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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (6): 1333-1345.doi: 10.3724/SP.J.1006.2022.14102


Genome wide association analysis of petiole angle based on 783 soybean resources (Glycine max L.)

CHEN Ling-Ling1,2(), LI Zhan1, LIU Ting-Xuan1, GU Yong-Zhe2, SONG Jian1,*(), WANG Jun1,*(), QIU Li-Juan1,2,*()   

  1. 1Yangtze University, Jingzhou 434025, Hubei, China
    2National Key Facility for Gene Resources and Genetic Improvement / Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture and Rural Affairs / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • Received:2021-06-10 Accepted:2021-10-19 Online:2022-06-12 Published:2021-11-15
  • Contact: SONG Jian,WANG Jun,QIU Li-Juan E-mail:905540072@qq.com;songhanxi2013@163.com;wangjagri@yangtzeu.edu.cn;qiulijuan@caas.cn
  • Supported by:
    Preservation of Soybean Germplasm Resources(19211205);Jingzhou Science and Technology Plan Project(2020CB21-28)


Petiole angle is one of the important factors that affects the high-efficiency light posture of plants. It is very important to improve soybean plant architecture by adjusting the leaf angle petioles. Soybean petiole angle is a quantitative trait, which is limited to QTLs mapping for most studies up to date. The reported gene GmILPA1controlling leaf petiole angle gene was cloned from mutants. Identification of more regulatory genes and elite alleles is urgent both for the clarification of genetic mechanism for petiole angle and its breeding utilization. In this study, 783 and 690 soybean germplasms were phenotypic for petiole angle in Hainan and Beijing in 2019 and 2020, respectively, and genome-wide associated study (GWAS) were performed using genome-wide distributed SNPs. Results showed that the petiole angle at different nodes (top, middle, and bottom nodes) were in normal distribution, suggesting that the trait of typical quantitative was inheritance. A total of 325 SNPs associated with petiole angle were identified by two-point GWAS analysis in two years, including 51, 230, 10, and 34 SNPs for petiole angles of the top, middle, bottom, and mean value of different nodes, respectively. Three candidate genes (Glyma.05G059700: auxin regulatory protein, Glyma.06G076900: AFR, and Glyma.06G076000: COP9) were obtained by LD block analysis. Transcriptional analysis revealed that all these three candidate genes had high expression level in shoot apical meristem (SAM), however, high expression level were also identified in leaf for Glyma.06G076900, leaf and stem for Glyma.06G076000.

Key words: soybean, leaf petiole angle, GWAS

Fig. 1

Distribution of 783 soybean resources"

Table 1

Basic data of the angle between the petioles of 690 materials in two years"

Max (°)
Min (°)
Average (°)
Standard deviation (°)
Coefficient of variation(%)
2019 Hainan
顶部Top 110.6 17.0 41.0 12.0 29.3
中部Middle 109.9 14.6 39.8 10.7 26.9
底部Bottom 99.8 21.7 57.6 13.0 22.6
平均值Average 104.2 24.4 46.1 9.9 21.5
2020 Beijing
顶部Top 111.9 22.0 48.4 14.1 29.1
中部Middle 119.5 22.0 49.5 10.3 20.8
底部Bottom 108.9 27.2 55.9 11.2 20.0
平均值Average 99.1 27.5 51.3 8.4 16.4

Fig. 2

Phenotypic distribution of petiole angle in natural population A, C, and E are the distribution frequency histograms of petiole angle at top, middle, and bottom nodes of Hainan in 2019, with three replicates per sample; B, D, and F are the distribution frequency histograms of petiole angle at top, middle, and bottom nodes of Beijing in 2020, with three replicates per sample."

Table 2

Correlation analysis of two different nodes in two years"

北京Beijing 海南Hainan
顶部Top 中部Middle 底部Bottom 顶部Top 中部Middle 底部Bottom
顶部Top 1
中部Middle 0.203** 1
底部Bottom 0.142** 0.419** 1
顶部Top 0.088* -0.068 -0.119* 1
中部Middle 0.042 -0.014 -0.048 0.601** 1
底部Bottom 0.004 -0.082* -0.068 0.426** 0.584** 1

Fig. 3

Analysis of phenotypic difference between two years A: the significance analysis of phenotypic differences at the same node in two years; B: the analysis of the proportion of different grade materials; C: the phenotypic difference between the two years was in the geographical distribution of 0°-20° materials; D: the analysis of the proportion of different grade materials; C: the phenotypic difference between the two years was in the geographical distribution of 21°-40°; E: the difference of phenotype in two years is more than 40° in material geographical distribution."

Fig. 4

Location of petiole angle GWAS at each node in two years A-D: the correlation analysis Q-Q plot and Manhattan plot of petiole angle at top, middle, and bottom nodes and average value of petiole angle at three nodes in Hainan; E-H: the correlation analysis Q-Q plot and Manhattan plot of petiole angle at top, middle, and bottom nodes and average value of petiole angle at three nodes in Beijing."

Table 3

SNPs were significantly associated with leaf petiole angle at each node"

SNP number
Position interval
Peak SNP position
-log10 P值极大值
(-log10 Pmax)
Reported interval
顶部Top 6 34 20081726-29191958 24044918 A/G 9.08
顶部Top 18 2 33523827-33523832 33523832 G/T 6.91
中部Middle 4 4 5596149-15210458 15210440 C/A 7.42
中部Middle 9 3 17234567-17234585 17234573 T/A 6.23
底部Bottom 1 5 3190286-3193332 3190286 A/T 7.21
平均值Average 5 3 5476726-5488204 5476976 A/C 11.37
顶部Top 3 2 10230350-10230362 10230350 A/T 7.72
顶部Top 3 6 17497236-17497310 17497236 C/T 8.41
顶部Top 7 2 21264942-26216740 21264942 G/A 8.08
顶部Top 11 3 17811042-17811056 17811042 C/T 7.45 [9]
顶部Top 17 2 37154449-39977197 37154449 C/A 12.11 [9]
中部Middle 6 131 5787577-5947566 5889343 A/G 8.33
中部Middle 6 5 20003640-20973899 20071106 A/G 11.92
中部Middle 13 49 37043663-37156881 37117542 A/G 8.71
中部Middle 14 5 15953346-19558649 15953346 A/G 9.23 [9]
中部Middle 14 6 24281424-25306741 24281424 A/G 9.35 [9]
中部Middle 14 3 27024699-27783925 27076700 C/T 9.35 [9]
中部Middle 14 5 29151458-30357161 29151458 A/G 9.96 [9]
中部Middle 14 19 32044124-41988610 32044124 A/G 9.35 [9]
中部Middle 19 2 37695290-37695805 37695805 G/T 7.13
中部Middle 19 3 46080617-46082050 46080617 C/G 10.25
底部Bottom 3 3 1997994-1998818 1997994 C/G 7.35
底部Bottom 19 2 41151600-41169499 41169499 C/T 7.27
平均值Average 6 31 5859032-5958396 5948057 A/G 8.06

Fig. 5

Analysis of significant loci A: peak SNP site Gm05_5476976 allele difference analysis, AA and CC represent the frequency of AA and CC homozygosity at this site, AC indicates the frequency of AC heterozygosity at this site; B: peak SNP site Gm05_5476976 LD block analysis, the red dot on the red threshold line indicates Gm05_ 5476976 LD block loci closely linked to petiole angle traits; C: peak SNP site Gm06_24044918 allele difference analysis, AA and GG represent the frequency of AA and GG homozygosity at this site, GA indicates the frequency of GA heterozygosity at this site; peak SNP site Gm06_5948057 LD block analysis, the red dot on the red threshold line indicates Gm06_5948057 LD block loci closely linked to petiole angle traits."

Fig. 6

Expression profile of candidate genes A: the relative expression profile of candidate genes in Gm05_5476976 LD block interval; B: the relative expression profile of candidate genes in Gm05_5476976 LD block interval."

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