Scientia Agricultura Sinica ›› 2023, Vol. 56 ›› Issue (18): 3487-3499.doi: 10.3864/j.issn.0578-1752.2023.18.001

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

Genome-Wide Association Analysis of Yield Traits in Xinjiang Winter Wheat Germplasm

MA YanMing1,2(), LOU HongYao3, ZHANG ShengJun4, WANG Wei1, GUO Ying5, NI ZhongFu2, LIU Jie2()   

  1. 1 Institute of Crop Germplasm Resource, Xinjiang Academy of Agricultural Sciences, Urumqi 830091
    2 College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193
    3 Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097
    4 Institute of Agricultural Sciences of Ili Prefecture, Yining 835011, Xinjiang
    5 College of Agronomy, Shandong Agricultural University, Tai’an 271018, Shandong
  • Received:2023-03-27 Accepted:2023-05-25 Online:2023-09-16 Published:2023-09-21
  • Contact: LIU Jie

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Abstract:

【Objective】To discover new high yield genes in wheat by association analysis, which can provide technical supports for the innovation and genetic improvement of high yield germplasm resources in wheat.【Method】Totally 188 bread wheat cultivars in Xinjiang were genotyped using the wheat 55K genotyping assay. GWAS was carried out to identify the signifcant single nucleotide polymorphisms (SNPs) which were associated with 9 wheat yield traits in 6 environments. The MLM algorithm in TASSEL5.0 was used to analyze the nine traits related to wheat yield traits.【Result】Totally 1309 SNPs explained 7.259%-70.792% of the phenotypic variation. 38 SNP loci were identifed, which were significantly correlated with 5 plant height weight SNP loci, 10 spike length weight SNP loci, 10 spikelet number SNP loci, 6 fertile spikelet number SNP loci, 6 spike grain number SNP loci, and 1 thousand grain weight SNP loci. These loci can explain 9.10%-23.81% of phenotypic variations. Comparing these 38 loci with the published wheat genome loci, only 3 functional genes were found, which annotated with gene function. There genes are: TraesCS2A01G448800 on chromosome 2A, which is close to the plant height associated site AX-108794050 and is related to the metabolic synthesis of transcription factor bHLH71; TraesCS2A01G448800, located on chromosome 1A at a distance similar to the spike length associated site AX-110689765, is related to protein coding; TraesCS4B01G031100, located on the 4B chromosome at a distance similar to the 1000 grain weight associated site AX-110399975, is associated with the encoding serine/threonine protein kinase SD1-8 and is involved in regulating cell proliferation and differentiation. 【Conclusion】38 QTL loci associated with wheat yield traits were detected. After verification, it was found that the associated excellent alleles have the effect of reducing plant height, increasing spike length, spikelet number, fertile spikelet number, grain number per spike, and thousand grain weight.

Key words: wheat, yield traits, SNP, association analysis, candidate genes

Fig. 1

Population structure analysis of 188 Xingjiang wheat accessions a: The ΔK statistic for each given K; b: PCA; c: Model-based ancestries"

Fig. 2

The relative kinship and LD of 188 Xinjiang wheat materials a: The relative kinship of the wheat association panel. b: The LD of 21 chromosomes in 188 wheat association panel"

Table 1

Physical locations, P values and interpreted phenotypic variation rates of 38 repeat sites"

性状
Trait 		标记
SNP		 染色体
Chr.		 物理位置
Position (bp)		 P PVE (%)
E1 E2 E3 E4 E5 E6 BLUP E1 E2 E3 E4 E5 E6 BLUP
PH AX-108794050 2A 698175277 3.76E-06 1.08E-05 1.06E-05 11.60 11.60 10.10
AX-108838330 4B 465981233 6.31E-05 4.80E-06 9.00 12.90
AX-109467555 6A 417439944 3.11E-05 4.28E-05 9.60 11.40
AX-109857508 2A 19661854 1.41E-05 8.26E-05 2.20E-05 12.40 9.50 11.40
AX-110969164 7B 53530940 1.37E-05 5.65E-05 1.84E-05 13.80 11.30 12.80
SL AX-111524633 1A 229272328 6.67E-08 1.67E-05 26.90 12.70
AX-110359663 2A 555501466 1.81E-08 3.06E-05 24.50 14.80
AX-110956005 5A 384438157 1.19E-10 1.987-08 28.80 21.90
AX-108852957 6A 611194075 1.61E-08 6.62E-05 26.40 12.10
AX-110689765 6A 12313027 1.63E-05 9.13E-05 11.40 9.10
AX-109282231 3B 138504166 8.79E-05 1.02E-05 11.60 14.90
AX-108758415 7B 687068740 7.82E-13 5.99E-05 36.60 11.10
AX-111722527 2D 527923732 7.31E-10 1.54E-05 26.70 12.80
AX-110568577 4D 200403065 1.64E-09 9.80E-05 27.40 11.10
AX-109822039 5D 154563929 1.78E-07 1.14E-06 22.80 16.10
SN AX-108825815 3A 526860477 2.49E-05 7.23E-05 12.60 10.80
AX-108977066 3A 526923011 8.55E-05 1.43E-05 1.40E-05 10.80 13.30 12.70
AX-109365068 5A 69079172 5.43E-06 5.21E-05 11.80 9.20
AX-110105180 4A 549802334 4.76E-05 7.71E-05 14.20 12.80
AX-110123746 4D 469869704 2.33E-06 6.47E-05 15.10 11.10
AX-110419722 3A 514225494 2.29E-05 1.61E-05 13.80 16.10
AX-111073226 7A 383199757 8.41E-05 8.90E-05 10.80 10.80
SN AX-111074553 6B 610906100 3.16E-07 1.19E-05 16.60 12.50
AX-111523929 1A 516381475 3.15E-07 1.18E-05 18.70 13.50
AX-111700650 7B 548781811 3.21E-07 4.72E-06 18.10 13.40
FSN AX-110123746 4D 469869704 3.52E-07 9.72E-05 1.08E-05 17.60 10.80 13.50
AX-111073226 7A 383199757 4.54E-05 7.21E-05 3.44E-05 11.50 9.30 12.00
AX-111523929 1A 516381475 4.63E-08 5.66E-05 1.81E-06 22.50 12.60 16.60
AX-111074553 6B 610906100 2.84E-07 7.44E-06 16.60 13.00
AX-111700650 7B 548781811 1.11E-06 2.58E-06 15.90 11.70
AX-109545508 2A 324629159 7.76E-07 1.92E-05 16.70 12.90
GNPS AX-108745367 1A 554125804 4.45E-05 2.18E-08 3.82E-05 11.60 25.70 12.92
AX-110509054 6A 71539737 7.04E-05 2.27E-08 1.91E-05 11.00 22.70 12.35
AX-112290916 4B 241185348 1.65E-06 1.24E-05 16.70 12.87
AX-110270363 4D 200804203 3.53E-08 3.69E-05 21.60 11.77
AX-111523929 1A 516381475 2.92E-08 1.35E-09 22.53 23.81
AX-110123746 4D 469869704 3.69E-05 8.14E-09 11.77 22.73
TKW AX-110399975 3B 23344933 4.66E-06 9.81E-05 11.60 10.30

Fig. 3

Selected yield characters’ Manhattan and Q-Q Plot diagrams of BLUP value a: Plant height; b: Spike length; c: Spikelet number; d: Grain number per spike; e: Fertile spikelet number per spike; f: Thousand kernel weight"

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