Genomic diversity in pearl millet inbred lines derived from landraces and improved varieties

Kanfany, G and Serba, D D and Rhodes, D and St. Amand, P and Bernardo, A and Gangashetty, P I and Kane, N A and Bai, G (2020) Genomic diversity in pearl millet inbred lines derived from landraces and improved varieties. BMC Genomics (TSI), 21 (1). pp. 1-12. ISSN 1471-2164

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Abstract

Background: Genetic improvement of pearl millet is lagging behind most of the major crops. Development of genomic resources is expected to expedite breeding for improved agronomic traits, stress tolerance, yield, and nutritional quality. Genotyping a breeding population with high throughput markers enables exploration of genetic diversity, population structure, and linkage disequilibrium (LD) which are important preludes for marker-trait association studies and application of genomic-assisted breeding. Results: Genotyping-by-sequencing (GBS) libraries of 309 inbred lines derived from landraces and improved varieties from Africa and India generated 54,770 high quality single nucleotide polymorphism (SNP) markers. On average one SNP per 29 Kb was mapped in the reference genome, with the telomeric regions more densely mapped than the pericentromeric regions of the chromosomes. Population structure analysis using 30,208 SNPs evenly distributed in the genome divided 309 accessions into five subpopulations with different levels of admixture. Pairwise genetic distance (GD) between accessions varied from 0.09 to 0.33 with the average distance of 0.28. Rapid LD decay implied low tendency of markers inherited together. Genetic differentiation estimates were the highest between subgroups 4 and 5, and the lowest between subgroups 1 and 2. Conclusions: Population genomic analysis of pearl millet inbred lines derived from diverse geographic and agroecological features identified five subgroups mostly following pedigree differences with different levels of admixture. It also revealed the prevalence of high genetic diversity in pearl millet, which is very useful in defining heterotic groups for hybrid breeding, trait mapping, and holds promise for improving pearl millet for yield and nutritional quality. The short LD decay observed suggests an absence of persistent haplotype blocks in pearl millet. The diverse genetic background of these lines and their low LD make this set of germplasm useful for traits mapping.

Item Type:	Article
Divisions:	Research Program : West & Central Africa
CRP:	UNSPECIFIED
Uncontrolled Keywords:	Genetic diversity, Population structure, Pennisetum glaucum, Cenchrus americanus, Genotyping-bysequencing, SNPs, Linkage disequilibrium
Subjects:	Others > Plant Breeding Mandate crops > Millets > Pearl Millet Others > Genetics and Genomics
Depositing User:	Mr Arun S
Date Deposited:	26 Mar 2021 03:51
Last Modified:	26 Mar 2021 03:53
URI:	http://oar.icrisat.org/id/eprint/11764
Official URL:	https://doi.org/10.1186/s12864-020-06796-4
Projects:	UNSPECIFIED
Funders:	United States Department of Agriculture Foreign Agricultural Service
Acknowledgement:	Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by any part herein. This is contribution number 20-185-J from the Kansas Agricultural Experiment Station.
Links:	Google Scholar

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