Candidate gene analysis of cabbage head-splitting resistance based on QTL mapping and omics profiling

doi:10.1016/j.jia.2025.11.020

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Xiaowei Zhu^1*, Min Wang^1*, Xiang Tai¹, Panling Lu¹, Hang Gui², Jinxiu Chen^1#, Tianyue Bo^1#

¹ Shanghai Key Lab of Protected Horticultural Technology, Protected Horticultural Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China

² Shanghai Shengeng Agricultural Development Corporation Limited, Shanghai 201824, China

Highlights

• Head-splitting resistance QTL(s) in cabbage were investigated using an F₂ population derived from a cross between 'ZF' and '103'.

• One head-splitting resistance QTL, qNLQ3.1, was identified through multiple approaches including QTL-seq, Graded Pool-seq (GPS), and traditional genetic linkage analysis.

• Integration of transcriptomic and metabolic profiling enabled the identification of Bol028000 as a plausible candidate gene within qNLQ3.1.

Abstract
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摘要

裂球是结球甘蓝常见的生理性病害之一，给甘蓝生产造成严重的经济损失。但迄今有关甘蓝耐裂球的遗传因子及分子机理知之甚少。因此，本研究通过利用两份甘蓝自交系，‘Dazhengfu’（‘ZF’，易裂球）和‘103’（耐裂球），杂交构建的F₂群体结合QTL-seq和Graded Pool-seq（GPS）分析获得1个位于C03染色体的耐裂球相关区段，qNLQ3.1，之后运用传统遗传作图分析将该位点缩小至74.6 kb的区间内。此外，通过转录组学和代谢组学对‘ZF’和‘103’进行比较分析，发现激素在调控耐裂球中起重要作用。Bol028000，编码一个拟南芥细胞分裂素响应因子（Cytokinin Response Factor 3，CRF3）的同源蛋白，被认为是与耐裂球相关的最有希望的候选基因，进一步利用Sanger测序和荧光定量PCR（Quantitative RT-PCR，qRT-PCR）对该基因进行了验证。亚细胞定位分析表明，Bol028000基因主要在细胞核中表达。另外，我们开发了基于Bol028000的KASP分子标记，并利用该分子标记对42份自交系进行了筛选。上述结果丰富了耐裂球的理论基础，对利用分子育种技术选育耐裂球甘蓝具有重要意义。

Abstract

Head-splitting is a prevalent physiological disorder in cabbage that causes substantial economic losses. However, the genetic factors and molecular mechanisms underlying head-splitting resistance remain largely unexplored. This study identified a genomic region (qNLQ3.1) for head-splitting resistance on chromosome C03 through the combination of QTL-seq and GPS analysis in an F₂ population derived from hybridizing two cabbage inbred lines, 'Dazhengfu' ('ZF', susceptible) and '103' (resistant). Traditional genetic linkage analysis narrowed qNLQ3.1 to a 74.6 kb region. Furthermore, comparative analysis of the two parental linesusing transcriptomic and metabolic profilingdemonstrated the crucial role of hormones in regulating head-splitting resistance. Bol028000, encoding a homologue of Arabidopsis Cytokinin Response Factor 3 (CRF3), emerged as a promising candidate for head-splitting resistance and was subsequently validated through Sanger sequencing and Quantitative RT-PCR (qRT-PCR). Subcellular localisation analysis revealed that Bol028000 was mainly expressed in the nucleus. Additionally, one kompetitive allele-specific PCR (KASP) marker from Bol028000 was developed and utilized to screen 42 inbred lines. These findings enhance the theoretical understanding of head-splitting resistance and provide valuable insights for the molecular breeding of head-splitting resistant cabbages.

Keywords: cabbage head-splitting resistance QTL transcriptomic and metabolic profiling

Online: 14 November 2025

Fund:

This research was funded by the Agricultural Development Program through Science and Technology of Shanghai (2022-02-08-00-12-F01099), the National Key R&D Program of China (2023YFD1201501), the Science and Technology Commission of Shanghai Municipality (22DX1900100), and the Excellent Team Project (Hu nong ke zhuo 2022(007)).

About author: #Jinxiu Chen, E-mail: cabbagecjx@126.com; Tianyue Bo, E-mail: tybo@saas.sh.cn * These authors contributed equally to this study.

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Xiaowei Zhu, Min Wang, Xiang Tai, Panling Lu, Hang Gui, Jinxiu Chen, Tianyue Bo. 2025. Candidate gene analysis of cabbage head-splitting resistance based on QTL mapping and omics profiling. Journal of Integrative Agriculture, Doi:10.1016/j.jia.2025.11.020

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