Genetic Diversity Patterns and Heterosis Prediction Based on SSRs and SNPs in Hybrid Parents of Pearl Millet

Singh, S and Gupta, S K and Thudi, M and Das, R R and Vemula, A and Garg, V and Varshney, R K and Rathore, A and Pahuja, S K and Yadav, D V (2018) Genetic Diversity Patterns and Heterosis Prediction Based on SSRs and SNPs in Hybrid Parents of Pearl Millet. Crop Science (TSI), 58 (6). pp. 2379-2390. ISSN 0011-183X

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Abstract

The present investigation was performed to assess genetic divergence and heterosis prediction in hybrid parents of pearl millet [Pennisetum glaucum (L.) R Br.] using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. Using 56 SSR loci, 412 alleles were detected in 147 lines with an average of 7.36 alleles per locus, and 75,007 SNP loci were detected in 117 lines. Both SSR- and SNP-based clustering and structure analysis partitioned all maintainer (B) and restorer (R) lines into two clear-cut separate groups, indicating the existence of two diverse gene pools, each representing the seed and restorer parents in pearl millet. Results of analysis of molecular variance and principal coordinate analysis also showed significant diversity between B and R lines. The correlation between parental genetic distances estimated based on SSRs and SNPs was high and significant (r = 0.58, p < .01). Similar clustering pattern of hybrid parents was observed with both marker systems, although the cost of genotyping was 41% less with SNPs than with SSRs, and the ratio of loci detected with SNPs was much higher (1:364 SSR/SNP), hence the use of SNPs is indicated over SSRs for germplasm characterization. A set of 136 hybrids (including all B × B, R × R, and B × R crosses) generated crossing 17 hybrid parents (nine B lines and eight R lines) in half diallel (without reciprocal) fashion, and evaluation at two locations revealed that the correlation between genetic distance and better parent heterosis for grain yield was moderate, positive, and significant (with SSR, 0.33, p < .01; with SNP, 0.35, p < .01), hence both SSRs and SNPs were found comparable in results for heterosis prediction.

Item Type: Article
Divisions: Research Program : Asia
Research Program : Genetic Gains
CRP: CGIAR Research Program on Dryland Cereals
Uncontrolled Keywords: Pearl Millet, SNPs, Hybrid Parents, Heterosis Prediction, SSRs, Genetic Diversity Patterns
Subjects: Others > Plant Genetics
Others > Plant Breeding
Mandate crops > Millets > Pearl Millet
Others > Genetics and Genomics
Depositing User: Mr Ramesh K
Date Deposited: 24 Oct 2018 03:28
Last Modified: 24 Oct 2018 03:28
URI: http://oar.icrisat.org/id/eprint/10911
Official URL: http://dx.doi.org/10.2135/cropsci2018.03.0163
Projects: UNSPECIFIED
Funders: ICRISAT Pearl Millet Hybrid Parent Research Consortium (PMHPRC)
Acknowledgement: The research reported here was financially supported by the ICRISAT Pearl Millet Hybrid Parent Research Consortium (PMHPRC) and was conducted under the CGIAR Research Program on Dryland Cereals.
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