Kinhoegbè, G and Djèdatin, G and Saxena, R K and Chitikineni, A and Bajaj, P and Molla, J and Agbangla, C and Dansi, A and Varshney, R K (2022) Genetic diversity and population structure of pigeonpea (Cajanus cajan [L.] Millspaugh) landraces grown in Benin revealed by Genotyping-By-Sequencing. PLoS ONE (TSI), 17. pp. 1-14. ISSN 1932-6203
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Abstract
Genetic diversity studies provide important details on target trait availability and its variability, for the success of breeding programs. In this study, GBS approach was used to reveal a new structuration of genetic diversity and population structure of pigeonpea in Benin. We used a total of 688 high-quality Single Nucleotide Polymorphism markers for a total of 44 pigeonpea genotypes. The distribution of SNP markers on the 11 chromosomes ranged from 14 on chromosome 5 to 133 on chromosome 2. The Polymorphism Information Content and gene diversity values were 0.30 and 0.34 respectively. The analysis of population structure revealed four clear subpopulations. The Weighted Neighbor Joining tree agreed with structure analyses by grouping the 44 genotypes into four clusters. The PCoA revealed that genotypes from subpopulations 1, 2 and 3 intermixed among themselves. The Analysis of Molecular Variance showed 7% of the total variation among genotypes while the rest of variation (93%) was within genotypes from subpopulations indicating a high gene exchange (Nm = 7.13) and low genetic differentiation (PhiPT = 0.07) between subpopulations. Subpopulation 2 presented the highest mean values of number of different alleles (Na = 1.57), number of loci with private alleles (Pa = 0.11) and the percentage of polymorphic loci (P = 57.12%). We discuss our findings and demonstrate how the genetic diversity and the population structure of this specie can be used through the Genome Wide Association Studies and Marker-Assisted Selection to enhance genetic gain in pigeonpea breeding programs in Benin.
| Item Type: | Article |
|---|---|
| Divisions: | Center of Excellence in Genomics and Systems Biology |
| CRP: | UNSPECIFIED |
| Uncontrolled Keywords: | Population genetics, Single nucleotide polymorphisms, Genetic polymorphism, Alleles, Conservation genetics, Benin, Species diversity, Variant genotypes |
| Subjects: | Mandate crops > Pigeonpea Others > Genetics and Genomics |
| Depositing User: | Mr Nagaraju T |
| Date Deposited: | 16 Jan 2024 03:42 |
| Last Modified: | 16 Jan 2024 03:42 |
| URI: | http://oar.icrisat.org/id/eprint/12359 |
| Official URL: | https://journals.plos.org/plosone/article?id=10.13... |
| Projects: | UNSPECIFIED |
| Funders: | UNSPECIFIED |
| Acknowledgement: | The authors are grateful to the Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) of India for their helpful assistance during the study. We thank the anonymous reviewers and editors for their comments on previous versions of the manuscript. We express our sincere gratitude to Doctors Ruth TAMADAHO and Aliu IBUKUN for English Language Editing. Our sincere grateful to Dr Vanika Garg from Murdoch University, Murdoch, Western Australia, Australia for their help when it has been to prepare and to upload Raw sequencing data in NCBI Sequence Read Archive. |
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