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作物学报

作物学报 ›› 2024, Vol. 50 ›› Issue (3): 590-602.doi: 10.3724/SP.J.1006.2024.31034

所属专题： 小麦：遗传育种·种质资源·分子遗传学

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

小麦胚芽鞘长度QTL定位和GWAS分析

郝倩琳1(), 杨廷志1, 吕新茹1, 秦慧敏1, 王亚林1, 贾晨飞1, 夏先春2, 马武军1, 徐登安1,*()   

  1. 1青岛农业大学农学院, 山东青岛 266109
    2中国农业科学院作物科学研究所, 北京 100081
  • 收稿日期:2023-05-18 接受日期:2023-09-13 出版日期:2024-03-12 网络出版日期:2023-09-27
  • 通讯作者: *徐登安, E-mail: xudengan200@126.com
  • 作者简介:E-mail: haoqianlin_0211@163.com
  • 基金资助:
    青岛农业大学高层次人才科研启动基金(663/1122023);山东省自然科学基金项目(ZR202103020229);国家自然科学基金青年科学基金项目(32101733)

QTL mapping and GWAS analysis of coleoptile length in bread wheat

HAO Qian-Lin1(), YANG Ting-Zhi1, LYU Xin-Ru1, QIN Hui-Min1, WANG Ya-Lin1, JIA Chen-Fei1, XIA Xian-Chun2, MA Wu-Jun1, XU Deng-An1,*()   

  1. 1College of Agronomy, Qingdao Agricultural University, Qingdao 266109, Shandong, China
    2Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • Received:2023-05-18 Accepted:2023-09-13 Published:2024-03-12 Published online:2023-09-27
  • Contact: *E-mail: xudengan200@126.com
  • Supported by:
    High-level Talents Project of Qingdao Agricultural University(663/1122023);Shandong Provincial Natural Science Foundation(ZR202103020229);National Natural Science Foundation of China(32101733)

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摘要：

在干旱条件下, 小麦(Triticum aestivum L.)适当深播可提高出苗率, 胚芽鞘长度决定了小麦播种的最大深度, 因此培育长胚芽鞘小麦品种至关重要。为了挖掘控制小麦胚芽鞘长度相关的数量性状位点(quantitative trait loci, QTL), 本研究以275份豆麦/石4185重组自交系(recombinant inbred lines, RIL)群体和186份自然群体为材料, 根据90K SNP芯片的分型结果, 利用3个环境下小麦胚芽鞘长度表型数据进行QTL鉴定。采用完备区间作图法(inclusive composite interval mapping, ICIM)在RIL群体中鉴定到2个稳定的QTL位点, 分别位于4BS (30.17~40.59 Mb)和6BL (700.08~703.53 Mb)染色体上, 解释表型变异率(PVE)分别为26.29%~28.46%和4.16%~4.36%; 全基因组关联分析(GWAS)采用混合线性模型(Mixed linear model, MLM)方法, 共鉴定到36个稳定的QTL位点, 分别位于1A (3)、1B (3)、1D (2)、2A (1)、3A (2)、3B (2)、4B (11)、5A (1)、5B (3)、6B (4)、7A (2)、7B (2)染色体上, 在3个环境中重复检测到的显著关联位点有7个, 其中3个位点与已报道的位点重叠或邻近, 其他4个位点推测为新位点, 分别位于1A (499.03 Mb)、3A (73.06 Mb)、4B (648.74~648.87 Mb)、7A (36.31 Mb)染色体上, 预测了5个候选基因(TraesCS1A03G0748300、Rht1、TraesCS4B03G0110000、TraesCS4B03G0112200和TraesCS7A03G0146600)。在两个群体中均鉴定到位于4BS (30.17~40.59 Mb)染色体上的主效QTL位点, 该位点的候选基因Rht1已被证实能降低小麦胚芽鞘长度。该研究结果为挖掘控制小麦胚芽鞘长度的基因以及胚芽鞘长度相关性状分子标记辅助选择育种奠定了基础。

关键词: 小麦, 胚芽鞘长度, QTL定位, 全基因组关联分析

Abstract:

Under drought conditions, the emergence rate of wheat (Triticum aestivum L.) can be improved by proper deep sowing. The maximum sowing depth of wheat is determined by the length of the coleoptile, so it is very important to cultivate wheat varieties with long coleoptile. In this study, a recombinant inbred line (RIL) population consisting of 275 lines derived from the cross of Doumai and Shi 4185, and 186 natural population materials were used as the experimental materials. Genotyping results of 90K SNP chip were used to identify QTL for wheat coleoptile length in three different environments. The results showed that two stable QTL sites were identified by inclusive composite interval mapping in the RIL population. The two QTL located on Chromosome 4BS (30.17-40.59 Mb) and 6BL (700.08-703.53 Mb), respectively, and explained 26.29%-28.46% and 4.16%- 4.36% of the phenotypic variance, respectively. A total of 36 stable QTL were identified in the genome-wide association study (GWAS) using the mixed linear model. They were located on Chromosome 1A (3), 1B (3), 1D (2), 2A (1), 3A (2), 3B (2), 4B (11), 5A (1), 5B (3), 6B (4), 7A (2), and 7B (2), respectively. Seven significant association loci were repeatedly detected in the three environments, three of which overlapped or were adjacent to reported loci, and the other four loci were presumed to be new loci. They were located on Chromosomes 1A (499.03 Mb), 3A (73.06 Mb), 4B (648.74-648.87 Mb), and 7A (36.31 Mb), respectively. Five candidate genes (TraesCS1A03G0748300, Rht1, TraesCS4B03G0110000, TraesCS4B03G0112200, and TraesCS7A03G0146600) were predicted. A major QTL locus on Chromosome 4BS (30.17-40.59 Mb) was identified in both RIL and natural populations, and the candidate gene Rht1 at this locus had been shown to reduce the length of wheat coleoptile. The results of this study lay a foundation for the identification of genes controlling the length of coleoptile in wheat and the maker-assisted selection breeding.

Key words: wheat, coleoptile length, QTL mapping, GWAS

表1

豆麦/石4185 RIL群体亲本及其275个家系胚芽鞘长度基本统计数据"

环境
Environment		 亲本 Parents RIL家系 RIL lines
豆麦
Doumai		 石4185
Shi 4185		 最小值
Min.		 最大值
Max.		 均值
Mean		 标准差
SD		 变异系数
CV (%)
E1 5.41 4.49 2.88 6.33 4.32 0.57 13.31
E2 5.65 4.57 3.23 6.16 4.29 0.56 13.06
E3 5.16 4.54 3.10 6.21 4.27 0.58 13.50
BLUE 5.40 4.54 3.14 6.20 4.29 0.55 12.76

图1

亲本(石4185和豆麦)幼苗图"

图2

豆麦/石4185 RIL群体亲本及其275个家系胚芽鞘长度频数分布图 E1、E2、E3分别代表2020-2021青岛、2021-2022青岛、2020-2021新乡3个环境下收获种子测定的胚芽鞘长度。"

表2

豆麦/石4185 RIL群体亲本及其275个家系胚芽鞘长度在不同环境间相关性分析及广义遗传力"

环境
Environment		 相关系数 Correlation coefficient 广义遗传力
H2
E1 E2 E3
E1 1 0.92
E2 0.89** 1
E3 0.80** 0.88** 1

图3

豆麦/石4185 RIL群体胚芽鞘长度QTL 图示连锁图谱仅展示了区间内的部分标记。位于4BS染色体的“绿色革命”基因Rht1未用于构建连锁图谱, 其在图谱上位置为根据基因及附近标记在中国春参考基因组IWGSC RefSeq v2.1 (http://www.wheatgenome.org/[40])上物理位置的示意。"

表3

豆麦/石4185 RIL群体中定位到的胚芽鞘长度QTL"

数量性状位点a
QTL a		 环境
Environment		 侧翼标记
Flanking marker		 物理区间b
Physiol interval (Mb) b		 LOD值c
LOD value c		 贡献率
PVE (%)		 加性效应
Add
QCL.qau-4BS E1 IWA102-IWB54814 30.17-40.59 18.43 27.84 0.32
E2 IWA102-IWB54814 30.17-40.59 15.51 26.29 0.30
E3 IWA102-IWB54814 30.17-40.59 16.99 26.66 0.31
BLUE IWA102-IWB54814 30.17-40.59 19.32 28.46 0.31
QCL.qau-6BL E1 IWB19986-IWB35852 702.16-703.53 3.15 4.16 -0.12
E3 IWB63870-IWB19986 700.08-702.16 3.02 4.36 -0.12
BLUE IWB19986-IWB35852 702.16-703.53 15.03 20.97 -0.25

表4

186份自然群体材料胚芽鞘长度统计分析"

环境
Environment		 均值
Mean		 标准差
SD		 变异系数
CV (%)		 相关系数 Correlation coefficient 遗传力
H2
E1 E2 E3
E1 3.98 0.55 13.74 1 0.91
E2 4.01 0.56 14.07 0.94** 1
E3 4.03 0.57 14.25 0.93** 0.93** 1
BLUE 4.01 0.55 13.70

图4

186份自然群体材料胚芽鞘长度频数分布图 E1、E2、E3分别代表2020-2021青岛、2021-2022青岛、2020-2021新乡3个环境下收获种子测定的胚芽鞘长度。"

图5

本研究中186份自然群体材料亲缘关系和群体结构 A: 亲缘关系; B: 主成分分析; C: 邻接进化树。"

表5

基于MLM模型在至少2个环境下检测到的CL关联位点"

环境a
Environment a		 标记名称
Marker name		 基因型b
Allele b		 物理位置c
Physical position (Mb) c		 P最小值d
P-value min. d		 P最大值d
P-value max. d
E1/BLUE IWB30674 G/A 1A:48.36 1.59E-04 3.16E-05
E1/E2/E3/BLUE IWB50788 G/A 1A:499.03 6.07E-04 1.40E-04
E3/BLUE IWA7871 G/A 1A:505.76 5.98E-04 1.23E-04
E1/E3/BLUE IWB21039 G/A 1B:30.67 9.25E-04 1.99E-04
E3/BLUE IWB53874 G/A 1B:588.25 2.83E-04 2.28E-04
E3/BLUE IWB74028 G/A 1B:690.58 8.03E-04 7.03E-04
E1/BLUE IWB18554 G/A 1D:42.77 1.00E-03 4.68E-04
E1/BLUE IWA830 G/A 1D:43.07 1.00E-03 4.68E-04
E1/E2/BLUE IWB64018 G/A 2A:757.65 3.83E-04 1.30E-05
E2/E3/BLUE IWB2733 G/A 3A:72.88 8.60E-04 6.15E-04
E1/E2/E3/BLUE IWB53051 G/A 3A:73.06 5.40E-04 1.52E-04
E1/E2/E3/BLUE IWB24605 G/A 3B:19.95 2.26E-04 1.17E-04
E1/BLUE IWB39644 G/A 3B:75.98 7.11E-04 5.20E-04
E1/E2/E3/BLUE IWB49875 G/A 4B:24.28 8.57E-04 5.50E-05
E1/E2/E3/BLUE IWB70449 G/A 4B:40.43 7.36E-04 9.01E-05
E1/E2/E3/BLUE IWB54814 G/A 4B:40.59 3.42E-05 7.35E-06
E1/BLUE IWA6850 G/A 4B:40.76 9.74E-04 8.55E-04
E1/E3/BLUE IWB4719 G/A 4B:40.77 5.04E-04 1.79E-04
E1/E3/BLUE IWB25737 G/A 4B:41.02 5.55E-04 2.55E-04
E1/BLUE IWB40899 G/A 4B:574.98 7.29E-04 5.86E-04
E1/BLUE IWB59718 G/A 4B:577.08 8.58E-04 8.18E-04
E1/BLUE IWB71859 G/A 4B:578.54 9.42E-04 7.17E-04
E1/E2/E3/BLUE IWB53155 G/A 4B:648.74 3.86E-04 5.06E-05
E1/E2/E3/BLUE IWB42023 G/A 4B:648.87 5.14E-04 6.61E-05
E1/E3 IWB35845 G/A 5A:710.07 5.69E-04 5.66E-04
E1/BLUE IWA6527 G/A 5B:211.64 7.49E-04 2.81E-04
E1/BLUE IWB71849 G/A 5B:607.90 9.62E-04 2.43E-04
E/E2 IWB63425 G/A 5B:75.60 9.64E-04 9.60E-04
E2/E3 IWB62054 G/A 6B:123.26 7.01E-04 6.74E-04
E2/BLUE IWB56800 G/A 6B:128.10 6.75E-04 4.32E-04
E2/E3 IWB68130 G/A 6B:146.70 9.96E-04 5.02E-04
E2/E3 IWB65561 G/A 6B:683.94 8.99E-04 7.31E-04
E2/E3 IWB22879 G/A 7A:31.41 7.50E-04 5.52E-04
E1/E2/E3/BLUE IWB11001 G/A 7A:36.31 8.74E-04 4.53E-05
E3/BLUE IWB72566 G/A 7B:203.84 9.80E-04 4.88E-04
E1/E3/BLUE IWB11945 G/A 7B:204.38 7.06E-04 1.98E-04

图6

186份自然群体材料胚芽鞘长度全基因组关联分析 A: 基于混合线性模型下胚芽鞘长度BLUE值曼哈顿图, X轴代表小麦21条染色体上的SNP标记, Y轴代表-log10 (P-value)值; B: 基于混合线性模型下胚芽鞘长度BLUE值Q-Q图, X轴代表经过负常数对数转换的期望P值; Y轴代表经过负常数对数转换观察到的P值。"

表6

CL关联位点候选基因"

标记名称
Marker name		 标记物理位置a
Position (Mb) a		 基因名称b
Gene name b		 基因物理位置c
Position (Mb) c		 同源基因d
Homologs d		 基因功能
Gene function
IWB50788 1A:499.03 1A03G0748300 1A:496.71 OsEXP4[48] Alpha-expansin OsEXPA4
IWB70449 4B:40.43 Rht1 4B:33.61 DELLA protein
IWB54814 4B:40.59 4B03G0110000 4B:42.02 AT5G39760[50] Zinc finger homeodomain protein
IWB54814 4B:40.59 4B03G0112200 4B:43.56 AT1G09570[51] Phytochrome A
IWB11001 7A:36.31 7A03G0146600 7A:32.23 AT5G13320[52] Auxin-responsive GH3 protein
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