Welcome to Acta Agronomica Sinica，

Acta Agronomica Sinica ›› 2018, Vol. 44 ›› Issue (8): 1142-1151.doi: 10.3724/SP.J.1006.2018.01142

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

QTL Mapping for Shelling Percentage and Plant Height in Cultivated Peanut (Arachis hypogaea L.)

Wei-Gang CHEN(),Jian-Bin GUO(),Zhi-Jun XU,Bo-Lun YU,Xi-Ke QIU,Li HUANG,Yan-Bin SONG,Yu-Ning CHEN,Xiao-Jing ZHOU,Huai-Yong LUO,Nian LIU,Xiao-Ping REN,Hui-Fang JIANG()   

  1. Oil Crops Research Institute, China Academy of Agricultural Sciences / Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, Hubei, China
  • Received:2017-12-20 Accepted:2018-03-26 Online:2018-08-10 Published:2018-04-20
  • Contact: Wei-Gang CHEN,Jian-Bin GUO,Hui-Fang JIANG E-mail:wgchen2015@163.com;guojianbin1990@163.com;peanutlab@oilcrops.cn
  • Supported by:
    the National Natural Science Foundation of China(31471534);the National Natural Science Foundation of China(31571713);the Crop Germplasm Resources Protection Project(2017NWB033);the Plant Germplasm Resources Sharing Platform(NICGR2017-36);the China Agriculture Research System (CARS-13-Germplasm Resource Evaluation for Peanut).(CARS-13-花生种质资源评价)

RichHTML335

21

PDF

735

PDF

17

Abstract:

Peanut yield is greatly influenced by shelling percentage (SP) and plant height (PH). Marker-assisted selection for shelling percentage and plant height improvement can be facilitated by detecting additive and epistatic QTLs, understanding their interactions with environment, as well as the genetic relationship between SP and PH. In a four-year experiment, the variations of SP and PH were evaluated with the recombinant inbred line population derived from the cross between Yuanza 9102 and Xuzhou 68-4. QTLs associated with SP and PH were analyzed using a high density linkage map and QTLNetwork 2.0 software. The results showed that SP and PH were negatively correlated (P < 0.01). Thirteen and eight additive QTLs were identified for SP and PH, respectively. Major loci qSPA05.2 and qSPA09.1 for SP and major locus qPHA09.1 for PH were repeatedly detected in three or four years. Six pairs of epistatic QTLs for SP and five pairs of epistatic QTLs for PH were identified, and they all had interaction effects with environment. qSPA09.1 and qPHA09.1 were located in the same interval (Ad91I24-AGGS2492) on chromosome A09. The additive effect of this locus for SP variation decreased from 14.37% to 5.50% after eliminating the PH effect, suggesting the pleiotropism of qSPA09.1 for SP and qPHA09.1 for PH.

Key words: cultivated peanut, shelling percentage, plant height, QTL

Fig. 1

Phenotypic distribution of shelling percentage in the RIL population across four years Dotted arrow: Yuanza 9102; solid arrow: Xuzhou 68-4."

Fig. 2

Phenotypic distribution of plant height in the RIL population across four years Dotted arrow: Yuanza 9102; solid arrow: Xuzhou 68-4."

Table 1

Phenotypic variation for shelling percentage and plant height in the peanut RILs population"

性状
Trait		 年份
Year		 亲本 Parents 重组自交系群体 RILs population
远杂9102
Yuanza 9102		 徐州68-4
Xuzhou 68-4		 差异
Difference		 最小值
Min.		 最大值
Max.		 平均值±标准差
Mean±SD		 变异系数
CV (%)
出仁率
Shelling
percentage (%)		 2013 80.32 75.31 5.01** 65.39 83.33 76.92±3.72 4.84
2014 79.99 74.25 5.74** 66.74 84.79 78.05±3.65 4.68
2015 82.12 75.96 6.16** 68.28 83.72 78.18±3.03 3.88
2016 82.03 76.56 5.47** 67.04 83.52 78.16±3.12 3.99
株高
Plant height (cm)		 2013 29.22 53.50 -24.28** 25.80 62.90 42.41±8.69 20.48
2014 34.58 58.15 -23.57** 25.80 61.45 41.67±6.60 15.83
2015 32.62 46.85 -14.23** 28.35 60.30 41.06±5.70 13.88
2016 32.50 47.85 -15.35** 26.65 48.71 35.29±4.25 12.03

Table 2

Analysis of variance for shelling percentage and plant height traits in the RIL population across four years"

性状
Trait		 变异来源
Source		 平方和
SS		 自由度
df		 均方
MS		 F值
F-value		 P值
P-value		 遗传力
h2
出仁率
Shelling
percentage		 基因型 Genotype (G) 13283.621 194 68.472 17.401 <0.001 0.958
环境 Environment (E) 253.848 3 84.616 21.504 <0.001
基因型×环境G × E 2083.076 577 3.610 0.917 0.849
误差 Error 2262.604 575 3.935
株高
Plant height		 基因型 Genotype (G) 31363.468 194 161.667 11.354 <0.001 0.886
环境 Environment (E) 11021.132 3 3673.711 257.999 <0.001
基因型×环境G × E 17812.325 578 30.817 2.164 <0.001
误差 Error 8329.958 585 14.239

Fig. 3

Location of additive effects QTL and epistatic QTL on linkage groups"

Table 3

Additive QTLs and their genetic effects for shelling percentage and plant height"

性状
Trait		 QTL 环境
Environment		 标记区间
Marker interval		 位置
Position
(cM)		 置信区间
CI (cM)		 加性效应
A		 贡献率
R2A (%)		 贡献率
R2AE (%)
出仁率 qSPA05.1 ME Ad05A19296-Ad05A19142 36.7 35.7-37.1 0.65 1.47 0.09
Shelling qSPA05.2 E2 Ad05A20617-AGGS2372 93.5 91.9-94.5 -1.16 10.44
percentage E3 Ad05A20617-AGGS2372 93.5 91.9-94.5 -1.09 10.81
ME Ad05A20617-AGGS2372 93.5 91.9-94.5 -1.00 10.06
qSPA09.1 E2 Ad91I24-AHGS2130 27.6 26.9-27.9 -1.43 11.72
E3 AGGS1606-AHGA98567 27.2 26.9-27.7 -1.29 14.79
E4 AGGS1606-AHGA98567 27.2 26.9-27.9 -1.45 14.11
ME Ad91I24-AHGS2130 27.6 26.9-27.7 -1.36 14.37 0.21
qSPA09.2 E1 Ad09A3779-GNB377 33.9 32.9-36.0 -1.82 16.86
qSPB01.1 E2 TC23C08-TC1A08 66.5 65.9-67.0 0.87 7.95
qSPB03.1 E4 Ai08B16802-AGGS1276 32.9 24.9-41.3 -1.23 6.45
qSPB03.2 E2 AHGS1561-AGGS1369 45.7 44.7-46.6 -0.97 6.91
qSPB03.3 ME AGGS1369-GM1854 47.6 46.6-50.6 -0.70 3.58 0.11
qSPB04.1 ME pPGSseq15C12-1-AGGS0396-2 101.3 100.3-101.9 -0.41 4.28 0.16
qSPB05.1 ME AGGS0243-AHGS1624 52.8 51.8-52.9 -1.28 5.78 0.04
qSPB05.2 ME AhTE0319-AhTE0446 84.6 83.6-84.7 0.79 4.09 0.06
qSPB10.1 ME Ai10B12455-AGGS0675 47.2 46.9-47.6 0.74 4.04
qSPB10.2 E2 AhTE0709-GA156 59.8 58.8-60.0 1.02 6.17
E3 AhTE0709-GA156 59.8 58.8-60.0 1.04 7.92
E4 AhTE0709-GA156 59.8 58.8-60.0 1.36 8.31
株高 qPHA05.1 ME AGGS1589-AHGS1143 4.7 3.7-6.7 -0.95 0.51 0.76
Plant qPHA05.2 E3 pPGPSeq2F10-AGGS1167 85.6 83.7-85.8 1.96 14.19
height ME pPGPSeq2F10-AGGS1167 84.6 83.7-85.8 1.59 5.04 0.31
qPHA09.1 E1 AHGS2130-AGGS2492 27.7 27.3-27.9 3.78 21.60
E4 Ad91I24-AHGS2130 27.6 27.3-27.7 1.99 21.87
ME AHGS2130-AGGS2492 27.7 27.3-27.9 2.10 11.17 1.98
qPHB03.1 E1 AGGS1276-AHGS1561 44.3 41.3-44.7 2.19 6.77
ME AGGS1276-AHGS1561 44.3 42.3-44.7 1.49 4.79 0.60
qPHB03.2 E2 AGGS1369-GM1854 50.6 46.6-59.6 2.60 12.15
qPHB04.1 ME AhTE0908-AHGS1703 26.6 25.6-26.9 1.50 1.45 1.25
qPHB04.2 E2 Ai04B2241-AGGS1601 44.7 43.7-45.0 2.42 10.30
qPHB08 E3 AHGS1470-AGGS2186 21.1 19.5-22.9 1.80 9.77

Table 4

Interaction of epistatic QTLs for shelling percentage and plant height with environment in the RIL population"

QTL 标记区间
Marker interval		 位置
Position		 QTL 标记区间
Marker interval		 位置
Position		 上位性
效应
AA		 贡献率
R2AA (%)		 贡献率
R2AAE (%)
出仁率 Shelling percentage
qSPA09.1 Ad91I24-AHGS2130 27.6 qSPB03.3 AGGS1369-GM1854 47.6 -0.6479 3.72 0.01
qSPA01.1 AGGS1451-AhTE0678 18.4 qSPA06 AGGS0978-Ai06B19288 12.3 0.6695 2.33 0.08
qSPA01.2 AHGS1846-AGGS0633 33.7 qSPB01.2 AHGS1369-AHGS3627 63.1 -0.4537 1.02 0.02
qSPA05.2 Ad05A20617-AGGS2372 93.5 qSPB05.2 AhTE0319-AhTE0446 84.6 0.2599 0.45 0.01
qSPA09.3 AHGS0344-Ad10A10685 40.5 qSPB01.3 AHTE0674-Ai01B7136 43.8 0.5093 1.44 0.05
qSPB05.3 AGGS2216-AHGS1532 70.7 qSPB07 Ai07B12485-AGGS2425 38.4 0.522 1.56 0.05
株高 Plant height
qPHA06 AGGS0978-Ai06B19288 13.3 qPHA09.2 AhTE0794-AhTE0381 55.3 -2.3216 3.13 0.25
qPHA06 AGGS0978-Ai06B19288 13.3 qPHA09.3 AGGS2380-AhTE0888 68.4 -0.7828 0.04 0.05
qPHB01.1 AHTE0674-Ai01B7136 43.8 qPHB04.3 AGGS0284-AHGS1773 72.1 0.5921 1.06 0.13
qPHB01.2 Ai01B7136-AHGA364915 46.9 qPHB04.4 AhTE0796-GM2106 91.9 -7.7112 0.13 1.11
qPHB01.3 AGGS1376-AHGS1130 70.8 qPHB04.3 AGGS0284-AHGS1773 72.1 0.6076 0.46 0.18

Table 5

Estimated additive effect of conditional QTLs for shelling percentage in multi-environments"

QTL 标记区间
Marker interval		 非条件QTL贡献率
R2A (%) SP		 条件QTL贡献率
R2A (%) SP|PH
qSPA05.1 Ad05A19296-Ad05A19142 1.47
qSPA05.2 Ad05A20617-AGGS2372 10.06 5.30
qSPA09.1 Ad91I24-AHGS2130 14.37 5.50
qSPB03.3 AGGS1369-GM1854 3.58
qSPB04.1 pPGSseq15C12-1-AGGS0396-2 4.28
qSPB04.2 AHGA161495-AHGA161468 4.75
qSPB04.3 AhTE0107-AGGS2509 5.27
qSPB05.1 AGGS0243-AHGS1624 5.78 1.26
qSPB05.2 AhTE0319-AhTE0446 4.09 6.90
qSPB10.1 Ai10B12455-AGGS0675 4.04

Fig. 4

QTLs and their LOD values for shelling percentage and plant height in the same range of chromosome A09"

Fig. 5

Distribution of QTLs repeatedly detected for shelling percentage and plant height on the genetic maps"

[1] 李振动, 李新平, 黄莉, 任小平, 陈玉宁, 周小静, 廖伯寿, 姜慧芳 . 栽培种花生荚果大小相关性状QTL定位. 作物学报, 2015,41:1313-1323
doi: 10.3724/SP.J.1006.2015.01313
Li Z D, Li X P, Huang L, Ren X P, Chen Y N, Zhou X J, Liao B S, Jiang H F . Mapping of QTLs for pod size related traits in cultivated peanut (Arachis hypogaea L.). Acta Agron Sin, 2015,41:1313-1323 (in Chinese with English abstract)
doi: 10.3724/SP.J.1006.2015.01313
[2] Chen W, Jiao Y, Cheng L, Huang L, Liao B, Tang M, Ren X, Zhou X, Chen Y, Jiang H . Quantitative trait locus analysis for pod- and kernel-related traits in the cultivated peanut (Arachis hypogaea L.). BMC Genet, 2016,17:25
[3] Chen Y, Ren X, Zheng Y, Zhou X, Huang L, Yan L, Jiao Y, Chen W, Huang S, Wan L, Liao B, Huai D, Wei W, Jiang H . Genetic mapping of yield traits using RIL population derived from Fuchuan Dahuasheng and ICG6375 of peanut ( Arachis hypogaea L.). Mol Breed, 2017,37:17
[4] Luo H, Ren X, Li Z, Xu Z, Li X, Huang L, Zhou X, Chen Y, Chen W, Lei Y, Liao B, Pandey M, Varsheny R, Guo B, Jiang X, Liu F, Jiang H . Co-localization of major quantitative trait loci for pod size and weight to a 3.7 cM interval on chromosome A05 in cultivated peanut (Arachis hypogaea L.). BMC Genomics, 2017,18:58
[5] Luo H, Guo J, Ren X, Chen W, Huang L, Zhou X, Chen Y, Liu N, Xiong F, Lei Y, Liao B, Jiang H . Chromosomes A07 and A05 associated with stable and major QTLs for pod weight and size in cultivated peanut (Arachis hypogaea L.). Theor Appl Genet, 2017,131:267-282
[6] Faye I, Pandey M K, Hamidou F, Rothore A, Ndoye O, Vadez V, Varshney R K . Identification of quantitative trait loci for yield and yield related traits in groundnut (Arachis hypogaea L.) under different water regimes in Niger and Senegal. Euphytica, 2015,206:631-647
[7] Huang L, He H, Chen W, Ren X, Chen Y, Zhou X, Xia Y, Wang X, Jiang X, Liao B, Jiang H . Quantitative trait locus analysis of agronomic and quality-related traits in cultivated peanut (Arachis hypogaea L.). Theor Appl Genet, 2015,128:1103-1115
[8] 成良强, 唐梅, 任小平, 黄莉, 陈伟刚, 李振动, 周小静, 陈玉宁, 廖伯寿, 姜慧芳 . 栽培种花生遗传图谱的构建及主茎高和总分枝数QTL分析. 作物学报, 2015,41:979-987
doi: 10.3724/SP.J.1006.2015.00979
Cheng L Q, Tang M, Ren X P, Huang L, Chen W G, Li Z D, Zhou X J, Chen Y N, Liao B S, Jiang H F . Construction of genetic map and QTL analysis for main stem height and total branch number in peanut (Arachis hypogaea L.). Acta Agron Sin, 2015,41:979-987 (in Chinese with English abstract)
doi: 10.3724/SP.J.1006.2015.00979
[9] Li Y, Li L, Zhang X, Zhang K, Ma D, Liu J, Wang X, Liu F, Wan Y . QTL mapping and marker analysis of main stem height and the first lateral branch length in peanut (Arachis hypogaea L.). Euphytica, 2017,213:57
[10] Huang L, Ren X, Wu B, Li X, Chen W, Zhou X, Chen Y, Pandey M, Jiao Y, Luo H, Lei Y, Varsheny R, Liao B, Jiang H . Development and deployment of a high-density linkage map identified quantitative trait loci for plant height in peanut (Arachis hypogaea L.). Sci Rep, 2016,6:39478
[11] 蔡岩, 徐志军, 李振动, 李新平, 郭建斌, 任小平, 黄莉, 陈伟刚, 陈玉宁, 周小静, 罗怀勇, 姜慧芳 . 花生出仁率QTL分析及其与荚果大小的相关性. 作物学报, 2017,43:701-707
Cai Y, Xu Z J, Li Z D, Li X P, Guo J B, Ren X P, Huang L, Chen W G, Chen Y N, Zhou X J, Luo H Y, Jiang H F . Quantitative trait locus analysis for shelling percentage and correlation between shelling percentage and pod size related traits in Arachis hypogaea. Acta Agron Sin, 2017,43:701-707 (in Chinese with English abstract)
[12] Yang J, Hu C, Hu H, Yu R, Xia Z, Ye X, Zhu J . QTLNetwork: mapping and visualizing genetic architecture of complex traits in experimental populations. Bioinformatics, 2008,24:721-723
doi: 10.1093/bioinformatics/btm494
[13] Zhu J . Analysis of conditional genetic effects and variance components in developmental genetics. Genetics, 1995,141:1633
[14] Wang D, Zhu J, Li Z, Paterson A . Mapping QTLs with epistatic effects and QTL × environment interactions by mixed linear model approaches. Theor Appl Genet, 1999,99:1255-1264
doi: 10.1007/s001220051331
[15] 刘华, 张新友, 韩锁义, 严玫, 徐静, 董文召, 孙子淇 . 花生主茎高、侧枝长的遗传分析及QTL检测. 中国油料作物学报, 2013,35:508-514
Liu H, Zhang X Y, Han S Y, Yan M, Xu J, Dong W Z, Sun Z Q . Inheritance analysis and QTL mapping of main stem height and lateral branch length in peanut (Arachis hypogaea L.). Chin J Oil Crop Sci, 2013,35:508-514 (in Chinese with English abstract)
[16] 周小静, 董洋, 张芳, 任小平, 陈玉宁, 黄莉, 陈伟刚, 廖伯寿, 雷永, 晏立英, 罗怀勇, 姜慧芳 . 利用SNP标记高密度遗传图谱进行花生出仁率QTL定位. 中国油料作物学报, 2016,38:750-756
Zhou X J, Dong Y, Zhang F, Ren X P, Chen Y N, Huang L, Chen W G, Liao B S, Luo H Y, Jiang H F . QTL mapping of shelling percentage using SNP-based high density genetic map in cultivated peanut. Chin J Oil Crop Sci, 2016,38:750-756 (in Chinese with English abstract)
[1] Tang Kuan-Qiang, Li Gong-Yun, Song Mei-Yi, Zhao Xue, Chang Chun-Ling. Genome-wide association analysis and prediction model construction for soybean plant height [J]. Acta Agronomica Sinica, 2026, 52(6): 1743-1756.
[2] Zheng Yu-Zhen, Qi Fei-Yan, Sun Zi-Qi, Liu Hua, Qin Li, Shi Lei, Wang Juan, Wang Meng-Meng, Han Suo-Yi, Xu Jing, Miao Li-Juan, Huang Bing-Yan, Dong Wen-Zhao, Zheng Zheng, Zhang Xin-You. QTL mapping of total very long-chain fatty acids and seven fatty acid components in peanut seeds [J]. Acta Agronomica Sinica, 2026, 52(6): 1646-1657.
[3] Liu Chang-You, Wang Shen, Shi Hui-Ying, Shen Ying-Chao, Sun Lei, Wang Yan, Zhang Zhi-Xiao, Su Qiu-Zhu, Tian Jing, Fan Bao-Jie. QTL mapping for bruchid resistance in an adzuki bean distant hybridization population using rice bean genetic resources [J]. Acta Agronomica Sinica, 2026, 52(3): 936-944.
[4] ZHANG Fei-Fei, HE Wan-Long, JIAO Wen-Juan, BAI Bin, GENG Hong-Wei, CHENG Yu-Kun. Meta-analysis of stripe rust resistance-associated traits and candidate gene identification in wheat [J]. Acta Agronomica Sinica, 2025, 51(8): 2111-2127.
[5] HU Meng, SHA Dan, ZHANG Sheng-Rui, GU Yong-Zhe, ZHANG Shi-Bi, LI Jing, SUN Jun-Ming, QIU Li-Juan, LI Bin. QTL mapping and candidate gene screening for branch number in soybean [J]. Acta Agronomica Sinica, 2025, 51(7): 1747-1756.
[6] SHAO Shun-Wei, CHEN Zhuo, LAN Zhen-Dong, CAI Xing-Kui, ZOU Hua-Fen, LI Chen-Xi, TANG Jing-Hua, ZHU Xi, ZHANG Yu, DONG Jian-Ke, JIN Hui, SONG Bo-Tao. QTL mapping of tuber eye depth based on BSA-seq technique [J]. Acta Agronomica Sinica, 2025, 51(7): 1725-1735.
[7] YANG Hai-Yang, WU Lin-Xuan, LI Bo-Wen, SHI Han-Feng, YUAN Xi-Long, LIU Jin-Zhao, CAI Hai-Rong, CHEN Shi-Yi, GUO Tao, WANG Hui. OsWRI3, identified based on QTL mapping, regulates seed shattering in rice [J]. Acta Agronomica Sinica, 2025, 51(7): 1712-1724.
[8] GUO Dong-Cai, LYU Tao, CAI Yong-Sheng, MAI WU-LU-DA·AI He-Mai-Ti, CHEN Quan-Jia, QU Yan-Ying, ZHENG Kai. Meta-analysis of QTL and identification of candidate genes for fiber quality in cotton [J]. Acta Agronomica Sinica, 2025, 51(6): 1445-1466.
[9] ZHANG Jin-Ze, ZHOU Qing-Guo, XIAO Li-Jing, JIN Hai-Run, OU-YANG Qing-Jing, LONG Xu, YAN Zhong-Bin, TIAN En-Tang. QTL mapping and candidate gene analysis of glucosinolate content in various tissues of Brassica juncea [J]. Acta Agronomica Sinica, 2025, 51(5): 1166-1177.
[10] LIN Wei-Jin, GUO Ze-Jia, LIU Hao, LI Hai-Fen, WANG Run-Feng, HUANG Lu, YU Qian-Xia, CHEN Xiao-Ping, HONG Yan-Bin, LI Shao-Xiong, LU Qing. QTL mapping and candidate gene analysis of peanut pod yield-related traits [J]. Acta Agronomica Sinica, 2025, 51(4): 969-981.
[11] WANG Xiao-Lin, LIU Zhong-Song, KANG Lei, YANG Liu. Mapping of silique length and seeds per silique and transcriptome profiling of pod walls in Brassica napus L. [J]. Acta Agronomica Sinica, 2025, 51(4): 888-899.
[12] GUO Xu-Hu, LI Ling-Zhi, LI Feng, MA Bo-Yan, JIA Xiao-Yu. Functional study on the regulation of plant architecture by tomato type I MADS-box gene SlMADS79 [J]. Acta Agronomica Sinica, 2025, 51(4): 982-991.
[13] XU Jian-Xia, DING Yan-Qing, CAO Ning, CHENG Bin, GAO Xu, LI Wen-Zhen, ZHANG Li-Yi. Genome-wide association analysis and prediction of candidate genes for plant height and internode number in Chinese sorghum [J]. Acta Agronomica Sinica, 2025, 51(3): 568-585.
[14] YONG Rui, HU Wen-Jing, WU Di, WANG Zun-Jie, LI Dong-Sheng, ZHAO Die, YOU Jun-Chao, XIAO Yong-Gui, WANG Chun-Ping. Identification and validation of quantitative trait loci for grain number per spike showing pleiotropic effect on thousand grain weight in bread wheat (Triticum aestivum L.) [J]. Acta Agronomica Sinica, 2025, 51(2): 312-323.
[15] HU Peng-Ju, GUO Song, SONG Ya-Hui, JIN Xin-Xin, SU Qiao, YANG Yong-Qing, WANG Jin. Genetic and QTL mapping analysis of oil content in peanut across multiple environments [J]. Acta Agronomica Sinica, 2025, 51(2): 324-333.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
Add: No. 80 Xueyuan South Rd, Beijing 100081, P. R. China E-mail: zwxb301@caas.cn
Supported by Beijing Magtech Co.Ltd