Genetic Diversity and Population Structure of Tomato (<i>Solanum lycopersicum</i>) from the USDA-GRIN Germplasm Collection

The genetic diversity and population structure of tomato (<i>Solanum lycopersicum</i>) were investigated to support breeding strategies and germplasm conservation. A total of 276 accessions from the USDA-GRIN collection were analyzed using single-nucleotide polymorphisms (SNPs) generated...

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Main Authors: Ibtisam Alatawi, Haizheng Xiong, Hanan Alkabkabi, Kenani Chiwina, Qun Luo, Kai-Shu Ling, Yuejun Qu, Renjie Du, Ainong Shi
Format: Article
Language:English
Published: MDPI AG 2024-12-01
Series:Agronomy
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Online Access:https://www.mdpi.com/2073-4395/15/1/22
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author Ibtisam Alatawi
Haizheng Xiong
Hanan Alkabkabi
Kenani Chiwina
Qun Luo
Kai-Shu Ling
Yuejun Qu
Renjie Du
Ainong Shi
author_facet Ibtisam Alatawi
Haizheng Xiong
Hanan Alkabkabi
Kenani Chiwina
Qun Luo
Kai-Shu Ling
Yuejun Qu
Renjie Du
Ainong Shi
author_sort Ibtisam Alatawi
collection DOAJ
description The genetic diversity and population structure of tomato (<i>Solanum lycopersicum</i>) were investigated to support breeding strategies and germplasm conservation. A total of 276 accessions from the USDA-GRIN collection were analyzed using single-nucleotide polymorphisms (SNPs) generated through genotyping by sequencing (GBS). After stringent filtering, 5162 high-quality polymorphic SNPs were retained for analysis. Population structure analysis revealed three distinct genetic groups (Q1, Q2, and Q3) among the accessions. Accessions from the USA, Asia, and Central and South America were assigned to all three groups, while accessions from Europe and Oceania were predominantly clustered within Q2. Genetic diversity indices, including major allele frequency, heterozygosity, and polymorphism information content (PIC), indicated moderate-to-high levels of genetic variation. These findings provide essential insights into the genetic diversity and population structure of tomato, offering valuable information for breeding programs aimed at improving traits such as yield, stress tolerance, and disease resistance. The results further underscore the role of global germplasm exchange in shaping the genetic landscape of tomato accessions.
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series Agronomy
spelling doaj-art-fd0901965ceb4b909a6fdab2e5cc6fb92025-01-24T13:16:23ZengMDPI AGAgronomy2073-43952024-12-011512210.3390/agronomy15010022Genetic Diversity and Population Structure of Tomato (<i>Solanum lycopersicum</i>) from the USDA-GRIN Germplasm CollectionIbtisam Alatawi0Haizheng Xiong1Hanan Alkabkabi2Kenani Chiwina3Qun Luo4Kai-Shu Ling5Yuejun Qu6Renjie Du7Ainong Shi8Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USADepartment of Horticulture, University of Arkansas, Fayetteville, AR 72701, USADepartment of Horticulture, University of Arkansas, Fayetteville, AR 72701, USADepartment of Horticulture, University of Arkansas, Fayetteville, AR 72701, USADepartment of Horticulture, University of Arkansas, Fayetteville, AR 72701, USAUSDA-ARS, 2700 Savannah Highway, Charleston, SC 29414, USADepartment of Horticulture, University of Arkansas, Fayetteville, AR 72701, USADepartment of Horticulture, University of Arkansas, Fayetteville, AR 72701, USADepartment of Horticulture, University of Arkansas, Fayetteville, AR 72701, USAThe genetic diversity and population structure of tomato (<i>Solanum lycopersicum</i>) were investigated to support breeding strategies and germplasm conservation. A total of 276 accessions from the USDA-GRIN collection were analyzed using single-nucleotide polymorphisms (SNPs) generated through genotyping by sequencing (GBS). After stringent filtering, 5162 high-quality polymorphic SNPs were retained for analysis. Population structure analysis revealed three distinct genetic groups (Q1, Q2, and Q3) among the accessions. Accessions from the USA, Asia, and Central and South America were assigned to all three groups, while accessions from Europe and Oceania were predominantly clustered within Q2. Genetic diversity indices, including major allele frequency, heterozygosity, and polymorphism information content (PIC), indicated moderate-to-high levels of genetic variation. These findings provide essential insights into the genetic diversity and population structure of tomato, offering valuable information for breeding programs aimed at improving traits such as yield, stress tolerance, and disease resistance. The results further underscore the role of global germplasm exchange in shaping the genetic landscape of tomato accessions.https://www.mdpi.com/2073-4395/15/1/22tomato<i>Solanum lycopersicum</i>SNPpopulation structuregenetic diversity
spellingShingle Ibtisam Alatawi
Haizheng Xiong
Hanan Alkabkabi
Kenani Chiwina
Qun Luo
Kai-Shu Ling
Yuejun Qu
Renjie Du
Ainong Shi
Genetic Diversity and Population Structure of Tomato (<i>Solanum lycopersicum</i>) from the USDA-GRIN Germplasm Collection
Agronomy
tomato
<i>Solanum lycopersicum</i>
SNP
population structure
genetic diversity
title Genetic Diversity and Population Structure of Tomato (<i>Solanum lycopersicum</i>) from the USDA-GRIN Germplasm Collection
title_full Genetic Diversity and Population Structure of Tomato (<i>Solanum lycopersicum</i>) from the USDA-GRIN Germplasm Collection
title_fullStr Genetic Diversity and Population Structure of Tomato (<i>Solanum lycopersicum</i>) from the USDA-GRIN Germplasm Collection
title_full_unstemmed Genetic Diversity and Population Structure of Tomato (<i>Solanum lycopersicum</i>) from the USDA-GRIN Germplasm Collection
title_short Genetic Diversity and Population Structure of Tomato (<i>Solanum lycopersicum</i>) from the USDA-GRIN Germplasm Collection
title_sort genetic diversity and population structure of tomato i solanum lycopersicum i from the usda grin germplasm collection
topic tomato
<i>Solanum lycopersicum</i>
SNP
population structure
genetic diversity
url https://www.mdpi.com/2073-4395/15/1/22
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