Genome wide association study and genomic prediction for stover quality traits in tropical maize (Zea mays L.)

Abstract Maize is rapidly replacing traditionally cultivated dual purpose crops of South Asia, primarily due to the better economic remuneration. This has created an impetus for improving maize for both grain productivity and stover traits. Molecular techniques can largely assist breeders in determi...

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Autores principales:	M. T. Vinayan, K. Seetharam, Raman Babu, P. H. Zaidi, M. Blummel, Sudha K. Nair
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/9e1b7bfc74e34711ad2a9df77049e96e
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spelling	oai:doaj.org-article:9e1b7bfc74e34711ad2a9df77049e96e2021-12-02T14:01:33ZGenome wide association study and genomic prediction for stover quality traits in tropical maize (Zea mays L.)10.1038/s41598-020-80118-22045-2322https://doaj.org/article/9e1b7bfc74e34711ad2a9df77049e96e2021-01-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-80118-2https://doaj.org/toc/2045-2322Abstract Maize is rapidly replacing traditionally cultivated dual purpose crops of South Asia, primarily due to the better economic remuneration. This has created an impetus for improving maize for both grain productivity and stover traits. Molecular techniques can largely assist breeders in determining approaches for effectively integrating stover trait improvement in their existing breeding pipeline. In the current study we identified a suite of potential genomic regions associated to the two major stover quality traits—in-vitro organic matter digestibility (IVOMD) and metabolizable energy (ME) through genome wide association study. However, considering the fact that the loci identified for these complex traits all had smaller effects and accounted only a small portion of phenotypic variation, the effectiveness of following a genomic selection approach for these traits was evaluated. The testing set consists of breeding lines recently developed within the program and the training set consists of a panel of lines from the working germplasm comprising the founder lines of the newly developed breeding lines and also an unrelated diversity set. The prediction accuracy as determined by the Pearson’s correlation coefficient between observed and predicted values of these breeding lines were high even at lower marker density (200 random SNPs), when the training and testing set were related. However, the accuracies were dismal, when there was no relationship between the training and the testing set.M. T. VinayanK. SeetharamRaman BabuP. H. ZaidiM. BlummelSudha K. NairNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q M. T. Vinayan K. Seetharam Raman Babu P. H. Zaidi M. Blummel Sudha K. Nair Genome wide association study and genomic prediction for stover quality traits in tropical maize (Zea mays L.)
description	Abstract Maize is rapidly replacing traditionally cultivated dual purpose crops of South Asia, primarily due to the better economic remuneration. This has created an impetus for improving maize for both grain productivity and stover traits. Molecular techniques can largely assist breeders in determining approaches for effectively integrating stover trait improvement in their existing breeding pipeline. In the current study we identified a suite of potential genomic regions associated to the two major stover quality traits—in-vitro organic matter digestibility (IVOMD) and metabolizable energy (ME) through genome wide association study. However, considering the fact that the loci identified for these complex traits all had smaller effects and accounted only a small portion of phenotypic variation, the effectiveness of following a genomic selection approach for these traits was evaluated. The testing set consists of breeding lines recently developed within the program and the training set consists of a panel of lines from the working germplasm comprising the founder lines of the newly developed breeding lines and also an unrelated diversity set. The prediction accuracy as determined by the Pearson’s correlation coefficient between observed and predicted values of these breeding lines were high even at lower marker density (200 random SNPs), when the training and testing set were related. However, the accuracies were dismal, when there was no relationship between the training and the testing set.
format	article
author	M. T. Vinayan K. Seetharam Raman Babu P. H. Zaidi M. Blummel Sudha K. Nair
author_facet	M. T. Vinayan K. Seetharam Raman Babu P. H. Zaidi M. Blummel Sudha K. Nair
author_sort	M. T. Vinayan
title	Genome wide association study and genomic prediction for stover quality traits in tropical maize (Zea mays L.)
title_short	Genome wide association study and genomic prediction for stover quality traits in tropical maize (Zea mays L.)
title_full	Genome wide association study and genomic prediction for stover quality traits in tropical maize (Zea mays L.)
title_fullStr	Genome wide association study and genomic prediction for stover quality traits in tropical maize (Zea mays L.)
title_full_unstemmed	Genome wide association study and genomic prediction for stover quality traits in tropical maize (Zea mays L.)
title_sort	genome wide association study and genomic prediction for stover quality traits in tropical maize (zea mays l.)
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/9e1b7bfc74e34711ad2a9df77049e96e
work_keys_str_mv	AT mtvinayan genomewideassociationstudyandgenomicpredictionforstoverqualitytraitsintropicalmaizezeamaysl AT kseetharam genomewideassociationstudyandgenomicpredictionforstoverqualitytraitsintropicalmaizezeamaysl AT ramanbabu genomewideassociationstudyandgenomicpredictionforstoverqualitytraitsintropicalmaizezeamaysl AT phzaidi genomewideassociationstudyandgenomicpredictionforstoverqualitytraitsintropicalmaizezeamaysl AT mblummel genomewideassociationstudyandgenomicpredictionforstoverqualitytraitsintropicalmaizezeamaysl AT sudhaknair genomewideassociationstudyandgenomicpredictionforstoverqualitytraitsintropicalmaizezeamaysl
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Genome wide association study and genomic prediction for stover quality traits in tropical maize (Zea mays L.)

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