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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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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.)
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Creator Singh Devendra K.
Pandey Avinash
Choudhary Shashi Bhushan
Kumar Sudhir
Mishra Dwijesh C.
Bhati Jyotika
Kumar Madan
Tribhuvan Kishor U.,
Tomar J.B.
Bishnoi S.K.
Mallick M.A.
Bhadana V.P.
Sharma T.R.
Pattanayak A.
Singh. Binay K.
 
Subject Moraceae
Transcriptome
Illumina sequencing
Molecular markers
Genetic variation
 
Description Not Available
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.
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Date 2022-04-19T08:33:12Z
2022-04-19T08:33:12Z
2021-11-01
 
Type Research Paper
 
Identifier 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 (2021). 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.), Ecological Indicators, 131, 108143.
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http://krishi.icar.gov.in/jspui/handle/123456789/71631
 
Language English
 
Relation Not Available;
 
Publisher Elsevier