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High-Density Genetic Variation Map Reveals Key Candidate Loci and Genes Associated With Important Agronomic Traits in Peanut

Peanut is one of the most important cash crops with high quality oil, high protein content, and many other nutritional elements, and grown globally. Cultivated peanut (Arachis hypogaea L.) is allotetraploid with a narrow genetic base, and its genetics and molecular mechanisms controlling the agronom...

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Autores principales: Zhao, Huiling, Tian, Ruizheng, Xia, Han, Li, Changsheng, Li, Guanghui, Li, Aiqin, Zhang, Xianying, Zhou, Ximeng, Ma, Jing, Huang, Huailing, Zhang, Kun, Thudi, Mahendar, Ma, Changle, Wang, Xingjun, Zhao, Chuanzhi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8990815/
https://www.ncbi.nlm.nih.gov/pubmed/35401655
http://dx.doi.org/10.3389/fgene.2022.845602
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author Zhao, Huiling
Tian, Ruizheng
Xia, Han
Li, Changsheng
Li, Guanghui
Li, Aiqin
Zhang, Xianying
Zhou, Ximeng
Ma, Jing
Huang, Huailing
Zhang, Kun
Thudi, Mahendar
Ma, Changle
Wang, Xingjun
Zhao, Chuanzhi
author_facet Zhao, Huiling
Tian, Ruizheng
Xia, Han
Li, Changsheng
Li, Guanghui
Li, Aiqin
Zhang, Xianying
Zhou, Ximeng
Ma, Jing
Huang, Huailing
Zhang, Kun
Thudi, Mahendar
Ma, Changle
Wang, Xingjun
Zhao, Chuanzhi
author_sort Zhao, Huiling
collection PubMed
description Peanut is one of the most important cash crops with high quality oil, high protein content, and many other nutritional elements, and grown globally. Cultivated peanut (Arachis hypogaea L.) is allotetraploid with a narrow genetic base, and its genetics and molecular mechanisms controlling the agronomic traits are poorly understood. Here, we report a comprehensive genome variation map based on the genotyping of a panel of 178 peanut cultivars using Axiom_Arachis2 SNP array, including 163 representative varieties of different provinces in China, and 15 cultivars from 9 other countries. According to principal component analysis (PCA) and phylogenetic analysis, the peanut varieties were divided into 7 groups, notable genetic divergences between the different areas were shaped by environment and domestication. Using genome-wide association study (GWAS) analysis, we identified several marker-trait associations (MTAs) and candidate genes potentially involved in regulating several agronomic traits of peanut, including one MTA related with hundred seed weight, one MTA related with total number of branches, and 14 MTAs related with pod shape. This study outlines the genetic basis of these peanut cultivars and provides 13,125 polymorphic SNP markers for further distinguishing and utility of these elite cultivars. In addition, the candidate loci and genes provide valuable information for further fine mapping of QTLs and improving the quality and yield of peanut using a genomic-assisted breeding method.
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spelling pubmed-89908152022-04-09 High-Density Genetic Variation Map Reveals Key Candidate Loci and Genes Associated With Important Agronomic Traits in Peanut Zhao, Huiling Tian, Ruizheng Xia, Han Li, Changsheng Li, Guanghui Li, Aiqin Zhang, Xianying Zhou, Ximeng Ma, Jing Huang, Huailing Zhang, Kun Thudi, Mahendar Ma, Changle Wang, Xingjun Zhao, Chuanzhi Front Genet Genetics Peanut is one of the most important cash crops with high quality oil, high protein content, and many other nutritional elements, and grown globally. Cultivated peanut (Arachis hypogaea L.) is allotetraploid with a narrow genetic base, and its genetics and molecular mechanisms controlling the agronomic traits are poorly understood. Here, we report a comprehensive genome variation map based on the genotyping of a panel of 178 peanut cultivars using Axiom_Arachis2 SNP array, including 163 representative varieties of different provinces in China, and 15 cultivars from 9 other countries. According to principal component analysis (PCA) and phylogenetic analysis, the peanut varieties were divided into 7 groups, notable genetic divergences between the different areas were shaped by environment and domestication. Using genome-wide association study (GWAS) analysis, we identified several marker-trait associations (MTAs) and candidate genes potentially involved in regulating several agronomic traits of peanut, including one MTA related with hundred seed weight, one MTA related with total number of branches, and 14 MTAs related with pod shape. This study outlines the genetic basis of these peanut cultivars and provides 13,125 polymorphic SNP markers for further distinguishing and utility of these elite cultivars. In addition, the candidate loci and genes provide valuable information for further fine mapping of QTLs and improving the quality and yield of peanut using a genomic-assisted breeding method. Frontiers Media S.A. 2022-03-25 /pmc/articles/PMC8990815/ /pubmed/35401655 http://dx.doi.org/10.3389/fgene.2022.845602 Text en Copyright © 2022 Zhao, Tian, Xia, Li, Li, Li, Zhang, Zhou, Ma, Huang, Zhang, Thudi, Ma, Wang and Zhao. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Zhao, Huiling
Tian, Ruizheng
Xia, Han
Li, Changsheng
Li, Guanghui
Li, Aiqin
Zhang, Xianying
Zhou, Ximeng
Ma, Jing
Huang, Huailing
Zhang, Kun
Thudi, Mahendar
Ma, Changle
Wang, Xingjun
Zhao, Chuanzhi
High-Density Genetic Variation Map Reveals Key Candidate Loci and Genes Associated With Important Agronomic Traits in Peanut
title High-Density Genetic Variation Map Reveals Key Candidate Loci and Genes Associated With Important Agronomic Traits in Peanut
title_full High-Density Genetic Variation Map Reveals Key Candidate Loci and Genes Associated With Important Agronomic Traits in Peanut
title_fullStr High-Density Genetic Variation Map Reveals Key Candidate Loci and Genes Associated With Important Agronomic Traits in Peanut
title_full_unstemmed High-Density Genetic Variation Map Reveals Key Candidate Loci and Genes Associated With Important Agronomic Traits in Peanut
title_short High-Density Genetic Variation Map Reveals Key Candidate Loci and Genes Associated With Important Agronomic Traits in Peanut
title_sort high-density genetic variation map reveals key candidate loci and genes associated with important agronomic traits in peanut
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8990815/
https://www.ncbi.nlm.nih.gov/pubmed/35401655
http://dx.doi.org/10.3389/fgene.2022.845602
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