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作物学报

作物学报 ›› 2025, Vol. 51 ›› Issue (8): 2020-2032.doi: 10.3724/SP.J.1006.2025.51020

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

小麦幼苗根系性状全基因组关联分析及TaSRL-3B优异等位基因发掘

蔡金珊1(), 李超男2, 王景一2, 李宁1, 柳玉平2, 景蕊莲2, 李龙2,*(), 孙黛珍1,*()   

  1. 1山西农业大学农学院, 山西太谷 030801
    2作物基因资源与育种全国重点实验室 / 中国农业科学院作物科学研究所, 北京 100081
  • 收稿日期:2025-02-24 接受日期:2025-06-01 出版日期:2025-08-12 网络出版日期:2025-06-10
  • 通讯作者: *孙黛珍, E-mail: sdz64@126.com;李龙, E-mail: lilong01@caas.cn
  • 作者简介:E-mail: 2743445979@qq.com
  • 基金资助:
    国家重点研发计划项目(2022YFD1200201);财政部和农业农村部国家现代农业产业技术体系建设专项(CARS-03-5)

Genome-wide association study of root traits in wheat seedlings and identification of a superior allele at TaSRL-3B

CAI Jin-Shan1(), LI Chao-Nan2, WANG Jing-Yi2, LI Ning1, LIU Yu-Ping2, JING Rui-Lian2, LI Long2,*(), SUN Dai-Zhen1,*()   

  1. 1College of Agriculture, Shanxi Agricultural University, Taigu 030801, Shanxi, China
    2State Key Laboratory of Crop Gene Resources and Breeding / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • Received:2025-02-24 Accepted:2025-06-01 Published:2025-08-12 Published online:2025-06-10
  • Contact: *E-mail: sdz64@126.com;E-mail: lilong01@caas.cn
  • Supported by:
    National Key R&D Program of China(2022YFD1200201);China Agriculture Research System of MOF and MARA(CARS-03-5)

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摘要：

根系是小麦吸收土壤水分和养分的器官, 其形态特征与产量及耐逆性密切相关。因此, 发掘根系形态相关遗传位点及优异等位基因对于小麦改良具有重要意义。本项目以277份小麦种质为材料, 采用凝胶根室法鉴定总根长、根表面积及根角度等8种幼苗根系性状, 结合小麦660K SNP芯片的分型结果开展3种模型(GLM、MLM和FarmCPU)全基因组关联分析(GWAS)。共检测到52个关联位点, 其中包括6个与多个根系性状相关的一因多效性遗传位点(Loci17、Loci20、Loci22、Loci38、Loci46、Loci47), 分别位于染色体3A、3B、3D、5A、6A和6B上。在位点Loci20中克隆到调控根系性状候选基因TaSRL-3B, 其序列全长1089 bp, 无内含子, 第78~235位氨基酸处有1个保守的NAC结构域。在该基因编码区检测到1个20 bp的插入/缺失变异(InDel717), 该变异导致移码突变且与Loci20位点的候选SNP (cSNP, AX-108758584)紧密连锁(R2 = 0.84)。277份供试小麦材料中携带等位基因TaSRL-3BIn的种质平均最大根长、总根长及根表面积均显著大于携带等位基因TaSRL-3BDel的种质。以携带TaSRL-3BDel的鲁麦14 (LM14)为受体亲本、携带TaSRL-3BIn的陕合6号 (SH6)为供体亲本, 创制回交导入系群体(BC3F5)。利用基于InDel717开发的分子标记从中鉴定出5个携带TaSRL-3BIn的鲁麦14近等基因系。与鲁麦14相比, 其近等基因系的最大根长、总根长、根表面积及根体积均显著增加, 进一步表明TaSRL-3B参与调控小麦幼苗根系形态。与小麦地方品种相比, 我国现代育成品种中长根型等位基因TaSRL-3BIn频率减少。本研究为加快小麦根系遗传调控网络构建和功能解析提供了重要信息, 有助于小麦根系的遗传改良。

关键词: 小麦, 幼苗, 根系形态, 全基因组关联分析, 候选基因

Abstract:

The root system is the primary organ responsible for water and nutrient uptake in wheat, and its morphological characteristics are closely associated with yield and tolerance to abiotic stress. Therefore, identifying genetic loci and favorable alleles that control root morphology is of great importance for wheat improvement. In this study, 277 wheat accessions were evaluated using a gel-chamber-based observation method to characterize eight root morphological traits at the seedling stage, including total root length, root surface area, and root angle. Based on genotyping with the Wheat 660K SNP Array, a genome-wide association study (GWAS) was performed using three models (GLM, MLM, and FarmCPU), leading to the identification of 52 associated loci. Among them, six pleiotropic loci (Loci17, Loci20, Loci22, Loci38, Loci46, and Loci47) were located on chromosomes 3A, 3B, 3D, 5A, 6A, and 6B, respectively. Within Loci20, the candidate gene TaSRL-3B, associated with root morphology, was cloned. This gene has a full-length sequence of 1089 bp, lacks introns, and contains a conserved NAC domain between amino acids 78 and 235. A 20-bp insertion/deletion (InDel717) in the coding region of TaSRL-3B caused a frameshift mutation and showed strong linkage (R2 = 0.84) with the candidate SNP (AX-108758584) in Loci20. Accessions carrying the TaSRL-3BIn allele exhibited significantly greater maximum root length, total root length, and root surface area compared to those with the TaSRL-3BIn. A backcross introgression line population (BC3F5) was developed using Lumai 14 (LM14, carrying TaSRL-3BDel as the recurrent parent and Shaanhe 6 (SH6, carrying TaSRL-3BIn as the donor. A molecular marker based on InDel717 was used to identify five near-isogenic lines (NILs) carrying TaSRL-3BIn from this population. Compared to LM14, these lines showed significant improvements in maximum root length, total root length, root surface area, and root volume, further confirming the role of TaSRL-3B in shaping seedling root morphology. Notably, the frequency of the long-root allele TaSRL-3BIn has declined in modern Chinese cultivars compared to landraces. This study provides valuable insights into the genetic regulation of wheat root traits and supports the genetic improvement of root systems for enhanced wheat performance.

Key words: wheat, seedling, root morphology, genome-wide association analysis, candidate gene

表1

根系表型统计分析"

性状
Trait		 变异范围
Range		 均值
Mean		 标准差
SD		 变异系数
CV (%)		 广义遗传力
Broad-sense heritability (%)
最大根长 MRL (cm) 7.59-20.30 16.02 1.56 9.74 83.41
总根长 TRL (cm) 32.88-71.89 51.37 7.85 15.28 79.16
根直径 RD (mm) 0.40-0.57 0.49 0.03 6.12 78.10
根数目 RN 3.11-5.67 4.49 0.55 12.25 74.13
根表面积 RS (cm2) 4.70-11.57 7.85 1.23 15.67 76.32
根体积 RV (cm3) 0.06-0.17 0.09 0.02 22.22 74.05
根鲜重 RFW (g) 0.03-0.11 0.07 0.01 14.29 69.13
根角度 RA (°) 25.90-155.82 108.26 28.29 26.13 77.79

图1

小麦幼苗根系性状相关性矩阵 对角线为各性状的名称及频率直方图, 左下侧为根系性状散点图, 红色线条表示线性回归, 右上侧为皮尔逊相关系数。*和**分别表示在0.05和0.01水平上显著相关, 颜色越深相关性越强。缩写同表1。"

图2

小麦幼苗根系性状全基因组关联分析 A~C: 基于GLM、MLM和FarmCPU模型的根系性状全基因组关联分析曼哈顿图, 从里环到外环分别表示最大根长、总根长、根直径、根数目、根表面积、根体积、根鲜重和根角度的全基因组关联分析结果。D: 基于不同模型的根系性状全基因组关联分析结果韦恩图。E: 关联位点在染色体上的分布, 红色标示一因多效性位点。GLM: 一般线性模型; MLM: 混合线性模型; FarmCPU: 固定与随机模型循环概率统一模型。"

附表1

小麦根系性状显著关联位点"

关联位点 性状 候选SNP 染色体 位置 P值GLM P值MLM P值FarmCPU
Associated loci Trait Candidate SNP Chromosome Position (bp) -log10 (PGLM) -log10(PMLM) -log10(PFarmCPU)
Loci1 RA AX-94530450 1A 1,174,785 6.36 4.59 6.36
Loci2 TRL AX-94938835 1A 45,797,074 4.80 3.86 6.81
Loci3 RV AX-108830982 1A 49,331,465 4.96 4.20 4.96
Loci4 RD AX-95211457 1A 57,764,436 4.80 2.51 4.80
Loci5 RA AX-110550989 1A 363,636,440 5.10 2.47 5.10
Loci6 RD AX-95151393 1B 94,831,699 4.95 2.73 4.95
Loci7 RA AX-109887764 1B 684,214,070 5.25 4.32 5.25
Loci8 RD AX-94783903 1D 58,760,372 5.67 2.92 5.67
Loci9 RD AX-94763625 1D 62,415,780 4.79 2.54 4.79
Loci10 RA AX-108748925 1D 293,524,586 4.74 2.14 4.74
Loci11 RN AX-108757188 2A 14,946,475 6.45 5.35 6.45
Loci12 RN AX-110058193 2B 27,539,477 4.88 2.66 4.88
Loci13 RN AX-95124238 2D 598,329,680 5.08 4.15 5.08
Loci14 RD AX-111129296 3A 15,334,246 5.06 4.57 5.06
Loci15 RV AX-94413327 3A 33,200,963 5.60 4.43 5.60
Loci16 RN AX-94531407 3A 355,255,702 5.11 3.97 5.11
Loci17 TRL AX-95170863 3A 642,157,356 8.74 4.90 0.07
Loci17 RS AX-95170863 3A 642,157,356 9.02 5.31 0.78
Loci18 RN AX-110919402 3B 272,543,663 5.80 3.26 5.80
Loci19 TRL AX-109991407 3B 627,748,254 7.07 4.73 8.57
Loci20 MRL AX-108758584 3B 658,464,182 8.00 5.16 13.56
Loci20 TRL AX-108758584 3B 658,464,182 10.28 4.78 0.03
Loci20 RS AX-108758584 3B 658,464,182 9.51 5.01 13.92
Loci21 RD AX-108861242 3D 41,269,285 4.80 5.37 4.80
Loci22 MRL AX-95079631 3D 496,787,830 7.37 5.01 0.14
Loci22 TRL AX-95079631 3D 496,787,830 10.33 5.94 9.82
Loci22 RS AX-95079631 3D 496,787,830 8.90 5.65 0.09
Loci23 TRL AX-94519825 3D 504,057,903 8.55 4.98 0.13
Loci24 RN AX-111498171 3D 587,502,221 5.07 3.73 5.07
Loci25 RN AX-109907879 3D 611,193,094 4.77 3.66 4.77
Loci26 RFW AX-110691523 4A 2,981,188 4.83 3.52 4.83
Loci27 RA AX-110721031 4A 601,774,555 4.91 2.99 4.91
Loci28 RA AX-109400915 4A 614,230,276 6.70 4.77 6.70
Loci29 RD AX-110473901 4A 719,247,368 4.83 2.68 4.83
Loci30 RA AX-95229763 4B 14,112,442 4.83 3.02 4.83
Loci31 RA AX-109453026 4B 217,485,661 5.36 2.92 5.36
Loci32 RA AX-111556840 4B 226,194,248 4.88 2.47 4.88
Loci33 RA AX-111593000 4B 237,489,681 5.29 2.66 5.29
Loci34 RA AX-94629126 4B 281,732,587 5.06 3.69 5.06
Loci35 RA AX-109330449 4B 306,933,435 4.80 2.36 4.80
Loci36 RA AX-110103911 4B 361,732,573 4.96 2.57 4.96
Loci37 RV AX-109216467 4D 206,954,832 5.12 4.61 5.12
Loci38 TRL AX-109929811 5A 39,928,718 6.15 4.87 7.16
Loci38 RFW AX-109929811 5A 39,928,718 5.17 4.69 5.17
Loci38 RS AX-109929811 5A 39,928,718 5.77 4.66 11.90
Loci39 RN AX-94790761 5B 15,321,516 4.74 3.88 4.74
Loci40 MRL AX-109840604 5B 604,060,280 4.77 3.46 6.71
Loci41 RA AX-110957626 5B 691,956,913 7.53 6.64 7.53
Loci42 RD AX-110048366 5D 31,117,168 5.04 2.98 5.04
Loci43 RA AX-94486801 5D 553,010,006 5.16 3.70 5.16
Loci44 RD AX-108863773 6A 13,601,639 4.95 3.17 4.95
Loci45 RFW AX-109936313 6A 50,437,525 5.53 4.24 5.53
Loci46 TRL AX-110579044 6A 58,050,390 6.32 3.48 6.99
Loci46 RFW AX-110579044 6A 58,050,390 6.58 4.57 6.58
Loci46 RS AX-110579044 6A 58,050,390 6.93 3.96 9.22
Loci47 MRL AX-95018127 6B 19,999,314 7.67 5.22 0.34
Loci47 TRL AX-95018127 6B 19,999,314 8.97 5.08 0.29
Loci47 RS AX-95018127 6B 19,999,314 7.72 4.83 0.01
Loci48 RV AX-108958707 6B 93,414,710 5.08 4.03 5.08
Loci49 RFW AX-109954348 6B 94,122,920 6.60 4.56 6.60
Loci50 TRL AX-108776159 6B 713,461,853 5.00 2.75 5.56
Loci51 RA AX-109078183 6D 7,469,443 5.18 3.40 5.18
Loci52 RN AX-94519359 7A 538,102,732 4.93 3.59 4.93

表2

小麦根系性状的一因多效关联位点"

关联位点 性状 候选SNP 染色体 位置 P值GLM P值MLM P值FarmCPU
Associated loci Trait Candidate SNP Chromosome Position (bp) -log10(PGLM) -log10(PMLM) -log10(PFarmCPU)
Loci17 TRL AX-95170863 3A 642,157,356 8.74 4.90 0.07
Loci17 RS AX-95170863 3A 642,157,356 9.02 5.31 0.78
Loci20 MRL AX-108758584 3B 658,464,182 8.00 5.16 13.56
Loci20 TRL AX-108758584 3B 658,464,182 10.28 4.78 0.03
Loci20 RS AX-108758584 3B 658,464,182 9.51 5.01 13.92
Loci22 MRL AX-95079631 3D 496,787,830 7.37 5.01 0.14
Loci22 TRL AX-95079631 3D 496,787,830 10.33 5.94 9.82
Loci22 RS AX-95079631 3D 496,787,830 8.90 5.65 0.09
Loci38 TRL AX-109929811 5A 39,928,718 6.15 4.87 7.16
Loci38 RFW AX-109929811 5A 39,928,718 5.17 4.69 5.17
Loci38 RS AX-109929811 5A 39,928,718 5.77 4.66 11.90
Loci46 TRL AX-110579044 6A 58,050,390 6.32 3.48 6.99
Loci46 RFW AX-110579044 6A 58,050,390 6.58 4.57 6.58
Loci46 RS AX-110579044 6A 58,050,390 6.93 3.96 9.22
Loci47 MRL AX-95018127 6B 19,999,314 7.67 5.22 0.34
Loci47 TRL AX-95018127 6B 19,999,314 8.97 5.08 0.29
Loci47 RS AX-95018127 6B 19,999,314 7.72 4.83 0.01

表3

Loci20关联位点基因功能注释"

基因号 Gene ID 物理位置 Physical position (bp) 功能注释 Gene annotation
TraesCS3B02G421100 Chr.3B: 658,058,978-658,060,408 多巴双加氧酶 4,5-DOPA dioxygenase extradiol
TraesCS3B02G421200 Chr.3B: 658,062,268-658,065,391 外二醇双加氧酶 Extradiol dioxygenase
TraesCS3B02G421300 Chr.3B: 658,462,627-658,463,973 含NAC结构域蛋白 NAC domain containing protein
TraesCS3B02G421400 Chr.3B: 658,486,988-658,488,416 邻氨基苯甲酸 O-甲基转移酶1 Anthranilate O-methyltransferase 1
TraesCS3B02G421500 Chr.3B: 658,489,846-658,491,612 邻氨基苯甲酸 O-甲基转移酶1 Anthranilate O-methyltransferase 1
TraesCS3B02G421600 Chr.3B: 658,494,276-658,498,604 转录起始因子TFIID 亚基9 TFIID subunit 9

图3

TaSRL-3B等位变异与cSNP及根系表型的相关性 A: TaSRL-3B基因等位变异及其与根系性状的关联分析(MLM模型)。红、黄、蓝点分别表示TaSRL-3B基因等位变异与最大根长、根表面积和总根长关联分析结果。B: TaSRL-3B等位变异及cSNP的连锁不平衡分析。C~E: 携带插入型(In717)等位变异小麦材料与携带缺失型(Del717)等位变异小麦材料的根系性状差异比较。**表示在0.01水平上显著相关。缩写同表1。cSNP: 编码区单核苷酸多态性; In: 插入; Del: 缺失。"

图4

鲁麦14近等基因系创制及其根系表型分析 A: 利用STSTaSRL-3B分子标记鉴定鲁麦14和陕合6号基因型。B: 鲁麦14近等基因系创制流程。C: 鲁麦14及其近等基因系幼苗根系照片, 标尺为2 cm。D~G: 鲁麦14及其近等基因系幼苗根系性状比较, 柱状图顶部的字母表示组间差异显著性, 小写字母表示显著水平α = 0.05。LM14: 鲁麦14; SH6: 陕合6号。"

图5

TaSRL-3B等位基因在我国十大麦区的频率分布 A: TaSRL-3B等位基因在地方品种中的分布。B: TaSRL-3B等位基因在现代育成品种中的分布。麦区I: 北部冬麦区; 麦区II: 黄淮冬麦区; 麦区III: 长江中下游冬麦区; 麦区IV: 西南冬麦区; 麦区V: 华南冬麦区; 麦区VI: 东北春麦区; 麦区VII: 北部春麦区; 麦区VIII: 西北春麦区; 麦区IX: 青藏春冬麦区; 麦区X: 新疆冬春麦区。"

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