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Acta Agronomica Sinica ›› 2025, Vol. 51 ›› Issue (2): 548-556.doi: 10.3724/SP.J.1006.2025.44090

• RESEARCH NOTES • Previous Articles    

Association mapping of internode and lateral branch internode length of peanut main stem and analysis of candidate genes

ZHAO Fei-Fei1,2(), LI Shao-Xiong2, LIU Hao2, LI Hai-Fen2, WANG Run-Feng2, HUANG Lu2, YU Qian-Xia2, HONG Yan-Bin2, CHEN Xiao-Ping2, LU Qing2,*(), CAO Yu-Man1,*()   

  1. 1College of Grassland Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, China
    2Crops Research Institute, Guangdong Academy of Agricultural Sciences / Guangdong Provincial Key Laboratory of Crop Genetic Improvement / South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou 510640, Guangdong, China
  • Received:2024-06-03 Accepted:2024-09-18 Online:2025-02-12 Published:2024-10-11
  • Contact: E-mail: yumancao@nwafu.edu.cn; E-mail: luqing2016@126.com
  • Supported by:
    National Key Research and Development Program of China(2023YFD1202800);China Agriculture Research System of MOF and MARA(CARS-13);Open Competition Program of Top Ten Critical Priorities of Agricultural Science and Technology Innovation for the 14th Five-Year Plan in Guangdong Province(2022SDZG05);Guangdong Provincial Key Research and Development Program-Modern Seed Industry(2022B0202060004);Special Support Program of Guangdong Province(2021TX06N789)

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Abstract:

The internode length of the main stem and lateral branches is a key agronomic trait influencing the yield per plant in peanuts. In this study, 390 natural peanut populations were used to measure the length of the first, second, and third internodes of both the main stem and lateral branches at maturity. A genome-wide association analysis was conducted using the mixed linear model (PCA+K model) in GAPIT3.0 software. The results showed that the internode lengths of the main stem and lateral branches followed a normal distribution and were significantly positively correlated. A total of 63 loci associated with the internode length of the main stem and lateral branches were identified. Three significant association sites and site clusters were discovered, including a notable association at A04_57397319 that co-located with findings from previous research. Five candidate genes were predicted within this region. These findings provide valuable insights into the genetic basis and regulatory mechanisms of internode length in both the main stem and lateral branches of peanuts, laying a foundation for plant architecture improvement.

Key words: peanut, main stem internode length, lateral branch internode length, GWAS

Table 1

Statistical analysis of internode length-related traits in peanut population in 2017"

性状
Trait		 最大值
Max.		 最小值
Min.		 平均值±标准数
Mean ± SD		 变异系数
CV (%)		 偏度
Skewness		 峰度
Kurtosis
主茎第一节间长度Main stem first internode length 6.00 1.00 2.09±0.61 0.29 1.953 8.880
主茎第二节间长度Main stem second internode length 3.50 0.50 1.55±0.56 0.36 0.560 0.149
主茎第三节间长度Main stem third internode length 4.25 0.26 1.64±0.63 0.38 0.818 1.175
侧枝第一节间长度Lateral branch first internode length 8.00 0.65 2.25±0.92 0.40 1.734 6.093
侧枝第二节间长度Lateral branch second internode length 7.00 1.00 2.40±0.85 0.35 1.526 4.486
侧枝第三节间长度Lateral branch third internode length 7.50 0.20 2.81±0.97 0.35 1.215 3.067

Fig. 1

Distribution of related characters of internode length in peanut associated population MSF: main stem first internode length; MSS: main stem second internode length; MST: main stem third internode length; LBF: lateral branch first internode length; LBS: lateral branch second internode length; LBT: lateral branch third internode length."

Fig. 2

Correlation coefficient between internode traits of the main stem and lateral branches of peanut Abbreviations are the same as those given in Fig. 1. ** indicates significant correlation at the 0.01 probability level."

Table 2

Significant association sites of node length traits of main stem and lateral branches"

性状
Trait		 关联位点
Associated sites		 染色体
Chromosome		 位置
Position		 P值
P-value
MSF A01_106043972 A01 106,043,972 1.51E-07
A03_96536142 A03 96,536,142 1.08E-08
A04_57397319 A04 57,397,319 2.29E-07
A05_51337016 A05 51,337,016 1.08E-08
A05_74958968 A05 74,958,968 1.08E-08
A06_30420867 A06 30,420,867 1.08E-08
A07_34955668 A07 34,955,668 1.08E-08
A07_48095361 A07 48,095,361 3.72E-07
A07_49223806 A07 49,223,806 1.32E-07
A07_52783226 A07 52,783,226 1.61E-07
A07_58125963 A07 58,125,963 2.84E-07
A07_66360549 A07 66,360,549 3.09E-07
A07_71636384 A07 71,636,384 1.84E-07
A07_73981302 A07 73,981,302 1.62E-08
A07_75712072 A07 75,712,072 1.61E-07
A07_81744376 A07 81,744,376 6.20E-08
A07_83570736 A07 83,570,736 7.46E-08
A07_87296838 A07 87,296,838 1.08E-08
A07_93491105 A07 93,491,105 4.48E-08
A07_109121009 A07 109,121,009 1.61E-07
A07_111031457 A07 111,031,457 2.14E-07
A08_24070999 A08 24,070,999 1.08E-08
A09_62081202 A09 62,081,202 1.92E-07
A09_67453035 A09 67,453,035 2.71E-07
A10_37985014 A10 37,985,014 3.00E-07
B01_137273357 B01 137,273,357 1.08E-08
B02_49773743 B02 49,773,743 1.08E-08
B02_52441346 B02 52,441,346 1.45E-07
B04_14356520 B04 14,356,520 1.08E-08
B05_37369887 B05 37,369,887 1.08E-08
B05_153066632 B05 153,066,632 1.08E-08
B07_4160712 B07 4,160,712 1.21E-07
B08_21939742 B08 21,939,742 1.08E-08
B10_9639595 B10 9,639,595 1.08E-08
B10_13221609 B10 13,221,609 1.08E-08
B10_45639904 B10 45,639,904 3.66E-08
B10_119864830 B10 119,864,830 1.08E-08
B10_132271423 B10 132,271,423 1.08E-08
MST A01_73271598 A01 73,271,598 2.14E-07
LBF A01_23488952 A01 23,488,952 2.29E-07
A01_55372401 A01 55,372,401 2.14E-07
A01_68297303 A01 68,297,303 2.49E-07
A02_8875457 A02 8,875,457 2.61E-07
A03_2953786 A03 2,953,786 2.33E-07
A06_4380158 A06 4,380,158 2.68E-07
A06_86359952 A06 86,359,952 2.52E-07
A06_103855231 A06 103,855,231 2.60E-07
A07_129887507 A07 129,887,507 2.98E-07
A09_62083927 A09 62,083,927 2.05E-07
A09_114516939 A09 114,516,939 2.69E-07
A10_79235001 A10 79,235,001 2.37E-07
A10_104046269 A10 104,046,269 2.15E-07
B01_104941977 B01 104,941,977 2.96E-07
B01_150609234 B01 150,609,234 2.26E-07
B03_52115966 B03 52,115,966 2.80E-07
B03_143095996 B03 143,095,996 2.12E-07
B05_18845147 B05 18,845,147 2.10E-07
B05_95256042 B05 95,256,042 1.18E-07
B06_16502781 B06 16,502,781 3.12E-07
B06_42455491 B06 42,455,491 2.01E-07
B07_61224 B07 61,224 3.12E-07
B07_47200539 B07 47,200,539 2.01E-07

Fig. 3

Manhattan plot of genome-wide association analysis for main stem and lateral branch internode length in peanut"

Fig. 4

Manhattan diagram of candidate gene analysis"

Table 3

Notes on candidate genes"

染色体
Chr.		 预测基因
Predictive genes		 起始位置
Start
position		 终止位置
End
position		 描述
Description		 功能
Function		 PFAMs功能结构域
Functional domain of PFAMs
A04 Ahy_A04g019832 57,318,253 57,319,719 — — Asp_protease_2, Retrotrans_gag
A04 Ahy_A04g019833 57,392,913 57,401,960 清除剂mRNA解旋酶C端结合
Scavenger mRNA decapping enzyme C-term binding		 — HIT
A04 Ahy_A04g019834 57,405,637 57,406,221 — — —
A04 Ahy_A04g019835 57,410,765 57,415,546 肽基脯氨酰顺反异构酶
Peptidyl-prolyl cis-trans isomerase		 — FKBP_C, Ribosomal_S8e, TPR_1, TPR_2, TPR_8
A04 Ahy_A04g019837 57,493,974 57,498,876 肽基脯氨酰顺反异构酶
Peptidyl-prolyl cis-trans isomerase		 FKBP15-2 FKBP_C

Fig. 5

Candidate gene expression analysis"

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