Identification of quantitative trait nucleotides and candidate genes for tuber yield and mosaic virus tolerance in an elite population of white guinea yam (Dioscorea rotundata) using genome-wide association scan

Abstract Background Improvement of tuber yield and tolerance to viruses are priority objectives in white Guinea yam breeding programs. However, phenotypic selection for these traits is quite challenging due to phenotypic plasticity and cumbersome screening of phenotypic-induced variations. This stud...

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Autores principales:	Paterne A. Agre, Prince E. Norman, Robert Asiedu, Asrat Asfaw
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Genetic diversity population structure GWAS SNP markers white Guinea yam Botany QK1-989
Acceso en línea:	https://doaj.org/article/4a3c80987b36488d9dd68b36111aa615
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spelling	oai:doaj.org-article:4a3c80987b36488d9dd68b36111aa6152021-11-28T12:07:24ZIdentification of quantitative trait nucleotides and candidate genes for tuber yield and mosaic virus tolerance in an elite population of white guinea yam (Dioscorea rotundata) using genome-wide association scan10.1186/s12870-021-03314-w1471-2229https://doaj.org/article/4a3c80987b36488d9dd68b36111aa6152021-11-01T00:00:00Zhttps://doi.org/10.1186/s12870-021-03314-whttps://doaj.org/toc/1471-2229Abstract Background Improvement of tuber yield and tolerance to viruses are priority objectives in white Guinea yam breeding programs. However, phenotypic selection for these traits is quite challenging due to phenotypic plasticity and cumbersome screening of phenotypic-induced variations. This study assessed quantitative trait nucleotides (QTNs) and the underlying candidate genes related to tuber yield per plant (TYP) and yam mosaic virus (YMV) tolerance in a panel of 406 white Guinea yam (Dioscorea rotundata) breeding lines using a genome-wide association study (GWAS). Results Population structure analysis using 5,581 SNPs differentiated the 406 genotypes into seven distinct sub-groups based delta K. Marker-trait association (MTA) analysis using the multi-locus linear model (mrMLM) identified seventeen QTN regions significant for TYP and five for YMV with various effects. The seveteen QTNs were detected on nine chromosomes, while the five QTNs were identified on five chromosomes. We identified variants responsible for predicting higher yield and low virus severity scores in the breeding panel through the marker-effect prediction. Gene annotation for the significant SNP loci identified several essential putative genes associated with the growth and development of tuber yield and those that code for tolerance to mosaic virus. Conclusion Application of different multi-locus models of GWAS identified 22 QTNs. Our results provide valuable insight for marker validation and deployment for tuber yield and mosaic virus tolerance in white yam breeding. The information on SNP variants and genes from the present study would fast-track the application of genomics-informed selection decisions in breeding white Guinea yam for rapid introgression of the targeted traits through markers validation.Paterne A. AgrePrince E. NormanRobert AsieduAsrat AsfawBMCarticleGenetic diversitypopulation structureGWASSNP markerswhite Guinea yamBotanyQK1-989ENBMC Plant Biology, Vol 21, Iss 1, Pp 1-16 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Genetic diversity population structure GWAS SNP markers white Guinea yam Botany QK1-989
spellingShingle	Genetic diversity population structure GWAS SNP markers white Guinea yam Botany QK1-989 Paterne A. Agre Prince E. Norman Robert Asiedu Asrat Asfaw Identification of quantitative trait nucleotides and candidate genes for tuber yield and mosaic virus tolerance in an elite population of white guinea yam (Dioscorea rotundata) using genome-wide association scan
description	Abstract Background Improvement of tuber yield and tolerance to viruses are priority objectives in white Guinea yam breeding programs. However, phenotypic selection for these traits is quite challenging due to phenotypic plasticity and cumbersome screening of phenotypic-induced variations. This study assessed quantitative trait nucleotides (QTNs) and the underlying candidate genes related to tuber yield per plant (TYP) and yam mosaic virus (YMV) tolerance in a panel of 406 white Guinea yam (Dioscorea rotundata) breeding lines using a genome-wide association study (GWAS). Results Population structure analysis using 5,581 SNPs differentiated the 406 genotypes into seven distinct sub-groups based delta K. Marker-trait association (MTA) analysis using the multi-locus linear model (mrMLM) identified seventeen QTN regions significant for TYP and five for YMV with various effects. The seveteen QTNs were detected on nine chromosomes, while the five QTNs were identified on five chromosomes. We identified variants responsible for predicting higher yield and low virus severity scores in the breeding panel through the marker-effect prediction. Gene annotation for the significant SNP loci identified several essential putative genes associated with the growth and development of tuber yield and those that code for tolerance to mosaic virus. Conclusion Application of different multi-locus models of GWAS identified 22 QTNs. Our results provide valuable insight for marker validation and deployment for tuber yield and mosaic virus tolerance in white yam breeding. The information on SNP variants and genes from the present study would fast-track the application of genomics-informed selection decisions in breeding white Guinea yam for rapid introgression of the targeted traits through markers validation.
format	article
author	Paterne A. Agre Prince E. Norman Robert Asiedu Asrat Asfaw
author_facet	Paterne A. Agre Prince E. Norman Robert Asiedu Asrat Asfaw
author_sort	Paterne A. Agre
title	Identification of quantitative trait nucleotides and candidate genes for tuber yield and mosaic virus tolerance in an elite population of white guinea yam (Dioscorea rotundata) using genome-wide association scan
title_short	Identification of quantitative trait nucleotides and candidate genes for tuber yield and mosaic virus tolerance in an elite population of white guinea yam (Dioscorea rotundata) using genome-wide association scan
title_full	Identification of quantitative trait nucleotides and candidate genes for tuber yield and mosaic virus tolerance in an elite population of white guinea yam (Dioscorea rotundata) using genome-wide association scan
title_fullStr	Identification of quantitative trait nucleotides and candidate genes for tuber yield and mosaic virus tolerance in an elite population of white guinea yam (Dioscorea rotundata) using genome-wide association scan
title_full_unstemmed	Identification of quantitative trait nucleotides and candidate genes for tuber yield and mosaic virus tolerance in an elite population of white guinea yam (Dioscorea rotundata) using genome-wide association scan
title_sort	identification of quantitative trait nucleotides and candidate genes for tuber yield and mosaic virus tolerance in an elite population of white guinea yam (dioscorea rotundata) using genome-wide association scan
publisher	BMC
publishDate	2021
url	https://doaj.org/article/4a3c80987b36488d9dd68b36111aa615
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Identification of quantitative trait nucleotides and candidate genes for tuber yield and mosaic virus tolerance in an elite population of white guinea yam (Dioscorea rotundata) using genome-wide association scan

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