Allan, V and Vetriventhan, M and Senthil, R and Geetha, S and Deshpande, S and Rathore, A and Kumar, V and Singh, P and Reddymalla, S and Azevedo, V C R (2020) Genome-Wide DArTSeq Genotyping and Phenotypic Based Assessment of Within and Among Accessions Diversity and Effective Sample Size in the Diverse Sorghum, Pearl Millet, and Pigeonpea Landraces. Frontiers in Plant Science (TSI), 11 (587426). pp. 1-20. ISSN 1664-462X
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Abstract
Germplasm should be conserved in such a way that the genetic integrity of a given accession is maintained. In most genebanks, landraces constitute a major portion of collections, wherein the extent of genetic diversity within and among landraces of crops vary depending on the extent of outcrossing and selection intensity infused by farmers. In this study, we assessed the level of diversity within and among 108 diverse landraces and wild accessions using both phenotypic and genotypic characterization. This included 36 accessions in each of sorghum, pearl millet, and pigeonpea, conserved at ICRISAT genebank. We genotyped about 15 to 25 individuals within each accession, totaling 1,980 individuals using the DArTSeq approach. This resulted in 45,249, 19,052, and 8,211 high-quality single nucleotide polymorphisms (SNPs) in pearl millet, sorghum, and pigeonpea, respectively. Sorghum had the lowest average phenotypic (0.090) and genotypic (0.135) within accession distances, while pearl millet had the highest average phenotypic (0.227) and genotypic (0.245) distances. Pigeonpea had an average of 0.203 phenotypic and 0.168 genotypic within accession distances. Analysis of molecular variance also confirms the lowest variability within accessions of sorghum (26.3%) and the highest of 80.2% in pearl millet, while an intermediate in pigeonpea (57.0%). The effective sample size required to capture maximum variability and to retain rare alleles while regeneration ranged from 47 to 101 for sorghum, 155 to 203 for pearl millet, and 77 to 89 for pigeonpea accessions. This study will support genebank curators, in understanding the dynamics of population within and among accessions, in devising appropriate germplasm conservation strategies, and aid in their utilization for crop improvement.
| Item Type: | Article |
|---|---|
| Divisions: | Genebank |
| CRP: | UNSPECIFIED |
| Uncontrolled Keywords: | DArTseq, Within accession diversity, Effective population size, Landraces, Pearl millet, Pigeonpea, Regeneration, Sorghum |
| Subjects: | Mandate crops > Millets > Pearl Millet Mandate crops > Pigeonpea Mandate crops > Sorghum Others > Genetics and Genomics |
| Depositing User: | Mr Arun S |
| Date Deposited: | 08 Mar 2021 15:18 |
| Last Modified: | 08 Mar 2021 15:18 |
| URI: | http://oar.icrisat.org/id/eprint/11728 |
| Official URL: | https://doi.org/10.3389/fpls.2020.587426 |
| Projects: | UNSPECIFIED |
| Funders: | Global Crop Diversity Trust (GCDT) |
| Acknowledgement: | We thank Dr. Juan Andres (Biometrics and Statistics Unit Head, CIMMYT, Mexico) for his kind help in AMOVA for the DArTSeq data and Shannon diversity. Also, we extend our thanks to Dr. Jorge Franco (Professor of Biometrics and Statistics, Universidad de la República, Uruguay), Dr. Carolina Paola Sansaloni (High-throughput genotyping and sequencing specialist, CIMMYT, Mexico) and Dr. Fernando Henrique Ribeiro (Associate Scientist-Agricultural Statistics, CIMMYT, Mexico) for their kind support in calculation of genotypic diversity. |
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