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作物学报

作物学报 ›› 2022, Vol. 48 ›› Issue (10): 2451-2462.doi: 10.3724/SP.J.1006.2022.13052

所属专题： 玉米：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

基于杂交群体解析玉米籽粒大小相关性状及其配合力的分子遗传机制

李婷1,2(), 王亚鹏1,2, 董远1,2, 郭瑞士1, 李冬梅1, 唐雅伶1, 张兴华1,2, 薛吉全1,2, 徐淑兔1,2,*()   

  1. 1西北农林科技大学农学院 / 农业农村部西北旱区玉米生物与遗传改良重点实验室, 陕西杨凌 712100
    2陕西省玉米工程技术研究中心, 陕西杨凌 712100
  • 收稿日期:2021-09-07 接受日期:2022-02-25 出版日期:2022-10-12 网络出版日期:2022-03-22
  • 通讯作者: 徐淑兔
  • 作者简介:第一作者联系方式: E-mail: ltstime@163.com
  • 基金资助:
    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(玉米, CARS-02-77);陕西省重点研发计划项目(2021ZDLNY01-06)

Dissecting the genetic basis of kernel size related traits and their combining ability based on a hybrid population in maize

LI Ting1,2(), WANG Ya-Peng1,2, DONG Yuan1,2, GUO Rui-Shi1, LI Dong-Mei1, TANG Ya-Ling1, ZHANG Xing-Hua1,2, XUE Ji-Quan1,2, XU Shu-Tu1,2,*()   

  1. 1Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
    2Maize Engineering Technology Research Centre of Shaanxi Province, Yangling 712100, Shaanxi, China
  • Received:2021-09-07 Accepted:2022-02-25 Published:2022-10-12 Published online:2022-03-22
  • Contact: XU Shu-Tu
  • Supported by:
    China Agriculture Research System (Maize, CARS-02-77) of MOF and MARA;Key Research and Development Program of Shaanxi Province(2021ZDLNY01-06)

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摘要：

配合力是育种过程中评价自交系潜力、筛选优良杂交组合的重要指标。籽粒大小相关性状是产量的重要构成因子, 解析籽粒大小相关性状及其配合力的遗传基础有助于高产玉米品种的培育。本研究以NCII遗传交配设计获得的246份玉米杂交组合为材料展开籽粒大小相关性状及其配合力的全基因组关联分析。研究表明, 粒长、粒宽、粒厚3个性状的广义遗传力分别为76.20%、86.52%和81.14%, 各性状与其配合力均呈显著正相关(0.58~0.82)。基于EMMAX (efficient mixed-model association expedited)算法检测到31、21、5个显著的SNP (single nucleotide polymorphism), 它们分别与性状、GCA (general combining ability)和SCA (special combining ability)关联, 其中10个SNP为性状与配合力共定位的。对共定位的SNP进行效应分析, 发现3个为加性效应、4个为部分显性效应、1个为超显性效应。结合公共数据库中基因注释及籽粒发育相关转录组数据, 在共定位、主效SNP位点附近共筛选到17个候选基因, 包括被报道与玉米籽粒发育相关的shrunken1、emp6等。本研究结果有助于进一步解析玉米籽粒大小及其配合力的遗传机制, 可为籽粒大小相关性状的遗传改良提供参考。

关键词: 玉米, 杂交种, 籽粒大小, 配合力, 全基因组关联分析

Abstract:

Combining ability is a crucial index for evaluating elite inbred lines and selecting superior hybrids during maize breeding processes. Kernel size related traits are important components of grain yield. Therefore, dissecting the genetic basis of kernel size related traits and their combining ability is beneficial for improving maize yield. In this study, we performed genome-wide association study (GWAS) of kernel size related traits and their combining ability using 246 hybrids breed by designed as NCII mating. The broad-sense heritability of kernel length (KL), kernel width (KW), and kernel thickness (KT) was 76.20%, 86.52%, and 81.14%, respectively. The correlation coefficient between each trait and their combining ability was more than 0.58, indicating there was significant positive correlation. Based on the efficient mixed-model association expedited (EMMAX) algorithm, we identified 31, 21, and 5 significant single nucleotide polymorphisms (SNPs) associated with the best linear unbiased estimation (BLUE), general combining ability (GCA), and special combining ability (SCA) of kernel size related traits, respectively. Among these significant SNPs, 10 SNPs were co-located both kernel size related traits and their combining ability. The effect analysis of co-located significant SNPs showed that three SNPs were additive, four were partial dominance and one was overdominance. Further, 17 candidate genes were predicted from candidate regions of co-located SNPs or SNPs with large effect, such as shrunken 1, emp6 and so on. The results further dissect the genetic architecture of maize kernel size related traits and their combining ability and provide useful information for improving grain yield in maize breeding.

Key words: maize, hybrids, kernel size, combining ability, genome-wide association study

表1

籽粒大小相关性状的基本描述统计及方差分析"

来源 Source 粒长 KL 粒宽 KW 粒厚 KT
均值±标准差 Mean ± SD 12.62 ± 0.66 7.55 ± 0.44 4.30 ± 0.23
变异系数 CV 5.21% 5.78% 5.38%
偏度 Skewness 0.08 0.30 0.24
峰度 Kurtosis 0.15 0.41 -0.25
母本一般配合力 GCA female 2.22*** 0.26*** 1.55***
父本一般配合力 GCA male 25.86*** 3.89*** 6.60***
特殊配合力 SCA 0.56*** 0.08*** 0.18***
母本一般配合力×环境 GCA female × Environment 0.44 0.05** 0.11
父本一般配合力×环境GCA male × Environment 0.57 0.04 0.22*
特殊配合力×环境 SCA × Environment 0.35 0.04 0.09
基因型方差 $\sigma _{\text{g}}^{2}$ 0.31 0.17 0.04
基因型×环境方差 $\sigma _{\text{ge}}^{2}$ 0.02 0.00 0.00
广义遗传力 H2 (%) 76.20 86.52 81.14

图1

籽粒大小相关性状及其配合力的相关性分析 A: 不同环境下籽粒大小性状的相关性分析; B: 籽粒大小与其配合力的相关性分析。*、**和***分别表示在P < 0.05、P < 0.01和P < 0.001水平显著; KL: 粒长; KW: 粒宽; KT: 粒厚; XY: 旬邑; YL: 榆林; BLUE: 最佳线性无偏估计; GCA: 一般配合力; SCA: 特殊配合力。"

图2

籽粒大小相关性状及其配合力的显著SNP分布及统计 缩写同图1。"

表2

籽粒大小相关性状及其一般配合力、特殊配合力显著关联的SNP"

序号
Number		 性状
Trait		 SNP标记
SNP marker		 染色体
Chr.		 位置
Position		 等位基因
Allele		 P值
P-value		 模型
Model		 表型解释率
R2 (%)
1 KL_BLUE Affx-291427653 2 172,900,382 A/C 1.17E-05 加性Additive 2.65
2 KL_BLUE Affx-291399192 2 174,990,230 C/T 6.00E-05 显性Dominance 5.20
3 KL_BLUE Affx-291415239 2 188,723,861 A/G 1.23E-04 加性Additive 3.36
4 KL_BLUE Affx-291421576 3 4,667,059 C/T 1.17E-04 显性Dominance 0.59
5 KL_BLUE Affx-291388159 4 161,189,573 G/T 9.25E-05 显性Dominance 7.87
6 KL_BLUE Affx-291414096 5 19,152,693 G/A 1.12E-04 显性Dominance 7.50
7 KL_BLUE Affx-291382102 5 45,936,956 A/T 6.34E-05 显性Dominance 0.75
8 KL_BLUE Affx-291430485 5 199,891,583 T/C 3.77E-05 显性Dominance 0.84
序号
Number		 性状
Trait		 SNP标记
SNP marker		 染色体
Chr.		 位置
Position		 等位基因
Allele		 P值
P-value		 模型
Model		 表型解释率
R2 (%)
9 KL_GCA Affx-88981164 2 109,561,515 G/A 2.62E-05 加性Additive 25.52
10 KL_GCA Affx-291438859 2 147,075,651 C/T 1.25E-04 加性Additive 7.29
11 KL_GCA Affx-291381936 2 172,197,055 G/A 7.39E-05 加性Additive 13.35
12 KL_GCA Affx-291427653 2 172,900,382 A/C 7.93E-07 加性Additive 0.80
13 KL_GCA Affx-291383897 2 173,344,526 G/C 1.86E-05 加性Additive 0.90
14 KL_GCA Affx-291399192 2 174,990,230 C/T 3.45E-05 加性Additive 0.03
15 KL_GCA Affx-291400614 2 177,112,609 C/T 4.06E-05 加性Additive 1.11
16 KL_GCA Affx-291415239 2 188,723,861 A/G 4.76E-06 加性Additive 0.42
17 KL_GCA Affx-291419252 2 194,294,110 T/C 9.17E-06 加性Additive 0.02
18 KL_SCA Affx-291414096 5 19,152,693 G/A 6.68E-05 显性Dominance 3.54
19 KW_BLUE Affx-291445199 1 180,428,491 C/T 1.16E-04 显性Dominance 10.90
20 KW_BLUE Affx-158946352 1 224,324,098 G/A 5.83E-05 加性Additive 0.65
21 KW_BLUE Affx-291438736 1 292,427,178 C/A 4.06E-05
5.00E-11		 加性Additive
显性Dominance		 28.23
0.07
22 KW_BLUE Affx-291386203 2 28,660,634 C/A 3.98E-05
2.31E-05		 加性Additive
显性Dominance		 3.79
0.44
23 KW_BLUE Affx-291438094 2 235,818,735 C/G 1.09E-05 显性Dominance 0.07
24 KW_BLUE Affx-291404824 3 1,338,197 C/A 2.84E-05
8.58E-06		 加性Additive
显性Dominance		 6.41
12.47
25 KW_BLUE Affx-291426461 4 35,122,656 T/C 3.23E-05 显性Dominance 0.11
26 KW_BLUE Affx-159061154 5 2,145,982 T/G 8.59E-05 显性Dominance 0.15
27 KW_BLUE Affx-291435207 7 277,626 A/G 5.33E-05 加性Additive 12.96
28 KW_BLUE Affx-291438357 9 38,415,742 T/C 8.18E-05 显性Dominance 0.18
29 KW_GCA Affx-291445199 1 180,428,491 C/T 1.34E-04 加性Additive 16.83
30 KW_GCA Affx-158946352 1 224,324,098 G/A 1.36E-04 加性Additive 6.47
31 KW_GCA Affx-158948129 1 235,021,563 C/T 7.38E-05 加性Additive 10.69
32 KW_GCA Affx-291438736 1 292,427,178 C/A 4.28E-06 加性Additive 16.97
33 KW_GCA Affx-291385173 2 5,147,139 T/C 3.83E-05 加性Additive 1.67
34 KW_GCA Affx-291420744 5 80,480,359 A/C 3.51E-05 加性Additive 7.50
35 KW_GCA Affx-291401044 9 129,309,960 A/G 2.72E-05 加性Additive 8.28
36 KW_SCA Affx-291436386 2 27,498,155 C/T 1.11E-04 显性Dominance 2.92
37 KT_BLUE Affx-291413666 1 118,986,201 A/C 8.08E-05 显性Dominance 7.95
38 KT_BLUE Affx-159032175 1 262,226,149 T/C 6.04E-06 显性Dominance 0.37
39 KT_BLUE Affx-291390855 1 262,368,074 C/T 4.17E-05
1.60E-05		 加性Additive
显性Dominance		 12.47
7.33
40 KT_BLUE Affx-158839028 1 280,195,356 C/A 7.78E-05 显性Dominance 3.39
41 KT_BLUE Affx-291410051 1 285,592,051 C/T 5.51E-05 显性Dominance 4.21
42 KT_BLUE Affx-291443747 2 23,623,257 G/A 8.77E-05 加性Additive 25.58
43 KT_BLUE Affx-291388256 2 195,694,458 C/T 1.19E-04 显性Dominance 0.34
44 KT_BLUE Affx-291401517 2 235,207,369 G/A 1.26E-05 显性Dominance 0.26
45 KT_BLUE Affx-291441620 3 85,891,477 T/C 6.06E-06 显性Dominance 2.57
46 KT_BLUE Affx-291422512 9 11,615,037 G/A 1.36E-04 显性Dominance 0.53
47 KT_BLUE Affx-291445448 9 15,315,557 A/C 8.53E-05 显性Dominance 3.25
48 KT_BLUE Affx-291438777 9 107,428,822 G/A 2.59E-05 显性Dominance 0.04
49 KT_BLUE Affx-291378767 10 144,701,539 C/A 1.09E-04 显性Dominance 2.76
50 KT_GCA Affx-291399215 1 104,625,663 C/T 3.57E-05 加性Additive 21.69
序号
Number		 性状
Trait		 SNP标记
SNP marker		 染色体
Chr.		 位置
Position		 等位基因
Allele		 P值
P-value		 模型
Model		 表型解释率
R2 (%)
51 KT_GCA Affx-291390855 1 262,368,074 C/T 7.69E-05 加性Additive 10.71
52 KT_GCA Affx-291418355 3 1,713,800 A/G 1.18E-04 加性Additive 9.51
53 KT_GCA Affx-291442108 4 12,611,068 G/A 9.26E-05 加性Additive 0.03
54 KT_GCA Affx-291425118 5 37,099,257 C/T 1.14E-04 加性Additive 4.83
55 KT_SCA Affx-291399798 3 11,407,826 G/A 9.19E-05 显性Dominance 3.52
56 KT_SCA Affx-291422512 9 11,615,037 G/A 4.99E-05 显性Dominance 5.84
57 KT_SCA Affx-291438777 9 107,428,822 G/A 8.20E-05 显性Dominance 1.66

表3

BLUE与配合力(一般配合力和特殊配合力)共定位SNP的效应分析"

序号
Number		 性状
Trait		 SNP名称
SNP marker		 染色体
Chr.		 位置
Position		 显性度
Dominance effect index		 效应
Effect
1 KL_BLUE, KL_GCA Affx-291427653 2 172,900,382 0.03 加性 Additive
2 KL_BLUE, KL_GCA Affx-291399192 2 174,990,230 -0.12 加性 Additive
3 KL_BLUE, KL_GCA Affx-291415239 2 188,723,861 -0.55 部分显性 Partial dominance
4 KL_BLUE, KL_SCA Affx-291414096 5 19,152,693 2.64 超显性 Overdominance
5 KW_BLUE, KW_GCA Affx-291445199 1 180,428,491 — —
6 KW_BLUE, KW_GCA Affx-158946352 1 224,324,098 -0.08 加性Additive
7 KW_BLUE, KW_GCA Affx-291438736 1 292,427,178 -0.57 部分显性 Partial dominance
8 KT_BLUE, KT_GCA Affx-291390855 1 262,368,074 — —
9 KT_BLUE, KT_SCA Affx-291422512 9 11,615,037 -0.60 部分显性 Partial dominance
10 KT_BLUE, KT_SCA Affx-291438777 9 107,428,822 -0.57 部分显性 Partial dominance

图3

性状与配合力共定位SNP的不同等位基因的表型差异分析 **和***分别表示在P < 0.01和P < 0.001水平显著。缩写同表1。"

图4

候选区间内在籽粒中表达基因的功能富集分析 A: GO分析; B: KEGG通路分析。BP: 生物过程; CC: 细胞组分; MF: 分子功能。"

表4

玉米粒长、粒宽、粒厚及其配合力(一般配合力和特殊配合力)的候选基因和功能注释"

序号
Number		 性状
Trait		 SNP标记
SNP marker		 染色体
Chr.		 候选基因
Candidate gene		 注释
Description
1 KT_GCA Affx-291399215 1 GRMZM2G025157 Putative pentatricopeptide repeat-containing protein
2 KW_BLUE, KW_GCA Affx-291445199 1 GRMZM2G085474 Thiolase1 (thl1)
3 KW_BLUE, KW_GCA Affx-158946352 1 GRMZM2G031572 Putative serine peptidase S28 family protein
4 KW_GCA Affx-158948129 1 GRMZM2G464680 Xyloglucan galactosyltransferase KATAMARI 1
5 KT_BLUE, KT_GCA Affx-291390855 1 GRMZM2G022997 Inositol hexakisphosphate and diphosphoinositol- pentakisphosphatekinase VIP2
6 KW_BLUE, KW_GCA Affx-291438736 1 GRMZM2G450920 Protein SCAR2
7 KT_BLUE Affx-291443747 2 GRMZM2G505380 Protein O-glucosyltransferase 1
8 KL_GCA Affx-88981164 2 GRMZM2G158043 Pullulanase-type starch debranching enzyme1 (zpu1)
9 KL_BLUE, KL_GCA Affx-291427653 2 GRMZM2G014106 Enhancer of polycomb-like transcription factor
10 KL_GCA Affx-291381936 2 GRMZM2G104546 Aspartate kinase homoserine dehydrogenase 2
11 KL_BLUE, KL_GCA Affx-291399192 2 AC203957.3_FG004 BZIP-transcription factor 40
12 KL_BLUE, KL_GCA Affx-291415239 2 GRMZM2G048392 Empty pericarp6 (emp6)
13 KW_BLUE Affx-291404824 3 GRMZM2G175218 Beta amylase4 (amyb4)
14 KL_BLUE, KL_SCA Affx-291414096 5 GRMZM2G081221 Protein phosphatase 1 regulatory inhibitor
15 KW_BLUE Affx-291435207 7 GRMZM5G800488 Laccase20 (lac20)
16 KT_BLUE, KT_SCA Affx-291422512 9 GRMZM2G089713 Sucrose synthase (shrunken1)
17 KT_BLUE, KT_SCA Affx-291438777 9 GRMZM2G048472 Homogentisate phytyltransferase VTE2-1
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