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Journal of Integrative Agriculture  2026, Vol. 25 Issue (4): 1373-1383    DOI: 10.1016/j.jia.2024.08.028
Crop Science Advanced Online Publication | Current Issue | Archive | Adv Search |
High-resolution mapping through whole-genome resequencing identifies two novel QTLs controlling oil content in peanut

Nian Liu, Huaiyong Luo, Li Huang, Xiaojing Zhou, Weigang Chen, Bei Wu, Jianbin Guo, Dongxin Huai, Yuning Chen, Yong Lei, Boshou Liao, Huifang Jiang#

Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs/Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
 Highlights 
Two novel stable QTLs with two candidate genes each were identified for oil content.
Markers developed from two QTLs were verified to increase 1.6% of peanut oil content.
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摘要  

提高含油量是花生育种的重要目标。精准鉴定含油量相关位点及其连锁标记能够有助于在高油育种中开展分子标记辅助选择。通过对包含295个家系的重组自交系(ZH16×J11)开展全基因组重测序,构建了一张高密度的遗传连锁图谱。该图谱的遗传长度为1162.3cM,包含了4212位点。在该图谱的6个连锁群上共发现了10个含油量的遗传位点(QTLs)。其中两个QTLsqOCB03.1  qOCB06.1)能够在至少三个环境下被重复检测到,其遗传解释率可达13.62%。这两个QTL尚未在之前的研究中被报道,推测可能是两个新的位点。在该重组自交系群体中,聚合了这两个优异等位位点的家系的含油量,比没有聚合的家系在四个环境下高出1.50%2.46%。针对这两个新位点开发的紧密连锁的分子标记在其它群体中(ZH10×ICG12625)也被证实跟含油量性状密切相关。这个两个位点分别被定位到B03染色体的1.77MbB06染色体的1.51Mb物理区间内。进一步通过目标位点基因组序列变异分析,转录组测序分析以及对目标变异位点的表型效应分析,在qOCB03.1  qOCB06.1定位区间内各发现了两个候选基因与含油量相关。该候选基因的挖掘可以为下一步的图位克隆含油量关键基因提供参考。本文发现的新的稳定QTL及其连锁分子标记对于指导分子标记辅助选择育种提高花生含油量具有重要价值。



Abstract  

Increasing the oil content is a key objective in peanut breeding programs.  Accurate identification of quantitative trait loci (QTLs) with linked markers for oil content can facilitate marker-assisted selection for high-oil breeding.  In this study, a high-density bin map was constructed by resequencing a recombinant inbred line (RIL) population (ZH16×J11) consisting of 295 lines.  The bin map contained 4,212 loci and had a total length of 1,162.3 cM.  Ten QTLs for oil content were identified in six linkage groups.  Notably, two of these QTLs, qOCB03.1 and qOCB06.1, were consistently detected in a minimum of three environments and explained up to 13.62% of the phenotypic variation.  They have not been reported in previous studies and thus are novel QTLs.  The combination of favorable alleles from qOCB03.1 and qOCB06 in the RIL population could increase oil content across multiple environments from 1.50 to 2.46%.  Two insertions/deletions (InDels) markers linked to qOCB03.1 and qOCB06.1 were developed, and their association with oil content was validated in another RIL population (ZH10×ICG12625) with diverse phenotypes.  In addition, the high-resolution map allowed for the precise positioning of qOCB03.1 and qOCB06.1 within a 1.77 Mb interval on chromosome B03 and a 1.51 Mb interval on chromosome B06, respectively.  The annotation of genomic variants, analysis of transcriptome sequencing, and evaluation of the allelic effects in 292 peanut varieties revealed two candidate genes associated with oil content for each of the two QTLs.  The candidate genes identified in this study can enable the map-based cloning of key genes controlling oil content in peanut.  Furthermore, these novel and stable QTLs and their tightly linked markers are valuable for marker-assisted breeding for greater oil content in peanut.

Keywords:  peanut       oil content        QTL mapping        whole genome resequencing  
Received: 08 August 2024   Accepted: 01 July 2024 Online: 30 August 2024  
Fund: 

This work was supported by the National Key Research and Development Program of China (2022YFD1200400), the National Natural Science Foundation of China (32161143006 and 31971903), the National Peanut Industry Technology System Construction, China (CARS13), the National Crop Germplasm Resources Center, China (NCGRC-2022-036), the National Program for Crop Germplasm Protection of China (19210163), the Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences (CAAS-ASTIP-2021-OCRI), and the Guangdong Provincial Key Research and Development Program-Modern Seed Industry, China (2022B0202060004).

About author:  Nian Liu, E-mail: lnian0531@163.com; #Correspondence Huifang Jiang, Tel: +86-28-87283955, E-mail: peanutlab@oilcrops.cn

Cite this article: 

Nian Liu, Huaiyong Luo, Li Huang, Xiaojing Zhou, Weigang Chen, Bei Wu, Jianbin Guo, Dongxin Huai, Yuning Chen, Yong Lei, Boshou Liao, Huifang Jiang. 2026. High-resolution mapping through whole-genome resequencing identifies two novel QTLs controlling oil content in peanut. Journal of Integrative Agriculture, 25(4): 1373-1383.

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