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Acta Agronomica Sinica ›› 2025, Vol. 51 ›› Issue (2): 312-323.doi: 10.3724/SP.J.1006.2025.41045

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• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Identification and validation of quantitative trait loci for grain number per spike showing pleiotropic effect on thousand grain weight in bread wheat (Triticum aestivum L.)

YONG Rui1,2(), HU Wen-Jing2,*(), WU Di2, WANG Zun-Jie2, LI Dong-Sheng2, ZHAO Die2, YOU Jun-Chao2, XIAO Yong-Gui3, WANG Chun-Ping1,*()   

  1. 1College of Agriculture, Henan University of Science and Technology, Luoyang 471023, Henan, China
    2Lixiahe Institute of Agriculture Sciences / Key Laboratory of Wheat Biology and Genetic Improvement for Low and Middle Yangtze Valley, Ministry of Agriculture and Rural Affairs, Yangzhou 225007, Jiangsu, China
    3Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • Received:2024-06-25 Accepted:2024-10-25 Online:2025-02-12 Published:2024-11-11
  • Contact: E-mail: huren2008@126.com; E-mail: chunpingw@haust.edu.cn E-mail:15202659168@163.com;huren2008@126.com;chunpingw@haust.edu.cn
  • Supported by:
    National Natural Science Foundation of China(32341037);Jiangsu Modern Agricultural Industry Single Technology Research and Development Project(CX (23) 3089);Major Science and Technology of Henan Province Project “the Wheat Nutrigenomics Analysis and Functional Food Creation and Industrialization Fund Project”(231100110300);Shennong Laboratory “First-Class Subject” Project(SN01-2022-01)

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Abstract:

Grain number per spike (GNS) is a key quantitative trait closely associated with wheat yield. To further investigate the quantitative trait loci (QTL) associated with GNS in wheat, 151 recombinant inbred lines (RILs) derived from a cross between Yangmai 4 (YM4) and Yanzhan 1 (YZ1) were used to construct a wheat hexaploid genetic linkage map. GNS was evaluated across four environments over three years. Three QTLs for GNS were identified on chromosomes 4A, 5A, and 5B. Among these, QGns.yaas-4A and QGns.yaas-5B were detected in two environments, with the favorable effect contributed by YM4. The phenotypic variation explained (PVE) by QGns.yaas-4A and QGns.yaas-5B ranged from 11.50% to 13.27% and from 5.59% to 10.99%, respectively, with physical intervals of 703.41-710.25 Mb and 77.62-365.60 Mb. QGns.yaas-5A was detected in all four environments, with the favorable effect contributed by YZ1. The PVE for QGns.yaas-5A ranged from 8.99% to 11.13%, with a physical interval of 495.34-512.39 Mb. The YZ1 allele at QGns.yaas-5A and the YM4 allele at QGns.yaas-5B significantly increased thousand-grain weight by 3.39% (P < 0.05) and 4.45% (P < 0.01), respectively. Kompetitive Allele-Specific PCR (KASP) markers for QGns.yaas-4A, QGns.yaas-5A, and QGns.yaas-5B were developed and validated in a natural population. Pyramiding the three favorable alleles showed a significant additive effect, increasing GNS by 13.75%. These findings provide theoretical and technical support for molecular marker-assisted breeding to improve GNS in wheat.

Key words: Triticum aestivum L., grain number per spike, thousand-grain weight, QTL mapping, KASP

Table S1

Source, value of grain number per spike and QTL alleles of 137 varieties/lines"

数目 品种名称 来源 穗粒数 KASP.Y4.4A KASP.YZ1.5A KASP.Y4.5B
Number Name of cultivars/lines Source GNS
1 新乡 197 Xinxiang 197 中国河南 Henan, China 49.50 A A B
2 鲁麦 14 Lumai 14 中国山东 Shandong, China 50.50 A A B
3 淮麦 39 Huaimai 39 中国江苏 Jiangsu, China 52.25 A A B
4 LJ 041 中国山东 Shandong, China 53.75 A A B
5 鲁原 502 Luyuan 502 中国山东 Shandong, China 54.75 A A B
6 鄂西 84-1031 Exi 84-1031 中国湖北 Hubei, China 57.00 A A B
7 博爱 7023 Bo’ai 7023 中国河南 Henan, China 58.25 A A B
8 淮麦 1403 Huaimai 1403 中国江苏 Jiangsu, China 58.25 A A B
9 淮麦 33 Huaimai 33 中国江苏 Jiangsu, China 59.25 A A B
10 济麦 23 Jimai 23 中国山东 Shandong, China 61.25 A A B
11 新乡 289 Xinxiang 289 中国河南 Henan, China 62.00 A A B
12 济麦 52 Jimai 52 中国山东 Shandong, China 62.25 A A B
13 徐麦 2023 Xumai 2023 中国江苏 Jiangsu, China 63.50 A A B
14 淮麦 25 Huaimai 25 中国江苏 Jiangsu, China 64.75 A A B
15 淮麦 40 Huaimai 40 中国江苏 Jiangsu, China 64.75 A A B
16 宁春 10号 Ningchun 10 中国宁夏 Ningxia, China 65.25 A A B
17 W 16 国外 Foreign 66.88 A A B
18 扬辐麦 5242 变异
Yangfumai 5242 Bianyi		 中国江苏 Jiangsu, China 68.00 A A B
19 绵阳 15 Mianyang 15 中国四川 Sichuan, China 68.25 A A B
20 江东门 Jiangdongmen 地方 Local, China 69.75 A A B
21 皖麦 32 Wanmai 32 中国安徽 Anhui, China 60.50 A B A
22 早熟 5号 Zaoshu 5 中国山东 Shandong, China 61.50 A B A
23 扬辐麦 2 号 Yangfumai 2 中国江苏 Jiangsu, China 61.75 A B A
24 镇 7495 Zhen 7495 中国江苏 Jiangsu, China 62.25 A B A
25 宁麦 12 Ningmai 12 中国江苏 Jiangsu, China 64.00 A B A
26 镇麦 1 号 Zhenmai 1 中国江苏 Jiangsu, China 65.75 A B A
27 欧柔 Ourou 国外 Foreign 67.50 A B A
28 皖麦 33 Wanmai 33 中国安徽 Anhui, China 72.00 A B A
29 S 42 中国江苏 Jiangsu, China 72.25 A B A
30 扬麦 28 Yangmai 28 中国江苏 Jiangsu, China 56.00 A B B
31 延岗坊主 Yangangfangzhu 地方 Local, China 56.00 A B B
32 万年 2 号 Wannian 2 地方 Local, China 56.50 A B B
33 扬麦 27 Yangmai 27 中国江苏 Jiangsu, China 57.25 A B B
34 宁 7840 Ning 7840 中国江苏 Jiangsu, China 57.25 A B B
35 NMAS 2020 中国江苏 Jiangsu, China 57.50 A B B
36 武麦 1 号 Wumai 1 中国江苏 Jiangsu, China 58.25 A B B
37 C 19212-11 中国江苏 Jiangsu, China 58.25 A B B
38 扬麦3 号 Yangmai 3 中国江苏 Jiangsu, China 58.50 A B B
39 矮孟牛 Ⅴ Aimengniu Ⅴ 中国山东 Shandong, China 58.50 A B B
40 扬糯麦 1 号 Yangnuomai 1 中国江苏 Jiangsu, China 58.50 A B B
41 扬麦 15 Yangmai 15 中国江苏 Jiangsu, China 59.00 A B B
42 扬麦 22 Yangmai 22 中国江苏 Jiangsu, China 59.00 A B B
43 徐麦 30 Xumai 30 中国江苏 Jiangsu, China 59.00 A B B
44 LJ 803 中国山东 Shandong, China 59.25 A B B
45 淮麦 22 Huaimai 22 中国江苏 Jiangsu, China 59.50 A B B
46 济麦 20 Jimai 20 中国山东 Shandong, China 59.50 A B B
47 白慈麦 Baicimai 地方 Local, China 59.75 A B B
48 周麦 36 Zhoumai 36 中国河南 Henan, China 59.75 A B B
49 鄂麦 12 Emai 12 中国湖北 Hubei, China 60.00 A B B
50 镇麦 4号 Zhenmai 4 中国江苏 Jiangsu, China 60.00 A B B
51 百农 4199 Bainong 4199 中国河南 Henan, China 60.00 A B B
52 蚰子头 Youzitou 地方 Local, China 60.25 A B B
53 宁糯麦 1 号 Ningnuomai 中国江苏 Jiangsu, China 60.25 A B B
54 皖麦 19 Wanmai 19 中国安徽 Anhui, China 60.25 A B B
55 扬麦 16 Yangmai 16 中国江苏 Jiangsu, China 60.25 A B B
56 翻山小麦 Fanshanxiaomai 地方 Local, China 60.25 A B B
57 糯麦 Nuomai 地方 Local, China 60.38 A B B
58 鄂恩 1 号 E’en 1 中国湖北 Hubei, China 60.50 A B B
59 扬麦 9 号 Yangmai 9 中国江苏 Jiangsu, China 61.25 A B B
60 矮秆红 Aiganhong 国外 Foreign 61.25 A B B
61 宁 17110 Ning 17110 中国江苏 Jiangsu, China 61.50 A B B
62 存麦 5 号 Cunmai 5 中国河南 Henan, China 61.75 A B B
63 扬麦 25 Yangmai 25 中国江苏 Jiangsu, China 62.25 A B B
64 中麦 175 Zhongmai 175 中国河南 Henan, China 63.25 A B B
65 扬麦 2 号 Yangmai 2 中国江苏 Jiangsu, China 65.25 A B B
66 扬麦 20 Yangmai 20 中国江苏 Jiangsu, China 65.50 A B B
67 皖麦 31 Wanmai 31 中国安徽 Anhui, China 65.75 A B B
68 鄂 133 E 133 中国湖北 Hubei, China 65.75 A B B
69 扬麦 23 Yangmai 23 中国江苏 Jiangsu, China 66.00 A B B
70 C 190245474 C 19027-1 中国江苏 Jiangsu, China 66.50 A B B
71 C 192145310 C 19211-19 中国江苏 Jiangsu, China 66.50 A B B
72 宁麦 3 号 Ningmai 3 中国江苏 Jiangsu, China 67.00 A B B
73 和尚头 Heshangtou 地方 Local, China 67.25 A B B
74 丰产 3 号 Fengchan 3 中国陕西 Shaanxi, China 67.25 A B B
75 浙麦 1 号 Zhemai 1 中国浙江 Zhejiang, China 67.25 A B B
76 西农 511 Xinong 511 中国陕西 Shaanxi, China 67.25 A B B
77 红袖子 Hongxiuzi 地方 Local, China 68.00 A B B
78 复壮 30 Fuzhuang 30 中国山东 Shandong, China 68.13 A B B
79 C19008-1 中国江苏 Jiangsu, China 68.75 A B B
80 生选 6 号 Shengxuan 6 中国江苏 Jiangsu, China 49.00 B A B
81 扬辐 9 Yangfu 9 中国江苏 Jiangsu, China 49.75 B A B
82 连麦 2 号 Lianmai 2 中国江苏 Jiangsu, China 50.00 B A B
83 徐麦 178 Xumai 178 中国江苏 Jiangsu, China 50.25 B A B
84 徐农 029 Xunong 029 中国江苏 Jiangsu, China 51.00 B A B
85 济南 17 Jinan 17 中国山东 Shandong, China 51.25 B A B
86 扬辐 3046 Yangfu 3046 中国江苏 Jiangsu, China 53.00 B A B
87 宁 12188 Ning 12188 中国江苏 Jiangsu, China 53.50 B A B
88 徐麦 36 Xumai 36 中国江苏 Jiangsu, China 53.75 B A B
89 丰抗 8 号 Fengkang 8 中国北京 Beijing, China 55.50 B A B
90 淮麦 20 Huaimai 20 中国江苏 Jiangsu, China 56.75 B A B
91 济麦 19 Jimai 19 中国山东 Shandong, China 58.50 B A B
92 淮麦 302 Huaimai 302 中国江苏 Jiangsu, China 58.50 B A B
93 徐麦 17258 Xumai 17258 中国江苏 Jiangsu, China 59.00 B A B
94 烟农 1212 Yannong 1212 中国山东 Shandong, China 59.50 B A B
95 徐麦 14123 Xumai 14123 中国江苏 Jiangsu, China 60.25 B A B
96 扬辐 6 Yangfu 6 中国江苏 Jiangsu, China 61.25 B A B
97 宁麦 21 Ningmai 21 中国江苏 Jiangsu, China 63.50 B A B
98 宁麦 8号 Ningmai 8 中国江苏 Jiangsu, China 64.00 B A B
99 淮麦 1558 Huaimai 1558 中国江苏 Jiangsu, China 65.75 B A B
100 徐麦 16144 Xumai 16144 中国江苏 Jiangsu, China 68.25 B A B
101 18 G 375 (刘) 18 G 375 (Liu) 中国江苏 Jiangsu, China 70.25 B A B
102 宁麦 24 Ningmai 24 中国江苏 Jiangsu, China 54.75 B B B
103 淮麦 36 Huaimai 36 中国江苏 Jiangsu, China 55.00 B B B
104 骊英 6 号 Liying 6 地方 Local, China 55.00 B B B
105 宁17001 Ning 17001 中国江苏 Jiangsu, China 55.75 B B B
106 怀川 Sz 16 Huaichuan Sz 16 中国河南 Henan, China 56.25 B B B
107 扬辐麦 11 号 Yangfumai 11 中国江苏 Jiangsu, China 56.25 B B B
108 宁麦 16 Ningmai 16 中国江苏 Jiangsu, China 56.50 B B B
109 扬 17346 Yang 173046 中国江苏 Jiangsu, China 57.00 B B B
110 滑育麦 1 号 Huayumai 1 中国河南 Henan, China 57.50 B B B
111 宁 17396 Ning 17396 中国江苏 Jiangsu, China 57.50 B B B
112 扬麦 11 号 Yangmai 11 中国江苏 Jiangsu, China 58.25 B B B
113 宁麦资 14213 Ningmaizi 14213 中国江苏 Jiangsu, China 58.50 B B B
114 宁丰小麦 Ningfengxiaomai 中国江苏 Jiangsu, China 59.00 B B B
115 K 122 K 122 中国江苏 Jiangsu, China 59.00 B B B
116 镇 13056 Zhen 13056 中国江苏 Jiangsu, China 59.00 B B B
117 鄂 177 E 177 中国湖北 Hubei, China 59.25 B B B
118 徐麦 14017 Xumai 14017 中国江苏 Jiangsu, China 59.50 B B B
119 徐麦 32 Xumai 32 中国江苏 Jiangsu, China 60.25 B B B
120 豫麦 2 号 Yumai 2 中国河南 Henan, China 61.00 B B B
121 鄂麦 15 Emai 15 中国湖北 Hubei, China 61.50 B B B
122 骊英 3 号 Liying 3 地方 Local, China 61.50 B B B
123 宁麦 1529 Ningmai 1529 中国江苏 Jiangsu, China 61.50 B B B
124 阿勃 Abo 国外 Foreign 62.00 B B B
125 徐麦 35 Xumai 35 中国江苏 Jiangsu, China 63.00 B B B
126 濮兴 5 号 Puxing 5 中国河南 Henan, China 65.25 B B B
127 宁春 13 Ningchun 13 中国宁夏 Ningxia, China 65.50 B B B
128 徐麦 33 Xumai 33 中国江苏 Jiangsu, China 65.50 B B B
129 扬辐 5242 Yangfu 5242 中国江苏 Jiangsu, China 65.50 B B B
130 望水白 7426 Wangshuibai 7426 地方 Local, China 65.63 B B B
131 宁 15186 Ning 15186 中国江苏 Jiangsu, China 67.00 B B B
132 宁 17104 Ning 17104 中国江苏 Jiangsu, China 67.50 B B B
133 扬麦 12 Yangmai 12 中国江苏 Jiangsu, China 68.00 B B B
134 扬辐 5054 Yangfu 5054 中国江苏 Jiangsu, China 68.75 B B B
135 宁 17329 Ning 17329 中国江苏 Jiangsu, China 69.00 B B B
136 马场 2号 Machang 2 中国河南 Henan, China 69.25 B B B
137 扬麦 18 Yangmai 18 中国江苏 Jiangsu, China 69.25 B B B

Table 1

Phenotypic variation of grain number per spike for Yangmai 4, Yanzhan 1, and recombinant inbred lines population in different environments"

环境
Environment		 亲本 Parent 群体 Population
YM4 YZ1 平均值
Mean		 标准差
SD		 偏度
Skewness		 峰度
Kurtosis
2019JZ 61.33** 43.33 52.10 6.92 0.30 0.30
2020YZ 61.00** 48.00 54.17 5.37 0.67 0.90
2021YZ 54.00** 43.33 51.15 4.27 0.22 -0.23
2021NJ 56.00** 43.00 50.78 4.38 0.03 -0.29
BLUE 58.08** 44.42 52.05 4.31 0.45 0.28

Fig. 1

Frequency distribution of grain number per spike of Yangmai 4/Yanzhan 1 recombinant inbred lines population in four environments Abbreviations are the same as those given in Table 1."

Fig. 2

Genetic linkage maps of grain number per spike QTL in Yangmai 4/Yanzhan 1 recombinant inbred lines population The right side of the linkage group is the marker name, and the left is the genetic position (cM). The bold black rectangles in the linkage group represent the QTL positioning interval."

Table 2

QTL for grain number per spike in Yangmai 4/Yanzhan 1 recombinant inbred lines population"

染色体
Chr.		 环境
Environment		 数量性状
遗传位点
QTL		 物理位置
Physical interval
(Mb)		 侧翼标记
Flanking marker		 LOD 贡献率
PVE (%)		 加性效应
Add
4A 2019JZ, 2021NJ QGns.yaas-4A 703.41-710.25 AX110024919-
AX109551603		 5.28-8.54 11.50-13.27 1.61-2.36
5A 2019JZ, 2020YZ, 2021YZ, 2021NJ QGns.yaas-5A 495.34-512.39 AX110494964-
AX109322572		 6.33-9.18 8.99-11.13 -2.97- -1.89
5B 2020YZ, 2021YZ QGns.yaas-5B 77.62-365.60 AX94764048-
AX95657974		 3.37-5.32 5.59-10.99 1.06-1.41

Fig. 3

Genetic effects analysis of QGns.yaas-4A, QGns.yaas-5A, and QGns.yaas-5B on grain number per spike in Yangmai 4/Yanzhan 1 recombinant inbred lines population GNS: grain number per spike; × in the data box indicates the mean value, and the horizontal line in the data box indicates the median, and the dots in the boxplots are the outliers. ** represents significance at P < 0.01 compared with Yanzhan 1. A and B represent the Yangmai 4 allele and Yanzhan 1 allele, respectively."

Fig. 4

Effects of pyramiding QGns.yaas-4A, QGns.yaas-5A, and QGns.yaas-5B on grain number per spike in Yangmai 4/Yanzhan 1 recombinant inbred lines population GNS: grain number per spike; × in the data box indicates the mean value, and the horizontal line in the data box indicates the median, and the dots in the boxplots are the outliers. The letters (a, b, and c) in the graph indicate a significance level of P < 0.01 between the numbers. No. represents the number of lines. A and B represent the Yangmai 4 allele and Yanzhan 1 allele, respectively."

Fig. 5

Genetic effects of QGns.yaas-4A, QGns.yaas-5A, and QGns.yaas-5B on thousand grain weight in Yangmai 4/Yanzhan 1 recombinant inbred lines population TGW: thousand-grain weight; × in the data box indicates the mean value, and the horizontal line in the data box indicates the median, and the dots in the boxplots are the outliers. * and ** represent significance at P < 0.05 and P < 0.01 compared with Yanzhan 1, respectively. A and B represent allelic variations from the Yangmai 4 and Yanzhan 1, respectively."

Fig. 6

Effects of QGns.yaas-5A and QGns.yaas-5B on thousand grain weight in Yangmai 4/Yanzhan 1 recombinant inbred lines population TGW: thousand-grain weight; × in the data box indicates the mean value, and the horizontal line in the data box indicates the median; and the letters (a and b) in the graph indicate a significance level of P < 0.01 between the numbers. No. represents the number of lines. A and B represent the Yangmai 4 allele and Yanzhan 1 allele, respectively."

Table 3

Protocols for assaying markers KASP.Y4.4A, KASP.YZ1.5A, and KASP.Y4.5B"

侧翼标记
Flanking marker		 标记
Marker		 引物序列
Primer sequence (5′-3′)
AX110024919-AX109551603 KASP.Y4.4A F1: GAAGGTGACCAAGTTCATGCTCCAAACGAACCTTTCCTCCA
F2: GAAGGTCGGAGTCAACGGATTCCAAACGAACCTTTCCTCCG
R: ACGTCGAAAGTACGCTTAGCA
AX110494964-AX109322572 KASP.YZ1.5A F1: GAAGGTGACCAAGTTCATGCTGTGCAGAGCCATTTTGGATGAA
F2: GAAGGTCGGAGTCAACGGATTGTGCAGAGCCATTTTGGATGAG
R: CCTTATGCCCATTGCTGCAC
AX94764048-AX95657974 KASP.Y4.5B F1: GAAGGTGACCAAGTTCATGCTTCCTGAGAAAATGTACGAGTTCA
F2: GAAGGTCGGAGTCAACGGATTTCCTGAGAAAATGTACGAGTTCG
R: GATGGACACGAGCAGCTCT

Fig. 7

Effects of QGns.yaas-4A, QGns.yaas-5A, and QGns.yaas-5B on grain number per spike in natural populations GNS: grain number per spike; × in the data box indicates the mean value, and the horizontal line in the data box indicates the median, and the dots in the boxplots are the outliers. * and ** represent significance at P < 0.05 and P < 0.01 compared with YZ1, respectively. A and B represent the Yangmai 4 allele and Yanzhan 1 allele, respectively."

Table 4

Number of cultivars with different allelic combinations of QGns.yaas-4A, QGns.yaas-5A, and QGns.yaas-5B in natural population"

家系个数
Number of lines		 基因型 Genotype
QGns.yaas-4A QGns.yaas-5A QGns.yaas-5B
22 B A B
20 A A B
36 B B B
50 A B B
9 A B A
0 B B A
0 A A A
0 B A A

Fig. 8

Effects of QGns.yaas-4A, QGns.yaas-5A, and QGns.yaas- 5B on grain number per spike in natural populations GNS: grain number per spike; × in the data box indicates the mean value, and the horizontal line in the data box indicates the median. The letters (a, b, and c) in the graph indicate a significance level of P < 0.01 between the numbers. No. represents the number of wheat cultivars."

Table S2

Genotypic and phenotypic values of RIL with three excellent allelic variation"

家系编号
Line No.		 基因型Genotype 穗粒数
Grain number per spike		 千粒重
1000-grain weight (g)
QGNS.yaas-4A QGNS.yaas-5A QGNS.yaas-5B
12 A B A 52.75 52.05
18 A B A 59.55 44.61
22 A B A 53.90 42.74
33 A B A 56.28 39.93
35 A B A 52.40 44.01
37 A B A 49.21 43.81
42 A B A 58.31 41.72
48 A B A 56.56 46.39
49 A B A 59.15 38.75
59 A B A 60.76 42.54
60 A B A 50.79 41.36
62 A B A 58.69 45.34
68 A B A 56.55 43.72
70 A B A 52.24 41.61
76 A B A 53.88 37.22
92 A B A 59.03 41.94
93 A B A 64.81 47.10
95 A B A 60.23 41.84
96 A B A 62.02 51.01
101 A B A 54.62 37.90
104 A B A 56.79 43.17
108 A B A 59.00 42.70
117 A B A 59.28 41.04
118 A B A 59.74 50.39
133 A B A 56.50 38.01
134 A B A 56.67 37.09
135 A B A 56.62 39.69
139 A B A 56.08 38.01
141 A B A 60.60 50.16
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