SNP- and Haplotype-Based GWAS of Flowering-Related Traits in Brassica napus

Traits related to flowering time are the most promising agronomic traits that directly impact the seed yield and oil quality of rapeseed (Brassica napus L.). Developing early flowering and maturity rapeseed varieties is an important breeding objective in B. napus...

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Autores principales:	MMU Helal, Rafaqat Ali Gill, Minqiang Tang, Li Yang, Ming Hu, Lingli Yang, Meili Xie, Chuanji Zhao, Xiaohui Cheng, Yuanyuan Zhang, Xiong Zhang, Shengyi Liu
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	flowering time <i>Brassica napus</i> SNP haplotypes QTL Botany QK1-989
Acceso en línea:	https://doaj.org/article/90dccfda44fc423b8f6012721a82cf0d
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id	oai:doaj.org-article:90dccfda44fc423b8f6012721a82cf0d
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spelling	oai:doaj.org-article:90dccfda44fc423b8f6012721a82cf0d2021-11-25T18:46:54ZSNP- and Haplotype-Based GWAS of Flowering-Related Traits in <i>Brassica napus</i>10.3390/plants101124752223-7747https://doaj.org/article/90dccfda44fc423b8f6012721a82cf0d2021-11-01T00:00:00Zhttps://www.mdpi.com/2223-7747/10/11/2475https://doaj.org/toc/2223-7747Traits related to flowering time are the most promising agronomic traits that directly impact the seed yield and oil quality of rapeseed (<i>Brassica napus</i> L.). Developing early flowering and maturity rapeseed varieties is an important breeding objective in <i>B. napus</i>. Many studies have reported on days to flowering, but few have reported on budding, bolting, and the interval between bolting and DTF. Therefore, elucidating the genetic architecture of QTLs and genes regulating flowering time, we presented an integrated investigation on SNP and haplotype-based genome-wide association study of 373 diverse <i>B. napus</i> germplasm, which were genotyped by the 60K SNP array and were phenotyped in the four environments. The results showed that a total of 15 and 37 QTLs were detected from SNP and haplotype-based GWAS, respectively. Among them, seven QTL clusters were identified by haplotype-based GWAS. Moreover, three and eight environmentally stable QTLs were detected by SNP-GWAS and haplotype-based GWAS, respectively. By integrating the above two approaches and by co-localizing the four traits, ten (10) genomic regions were under selection on chromosomes A03, A07, A08, A10, C06, C07, and C08. Interestingly, the genomic regions FT.A07.1, FT.A08, FT.C06, and FT.C07 were identified as novel. In these ten regions, a total of 197 genes controlling FT were detected, of which 14 highly expressed DEGs were orthologous to 13 <i>Arabidopsis thaliana</i> genes after integration with transcriptome results. In a nutshell, the above results uncovered the genetic architecture of important agronomic traits related to flowering time and provided a basis for multiple molecular marker-trait associations in <i>B. napus</i>.MMU HelalRafaqat Ali GillMinqiang TangLi YangMing HuLingli YangMeili XieChuanji ZhaoXiaohui ChengYuanyuan ZhangXiong ZhangShengyi LiuMDPI AGarticleflowering time<i>Brassica napus</i>SNPhaplotypesQTLBotanyQK1-989ENPlants, Vol 10, Iss 2475, p 2475 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	flowering time <i>Brassica napus</i> SNP haplotypes QTL Botany QK1-989
spellingShingle	flowering time <i>Brassica napus</i> SNP haplotypes QTL Botany QK1-989 MMU Helal Rafaqat Ali Gill Minqiang Tang Li Yang Ming Hu Lingli Yang Meili Xie Chuanji Zhao Xiaohui Cheng Yuanyuan Zhang Xiong Zhang Shengyi Liu SNP- and Haplotype-Based GWAS of Flowering-Related Traits in <i>Brassica napus</i>
description	Traits related to flowering time are the most promising agronomic traits that directly impact the seed yield and oil quality of rapeseed (<i>Brassica napus</i> L.). Developing early flowering and maturity rapeseed varieties is an important breeding objective in <i>B. napus</i>. Many studies have reported on days to flowering, but few have reported on budding, bolting, and the interval between bolting and DTF. Therefore, elucidating the genetic architecture of QTLs and genes regulating flowering time, we presented an integrated investigation on SNP and haplotype-based genome-wide association study of 373 diverse <i>B. napus</i> germplasm, which were genotyped by the 60K SNP array and were phenotyped in the four environments. The results showed that a total of 15 and 37 QTLs were detected from SNP and haplotype-based GWAS, respectively. Among them, seven QTL clusters were identified by haplotype-based GWAS. Moreover, three and eight environmentally stable QTLs were detected by SNP-GWAS and haplotype-based GWAS, respectively. By integrating the above two approaches and by co-localizing the four traits, ten (10) genomic regions were under selection on chromosomes A03, A07, A08, A10, C06, C07, and C08. Interestingly, the genomic regions FT.A07.1, FT.A08, FT.C06, and FT.C07 were identified as novel. In these ten regions, a total of 197 genes controlling FT were detected, of which 14 highly expressed DEGs were orthologous to 13 <i>Arabidopsis thaliana</i> genes after integration with transcriptome results. In a nutshell, the above results uncovered the genetic architecture of important agronomic traits related to flowering time and provided a basis for multiple molecular marker-trait associations in <i>B. napus</i>.
format	article
author	MMU Helal Rafaqat Ali Gill Minqiang Tang Li Yang Ming Hu Lingli Yang Meili Xie Chuanji Zhao Xiaohui Cheng Yuanyuan Zhang Xiong Zhang Shengyi Liu
author_facet	MMU Helal Rafaqat Ali Gill Minqiang Tang Li Yang Ming Hu Lingli Yang Meili Xie Chuanji Zhao Xiaohui Cheng Yuanyuan Zhang Xiong Zhang Shengyi Liu
author_sort	MMU Helal
title	SNP- and Haplotype-Based GWAS of Flowering-Related Traits in <i>Brassica napus</i>
title_short	SNP- and Haplotype-Based GWAS of Flowering-Related Traits in <i>Brassica napus</i>
title_full	SNP- and Haplotype-Based GWAS of Flowering-Related Traits in <i>Brassica napus</i>
title_fullStr	SNP- and Haplotype-Based GWAS of Flowering-Related Traits in <i>Brassica napus</i>
title_full_unstemmed	SNP- and Haplotype-Based GWAS of Flowering-Related Traits in <i>Brassica napus</i>
title_sort	snp- and haplotype-based gwas of flowering-related traits in <i>brassica napus</i>
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/90dccfda44fc423b8f6012721a82cf0d
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SNP- and Haplotype-Based GWAS of Flowering-Related Traits in <i>Brassica napus</i>

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