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Acta Agronomica Sinica ›› 2021, Vol. 47 ›› Issue (10): 1891-1902.doi: 10.3724/SP.J.1006.2021.01078


Genome-wide association study of pre-harvest sprouting traits in wheat

XIE Lei1,2(), REN Yi1,2, ZHANG Xin-Zhong1,3, WANG Ji-Qing1,2, ZHANG Zhi-Hui1,2, SHI Shu-Bing1,2, GENG Hong-Wei1,2,*()   

  1. 1Agricultural College of Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
    2Key Laboratory of Biotechnology, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
    3Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, Xinjiang, China
  • Received:2020-10-04 Accepted:2021-01-13 Online:2021-10-12 Published:2021-02-24
  • Contact: GENG Hong-Wei E-mail:1784462634@qq.com;hw-geng@163.com
  • Supported by:
    National Natural Science Foundation of China(31771786);Technical Innovation Bases Construction Project of Xinjiang Uygur Autonomous Region(PT1910)


To understand the genetic mechanism of wheat pre-harvest sprouting (PHS) in wheat breeding, it is significant to explore marker loci and candidate genes associated with PHS resistance using intact spikes. In this study, a total of 207 wheat varieties (lines) from China and 16,686 SNP markers were analyzed in wheat whole genome. The mixed liner model (Q + K) was used to analyze PHS phenotypic data in three environments. Genome-wide association study showed that there were abundant phenotypic variations in different environments and wheat varieties (lines). The coefficient of variation was 0.34 and 0.25, the polymorphic information content of value (PIC) was from 0.01 to 0.38, and the attenuation distance of whole genome LD was 3 Mb. The population structure and principal component analysis revealed that 207 wheat varieties (lines) could be divided into three subgroups. GWAS results indicated that 34 SNP markers were detected, which were significantly associated with pre-harvest sprouting at P < 0.001. They were located on chromosomes 3A, 3B, 4A, 4B, 5D, 6A, 6B, 6D, 7B, and 7D, and each explained 5.55%-11.63% of phenotypic variation. There were 16 markers loci detected in more than two environments, and the marker Np_Ex_c14101_22,012,676 on 6B chromosome detected in E1, E2, and average environment. Meanwhile, 13 candidate genes were screened out by mining association loci with large phenotypic effect value and stable inheritance. TraesCS3A01G589400LC, TraesCS6B01G138600/TraesCS6B01G516700LC/TraesCS6B01G548900LC, TraesCS6D01G103600, and TraesCS7B01G200100 could affect seed dormancy by regulating the sensitivity of endogenous ABA in plants. The F-box proteins were encoded by TraesCS3B01G415900LC, TraesCS6A01G144700LC, and TraesCS6B01G294800, which played major roles in plant hormone signal transduction, light signal transduction, and flower organ development. TraesCS6A01G108800, TraesCS6B01G138200/ TraesCS6B01G293700 encoded Myb transcription factor family. These candidate genes are important genes related to wheat sprouting.

Key words: wheat, pre-harvest sprouting, genome-wide association analysis, SNP, candidate gene

Fig. 1

Pre-harvest sprouting diagram of some tested materials A: Jingdong 8; B: Huaimai 20; C: Zhengmai 2."

Fig. 2

Variation of germination rate of intact spike in 207 wheat genotypes detected in two environments SR: sprouting rate."

Table 1

ANOVA of sprouting in 207 genotypes used in this study"

Source of variance
基因型Genotype (G) 206 95,102,272.00 312,836.40 540.38 0.00001 0.60
环境Environment (E) 1 756,525,632.00 378,262,816.00 653,396.18 0.00001
基因型×环境G×E 443 94,041,216.00 212,282.65 366.68 0.00001
误差Error 747 432,451.71 578.91
总变异Total 1397 946,109,312.00

Table 2

Genome coverage and polymorphism of markers"

No. of markers
Chromosome length (Mb)
Density of marker
多态信息量 PIC
平均值Mean 变异范围Range
1A 1263 592.38 0.47 0.27 0.01-0.38
2A 1145 780.46 0.68 0.24 0.01-0.38
3A 891 749.46 0.84 0.25 0.01-0.38
4A 708 741.73 1.05 0.25 0.01-0.38
5A 960 709.43 0.74 0.28 0.01-0.38
6A 1006 617.40 0.61 0.27 0.03-0.38
7A 1172 736.44 0.63 0.25 0.01-0.38
1B 1292 688.60 0.53 0.27 0.01-0.38
2B 1291 799.62 0.62 0.26 0.01-0.38
3B 1087 829.32 0.76 0.27 0.01-0.38
4B 571 672.56 1.18 0.26 0.01-0.38
5B 1156 712.82 0.62 0.28 0.01-0.38
6B 1085 720.82 0.66 0.25 0.01-0.38
7B 861 750.49 0.87 0.26 0.02-0.38
1D 568 495.14 0.87 0.13 0.01-0.38
2D 482 650.94 1.35 0.25 0.02-0.38
3D 232 613.92 2.65 0.24 0.01-0.38
4D 99 508.58 5.14 0.25 0.08-0.38
5D 240 563.41 2.35 0.26 0.02-0.38
6D 319 472.61 1.48 0.25 0.03-0.38
7D 260 637.17 2.45 0.23 0.01-0.38
A染色体组 Total genome A 7145 4927.30 0.72 0.26 0.01-0.38
B染色体组 Total genome B 7343 5174.23 0.75 0.27 0.01-0.38
D染色体组 Total genome D 2198 3941.77 2.33 0.23 0.01-0.38
总计Total 16686 14043.30 1.27 0.25 0.01-0.38

Fig. 3

Population structure analysis of 207 wheat varieties (lines)"

Fig. 4

Manhattan and Q-Q diagrams of pre-harvest sprouting traits in different environments E1: 2017 and 2018 in Manasi; E2: 2018 and 2019 in Manasi; E3: average environment."

Table 3

Information of significant association sites for PHS"

Position (Mb)
MLM 环境
已报道的QTL/标记/基因Known QTL/marker/gene
R2 (%)
Kukri_c8465_54 3A 684.04-685.36 2.35E-04-9.14E-04 5.55-8.75 E2/E3 TaVp-1[32]
Kukri_c9259_421 4A 673.07 5.95E-04 6.34 E2 IWB23723[23]
RAC875_rep_c107892_142 6A 77.78 2.56E-05-9.28E-05 8.04-9.25 E1/E3
Kukri_c5744_92 6A 483.90 2.78E-05-7.41E-04 8.34-9.25 E1/E3
RAC875_c43536_193 6A 490.50 3.03E-04 6.94 E1
IAAV8536 3B 422.52 6.78E-05 9.81 E1 TaDFR[33]
Tdurum_contig60051_838 4B 644.68 7.10E-04 9.42 E2 Xwmc349[34]
CAP11_c2542_147 6B 24.92 7.71E-05-3.83E-04 6.71-8.29 E1/E3 TaCYP707A1[35]
Kukri_c33668_877 6B 119.53 4.55E-04-5.32E-04 6.05-6.16 E2/E3 AX-108844376[24]
GENE-3171_203 6B 135.11-138.65 2.15E-05-5.50E-04 6.09-9.71 E1/E3
BS00069412_51 6B 143.20 9.03E-04 5.64 E1
Excalibur_c18382_760 6B 151.13 9.24E-04 5.60 E3
wsnp_Ku_c2614_4970880 6B 226.87 8.44E-04 5.59 E3
Tdurum_contig13698_141 6B 475.73 7.54E-04 5.70 E3
RFL_Contig6050_941 6B 481.47-481.86 3.10E-06-1.63E-04 8.83-11.63 E1/E3
wsnp_Ex_c3640_6644345 6B 485.54 2.36E-05-1.08E-04 8.21-11.04 E1/E3 IWB2831[24]
wsnp_Ex_c14101_22012676 6B 492.02 2.26E-06-6.77E-04 5.86-11.61 E1/E2/E3
wsnp_Ex_c6143_10747643 6B 516.08-519.15 1.30E-05-1.65E-04 8.30-10.65 E1/E3
Kukri_c16568_287 6B 522.49 4.81E-05-1.69E-04 7.21-8.45 E1/E3
Excalibur_c7785_123 6B 526.48-528.92 1.19E-056.21E-04 5.94-10.02 E1/E3
Excalibur_c11245_880 6B 530.57 2.79E-04-5.34E-04 6.06-6.83 E1/E3
wsnp_Ex_c3990_7223090 6B 577.48 1.67E-05-6.19E-05 8.45-9.95 E1/E3 Qphs.ahau-6B[36]
RAC875_c57261_265 6B 609.38 6.10E-04-6.34E-04 5.99-6.02 E1
Position (Mb)
MLM 环境
已报道的QTL/标记/基因Known QTL/marker/gene
R2 (%)
RAC875_rep_c117796_352 6B 632.97 5.23E-04-5.35E-04 6.19-6.21 E3
wsnp_CV776265A_Ta_2_1 6B 651.01-652.00 1.21E-04-7.21E-04 5.78-7.51 E1/E3
BS00023032_51 6B 664.38 8.28E-04 5.90 E3
IAE36519 6B 701.98-704.04 7.44E-04-9.92E-04 5.87-6.09 E2
wsnp_Ku_c18780_28136150 7B 223.61 8.12E-05 10.12 E2
Excalibur_c25719_238 7B 363.24 3.92E-05-3.24E-04 6.64-8.89 E2/E3
RAC875_c4834_694 7B 613.38 7.14E-04 5.87 E2 Dorm-1[37]
BobWhite_c8092_726 5D 246.30 4.94E-04 6.22 E3
wsnp_Ex_c1249_2399894 6D 67.39-68.10 8.81E-04-9.23E-04 5.72-5.78 E1
D_wsnpbe403818_Contig1_1 6D 389.70 6.71E-04 5.79 E3
D_contig10382_335 7D 23.50-55.42 7.24E-04-9.41E-04 5.70-6.15 E2 MST101[37]

Table 4

Information of candidate genes"

Position (Mb)
Gene annotation or coding protein
Kukri_c8465_54 3A 684.76 TraesCS3A01G589400LC Zinc finger MYM-type-like protein
IAAV8536 3B 421.53 TraesCS3B01G415900LC F-box protein
RAC875_rep_c107892_142 6A 77.61 TraesCS6A01G144700LC F-box family protein
6A 77.54 TraesCS6A01G108800 Myb-like transcription factor family protein
GENE-3171_203 6B 135.71 TraesCS6B01G138200 Myb family transcription factor-like
6B 135.94 TraesCS6B01G138600 RING/U-box superfamily protein
RFL_Contig6050_941 6B 481.79 TraesCS6B01G511400LC Anaerobic nitric oxide reductase transcription regulator NorR
wsnp_Ex_c14101_22012676 6B 491.55 TraesCS6B01G516700LC Zinc finger (C3HC4-type RING finger) family protein
Excalibur_c7785_123 6B 528.92 TraesCS6B01G294800 F-box protein
6B 527.93 TraesCS6B01G293700 Myb family transcription factor-like
6B 526.49 TraesCS6B01G548900LC Zinc finger MYM-type-like protein
Excalibur_c25719_238 7B 363.00 TraesCS7B01G200100 Zinc finger C-x8-C-x5-C-x3-H type family protein
wsnp_Ex_c1249_2399894 6D 67.39 TraesCS6D01G103600 Zinc finger BED domain-containing protein DAYSLEEPER
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doi: 10.1007/s00122-011-1555-2
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