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Journal of Integrative Agriculture  2026, Vol. 25 Issue (7): 2723-2738    DOI: 10.1016/j.jia.2024.11.013
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A genome-wide association study integrated with transcriptome analysis to identify boron efficiency-related candidate genes and favorable haplotypes in Brassica napus L.

Ziwei Zhang1, 2, Haoqiang Zhai3, Yingpeng Hua4, Sheliang Wang2, Fangsen Xu1, 2#

1 National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China

2 Microelement Research Center, College of Resources & Environment, Huazhong Agricultural University, Wuhan 430070, China

3 Hubei Yishizhuang Agricultural Technology Co., Ltd., Yichang 443000, China

4 School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China

 Highlights 
A natural population of Brassica napus with 391 accessions was employed to identify boron (B) efficiency-related beneficial alleles with genome-wide association study (GWAS).
BnaA03g29020D, BnaA03g29440D, BnaC03g33010D, and BnaC03g34490D were identified as candidate genes potentially involved in the efficient utilization of B in B. napus.
The favorable haplotypes had better seedling growth and productivity within the rapeseed population under B deficiency conditions.

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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B是植物生长发育必需微量营养元素,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106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chrA03:14087835–14764672chrC03:20110319–22135492两个显著的SNP簇。结合转录组分析,四个基因BnaA03g29020DBnaA03g29440DBnaC03g33010D  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硼胁迫遗传机制研究,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.

Keywords:  rapeseed       boron deficiency        GWAS        transcriptomic analysis        favorable haplotypes        B efficiency  
Received: 25 June 2024   Accepted: 24 September 2024 Online: 05 November 2024  
Fund: 

This work was supported by the National Natural Science Foundation of China (32372805 and 31972483).  

About author:  #Correspondences Fangsen Xu, E-mail: fangsenxu@mail.hzau.edu.cn

Cite this article: 

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

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