Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

Abstract This study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic inf...

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Autores principales:	Grimar Abdiel Perez, Pumipat Tongyoo, Julapark Chunwongse, Hans de Jong, Anucha Wongpraneekul, Waraporn Sinsathapornpong, Paweena Chuenwarin
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/180e3b4e7deb436f810bad05af071023
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spelling	oai:doaj.org-article:180e3b4e7deb436f810bad05af0710232021-12-02T18:47:03ZGenetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers10.1038/s41598-021-94802-42045-2322https://doaj.org/article/180e3b4e7deb436f810bad05af0710232021-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-94802-4https://doaj.org/toc/2045-2322Abstract This study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of F ST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (F IS = − 0.092) and low total fixation index (F IT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.Grimar Abdiel PerezPumipat TongyooJulapark ChunwongseHans de JongAnucha WongpraneekulWaraporn SinsathapornpongPaweena ChuenwarinNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Grimar Abdiel Perez Pumipat Tongyoo Julapark Chunwongse Hans de Jong Anucha Wongpraneekul Waraporn Sinsathapornpong Paweena Chuenwarin Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers
description	Abstract This study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of F ST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (F IS = − 0.092) and low total fixation index (F IT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.
format	article
author	Grimar Abdiel Perez Pumipat Tongyoo Julapark Chunwongse Hans de Jong Anucha Wongpraneekul Waraporn Sinsathapornpong Paweena Chuenwarin
author_facet	Grimar Abdiel Perez Pumipat Tongyoo Julapark Chunwongse Hans de Jong Anucha Wongpraneekul Waraporn Sinsathapornpong Paweena Chuenwarin
author_sort	Grimar Abdiel Perez
title	Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers
title_short	Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers
title_full	Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers
title_fullStr	Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers
title_full_unstemmed	Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers
title_sort	genetic diversity and population structure of ridge gourd (luffa acutangula) accessions in a thailand collection using snp markers
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/180e3b4e7deb436f810bad05af071023
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Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

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