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Genome-wide association studies and whole-genome prediction reveal the genetic architecture of KRN in maize

BACKGROUND: Kernel row number (KRN) is an important trait for the domestication and improvement of maize. Exploring the genetic basis of KRN has great research significance and can provide valuable information for molecular assisted selection. RESULTS: In this study, one single-locus method (MLM) an...

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Autores principales: An, Yixin, Chen, Lin, Li, Yong-Xiang, Li, Chunhui, Shi, Yunsu, Zhang, Dengfeng, Li, Yu, Wang, Tianyu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7590725/
https://www.ncbi.nlm.nih.gov/pubmed/33109077
http://dx.doi.org/10.1186/s12870-020-02676-x
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author An, Yixin
Chen, Lin
Li, Yong-Xiang
Li, Chunhui
Shi, Yunsu
Zhang, Dengfeng
Li, Yu
Wang, Tianyu
author_facet An, Yixin
Chen, Lin
Li, Yong-Xiang
Li, Chunhui
Shi, Yunsu
Zhang, Dengfeng
Li, Yu
Wang, Tianyu
author_sort An, Yixin
collection PubMed
description BACKGROUND: Kernel row number (KRN) is an important trait for the domestication and improvement of maize. Exploring the genetic basis of KRN has great research significance and can provide valuable information for molecular assisted selection. RESULTS: In this study, one single-locus method (MLM) and six multilocus methods (mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, pKWmEB and ISIS EM-BLASSO) of genome-wide association studies (GWASs) were used to identify significant quantitative trait nucleotides (QTNs) for KRN in an association panel including 639 maize inbred lines that were genotyped by the MaizeSNP50 BeadChip. In three phenotyping environments and with best linear unbiased prediction (BLUP) values, the seven GWAS methods revealed different numbers of KRN-associated QTNs, ranging from 11 to 177. Based on these results, seven important regions for KRN located on chromosomes 1, 2, 3, 5, 9, and 10 were identified by at least three methods and in at least two environments. Moreover, 49 genes from the seven regions were expressed in different maize tissues. Among the 49 genes, ARF29 (Zm00001d026540, encoding auxin response factor 29) and CKO4 (Zm00001d043293, encoding cytokinin oxidase protein) were significantly related to KRN, based on expression analysis and candidate gene association mapping. Whole-genome prediction (WGP) of KRN was also performed, and we found that the KRN-associated tagSNPs achieved a high prediction accuracy. The best strategy was to integrate all of the KRN-associated tagSNPs identified by all GWAS models. CONCLUSIONS: These results aid in our understanding of the genetic architecture of KRN and provide useful information for genomic selection for KRN in maize breeding.
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spelling pubmed-75907252020-10-27 Genome-wide association studies and whole-genome prediction reveal the genetic architecture of KRN in maize An, Yixin Chen, Lin Li, Yong-Xiang Li, Chunhui Shi, Yunsu Zhang, Dengfeng Li, Yu Wang, Tianyu BMC Plant Biol Research Article BACKGROUND: Kernel row number (KRN) is an important trait for the domestication and improvement of maize. Exploring the genetic basis of KRN has great research significance and can provide valuable information for molecular assisted selection. RESULTS: In this study, one single-locus method (MLM) and six multilocus methods (mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, pKWmEB and ISIS EM-BLASSO) of genome-wide association studies (GWASs) were used to identify significant quantitative trait nucleotides (QTNs) for KRN in an association panel including 639 maize inbred lines that were genotyped by the MaizeSNP50 BeadChip. In three phenotyping environments and with best linear unbiased prediction (BLUP) values, the seven GWAS methods revealed different numbers of KRN-associated QTNs, ranging from 11 to 177. Based on these results, seven important regions for KRN located on chromosomes 1, 2, 3, 5, 9, and 10 were identified by at least three methods and in at least two environments. Moreover, 49 genes from the seven regions were expressed in different maize tissues. Among the 49 genes, ARF29 (Zm00001d026540, encoding auxin response factor 29) and CKO4 (Zm00001d043293, encoding cytokinin oxidase protein) were significantly related to KRN, based on expression analysis and candidate gene association mapping. Whole-genome prediction (WGP) of KRN was also performed, and we found that the KRN-associated tagSNPs achieved a high prediction accuracy. The best strategy was to integrate all of the KRN-associated tagSNPs identified by all GWAS models. CONCLUSIONS: These results aid in our understanding of the genetic architecture of KRN and provide useful information for genomic selection for KRN in maize breeding. BioMed Central 2020-10-27 /pmc/articles/PMC7590725/ /pubmed/33109077 http://dx.doi.org/10.1186/s12870-020-02676-x Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research Article
An, Yixin
Chen, Lin
Li, Yong-Xiang
Li, Chunhui
Shi, Yunsu
Zhang, Dengfeng
Li, Yu
Wang, Tianyu
Genome-wide association studies and whole-genome prediction reveal the genetic architecture of KRN in maize
title Genome-wide association studies and whole-genome prediction reveal the genetic architecture of KRN in maize
title_full Genome-wide association studies and whole-genome prediction reveal the genetic architecture of KRN in maize
title_fullStr Genome-wide association studies and whole-genome prediction reveal the genetic architecture of KRN in maize
title_full_unstemmed Genome-wide association studies and whole-genome prediction reveal the genetic architecture of KRN in maize
title_short Genome-wide association studies and whole-genome prediction reveal the genetic architecture of KRN in maize
title_sort genome-wide association studies and whole-genome prediction reveal the genetic architecture of krn in maize
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7590725/
https://www.ncbi.nlm.nih.gov/pubmed/33109077
http://dx.doi.org/10.1186/s12870-020-02676-x
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