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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (7): 1813-1821.doi: 10.3724/SP.J.1006.2022.12047

• RESEARCH NOTES • Previous Articles     Next Articles

Genome-wide association analysis and candidate gene selection of yield related traits in rice

YANG Fei1(), ZHANG Zheng-Feng2(), NAN Bo1, XIAO Ben-Ze1,*()   

  1. 1College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
    2School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China
  • Received:2021-07-13 Accepted:2021-11-30 Online:2022-07-12 Published:2021-12-24
  • Contact: XIAO Ben-Ze E-mail:1044708754@163.com;zhengfeng@mail.ccnu.edu.cn;benzexiao@mail.hzau.edu.cn
  • About author:First author contact:

    ** Contributed equally to this work

  • Supported by:
    National Major Project for Developing New GM Crops(2016ZX 08001-003)

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Abstract:

Rice is the most important food crop for more than half of the world’s population, and the cultivation of rice varieties with high and stable yield is crucial for solving the world’s food problems. In this study, 226 rice core materials with relatively consistent growth stage were selected from “3K Rice Genome Project” and 2429 kb of high density genotype and 10 agronomic traits including growth period, plant height, effective panicle number, panicle length, spikelet density, seed setting rate, thousand-grains weight, yield per plant, spikelet per panicle, and grains per panicle were investigated by genome-wide associate study combined with 2429 kb of high-density genotype data. A total of 43 loci significantly associated with main agronomic traits were identified, including seven known loci, such as qRGP7.2, qPH12, qPL6.2, qSD6.2, qTGW1.1, qGP1, and qGP5.2. Six candidate genes were screened out, including LOC_Os12g18760 related to plant height, LOC_Os03g33530 related to effective panicle number, LOC_Os06g30940 related to panicle length, LOC_Os01g49810 related to thousand grains weight, LOC_Os09g25260 related to yield per plant, and LOC_Os09g32620 related to spikelet density and spikelet per panicle. These results provide important gene resources and the theoretical reference for genetic improvement of rice yield.

Key words: rice, yield, GWAS, candidate genes, genetic improvement

Fig. 1

LD decay diagram of different category groups of materials"

Fig. 2

Phylogenetic tree of population and kinship heatmap"

Table 1

Phenotypic performance of main agronomic traits"

性状
Trait		 最小值
Max.		 最大值
Min.		 平均值±标准差
Mean±SD		 变异系数
CV		 偏度
Skewness		 峰度
Kurtosis
生育期RGP 88.00 141.00 113.69±12.49 0.11 -0.22 -0.33
株高PH 70.83 212.52 125.40±29.63 0.24 0.47 -0.70
有效穗数EPN 1.50 30.00 11.26±4.01 0.36 0.75 2.58
穗长PL 12.19 35.32 24.93±3.78 0.15 -0.12 0.82
穗着粒密度SD 26.71 125.40 55.79±15.95 0.29 0.95 1.45
结实率SSR 2.72 94.48 54.35±21.74 0.40 -0.37 -0.68
千粒重TGW 13.63 34.67 21.48±3.07 0.14 0.52 1.52
单株产量YP 2.09 55.62 18.91±10.26 0.54 0.47 -0.23
每穗颖花数SP 32.56 320.96 139.25±42.67 0.31 0.62 1.28
每穗实粒数GP 10.20 182.85 76.00±37.61 0.49 0.41 -0.35

Table 2

Correlation coefficient for main agronomic traits"

性状
Trait		 生育期
RGP		 株高
PH		 有效穗数
EPN		 穗长
PL		 穗着粒密度SD 结实率
SSR		 千粒重
TGW		 单株产量YP 每穗颖花数SP
株高PH 0.334**
有效穗数EPN -0.322** -0.118
穗长PL 0.409** 0.592** -0.068
穗着粒密度SD 0.285** -0.141* -0.194** -0.035
结实率SSR -0.114 0.117 0.265** 0.013 -0.003
千粒重TGW -0.043 0.127 -0.014 0.017 -0.357** -0.064
单株产量YP 0.006 0.148* 0.536** 0.247** 0.242** 0.740** -0.045
每穗颖花数SP 0.419** 0.137* -0.208** 0.420** 0.878** 0.008 -0.299** 0.340**
每穗实粒数GP 0.145* 0.191** 0.067 0.274** 0.459** 0.780** -0.246** 0.799** 0.560**

Fig. 3

Manhattan plot and QQ (quantile-quantile) plot of main agronomic traits"

Table 3

Sites detected by genome-wide association analysis of main agronomic traits"

性状
Trait		 位点
Loci		 染色体
Chr.		 峰值SNP位置
Lead SNP location		 等位基因
Allele		 P值
P-value		 表型解释率
R2 (%)		 已知基因或QTL
Known gene/QTL
着粒密度SD qSD2 2 23,186,794 G/A 4.62E-08 13.70
qSD3.1 3 1,157,127 G/T 2.32E-07 13.21
qSD3.2 3 1,237,405 C/T 3.23E-07 12.91
qSD4.1 4 624,883 A/G 3.95E-07 12.45
qSD4.2 4 21,988,379 A/T 9.13E-07 11.99
qSD6.1 6 1,288,379 C/G 3.95E-07 13.73
qSD6.2 6 4,195,628 A/C 4.43E-07 13.08 qSD-6[12]
qSD8 8 4,256,879 G/A 5.45E-07 11.94
qSD9 9 19,467,675 C/T 3.61E-10 18.35
qSD11 11 21,384,141 A/T 4.47E-07 13.46
结实率SSR qSSR1 1 5,869,453 C/T 3.99E-07 13.12
qSSR5 5 1,034,218 G/A 7.89E-07 14.62
千粒重TGW qTGW1.1 1 23,551,474 G/T 3.66E-07 12.34 gw1.6[9]
qTGW1.2 1 28,602,321 C/T 1.09E-07 14.27
单株产量YP qYP9 9 15,090,090 C/T 2.05E-07 15.40
每穗颖花数SP qSP9 9 19,467,675 C/T 2.25E-08 15.37
每穗实粒数GP qGP1 1 5,016,026 C/T 4.74E-07 12.88 Gn1a[5]
qGP4 4 4,823,582 A/T 8.26E-08 14.67
qGP5.1 5 4,768,623 G/C 1.70E-07 14.00
qGP5.2 5 24,181,775 G/C 6.36E-07 13.76 qFGP-5[12]
qGP7 7 19,529,904 A/T 9.90E-07 11.90
qGP10 10 1,461,247 C/G 7.41E-07 13.35
qGP12 12 18,869,520 C/T 5.68E-07 13.19
生育期RGP qRGP3 3 9,022,002 G/A 9.18E-08 8.00
qRGP7.1 7 8,213,977 C/T 6.75E-07 8.89
qRGP7.2 7 10,550,765 T/C 5.47E-07 4.61 Ghd7[10]
qRGP7.3 7 26,977,462 G/T 8.28E-07 8.39
qRGP9.1 9 5,217,056 G/A 2.15E-07 7.09
qRGP9.2 9 9,452,746 C/T 4.25E-07 9.68
株高PH qPH12 12 10,850,670 A/G 9.52E-09 13.74 rs10809004[26]
有效穗数EPN qEPN2.1 2 8,414,057 T/G 5.52E-07 12.87
qEPN2.2 2 21,565,076 G/A 4.42E-07 8.32
qEPN2.3 2 23,524,522 G/A 9.55E-08 14.15
qEPN3 3 19,153,885 A/C 3.25E-07 14.46
qEPN4 4 8,551,259 G/A 2.36E-07 13.85
qEPN7 7 9,522,613 C/A 6.85E-07 11.96
qEPN9 9 11,661,903 C/T 4.08E-07 13.23
qEPN10 10 11,248,685 G/A 1.89E-07 12.11
qEPN12 12 23,941,955 C/G 3.44E-07 14.09
穗长PL qPL3 3 4,492,601 A/G 1.31E-07 7.10
qPL6.1 6 7,837,937 G/A 7.68E-07 11.20
qPL6.2 6 18,006,896 C/T 2.95E-07 4.87 PL6-4[13]
qPL10 10 22,711,072 C/T 2.35E-08 4.22

Table 4

Candidate genes related to main agronomic traits"

性状
Trait		 染色体
Chr.		 Block区间
Block interval		 SNP位置
SNP location		 P值
P-value		 突变类型
Mutation type		 候选基因
Candidate gene
株高PH 12 9,980,244-10,892,970 10,850,670 9.52E-09 Ile341Val LOC_Os12g18760
10,852,412 2.62E-07 Arg427Trp LOC_Os12g18760
有效穗数EPN 3 18,869,017-19,653,830 19,153,885 3.25E-07 His1596Gln LOC_Os03g33530
穗长PL 6 17,508,688-18,018,169 17,998,194 6.38E-07 Arg145Trp LOC_Os06g30940
17,998,633 5.87E-07 Val291Ala LOC_Os06g30940
17,998,980 5.42E-07 Ser407Pro LOC_Os06g30940
着粒密度SD 9 19,299,911-19,490,308 19,465,897 1.78E-09 Gln242* LOC_Os09g32620
千粒重TGW 1 28,102,929-28,992,862 28,600,008 4.75E-07 Asp238Glu LOC_Os01g49810
单株产量YP 9 14,973,503-15,128,976 15,126,639 3.38E-07 Ser89Leu LOC_Os09g25260
每穗实粒数SP 9 19,299,911-19,490,308 19,465,897 4.89E-08 Gln242* LOC_Os09g32620
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