Genetic diversity and population structure of advanced clones selected over forty years by a potato breeding program in the USA

Abstract Knowledge regarding genetic diversity and population structure of breeding materials is essential for crop improvement. The Texas A&M University Potato Breeding Program has a collection of advanced clones selected and maintained in-vitro over a 40-year period. Little is known about its...

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Autores principales:	Jeewan Pandey, Douglas C. Scheuring, Jeffrey W. Koym, Joseph Coombs, Richard G. Novy, Asunta L. Thompson, David G. Holm, David S. Douches, J. Creighton Miller, M. Isabel Vales
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/9d6777fba96746a19f785a19d53c32a0
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spelling	oai:doaj.org-article:9d6777fba96746a19f785a19d53c32a02021-12-02T14:27:46ZGenetic diversity and population structure of advanced clones selected over forty years by a potato breeding program in the USA10.1038/s41598-021-87284-x2045-2322https://doaj.org/article/9d6777fba96746a19f785a19d53c32a02021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-87284-xhttps://doaj.org/toc/2045-2322Abstract Knowledge regarding genetic diversity and population structure of breeding materials is essential for crop improvement. The Texas A&M University Potato Breeding Program has a collection of advanced clones selected and maintained in-vitro over a 40-year period. Little is known about its genetic makeup and usefulness for the current breeding program. In this study, 214 potato clones were genotyped with the Infinium Illumina 22 K V3 Potato Array. After filtering, a total of 10,106 single nucleotide polymorphic (SNP) markers were used for analysis. Heterozygosity varied by SNP, with an overall average of 0.59. Three groups of tetraploid clones primarily based on potato market classes, were detected using STRUCTURE software and confirmed by discriminant analysis of principal components. The highest coefficient of differentiation observed between the groups was 0.14. Signatures of selection were uncovered in genes controlling potato flesh and skin color, length of plant cycle and tuberization, and carbohydrate metabolism. A core set of 43 clones was obtained using Core Hunter 3 to develop a sub-collection that retains similar genetic diversity as the whole population, minimize redundancies, and facilitates long-term conservation of genetic resources. The comprehensive molecular characterization of our breeding clone bank collection contributes to understanding the genetic diversity of existing potato resources. This analysis could be applied to other breeding programs and assist in the selection of parents, fingerprinting, protection, and management of the breeding collections.Jeewan PandeyDouglas C. ScheuringJeffrey W. KoymJoseph CoombsRichard G. NovyAsunta L. ThompsonDavid G. HolmDavid S. DouchesJ. Creighton MillerM. Isabel ValesNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-18 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jeewan Pandey Douglas C. Scheuring Jeffrey W. Koym Joseph Coombs Richard G. Novy Asunta L. Thompson David G. Holm David S. Douches J. Creighton Miller M. Isabel Vales Genetic diversity and population structure of advanced clones selected over forty years by a potato breeding program in the USA
description	Abstract Knowledge regarding genetic diversity and population structure of breeding materials is essential for crop improvement. The Texas A&M University Potato Breeding Program has a collection of advanced clones selected and maintained in-vitro over a 40-year period. Little is known about its genetic makeup and usefulness for the current breeding program. In this study, 214 potato clones were genotyped with the Infinium Illumina 22 K V3 Potato Array. After filtering, a total of 10,106 single nucleotide polymorphic (SNP) markers were used for analysis. Heterozygosity varied by SNP, with an overall average of 0.59. Three groups of tetraploid clones primarily based on potato market classes, were detected using STRUCTURE software and confirmed by discriminant analysis of principal components. The highest coefficient of differentiation observed between the groups was 0.14. Signatures of selection were uncovered in genes controlling potato flesh and skin color, length of plant cycle and tuberization, and carbohydrate metabolism. A core set of 43 clones was obtained using Core Hunter 3 to develop a sub-collection that retains similar genetic diversity as the whole population, minimize redundancies, and facilitates long-term conservation of genetic resources. The comprehensive molecular characterization of our breeding clone bank collection contributes to understanding the genetic diversity of existing potato resources. This analysis could be applied to other breeding programs and assist in the selection of parents, fingerprinting, protection, and management of the breeding collections.
format	article
author	Jeewan Pandey Douglas C. Scheuring Jeffrey W. Koym Joseph Coombs Richard G. Novy Asunta L. Thompson David G. Holm David S. Douches J. Creighton Miller M. Isabel Vales
author_facet	Jeewan Pandey Douglas C. Scheuring Jeffrey W. Koym Joseph Coombs Richard G. Novy Asunta L. Thompson David G. Holm David S. Douches J. Creighton Miller M. Isabel Vales
author_sort	Jeewan Pandey
title	Genetic diversity and population structure of advanced clones selected over forty years by a potato breeding program in the USA
title_short	Genetic diversity and population structure of advanced clones selected over forty years by a potato breeding program in the USA
title_full	Genetic diversity and population structure of advanced clones selected over forty years by a potato breeding program in the USA
title_fullStr	Genetic diversity and population structure of advanced clones selected over forty years by a potato breeding program in the USA
title_full_unstemmed	Genetic diversity and population structure of advanced clones selected over forty years by a potato breeding program in the USA
title_sort	genetic diversity and population structure of advanced clones selected over forty years by a potato breeding program in the usa
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/9d6777fba96746a19f785a19d53c32a0
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Genetic diversity and population structure of advanced clones selected over forty years by a potato breeding program in the USA

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