Genome-Wide Association Study of Major Agronomic Traits in Foxtail Millet (Setaria italica L.) Using ddRAD Sequencing

Abstract Foxtail millet (Setaria italica), the second largest cultivated millet crop after pearl millet, is utilized for food and forage globally. Further, it is also considered as a model crop for studying agronomic, nutritional and biofuel traits. In the present study, a genome-wide association st...

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Autores principales:	Vandana Jaiswal, Sarika Gupta, Vijay Gahlaut, Mehanathan Muthamilarasan, Tirthankar Bandyopadhyay, Nirala Ramchiary, Manoj Prasad
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2019
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/6408cc9636234f9d8d6ce7143daabef3
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spelling	oai:doaj.org-article:6408cc9636234f9d8d6ce7143daabef32021-12-02T15:09:41ZGenome-Wide Association Study of Major Agronomic Traits in Foxtail Millet (Setaria italica L.) Using ddRAD Sequencing10.1038/s41598-019-41602-62045-2322https://doaj.org/article/6408cc9636234f9d8d6ce7143daabef32019-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-019-41602-6https://doaj.org/toc/2045-2322Abstract Foxtail millet (Setaria italica), the second largest cultivated millet crop after pearl millet, is utilized for food and forage globally. Further, it is also considered as a model crop for studying agronomic, nutritional and biofuel traits. In the present study, a genome-wide association study (GWAS) was performed for ten important agronomic traits in 142 foxtail millet core eco-geographically diverse genotypes using 10 K SNPs developed through GBS-ddRAD approach. Number of SNPs on individual chromosome ranged from 844 (chromosome 5) to 2153 (chromosome 8) with an average SNP frequency of 25.9 per Mb. The pairwise linkage disequilibrium (LD) estimated using the squared-allele frequency correlations was found to decay rapidly with the genetic distance of 177 Kb. However, for individual chromosome, LD decay distance ranged from 76 Kb (chromosome 6) to 357 Kb (chromosome 4). GWAS identified 81 MTAs (marker-trait associations) for ten traits across the genome. High confidence MTAs for three important agronomic traits including FLW (flag leaf width), GY (grain yield) and TGW (thousand-grain weight) were identified. Significant pyramiding effect of identified MTAs further supplemented its importance in breeding programs. Desirable alleles and superior genotypes identified in the present study may prove valuable for foxtail millet improvement through marker-assisted selection.Vandana JaiswalSarika GuptaVijay GahlautMehanathan MuthamilarasanTirthankar BandyopadhyayNirala RamchiaryManoj PrasadNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 9, Iss 1, Pp 1-11 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Vandana Jaiswal Sarika Gupta Vijay Gahlaut Mehanathan Muthamilarasan Tirthankar Bandyopadhyay Nirala Ramchiary Manoj Prasad Genome-Wide Association Study of Major Agronomic Traits in Foxtail Millet (Setaria italica L.) Using ddRAD Sequencing
description	Abstract Foxtail millet (Setaria italica), the second largest cultivated millet crop after pearl millet, is utilized for food and forage globally. Further, it is also considered as a model crop for studying agronomic, nutritional and biofuel traits. In the present study, a genome-wide association study (GWAS) was performed for ten important agronomic traits in 142 foxtail millet core eco-geographically diverse genotypes using 10 K SNPs developed through GBS-ddRAD approach. Number of SNPs on individual chromosome ranged from 844 (chromosome 5) to 2153 (chromosome 8) with an average SNP frequency of 25.9 per Mb. The pairwise linkage disequilibrium (LD) estimated using the squared-allele frequency correlations was found to decay rapidly with the genetic distance of 177 Kb. However, for individual chromosome, LD decay distance ranged from 76 Kb (chromosome 6) to 357 Kb (chromosome 4). GWAS identified 81 MTAs (marker-trait associations) for ten traits across the genome. High confidence MTAs for three important agronomic traits including FLW (flag leaf width), GY (grain yield) and TGW (thousand-grain weight) were identified. Significant pyramiding effect of identified MTAs further supplemented its importance in breeding programs. Desirable alleles and superior genotypes identified in the present study may prove valuable for foxtail millet improvement through marker-assisted selection.
format	article
author	Vandana Jaiswal Sarika Gupta Vijay Gahlaut Mehanathan Muthamilarasan Tirthankar Bandyopadhyay Nirala Ramchiary Manoj Prasad
author_facet	Vandana Jaiswal Sarika Gupta Vijay Gahlaut Mehanathan Muthamilarasan Tirthankar Bandyopadhyay Nirala Ramchiary Manoj Prasad
author_sort	Vandana Jaiswal
title	Genome-Wide Association Study of Major Agronomic Traits in Foxtail Millet (Setaria italica L.) Using ddRAD Sequencing
title_short	Genome-Wide Association Study of Major Agronomic Traits in Foxtail Millet (Setaria italica L.) Using ddRAD Sequencing
title_full	Genome-Wide Association Study of Major Agronomic Traits in Foxtail Millet (Setaria italica L.) Using ddRAD Sequencing
title_fullStr	Genome-Wide Association Study of Major Agronomic Traits in Foxtail Millet (Setaria italica L.) Using ddRAD Sequencing
title_full_unstemmed	Genome-Wide Association Study of Major Agronomic Traits in Foxtail Millet (Setaria italica L.) Using ddRAD Sequencing
title_sort	genome-wide association study of major agronomic traits in foxtail millet (setaria italica l.) using ddrad sequencing
publisher	Nature Portfolio
publishDate	2019
url	https://doaj.org/article/6408cc9636234f9d8d6ce7143daabef3
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Genome-Wide Association Study of Major Agronomic Traits in Foxtail Millet (Setaria italica L.) Using ddRAD Sequencing

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