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Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (8): 2160-2170.doi: 10.3724/SP.J.1006.2023.24190

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

QTLs mapping for single-seed weight of cultivated peanut

LI Xing, YANG Hui, LUO Lu, LI Hua-Dong, ZHANG Kun, ZHANG Xiu-Rong, LI Yu-Ying, YU Hai-Yang, WANG Tian-Yu, LIU Jia-Qi, WANG Yao, LIU Feng-Zhen(), WAN Yong-Shan()   

  1. College of Agronomy, Shandong Agricultural University / State Key Laboratory of Crop Biology, Tai’an 271018, Shandong, China
  • Received:2022-08-16 Accepted:2023-02-10 Online:2023-08-12 Published:2023-03-02
  • Contact: LIU Feng-Zhen,WAN Yong-Shan E-mail:liufz@sdau.edu.cn;yswan@sdau.edu.cn
  • Supported by:
    Construction Project of Shandong Peanut Industrial Technology System(SDAIT-04-03);Shandong Agricultural Improved Varieties Engineering Project(2020LZGC001);Shandong Provincial Key Research and Development Program(2019GNC106002);China Agriculture Research System of MOF and MARA(CARS-13)

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Abstract:

Peanut (Arachis hypogaea L.) is an important oil and cash crop in China, and the single-seed weight is one of the important traits that determine the yield and commodity of peanut. In this study, QTLs mapping for single-seed weight of peanut was performed using RIL population constructed from a cross between large-kernel variety Shanhua 15 (female) and small-kernel variety Zhonghua 12 (male), based on a high-density genetic map. Nine QTLs related to single-seed weight were identified on seven chromosomes (A04, A06, A07, B05, B07, B09, and B10). The LOD values of these QTLs was 3.01-33.97, phenotypic variation contribution rates was 2.61%-34.28%, the additive effect values were -0.03 to 0.15 g, and the physical range of positioning was 0.03-4.32 Mb. qSSWA07.1 was a stable major QTL repeatedly detected in six planting environments, and qSSWA06.1 and qSSWB09.1 were repeatedly detected in four planting environments. The additive effect of qSSWA07.1 and qSSWA06.1 were positive, and the favorable alleles were inherited from Shanhua 15. The additive effect of qSSWB09.1 was negative, and the favorable allele was inherited from Zhonghua 12. The additive effect of qSSWA06.1, qSSWA07.1, and qSSWB09.1 on peanut single-seed weight was analyzed with the genotype of three bin markers (A06: Block3344, A07: Block3373, and B09: Block10032) closely-linked with QTLs. The mean value of single-seed weight of lines with three favorable alleles was the largest, and that of the lines without the favorable alleles was the smallest. The candidate genes in qSSWA06.1, qSSWA07.1, and qSSWB09.1 were analyzed by KEGG enrichment pathway, according to the expression in different tissues and functional annotation of these genes, four candidate genes were predicted, Arahy.9UY90I, Arahy.RX7YKY, Arahy.3ZC2CN, and Arahy.9V2WXE, which may play a significant role in the regulation of peanut seed growth and development. The results provided the reference for the genetic improvement of yield related traits in peanut.

Key words: peanut, single-seed weight, QTLs mapping, candidate genes

Table 1

Statistical analysis of single-seed weight traits in parental and RIL populations"

种植环境
Planting environment		 亲本Parent RIL群体 RIL population
山花15号
Shanhua 15		 中花12号
Zhonghua 12		 最大值
Max.		 最小值
Min.		 平均值
Mean		 标准差
SD		 变异系数
CV (%)		 偏度
Skewness		 峰度
Kurtosis
2014 1.39 0.71** 1.63 0.41 0.93 0.25 26.88 0.291 -0.413
2015 1.21 0.58** 1.33 0.22 0.74 0.18 24.32 0.283 0.286
2016 1.08 0.42** 1.24 0.24 0.64 0.18 28.13 0.414 0.217
2017 1.14 0.75** 1.52 0.59 0.94 0.19 20.21 0.354 -0.209
2020 1.18 0.76** 1.57 0.48 0.97 0.21 21.68 0.116 -0.543
2021 1.16 0.76** 1.21 0.33 0.76 0.17 22.37 0.027 -0.437

Fig. 1

Distribution of single-seed weight in peanut RIL population 2014, 2015, 2016, 2017, 2020, and 2021 represent different planting environments, respectively. RIL: recombinant inbred lines."

Fig. 2

Genomic distribution of QTL related to single-seed weight of peanut 2014, 2015, 2016, 2017, 2020, and 2021 represent planting environments, respectively. A04, A06, A07, B05, B07, B09, and B10 represent different chromosomes, respectively."

Table 2

QTLs information of peanut seed-single weight"

QTL 种植环境
Planting environment		 染色体
Chr.		 标记区间
Marker interval		 物理区间长度
Physical interval length (Mb)		 阈值
LOD		 贡献率
PVE (%)		 加性效应
ADD (g)
qSSWA04.1 2015 A04 Block1622-Block1625 2.05 3.01 3.41 -0.03
qSSWA06.1 2021 A06 Block3360-Block3309 4.32 6.82 5.83 0.05
2020 8.30 7.61 0.05
2017 10.24 9.40 0.06
2014 8.11 7.39 0.07
qSSWA07.1 2021 A07 Block3421-Block3366 1.39 31.02 32.30 0.10
2020 33.62 34.06 0.11
2017 33.97 34.28 0.12
2016 13.75 16.36 0.07
2015 18.57 21.34 0.08
2014 30.17 31.34 0.15
qSSWB05.1 2020 B05 Block7608-Block7556 0.84 3.12 2.92 0.04
qSSWB05.2 2017 B05 Block7651-Block7587 3.01 4.34 3.33 0.03
qSSWB07.1 2014 B07 Block8272-Block8264 0.40 3.80 4.12 0.05
qSSWB07.2 2020 B07 Block8284-Block8285 0.03 3.08 2.61 0.04
qSSWB09.1 2021 B09 Block10054-Block10004 1.45 5.27 4.21 -0.04
2020 5.79 4.48 -0.04
2017 7.12 6.38 -0.04
2014 6.30 5.39 -0.06
qSSWB10.1 2015 B10 Block10084-Block10083 0.58 3.16 3.36 0.03

Fig. 3

Phenotypic effects of qSSWA06.1, qSSWA07.1, and qSSWB09.1 in population 2014, 2015, 2016, 2017, 2020, and 2021 represent different planting environments, respectively. AABBCC, AAbbcc, AABBcc, AAbbCC, aaBBCC, aaBBcc, aabbCC, and aabbcc represent different genotypes, respectively."

Fig. 4

KEGG enrichment pathway of candidate genes in physical interval of QTL for peanut single-seed weight A07, B09, and A06 represent different chromosomes, respectively."

Fig. 5

Relative expression pattern of 12 candidate genes in different tissues of peanut The darker the color, the higher the expression, and the lower the vice versa."

Table 3

Candidate genes of qSSWA06.1, qSSWA07.1, and qSSWB09.1"

基因 ID
Gene ID		 染色体
Chr.		 物理区间
Physical interval (bp)		 基因家族
Gene family		 功能注释
Functional description
Arahy.9UY90I A07 447423-452848 legfed_v1_0.L_MWNP2J 烯醇酶
Enolase
Arahy.KE1FF5 A07 955911-958635 legfed_v1_0.L_KG5CQL 半胱氨酸合酶/半胱氨酸β合酶
Cysteine synthase/cystathionine β-synthase
Arahy.K4CMZR A07 1001166-1002296 legfed_v1_0.L_1XK45N 丝氨酸O-乙酰转移酶
Serine O-acetyltransferase
Arahy.K0DIZR A07 1218259-1224643 legfed_v1_0.L_0GKWV0 ABC转运蛋白1型
ABC transporter type 1
Arahy.RX7YKY B09 157391371-157396195 legfed_v1_0.L_BH5DLF 甜菜碱同型半胱氨酸甲基转移酶
Betaine-homocysteine methyltransferase
Arahy.E9249P B09 157550706-157553539 legfed_v1_0.L_0C7SKC 类RmlC-like cupins蛋白
Proteins similar to the RmlC-like cupins
Arahy.IQP7TJ B09 157714814-157717184 legfed_v1_0.L_FMT5KJ 糖苷水解酶
Glycoside hydrolase
Arahy.QJT344 A06 110434786-110446942 legfed_v1_0.L_9WXLVF 泛素特异性蛋白酶
Ubiquitin specific proteases
Arahy.3ZC2CN A06 110489370-110491090 legfed_v1_0.L_63KDF3 LSM蛋白质
LSM proteins
Arahy.S90AI0 A06 112231732-112241188 legfed_v1_0.L_J3GGX7 核转录和剪接因子
Nuclear transcription and splicing factors
Arahy.57RIKC A06 110715861-110721136 legfed_v1_0.L_F86644 磷酸吡哆醛依赖性转移酶
Pyridoxal phosphate-dependent transferase
Arahy.9V2WXE A06 111734794-111743008 legfed_v1_0.L_RNPQZ0 真核翻译起始因子
Eukaryotic translation initiation factor
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[3] YANG Jian-Chang;ZHANG Jian-Hua;WANG Zhi-Qin;ZH0U Qing-Sen. Changes in Contents of Polyamines in the Flag Leaf and Their Relationship with Drought-resistance of Rice Cultivars under Water Deficiency Stress[J]. Acta Agron Sin, 2004, 30(11): 1069 -1075 .
[4] Yan Mei;Yang Guangsheng;Fu Tingdong;Yan Hongyan. Studies on the Ecotypical Male Sterile-fertile Line of Brassica napus L.Ⅲ. Sensitivity to Temperature of 8-8112AB and Its Inheritance[J]. Acta Agron Sin, 2003, 29(03): 330 -335 .
[5] Wang Yongsheng;Wang Jing;Duan Jingya;Wang Jinfa;Liu Liangshi. Isolation and Genetic Research of a Dwarf Tiilering Mutant Rice[J]. Acta Agron Sin, 2002, 28(02): 235 -239 .
[6] WANG Li-Yan;ZHAO Ke-Fu. Some Physiological Response of Zea mays under Salt-stress[J]. Acta Agron Sin, 2005, 31(02): 264 -268 .
[7] TIAN Meng-Liang;HUNAG Yu-Bi;TAN Gong-Xie;LIU Yong-Jian;RONG Ting-Zhao. Sequence Polymorphism of waxy Genes in Landraces of Waxy Maize from Southwest China[J]. Acta Agron Sin, 2008, 34(05): 729 -736 .
[8] HU Xi-Yuan;LI Jian-Ping;SONG Xi-Fang. Efficiency of Spatial Statistical Analysis in Superior Genotype Selection of Plant Breeding[J]. Acta Agron Sin, 2008, 34(03): 412 -417 .
[9] WANG Yan;QIU Li-Ming;XIE Wen-Juan;HUANG Wei;YE Feng;ZHANG Fu-Chun;MA Ji. Cold Tolerance of Transgenic Tobacco Carrying Gene Encoding Insect Antifreeze Protein[J]. Acta Agron Sin, 2008, 34(03): 397 -402 .
[10] ZHENG Xi;WU Jian-Guo;LOU Xiang-Yang;XU Hai-Ming;SHI Chun-Hai. Mapping and Analysis of QTLs on Maternal and Endosperm Genomes for Histidine and Arginine in Rice (Oryza sativa L.) across Environments[J]. Acta Agron Sin, 2008, 34(03): 369 -375 .
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