Scientia Agricultura Sinica ›› 2023, Vol. 56 ›› Issue (12): 2237-2248.doi: 10.3864/j.issn.0578-1752.2023.12.001


QTL Identification and Genetic Analysis of Plant Height in Wheat Based on 16K SNP Array

YAO QiFu1(), CHEN HuangXin2(), ZHOU JieGuang2, MA RuiYing3, DENG Liang3, TAN ChenXinYu3, SONG JingHan4, LÜ JiJuan5(), MA Jian2,()   

  1. 1 College of Agroforestry Engineering and Planning, Tongren University/Guizhou Key Laboratory of Biodiversity Conservation and Utilization in the Fanjing Mountain Region, Tongren 554300, Guizhou
    2 Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130
    3 College of Agronomy, Sichuan Agricultural University, Chengdu 611130
    4 Beijing Foreign Studies University, Beijing 100089
    5 Sichuan Provincial Seed Station, Chengdu 610041
  • Received:2023-02-14 Accepted:2023-03-17 Online:2023-06-16 Published:2023-06-27


【Objective】There is a close relationship between plant height (PH) and yield. The aim of this study is to further explore quantitative trait loci (QTL) of PH with breeding value in wheat and analyze the genetic effects of major QTL for PH on other yield related traits toward to providing a theoretical basis for molecular breeding. 【Method】A recombinant inbred line population (MC) derived from a cross between the natural mutant msf and Chuannong 16 (CN16) was used for QTL analysis. During 2020 to 2022, planting and PH phenotype identification were conducted at five environments in Wenjiang, Chongzhou, and Ya’an of Sichuan Province. The high-quality genetic linkage map constructed using the 16K SNP array was used for QTL mapping of PH. Genotypes of flanking markers of major QTL for PH were used to analyze the genetic effects of positive alleles on yield related traits and evaluate the potentiality of QTL for yield improvement. 【Result】Eight QTL controlling PH were identified on chromosomes 1A, 3D, 4D, 5A, and 7B, respectively. Among them, two stable and major QTL, QPh.sau-MC-1A and QPh.sau-MC-5A, were located, which explained 9.09% to 25.56% and 3.91% to 13.09% of the phenotypic variation rate, respectively. Their positive alleles were all from CN16. The additive effect analysis showed that PH of the lines carrying positive alleles from QPh.sau-MC-1A and QPh.sau-MC-5A was significantly higher than that of the lines carrying only a single positive allele or none. Correlation analysis showed that PH has a significantly positive correlation with effective tiller number (ETN), a significantly negative correlation with flag leaf width (FLW), and no significant correlation with kernel number per spike (KNPS), kernel weight per spike (KWPS), thousand kernel weight (TKW), flag leaf length (FLL) and anthesis date (AD). Genetic effects analysis showed that positive allele of QPh.sau-MC-1A had a significant effect on improving ETN (56.51%), a significant effect on decreasing KNPS (-11.26%), KWPS (-13.04%), TKW (-5.47%), and FLW (-2.85%), and a significant effect on advancing AD (-0.61%). Positive allele of QPh.sau-MC-5A had a significant effect on improving ETN (10.57%), KNPS (4.32%), and TKW (2.92%), and a significant effect on delaying AD (1.07%). 【Conclusion】A major QTL QPh.sau-MC-5A for PH was mapped on chromosome 5A, and its positive allele significantly increased ETN, KNPS, and TKW, indicating that it may have a positive impact on yield.

Key words: wheat, 16K SNP array, QTL, plant height, yield

Fig. 1

Parental phenotype of MC population"

Table 1

Phenotypic distribution of plant height for parents and RIL in MC population (cm)"

亲本Parents 重组自交系RIL
msf CN16 范围 Range 均值 Mean 标准差 SD
2021WJ 109.4±2.4** 77.8±2.7 44.0—120.0 93.6 11.8
2021CZ 101.1±4.4** 83.6±9.9 67.4—106.2 86.4 7.8
2021YA 80.0±8.0 67.0N 60.0—102.0 78.1 8.8
2022WJ 92.6±3.8** 69.0±3.7 44.1—105.8 75.8 10.8
2022CZ 93.3±3.1** 65.1±1.9 40.0—98.0 71.2 10.4
BLUP 91.9 74.5 68.1—94.7 81.0 5.5

Fig. 2

Frequency distribution and correlations of plant height for MC population in different environments * and **: Significant difference at level 0.05 and 0.01. The same as below"

Table 2

Analysis of variance for plant height in MC population"

G×E interaction
自由度Degrees of freedom 197 4 739 5 929
均方Mean square 501.25 31662.90 131.60 19.45 15.39
F 32.57 2057.66 8.55 1.26
PP value <0.001 <0.001 <0.001 0.28

Table 3

Correlations between plant height and yield related traits in MC population"

Plant height
有效分蘖数Effective tiller number 0.54**
每穗粒数Kernel number per spike -0.13
每穗粒重Kernel weight per spike -0.10
千粒重Thousand kernel weight -0.12
旗叶长Flag leaf length 0.01
旗叶宽Flag leaf width -0.16*
开花期Anthesis date 0.10

Table 4

QTL related to plant height in MC population"

QTL 生态环境
Marker interval
Genetic position (cM)
PVE (%)
QPh.sau-MC-1A 2021WJ 1A_12082541A_3911208 0 6.23 13.83 -4.22
2021YA 1A_39112081A_10060497 1 3.31 9.09 -2.62
2022WJ 1A_39112081A_10060497 1 16.28 25.56 -5.31
2022CZ 1A_39112081A_10060497 1 13.71 25.03 -5.17
BLUP 1A_39112081A_10060497 1 14.26 23.67 -2.65
QPh.sau-MC-3D.1 2022WJ 3D_680397633D_70735603 55 2.59 3.33 1.92
QPh.sau-MC-3D.2 BLUP 3D_1909763413D_147552757 61 3.28 4.61 1.17
QPh.sau-MC-4D BLUP 4D_4566769704D_467767587 42 2.69 3.82 -1.07
2022WJ 4D_4677675874D_474629240 43 3.88 5.10 -2.38
QPh.sau-MC-5A 2022WJ 5A_5638337045A_568561734 101 9.05 13.09 -3.81
BLUP 5A_5695438925A_572006166 105 3.75 5.54 -1.29
2022CZ 5A_5720061665A_572980290 106 2.55 3.91 -2.06
QPh.sau-MC-7B.1 2022CZ 7B_438497B_3090779 0 2.68 7.02 2.31
QPh.sau-MC-7B.2 2021YA 7B_117088417B_19685092 31 2.82 3.66 2.01
QPh.sau-MC-7B.3 2022WJ 7B_315564037B_33812777 38 2.98 4.59 2.21

Table 5

Multi-environment QTL related to plant height in MC population"

QTL 标记区间
Marker interval
LOD (AbyE) 表型变异率
PVE (%)
QPh.sau-MC-1A 1A_39112081A_10060497 43.35 33.92 9.43 25.91 19.12 6.79 -3.42
- 3D_1223965893D_138793245 6.91 5.52 1.39 4.17 2.89 1.28 1.33
QPh.sau-MC-4D 4D_4566769704D_467767587 7.19 5.15 2.04 3.33 2.69 0.64 -1.29
QPh.sau-MC-5A 5A_5638337045A_568561734 11.01 5.27 5.74 5.23 2.69 2.53 -1.28
QPh.sau-MC-7B.1 7B_438497B_3090779 5.18 3.48 1.70 2.62 1.81 0.80 1.05

Fig. 3

Genetic effect of major QTL for plant height in MC population + and −: Lines carrying and not carrying the positive allele of corresponding QTL; n: Lines. The same as below"

Fig. 4

Additive effect of major QTL for plant height in MC population Different lowercase letters indicate significant differences"

Fig. 5

Effect of the major QTL for plant height on yield related traits a-g: Effects of QPh.sau-MC-1A on yield related traits, + and - contain 84 and 93 lines; h-n: Effects of QPh.sau-MC-5A on yield related traits, + and - contain 70 and 92 lines"

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doi: 10.1016/j.jgg.2015.08.007
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