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Genetic Diversity and Selection Footprints in the Genome of Brazilian Soybean Cultivars

Although Brazil is currently the largest soybean producer in the world, only a small number of studies have analyzed the genetic diversity of Brazilian soybean. These studies have shown the existence of a narrow genetic base. The objectives of this work were to analyze the population structure and g...

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Autores principales: Mendonça, Heitor Calux, Pereira, Luiz Filipe Protasio, Maldonado dos Santos, João Vitor, Meda, Anderson Rotter, Sant’ Ana, Gustavo César
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9006619/
https://www.ncbi.nlm.nih.gov/pubmed/35432410
http://dx.doi.org/10.3389/fpls.2022.842571
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author Mendonça, Heitor Calux
Pereira, Luiz Filipe Protasio
Maldonado dos Santos, João Vitor
Meda, Anderson Rotter
Sant’ Ana, Gustavo César
author_facet Mendonça, Heitor Calux
Pereira, Luiz Filipe Protasio
Maldonado dos Santos, João Vitor
Meda, Anderson Rotter
Sant’ Ana, Gustavo César
author_sort Mendonça, Heitor Calux
collection PubMed
description Although Brazil is currently the largest soybean producer in the world, only a small number of studies have analyzed the genetic diversity of Brazilian soybean. These studies have shown the existence of a narrow genetic base. The objectives of this work were to analyze the population structure and genetic diversity, and to identify selection signatures in the genome of soybean germplasms from different companies in Brazil. A panel consisting of 343 soybean lines from Brazil, North America, and Asia was genotyped using genotyping by sequencing (GBS). Population structure was assessed by Bayesian and multivariate approaches. Genetic diversity was analyzed using metrics such as the fixation index, nucleotide diversity, genetic dissimilarity, and linkage disequilibrium. The software BayeScan was used to detect selection signatures between Brazilian and Asian accessions as well as among Brazilian germplasms. Region of origin, company of origin, and relative maturity group (RMG) all had a significant influence on population structure. Varieties belonging to the same company and especially to the same RMG exhibited a high level of genetic similarity. This result was exacerbated among early maturing accessions. Brazilian soybean showed significantly lower genetic diversity when compared to Asian accessions. This was expected, because the crop’s region of origin is its main genetic diversity reserve. We identified 7 genomic regions under selection between the Brazilian and Asian accessions, and 27 among Brazilian varieties developed by different companies. Associated with these genomic regions, we found 96 quantitative trait loci (QTLs) for important soybean breeding traits such as flowering, maturity, plant architecture, productivity components, pathogen resistance, and seed composition. Some of the QTLs associated with the markers under selection have genes of great importance to soybean’s regional adaptation. The results reported herein allowed to expand the knowledge about the organization of the genetic variability of the Brazilian soybean germplasm. Furthermore, it was possible to identify genomic regions under selection possibly associated with the adaptation of soybean to Brazilian environments.
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spelling pubmed-90066192022-04-14 Genetic Diversity and Selection Footprints in the Genome of Brazilian Soybean Cultivars Mendonça, Heitor Calux Pereira, Luiz Filipe Protasio Maldonado dos Santos, João Vitor Meda, Anderson Rotter Sant’ Ana, Gustavo César Front Plant Sci Plant Science Although Brazil is currently the largest soybean producer in the world, only a small number of studies have analyzed the genetic diversity of Brazilian soybean. These studies have shown the existence of a narrow genetic base. The objectives of this work were to analyze the population structure and genetic diversity, and to identify selection signatures in the genome of soybean germplasms from different companies in Brazil. A panel consisting of 343 soybean lines from Brazil, North America, and Asia was genotyped using genotyping by sequencing (GBS). Population structure was assessed by Bayesian and multivariate approaches. Genetic diversity was analyzed using metrics such as the fixation index, nucleotide diversity, genetic dissimilarity, and linkage disequilibrium. The software BayeScan was used to detect selection signatures between Brazilian and Asian accessions as well as among Brazilian germplasms. Region of origin, company of origin, and relative maturity group (RMG) all had a significant influence on population structure. Varieties belonging to the same company and especially to the same RMG exhibited a high level of genetic similarity. This result was exacerbated among early maturing accessions. Brazilian soybean showed significantly lower genetic diversity when compared to Asian accessions. This was expected, because the crop’s region of origin is its main genetic diversity reserve. We identified 7 genomic regions under selection between the Brazilian and Asian accessions, and 27 among Brazilian varieties developed by different companies. Associated with these genomic regions, we found 96 quantitative trait loci (QTLs) for important soybean breeding traits such as flowering, maturity, plant architecture, productivity components, pathogen resistance, and seed composition. Some of the QTLs associated with the markers under selection have genes of great importance to soybean’s regional adaptation. The results reported herein allowed to expand the knowledge about the organization of the genetic variability of the Brazilian soybean germplasm. Furthermore, it was possible to identify genomic regions under selection possibly associated with the adaptation of soybean to Brazilian environments. Frontiers Media S.A. 2022-03-30 /pmc/articles/PMC9006619/ /pubmed/35432410 http://dx.doi.org/10.3389/fpls.2022.842571 Text en Copyright © 2022 Mendonça, Pereira, Maldonado dos Santos, Meda and Sant’ Ana. 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 Plant Science
Mendonça, Heitor Calux
Pereira, Luiz Filipe Protasio
Maldonado dos Santos, João Vitor
Meda, Anderson Rotter
Sant’ Ana, Gustavo César
Genetic Diversity and Selection Footprints in the Genome of Brazilian Soybean Cultivars
title Genetic Diversity and Selection Footprints in the Genome of Brazilian Soybean Cultivars
title_full Genetic Diversity and Selection Footprints in the Genome of Brazilian Soybean Cultivars
title_fullStr Genetic Diversity and Selection Footprints in the Genome of Brazilian Soybean Cultivars
title_full_unstemmed Genetic Diversity and Selection Footprints in the Genome of Brazilian Soybean Cultivars
title_short Genetic Diversity and Selection Footprints in the Genome of Brazilian Soybean Cultivars
title_sort genetic diversity and selection footprints in the genome of brazilian soybean cultivars
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9006619/
https://www.ncbi.nlm.nih.gov/pubmed/35432410
http://dx.doi.org/10.3389/fpls.2022.842571
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