Development of genic-SSR markers and their application in revealing genetic diversity and population structure in an Eastern and North-Eastern Indian collection of Jack (Artocarpus heterophyllus Lam.)

Jack (Artocarpus heterophyllus) is a multi-purpose out-breeding tree species of the family Moraceae. We generated 42,928,887 high-quality expressed sequence reads, assembled them into 89,356 unigenes, and discovered 16,853 unigene-based perfect SSRs in A. heterophyllus. Thirty-eight polymorphic SSRs...

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Autores principales:	Devendra K. Singh, Avinash Pandey, Shashi Bhushan Choudhary, Sudhir Kumar, Kishor U. Tribhuvan, Dwijesh C. Mishra, Jyotika Bhati, Madan Kumar, J.B. Tomar, S.K. Bishnoi, M.A. Mallick, V.P. Bhadana, T.R. Sharma, A. Pattanayak, Binay K. Singh
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	Moraceae Transcriptome Illumina sequencing Molecular markers Genetic variation Ecology QH540-549.5
Acceso en línea:	https://doaj.org/article/519e668bffa3461494f41ef4d905b496
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spelling	oai:doaj.org-article:519e668bffa3461494f41ef4d905b4962021-12-01T04:59:39ZDevelopment of genic-SSR markers and their application in revealing genetic diversity and population structure in an Eastern and North-Eastern Indian collection of Jack (Artocarpus heterophyllus Lam.)1470-160X10.1016/j.ecolind.2021.108143https://doaj.org/article/519e668bffa3461494f41ef4d905b4962021-11-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S1470160X21008086https://doaj.org/toc/1470-160XJack (Artocarpus heterophyllus) is a multi-purpose out-breeding tree species of the family Moraceae. We generated 42,928,887 high-quality expressed sequence reads, assembled them into 89,356 unigenes, and discovered 16,853 unigene-based perfect SSRs in A. heterophyllus. Thirty-eight polymorphic SSRs were used to analyze the genetic diversity and population structure of 224 germplasm accessions of A. heterophyllus constituting three populations from three agro-climatic zones, namely Eastern Plateau and Hills, Middle Gangetic Plain Region, and Eastern Himalayan Region, encompassing five Eastern and North-Eastern states of India. At the 38 SSR loci, we detected 142 alleles with a mean of 3.74 alleles per locus. The PIC values for the loci ranged from 0.25 to 0.69. The maximum genetic diversity was recorded in Eastern Plateau and Hills (I = 0.98, He = 0.52). The ANOVA analysis indicated significantly higher within-population variation (90%) than between populations (10%). The indirect estimation of gene flow (Nm) from PhiPT indicated significant gene flow among all three populations. The population structure analysis showed at least four distinct groups among the three populations with different introgression degrees. The NJ-based clustering grouped the 224 germplasm accessions into three main clusters, each with three sub-clusters. However, we did not observe distinct geographical structure among populations except some clustering among the germplasm accessions of the populations of geographically close locations. The transcriptome dataset and the SSR markers developed in the study would boost the species' molecular characterization, conservation, and specific need-based improvement.Devendra K. SinghAvinash PandeyShashi Bhushan ChoudharySudhir KumarKishor U. TribhuvanDwijesh C. MishraJyotika BhatiMadan KumarJ.B. TomarS.K. BishnoiM.A. MallickV.P. BhadanaT.R. SharmaA. PattanayakBinay K. SinghElsevierarticleMoraceaeTranscriptomeIllumina sequencingMolecular markersGenetic variationEcologyQH540-549.5ENEcological Indicators, Vol 131, Iss , Pp 108143- (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Moraceae Transcriptome Illumina sequencing Molecular markers Genetic variation Ecology QH540-549.5
spellingShingle	Moraceae Transcriptome Illumina sequencing Molecular markers Genetic variation Ecology QH540-549.5 Devendra K. Singh Avinash Pandey Shashi Bhushan Choudhary Sudhir Kumar Kishor U. Tribhuvan Dwijesh C. Mishra Jyotika Bhati Madan Kumar J.B. Tomar S.K. Bishnoi M.A. Mallick V.P. Bhadana T.R. Sharma A. Pattanayak Binay K. Singh Development of genic-SSR markers and their application in revealing genetic diversity and population structure in an Eastern and North-Eastern Indian collection of Jack (Artocarpus heterophyllus Lam.)
description	Jack (Artocarpus heterophyllus) is a multi-purpose out-breeding tree species of the family Moraceae. We generated 42,928,887 high-quality expressed sequence reads, assembled them into 89,356 unigenes, and discovered 16,853 unigene-based perfect SSRs in A. heterophyllus. Thirty-eight polymorphic SSRs were used to analyze the genetic diversity and population structure of 224 germplasm accessions of A. heterophyllus constituting three populations from three agro-climatic zones, namely Eastern Plateau and Hills, Middle Gangetic Plain Region, and Eastern Himalayan Region, encompassing five Eastern and North-Eastern states of India. At the 38 SSR loci, we detected 142 alleles with a mean of 3.74 alleles per locus. The PIC values for the loci ranged from 0.25 to 0.69. The maximum genetic diversity was recorded in Eastern Plateau and Hills (I = 0.98, He = 0.52). The ANOVA analysis indicated significantly higher within-population variation (90%) than between populations (10%). The indirect estimation of gene flow (Nm) from PhiPT indicated significant gene flow among all three populations. The population structure analysis showed at least four distinct groups among the three populations with different introgression degrees. The NJ-based clustering grouped the 224 germplasm accessions into three main clusters, each with three sub-clusters. However, we did not observe distinct geographical structure among populations except some clustering among the germplasm accessions of the populations of geographically close locations. The transcriptome dataset and the SSR markers developed in the study would boost the species' molecular characterization, conservation, and specific need-based improvement.
format	article
author	Devendra K. Singh Avinash Pandey Shashi Bhushan Choudhary Sudhir Kumar Kishor U. Tribhuvan Dwijesh C. Mishra Jyotika Bhati Madan Kumar J.B. Tomar S.K. Bishnoi M.A. Mallick V.P. Bhadana T.R. Sharma A. Pattanayak Binay K. Singh
author_facet	Devendra K. Singh Avinash Pandey Shashi Bhushan Choudhary Sudhir Kumar Kishor U. Tribhuvan Dwijesh C. Mishra Jyotika Bhati Madan Kumar J.B. Tomar S.K. Bishnoi M.A. Mallick V.P. Bhadana T.R. Sharma A. Pattanayak Binay K. Singh
author_sort	Devendra K. Singh
title	Development of genic-SSR markers and their application in revealing genetic diversity and population structure in an Eastern and North-Eastern Indian collection of Jack (Artocarpus heterophyllus Lam.)
title_short	Development of genic-SSR markers and their application in revealing genetic diversity and population structure in an Eastern and North-Eastern Indian collection of Jack (Artocarpus heterophyllus Lam.)
title_full	Development of genic-SSR markers and their application in revealing genetic diversity and population structure in an Eastern and North-Eastern Indian collection of Jack (Artocarpus heterophyllus Lam.)
title_fullStr	Development of genic-SSR markers and their application in revealing genetic diversity and population structure in an Eastern and North-Eastern Indian collection of Jack (Artocarpus heterophyllus Lam.)
title_full_unstemmed	Development of genic-SSR markers and their application in revealing genetic diversity and population structure in an Eastern and North-Eastern Indian collection of Jack (Artocarpus heterophyllus Lam.)
title_sort	development of genic-ssr markers and their application in revealing genetic diversity and population structure in an eastern and north-eastern indian collection of jack (artocarpus heterophyllus lam.)
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/519e668bffa3461494f41ef4d905b496
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Development of genic-SSR markers and their application in revealing genetic diversity and population structure in an Eastern and North-Eastern Indian collection of Jack (Artocarpus heterophyllus Lam.)

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