Identification of a Diverse Core Set Panel of Rice From the East Coast Region of India Using SNP Markers

In India, rice (Oryza sativa L.) is cultivated under a variety of climatic conditions. Due to the fragility of the coastal ecosystem, rice farming in these areas has lagged behind. Salinity coupled with floods has added to this trend. Hence, to prevent genetic erosion, conserving and characterizing...

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Autores principales:	Debjani Roy Choudhury, Ramesh Kumar, Vimala Devi S, Kuldeep Singh, N. K. Singh, Rakesh Singh
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	rice SNP markers genetic diversity genotyping SNP coastal rice Genetics QH426-470
Acceso en línea:	https://doaj.org/article/9dea06a2165142ca857b0e355a12edb8
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spelling	oai:doaj.org-article:9dea06a2165142ca857b0e355a12edb82021-12-01T01:17:18ZIdentification of a Diverse Core Set Panel of Rice From the East Coast Region of India Using SNP Markers1664-802110.3389/fgene.2021.726152https://doaj.org/article/9dea06a2165142ca857b0e355a12edb82021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fgene.2021.726152/fullhttps://doaj.org/toc/1664-8021In India, rice (Oryza sativa L.) is cultivated under a variety of climatic conditions. Due to the fragility of the coastal ecosystem, rice farming in these areas has lagged behind. Salinity coupled with floods has added to this trend. Hence, to prevent genetic erosion, conserving and characterizing the coastal rice, is the need of the hour. This work accessed the genetic variation and population structure among 2,242 rice accessions originating from India’s east coast comprising Andhra Pradesh, Orissa, and Tamil Nadu, using 36 SNP markers, and have generated a core set (247 accessions) as well as a mini-core set (30 accessions) of rice germplasm. All the 36 SNP loci were biallelic and 72 alleles found with average two alleles per locus. The genetic relatedness of the total collection was inferred using the un-rooted neighbor-joining tree, which grouped all the genotypes (2,242) into three major clusters. Two groups were obtained with a core set and three groups obtained with a mini core set. The mean PIC value of total collection was 0.24, and those of the core collection and mini core collection were 0.27 and 0.32, respectively. The mean heterozygosity and gene diversity of the overall collection were 0.07 and 0.29, respectively, and the core set and mini core set revealed 0.12 and 0.34, 0.20 and 0.40 values, respectively, representing 99% of distinctiveness in the core and mini core sets. Population structure analysis showed maximum population at K = 4 for total collection and core collection. Accessions were distributed according to their population structure confirmed by PCoA and AMOVA analysis. The identified small and diverse core set panel will be useful in allele mining for biotic and abiotic traits and managing the genetic diversity of the coastal rice collection. Validation of the 36-plex SNP assay was done by comparing the genetic diversity parameters across two different rice core collections, i.e., east coast and northeast rice collection. The same set of SNP markers was found very effective in deciphering diversity at different genetic parameters in both the collections; hence, these marker sets can be utilized for core development and diversity analysis studies.Debjani Roy ChoudhuryRamesh KumarVimala Devi SKuldeep SinghN. K. SinghRakesh SinghFrontiers Media S.A.articlericeSNP markersgenetic diversitygenotypingSNPcoastal riceGeneticsQH426-470ENFrontiers in Genetics, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	rice SNP markers genetic diversity genotyping SNP coastal rice Genetics QH426-470
spellingShingle	rice SNP markers genetic diversity genotyping SNP coastal rice Genetics QH426-470 Debjani Roy Choudhury Ramesh Kumar Vimala Devi S Kuldeep Singh N. K. Singh Rakesh Singh Identification of a Diverse Core Set Panel of Rice From the East Coast Region of India Using SNP Markers
description	In India, rice (Oryza sativa L.) is cultivated under a variety of climatic conditions. Due to the fragility of the coastal ecosystem, rice farming in these areas has lagged behind. Salinity coupled with floods has added to this trend. Hence, to prevent genetic erosion, conserving and characterizing the coastal rice, is the need of the hour. This work accessed the genetic variation and population structure among 2,242 rice accessions originating from India’s east coast comprising Andhra Pradesh, Orissa, and Tamil Nadu, using 36 SNP markers, and have generated a core set (247 accessions) as well as a mini-core set (30 accessions) of rice germplasm. All the 36 SNP loci were biallelic and 72 alleles found with average two alleles per locus. The genetic relatedness of the total collection was inferred using the un-rooted neighbor-joining tree, which grouped all the genotypes (2,242) into three major clusters. Two groups were obtained with a core set and three groups obtained with a mini core set. The mean PIC value of total collection was 0.24, and those of the core collection and mini core collection were 0.27 and 0.32, respectively. The mean heterozygosity and gene diversity of the overall collection were 0.07 and 0.29, respectively, and the core set and mini core set revealed 0.12 and 0.34, 0.20 and 0.40 values, respectively, representing 99% of distinctiveness in the core and mini core sets. Population structure analysis showed maximum population at K = 4 for total collection and core collection. Accessions were distributed according to their population structure confirmed by PCoA and AMOVA analysis. The identified small and diverse core set panel will be useful in allele mining for biotic and abiotic traits and managing the genetic diversity of the coastal rice collection. Validation of the 36-plex SNP assay was done by comparing the genetic diversity parameters across two different rice core collections, i.e., east coast and northeast rice collection. The same set of SNP markers was found very effective in deciphering diversity at different genetic parameters in both the collections; hence, these marker sets can be utilized for core development and diversity analysis studies.
format	article
author	Debjani Roy Choudhury Ramesh Kumar Vimala Devi S Kuldeep Singh N. K. Singh Rakesh Singh
author_facet	Debjani Roy Choudhury Ramesh Kumar Vimala Devi S Kuldeep Singh N. K. Singh Rakesh Singh
author_sort	Debjani Roy Choudhury
title	Identification of a Diverse Core Set Panel of Rice From the East Coast Region of India Using SNP Markers
title_short	Identification of a Diverse Core Set Panel of Rice From the East Coast Region of India Using SNP Markers
title_full	Identification of a Diverse Core Set Panel of Rice From the East Coast Region of India Using SNP Markers
title_fullStr	Identification of a Diverse Core Set Panel of Rice From the East Coast Region of India Using SNP Markers
title_full_unstemmed	Identification of a Diverse Core Set Panel of Rice From the East Coast Region of India Using SNP Markers
title_sort	identification of a diverse core set panel of rice from the east coast region of india using snp markers
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/9dea06a2165142ca857b0e355a12edb8
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Identification of a Diverse Core Set Panel of Rice From the East Coast Region of India Using SNP Markers

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