Genetic variation and population structure in China summer maize germplasm

Abstract Maize (Zea mays L.) germplasm in China Summer maize ecological region (CSM) or central corn-belt of China is diverse but has not been systematically characterized at molecular level. In this study, genetic variation, genome diversity, linkage disequilibrium patterns, population structure, a...

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Autores principales:	Guoping Shu, Gangqiang Cao, Niannian Li, Aifang Wang, Fang Wei, Ting Li, Li Yi, Yunbi Xu, Yibo Wang
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/fc52292dcac34c5d8f682b04bb2f6be9
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spelling	oai:doaj.org-article:fc52292dcac34c5d8f682b04bb2f6be92021-12-02T15:51:13ZGenetic variation and population structure in China summer maize germplasm10.1038/s41598-021-84732-62045-2322https://doaj.org/article/fc52292dcac34c5d8f682b04bb2f6be92021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-84732-6https://doaj.org/toc/2045-2322Abstract Maize (Zea mays L.) germplasm in China Summer maize ecological region (CSM) or central corn-belt of China is diverse but has not been systematically characterized at molecular level. In this study, genetic variation, genome diversity, linkage disequilibrium patterns, population structure, and characteristics of different heterotic groups were studied using 525,141 SNPs obtained by Genotyping-By-Sequencing (GBS) for 490 inbred lines collected from researchers at CSM region. The SNP density is lower near centromere, but higher near telomere region of maize chromosome, the degree of linkage disequilibrium (r2) vary at different chromosome regions. Majority of the inbred lines (66.05%) show pairwise relative kinship near zero, indicating a large genetic diversity in the CSM breeding germplasm. Using 4849 tagSNPs derived from 3618 haplotype blocks, the 490 inbred lines were delineated into 3 supergroups, 6 groups, and 10 subgroups using ADMIXTURE software. A procedure of assigning inbred lines into heterotic groups using genomic data and tag-SNPs was developed and validated. Genome differentiation among different subgroups measured by Fst, and the genetic diversity within each subgroup measured by GD are both large. The share of heterotic groups that have significant North American germplasm contribution: P, SS, IDT, and X, accounts about 54% of the CSM breeding germplasm collection and has increased significantly in the last two decades. Two predominant types of heterotic pattern in CSM region are: M-Reid group × TSPT group, and X subgroup × Local subgroups.Guoping ShuGangqiang CaoNiannian LiAifang WangFang WeiTing LiLi YiYunbi XuYibo WangNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-13 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Guoping Shu Gangqiang Cao Niannian Li Aifang Wang Fang Wei Ting Li Li Yi Yunbi Xu Yibo Wang Genetic variation and population structure in China summer maize germplasm
description	Abstract Maize (Zea mays L.) germplasm in China Summer maize ecological region (CSM) or central corn-belt of China is diverse but has not been systematically characterized at molecular level. In this study, genetic variation, genome diversity, linkage disequilibrium patterns, population structure, and characteristics of different heterotic groups were studied using 525,141 SNPs obtained by Genotyping-By-Sequencing (GBS) for 490 inbred lines collected from researchers at CSM region. The SNP density is lower near centromere, but higher near telomere region of maize chromosome, the degree of linkage disequilibrium (r2) vary at different chromosome regions. Majority of the inbred lines (66.05%) show pairwise relative kinship near zero, indicating a large genetic diversity in the CSM breeding germplasm. Using 4849 tagSNPs derived from 3618 haplotype blocks, the 490 inbred lines were delineated into 3 supergroups, 6 groups, and 10 subgroups using ADMIXTURE software. A procedure of assigning inbred lines into heterotic groups using genomic data and tag-SNPs was developed and validated. Genome differentiation among different subgroups measured by Fst, and the genetic diversity within each subgroup measured by GD are both large. The share of heterotic groups that have significant North American germplasm contribution: P, SS, IDT, and X, accounts about 54% of the CSM breeding germplasm collection and has increased significantly in the last two decades. Two predominant types of heterotic pattern in CSM region are: M-Reid group × TSPT group, and X subgroup × Local subgroups.
format	article
author	Guoping Shu Gangqiang Cao Niannian Li Aifang Wang Fang Wei Ting Li Li Yi Yunbi Xu Yibo Wang
author_facet	Guoping Shu Gangqiang Cao Niannian Li Aifang Wang Fang Wei Ting Li Li Yi Yunbi Xu Yibo Wang
author_sort	Guoping Shu
title	Genetic variation and population structure in China summer maize germplasm
title_short	Genetic variation and population structure in China summer maize germplasm
title_full	Genetic variation and population structure in China summer maize germplasm
title_fullStr	Genetic variation and population structure in China summer maize germplasm
title_full_unstemmed	Genetic variation and population structure in China summer maize germplasm
title_sort	genetic variation and population structure in china summer maize germplasm
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/fc52292dcac34c5d8f682b04bb2f6be9
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_version_	1718385670041370624

Genetic variation and population structure in China summer maize germplasm

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