基于BSA-seq和QTL定位挖掘棉花早熟相关性状候选基因

doi:10.1016/j.jia.2024.04.024

摘要/Abstract

摘要：

培育早熟棉品种是提高我国复种指数、缓解粮棉争地矛盾的有效途径。本研究旨在挖掘与棉花早熟性状相关的数量性状位点（QTL）和候选基因，包括全生育期（WGP）、开花时间（FT）、第一结果枝节位（NFFB）、第一果枝节位高度（HNFFB）和株高（PH）。以早熟棉品种中棉所50和晚熟棉品种国欣棉11为亲本分别在2020年和2021年构建得到两个F₂分离群体，用于BSA-seq和QTL定位。在2020年，基于F2分离群体的表型数据，构建极端混池进行BSA-seq测序，分析发现早熟相关性状的候选区间位于D03染色体上。为进一步缩小候选区间，我们开发得到22个多态性InDel标记，在2020年和2021年群体中分别检测到5个和4个早熟性状相关的QTL位点，这些QTL位于两个候选区域内（InDel_G286-InDel_G144和InDel_G24-InDel_G43）。两个候选区间内，三个基因（GH_D03G0451、GH_D03GO649和GH_D03G1180）的外显子在两个亲本中存在非同义突变，一个基因（GH_D03G0450）的上游序列在两个亲本中存在SNP变异。上述四个基因在花器官中均具有较高的表达。在花芽分化阶段，GH_D03G0451、GH_D03GO649和GH_D03G1180在中棉所50中的表达量显著高于国欣棉11，而GH_D03G0450则表现出相反的趋势。对GH_D03G0451的进一步功能验证显示沉默GH_D03GO451的植株表现出开花延迟。本研究将为棉花早熟分子改良提供理论支撑和基因资源。

Abstract:

Cotton breeding for the development of early-maturing varieties is an effective way to improve multiple cropping indexes and alleviate the conflict between grains and cotton in the cultivated fields in China. In the present study, we aimed to identify upland cotton quantitative trait loci (QTLs) and candidate genes related to early-maturity traits, including whole growth period (WGP), flowering timing (FT), node of the first fruiting branch (NFFB), height of the node of the first fruiting branch (HNFFB), and plant height (PH). An early-maturing variety, CCRI50, and a late-maturing variety, Guoxinmian 11, were crossed to obtain biparental populations. These populations were used to map QTLs for the early-maturity traits for two years (2020 and 2021). With BSA-seq analysis based on the data of population 2020, the candidate regions related to early maturity were found to be located on chromosome D03. We then developed 22 polymorphic insertions or deletions (InDel) markers to further narrow down the candidate regions, resulting in the detection of five and four QTLs in the 2020 and 2021 populations, respectively. According to the results of QTL mapping, two candidate regions (InDel_G286-InDel_G144 and InDel_G24-InDel_G43) were detected. In these regions, three genes (GH_D03G0451, GH_D03G0649, and GH_D03G1180) have non-synonymous mutations in their exons and one gene (GH_D03G0450) has SNP variations in the upstream sequence between CCRI50 and Guoxinmian 11. These four genes also showed dominant expression in the floral organs. The expression levels of GH_D03G0451, GH_D03G0649 and GH_D03G1180 were significantly higher in CCRI50 than in Guoxinmian 11 during the bud differentiation stages, while GH_D03G0450 showed the opposite trend. Further functional verification of GH_D03G0451 indicated that the GH_D03G0451-silenced plants showed a delay in the flowering time. The results suggest that these are the candidate genes for cotton early maturity, and they may be used for breeding early-maturity cotton varieties.

Key words: cotton genomics , early maturity traits , BSA-seq , QTL mapping , molecular breeding

Liang Ma, Tingli Hu, Meng Kang, Xiaokang Fu, Pengyun Chen, Fei Wei, Hongliang Jian, Xiaoyan Lü, Meng Zhang, Yonglin Yang. 基于BSA-seq和QTL定位挖掘棉花早熟相关性状候选基因[J]. Journal of Integrative Agriculture, 2024, 23(10): 3472-3486.

Liang Ma, Tingli Hu, Meng Kang, Xiaokang Fu, Pengyun Chen, Fei Wei, Hongliang Jian, Xiaoyan Lü, Meng Zhang, Yonglin Yang. Identification of candidate genes for early-maturity traits by combining BSA-seq and QTL mapping in upland cotton (Gossypium hirsutum L.)[J]. Journal of Integrative Agriculture, 2024, 23(10): 3472-3486.

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