Agronomic and Seed Quality Traits Dissected by Genome-Wide Association Mapping in Brassica napus

In Brassica napus breeding, traits related to commercial success are of highest importance for plant breeders. However, such traits can only be assessed in an advanced developmental stage. Molecular markers genetically linked to such traits have the potential to accelerate the breeding process of B....

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Main Authors:	Körber, Niklas, Bus, Anja, Li, Jinquan, Parkin, Isobel A. P., Wittkop, Benjamin, Snowdon, Rod J., Stich, Benjamin
Format:	Online
Language:	English
Published:	Frontiers Media S.A. 2016
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4814720/

id	pubmed-4814720
recordtype	oai_dc
spelling	pubmed-48147202016-04-08 Agronomic and Seed Quality Traits Dissected by Genome-Wide Association Mapping in Brassica napus Körber, Niklas Bus, Anja Li, Jinquan Parkin, Isobel A. P. Wittkop, Benjamin Snowdon, Rod J. Stich, Benjamin Plant Science In Brassica napus breeding, traits related to commercial success are of highest importance for plant breeders. However, such traits can only be assessed in an advanced developmental stage. Molecular markers genetically linked to such traits have the potential to accelerate the breeding process of B. napus by marker-assisted selection. Therefore, the objectives of this study were to identify (i) genome regions associated with the examined agronomic and seed quality traits, (ii) the interrelationship of population structure and the detected associations, and (iii) candidate genes for the revealed associations. The diversity set used in this study consisted of 405 B. napus inbred lines which were genotyped using a 6K single nucleotide polymorphism (SNP) array and phenotyped for agronomic and seed quality traits in field trials. In a genome-wide association study, we detected a total of 112 associations between SNPs and the seed quality traits as well as 46 SNP-trait associations for the agronomic traits with a P < 1.28e-05 (Bonferroni correction of α = 0.05) for the inbreds of the spring and winter trial. For the seed quality traits, a single SNP-sulfur concentration in seeds (SUL) association explained up to 67.3% of the phenotypic variance, whereas for the agronomic traits, a single SNP-blossom color (BLC) association explained up to 30.2% of the phenotypic variance. In a basic local alignment search tool (BLAST) search within a distance of 2.5 Mbp around these SNP-trait associations, 62 hits of potential candidate genes with a BLAST-score of ≥100 and a sequence identity of ≥70% to A. thaliana or B. rapa could be found for the agronomic SNP-trait associations and 187 hits of potential candidate genes for the seed quality SNP-trait associations. Frontiers Media S.A. 2016-03-31 /pmc/articles/PMC4814720/ /pubmed/27066036 http://dx.doi.org/10.3389/fpls.2016.00386 Text en Copyright © 2016 Körber, Bus, Li, Parkin, Wittkop, Snowdon and Stich. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Körber, Niklas Bus, Anja Li, Jinquan Parkin, Isobel A. P. Wittkop, Benjamin Snowdon, Rod J. Stich, Benjamin
spellingShingle	Körber, Niklas Bus, Anja Li, Jinquan Parkin, Isobel A. P. Wittkop, Benjamin Snowdon, Rod J. Stich, Benjamin Agronomic and Seed Quality Traits Dissected by Genome-Wide Association Mapping in Brassica napus
author_facet	Körber, Niklas Bus, Anja Li, Jinquan Parkin, Isobel A. P. Wittkop, Benjamin Snowdon, Rod J. Stich, Benjamin
author_sort	Körber, Niklas
title	Agronomic and Seed Quality Traits Dissected by Genome-Wide Association Mapping in Brassica napus
title_short	Agronomic and Seed Quality Traits Dissected by Genome-Wide Association Mapping in Brassica napus
title_full	Agronomic and Seed Quality Traits Dissected by Genome-Wide Association Mapping in Brassica napus
title_fullStr	Agronomic and Seed Quality Traits Dissected by Genome-Wide Association Mapping in Brassica napus
title_full_unstemmed	Agronomic and Seed Quality Traits Dissected by Genome-Wide Association Mapping in Brassica napus
title_sort	agronomic and seed quality traits dissected by genome-wide association mapping in brassica napus
description	In Brassica napus breeding, traits related to commercial success are of highest importance for plant breeders. However, such traits can only be assessed in an advanced developmental stage. Molecular markers genetically linked to such traits have the potential to accelerate the breeding process of B. napus by marker-assisted selection. Therefore, the objectives of this study were to identify (i) genome regions associated with the examined agronomic and seed quality traits, (ii) the interrelationship of population structure and the detected associations, and (iii) candidate genes for the revealed associations. The diversity set used in this study consisted of 405 B. napus inbred lines which were genotyped using a 6K single nucleotide polymorphism (SNP) array and phenotyped for agronomic and seed quality traits in field trials. In a genome-wide association study, we detected a total of 112 associations between SNPs and the seed quality traits as well as 46 SNP-trait associations for the agronomic traits with a P < 1.28e-05 (Bonferroni correction of α = 0.05) for the inbreds of the spring and winter trial. For the seed quality traits, a single SNP-sulfur concentration in seeds (SUL) association explained up to 67.3% of the phenotypic variance, whereas for the agronomic traits, a single SNP-blossom color (BLC) association explained up to 30.2% of the phenotypic variance. In a basic local alignment search tool (BLAST) search within a distance of 2.5 Mbp around these SNP-trait associations, 62 hits of potential candidate genes with a BLAST-score of ≥100 and a sequence identity of ≥70% to A. thaliana or B. rapa could be found for the agronomic SNP-trait associations and 187 hits of potential candidate genes for the seed quality SNP-trait associations.
publisher	Frontiers Media S.A.
publishDate	2016
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4814720/
_version_	1613560064430309376

Agronomic and Seed Quality Traits Dissected by Genome-Wide Association Mapping in Brassica napus

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