Genomic variation within the maize stiff‐stalk heterotic germplasm pool

Abstract The stiff‐stalk heterotic group in Maize (Zea mays L.) is an important source of inbreds used in U.S. commercial hybrid production. Founder inbreds B14, B37, B73, and, to a lesser extent, B84, are found in the pedigrees of a majority of commercial seed parent inbred lines. We created high‐q...

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Autores principales:	Nolan Bornowski, Kathryn J. Michel, John P. Hamilton, Shujun Ou, Arun S. Seetharam, Jerry Jenkins, Jane Grimwood, Chris Plott, Shengqiang Shu, Jayson Talag, Megan Kennedy, Hope Hundley, Vasanth R. Singan, Kerrie Barry, Chris Daum, Yuko Yoshinaga, Jeremy Schmutz, Candice N. Hirsch, Matthew B. Hufford, Natalia deLeon, Shawn M. Kaeppler, C. Robin Buell
Formato:	article
Lenguaje:	EN
Publicado:	Wiley 2021
Materias:	Plant culture SB1-1110 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/579f35ac5f934dc5a2375d794f0ae176
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spelling	oai:doaj.org-article:579f35ac5f934dc5a2375d794f0ae1762021-12-05T07:50:12ZGenomic variation within the maize stiff‐stalk heterotic germplasm pool1940-337210.1002/tpg2.20114https://doaj.org/article/579f35ac5f934dc5a2375d794f0ae1762021-11-01T00:00:00Zhttps://doi.org/10.1002/tpg2.20114https://doaj.org/toc/1940-3372Abstract The stiff‐stalk heterotic group in Maize (Zea mays L.) is an important source of inbreds used in U.S. commercial hybrid production. Founder inbreds B14, B37, B73, and, to a lesser extent, B84, are found in the pedigrees of a majority of commercial seed parent inbred lines. We created high‐quality genome assemblies of B84 and four expired Plant Variety Protection (ex‐PVP) lines LH145 representing B14, NKH8431 of mixed descent, PHB47 representing B37, and PHJ40, which is a Pioneer Hi‐Bred International (PHI) early stiff‐stalk type. Sequence was generated using long‐read sequencing achieving highly contiguous assemblies of 2.13–2.18 Gbp with N50 scaffold lengths >200 Mbp. Inbred‐specific gene annotations were generated using a core five‐tissue gene expression atlas, whereas transposable element (TE) annotation was conducted using de novo and homology‐directed methodologies. Compared with the reference inbred B73, synteny analyses revealed extensive collinearity across the five stiff‐stalk genomes, although unique components of the maize pangenome were detected. Comparison of this set of stiff‐stalk inbreds with the original Iowa Stiff Stalk Synthetic breeding population revealed that these inbreds represent only a proportion of variation in the original stiff‐stalk pool and there are highly conserved haplotypes in released public and ex‐Plant Variety Protection inbreds. Despite the reduction in variation from the original stiff‐stalk population, substantial genetic and genomic variation was identified supporting the potential for continued breeding success in this pool. The assemblies described here represent stiff‐stalk inbreds that have historical and commercial relevance and provide further insight into the emerging maize pangenome.Nolan BornowskiKathryn J. MichelJohn P. HamiltonShujun OuArun S. SeetharamJerry JenkinsJane GrimwoodChris PlottShengqiang ShuJayson TalagMegan KennedyHope HundleyVasanth R. SinganKerrie BarryChris DaumYuko YoshinagaJeremy SchmutzCandice N. HirschMatthew B. HuffordNatalia deLeonShawn M. KaepplerC. Robin BuellWileyarticlePlant cultureSB1-1110GeneticsQH426-470ENThe Plant Genome, Vol 14, Iss 3, Pp n/a-n/a (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Plant culture SB1-1110 Genetics QH426-470
spellingShingle	Plant culture SB1-1110 Genetics QH426-470 Nolan Bornowski Kathryn J. Michel John P. Hamilton Shujun Ou Arun S. Seetharam Jerry Jenkins Jane Grimwood Chris Plott Shengqiang Shu Jayson Talag Megan Kennedy Hope Hundley Vasanth R. Singan Kerrie Barry Chris Daum Yuko Yoshinaga Jeremy Schmutz Candice N. Hirsch Matthew B. Hufford Natalia deLeon Shawn M. Kaeppler C. Robin Buell Genomic variation within the maize stiff‐stalk heterotic germplasm pool
description	Abstract The stiff‐stalk heterotic group in Maize (Zea mays L.) is an important source of inbreds used in U.S. commercial hybrid production. Founder inbreds B14, B37, B73, and, to a lesser extent, B84, are found in the pedigrees of a majority of commercial seed parent inbred lines. We created high‐quality genome assemblies of B84 and four expired Plant Variety Protection (ex‐PVP) lines LH145 representing B14, NKH8431 of mixed descent, PHB47 representing B37, and PHJ40, which is a Pioneer Hi‐Bred International (PHI) early stiff‐stalk type. Sequence was generated using long‐read sequencing achieving highly contiguous assemblies of 2.13–2.18 Gbp with N50 scaffold lengths >200 Mbp. Inbred‐specific gene annotations were generated using a core five‐tissue gene expression atlas, whereas transposable element (TE) annotation was conducted using de novo and homology‐directed methodologies. Compared with the reference inbred B73, synteny analyses revealed extensive collinearity across the five stiff‐stalk genomes, although unique components of the maize pangenome were detected. Comparison of this set of stiff‐stalk inbreds with the original Iowa Stiff Stalk Synthetic breeding population revealed that these inbreds represent only a proportion of variation in the original stiff‐stalk pool and there are highly conserved haplotypes in released public and ex‐Plant Variety Protection inbreds. Despite the reduction in variation from the original stiff‐stalk population, substantial genetic and genomic variation was identified supporting the potential for continued breeding success in this pool. The assemblies described here represent stiff‐stalk inbreds that have historical and commercial relevance and provide further insight into the emerging maize pangenome.
format	article
author	Nolan Bornowski Kathryn J. Michel John P. Hamilton Shujun Ou Arun S. Seetharam Jerry Jenkins Jane Grimwood Chris Plott Shengqiang Shu Jayson Talag Megan Kennedy Hope Hundley Vasanth R. Singan Kerrie Barry Chris Daum Yuko Yoshinaga Jeremy Schmutz Candice N. Hirsch Matthew B. Hufford Natalia deLeon Shawn M. Kaeppler C. Robin Buell
author_facet	Nolan Bornowski Kathryn J. Michel John P. Hamilton Shujun Ou Arun S. Seetharam Jerry Jenkins Jane Grimwood Chris Plott Shengqiang Shu Jayson Talag Megan Kennedy Hope Hundley Vasanth R. Singan Kerrie Barry Chris Daum Yuko Yoshinaga Jeremy Schmutz Candice N. Hirsch Matthew B. Hufford Natalia deLeon Shawn M. Kaeppler C. Robin Buell
author_sort	Nolan Bornowski
title	Genomic variation within the maize stiff‐stalk heterotic germplasm pool
title_short	Genomic variation within the maize stiff‐stalk heterotic germplasm pool
title_full	Genomic variation within the maize stiff‐stalk heterotic germplasm pool
title_fullStr	Genomic variation within the maize stiff‐stalk heterotic germplasm pool
title_full_unstemmed	Genomic variation within the maize stiff‐stalk heterotic germplasm pool
title_sort	genomic variation within the maize stiff‐stalk heterotic germplasm pool
publisher	Wiley
publishDate	2021
url	https://doaj.org/article/579f35ac5f934dc5a2375d794f0ae176
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Genomic variation within the maize stiff‐stalk heterotic germplasm pool

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