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

Journal of Integrative Agriculture

2026, Vol. 25

Issue (9): 3585-3594 DOI: 10.1016/j.jia.2024.11.015

Crop Science

Advanced Online Publication | Current Issue | Archive | Adv Search

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

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#}

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

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

³Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China

⁴Chongqing Academy of Agricultural Sciences, Chongqing 400216, China

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

Highlights
● Four candidate genes affecting seed palmitic acid content in Brassica napus were identified with combined genome-wide association study and transcriptome-wide association study.
● Four superior haplotypes were identified, and B. napus varieties carrying these haplotypes had lower palmitic acid content without affecting the seed oil content, protein content, or seed yield.
● Based on a functional single-nucleotide polymorphism, molecular marker Bn_A8_SPAC_Marker was developed to accelerate the breeding of rapeseed with low palmitic acid content.

Abstract
References

Download: PDF in ScienceDirect
Export: BibTeX | EndNote (RIS)

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, and the development of rapeseed varieties with high-quality oil is a long-term breeding goal. Reducing the content of palmitic acid, the main saturated fatty acid in rapeseed oil, can greatly improve oil quality. Here, a genome-wide association study (GWAS) and transcriptome-wide association study (TWAS) of seed palmitic acid content (SPAC) were performed 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, four low-SPAC haplotypes were identified 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, a molecular marker (Bn_A8_SPAC_Marker) was developed that can 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

Received: 28 August 2024 Accepted: 08 October 2024 Online: 05 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 and 32072093), the Natural Science Foundation of Chongqing, China (CSTB2022TIAD-KPX0010, CSTB2023NSCQ-MSX0744 and CSTB2022NSCQ-LZX0034), the earmarked Fund for China Agriculture Research System (CARS-12), and 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

	Service
	E-mail this article
	Add to citation manager
	E-mail Alert
	RSS
	Articles by authors

Cite this article:

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. 2026. Genome- and transcriptome-wide association studies reveal the genetic basis of seed palmitic acid content in Brassica napus. Journal of Integrative Agriculture, 25(9): 3585-3594.

Belide S, Petrie J R, Shrestha P, Singh S P. 2012. Modification of seed oil composition in Arabidopsis by artificial microRNA-mediated gene silencing. Frontiers in Plant Science, 3, 168.

Bradbury P J, Zhang Z, Kroon D E, Casstevens T M, Ramdoss Y, Buckler E S. 2007. TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics, 23, 2633–2638.

Cortés A J, Du H. 2023. Molecular genetics enhances plant breeding. International Journal of Molecular Sciences, 24, 9977.

Danecek P, Auton A, Abecasis G, Albers G A, Banks E, DePristo M A, Handsaker R E, Lunter G, Marth G T, Sherry S T, McVean G, Durbin R. 2011. The variant call format and VCFtools. Bioinformatics, 27, 2156–2164.

Gacek K, Bayer P E, Bartkowiak-Broda I, Szala L, Bocianowski J, Edwards D, Batley J. 2017. Genome-wide association study of genetic control of seed fatty acid biosynthesis in Brassica napus. Frontiers in Plant Science, 7, 2062.

Ge X Y, Chen J L, Li O Q, Zou M, Tao B L, Zhao L, Wen J, Yi B, Tu J X, Shen J X. 2025. ORF138 causes abnormal lipid metabolism in the tapetum that leads to Ogu cytoplasmic male sterility in Brassica napus. Journal of Integrative Agriculture, 24, 2080–2095.

Guan M, Huang X, Xiao Z, Jia L, Wang S, Zhu M, Qiao C, Wei L, Xu X, Liang Y, Wang R, Lu K, Li J, Qu C. 2019. Association mapping analysis of fatty acid content in different ecotypic rapeseed using mrMLM. Frontiers in Plant Science, 9, 1872.

Guyton J R, Ponder M, Kirkpatrick C F. 2023. Advances in understanding palmitic acid metabolism and health risks. Journal of Clinical Lipidology, 17, 571–573.

Huang K L, Tian J, Wang H, Fu Y, Li Y, Zheng Y, Bao X. 2021. Fatty acid export protein BnFAX6 functions in lipid synthesis and axillary bud growth in Brassica napus. Plant Physiology, 186, 2064–2077.

Khlestkina E, Shavrukov Y. 2022. Molecular-genetic basis of plant breeding. Biomolecules, 12, 1392.

Li H, Thrash A, Tang J D, He L, Yan J, Warburton M L. 2019. Leveraging GWAS data to identify metabolic pathways and networks involved in maize lipid biosynthesis. The Plant Journal, 98, 853–863.

Li L, Tian Z, Chen J, Tan Z, Zhang Y, Zhao H, Wu X, Yao X, Wen W, Chen W, Guo L. 2023. Characterization of novel loci controlling seed oil content in Brassica napus by marker metabolite-based multi-omics analysis. Genome Biology, 24, 141.

Li Y, Ali U, Cao Z, Cao Z, Zeng C, Xiao M, Wei F, Yao X, Guo L, Lu S. 2022. Fatty acid exporter 1 enhances seed oil content in Brassica napus. Molecular Breeding, 42, 75.

Lippert C, Listgarten J, Liu Y, Kadie C M, Davidson R I, Heckerman D. 2011. FaST linear mixed models for genome-wide association studies. Nature Methods, 8, 833–835.

Liu H, Wang J, Zhang B, Yang X, Hammond J, Ding G, Wang S, Cai H, Wang C, Xu F, Shi L. 2021. Genome-wide association study dissects the genetic control of plant height and branch number in response to low-phosphorus stress in Brassica napus. Annals of Botany, 128, 919–930.

Liu H J, Wang J C, Zhang B B, Yang X Y, Yuan P, Ding G D, Wang S L, Cai H M, Wang C, Xu F S, Shi L. 2022a. Genome-wide association study identifies new loci for 1000-seed weight in Brassica napus. Euphytica, 218, 142.

Liu H J, Wang W, Yang M, Yuan P, Hammond J P, King G J, Ding G D, White P, Wang S L, Cai H M, Wang C, Lu C G, Xu F S, Shi L. 2022b. Genome-wide association studies of important agronomic traits in Brassica napus: What we have learned and where we are headed. Annual Plant Review Online, 5, 151–180.

Liu H J, Zou M Y, Zhang B B, Yang X Y, Yuan P, Ding G D, Xu F S, Shi L. 2022c. Genome-wide association study identifies candidate genes and favorable haplotypes for seed yield in Brassica napus. Molecular Breeding, 42, 61.

Mai N T P, Nguyen L T T, Tran S G, To H T M. 2023. Genome-wide association study reveals useful QTL and genes controlling the fatty acid composition in rice bran oil using Vietnamese rice landraces. Functional & Integrative Genomics, 23, 150.

Mancini A, Imperlini E, Nigro E, Montagnese C, Daniele A, Orrù S, Buono P. 2015. Biological and nutritional properties of palm oil and palmitic acid: Effects on health. Molecules, 20, 17339–17361.

Qi Z, Guo C, Li H, Qiu H, Li H, Jong C, Yu G, Zhang Y, Hu L, Wu X, Xin D, Yang M, Liu C, Lv J, Wang X, Kong F, Chen Q. 2023. Natural variation in fatty acid 9 is a determinant of fatty acid and protein content. Plant Biotechnology Journal, 22, 759–773.

Qu C, Jia L, Fu F, Zhao H, Lu K, Wei L, Xu X, Liang Y, Li S, Wang R, Li J. 2017. Genome-wide association mapping and Identification of candidate genes for fatty acid composition in Brassica napus L. using SNP markers. BMC Genomics, 18, 232.

Rajcan I, Carrero-Colón M, Hudson K. 2022. Reduced palmitic acid content in soybean as a result of mutation in FATB1a. PLoS ONE, 17, e0262327.

Sinha P, Singh V K, Saxena R K, Khan A W, Abbai R, Chitikineni A, Desai A, Molla J, Upadhyaya H, Kumar A, Varshney R. 2020. Superior haplotypes for haplotype-based breeding for drought tolerance in pigeonpea (Cajanus cajan L.). Plant Biotechnology Journal, 18, 2482–2490.

Sivabharathi R C, Rajagopalan V R, Suresh R, Sudha M, Karthikeyan G, Jayakanthan M, Raveendran M. 2024. Haplotype-based breeding: A new insight in crop improvement. Plant Science, 346, 112129.

Song J, Guan Z, Hu J, Guo C, Yang Z, Wang S, Liu D, Wang B, Lu S, Zhou R, Xie W, Cheng Y, Zhang Y, Liu K, Yang Q, Chen L, Guo L. 2020. Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus. Nature Plants, 6, 34–45.

Tang S, Zhao H, Lu S, Yu L, Zhang G, Zhang Y, Yang Q, Zhou Y, Wang X, Ma W, Xie W, Guo L. 2021. Genome- and transcriptome-wide association studies provide insights into the genetic basis of natural variation of seed oil content in Brassica napus. Molecular Plant, 14, 470–487.

Wainberg M, Sinnott-Armstrong N, Mancuso N, Barbeira A, Knowles D, Golan D, Ermel R, Ruusalepp A, Quertermous T, Hao K, Björkegren J, Im H, Pasaniuc B, Rivas M, Kundaje A. 2019. Opportunities and challenges for transcriptome-wide association studies. Nature Genetics, 51, 592–599.

Wang M, Cheng J, Wu J, Chen J, Liu D, Wang C, Ma S, Guo W, Li G, Di D, Zhang Y, Han D, Kronzucker H, Xia G, Shi W. 2024. Variation in TaSPL6-D confers salinity tolerance in bread wheat by activating TaHKT1;5-D while preserving yield-related traits. Nature Genetics, 56, 1257–1269.

Wang Z, Wang Y, Shang P, Yang C, Yang M, Huang J, Ren B, Zuo Z, Zhang Q, Li W, Song B. 2022. Overexpression of soybean GmWRI1a stably increases the seed oil content in soybean. International Journal of Molecular Sciences, 23, 5084.

Xiao Z, Tang F, Zhang L, Li S, Wang S, Huo Q, Yang B, Zhang C, Wang D, Li Q, Wei L, Guo T, Qu C, Lu K, Zhang Y, Guo L, Li J, Li N. 2021. The Brassica napus fatty acid exporter FAX1-1 contributes to biological yield, seed oil content, and oil quality. Biotechnology for Biofuels, 14, 190.

Yang Z, Wang S, Wei L, Huang Y, Liu D, Jia Y, Luo C, Lin Y, Liang C, Hu Y, Dai C, Guo L, Zhou Y, Yang Q. 2023. BnIR: A multi-omics database with various tools for Brassica napus research and breeding. Molecular Plant, 16, 775–789.

Yin L, Zhang H, Tang Z, Xu J, Yin D, Zhang Z, Yuan X, Zhu M, Zhao S, Li X, Liu X. 2021. rMVP: A memory-efficient, visualization-enhanced, and parallel-accelerated tool for genome-wide association study. Genomics, Proteomics & Bioinformatics, 19, 619–628.

Zhang C, Dong S, Xu J, He W, Yang T. 2019. PopLDdecay: A fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics, 15, 1786–1788.

Zhang C, Gong R, Zhong H, Dai C, Zhang R, Dong J, Li Y, Liu S, Hu J. 2023. Integrated multi-locus genome-wide association studies and transcriptome analysis for seed yield and yield-related traits in Brassica napus. Frontiers in Plant Science, 14, 1153000.

Zhang Y, Zhang H, Zhao H, Xia Y Zheng X, Fan R, Tan Z, Duan C, Fu Y, Li L, Ye J, Tang S, Hu H, Xie W, Yao X, Guo L. 2022. Multi-omics analysis dissects the genetic architecture of seed coat content in Brassica napus. Genome Biology, 23, 86.

Zheng H, Zhao D, Shao W, Lu Y, Wang W, Hu Y, Li J, Zhu S, Wang X. 2022. GmWRI1c increases palmitic acid content to regulate seed oil content and nodulation in soybean (Glycine max). International Journal of Molecular Sciences, 23, 13793.

Zuo R, Xie M, Gao F, Liu J, Tang M, Cheng X, Liu Y, Bai Z, Liu S. 2022. Genome-wide identification and functional exploration of the legume lectin genes in Brassica napus and their roles in Sclerotinia disease resistance. Frontiers in Plant Science, 13, 963263.

[1]	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.
[2]	Li Zhe, Hui Wang, Jiping Chen, Xiaoge Fu, Liang Wang, Yang Yang, Tauqeer Ahmad Yasir, Huili Yan, Hongyan Chu, Chi Zhang, Yingang Hu, Xiaoyong Liao, Hanzhong Jia, Liang Chen. *Genome-wide association study of novel genetic loci for cadmium accumulation and germplasm screening for low cadmium accumulation in common wheat (Triticum* aestivum L.)**[J]. >Journal of Integrative Agriculture, 2026, 25(6): 2314-2328.
[3]	Shuo Yang, Qianru Jia, Qiong Wang, Junyan Wang, Jiahao Li, Shengyan Hu, Wei Zhang, Hongmei Zhang, Ya Guo, Xin Chen, Yuelin Zhu, Huatao Chen. Genome-wide association study of appearance quality traits and development of KASP markers in vegetable soybean[J]. >Journal of Integrative Agriculture, 2026, 25(6): 2341-2352.
[4]	Zhiying Zhao, Wanting Li, Yifei Wang, Meng Jin, Wenqiang Tang, Jiayi Li, Renliang Zhang, Yaxian Zhang, Peiyong Xin, Jinfang Chu, Yingjie Gao, Sha Tang, Xianmin Diao, Baowen Zhang. Proteomic investigation reveals the molecular mechanisms of plant height regulation in foxtail millet[J]. >Journal of Integrative Agriculture, 2026, 25(4): 1402-1417.
[5]	Sixian Yin, Taixia Wu, Shudong Wang, Ran Chen, Yingying Yang, Hongzhao Tang. Development of the FI-R model, a novel remote sensing method for fine-scale extraction of vegetation, using rapeseed as an example[J]. >Journal of Integrative Agriculture, 2026, 25(3): 1223-1242.
[6]	Mianyan Li, Lei Pu, David E. MacHugh, Jingjing Tian, Xiaoqing Wang, Qingyao Zhao, Lijun Shi, Hongmei Gao, Ying Yu, Lixian Wang, Fuping Zhao. Genome-wide association studies of novel resilience traits identify important immune QTL regions and candidate genes in Duroc pigs[J]. >Journal of Integrative Agriculture, 2025, 24(11): 4355-4369.
[7]	TAO Jian-bin, ZHANG Xin-yue, WU Qi-fan, WANG Yun. Mapping winter rapeseed in South China using Sentinel-2 data based on a novel separability index[J]. >Journal of Integrative Agriculture, 2023, 22(6): 1645-1657.
[8]	ZHANG Zhi-peng, LI Zhen, HE Fang, LÜ Ji-juan, XIE Bin, YI Xiao-yu, LI Jia-min, LI Jing, SONG Jing-han, PU Zhi-en, MA Jian, PENG Yuan-ying, CHEN Guo-yue, WEI Yu-ming, ZHENG You-liang, LI Wei. Genome-wide association and linkage mapping strategies reveal the genetic loci and candidate genes of important agronomic traits in Sichuan wheat[J]. >Journal of Integrative Agriculture, 2023, 22(11): 3380-3393.
[9]	NING Ning, HU Bing, BAI Chen-yang, LI Xiao-hua, KUAI Jie, HE Han-zi, REN Yi-lin, WANG Bo, JIA Cai-hua, ZHOU Guang-sheng, ZHAO Si-ming. *Influence of two-stage harvesting on the properties of cold-pressed rapeseed (Brassica napus* L.) oils**[J]. >Journal of Integrative Agriculture, 2023, 22(1): 265-278.
[10]	WU Bang-bang, SHI Meng-meng, Mohammad POURKHEIRANDISH, ZHAO Qi, WANG Ying, YANG Chen-kang, QIAO Ling, ZHAO Jia-jia, YAN Su-xian, ZHENG Xing-wei, ZHENG Jun. *Allele mining of wheat ABA receptor at TaPYL4* suggests neo-functionalization among the wheat homoeologs**[J]. >Journal of Integrative Agriculture, 2022, 21(8): 2183-2196.
[11]	RONG Hao, YANG Wen-jing, XIE Tao, WANG Yue, WANG Xia-qin, JIANG Jin-jin, WANG You-ping. *Transcriptional profiling between yellow- and black-seeded Brassica napus* reveals molecular modulations on flavonoid and fatty acid content**[J]. >Journal of Integrative Agriculture, 2022, 21(8): 2211-2226.
[12]	SUN Jing-xuan, LI Qian, TAN Xiao-ling, FAN Jia, ZHANG Yong, QIN Yao-guo, Frédéric FRANCIS, CHEN Ju-lian. *Population genetic structure of Sitobion miscanthi* in China**[J]. >Journal of Integrative Agriculture, 2022, 21(1): 178-187.
[13]	CAO Jian-bo, HE Li-min, Chinedu Charles NWAFOR, QIN Li-hong, ZHANG Chun-yu, SONG Yan-tun, HAO Rong. Ultrastructural studies of seed coat and cotyledon during rapeseed maturation[J]. >Journal of Integrative Agriculture, 2021, 20(5): 1239-1249.
[14]	ZHANG Zhi, CONG Ri-huan, REN Tao, LI Hui, ZHU Yun, LU Jian-wei. Optimizing agronomic practices for closing rapeseed yield gaps under intensive cropping systems in China[J]. >Journal of Integrative Agriculture, 2020, 19(5): 1241-1249.
[15]	MA Ni, WAN Lin, ZHAO Wei, LIU Hong-fang, LI Jun, ZHANG Chun-lei. Exogenous strigolactones promote lateral root growth by reducing the endogenous auxin level in rapeseed [J]. >Journal of Integrative Agriculture, 2020, 19(2): 465-482.

No Suggested Reading articles found!

Viewed

Full text

Abstract

Cited

Shared

Discussed

Cite this article:

About JIA

Editorial board

For authors