Identification of a pleiotropic QTL and development of KASP markers for 100-pod weight, 100-seed weight, and shelling percentage in peanut

doi:10.1016/j.jia.2024.06.013

Journal of Integrative Agriculture

2026, Vol. 25

Issue (3): 893-902 DOI: 10.1016/j.jia.2024.06.013

Crop Science

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Identification of a pleiotropic QTL and development of KASP markers for 100-pod weight, 100-seed weight, and shelling percentage in peanut

Xiukun Li^1*, Jing Hao^1*, Hongtao Deng^1*, Shunli Cui¹, Li Li², Mingyu Hou¹, Yingru Liu¹, Lifeng Liu^1#

¹State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory for Crop Germplasm Resources of Hebei/North China Key Laboratory for Crop Germplasm Resources, Ministry of Education/College of Agronomy, Hebei Agricultural University, Baoding 071001, China

²School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan 056038, China

Highlights
● A total of 46 QTLs and 115 SNPs associated with 100-pod weight (HPW), 100-seed weight (HSW), and shelling percentage (SP) were identified through combined linkage and association analyses.
● The locus qSP7, which influences SP, was consistently detected across two populations.
● Three KASP markers tightly linked to major QTL regions were developed and can be utilized for molecular marker-assisted breeding of peanut yield.

Abstract
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摘要

高产一直是花生育种的首要目标。百果重(HPW)、百仁重(HSW)和出仁率(SP)是花生产量的重要组成部分。本研究旨在通过对“四粒红”（多粒型）与“冀农黑3号”（普通型）杂交的重组自交系(RILs)进行重测序，构建高密度连锁图谱。该图谱由4499个bin组成，分布在20条染色体上，全长1712.32 cM，平均标记间距离为0.38 cM。在3种环境中共鉴定出46个QTL位点。其中，主效QTL位点qHPW5.2、qHPW18.1、qSP7.1、qSP8.1、qSP8.2、qSP18.1和qSP18.2的表型变异解释分别为12.04、11.41、16.53、24.17、10.49、10.82和29.89%。的14个QTL在多个环境中被检测到，认为是稳定的QTL。1个QTL (qHPW7、qHSW7.1、qSP7)与3个性状均相关，对HPW、HSW和SP的表型变异解释分别为8.91、9.04和16.53%。利用美国微核心种质进行全基因组关联来验证QTL定位的准确性。在两种环境中，共检测到115个SNP与百果重、百仁重和出仁率显著相关。6个SNP与2个性状同时相关，平均解释13.84%的表型变异。结合两个定位群体，关联分析群体中在 7号染色体上与SP显著相关的SNP，AX-176802178，同时位于RIL群体主效QTL qSP7置信区间内。此外，还开发了3个KASP标记，并在花生农家种和品种中进行了验证。这些QTL为了解花生HPW、HSW和SP的遗传基础提供了有价值的见解，并为花生标记辅助育种提供有用的分子标记。

Abstract

High yield remains the primary objective of peanut breeding. Key yield components, 100-pod weight (HPW), 100-seed weight (HSW), and shelling percentage (SP), are critical determinants of overall productivity. This study aimed to construct a high-density linkage map using resequencing data from recombinant inbred lines (RILs) derived from a cross between ‘Silihong’ (Arachis hypogaea var. fastigiate) and ‘Jinonghei 3’ (A. hypogaea var. hypogaea). The resulting map comprised 4,499 bins distributed across 20 chromosomes, spanning a total length of 1,712.32 cM with an average inter-marker distance of 0.38 cM. A total of 46 quantitative trait loci (QTLs) were identified across three environments. Major QTLs, including qHPW5.2, qHPW18.1, qSP7.1, qSP8.1, qSP8.2, qSP18.1, and qSP18.2, explained phenotypic variation (PVE) of 12.04, 11.41, 16.53, 24.17, 10.49, 10.82, and 29.89%, respectively. Fourteen QTLs detected across multiple environments were considered stable. Notably, one QTL region (qHPW7, qHSW7.1, and qSP7) was associated with all three traits, accounting for PVE values of 8.91, 9.04, and 16.53% for HPW, HSW, and SP, respectively. To validate the accuracy of QTL mapping, a genome-wide association study (GWAS) was conducted using the US mini-core collection. Across two environments, 115 single-nucleotide polymorphisms (SNPs) were significantly associated with HPW, HSW, and SP in the association panel. Six SNPs were linked to two traits, explaining an average phenotypic variation of 13.84%. Integration of both mapping populations revealed that AX-176802178, detected on chromosome 7 in the association panel and associated with SP, was located within the confidence interval of QTL qSP7 defined by the recombined inbred lines (RIL) population. Furthermore, three KASP markers were developed and validated in peanut landraces and cultivated varieties. These findings provide valuable insights into the genetic architecture underlying HPW, HSW, and SP, and offer useful molecular tools for marker-assisted selection in peanut breeding programs.

Keywords: Arachis hypogaea L. GWAS KASP QTL mapping shelling percentage

Received: 11 March 2024 Accepted: 30 May 2024 Online: 27 June 2024

Fund: This study was financially sponsored by the National Natural Science Foundation of China (320720977), the China Agriculture Research System (CARS-13), the Hebei Agriculture Research System, China (HBCT2024040205), the S&T Program of Hebei, China (23567601H), the Peanut Modern Seed Industry Technology Innovation Team in Hebei Province, China (21326316D-2), the State Key Laboratory of North China Crop Improvement and Regulation, China (NCCIR2020RC-2), and the Startup Fund of Hebei Agricultural University, China (YJ2020044).

About author: #Correspondence Lifeng Liu, E-mail: liulifeng@hebau.edu.cn * These authors contributed equally to this study.

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Xiukun Li, Jing Hao, Hongtao Deng, Shunli Cui, Li Li, Mingyu Hou, Yingru Liu, Lifeng Liu. 2026. Identification of a pleiotropic QTL and development of KASP markers for 100-pod weight, 100-seed weight, and shelling percentage in peanut. Journal of Integrative Agriculture, 25(3): 893-902.

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