GWAS联合转录组分析鉴定甘蓝型油菜硼高效相关的候选基因及优异单倍型

doi:10.1016/j.jia.2024.11.013

Journal of Integrative Agriculture ›› 2026, Vol. 25 ›› Issue (7): 2723-2738.DOI: 10.1016/j.jia.2024.11.013

GWAS联合转录组分析鉴定甘蓝型油菜硼高效相关的候选基因及优异单倍型

收稿日期:2024-06-25 修回日期:2024-11-05 接受日期:2024-09-24 出版日期:2026-07-20 发布日期:2026-06-09

A genome-wide association study integrated with transcriptome analysis to identify boron efficiency-related candidate genes and favorable haplotypes in Brassica napus L.

Ziwei Zhang^{1, 2}, Haoqiang Zhai³, Yingpeng Hua⁴, Sheliang Wang², Fangsen Xu^{1, 2#}

¹National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
²Microelement Research Center, College of Resources & Environment, Huazhong Agricultural University, Wuhan 430070, China
³Hubei Yishizhuang Agricultural Technology Co., Ltd., Yichang 443000, China
⁴School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China

Received:2024-06-25 Revised:2024-11-05 Accepted:2024-09-24 Online:2026-07-20 Published:2026-06-09
About author:#Correspondences Fangsen Xu, E-mail: fangsenxu@mail.hzau.edu.cn
Supported by:
This work was supported by the National Natural Science Foundation of China (32372805 and 31972483).

摘要/Abstract

摘要：

油菜（Brassica napus L.）是全球重要的油料作物之一，我国大力推广种植甘蓝型油菜。硼（B）是植物生长发育必需的微量营养元素，我国甘蓝型油菜种植区土壤普遍缺硼或严重缺硼。因此，提高油菜的抗缺硼能力成为一个重要的育种目标。然而，目前关于硼高效相关性状变异的遗传基础尚不清楚，能用于遗传育种的优异等位基因变异有待系统深入研究。本研究以391份甘蓝型油菜自然群体品种为材料，通过营养液培养的方法考察硼高效相关性状，包括相对根长（RRL）、地上部干重（SDW）、根部干重（RDW）和硼效率系数（BEC），这些性状在缺硼条件下表现出广泛的表型变异。结合全基因组重测序获得的高密度SNP标记进行全基因组关联分析（GWAS），使用一般线性模型和混合线性模型，共鉴定出106个显著关联的SNP位点。其中，在低硼条件下多个性状的三次重复试验中，检测到chrA03:14087835–14764672和chrC03:20110319–22135492两个显著的SNP簇。结合转录组分析，四个基因（BnaA03g29020D、BnaA03g29440D、BnaC03g33010D 和 BnaC03g34490D）在启动子区域或编码区内具有优异单倍型，并表现出更高的差异表达倍数，被鉴定为可能参与硼高效利用的候选基因。这些优异单倍型在硼缺乏条件下促进了苗期生长与油菜产量。鉴于我国硼矿资源缺乏，快速准确地鉴定到更多的硼高效优异等位基因并用于作物响应缺硼胁迫的遗传机制研究，对于培育硼高效利用的甘蓝型油菜品种以促进油菜绿色可持续的农业生产具有重要的理论和实践意义。

Abstract:

Rapeseed (Brassica napus L.) is a major oil crop worldwide that is vigorously promoted for cultivation in China. Boron (B) is an essential micronutrient for plant growth and development. However, the agricultural soils in rapeseed planting areas often show either B deficiency or severe B deficiency. Increasing the resistance to B deficiency is a pivotal goal in the breeding of rapeseed, yet the genetic basis for variations in B efficiency-related traits remains unclear. In this study, a natural population with 391 rapeseed accessions and a nutrient solution system were used to investigate B efficiency-related traits, including relative root length (RRL), shoot dry weight (SDW), root dry weight (RDW), and B efficiency coefficient (BEC), all of which exhibited extensive phenotypic variations under B deficiency. Through a genome-wide association study (GWAS) of B efficiency-related traits using high-density SNP markers obtained from whole-genome resequencing, 106 significantly associated SNPs were identified by employing both the general linear model and the mixed linear model. Among these SNP loci, two prominent SNP clusters were detected on chrA03: 14,087,835–14,764,672 and chrC03: 20,110,319–22,135,492 at low B levels across three repeated experiments of multiple traits. Integrating those results with a transcriptome analysis, four genes exhibiting higher differentially expressed fold-change along with favorable haplotypes within the promoter or coding region, BnaA03g29020D, BnaA03g29440D, BnaC03g33010D, and BnaC03g34490D, were identified as candidate genes that could potentially be involved in efficient B utilization, and their favorable haplotypes were found to improve seedling growth and productivity under B deficiency. Considering the lack of B mineral resources in China, the rapid and accurate identification of more B-efficient alleles and studying the genetic mechanism underlying crop responses to B deficiency have important theoretical and practical significance for cultivating B-efficient varieties and maintaining green, sustainable agriculture.

Key words: rapeseed , boron deficiency , GWAS , transcriptomic analysis , favorable haplotypes , B efficiency

Ziwei Zhang, Haoqiang Zhai, Yingpeng Hua, Sheliang Wang, Fangsen Xu. GWAS联合转录组分析鉴定甘蓝型油菜硼高效相关的候选基因及优异单倍型[J]. Journal of Integrative Agriculture, 2026, 25(7): 2723-2738.

Ziwei Zhang, Haoqiang Zhai, Yingpeng Hua, Sheliang Wang, Fangsen Xu. A genome-wide association study integrated with transcriptome analysis to identify boron efficiency-related candidate genes and favorable haplotypes in Brassica napus L.[J]. Journal of Integrative Agriculture, 2026, 25(7): 2723-2738.

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GWAS联合转录组分析鉴定甘蓝型油菜硼高效相关的候选基因及优异单倍型

A genome-wide association study integrated with transcriptome analysis to identify boron efficiency-related candidate genes and favorable haplotypes in Brassica napus L.

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