Kandarkar, K and Palaniappan, V and Satpathy, S and Vemula, A K and Rajasekaran, R and Jeyakumar, P and Sevugaperumal, N and Gupta, S K (2024) Understanding genetic diversity in drought-adaptive hybrid parental lines in pearl millet. PLoS ONE (TSI), 19 (2). pp. 1-24. ISSN 1932-6203
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Abstract
Information on genetic diversity and population structure is helpful to strategize enhancing the genetic base of hybrid parental lines in breeding programs. The present study determined the population structure and genetic diversity of 109 pearl millet hybrid parental lines, known for their better adaptation and performance in drought-prone environments, using 16,472 single nucleotide polymorphic (SNP) markers generated from GBS (genotyping-by-sequencing) platforms. The SNPs were distributed uniformly across the pearl millet genome and showed considerable genetic diversity (0.337), expected heterozygosity (0.334), and observed heterozygosity (0.031). Most of the pairs of lines (78.36%) had Identity-by-State (IBS) based genetic distances of more than 0.3, indicating a significant amount of genetic diversity among the parental lines. Bayesian model-based population stratification, neighbor-joining phylogenetic analysis, and principal coordinate analysis (PCoA) differentiated all hybrid parental lines into two clear-cut major groups, one each for seed parents (B-lines) and pollinators (R-lines). Majority of parental lines sharing common parentages were found grouped in the same cluster. Analysis of molecular variance (AMOVA) revealed 7% of the variation among subpopulations, and 93% of the variation was attributable to within sub-populations. Chromosome 3 had the highest number of LD regions. Genomic LD decay distance was 0.69 Mb and varied across the different chromosomes. Genetic diversity based on 11 agro-morphological and grain quality traits also suggested that the majority of the B- and R-lines were grouped into two major clusters with few overlaps. In addition, the combined analysis of phenotypic and genotypic data showed similarities in the population grouping patterns. The present study revealed the uniqueness of most of the inbred lines, which can be a valuable source of new alleles and help breeders to utilize these inbred lines for the development of hybrids in drought-prone environments.
| Item Type: | Article |
|---|---|
| Divisions: | Global Research Program - Accelerated Crop Improvement |
| CRP: | UNSPECIFIED |
| Uncontrolled Keywords: | genetic diversity, drought-adaptive, drought, pearl millet |
| Subjects: | Mandate crops > Millets > Pearl Millet Others > Drought Others > Genetics and Genomics |
| Depositing User: | Mr Nagaraju T |
| Date Deposited: | 14 Mar 2024 10:28 |
| Last Modified: | 14 Mar 2024 10:28 |
| URI: | http://oar.icrisat.org/id/eprint/12584 |
| Official URL: | https://journals.plos.org/plosone/article?id=10.13... |
| Projects: | UNSPECIFIED |
| Funders: | UNSPECIFIED |
| Acknowledgement: | This research work was carried out as part of a Ph.D. thesis by Kuldeep Kandarkar and submitted to Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu. This study was financially supported by the ICRISAT-Pearl Millet Hybrid Parents Research Consortium (PMHPRC) and Sehgal Foundation. We also acknowledge Dr Rajeev Varshney and Annapurna Chitikineni from the ICRISAT-CEG for their assistance in genotyping work. We also thank Dr Dev Vart Yadav (CCHAU, Hisar), Dr R K Solanki (CAZRI, Jodhpur), Dr L.D. Sharma (SKNAU, Jaipur), Dr P.C. Gupta (SKRAU, Bikaner) and Dr Gopal Bele (Hytech seeds, Alwar) for their assistance in the field evaluation. |
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