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作物学报 ›› 2022, Vol. 48 ›› Issue (1): 138-150.doi: 10.3724/SP.J.1006.2022.03072

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玉米抗倒伏相关性状QTL的关联和连锁分析

于芮苏1(), 田小康1, 刘斌斌1, 段迎新1, 李婷1, 张秀英2, 张兴华1, 郝引川1, 李勤2, 薛吉全1,*(), 徐淑兔1,*()   

  1. 1西北旱区玉米生物学与遗传育种重点实验室 / 西北农林科技大学农学院, 陕西杨凌 712100
    2陕西省汉中农业科学研究所, 陕西汉中723000
  • 收稿日期:2020-12-10 接受日期:2021-04-14 出版日期:2022-01-12 网络出版日期:2021-06-18
  • 通讯作者: 薛吉全,徐淑兔
  • 作者简介:E-mail: 1169390776@qq.com
  • 基金资助:
    国家重点研发计划项目“七大农作物育种专项”(2018YFD0100203);国家现代农业产业技术体系建设专项(玉米)资助(CARS-02-64)

Dissecting the genetic architecture of lodging related traits by genome-wide association study and linkage analysis in maize

YU Rui-Su1(), TIAN Xiao-Kang1, LIU Bin-Bin1, DUAN Ying-Xin1, LI Ting1, ZHANG Xiu-Ying2, ZHANG Xing-Hua1, HAO Yin-Chuan1, LI Qin2, XUE Ji-Quan1,*(), XU Shu-Tu1,*()   

  1. 1Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest Agriculture and Technology University, Yangling 712100, Shaanxi, China
    2Hanzhong Institute of Agricultural Sciences, Hanzhong 723000, Shaanxi China
  • Received:2020-12-10 Accepted:2021-04-14 Published:2022-01-12 Published online:2021-06-18
  • Contact: XUE Ji-Quan,XU Shu-Tu
  • Supported by:
    Seven Major Crop Breeding Projects of the National Key Research and Development Program of China(2018YFD0100203);China Agriculture Research System (Maize).(CARS-02-64)

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摘要：

倒伏是影响玉米高产和机械化收获的重要因素, 明确玉米抗倒伏相关性状的遗传基础, 增强玉米品种抗倒伏能力, 可为玉米高产宜机收育种提供理论依据。本研究以国内外收集的153份自交系为材料, 利用6H90K SNP芯片检测的70,438个高质量SNP标记对地上第3节茎秆强度、株高、穗位高和穗位系数进行全基因组关联分析, 分别检测到与茎秆强度、株高、穗位高和穗位系数相关位点5个、14个、16个和21个, 单个关联位点最大效应值为13.24。同时以KA105/KB020的F5群体为试验材料, 采用QTL IciMapping V4.2软件的完备区间作图法进行QTL定位, 检测到21个与抗倒伏相关的QTL, 可解释表型变异3.86%~16.58%。结合关联分析和连锁分析结果发现, 2个QTL区间与关联分析的候选区间重合。经过候选区段的基因功能注释和文献查阅, 挖掘到GRMZM2G105391、GRMZM2G014119和GRMZM2G341410等与细胞壁生物合成、细胞分裂和细胞伸长的相关基因可供进一步分析。本研究结果为进一步解析玉米抗倒伏性状的遗传基础提供参考。

关键词: 玉米, 倒伏, 关联分析, 连锁分析

Abstract:

Lodging is one of the main factors affecting the grain yield and mechanized harvesting in maize. Dissecting the genetic basis of lodging related traits can provide a theoretical basis for high yield and mechanized harvest breeding of maize. In this study, genome-wide association study (GWAS) and linkage analysis were combined to identify the significant loci interrelated with lodging related traits using 153 inbred lines from China and abroad. We detected 5, 14, 16, and 21 SNPs significant SNPs related to stem strength, plant height, ear height, and ear height-to-plant height ratio, respectively. Among these significant SNPs, the maximum effect value of a single site was 13.24. Twenty-one QTLs related to lodging related traits were identified by linkage analysis, which explaining the phenotypic variations of 3.86%-16.58% in F5 population constructed by KA105 and KB020. Further, we noticed that two QTL intervals were coincided with the candidate intervals of association analysis. Finally, GRMZM2G105391, GRMZM2G014119, and GRMZM2G341410 candidate genes related to cell wall biosynthesis, cell division and elongation were predicted by functional annotation for these candidate regions. These results can provide a new reference for further analysis of the genetic basis of lodging resistance in maize.

Key words: maize, lodging, association analysis, linkage analysis

表1

AM153群体抗倒伏性状的基本统计描述"

性状
Trait		 年份
Year		 范围
Range		 平均值±标准差
Mean±SD		 偏度
Skewness		 峰度
Kurtosis		 变异系数
CV (%)
茎秆强度 2018 32.99-66.23 50.21±6.24 0.12 -0.01 12.43
SS 2019 33.34-72.28 53.3±7.57 -0.08 -0.17 14.20
SS-BLUP 43.74-60.62 52.04±3.32 0.24 0.13 6.38
株高 2018 170.30-280.70 221.92±23.11 0.28 -0.37 10.41
PH 2019 143.00-252.20 200.99±21.56 0.13 -0.42 10.73
PH-BLUP 160.99-277.91 212.22±20.14 0.41 0.12 9.49
穗位高 2018 48.00-108.30 79.73±12.58 -0.21 -0.28 15.78
EH 2019 49.00-108.30 70.95±9.69 0.3 0.79 13.66
EH-BLUP 53.08-110.48 75.88±9.82 0.38 0.98 12.94
穗位系数 2018 0.26-0.53 0.40±0.05 0.31 0.98 12.41
EH/PH 2019 0.25-0.47 0.35±0.04 0.4 0.82 10.47
EH/PH-BLUP 0.28-0.46 0.35±0.03 0.5 0.87 9.49

表2

AM153群体抗倒伏性状的方差份析"

变异
Variation		 茎秆强度SS 株高PH 穗位高EH 穗位系数EH/PH
MS F MS F MS F MS F
基因型Genotypes (G) 119.15 2.24*** 1756.59 16.72*** 401.50 10.49*** 0.005 8.90***
年份Year 1430.55 26.24*** 65,572.72 624.12*** 12,290.33 321.08*** 0.007 12.06***
基因型×年份G×Year 63.29 1.19 221.13 2.10*** 77.43 2.02*** 0.001 1.81***
误差Error 53.14 105.06 38.28 0.001
遗传力H2 (%) 72.62 92.77 89.26 86.96

图1

AM153群体(图A)和F5群体(图B)抗倒伏性状相关性分析 *、**和***分别表示在P < 0.05、P < 0.01和P < 0.001水平显著; 18、19分别表示2018年和2019年; YU、HZ分别表示榆林和汉中。缩写同表1。"

图2

抗倒伏性状显著SNP分布图 缩写同表1。"

表3

抗倒伏性状关联位点分析"

SNP序号 染色体 位置 候选区间 -log10 (P) 效应值 性状
SNP ID Chr. Position Candidate interval Effect Trait
SNP372 1 7,693,562 7,493,562-7,893,562 4.29 10.08 19EH, 19PH
SNP524 1 10,449,649 10,249,649-10,649,649 3.41 4.87 18EH, 18PH
SNP3638 1 84,326,155 84,126,155-84,526,155 4.81 -1.48 18SS, SS-BLUP
SNP6691 1 205,781,890 205,581,890-205,981,890 3.73 -0.01 19EH/PH, EH/PH-BLUP
SNP8730 1 253,324,984 253,124,984-253,524,984 3.28 7.56 19PH, PH-BLUP
SNP11723 2 13,290,858 13,090,858-13,490,858 3.59 9.47 19EH, 19PH
SNP13557 2 53,646,990 53,446,990-53,846,990 3.06 -5.12 18EH, 19EH
SNP19390 2 233,508,755 233,308,755-233,708,755 3.31 8.17 18PH,19PH
SNP20574 3 18,803,909 18,603,909-19,003,909 3.58 -0.02 19EH/PH, EH/PH-BLUP
SNP20816 3 24,476,830 24,276,830-24,676,830 4.23 3.99 19SS, SS-BLUP
SNP24414 3 155,835,074 155,635,074-156,035,074 4.18 -0.02 19EH/PH,19EH
SNP28310 4 10,227,629 10,027,629-10,427,629 4.72 4.48 18PH, 19PH, PH-BLUP
SNP29286 4 33,460,646 33,260,646-33,660,646 3.07 -9.27 19PH, PH-BLUP
SNP29306 4 33,912,195 33,712,195-34,112,195 4.23 -13.25 19PH, 19EH
SNP29662 4 43,179,107 42,979,107-43,379,107 3.06 7.25 19PH, 19EH
SNP30918 4 107,290,607 107,090,607-107,490,607 3.82 -0.04 19EH/PH, EH/PH-BLUP
SNP36977 5 27,793,091 27,593,091-27,993,091 3.50 -0.01 19EH/PH, EH/PH-BLUP
SNP37167 5 32,584,178 32,384,178-32,784,178 3.26 -0.02 19EH/PH, EH/PH-BLUP
SNP38017 5 61,705,387 61,505,387-61,905,387 4.11 -0.02 19EH/PH, EH/PH-BLUP
SNP38046 5 62,710,291 62,510,291-62,910,291 3.28 -0.02 19EH/PH, EH/PH-BLUP
SNP38174 5 68,434,295 68,234,295-68,634,295 4.32 -0.01 19EH/PH, EH/PH-BLUP
SNP38176 5 68,449,337 68,249,337-68,649,337 4.37 -0.01 19EH/PH, EH/PH-BLUP
SNP38400 5 78,025,941 77,825,941-78,225,941 3.62 -0.01 19EH/PH, EH/PH-BLUP
SNP39705 5 141,210,709 141,010,709-141,410,709 3.20 0.01 19EH/PH, EH/PH-BLUP
SNP40214 5 157,008,514 156,808,514-157,208,514 3.38 2.89 19SS, SS-BLUP
SNP40603 5 167,979,920 167,779,920-168,179,920 3.44 -0.01 19EH/PH, EH/PH-BLUP
SNP44092 6 45,709,401 45,509,401-45,909,401 3.22 -4.54 18EH, 18PH
SNP45353 6 96,088,816 95,888,816-96,288,816 3.40 3.70 19EH, EH-BLUP
SNP48778 7 1,222,716 1,022,716-1,422,716 3.02 -8.07 19EH, 19PH
SNP49397 7 14,735,621 14,535,621-14,935,621 3.99 2.30 18SS, SS-BLUP
SNP50621 7 75,380,048 75,180,048-75,580,048 6.01 2.00 18SS, SS-BLUP
SNP54911 8 13,140,414 12,940,414-13,340,414 3.41 -0.01 19EH/PH, EH/PH-BLUP
SNP56153 8 70,742,498 70,542,498-70,942,498 4.30 -0.03 19EH/PH, EH/PH-BLUP
SNP57890 8 129,488,487 129,288,487-129,688,487 4.14 -9.73 18EH, 19EH, EH-BLUP
18PH, 19PH, PH-BLUP
SNP58030 8 133,307,178 133,107,178-133,507,178 4.78 -6.36 18EH, 19EH, 19PH
SNP58106 8 135,487,306 135,287,306-135,687,306 3.46 0.01 19EH/PH, EH/PH-BLUP
SNP58751 8 152,898,327 152,698,327-153,098,327 4.62 0.02 18EH/PH, EH/PH-BLUP
SNP59767 8 172,230,824 172,030,824-172,430,824 3.83 4.61 19EH,19PH
SNP59786 8 172,434,870 172,234,870-172,634,870 3.23 0.01 18EH, EH/PH-BLUP
SNP62666 9 89,001,322 88,801,322-89,201,322 3.28 -0.01 19EH/PH, EH/PH-BLUP
SNP62670 9 89,192,523 88,992,523-89,392,523 3.46 -0.02 19EH/PH, EH/PH-BLUP
SNP62676 9 89,529,835 89,329,835-89,729,835 3.73 -0.01 19EH/PH, EH/PH-BLUP
SNP62844 9 93,667,191 93,467,191-93,867,191 3.13 4.19 18EH, 19EH
SNP64186 9 129,539,571 129,339,571-129,739,571 3.26 3.90 18EH, 19EH

表4

F5群体抗倒伏性状的基本统计描述"

性状
Trait		 环境
Environment		 亲本 Parents RILs群体 RILs population
KA105 KB020 范围
Range		 平均数±标准差
Mean±SD		 偏度
Skewness		 峰度
Kurtosis		 变异系数
CV (%)
茎秆强度 YU 55.78 b 63.30 a 30.44-74.01 53.24±8.32 -0.20 0.02 15.62
SS HZ 47.96 51.41 35.09-65.69 49.92±6.33 -0.11 -0.35 12.68
BLUP 51.87 b 57.35 a 29.33-62.81 51.28±4.51 -0.14 -0.07 8.79
株高 YU 223.90 234.70 159.90-275.10 222.37±28.25 -0.23 -0.29 12.70
EH HZ 201.10 b 254.44 a 145.20-300.00 217.86±24.03 -0.38 1.09 11.03
BLUP 213.00 b 244.54 a 158.90-281.24 219.78±21.95 -0.16 -0.10 9.99
穗位高 YU 65.70 62.60 38.50-94.80 72.60±10.98 -0.11 -0.42 15.12
PH HZ 58.80 b 76.67 a 42.50-96.50 68.15±11.51 -0.08 -0.39 16.88
BLUP 62.25 b 69.82 a 49.63-90.21 70.30±9.05 -0.11 -0.54 12.88
穗位系数 YU 0.29 0.26 0.22-0.45 0.33±0.03 -0.01 0.92 10.17
EH/PH HZ 0.29 0.30 0.20-0.43 0.31±0.03 0.01 0.55 12.35
BLUP 0.29 b 0.27 a 0.23-0.42 0.31±0.03 0.09 0.79 8.50

表5

F5群体抗倒伏性状方差分析"

变异 茎秆强度SS 株高PH 穗位高EH 穗位系数EH/PH
Variation MS F MS F MS F MS F
基因型 Genotype (G) 157.78 4.96*** 2429.31 11.75*** 431.22 11.75*** 0.004 2.64***
环境 Environment (E) 3748.35 117.72*** 5380.57 26.03*** 4153.35 26.03*** 0.150 95.67***
基因型×环境 G×E 46.94 1.47*** 274.35 1.33** 64.73 1.32* 0.003 1.85***
误差 Error 31.84 206.70 52.48 0.002
遗传力 H2 (%) 83.40 92.80 90.50 66.67

图3

抗倒伏性状QTL分布图 缩写同表1和图1。"

表6

F5群体抗倒伏性状QTL定位"

性状 QTL 染色体 左翼标记 右翼标记 环境 LOD 贡献率 加性效应
Trait Chr. Left marker Right marker Environment R2 (%) Add
茎秆强度 qSS5-1 5 5_140763773 5_140763857 YU 4.22 9.12 2.46
SS qSS5-2 5 5_156167500 5_157012388 BLUP 10.35 16.58 2.02
qSS5-3 5 5_158723309 5_159130066 HZ 7.66 9.99 2.39
qSS5-4 5 5_178122149 5_179051498 HZ 4.14 5.22 -1.73
qSS5-5 5 5_144226809 5_181226757 BLUP 3.59 5.52 -1.19
qSS5-6 5 5_199338390 5_199672364 HZ 4.38 5.53 1.81
qSS6 6 6_67861806 6_68984948 YU 4.24 9.05 -2.47
BLUP 3.43 5.05 -1.13
株高 qPH1-1 1 1_112646044 1_115306380 YU 24.56 9.40 18.83
PH qPH1-2 1 1_120199828 1_160600750 YU 36.96 16.53 -25.07
BLUP 6.25 5.31 -6.36
qPH2-1 2 2_9013265 2_10394566 HZ 3.97 4.46 -5.66
qPH2-2 2 2_18731394 2_19945073 BLUP 5.16 4.32 -5.70
性状 QTL 染色体 左翼标记 右翼标记 环境 LOD 贡献率 加性效应
Trait Chr. Left marker Right marker Environment R2 (%) Add
qPH5-1 5 5_135497925 5_135725252 BLUP 5.39 4.52 -5.80
qPH5-2 5 5_164963962 5_166327830 BLUP 10.49 9.44 8.40
qPH5-3 5 5_1683956 5_1727799 HZ 3.45 3.86 -5.27
qPH6 6 6_68984948 6_128701322 HZ 5.16 7.94 -7.65
YU 12.43 4.83 -13.55
BLUP 11.76 11.63 -9.44
qPH7 7 7_11482224 7_14968823 BLUP 4.78 4.04 5.50
穗位高 qEH1 1 1_107294393 1_109785426 HZ 4.88 9.07 -3.58
EH YU 5.33 5.96 -3.06
BLUP 7.16 10.16 -3.11
qEH2 2 2_190284923 2_192872800 YU 4.81 5.39 -2.90
qEH6-1 6 6_68984948 6_128701322 YU 7.56 11.33 -4.25
qEH6-2 6 6_112247546 6_117497921 BLUP 3.65 5.00 -2.18
qEH10 10 10_13473790 10_18247431 YU 4.02 4.49 2.66
BLUP 3.65 5.05 2.20
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