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Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (8): 2051-2063.doi: 10.3724/SP.J.1006.2023.24208

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

Haplotype analysis of soybean leaf type regulator gene Ln and its homologous genes

LI Gang1,3(), ZHOU Yan-Chen1, XIONG Ya-Jun1, CHEN Yi-Jie1, GUO Qing-Yuan1, GAO Jie1, SONG Jian2, WANG Jun1,*(), LI Ying-Hui3,*(), QIU Li-Juan3,*()   

  1. 1 College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China
    2 College of Life Science, Yangtze University, Jingzhou 434025, Hubei, China
    3 Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • Received:2022-09-10 Accepted:2023-02-21 Online:2023-08-12 Published:2023-03-01
  • Contact: WANG Jun,LI Ying-Hui,QIU Li-Juan E-mail:1073855911@qq.com;wangjagri@yangtzeu.edu.cn;liyinghui@caas.cn;qiulijuan@caas.cn
  • About author:First author contact:**Contributed equally to this work
  • Supported by:
    Key Science and Technology Project of Yunnan Province(202202AE090014)

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Abstract:

Soybean leaf type is an important component of ideal plant type, which is of great significance for the breeding of soybean varieties. In this study, we analyzed the haplotype of Ln and its homologous gene (Glyma.10G273800) in 598 materials from different regions of China. Ln gene and homologous gene contained three haplotypes (Hap1-Hap3), respectively. There was no significant difference in leaf length between the three haplotypes of Ln gene, and Hap2 was significantly different from Hap1/Hap3 in leaf width, leaf area, and leaf length width ratio. There were significant differences between Hap3 and Hap2 of Ln homologous gene in different leaf types. There was no difference in the ratio of leaf length to width between Hap1 and Hap2. There was no significant difference in leaf width phenotype at the 4th leaf site, and Hap1 at the 5th leaf site was significantly lower than Hap2. Leaf length, leaf area, and leaf circumference Hap1 were significantly lower than Hap2. In terms of geographical distribution, Hap2 of Ln gene was mainly distributed in high latitude and high altitude regions, and no obvious regional bias was detected in the distribution of the three haplotypes of its homologous genes. Genetic analysis showed that only D9H of Hap2 in Ln gene had artificial selection signal, while the other two mutation sites in Ln gene and two mutation sites in homologous gene had no artificial selection signal. This study provides the theoretical basis for soybean leaf type breeding and has positive significance for increasing soybean yield.

Key words: soybean, leaf type, haplotype, Ln gene

Table 1

Origin, classification, and geographic information of 598 soybean germplasm"

来源
Origin		 数量
Number		 改良品种
Improved		 地方品种
Landrace		 经度
Longitude		 纬度
Latitude
安徽Anhui 21 6 15 117.17E 31.52N
北京Beijing 25 22 3 116.28E 39.54N
福建Fujian 6 2 4 118.04E 24.26N
广东Guangdong 11 1 10 113.18E 23.10N
甘肃Gansu 6 0 6 103.50E 36.03N
广西Guangxi 10 1 9 108.21E 22.47N
贵州Guizhou 33 0 33 106.72E 26.57N
海南Hainan 1 0 1 111.10E 20.03N
河北Hebei 48 7 41 114.26E 38.03N
河南Henan 24 11 13 113.40E 34.46N
黑龙Heilongjiang 76 59 17 126.64E 45.76N
湖北Hubei 28 5 23 115.32E 30.52N
湖南Hunan 15 3 12 112.59E 28.12N
吉林Jilin 45 17 28 125.18E 43.55N
江苏Jiangsu 27 10 17 118.75E 32.04N
江西Jiangxi 6 0 6 115.53E 28.42N
辽宁Liaoning 39 12 27 123.23E 41.48N
内蒙古Inner Mongolia 6 2 4 111.65E 40.82N
宁夏Ningxia 3 0 3 106.13E 38.28N
陕西Shaanxi 18 0 18 108.55E 34.15N
四川Sichuan 44 3 41 104.06E 30.67N
山东Shandong 29 9 20 120.18E 36.03N
上海Shanghai 2 0 2 121.43E 34.50N
山西Shanxi 56 11 45 112.33E 37.51N
台湾Taiwan 1 1 0 121.31E 25.02N
新疆Xinjiang 1 1 0 87.36E 43.46N
云南Yunnan 11 0 11 102.42E 25.03N
浙江Zhejiang 6 4 2 120.10E 30.15N

Table 2

Descriptive statistics of different leaf type traits in 598 germplasms"

性状
Trait		 节点
Node		 均值
Mean		 标准差
SD		 最小值
Min.		 最大值
Max.		 正态性检验显著性a
Normality test for significance a
叶面积Leaf area (cm2) 4 42.517 13.851 13.329 80.056 <0.001
5 45.803 13.486 16.780 81.826 <0.001
叶长Leaf length (cm) 4 10.206 1.421 6.294 14.009 >0.100
5 10.405 1.331 6.562 13.879 >0.100
叶长宽比Leaf length to width ratio 4 1.808 0.266 1.243 2.876 <0.001
5 1.685 0.279 1.130 2.634 <0.001
叶周长Leaf perimeter (cm) 4 27.817 4.161 16.584 40.053 >0.100
5 28.698 3.990 16.992 39.039 >0.100
叶宽Leaf width (cm) 4 5.950 1.346 3.077 9.693 <0.001
5 6.324 1.337 3.132 10.139 <0.001

Table 3

Correlation analysis of different leaf type traits"

性状
Trait		 叶面积
Leaf area		 叶长
Leaf length		 叶长宽比
Leaf length to width ratio		 叶周长
Leaf perimeter		 叶宽
Leaf width
叶面积Leaf area 1
叶长Leaf length 0.777*** 1
叶长宽比Leaf length to width ratio -0.463*** 0.003 1
叶周长Leaf perimeter 0.801*** 0.772*** -0.231*** 1
叶宽Leaf width 0.956*** 0.612*** -0.654** 0.721*** 1

Fig. 1

Gene structure of Glyma.20G116200 and Glyma.10G273800"

Table 4

Frequency of different haplotypes of Ln (Glyma.20g116200) and its homologous genes (Glyma.10G273800) in germplasm resources"

基因
Gene name		 单倍型
Haplotype		 类型
Class		 基因型
Genotype		 频率
Frequency		 改良品种
Improved		 地方品种
Landrace
Glyma.20G116200 Hap1 参考Reference GTA 429 92 337
Hap2 特定Specific CTA 59 55 4
Hap3 特定Specific GGT 92 34 58
Glyma.10G273800 Hap1 特定Specific TG 253 92 161
Hap2 参考Reference GG 206 82 124
Hap3 特定Specific GT 116 11 105

Fig. 2

Haplotype analysis of Ln gene A: haplotype inference network; B: mutation type and site; C-F: the LLWR of middle leaves (C), and side leaf (D) on the fourth node, LLWR of middle leaves (E), and side leaf (F) on the fifth node. Significance was estimated by K-W test, P < 0.01 and P < 0.001 indicate different significance and extremely significance, respectively; G: geographical distribution of Ln gene haplotypes."

Fig. S1

Comparison of leaf type traits among different haplotypes based on Ln genes A-D: the leaf length of middle leaves (A), and side leaf (B) on the fourth node, leaf length of middle leaves (C), and side leaf (D) on the fifth node; E-H: the leaf width of middle leaves (E), and side leaf (F) on the fourth node, leaf width of middle leaves (G), and side leaf (H) on the fifth node; I-L: the leaf area of middle leaves (I), and side leaf (J) on the fourth node, leaf area of middle leaves (K), and side leaf (L) on the fifth node; M-P: the leaf perimeter of middle leaves (M), and side leaf (N) on the fourth node, leaf perimeter of middle leaves (O), and side leaf (P) on the fifth node."

Fig. 3

Haplotype analysis of Glyma.10G273800 gene A: haplotype inference network; B: mutation type and site; C-F: the LLWR of middle leaves (C), and side leaf (D) on the fourth node, LLWR of middle leaves (E), and side leaf (F) on the fifth node. Significance was estimated by K-W test, P < 0.01 and P < 0.001 indicate different significance and extremely significance, respectively; G: geographical distribution of Ln gene haplotypes."

Fig. S2

Comparison of leaf type traits among different haplotypes based on Ln genes A-D: the leaf length of middle leaves (A), and side leaf (B) on the fourth node, leaf lengtth of middle leaves (C), and side leaf (D) on the fifth node; E-H: the leaf width of middle leaves (E), and side leaf (F) on the fourth node, leaf width of middle leaves (G), and side leaf (H) on the fifth node; I-L: the leaf area of middle leaves (I), and side leaf (J) on the fourth node, leaf area of middle leaves (K), and side leaf (L) on the fifth node; M-P: the leaf perimeter of middle leaves (M), and side leaf (N) on the fourth node, leaf perimeter of middle leaves (O), and side leaf (P) on the fifth node."

Fig. 4

Genetic differentiation analysis of Ln gene and homologous genes A: genetic differentiation index between populations based on Ln gene: B: the neutral test based on Ln gene: C: the analysis of nucleotide diversity in population based on Ln gene; D: the genetic differentiation index between populations based on Glyma.10g273800; E: the neutral test based on Glyma.10g273800; F: the analysis of nucleotide diversity in population based on Glyma.10g273800. Fst: genetic differentiation index between populations; Tajima’s D: neutral test; π: the analysis of nucleotide diversity in population."

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