Genetic diversity and population structure of soybean lines adapted to Sub-Saharan Africa using single nucleotide polymorphism (SNP) markers

Soybean productivity in sub-Saharan Africa (SSA) is less than half of the global average yield. To plug the productivity gap, further improvement in grain yield must be attained by enhancing the genetic potential of new cultivars that depends on the genetic diversity of the parents. Hence, our aim was to assess genetic diversity and population structure of elite soybean genotypes, mainly released cultivars and advanced selections in SSA. In this study, a set of 165 lines was genotyped with high-throughput single nucleotide polymorphism (SNP) markers covering the complete genome of soybean. The genetic diversity (0.414) was high considering the bi-allelic nature of SNP markers. The polymorphic information content (PIC) varied from 0.079 to 0.375, with an average of 0.324 and about 49% of the markers had a PIC value above 0.350. Cluster analysis grouped all the genotypes into three major clusters. The model-based STRUCTURE and discriminant analysis of principal components (DAPC) exhibited high consistency in the allocation of lines in subpopulations or groups. Nonetheless, they presented some discrepancy and identified the presence of six and five subpopulations or groups, respectively. Principal coordinate analysis revealed more consistency with subgroups suggested by DAPC analysis. Our results clearly revealed the broad genetic base of TGx (Tropical Glycine max) lines that soybean breeders may select parents for crossing, testing and selection of future cultivars with desirable traits for SSA.

Saved in:
Bibliographic Details
Main Authors: Chander, S., Garcia Oliveira, A.L., Gedil, M., Shah, T., Otusanya, G.O., Asiedu, R., Chigeza, G.
Format: Article biblioteca
Language:English
Published: MDPI 2021
Subjects:AGRICULTURAL SCIENCES AND BIOTECHNOLOGY, Kompetitive Allele Specific PCR, GENETIC DIVERSITY, POPULATION STRUCTURE, SINGLE NUCLEOTIDE POLYMORPHISM, SOYBEANS,
Online Access:https://hdl.handle.net/10883/21806
Tags: Add Tag
No Tags, Be the first to tag this record!
id dig-cimmyt-10883-21806
record_format koha
spelling dig-cimmyt-10883-218062023-01-30T16:32:33Z Genetic diversity and population structure of soybean lines adapted to Sub-Saharan Africa using single nucleotide polymorphism (SNP) markers Chander, S. Garcia Oliveira, A.L. Gedil, M. Shah, T. Otusanya, G.O. Asiedu, R. Chigeza, G. AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Kompetitive Allele Specific PCR GENETIC DIVERSITY POPULATION STRUCTURE SINGLE NUCLEOTIDE POLYMORPHISM SOYBEANS Soybean productivity in sub-Saharan Africa (SSA) is less than half of the global average yield. To plug the productivity gap, further improvement in grain yield must be attained by enhancing the genetic potential of new cultivars that depends on the genetic diversity of the parents. Hence, our aim was to assess genetic diversity and population structure of elite soybean genotypes, mainly released cultivars and advanced selections in SSA. In this study, a set of 165 lines was genotyped with high-throughput single nucleotide polymorphism (SNP) markers covering the complete genome of soybean. The genetic diversity (0.414) was high considering the bi-allelic nature of SNP markers. The polymorphic information content (PIC) varied from 0.079 to 0.375, with an average of 0.324 and about 49% of the markers had a PIC value above 0.350. Cluster analysis grouped all the genotypes into three major clusters. The model-based STRUCTURE and discriminant analysis of principal components (DAPC) exhibited high consistency in the allocation of lines in subpopulations or groups. Nonetheless, they presented some discrepancy and identified the presence of six and five subpopulations or groups, respectively. Principal coordinate analysis revealed more consistency with subgroups suggested by DAPC analysis. Our results clearly revealed the broad genetic base of TGx (Tropical Glycine max) lines that soybean breeders may select parents for crossing, testing and selection of future cultivars with desirable traits for SSA. 2022-01-11T01:10:20Z 2022-01-11T01:10:20Z 2021 Article Published Version https://hdl.handle.net/10883/21806 10.3390/agronomy11030604 English http://bms.iita.org:48080/ibpworkbench/main https://www.mdpi.com/2073-4395/11/3/604#supplementary CIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact CIMMYT-Knowledge-Center@cgiar.org indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose Open Access Basel (Switzerland) MDPI 3 11 2073-4395 Agronomy 604
institution CIMMYT
collection DSpace
country México
countrycode MX
component Bibliográfico
access En linea
databasecode dig-cimmyt
tag biblioteca
region America del Norte
libraryname CIMMYT Library
language English
topic AGRICULTURAL SCIENCES AND BIOTECHNOLOGY
Kompetitive Allele Specific PCR
GENETIC DIVERSITY
POPULATION STRUCTURE
SINGLE NUCLEOTIDE POLYMORPHISM
SOYBEANS
AGRICULTURAL SCIENCES AND BIOTECHNOLOGY
Kompetitive Allele Specific PCR
GENETIC DIVERSITY
POPULATION STRUCTURE
SINGLE NUCLEOTIDE POLYMORPHISM
SOYBEANS
spellingShingle AGRICULTURAL SCIENCES AND BIOTECHNOLOGY
Kompetitive Allele Specific PCR
GENETIC DIVERSITY
POPULATION STRUCTURE
SINGLE NUCLEOTIDE POLYMORPHISM
SOYBEANS
AGRICULTURAL SCIENCES AND BIOTECHNOLOGY
Kompetitive Allele Specific PCR
GENETIC DIVERSITY
POPULATION STRUCTURE
SINGLE NUCLEOTIDE POLYMORPHISM
SOYBEANS
Chander, S.
Garcia Oliveira, A.L.
Gedil, M.
Shah, T.
Otusanya, G.O.
Asiedu, R.
Chigeza, G.
Genetic diversity and population structure of soybean lines adapted to Sub-Saharan Africa using single nucleotide polymorphism (SNP) markers
description Soybean productivity in sub-Saharan Africa (SSA) is less than half of the global average yield. To plug the productivity gap, further improvement in grain yield must be attained by enhancing the genetic potential of new cultivars that depends on the genetic diversity of the parents. Hence, our aim was to assess genetic diversity and population structure of elite soybean genotypes, mainly released cultivars and advanced selections in SSA. In this study, a set of 165 lines was genotyped with high-throughput single nucleotide polymorphism (SNP) markers covering the complete genome of soybean. The genetic diversity (0.414) was high considering the bi-allelic nature of SNP markers. The polymorphic information content (PIC) varied from 0.079 to 0.375, with an average of 0.324 and about 49% of the markers had a PIC value above 0.350. Cluster analysis grouped all the genotypes into three major clusters. The model-based STRUCTURE and discriminant analysis of principal components (DAPC) exhibited high consistency in the allocation of lines in subpopulations or groups. Nonetheless, they presented some discrepancy and identified the presence of six and five subpopulations or groups, respectively. Principal coordinate analysis revealed more consistency with subgroups suggested by DAPC analysis. Our results clearly revealed the broad genetic base of TGx (Tropical Glycine max) lines that soybean breeders may select parents for crossing, testing and selection of future cultivars with desirable traits for SSA.
format Article
topic_facet AGRICULTURAL SCIENCES AND BIOTECHNOLOGY
Kompetitive Allele Specific PCR
GENETIC DIVERSITY
POPULATION STRUCTURE
SINGLE NUCLEOTIDE POLYMORPHISM
SOYBEANS
author Chander, S.
Garcia Oliveira, A.L.
Gedil, M.
Shah, T.
Otusanya, G.O.
Asiedu, R.
Chigeza, G.
author_facet Chander, S.
Garcia Oliveira, A.L.
Gedil, M.
Shah, T.
Otusanya, G.O.
Asiedu, R.
Chigeza, G.
author_sort Chander, S.
title Genetic diversity and population structure of soybean lines adapted to Sub-Saharan Africa using single nucleotide polymorphism (SNP) markers
title_short Genetic diversity and population structure of soybean lines adapted to Sub-Saharan Africa using single nucleotide polymorphism (SNP) markers
title_full Genetic diversity and population structure of soybean lines adapted to Sub-Saharan Africa using single nucleotide polymorphism (SNP) markers
title_fullStr Genetic diversity and population structure of soybean lines adapted to Sub-Saharan Africa using single nucleotide polymorphism (SNP) markers
title_full_unstemmed Genetic diversity and population structure of soybean lines adapted to Sub-Saharan Africa using single nucleotide polymorphism (SNP) markers
title_sort genetic diversity and population structure of soybean lines adapted to sub-saharan africa using single nucleotide polymorphism (snp) markers
publisher MDPI
publishDate 2021
url https://hdl.handle.net/10883/21806
work_keys_str_mv AT chanders geneticdiversityandpopulationstructureofsoybeanlinesadaptedtosubsaharanafricausingsinglenucleotidepolymorphismsnpmarkers
AT garciaoliveiraal geneticdiversityandpopulationstructureofsoybeanlinesadaptedtosubsaharanafricausingsinglenucleotidepolymorphismsnpmarkers
AT gedilm geneticdiversityandpopulationstructureofsoybeanlinesadaptedtosubsaharanafricausingsinglenucleotidepolymorphismsnpmarkers
AT shaht geneticdiversityandpopulationstructureofsoybeanlinesadaptedtosubsaharanafricausingsinglenucleotidepolymorphismsnpmarkers
AT otusanyago geneticdiversityandpopulationstructureofsoybeanlinesadaptedtosubsaharanafricausingsinglenucleotidepolymorphismsnpmarkers
AT asiedur geneticdiversityandpopulationstructureofsoybeanlinesadaptedtosubsaharanafricausingsinglenucleotidepolymorphismsnpmarkers
AT chigezag geneticdiversityandpopulationstructureofsoybeanlinesadaptedtosubsaharanafricausingsinglenucleotidepolymorphismsnpmarkers
_version_ 1756515231921602560