Genome- and transcriptome-wide association studies reveal the genetic basis of seed palmitic acid content in Brassica napus

doi:10.1016/j.jia.2024.11.015

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Haijiang Liu^1,^2,³, Yongheng Yuan^1,^2,³, YunShan Tang^1,^2,³, RuoShui Li^1,^2,³, Kaijie Ye^1,^2,³, Mengzhen Zhang^1,^2,³, Kun Lu^1,^2,³, Nengwen Yin^1,^2,³, Huiyan Zhao^1,^2,³, Yuanyuan Liu^1,^2,³, Taocui Huang⁴, Rui Wang^1,^2,³, Lei Shi⁵, Hai Du^1,^2,³^#, Cunmin Qu^1,^2,³^#

¹ Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and college of Agronomy and Biotechnology, Southwest University, Chongqing 401335, China

² Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing 400715, China

³ Academy of Agricultural Sciences, Southwest University, Chongqing400715, China

⁴ Chongqing Academy of Agricultural Sciences, Chongqing 40216, China

⁵ National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China

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摘要

油菜是世界上最重要的油料作物之一。培育优质油菜品种是一个长期的育种目标。降低菜籽油中的主要饱和脂肪酸棕榈酸的含量，可以极大的改善菜籽油的品质。本研究对393份甘蓝型油菜种子中的棕榈酸含量进行全基因组关联分析和全转录组关联分析，确定4个（BnaA08.DAP、BnaA08.PAA1、BnaAO8.DUF106和BnaC03.DAP）影响种子棕榈酸含量的候选基因。以上候选基因在开花后20和40天的基因表达量与SPAC呈显著相关。基于以上候选基因内的遗传变异，我们结合候选基因关联分析和单倍型分析，鉴定出4种低棕榈酸单倍型。携带低棕榈酸单倍型的油菜种子中的棕榈酸含量要显著低于携带高棕榈酸单倍型的油菜品种，但不影响种子含油量、蛋白质含量和产量。基于BnaA08.DUF106启动子上的与棕榈酸含量显著关联的功能SNP chrA08_9529850（C/A），开发了一个可用于甘蓝型油菜低棕榈酸的选育的分子标记Bn_A8_SPAC_Marker。本研究结果为解析甘蓝型油菜种子棕榈酸含量的遗传基础提供了有价值的信息。此外，本研究中确定的候选基因、优异单倍型和分子标记将为低棕榈酸油菜品种的选育提供参考。

Abstract

Rapeseed (Brassica napus L.) is one of the most important oilseed crops worldwide. Development of rapeseed varieties with high-quality oil is a long-term breeding goal. Reducing the contents of palmitic acid, the main saturated fatty acid in rapeseed oil, could greatly improve oil quality. Here, we performed genome-wide association study (GWAS) and transcriptome-wide association study (TWAS) of seed palmitic acid content (SPAC) using 393 diverse B. napus accessions. Four genes (BnaA08.DAP, BnaA08.PAA1, BnaA08. DUF106, and BnaC03.DAP) were identified by both GWAS and TWAS. The transcripts per million (TPM) values of these candidate genes at 20 and 40 days after flowering (DAF) were significantly correlated with SPAC in this association panel. Based on genetic variation in the candidate genes, we identified four low-SPAC haplotypes by combining candidate gene association analysis and haplotype analysis. Brassica napus accessions carrying low-SPAC haplotypes had lower SPAC than those carrying high-SPAC haplotypes without affecting seed oil content, seed protein content, or seed yield. Based on the functional single-nucleotide polymorphism (SNP) chrA08_9529850 (C/A) in the promoter of BnaA08.DUF106, we developed a molecular marker (Bn_A8_SPAC_Marker) that could be used to facilitate breeding for low SPAC in B. napus. Our findings provide valuable information for studying the genetic control of SPAC in B. napus. Moreover, the candidate genes, favorable haplotypes, and molecular marker identified in this study will be useful for breeding low-SPAC B. napus varieties.

Keywords: rapeseed genome-wide association study transcriptome-wide association study seed palmitic acid content haplotype analysis molecular marker

Online: 12 November 2024

Fund:

The authors are grateful for the financial support provided by the National Key Research and Development Program of China (2023YFD1201405), the National Natural Science Foundation of China (32272150, 32072093), the Natural Science Foundation of Chongqing, China (CSTB2022TIAD-KPX0010 and CSTB2022NSCQ-LZX0034), the Innovation and Entrepreneurship Training Program for Undergraduates, China (S202410635206).

About author: #Correspondence Cunmin Qu, E-mail: drqucunmin@swu.edu.cn; Hai Du, E-mail: haidu81@126.com

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Haijiang Liu, Yongheng Yuan, YunShan Tang, RuoShui Li, Kaijie Ye, Mengzhen Zhang, Kun Lu, Nengwen Yin, Huiyan Zhao, Yuanyuan Liu, Taocui Huang, Rui Wang, Lei Shi, Hai Du, Cunmin Qu. 2024. Genome- and transcriptome-wide association studies reveal the genetic basis of seed palmitic acid content in Brassica napus. Journal of Integrative Agriculture, Doi:10.1016/j.jia.2024.11.015

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