生菜全基因组关联研究揭示了高温下种子年龄、颜色和发芽的相互作用-动脉网

Genome-wide association studies in lettuce reveal the interplay of seed age, color, and germination under high temperatures

Nature 等信源发布 2025-01-03 03:44



可切换为仅中文







Abstract

摘要

Thermoinhibition, the suppression of seed germination by high temperatures, is an adaptive trait that ensures successful seedling establishment in natural environments. While beneficial for wild plants, thermoinhibition can adversely affect crop yields due to uneven and reduced germination rates, particularly in the face of climate change.

高温抑制种子萌发是一种适应性特征，可确保在自然环境中成功建立幼苗。虽然热抑制对野生植物有益，但由于发芽率不均匀和降低，特别是在面临气候变化的情况下，热抑制会对作物产量产生不利影响。

To understand the genetic basis of thermoinhibition, we conducted a comprehensive genetic analysis of a diverse panel of .

为了了解热抑制的遗传基础，我们对一组不同的基因进行了全面的遗传分析。

Lactuca

乳酸菌

spp. accessions. Our findings revealed that

属种质。我们的发现表明

L. serriola

L.Serriola

, a wild ancestor of cultivated lettuce, showed relaxed thermoinhibition response compared to cultivated lettuce, suggesting that this trait may have been positively selected during early domestication in the Mediterranean region with hot, dry summers. Additionally, we found that thermoinhibition intensified with seed age but was less pronounced in dark-colored seeds, which showed increased germination under high temperatures.

与栽培莴苣相比，栽培莴苣的野生祖先表现出放松的热抑制反应，这表明在地中海地区炎热干燥的夏季早期驯化过程中，这种性状可能已被积极选择。此外，我们发现热抑制随着种子年龄的增长而增强，但在深色种子中不太明显，这表明在高温下发芽增加。

Genome-wide association studies identified genomic regions associated with thermoinhibition, including genes involved in ethylene and ABA signaling. Interestingly, some of these regions were also linked to seed color, suggesting a potential genetic coupling between black seed color and reduced thermoinhibition.

全基因组关联研究确定了与热抑制相关的基因组区域，包括涉及乙烯和ABA信号传导的基因。有趣的是，其中一些区域也与种子颜色有关，这表明黑色种子颜色与热抑制降低之间存在潜在的遗传耦合。

These results highlighted the complex interplay between thermoinhibition, seed color, and domestication in lettuce, indicating a complicated nature of thermoinhibition regulation. By elucidating the genetic architecture of thermoinhibition, our study provides a valuable foundation for breeding strategies to enhance lettuce resilience to climate change..

这些结果突出了生菜中热抑制，种子颜色和驯化之间复杂的相互作用，表明热抑制调节的复杂性。通过阐明热抑制的遗传结构，我们的研究为提高莴苣对气候变化的适应能力的育种策略提供了有价值的基础。。

Introduction

导言

Seed dormancy and thermoinhibition are two pivotal physiological mechanisms that regulate the timing of seed germination, ensuring that seedling emergence aligns with favorable environmental conditions. While both processes serve to optimize the survival and establishment of seedlings, they are distinct in their environmental triggers and ecological implications.

种子休眠和热抑制是调节种子萌发时间的两个关键生理机制，确保幼苗出苗符合有利的环境条件。虽然这两个过程都有助于优化幼苗的存活和建立，但它们在环境触发因素和生态影响方面是截然不同的。

Seed dormancy is an adaptive mechanism that prevents premature germination of viable seeds, even under favorable conditions that might be transient. This mechanism is critical for synchronizing germination with optimal environmental cues, primarily temperature changes that signal the appropriate season for growth.

种子休眠是一种适应性机制，即使在可能是短暂的有利条件下，也可以防止活种子过早发芽。。

In contrast to seed dormancy, seed thermoinhibition is a response mechanism that temporarily suspends germination during periods of excessively high temperatures

与种子休眠相反，种子热抑制是一种反应机制，在高温期间暂时停止发芽

. Unlike dormancy, which is a more static state, thermoinhibition can be quickly reversed upon the return to favorable temperature conditions. This process is exemplified by lettuce seeds, which exhibit minimal primary dormancy but are highly susceptible to thermoinhibition

与休眠不同，休眠是一种更静态的状态，热抑制可以在恢复到有利的温度条件后迅速逆转。莴苣种子就是这个过程的例子，它表现出最小的初级休眠，但对热抑制非常敏感

. Originating from the Mediterranean region

源自地中海地区

—a climate characterized by hot, dry summers—lettuce seeds may have evolved thermoinhibition as a protective adaptation to delay germination until the decline of summer heat, thereby aligning seedling emergence with cooler, moist conditions conducive to growth

-以炎热干燥的夏季为特征的气候莴苣种子可能已经进化出热抑制作用，作为一种保护性适应，可以延迟发芽，直到夏季热量下降，从而使幼苗出苗与有利于生长的凉爽潮湿条件保持一致

While thermoinhibition may confer advantages in natural settings, it poses significant challenges in agriculture, particularly as global temperatures continue to rise. The increasing prevalence of heat waves and altered thermal profiles due to climate change threaten to disrupt germination uniformity, leading to reduced agricultural yields.

。由于气候变化，热浪的日益流行和热剖面的改变有可能破坏发芽的均匀性，导致农业产量下降。

The upper temperature threshold for germination varies significantly across lettuce genotypes

不同生菜基因型的发芽上限温度差异很大

, reflecting a broad spectrum of ecological adaptations. Most cultivars, including cv Salinas, fail to germinate at 29 °C or higher temperatures due to strong thermoinhibition. In contrast, certain thermotolerant genotypes exhibit remarkably high germination rates–above 90%–even at even at 36 °C

，反映了广泛的生态适应。大多数品种，包括cv Salinas，由于强烈的热抑制作用，无法在29°C或更高的温度下发芽。相比之下，即使在36°C的温度下，某些耐热基因型的发芽率也非常高，超过90%

, with

，带有

L. serriola

L.Serriola

, the wild progenitor of cultivated lettuce, showing greater thermotolerance

, possibly as a consequence of its adaptation to hotter, drier climate conditions.

，可能是由于它适应了更热，更干燥的气候条件。

Seed priming–prehydrating seeds at low temperatures followed by drying before sowing–has been employed to mitigate thermoinhibition by allowing seeds to initiate but not complete germination processes. This partial hydration enhances seed resilience to high-temperature stresses

种子引发-在低温下预水化种子，然后在播种前干燥-已被用于通过允许种子启动但不完成发芽过程来减轻热抑制。这种部分水合作用增强了种子对高温胁迫的抵抗力

. Despite its effectiveness, seed priming faces several practical challenges on a large scale. Increased moisture levels can lead to seed decay and disease, necessitating strict sanitation protocols that add cost and complexity

尽管种子引发有效，但它在大规模上面临着一些实际挑战。水分含量的增加会导致种子腐烂和疾病，因此需要严格的卫生协议，从而增加成本和复杂性

. Therefore, leveraging natural genetic variations to counter seed thermoinhibition presents a sustainable alternative to enhance crop establishment and productivity in lettuce, helping to combat the impacts of global warming.

因此，利用自然遗传变异来对抗种子热抑制是一种可持续的替代方法，可以提高莴苣的作物产量和生产力，有助于应对全球变暖的影响。

Phytohormones play critical roles in seed germination. Abscisic acid (ABA), the primary hormone responsible for inhibiting germination, is crucial in maintaining dormancy

植物激素在种子萌发中起关键作用。脱落酸（ABA）是抑制发芽的主要激素，对维持休眠至关重要

. ABA is synthesized during seed development, contributing to storage reserve accumulation and desiccation tolerance and counteracting the effects of gibberellic acid (GA) that promote germination. In-depth genetic studies have identified key genes in thermoinhibition such as

ABA在种子发育过程中合成，有助于储存储备积累和耐干燥性，并抵消赤霉素（GA）促进发芽的作用。深入的遗传学研究已经确定了热抑制的关键基因，例如

9-CIS-EPOXYCAROTENOID DIOXYGENASE4

9-顺式-环氧类胡萝卜素双加氧酶4

(

LsNCED4

), which is essential for ABA synthesis and contributes significantly to the thermotolerance observed in

)，这对于ABA的合成至关重要，并且对在

L. serriola

L.Serriola

US96UC23

. Additionally, mutant screening in lettuce has identified genes like

此外，莴苣中的突变筛选已鉴定出以下基因

LsABA1

, which negatively influences ABA-mediated germination inhibition. Mutations in

，这会对ABA介导的发芽抑制产生负面影响。突变

LsABA1

have been shown to reduce thermoinhibition, underscoring the critical role of ABA signaling in seed thermoinhibition

已经证明可以减少热抑制，强调了ABA信号在种子热抑制中的关键作用

Ethylene is also known for its significant role in modulating germination and thermoinhibition

乙烯也因其在调节发芽和热抑制中的重要作用而闻名

. Recognized for breaking dormancy in Compositae family members like lettuce and sunflower, ethylene application can alleviate the inhibitory effects of high temperatures on seed germination and reduce overall seed dormancy

乙烯被认为可以打破莴苣和向日葵等菊科植物的休眠，乙烯的应用可以减轻高温对种子萌发的抑制作用，并降低整体种子休眠

. Ethylene production in lettuce seeds decreases with rising temperatures during water uptake, indicating a temperature-sensitive synthesis pathway that may impact dormancy and thermoinhibition dynamics

莴苣种子中乙烯的产生随着水分吸收过程中温度的升高而降低，表明温度敏感的合成途径可能影响休眠和热抑制动力学

. Moreover, ethylene may enhance germination indirectly through interactions with GA and ABA. Ethylene can enhance GA biosynthesis or activity, which facilitates germination even under higher temperatures. It can also reduce ABA synthesis, increase ABA degradation, or decrease the sensitivity to ABA, effectively modulating the inhibitory role of ABA in seed germination.

此外，乙烯可能通过与GA和ABA的相互作用间接促进发芽。乙烯可以增强GA的生物合成或活性，即使在较高温度下也有利于发芽。它还可以减少ABA的合成，增加ABA的降解，或降低对ABA的敏感性，有效调节ABA在种子萌发中的抑制作用。

. This hormonal interplay was further evidenced by the coordinated expression of genes involved in ethylene and GA synthesis in response to germination-inducing temperatures

这种激素的相互作用进一步证明了乙烯和GA合成相关基因在发芽诱导温度下的协调表达

. Additionally, recent genetic and transcriptomic analyses have reinforced the importance of ethylene signaling in seed germination during high-temperature imbibition. A lettuce homolog of

此外，最近的遗传和转录组学分析增强了乙烯信号在高温吸胀期间种子萌发中的重要性。莴苣的同源物

ETHYLENE RESPONSE FACTOR1

乙烯响应因子1

LsERF1

that is also known as

这也被称为

LsERF172

, was identified as a causal locus for thermoinhibition in a quantitative trait locus (QTL) analysis

在数量性状位点（QTL）分析中，被确定为热抑制的因果位点

Gibberellic acid is essential for overcoming seed thermoinhibition by counterbalancing the inhibitory effects of ABA

赤霉素通过抵消ABA的抑制作用，对克服种子热抑制至关重要

. GA enhances seed germination by promoting ABA catabolism or reducing ABA sensitivity. Moreover, GA has been shown to induce the expression of enzymes responsible for ethylene biosynthesis, thus facilitating a hormonal synergy that supports germination. Conversely, inhibiting ethylene synthesis can lead to a decrease in the expression of GA biosynthesis enzymes, demonstrating the tightly linked regulatory network governing seed hormonal responses.

。此外，GA已被证明可诱导负责乙烯生物合成的酶的表达，从而促进支持发芽的激素协同作用。相反，抑制乙烯合成可导致GA生物合成酶表达的降低，证明了控制种子激素反应的紧密连接的调控网络。

Lettuce is a world-wide popular leafy vegetable for its health and nutritional benefits, including dietary fiber, minerals, and vitamins

莴苣是一种世界范围内受欢迎的叶菜，因为它具有健康和营养益处，包括膳食纤维、矿物质和维生素

. However, the increasing occurrence of unseasonal and erratic high temperatures associated with climate change poses significant challenges to its cultivation. Unseasonal high temperatures can disrupt the synchronization of germination, leading to decreased and uneven lettuce yields. Therefore, the development of cultivars with enhanced thermotolerant germination has emerged as a crucial objective in lettuce breeding.

然而，与气候变化相关的非季节性和不稳定的高温越来越多，对其种植提出了重大挑战。反常的高温会破坏发芽的同步性，导致莴苣产量下降且不均匀。因此，开发耐热发芽增强的品种已成为生菜育种的关键目标。

Current knowledge of thermoinhibition in lettuce has primarily focused on certain cultivars, with extensive studies on

目前关于生菜热抑制的知识主要集中在某些品种上，并对其进行了广泛的研究

L. serriola

L.Serriola

leading to the identification of several genes involved in this process

导致鉴定出参与这一过程的几个基因

. However, the rich genetic diversity observed among lettuce accessions for thermoinhibition suggested that multiple regulatory mechanisms were involved, highlighting the complexity of this trait

然而，在生菜种质中观察到的丰富的热抑制遗传多样性表明，涉及多种调控机制，突出了这一性状的复杂性

. To address this knowledge gap, our study explored the genetic basis of thermoinhibition by analyzing a diverse panel of lettuce accessions through genome-wide association studies (GWAS). This analysis led to the discovery of novel loci associated with thermoinhibition, underscoring the potential presence of various genetic mechanisms regulating this trait.

为了解决这一知识差距，我们的研究通过全基因组关联研究（GWAS）分析了一组不同的生菜种质，探索了热抑制的遗传基础。。

Additionally, our study expanded to examine how seed age and color influence thermoinhibition. These factors were systematically analyzed to understand their impact on germination rates under high temperatures. Our findings revealed a potential interplay of seed color, seed age, and thermoinhibition.

此外，我们的研究扩展到研究种子年龄和颜色如何影响热抑制。系统地分析了这些因素，以了解它们对高温下发芽率的影响。我们的研究结果揭示了种子颜色，种子年龄和热抑制的潜在相互作用。

This research not only broadens our understanding of the genetic factors governing thermoinhibition but also provides breeders with valuable genetic tools to develop lettuce varieties that are better adapted to the challenges posed by climate change..

这项研究不仅拓宽了我们对控制热抑制的遗传因素的理解，而且为育种者提供了有价值的遗传工具，以开发更好地适应气候变化挑战的莴苣品种。。

Results

结果

Seed age effect on thermoinhibition

种子年龄对热抑制的影响

The seeds from 521

521的种子

Lactuca

乳酸菌

spp. accessions (Table

物种种质（表

S1级

) were evaluated for germination rate under high-temperature (34 °C) and control (21 °C) conditions, where the seeds were harvested at various years between 1977 and 2017 (Fig.

)在高温（34°C）和对照（21°C）条件下评估发芽率，其中种子在1977年至2017年的不同年份收获（图）。

A). Under control conditions, the seeds exhibited a high average germination rate of 87.4%. To assess the possible age effect on germination rates, the seeds were grouped into seven groups by harvest year. The harvest groups exhibited similar germination rates under control conditions (Fig.

A）。在对照条件下，种子的平均发芽率高达87.4%。为了评估年龄对发芽率的可能影响，按收获年份将种子分为七组。收获组在对照条件下表现出相似的发芽率（图）。

B). For example, the seeds harvested from 2006 to 2010 displayed the highest germination rate at

B）。例如，2006年至2010年收获的种子在

88.2

%, whereas those from 2016 to 2017 showed the lowest at

%，而2016年至2017年的数据最低

87.1

%. An ANOVA test confirmed that these differences between harvest years were not statistically significant (P-value = 0.59), suggesting no correlation between germination rate under control conditions and seed harvest year.

%。方差分析检验证实，收获年份之间的这些差异无统计学意义（P值 = 0.59), 表明对照条件下的发芽率与种子收获年份之间没有相关性。

However, under high temperature conditions, an inverse correlation was observed between seed age and germination rate. The oldest seed group (harvested in 1990 or before) exhibited the lowest germination rate at

然而，在高温条件下，种子年龄与发芽率呈负相关。最古老的种子组（1990年或之前收获）在

27.7

%, while most recently harvested seeds (years 2016 and 2017) achieved the highest rate at

%，而最近收获的种子（2016年和2017年）在

64.7

% (Fig.

%（图。

C). Significance of the variation between harvest year groups was supported by an ANOVA test (P-value = 5.45E-14) (Table

C）。方差分析检验（P值=5.45E-14）支持了收获年份组之间差异的显着性（表

S2级

), indicating a pronounced effect of seed age on thermoinhibition, with thermoinhibition strengthening over time after harvest.

)，表明种子年龄对热抑制有明显影响，收获后随着时间的推移，热抑制作用增强。

Fig. 1

图1

Impact of harvest year on lettuce seed germination under high-temperature conditions (34 °C). (

。（笑声）(

) Distribution of lettuce seeds across different harvest years. (

)莴苣种子在不同收获年份的分布。（笑声）(

B类

) Germination rates of lettuce seeds from various harvest years under control temperature conditions (21 °C). (

)在控制温度条件下（21°C），不同收获年份的莴苣种子的发芽率。（笑声）(

C级

) Thermoinhibition rates, calculated as the ratio of germination rates under high-temperature conditions to those under control conditions. Different letters at the top indicate statistically significant differences among groups (Tukey’s HSD test, alpha = 0.01).

)热抑制率，以高温条件下的发芽率与对照条件下的发芽率之比计算。顶部的不同字母表示各组之间的统计学显着差异（Tukey的HSD测试，alpha = 0.01).

Full size image

全尺寸图像

Heat-tolerant germination of

耐热发芽

L. Serriola

L.Serriola

To control for seed age variability, we conducted the germination test using freshly harvested seeds from the same accessions. The germination test revealed an average thermoinhibition rate of 41.5% under high-temperature conditions at 34 °C. Among the 521 accessions, 12% (

为了控制种子年龄的变异性，我们使用来自相同种质的新鲜收获的种子进行了发芽试验。发芽试验显示，在34℃的高温条件下，平均热抑制率为41.5%。在521份材料中，有12%(

= 62) were unable to germinate at 34 °C. The remaining accessions displayed a wide range of thermoinhibition rates: 1–25% (164 lines), 26–50% (68 lines), 51–75% (105 lines), and 76–100% (115 lines), while seven lines exhibited slightly higher germination rate under high temperatures compared to control temperatures (Fig.

=62）无法在34°C下发芽。其余种质表现出广泛的热抑制率：1-25%（164系），26-50%（68系），51-75%（105系）和76-100%（115系），而7系在高温下的发芽率略高于对照温度（图）。

S1级

, Table

S1级

). When thermoinhibition rate was evaluated for four different horticultural types of cultivated lettuce and wild lettuce (

)。当评估四种不同园艺类型的栽培生菜和野生生菜的热抑制率时(

L. serriola

L.Serriola

), the wild lettuce showed less pronounced thermoinhibition with a rate of 63%, while cultivated lettuce types showed an average of 40.7% (33% for butterhead, 41% for romaine, and 44% for crisphead and leaf type) (Fig.

)，野生莴苣的热抑制率较低，为63%，而栽培莴苣类型的平均热抑制率为40.7%（牛头莴苣为33%，生菜为41%，脆头莴苣和叶型为44%）（图）。

A; Table

A、表

S1级

). The significance of these differences was confirmed by an ANOVA test (P-value = 0.014) (Table S3), and Tukey’s HSD test (alpha = 0.05) supported significant difference between

)。方差分析检验（P值=0.014）（表S3）证实了这些差异的显着性，Tukey的HSD检验（alpha=0.05）支持了两者之间的显着差异

L. serriola

L.Serriola

and butterhead type (Fig.

和蝴蝶头型（图）。

A).

A）。

Fig. 2

图2

Influence of horticultural types and seed colors on thermoinhibition at 34 °C. (

园艺类型和种子颜色对34℃温度抑制的影响。（笑声）(

) Comparison of thermoinhibition rates among horticultural types including butterhead (BUT), crisphead (CRP), leaf (LEF), and romaine (ROM), and

)园艺类型之间的热抑制率比较，包括牛头草（BUT），crisphead（CRP），叶（LEF）和罗曼（ROM），以及

L. serriola

L.Serriola

(SER). (

（SER）。（笑声）(

B类

) Thermoinhibition rate based on seed colors–black, brown, and white–where thermoinhibition rate is represented as the ratio of germination rates under high-temperature conditions relative to those under control conditions. Statistically significant differences are indicated by different letters at the top of the plots (Tukey’s HSD, alpha = 0.01)..

)基于种子颜色（黑色、棕色和白色）的热抑制率，其中热抑制率表示为高温条件下相对于对照条件下的发芽率的比率。统计学上显着的差异由图顶部的不同字母表示（Tukey的HSD，alpha = 0.01)..

Full size image

全尺寸图像

Thermoinhibition variation by seed color

种子颜色对热抑制的影响

Seeds from the GWAS panel displayed different colors, divided into three groups: 237 accessions for black, 17 for brown, and 259 for white. To assess an association between seed color and thermoinhibition, we examined germination rate among seed color groups. Seeds with a black pericarp exhibited the highest germination rate under heat conditions of 55.4%, followed by brown at 44% and white at 27.8% (Fig. .

GWAS小组的种子显示出不同的颜色，分为三组：237份为黑色，17份为棕色，259份为白色。。在高温条件下，黑色果皮的种子发芽率最高，为55.4%，其次是棕色，为44%，白色，为27.8%（图）。

B). The significance of this difference across seed colors was confirmed by the ANOVA test (P-value = 2E-16) (Table S4) and further substantiated by the Tukey’s HSD test, particularly noting the significant disparity between black and white seeds (Fig.

B）。ANOVA检验（P值2E-16）（表S4）证实了这种种子颜色差异的显着性，并通过Tukey的HSD检验进一步证实，特别是注意到黑色和白色种子之间的显着差异（图4）。

B). These results indicated that germination inhibition by heat (thermoinhibition effect) was attenuated in darker-colored seeds compared to white-colored seeds.

B）。这些结果表明，与白色种子相比，深色种子中的热抑制（热抑制效应）减弱了发芽抑制。

Genome-wide association study on seed thermoinhibition

种子热抑制的全基因组关联研究

To explore the genetic basis of variation in thermoinhibition, we conducted a GWAS using SNP data from various

为了探索热抑制变异的遗传基础，我们使用来自各种SNP数据进行了GWAS

Lactuca

乳酸菌

spp. accessions. We identified 84 SNPs significantly associated with thermoinhibition, with a cutoff of Bonferroni-corrected P-value of 2.7E-7 (Table S5). These SNPs were distributed across five chromosomes including 4, 5, 7, 8, and 9 (Fig.

属种质。我们确定了84个与热抑制显着相关的SNP，Bonferroni校正的P值截止值为2.7E-7（表S5）。这些SNP分布在五条染色体上，包括4、5、7、8和9（图）。

A). To identify potential candidate genes, we determined linkage disequilibrium (LD) blocks where the significant SNPs were linked to their neighboring SNPs by an LD of

A）。为了鉴定潜在的候选基因，我们确定了连锁不平衡（LD）区块，其中重要的SNP通过LD与相邻的SNP相连

> 0.5. The blocks spanned a total length of 4.6 Mb in the genome with an average size of approximately 0.52 Mb (Table S6). Chromosome 4, 8, and 9 each contained a single LD block, while chromosome 5 contained two and chromosome 7 contained four blocks, among which the largest block spanned 2.3 Mb on chromosome 7 (Fig. .

>0.5。这些区块在基因组中的总长度为4.6 Mb，平均大小约为0.52 Mb（表S6）。染色体4、8和9各自包含一个LD区块，而染色体5包含两个，染色体7包含四个区块，其中最大的区块跨越7号染色体上的2.3 Mb（图）。

B and C). Within the blocks, a total of 91 genes were identified based on the lettuce reference genome annotation (version 8) (Table S7).

B和C）。在这些区块内，基于莴苣参考基因组注释（版本8）（表S7），共鉴定出91个基因。

Fig. 3

图3

Analysis of SNPs associated with thermoinhibition. (

与热抑制相关的SNP分析。（笑声）(

) Manhattan plot illustrating significant SNPs associated with thermoinhibition across the genome. The red horizontal dashed line represents the genome-wide significance threshold (P-value < 2.7E-7, −log

)曼哈顿图说明了与整个基因组中的热抑制相关的重要SNP。红色水平虚线表示全基因组显著性阈值（P值<2.7E-7，-log

(

p) =

6.57). (

B类

) Detailed Manhattan plot for chromosome 7 showing significant SNPs. The blue vertical dashed line indicates the positions of candidate genomic regions identified by LD block analysis. (

)7号染色体的详细曼哈顿图显示了重要的SNP。蓝色垂直虚线表示通过LD区块分析鉴定的候选基因组区域的位置。（笑声）(

C级

) Visualization of the largest LD block (indicated by a blue arrow in panel B), with LD strength expressed as

)

Full size image

全尺寸图像

Further annotation of these 91 genes using Gene Ontology (GO) biological process highlighted their potential biological functions. We particularly focused on genes associated with heat, seed germination, or phytohormone-signaling as phytohormones, including ABA, ethylene, and GA, are known to play important roles in seed germination.

使用基因本体论（GO）生物学过程对这91个基因进行进一步注释，突出了它们潜在的生物学功能。我们特别关注与热，种子萌发或植物激素信号传导相关的基因，因为已知植物激素（包括ABA，乙烯和GA）在种子萌发中起重要作用。

Among the 91 genes, six genes were associated with the focused functions (Table .

在91个基因中，有6个基因与聚焦功能相关（表）。

). A gene associated with a GO function of ‘response to heat’ (GO:0009408) encoded a chaperone protein, similar to Gametophytic factor 2 (GFA2, At5g48030) of

)。与“热反应”的GO功能相关的基因（GO:0009408）编码一种伴侣蛋白，类似于配子体因子2（GFA2，At5g48030）

Arabidopsis

拟南芥

, which has been known for its responsiveness to heat stress

，以其对热应激的反应而闻名

and its involvement in female gamete development

及其参与雌性配子发育

. A gene encoding GATA transcription factor 22 was associated with ‘response to gibberellin’ (GO:0010029) and ‘regulation of seed germination’ (GO:0009739). Additionally, two genes were associated with ethylene signaling: one gene encoded a protein closely related to ENHANCED ETHYLENE RESPONSE PROTEIN 5 (EER5, AT2G19560) of .

编码GATA转录因子22的基因与“对赤霉素的反应”（GO:0010029）和“种子萌发的调节”（GO:0009739）相关。此外，有两个基因与乙烯信号传导有关：一个基因编码与增强的乙烯反应蛋白5（EER5，AT2G19560）密切相关的蛋白质。

Arabidopsis

拟南芥

, whose mutation showed ethylene hypersensitivity in

，其突变显示乙烯超敏反应

Arabidopsis

拟南芥

and the other gene encoded an enzyme, 1-aminocyclopropane-1-carboxylate oxidase 1 (ACO1, At2g19590), which is involved in the final step of ethylene biosynthesis in plants

另一个基因编码一种酶，1-氨基环丙烷-1-羧酸氧化酶1（ACO1，At2g19590），它参与植物乙烯生物合成的最后一步

. ACO1 has been previously reported to enhance seed germination under heat stress conditions

先前已报道ACO1可在热应激条件下增强种子发芽

. Two genes were identified to be associated with abscisic acid signaling: one gene was closely related to ABA INCENTIVE 1 (ABI1, At4g26080), a negative regulator of ABA signaling

.鉴定出两个与脱落酸信号传导相关的基因：一个基因与ABA信号传导的负调节剂ABA激励1（ABI1，At4g26080）密切相关

and the other gene encoding Calcium-dependent protein kinase 13 was known for its involvement in ABA-signaling

另一个编码钙依赖性蛋白激酶13的基因因其参与ABA信号传导而闻名

Table 1 Candidate genes associated with thermoinhibition and seed color, and their functional annotations.

表1与热抑制和种子颜色相关的候选基因及其功能注释。

Full size table

全尺寸表

Association between seed color and thermoinhibition

种子颜色与热抑制的关系

Given the significant difference in thermoinhibition rate among seeds of different colors (Fig.

鉴于不同颜色种子之间热抑制率的显着差异（图）。

B), we examined whether genes influencing seed color might be associated with thermoinhibition. The GWAS population had 211 accessions with black seeds, 235 with white seeds, and 14 with brown seeds, and we conducted a GWAS to investigate the genetic basis of the seed color variation.

B），我们检查了影响种子颜色的基因是否可能与热抑制有关。GWAS群体有211份黑色种子，235份白色种子和14份棕色种子，我们进行了GWAS研究种子颜色变异的遗传基础。

By applying the same significance threshold as for thermoinhibition, we identified 211 SNPs significantly associated with seed color variations (Fig.

。

A, Table S8). Most of these SNPs (

A、表S8）。大多数这些SNP(

= 206) were located on chromosome 7, while one SNP was located on chromosome 3 and four SNPs were located on chromosome 8.

==206）位于7号染色体上，而一个SNP位于3号染色体上，四个SNP位于8号染色体上。

Fig. 4

图4

Manhattan plot analysis for seed color. (

曼哈顿种子颜色的情节分析。（笑声）(

) Manhattan plot showing significant SNPs associated with seed color across the genome. (

)曼哈顿图显示了与整个基因组的种子颜色相关的重要SNP。（笑声）(

B类

) Manhattan plot for chromosome 7. The red horizontal dashed lines indicate the genome-wide significance threshold (P-value < 2.7E-7, −log

)曼哈顿7号染色体图。红色水平虚线表示全基因组显著性阈值（P值<2.7E-7，-log

(

p) =

6.57). The blue vertical dashed lines indicate the positions of candidate genomic regions identified by LD block analysis.

6.57）。蓝色垂直虚线表示通过LD区块分析鉴定的候选基因组区域的位置。

Full size image

全尺寸图像

Subsequent pairwise LD analysis resulted in six LD blocks, totaling 4.7 Mb. Four candidate LD blocks were located on chromosome 7, with sizes of 0.26 Mb, 0.35 Mb, 1.1 Mb, and 2.6 Mb, respectively (Fig.

随后的成对LD分析产生了六个LD块，总计4.7 Mb。四个候选LD区块位于7号染色体上，大小分别为0.26 Mb、0.35 Mb、1.1 Mb和2.6 Mb（图）。

B, Table S6). Chromosome 3 and 8 each contained a single block of 0.2 Mb (Table S6). These six blocks contained 91 genes (Table S9). Among these, there were two genes associated with pigment biosynthesis (Table

B、表S6）。染色体3和8各自包含一个0.2 Mb的单个区块（表S6）。这六个区块包含91个基因（表S9）。

). One gene encoded an enzyme, Lycopene epsilon cyclase, known for its involvement in carotenoid biosynthesis

)。一个基因编码一种酶，番茄红素ε环化酶，以其参与类胡萝卜素的生物合成而闻名

. The other gene encoded anthocyanin regulatory C1, a MYB transcription factor, previously recognized as a causal locus (

。另一个基因编码花青素调节C1，一种MYB转录因子，以前被认为是因果基因座(

LsTT2

) for lettuce seed color in a GWAS analysis

)GWAS分析中生菜种子的颜色

, where the authors showed that a stop codon point mutation of this gene resulted in white-colored seeds. The identification of this gene in our study reinforced the validity of our results.

，作者表明该基因的终止密码子点突变导致白色种子。在我们的研究中对该基因的鉴定增强了我们结果的有效性。

Interestingly, three of the seed color LD blocks on chromosome 7 colocalized with the candidate blocks of thermoinhibition trait (Fig.

有趣的是，7号染色体上的三个种子颜色LD区块与热抑制性状的候选区块共定位（图）。

). Specifically, 54 of the total 91 candidate genes on chromosome 7 were shared between seed color and thermoinhibition traits (Table S9), including the four key candidates,

)。具体而言，在7号染色体上的91个候选基因中，有54个在种子颜色和热抑制性状之间共享（表S9），包括四个关键候选基因，

GATA22

EER5

ACO1

ACO1公司

, and

，以及

ABI1

ABI1型

. This result suggested a potentially shared genetic pathway influencing both seed color and thermoinhibition.

。

Fig. 5

图5

Genomic distribution of QTNs and causal loci associated with thermoinhibition and seed color. Thermoinhibition QTNs (red bars) were compared with seed color QTNs (black bars). The co-localization of three QTN blocks on chromosome 7 suggested a potential genetic link between the two traits. Previously identified causal loci for thermoinhibition (.

QTN的基因组分布和与热抑制和种子颜色相关的因果基因座。将热抑制QTN（红色条）与种子颜色QTN（黑色条）进行比较。7号染色体上三个QTN区块的共定位表明这两个性状之间存在潜在的遗传联系。先前确定的热抑制因果基因座（。

LsERF1

LsNCED4

, and

，以及

LsABA1

) and seed color (

)和种子颜色(

LsTT2

) were indicated by blue arrows. The scale bar on the left indicates a chromosomal position in megabases (Mb).

)用蓝色箭头表示。左侧的比例尺表示以兆碱基（Mb）为单位的染色体位置。

Full size image

全尺寸图像

Discussion

讨论

Seed thermoinhibition, a natural adaptation that prevents germination during periods of heat stress, can hinder agricultural production, where consistent and timely germination is crucial regardless of temperature fluctuations

种子热抑制是一种自然适应，可以防止在热胁迫期间发芽，可能会阻碍农业生产，无论温度波动如何，持续及时的发芽都至关重要

. As climate change exacerbates temperature variability with rising temperatures and more frequent heat waves, reducing thermoinhibition is crucial for ensuring crop resilience and maintaining consistent germination across a broader temperature range. In this study, we investigated the genetic mechanisms underlying seed thermoinhibition in lettuce, an economically important vegetable crop..

由于气候变化加剧了气温的变化，气温升高和热浪频率增加，因此减少热抑制对于确保作物的抗逆性和在更广的温度范围内保持一致的发芽至关重要。。。

An intriguing observation from our study is that aged seeds exhibited stronger thermoinhibition (i.e., reduced germination rates under high temperatures) compared to freshly harvested seeds, suggesting that over time, lettuce seeds may enhance their thermoinhibitory responses. Prolonged seed storage often reduces seed viability and longevity, most likely due to accumulated oxidative damage to cell macromolecules such as proteins, sugars, lipids, and nucleic acids.

我们研究的一个有趣的观察结果是，与新鲜收获的种子相比，老化的种子表现出更强的热抑制作用（即高温下发芽率降低），这表明随着时间的推移，莴苣种子可能会增强其热抑制反应。。

. However, our findings indicated that the increased thermoinhibition was not attributable to reduced viability, as seeds of various ages showed comparable germination rates under control conditions (ANOVA test P-value = 0.59). Notably, the oldest seeds in our study, harvested as far back as 1977, maintained a high germination rate of nearly 85% at the control temperature of 21 °C.

然而，我们的研究结果表明，热抑制的增加并不是由于活力的降低，因为不同年龄的种子在对照条件下的发芽率相当（ANOVA检验P值 = 0.59). 值得注意的是，我们研究中最古老的种子早在1977年就收获了，在21°C的控制温度下保持了近85%的高发芽率。

This age-related increase in thermoinhibition underscores the dynamic nature of the mechanisms underlying thermoinhibition, which may involve complex physiological changes occurring during long-term storage of seeds at − 20 °C, the storage condition for USDA lettuce germplasm collections..

这种与年龄相关的热抑制增加强调了热抑制机制的动态性质，这可能涉及在美国农业部莴苣种质收集的储存条件-20°C下长期储存种子期间发生的复杂生理变化。。

One potential physiological change could be the accumulation of germination-inhibitory hormones, such as ABA, which plays a crucial role in inhibiting seed germination. Storing seeds at − 20 °C, a condition that simulates freezing and drought stresses, could promote ABA signaling

一个潜在的生理变化可能是发芽抑制激素的积累，例如ABA，其在抑制种子发芽中起关键作用。将种子储存在-20°C（一种模拟冻结和干旱胁迫的条件）可以促进ABA信号传导

, leading to enhanced thermoinhibition.

，导致增强的热抑制作用。

Alternatively, physical changes in the seed structure, like increased rigidity of the endosperm, might also enhance the thermoinhibitory effect

另外，种子结构的物理变化，如胚乳刚性的增加，也可能增强热抑制作用

. The endosperm plays a multifaceted role, acting as a physical barrier that regulates embryo growth and development while also providing nutrients and protection

胚乳起着多方面的作用，它是调节胚胎生长发育的物理屏障，同时也提供营养和保护

. Studies have shown that gradual hardening of the endosperm occurred during storage, which had a strong correlation with thermoinhibition

研究表明，胚乳在储存过程中逐渐硬化，这与热抑制有很强的相关性

To fully understand the mechanisms underlying thermoinhibition increase in aged seeds, further studies should focus on the biochemical and structural changes in seeds over time, particularly in those accessions where seed viability and low thermoinhibition rates were maintained during storage at − 20 °C.

为了充分了解老化种子中热抑制增加的潜在机制，进一步的研究应该集中在种子随时间的生化和结构变化上，特别是在那些在-20℃储存期间保持种子活力和低热抑制率的种质中。

Such studies could provide strategies for agricultural practices and seed storage aimed at optimizing germination and crop yields under varying climatic conditions..

这些研究可以为农业实践和种子储存提供策略，旨在优化不同气候条件下的发芽和作物产量。。

Our study highlighted a colocalization of casual loci for seed color and thermoinhibition on chromosome 7 (Fig.

我们的研究强调了7号染色体上种子颜色和热抑制的偶然基因座的共定位（图）。

), where three candidate LD blocks overlapped between these traits, sharing 56 candidate genes. This observation suggests two possible scenarios: (1) the traits are tightly linked due to the physical proximity of their associated genes on the chromosome 7, or (2) they share a common regulatory pathway, indicating pleiotropic effects..

)，其中三个候选LD区块在这些性状之间重叠，共享56个候选基因。这一观察结果表明了两种可能的情况：（1）这些性状由于其相关基因在7号染色体上的物理接近而紧密相关，或者（2）它们共享一个共同的调控途径，表明多效性。。

Previous research identified

先前的研究确定

LsTT2

, an R2R3-MYB transcription factor homologous to

，与R2R3-MYB转录因子同源

ARABIDOPSIS TRANSPARENT TESTA 2

拟南芥透明种皮2

, as a casual gene for seed color variation in lettuce through GWAS and fine mapping

，通过GWAS和精细定位作为莴苣种子颜色变异的偶然基因

. The authors demonstrated that knockout of the

作者证明了敲除

LsTT2

gene converted black seeds to white seeds in lettuce, indicating its key role in the seed color regulation. Notably, our GWAS analysis also identified this gene as a candidate for seed color variation, suggesting that the seed color variations among our diverse panel are likely regulated by the same genetic mechanism.

该基因将莴苣的黑色种子转化为白色种子，表明其在种子颜色调节中的关键作用。值得注意的是，我们的GWAS分析还将该基因鉴定为种子颜色变异的候选基因，这表明我们不同小组之间的种子颜色变异可能受相同的遗传机制调控。

This finding supported the hypothesis of a close linkage between seed color and thermoinhibition, or co-localization of their casual loci, and thereby each trait is regulated by distinct genetic pathways rather than a single pleiotropic pathway..

这一发现支持了种子颜色和热抑制之间紧密联系的假设，或者它们的偶然基因座的共定位，因此每个性状都受不同的遗传途径而不是单一的多效性途径调控。。

The prevalence of black seeds with reduced thermoinhibition in the lettuce population further suggested that two gene alleles, promoting darker color and low thermoinhibition, respectively, have become linked and fixed together in the lettuce population. This fixation may have resulted from a positive selection, particularly in accessions adapted to environments with intense ultraviolet (UV) radiation, such as hot, sunny climates.

。这种固定可能是由于积极的选择，特别是在适应强烈紫外线（UV）辐射环境的种质中，例如炎热，阳光充足的气候。

Anthocyanins, the pigments abundant in dark-colored seeds, can scavenge reactive oxygen species, thereby limiting oxidative stress during germination under high UV exposure.

花青素是深色种子中丰富的色素，可以清除活性氧，从而限制在高紫外线照射下萌发过程中的氧化应激。

. This protective effect likely enhances survival and successful germination, giving dark seeds with reduced thermoinhibition (thermotolerant germination) a selective advantage in hot summer climates, such as those found in the Mediterranean region. Consequently, both alleles may have become fixed in the lettuce population, contributing to the observed trait distribution..

这种保护作用可能会提高存活率和成功发芽率，使温度抑制（耐热发芽）降低的深色种子在炎热的夏季气候（如地中海地区）具有选择性优势。。。

However, the possibility that these traits are regulated by the same genetic pathway cannot be completely excluded. Our GWAS analysis on seed color variations uncovered additional candidate genomic regions on chromosome 3 and 8, which also appeared to be associated with the thermoinhibition trait. The region on chromosome 8 was located only 860 kb from a thermoinhibition-associated region, while the region on chromosome 3 co-localized with four SNPs displaying near-threshold P-values for thermoinhibition (< 3.7E-06) (Fig.

但是，不能完全排除这些性状受同一遗传途径调控的可能性。我们对种子颜色变异的GWAS分析揭示了3号和8号染色体上的其他候选基因组区域，这似乎也与热抑制性状有关。8号染色体上的区域距离热抑制相关区域仅860 kb，而3号染色体上的区域与四个SNP共定位，显示出接近热抑制阈值的P值（<3.7E-06）（图）。

S2级

). This result suggests potential pleiotropic effects of a shared mechanism on both traits, as the co-localization or nearby positioning of all three chromosomal candidate regions is highly improbable. Definitive determination of whether the correlation between seed color and thermoinhibition is due to pleiotropy or tight linkage warrants further genetic and molecular investigations, such as knockout of the casual genes..

)。这一结果表明，共享机制对两个性状都有潜在的多效性，因为所有三个染色体候选区域的共定位或附近定位极不可能。确定种子颜色和热抑制之间的相关性是由于多效性还是紧密连锁，需要进一步的遗传和分子研究，例如敲除偶然基因。。

Our germination data indicated that

L. serriola

L.Serriola

had a significantly greater germination rate under high temperature conditions compared to cultivated lettuce, suggesting that thermoinhibition is reduced in

与栽培生菜相比，在高温条件下的发芽率明显更高，这表明热抑制作用在

L. serriola

L.Serriola

. Typically, domestication is associated with the loss of dormancy and a relaxation of environmental controls on germination. However, our data revealed that cultivated lettuce exhibited greater sensitivity to temperature (i.e., greater thermoinhibition) during germination compared to wild

通常，驯化与休眠的丧失和对发芽的环境控制的放松有关。然而，我们的数据表明，与野生生菜相比，栽培生菜在发芽过程中对温度表现出更大的敏感性（即更大的热抑制作用）

L. serriola

L.Serriola

accessions, suggesting an increase in thermoinhibition during the domestication process.

。

Lettuce is believed to have been domesticated in the Mediterranean regions, which are characterized by hot summers

生菜被认为是在夏季炎热的地中海地区驯化的

. This evolutionary background suggests that thermoinhibition likely served as an adaptive trait in early

这种进化背景表明，热抑制可能是早期的一种适应性特征

L. sativa

五十、紫花苜蓿

accessions, preventing germination during unsuitably warm periods. On the other hand, since

种质，防止在不适宜的温暖时期发芽。另一方面，自从

L. serriola

L.Serriola

, a progenitor of cultivated lettuce, displays reduced thermoinhibition, it can be also proposed that

，一种栽培生菜的祖先，表现出降低的热抑制作用，也可以提出

L. serriola

L.Serriola

might evolve to weaken thermoinhibition.

可能会演变为削弱热抑制作用。

L. serriola

L.Serriola

is known to be more tolerant to abiotic stresses such as drought, heat, and cold compared to cultivated lettuce

. The enhanced thermotolerance likely allows this species to further lessen the constraint of thermoinhibition, expanding its geographical range

.增强的耐热性可能使该物种进一步减轻热抑制的限制，扩大其地理范围

Extensive studies on

广泛研究

L. serriola

L.Serriola

have identified critical genetic components related to thermoinhibition. Through QTL analysis, one study pinpointed

已经确定了与热抑制相关的关键遗传成分。通过QTL分析，一项研究确定了

LsNCED4

, a gene encoding an enzyme involved in ABA synthesis, as a causal gene for reduced thermoinhibition. In

，一种编码参与ABA合成的酶的基因，是降低热抑制的致病基因。在

L. serriola

L.Serriola

, a mutation in the stop codon of

，终止密码子的突变

LsNCED4

resulted in a non-functional protein, leading to lower levels of ABA in heat-exposed seeds, and facilitating germination under heat stress conditions. The presence of this mutated allele in

导致非功能性蛋白质，导致热暴露种子中ABA水平降低，并促进热胁迫条件下的发芽。这种突变等位基因的存在

L. serriola

L.Serriola

, likely derived from the wild-type allele, further supports the idea that reduced thermoinhibition in

，可能来自野生型等位基因，进一步支持了减少热抑制的想法

L. serriola

L.Serriola

may be a result of natural selection to adapt to a broader range of climates. A comprehensive survey of alleles among

可能是自然选择的结果，以适应更广泛的气候。等位基因的综合调查

L. serriola

L.Serriola

and cultivated lettuce populations is needed to provide a definitive answer.

栽培生菜种群需要提供明确的答案。

Previous studies discovered two causal loci for thermoinhibition variation:

先前的研究发现了两个热抑制变异的因果基因座：

LsNCED4

on chromosome 6

在6号染色体上

, and

，以及

LsERF1

on chromosome 9

在9号染色体上

. These studies utilized QTL analysis on biparental population, where genetic variation is inherently limited to two accessions. In contrast, our GWAS analysis, leveraging a genetically diverse panel, identified a region on chromosome 9 near the

这些研究利用双亲群体的QTL分析，其中遗传变异固有地限于两个种质。相比之下，我们的GWAS分析利用遗传多样性小组，确定了9号染色体上靠近

LsERF1

locus, potentially implicating the same gene, as well as additional quantitative trait nucleotides (QTNs) on chromosome 4, 5, and 8 (Fig.

基因座，可能涉及相同的基因，以及染色体4、5和8上的其他数量性状核苷酸（QTN）（图）。

). The discovery of these novel QTNs highlights the complexity of genetic regulation in thermoinhibition and demonstrates the benefits of using diverse germplasm in genetic studies. Overall, our GWAS analysis not only enriches our understanding of the genetic mechanisms underlying thermoinhibition but also provides lettuce breeding efforts with a broader toolkit for developing cultivars with enhanced heat resilience.

)。这些新型QTN的发现突显了热抑制中遗传调控的复杂性，并证明了在遗传研究中使用不同种质的益处。总体而言，我们的GWAS分析不仅丰富了我们对热抑制遗传机制的理解，而且为莴苣育种工作提供了更广泛的工具包，用于开发具有增强耐热性的品种。

This is crucial for mitigating the impact of climate change on crop productivity and agricultural sustainability..

这对于减轻气候变化对作物生产力和农业可持续性的影响至关重要。。

Methods

方法

Seed production of the GWAS mapping population

GWAS作图种群的种子生产

A diverse panel of 521

521人组成的多元化小组

Lactuca

乳酸菌

spp. accessions, including 12 wild lettuce accessions (eleven

包括12份野生莴苣种质（11份）

L. serriola

L.Serriola

and one

还有一个

L. saligna

L.柳树

) and 509 cultivated lettuce accessions (

)509份栽培莴苣(

L. sativa)

五十、紫花苜蓿）

(Table

（表

S1级

), were selected from the USDA-ARS germplasm collections in Salinas, CA. For an initial germination trial, we used seeds harvested between 1977 and 2017, which were stored at -20 °C in closed boxes with silica gel desiccant to control humidity. GWAS were conducted using freshly harvested seeds (May - July 2019) from plants grown in 6.4 cm (2.5 inches) diameter soil pots under natural light conditions in a greenhouse with mean air temperature ranging from 17 to 33 °C..

)，选自加利福尼亚州Salinas的USDA-ARS种质收集。对于初始发芽试验，我们使用1977年至2017年间收获的种子，将其在-20°C的密闭箱中用硅胶干燥剂储存以控制湿度。GWAS是使用新鲜收获的种子（2019年5月至7月）进行的，这些种子是在平均气温为17至33°C的温室中，在自然光照条件下，在直径6.4厘米（2.5英寸）的土壤盆中生长的植物。。

Phenotypic analyses

表型分析

Germination tests were conducted by sowing 25 seeds on Whatman grade 1 filter paper (85 mm diameter) in 100 × 15 mm Petri dishes (Fisher scientific), moistened with 4 mL of deionized water. The petri dishes were arranged in a randomized block design within a germination chamber (Percival GR-41 L), programmed to a 16-hour light/8-hour dark cycle.

通过在Whatman 1级滤纸（直径85毫米）上在100×15毫米培养皿（Fisher scientific）中播种25粒种子进行发芽试验，用4毫升去离子水润湿。。

For germination under high temperature conditions, the chamber temperature was set to 34 °C during the day and 27 °C at night. Conversely, for control germination, the chamber temperature was maintained at 21 °C. Germination success was quantified by the emergence of at least a 2 mm radicle and fully opened cotyledons at six days after imbibition.

为了在高温条件下发芽，室温白天设定为34°C，晚上设定为27°C。相反，对于对照发芽，室温度保持在21℃。通过在吸胀后6天出现至少2毫米胚根和完全开放的子叶来量化发芽成功率。

To minimize positional effects, the petri dishes were rotated every 24 h within the germination chamber. The thermoinhibition rate was calculated as the ratio of seeds germinated under heat stress conditions to those germinated under the control condition (21 °C) (Table .

为了使位置效应最小化，培养皿在发芽室内每24小时旋转一次。热抑制率计算为在热应激条件下发芽的种子与在对照条件（21°C）下发芽的种子的比率（表）。

S1级

). This experiment was replicated three times under identical conditions. Statistical analysis of the germination data was conducted using the ‘aov’ functiuon for Analysis of Variance (ANOVA), and the Tukey’s HSD test for pairwise comparison implemented in the R package

)。该实验在相同条件下重复三次。发芽数据的统计分析使用“aov”函数进行方差分析（ANOVA），Tukey的HSD检验在R包中进行成对比较

GWAS analysis

GWAS分析

The SNP data for the GWAS analysis was extracted from a public lettuce genotype dataset, (NCBI Project: PRJEB40369)

GWAS分析的SNP数据是从公共生菜基因型数据集（NCBI项目：PRJEB40369）中提取的

, where the variant SNPs (186,006) were identified based on the lettuce reference genome version 8

，其中基于莴苣参考基因组版本8鉴定了变异SNP（186006）

. Briefly explained, missing data within the initial SNP dataset were imputed using Beagle v5

简要说明，使用Beagle v5估算了初始SNP数据集中缺失的数据

, followed by filtering to retain SNPs with a minor allele frequency of at least 5%.

，然后过滤以保留次要等位基因频率至少为5%的SNP。

Association mapping analyses for seed thermoinhibition and seed color traits were conducted using the R-package Genome Association and Prediction Integrated Tool (GAPIT) version 3

使用R-package基因组关联和预测集成工具（GAPIT）版本3进行了种子热抑制和种子颜色性状的关联作图分析

. We employed the Settlement of MLM Under Progressively Exclusive Relationship (SUPER)

.我们采用逐步排他性关系下的传销结算（SUPER）

. Population stratification was corrected by PCA, setting PCA.total to 3, with all other parameters kept at their default settings. Significant associations were determined using a Bonferroni-corrected P-value threshold (0.05 divided by the total number of SNPs), corresponding to 2.69E-7 or − log

。通过PCA校正人口分层，将PCA.total设置为3，所有其他参数保持默认设置。使用Bonferroni校正的P值阈值（0.05除以SNP总数）确定显着关联，对应于2.69E-7或-log

(P-value) of 6.57.

（P值）为6.57。

Identification of candidate genes

候选基因的鉴定

To identify potential candidate genes, we determined linkage disequilibrium (LD) blocks by calculating pairwise LD values (

为了鉴定潜在的候选基因，我们通过计算成对的LD值来确定连锁不平衡（LD）区块(

) between significant SNPs and neighboring SNPs within a 100 kb window, using PLINK version 2

)使用PLINK版本2在100 kb窗口内的重要SNP和相邻SNP之间

. LD blocks were established by merging SNPs with a

通过将SNP与

value of at least 0.5, indicative of strong LD, which represent genomic regions where SNPs are co-inherited. If the resultant LD block was smaller than 200 kb, the genomic region was extended to up to 200 kb to ensure comprehensive candidate gene identification. These LD blocks were visualized using Haploview 4.2.

值至少为0.5，表示强LD，代表SNP共同遗传的基因组区域。如果产生的LD区块小于200 kb，则将基因组区域扩展至200 kb，以确保全面的候选基因鉴定。这些LD块使用Haploview 4.2可视化。

and candidate genes within the LD blocks were retrieved based on annotations of the lettuce reference genome

RNA expression levels of the candidate genes under heat stress conditions were obtained from public datasets (NCBI accession GSE241604). Hierarchical clustering analyses were conducted using the hcluster method from the R package amap (version 0.8.16)

从公共数据集（NCBI登录号GSE241604）获得热应激条件下候选基因的RNA表达水平。使用R包amap（版本0.8.16）中的hcluster方法进行分层聚类分析

. The resulting clusters were visualized using the heatmap.2 method from the R package ggplots version 3.1.3

。使用R包ggplots版本3.1.3中的热图2方法可视化生成的聚类

Gene ontology (GO) annotation

基因本体论（GO）注释

GO annotation of candidate genes was conducted using the Trinotate pipeline (

使用Trinotate管道对候选基因进行GO注释(

https://trinotate.github.io/

)

, and custom PERL scripts. Briefly explained, lettuce protein sequences were subjected to BLASTP searches against UniProtKB/Swiss-Prot database–a manually annotated, non-redundant protein sequence database. GO terms and biological functions were assigned to lettuce genes based on matches in the UniprotKB, with a stringent E-value threshold of less than 1E-20 to ensure high relevance and specificity..

，以及自定义PERL脚本。简而言之，对莴苣蛋白质序列进行了针对UniProtKB/Swiss-Prot数据库的BLASTP搜索，该数据库是一个手动注释的非冗余蛋白质序列数据库。根据UniprotKB中的匹配，将GO术语和生物学功能分配给莴苣基因，严格的E值阈值小于1E-20，以确保高度的相关性和特异性。。

Data availability

数据可用性

The lettuce SNP data for the GWAS analysis are available in the NCBI (Project ID: PRJEB40369). RNA-seq data for expression analysis of the candidate genes were obtained from public datasets (NCBI accession GSE241604). All additional relevant data are included in the manuscript and the Supporting Information files..

NCBI（项目编号：PRJEB40369）中提供了用于GWAS分析的莴苣SNP数据。用于候选基因表达分析的RNA-seq数据来自公共数据集（NCBI登录号GSE241604）。所有其他相关数据均包含在手稿和支持信息文件中。。

References

参考文献

Finkelstein, R., Reeves, W., Ariizumi, T. & Steber, C. Molecular aspects of seed dormancy.

Finkelstein，R.，Reeves，W.，Ariizumi，T。＆Steber，C。种子休眠的分子方面。

Annu. Rev. Plant. Biol.

年。工厂修订版。生物。

, 387–415.

https://doi.org/10.1146/annurev.arplant.59.032607.092740

(2008).

Article

文章

CAS

中科院

PubMed

MATH

数学

Google Scholar

谷歌学者

Koornneef, M., Bentsink, L. & Hilhorst, H. Seed dormancy and germination.

Koornneef，M.，Bentsink，L。＆Hilhorst，H。种子休眠和萌发。

Curr. Opin. Plant. Biol.

货币。奥平。工厂。生物。

, 33–36.

https://doi.org/10.1016/S1369-5266(01)00219-9

(2002).

Article

文章

CAS

中科院

PubMed

Google Scholar

谷歌学者

Huo, H. & Bradford, K. J. Molecular and hormonal regulation of thermoinhibition of seed germination. In

Huo，H。＆Bradford，K。J。种子萌发热抑制的分子和激素调节。在

Advances in Plant Dormancy

植物休眠研究进展

(ed. Anderson, J. V.), 3–33 (Springer International Publishing, 2015).

（ed.Anderson，J.V.），3-33（Springer International Publishing，2015）。

https://doi.org/10.1007/978-3-319-14451-1_1

Wei, J. et al. Advance in the thermoinhibition of lettuce (Lactuca sativa L.) seed germination.

Wei，J。等人。生菜（Lactuca sativa L.）种子萌发的热抑制研究进展。

Plants

植物

, 2051.

https://doi.org/10.3390/plants13152051

(2024).

Wei, T. et al. Whole-genome resequencing of 445 Lactuca accessions reveals the domestication history of cultivated lettuce.

Wei，T。等人。445份莴苣种质的全基因组重测序揭示了栽培莴苣的驯化历史。

Nat. Genet.

纳特，基因。

, 752–760.

https://doi.org/10.1038/s41588-021-00831-0

(2021).

Article

文章

CAS

中科院

PubMed

MATH

数学

Google Scholar

谷歌学者

Afroza, B. & Rana, M. K. Lettuce. In Vegetable Crop Science (CRC, 2017).

Afroza，B。和Rana，M.K。莴苣。在蔬菜作物科学（CRC，2017）。

Lebeda, A. et al. Egypt as one of the centers of lettuce domestication: morphological and genetic evidence.

埃及是莴苣驯化中心之一：形态学和遗传学证据。

Euphytica

Euphytica公司

218

https://doi.org/10.1007/s10681-021-02960-3

(2021).

Bita, C. & Gerats, T. Plant tolerance to high temperature in a changing environment: scientific fundamentals and production of heat stress-tolerant crops.

Bita，C。＆Gerats，T。在不断变化的环境中植物对高温的耐受性：科学基础和耐热作物的生产。

Front. Plant. Sci.

。工厂。科学。

https://doi.org/10.3389/fpls.2013.00273

(2013).

Cantliffe, D. J., Sung, Y. & Nascimento, W. M. Lettuce seed germination.

Cantliffe，D.J.，Sung，Y。和Nascimento，W.M。莴苣种子发芽。

Hortic. Rev.

Hortic。Rev.

, 229–275 (2000).

CAS

中科院

Google Scholar

谷歌学者

Gonai, T. et al. Abscisic acid in the thermoinhibition of lettuce seed germination and enhancement of its catabolism by gibberellin.

Gonai，T。等人。脱落酸在生菜种子萌发的热抑制和赤霉素对其分解代谢的增强中的作用。

J. Exp. Bot.

J、实验机器人。

, 111–118.

https://doi.org/10.1093/jxb/erh023

(2004).

Article

文章

CAS

中科院

PubMed

Google Scholar

谷歌学者

Argyris, J. et al. Quantitative trait loci associated with seed and seedling traits in Lactuca.

Argyris，J。等人。与乳菇种子和幼苗性状相关的数量性状基因座。

Theor. Appl. Genet.

西奥。掌声。基因。

111

, 1365–1376.

https://doi.org/10.1007/s00122-005-0066-4

(2005).

Article

文章

PubMed

MATH

数学

Google Scholar

谷歌学者

Argyris, J., Dahal, P., Hayashi, E., Still, D. W. & Bradford, K. J. Genetic variation for lettuce seed thermoinhibition is associated with temperature-sensitive expression of abscisic acid, gibberellin, and ethylene biosynthesis, metabolism, and response genes.

Argyris，J.，Dahal，P.，Hayashi，E.，Still，D.W。＆Bradford，K.J。莴苣种子热抑制的遗传变异与脱落酸，赤霉素和乙烯生物合成，代谢和响应基因的温度敏感表达有关。

Plant. Physiol.

工厂。生理学。

148

, 926–947.

https://doi.org/10.1104/pp.108.125807

(2008).

Article

文章

CAS

中科院

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Hayashi, E., Aoyama, N. & Still, D. W. Quantitative trait loci associated with lettuce seed germination under different temperature and light environments.

Hayashi，E.，Aoyama，N。＆Still，D.W。在不同温度和光照环境下与莴苣种子萌发相关的数量性状基因座。

Genome

基因组

, 928–947.

https://doi.org/10.1139/G08-077

(2008).

Article

文章

CAS

中科院

PubMed

Google Scholar

谷歌学者

Lafta, A. & Mou, B. Evaluation of lettuce genotypes for seed thermotolerance.

Lafta，A。＆Mou，B。评估莴苣基因型的种子耐热性。

https://doi.org/10.21273/HORTSCI.48.6.708

(2013).

Schwember, A. R. & Bradford, K. J. Quantitative trait loci associated with longevity of lettuce seeds under conventional and controlled deterioration storage conditions.

Schwember，A.R。＆Bradford，K.J。在常规和受控变质储存条件下，与莴苣种子寿命相关的数量性状基因座。

J. Exp. Bot.

J、实验机器人。

, 4423–4436.

https://doi.org/10.1093/jxb/erq248

(2010).

Article

文章

CAS

中科院

PubMed

PubMed Central

公共医学中心

MATH

数学

Google Scholar

谷歌学者

Cantliffe, D. J., Fischer, J. M. & Nell, T. A. Mechanism of seed priming in circumventing thermodormancy in lettuce 1.

Cantliffe，D.J.，Fischer，J.M。＆Nell，T.A。种子引发规避莴苣热休眠的机制1。

Plant. Physiol.

工厂。生理学。

, 290–294.

https://doi.org/10.1104/pp.75.2.290

(1984).

Article

文章

CAS

中科院

PubMed

PubMed Central

公共医学中心

MATH

数学

Google Scholar

谷歌学者

Zulfiqar, F. Effect of seed priming on horticultural crops.

Zulfiqar，F。种子引发对园艺作物的影响。

Sci. Hortic.

滑雪。园艺。

286

, 110197.

https://doi.org/10.1016/j.scienta.2021.110197

(2021).

Article

文章

CAS

中科院

MATH

数学

Google Scholar

谷歌学者

Ali, F., Qanmber, G., Li, F. & Wang, Z. Updated role of ABA in seed maturation, dormancy, and germination.

Ali，F.，Qanmber，G.，Li，F。＆Wang，Z。更新了ABA在种子成熟，休眠和萌发中的作用。

J. Adv. Res.

J.Adv.Res.

, 199–214.

https://doi.org/10.1016/j.jare.2021.03.011

(2022).

Article

文章

CAS

中科院

PubMed

Google Scholar

谷歌学者

Bertier, L. D. et al. High-Resolution Analysis of the Efficiency, Heritability, and Editing Outcomes of CRISPR/Cas9-Induced Modifications of NCED4 in Lettuce (Lactuca sativa).

Bertier，L.D.等人。CRISPR/Cas9诱导的莴苣（莴苣）NCED4修饰的效率，遗传力和编辑结果的高分辨率分析。

G3 GenesGenomesGenetics

G3基因基因组遗传学

, 1513–1521.

https://doi.org/10.1534/g3.117.300396

(2018).

Huo, H., Dahal, P., Kunusoth, K., McCallum, C. M. & Bradford, K. J. Expression of 9-cis-EPOXYCAROTENOID DIOXYGENASE4 is essential for Thermoinhibition of Lettuce seed germination but not for seed development or stress tolerance.

Huo，H.，Dahal，P.，Kunusoth，K.，McCallum，C.M。＆Bradford，K.J。9-顺式-环氧类胡萝卜素双加氧酶4的表达对于生菜种子萌发的热抑制至关重要，但对于种子发育或胁迫耐受性则不重要。

Plant. Cell.

工厂。细胞。

, 884–900.

https://doi.org/10.1105/tpc.112.108902

(2013).

Article

文章

CAS

中科院

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Huo, H. et al. Rapid identification of lettuce seed germination mutants by bulked segregant analysis and whole genome sequencing.

Huo，H.等人。通过批量分离分析和全基因组测序快速鉴定莴苣种子萌发突变体。

Plant. J.

工厂。J。

, 345–360.

https://doi.org/10.1111/tpj.13267

(2016).

Article

文章

CAS

中科院

PubMed

MATH

数学

Google Scholar

谷歌学者

Matilla, A. J. Ethylene in seed formation and germination.

Matilla，A.J。乙烯在种子形成和萌发中的作用。

Seed Sci. Res.

。研究。

, 111–126.

https://doi.org/10.1017/S096025850000012X

(2000).

Article

文章

CAS

中科院

MATH

数学

Google Scholar

谷歌学者

Corbineau, F., Rudnicki, R. M. & Côme, D. ACC conversion to ethylene by sunflower seeds in relation to maturation, germination and thermodormancy.

Corbineau，F.，Rudnicki，R.M。＆Côme，D。向日葵种子对乙烯的转化与成熟，萌发和热休眠有关。

Plant. Growth Regul.

工厂。生长调节。

, 105–115.

https://doi.org/10.1007/BF00024769

(1989).

Article

文章

CAS

中科院

Google Scholar

谷歌学者

Khan, A. A. & Prusinski, J. Kinetin enhanced 1-aminocyclopropane-1-carboxylic acid utilization during alleviation of high temperatures stress in lettuce seeds.

Khan，A.A.＆Prusinski，J.Kinetin在缓解莴苣种子高温胁迫期间增强了1-氨基环丙烷-1-羧酸的利用。

Plant. Physiol.

工厂。生理学。

, 733–737.

https://doi.org/10.1104/pp.91.2.733

(1989).

Article

文章

CAS

中科院

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Abeles, F. B. Role of ethylene in Lactuca sativa cv `Grand Rapids’ seed germination.

Abeles，F.B。乙烯在“大急流”莴苣种子萌发中的作用。

Plant. Physiol.

工厂。生理学。

, 780–787.

https://doi.org/10.1104/pp.81.3.780

(1986).

Article

文章

CAS

中科院

PubMed

PubMed Central

公共医学中心

MATH

数学

Google Scholar

谷歌学者

Dunlap, J. R. & Morgan, P. W. Characterization of ethylene/gibberellic acid control of germination in Lactuca sativa L.

Dunlap，J.R。＆Morgan，P.W。乙烯/赤霉素控制莴苣发芽的表征。

Plant. Cell. Physiol.

工厂。细胞。生理学。

, 561–568.

https://doi.org/10.1093/oxfordjournals.pcp.a075468

(1977).

Article

文章

CAS

中科院

MATH

数学

Google Scholar

谷歌学者

Sun, M., Tuan, P. A., Izydorczyk, M. S. & Ayele, B. T. Ethylene regulates post-germination seedling growth in wheat through spatial and temporal modulation of ABA/GA balance.

Sun，M.，Tuan，P.A.，Izydorczyk，M.S。和Ayele，B.T。乙烯通过ABA/GA平衡的时空调节来调节小麦发芽后的幼苗生长。

J. Exp. Bot.

J、实验机器人。

, 1985–2004.

https://doi.org/10.1093/jxb/erz566

(2020).

Article

文章

CAS

中科院

PubMed

Google Scholar

谷歌学者

Zuo, Y. & Xu, Y. Research Progress on the mechanism of GA and ABA during seed germination.

Zuo，Y.＆Xu，Y.种子萌发过程中GA和ABA机制的研究进展。

Mol. Plant. Breed.

摩尔植物。繁殖。

(2020).

Park, S., Shi, A., Meinhardt, L. W. & Mou, B. Genome-wide characterization and evolutionary analysis of the AP2/ERF gene family in lettuce (Lactuca sativa).

Park，S.，Shi，A.，Meinhardt，L.W。＆Mou，B。生菜（莴苣）中AP2/ERF基因家族的全基因组表征和进化分析。

Sci. Rep.

科学。代表。

, 21990.

https://doi.org/10.1038/s41598-023-49245-4

(2023).

Article

文章

ADS

CAS

中科院

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Yoong, F. Y. et al. Genetic variation for thermotolerance in lettuce seed germination is associated with temperature-sensitive regulation of ETHYLENE RESPONSE FACTOR1 (ERF1).

Yoong，F.Y.等人。莴苣种子萌发耐热性的遗传变异与乙烯响应因子1（ERF1）的温度敏感性调节有关。

Plant. Physiol.

工厂。生理学。

170

, 472–488.

https://doi.org/10.1104/pp.15.01251

(2016).

Article

文章

CAS

中科院

PubMed

Google Scholar

谷歌学者

Toh, S. et al. High temperature-induced abscisic acid biosynthesis and its role in the inhibition of gibberellin action in arabidopsis seeds.

Toh，S.等人。高温诱导的脱落酸生物合成及其在抑制拟南芥种子赤霉素作用中的作用。

Plant. Physiol.

工厂。生理学。

146

, 1368.

https://doi.org/10.1104/pp.107.113738

(2008).

Article

文章

CAS

中科院

PubMed

PubMed Central

公共医学中心

MATH

数学

Google Scholar

谷歌学者

Finch-Savage, W. E. & Leubner-Metzger, G. Seed dormancy and the control of germination.

Finch Savage，W.E。和Leubner Metzger，G。种子休眠和发芽控制。

New. Phytol

新建。植物醇

171

, 501–523.

https://doi.org/10.1111/j.1469-8137.2006.01787.x

(2006).

Article

文章

CAS

中科院

PubMed

MATH

数学

Google Scholar

谷歌学者

Mou, B. & Lettuce in

Mou，B。和莴苣

In Vegetables I: Asteraceae, Brassicaceae, Chenopodicaceae, and Cucurbitaceae

蔬菜I：菊科，十字花科，藜科和葫芦科

. 75–116 (eds Prohens, J. & Nuez, F.) (Springer, 2008).

75-116（Eds Prohens，J.和Nuto，F.）（斯普林格，2008年）。

https://doi.org/10.1007/978-0-387-30443-4_3

Argyris, J. et al. A gene encoding an abscisic acid biosynthetic enzyme (LsNCED4) collocates with the high temperature germination locus Htg6.1 in lettuce (Lactuca Sp).

Argyris，J。等人。一种编码脱落酸生物合成酶（LsNCED4）的基因与莴苣（Lactuca Sp。）中的高温发芽基因座Htg6.1配位。

Theor. Appl. Genet.

西奥。掌声。基因。

122

, 95–108.

https://doi.org/10.1007/s00122-010-1425-3

(2011).

Article

文章

CAS

中科院

PubMed

Google Scholar

谷歌学者

Yu, H. J., Hogan, P. & Sundaresan, V. Analysis of the female gametophyte transcriptome of arabidopsis by comparative expression profiling.

Yu，H.J.，Hogan，P。＆Sundaresan，V。通过比较表达谱分析拟南芥的雌配子体转录组。

Plant. Physiol.

工厂。生理学。

139

, 1853–1869.

https://doi.org/10.1104/pp.105.067314

(2005).

Article

文章

CAS

中科院

PubMed

PubMed Central

公共医学中心

MATH

数学

Google Scholar

谷歌学者

Christensen, C. A., Subramanian, S. & Drews, G. N. Identification of gametophytic mutations affecting female gametophyte development in

Christensen，C.A.，Subramanian，S。和Drews，G.N。鉴定影响雌性配子体发育的配子体突变

Arabidopsis

拟南芥

Dev. Biol.

发展生物学。

202

, 136–151.

https://doi.org/10.1006/dbio.1998.8980

(1998).

Article

文章

CAS

中科院

PubMed

Google Scholar

谷歌学者

Christians, M. J., Robles, L. M., Zeller, S. M. & Larsen, P. B. The eer5 mutation, which affects a novel proteasome-related subunit, indicates a prominent role for the COP9 signalosome in resetting the ethylene-signaling pathway in Arabidopsis.

Christians，M.J.，Robles，L.M.，Zeller，S.M。＆Larsen，P.B。影响新型蛋白酶体相关亚基的eer5突变表明COP9信号体在重置拟南芥中的乙烯信号传导途径中起着重要作用。

Plant. J.

工厂。J。

, 467–477.

https://doi.org/10.1111/j.1365-313X.2008.03521.x

(2008).

Article

文章

CAS

中科院

PubMed

Google Scholar

谷歌学者

Houben, M. & Van de Poel, B. 1-Aminocyclopropane-1-carboxylic acid oxidase (ACO): the enzyme that makes the plant hormone ethylene.

。

Front. Plant. Sci.

。工厂。科学。

, 695.

https://doi.org/10.3389/fpls.2019.00695

(2019).

Article

文章

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Wu, Y. S. & Yang, C. Y. Ethylene-mediated signaling confers thermotolerance and regulates transcript levels of heat shock factors in rice seedlings under heat stress.

Wu，Y.S.＆Yang，C.Y。乙烯介导的信号传导赋予耐热性并调节热胁迫下水稻幼苗中热激因子的转录水平。

Bot. Stud.

底部螺柱。

, 23.

https://doi.org/10.1186/s40529-019-0272-z

(2019).

Article

文章

CAS

中科院

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Leung, J. et al. Arabidopsis ABA response gene ABI1: features of a calcium-modulated protein phosphatase.

Leung，J。等人。拟南芥ABA反应基因ABI1：钙调节蛋白磷酸酶的特征。

Science

科学

264

, 1448–1452.

https://doi.org/10.1126/science.7910981

(1994).

Article

文章

ADS

CAS

中科院

PubMed

MATH

数学

Google Scholar

谷歌学者

Ronzier, E. et al. CPK13, a noncanonical Ca2+-Dependent protein kinase, specifically inhibits KAT2 and KAT1 Shaker K + channels and reduces stomatal opening.

Ronzier，E。等人CPK13是一种非典型的Ca2+依赖性蛋白激酶，可特异性抑制KAT2和KAT1 Shaker K+通道并减少气孔开放。

Plant. Physiol.

工厂。生理学。

166

, 314–326.

https://doi.org/10.1104/pp.114.240226

(2014).

Article

文章

CAS

中科院

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Ronen, G., Cohen, M., Zamir, D. & Hirschberg, J. Regulation of carotenoid biosynthesis during tomato fruit development: expression of the gene for lycopene epsilon-cyclase is down-regulated during ripening and is elevated in the mutant.

Ronen，G.，Cohen，M.，Zamir，D。＆Hirschberg，J。番茄果实发育过程中类胡萝卜素生物合成的调节：番茄红素ε环化酶基因的表达在成熟过程中下调，在突变体中升高。

Plant. J.

工厂。J。

, 341–351.

https://doi.org/10.1046/j.1365-313X.1999.00381.x

(1999).

Article

文章

CAS

中科院

PubMed

Google Scholar

谷歌学者

Bai, L., Kim, E. H., DellaPenna, D. & Brutnell, T. P. Novel lycopene epsilon cyclase activities in maize revealed through perturbation of carotenoid biosynthesis.

Bai，L.，Kim，E.H.，DellaPenna，D。＆Brutnell，T.P。通过类胡萝卜素生物合成的扰动揭示了玉米中新的番茄红素ε环化酶活性。

Plant. J.

工厂。J。

, 588–599.

https://doi.org/10.1111/j.1365-313X.2009.03899.x

(2009).

Article

文章

CAS

中科院

PubMed

Google Scholar

谷歌学者

Zhang, X. et al. Seed color in lettuce is determined by the LsTT2, LsCHS, and Ls2OGD genes from the flavonoid biosynthesis pathway.

Zhang，X。等人。莴苣的种子颜色由类黄酮生物合成途径中的LsTT2，LsCHS和Ls2OGD基因决定。

Theor. Appl. Genet.

西奥。掌声。基因。

136

, 241.

https://doi.org/10.1007/s00122-023-04491-y

(2023).

Article

文章

ADS

CAS

中科院

PubMed

Google Scholar

谷歌学者

Reed, R. C., Bradford, K. J. & Khanday, I. Seed germination and vigor: ensuring crop sustainability in a changing climate.

Reed，R.C.，Bradford，K.J。＆Khanday，I。种子发芽和活力：确保作物在不断变化的气候中的可持续性。

Heredity

遗传

128

, 450.

https://doi.org/10.1038/s41437-022-00497-2

(2022).

Article

文章

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Valdes, V. M., Bradford, K. J. & Mayberry, K. S. Alleviation of thermodormancy in coated lettuce seeds by seed priming.

Valdes，V.M.，Bradford，K.J。和Mayberry，K.S。通过种子引发减轻包被莴苣种子的热休眠。

https://doi.org/10.21273/HORTSCI.20.6.1112

(1985).

Sattler, S. E., Gilliland, L. U., Magallanes-Lundback, M., Pollard, M. & DellaPenna, D. Vitamin E is essential for seed longevity and for preventing lipid peroxidation during germination.

Sattler，S.E.，Gilliland，L.U.，Magallanes Lundback，M.，Pollard，M。＆DellaPenna，D。维生素E对于种子寿命和防止发芽过程中的脂质过氧化至关重要。

Plant. Cell.

工厂。细胞。

, 1419–1432.

https://doi.org/10.1105/tpc.021360

(2004).

Article

文章

CAS

中科院

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Debeaujon, I., Léon-Kloosterziel, K. M. & Koornneef, M. Influence of the testa on seed dormancy, germination, and longevity in Arabidopsis.

Debeaujon，I.，Léon Kloosterziel，K.M。＆Koornneef，M。种皮对拟南芥种子休眠，萌发和寿命的影响。

Plant. Physiol.

工厂。生理学。

122

, 403–414.

https://doi.org/10.1104/pp.122.2.403

(2000).

Article

文章

CAS

中科院

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Sano, N. et al. Staying alive: molecular aspects of seed longevity.

Sano，N.等人，《保持活力：种子寿命的分子方面》。

Plant. Cell. Physiol.

工厂。细胞。生理学。

, 660–674.

https://doi.org/10.1093/pcp/pcv186

(2016).

Article

文章

CAS

中科院

PubMed

MATH

数学

Google Scholar

谷歌学者

Mantyla, E., Lang, V. & Palva, E. T. Role of abscisic acid in drought-induced freezing tolerance, cold acclimation, and accumulation of LT178 and RAB18 proteins in Arabidopsis thaliana.

Mantyla，E.，Lang，V。＆Palva，E.T。脱落酸在干旱诱导的拟南芥耐寒性，冷驯化以及LT178和RAB18蛋白积累中的作用。

Plant. Physiol.

工厂。生理学。

107

, 141–148.

https://doi.org/10.1104/pp.107.1.141

(1995).

Article

文章

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Liu, X. et al. Auxin controls seed dormancy through stimulation of abscisic acid signaling by inducing ARF-mediated ABI3 activation in Arabidopsis.

Liu，X。等人。生长素通过诱导拟南芥中ARF介导的ABI3激活，通过刺激脱落酸信号传导来控制种子休眠。

Proc. Natl. Acad. Sci. U. S. A.

程序。纳特尔。阿卡德。科学。U、美国。

110

, 15485–15490.

https://doi.org/10.1073/pnas.1304651110

(2013).

Article

文章

ADS

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Sung, Y., Cantliffe, D. J. & Nagata, R. Using a puncture test to identify the role of seed coverings on thermotolerant lettuce seed germination.

Sung，Y.，Cantliffe，D.J。＆Nagata，R。使用穿刺试验来鉴定种子覆盖物对耐热莴苣种子萌发的作用。

https://doi.org/10.21273/JASHS.123.6.1102

(1998).

Yan, D., Duermeyer, L., Leoveanu, C. & Nambara, E. The functions of the endosperm during seed germination.

Yan，D.，Duermeyer，L.，Leoveanu，C。＆Nambara，E。胚乳在种子萌发过程中的功能。

Plant. Cell. Physiol.

工厂。细胞。生理学。

, 1521–1533.

https://doi.org/10.1093/pcp/pcu089

(2014).

Article

文章

CAS

中科院

PubMed

Google Scholar

谷歌学者

Bethke, P. C. et al. The Arabidopsis aleurone layer responds to nitric oxide, gibberellin, and abscisic acid and is sufficient and necessary for seed dormancy.

拟南芥糊粉层对一氧化氮、赤霉素和脱落酸有反应，是种子休眠所必需的。

Plant. Physiol.

工厂。生理学。

143

, 1173–1188.

https://doi.org/10.1104/pp.106.093435

(2007).

Article

文章

CAS

中科院

PubMed

PubMed Central

公共医学中心

MATH

数学

Google Scholar

谷歌学者

DREW, R. L. K. & BROCKLEHURST, P. A. Investigations on the control of lettuce seed germination at high temperatures.

DREW，R.L.K。和BROCKLEHURST，P.A。关于在高温下控制莴苣种子萌发的研究。

J. Exp. Bot.

J、实验机器人。

, 986–993.

https://doi.org/10.1093/jxb/35.7.986

(1984).

Article

文章

MATH

数学

Google Scholar

谷歌学者

Diederichsen, A. & Jones-Flory, L. L. Accelerated aging tests with seeds of 11 flax (Linum usitatissimum) cultivars.

Diederichsen，A.＆Jones Flory，L.L.用11种亚麻（Linum usitatissimum）品种的种子加速老化试验。

Seed Sci. Technol.

。技术。

, 419–429.

https://doi.org/10.15258/sst.2005.33.2.14

(2005).

Article

文章

Google Scholar

谷歌学者

Lionello, P. et al. Elsevier,. The Mediterranean climate: An overview of the main characteristics and issues. In

Lionello，P。等人，Elsevier，。地中海气候：主要特征和问题概述。在

Developments in Earth and Environmental Sciences

地球与环境科学的发展

(eds. Lionello, P., Malanotte-Rizzoli, P. & Boscolo, R.) vol. 4, 1–26.

（Lionello，P.，Malanotte Rizzoli，P.&Boscolo，R.编辑）第4卷，第1-26页。

https://doi.org/10.1016/S1571-9197(06)80003-0

(2006).

Lebeda, A., Křístková, E., Doležalová, I., Kitner, M. & Widrlechner, M. P. Wild Lactuca species in North America. In North American Crop Wild Relatives, Volume 2: Important Species (eds Greene, S. L., Williams, K. A., Khoury, C. K., Kantar, M. B. & Marek, L. F.) 131–194 (Springer International Publishing, 2019).

Lebeda，A.，Křístková，E.，Doležalová，I.，Kitner，M。＆Widrlechner，M.P。北美野生乳酸菌属物种。在北美作物野生近缘种中，第2卷：重要物种（eds Greene，S.L.，Williams，K.A.，Khoury，C.K.，Kantar，M.B。＆Marek，L.F。）131-194（Springer International Publishing，2019）。

https://doi.org/10.1007/978-3-319-97121-6_5

Werk, K. S. & Ehleringer, J. Effect of nonrandom leaf orientation on reproduction in Lactuca Serriola L.

Werk，K.S。＆Ehleringer，J。非随机叶片方向对莴苣繁殖的影响。

Evolution

进化

, 1334–1337.

https://doi.org/10.1111/j.1558-5646.1986.tb05756.x

(1986).

Article

文章

PubMed

Google Scholar

谷歌学者

Park, S., Shi, A. & Mou, B. Low frequency of the wild-type freezing-tolerance LsCBF7 allele among lettuce population suggests a negative selection during domestication and breeding.

Park，S.，Shi，A。＆Mou，B。生菜种群中野生型耐寒性LsCBF7等位基因的频率较低，表明在驯化和育种过程中存在负选择。

Theor. Appl. Genet.

西奥。掌声。基因。

137

, 135.

https://doi.org/10.1007/s00122-024-04643-8

(2024).

Article

文章

CAS

中科院

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Chadha, A. & Florentine, S. Biology, ecology, distribution and control of the invasive weed, Lactuca serriola L. (Wild Lettuce): a global review.

Chadha，A。和Florentine，S。入侵杂草Lactuca serriola L.（野生莴苣）的生物学，生态学，分布和控制：全球综述。

Plants

植物

, 2157.

https://doi.org/10.3390/plants10102157

(2021).

Article

文章

CAS

中科院

PubMed

PubMed Central

公共医学中心

MATH

数学

Google Scholar

谷歌学者

R core Team. R: A language and environment for statistical computing. Vienna, Austria: R foundation for statistical computing. Retrieved from

R核心团队。R：用于统计计算的语言和环境。奥地利维也纳：R统计计算基金会。检索自

https://www.R-project.org

A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing.

。奥地利维也纳：R统计计算基金会。

Retrieved from https://www.r-project.org/ (2024).

Park, S., Kumar, P., Shi, A. & Mou, B. Population genetics and genome-wide association studies provide insights into the influence of selective breeding on genetic variation in lettuce.

Park，S.，Kumar，P.，Shi，A。＆Mou，B。群体遗传学和全基因组关联研究为选择性育种对莴苣遗传变异的影响提供了见解。

Plant. Genome

工厂。基因组

, e20086.

，e20086年。

https://doi.org/10.1002/tpg2.20086

(2021).

Article

文章

PubMed

Google Scholar

谷歌学者

Reyes-Chin-Wo, S. et al. Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce.

Reyes Chin Wo，S.等人。莴苣中具有体外邻近连接数据和全基因组三倍体的基因组组装。

Nat. Commun.

Nat.普通。

, 14953.

https://doi.org/10.1038/ncomms14953

(2017).

Article

文章

ADS

CAS

中科院

PubMed

PubMed Central

公共医学中心

MATH

数学

Google Scholar

谷歌学者

Browning, B. L. & Browning, S. R. Genotype imputation with millions of reference samples.

Browning，B.L。和Browning，S.R。用数百万个参考样本进行基因型插补。

Am. J. Hum. Genet.

Am.J.Hum.Genet。

, 116–126.

https://doi.org/10.1016/j.ajhg.2015.11.020

(2016).

Article

文章

CAS

中科院

PubMed

PubMed Central

公共医学中心

MATH

数学

Google Scholar

谷歌学者

Lipka, A. E. et al. GAPIT: genome association and prediction integrated tool.

Lipka，A.E.等人。GAPIT：基因组关联和预测集成工具。

Bioinforma Oxf. Engl.

生物信息学。英格兰。

, 2397–2399.

https://doi.org/10.1093/bioinformatics/bts444

(2012).

Article

文章

CAS

中科院

MATH

数学

Google Scholar

谷歌学者

Wang, Q., Tian, F., Pan, Y., Buckler, E. S. & Zhang, Z. A SUPER powerful method for genome wide association study.

Wang，Q.，Tian，F.，Pan，Y.，Buckler，E.S.＆Zhang，Z。一种用于全基因组关联研究的超级强大方法。

PLoS One

公共科学图书馆一号

, e107684.

。

https://doi.org/10.1371/journal.pone.0107684

(2014).

Article

文章

ADS

CAS

中科院

PubMed

PubMed Central

公共医学中心

MATH

数学

Google Scholar

谷歌学者

Chang, C. C. et al. Second-generation PLINK: rising to the challenge of larger and richer datasets.

Chang，C.C.等人，《第二代PLINK：迎接更大、更丰富数据集的挑战》。

GigaScience

https://doi.org/10.1186/s13742-015-0047-8

(2015).

Barrett, J. C., Fry, B., Maller, J. & Daly, M. J. Haploview: analysis and visualization of LD and haplotype maps.

Barrett，J.C.，Fry，B.，Maller，J。＆Daly，M.J。Haploview：LD和单倍型图的分析和可视化。

Bioinforma Oxf. Engl.

生物信息学。英格兰。

, 263–265.

https://doi.org/10.1093/bioinformatics/bth457

(2005).

Article

文章

CAS

中科院

Google Scholar

谷歌学者

Lucas, A. & amap Another multidimensional analysis package.

Lucas，A。＆amap另一个多维分析软件包。

https://CRAN.R-project.org/package=amap

(2022).

Bryant, D. M. et al. A tissue-mapped axolotl de novo transcriptome enables identification of limb regeneration factors.

Bryant，D.M.等人。组织定位的axolotl从头转录组能够鉴定肢体再生因子。

Cell Rep.

细胞代表。

, 762–776.

https://doi.org/10.1016/j.celrep.2016.12.063

(2017).

Article

文章

CAS

中科院

PubMed

PubMed Central

公共医学中心

MATH

数学

Google Scholar

谷歌学者

Download references

下载参考资料

Acknowledgements

致谢

This research was funded by grants from the USDA-AMS Specialty Crop Multistate Program (Award No. 16SCCMAR0001), the USDA-NIFA Agriculture and Food Research Initiative (Award No. 2016-68004-24931), and the USDA-NIFA Specialty Crop Research Initiative (Award No. 2015-51181-24283, 2017-51181-26830, and 2021-51181-35903).

这项研究得到了美国农业部-美国农业科学院（USDA-AMS）特种作物多州计划（奖项编号16SCCMAR0001），美国农业部-美国国家粮食管理局（USDA-NIFA）农业和食品研究计划（奖项编号2016-68004-24931）和美国农业部-美国国家粮食管理局（USDA-NIFA）特种作物研究计划（奖项编号2015-51181-24283，2017-51181-26830和2021-51181-35903）的资助。

This research used resources provided by the SCINet project of the USDA Agricultural Research Service, ARS project number 0500-00093-001-00-D. Mention of a trade name, proprietary product, or vendor does not constitute an endorsement, guarantee, or warranty by the USDA and does not imply its approval to the exclusion of other products or vendors that may be suitable..

。。

Author information

作者信息

Authors and Affiliations

作者和隶属关系

U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD, 20705, USA

U、美国农业部，农业研究服务，贝尔茨维尔，马里兰州，20705，美国

Sookyung Oh, Ezekiel Ahn & Sunchung Park

Sookyung

Horticulture Department, University of Arkansas, Fayetteville, AR, 72701, USA

阿肯色大学园艺系，费耶特维尔，AR，72701，美国

Ainong Shi

艾农市

U.S. Department of Agriculture, Agricultural Research Service, Salinas, CA, 93905, USA

U、美国农业部，农业研究服务，萨利纳斯，加利福尼亚州，93905，美国

Beiquan Mou

北泉模式

Authors

作者

Sookyung Oh

吴秀京

View author publications

查看作者出版物

You can also search for this author in

您也可以在中搜索此作者

PubMed

Google Scholar

谷歌学者

Ezekiel Ahn

以西结·安

View author publications

查看作者出版物

You can also search for this author in

您也可以在中搜索此作者

PubMed

Google Scholar

谷歌学者

Ainong Shi

艾农市

View author publications

查看作者出版物

You can also search for this author in

您也可以在中搜索此作者

PubMed

Google Scholar

谷歌学者

Beiquan Mou

北泉模式

View author publications

查看作者出版物

You can also search for this author in

您也可以在中搜索此作者

PubMed

Google Scholar

谷歌学者

Sunchung Park

孙中公园

View author publications

查看作者出版物

You can also search for this author in

您也可以在中搜索此作者

PubMed

Google Scholar

谷歌学者

Contributions

捐款

B.M. and A.S. obtained funding for this investigation. S.P. and B.M. conceptualized the study and designed experiments. S.P and S.O conducted the experiments and analyzed the results with the help of E.A. The results were validated by B.M, E.A, and A.S, all of whom also contributed to writing the manuscript.

B、 M.和A.S.获得了这项调查的资金。S、 P.和B.M.将研究概念化并设计了实验。S、 P和S.O在E.A的帮助下进行了实验并分析了结果。结果得到了B.M，E.A和A.S的验证，他们都为撰写手稿做出了贡献。

All authors read and approved the final paper..

所有作者都阅读并批准了最终论文。。

Corresponding authors

通讯作者

Correspondence to

通信对象

Beiquan Mou

北泉模式

或

Sunchung Park

孙中公园

Ethics declarations

道德宣言

Competing interests

相互竞争的利益

The authors declare no competing interests.

作者声明没有利益冲突。

Additional information

其他信息

Publisher’s note

出版商注释

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Springer Nature在已发布的地图和机构隶属关系中的管辖权主张方面保持中立。

Electronic supplementary material

电子补充材料

Below is the link to the electronic supplementary material.

以下是电子补充材料的链接。

Supplementary Material 1

补充材料1

Supplementary Material 2

补充材料2

Rights and permissions

权限和权限

Open Access

开放存取

This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made.

本文根据知识共享署名4.0国际许可证进行许可，该许可证允许以任何媒体或格式使用，共享，改编，分发和复制，只要您对原始作者和来源给予适当的信任，提供知识共享许可证的链接，并指出是否进行了更改。

The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.

To view a copy of this licence, visit .

要查看此许可证的副本，请访问。

http://creativecommons.org/licenses/by/4.0/

Reprints and permissions

重印和许可

About this article

关于本文

Cite this article

引用本文

Oh, S., Ahn, E., Shi, A.

哦，S.，安，E.，石，A。

et al.