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

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.

Molecular Characterization and Genetic Diversity Analysis of Released Hybrids and Varieties of Pearl Millet [Pennisetum glaucum (L.) R. Br.]

“…Similar results regarding effectiveness of SSR markers in monitoring genetic diversity have also been reported by other investigators [12,15,27,[29][30][31]. Several reports have been observed on estimation of genetic diversity among parental lines of pearl millet on the basis of molecular profiling [14,15,16,11,17,27]. But, this study is the first report on molecular characterization and genetic diversity analysis of hybrids and varieties which will provide molecular database for the existing hybrids and varieties and will be helpful for developing genomic studies and DNA fingerprinting for pearl millet hybrids and varieties.…”

“…It has been proved that SSRs can be suitable and efficient tool for molecular characterization of many plant species including pearl millet. Similarly, clustering between genotypes of pearl millet based on molecular markers was also recorded in other studies [11,17,[44][45][46].…”

“…Thus, molecular markers put forward significant advantages over morphological markers for assessment of genetic diversity. Since past several years, various molecular markers were used to analyze genetic diversity among different cultivars and land races of pearl millet [12][13][14][15][16][17].…”

“…After this, several molecular makers including RFLPs, Sequence Tagged Sites (STSs), Amplified Fragment Length Polymorphism (AFLPs), genomic SSRs, Single-Strand Conformation Polymorphism (SSCPS) and genic SSRs were developed and applied in pearl millet improvement studies [14]. Later, high throughput platforms like Diversity Arrays Technology (DArT) [14], Genotyping-by-sequencing (GBS) [17], Single Nucleotide Polymorphism (SNPs) [18] were developed and used for profiling genome-wide nucleotide variations in pearl millet. Although nowadays, Next Generation Sequencing (NGS)-based single-nucleotide polymorphisms have become the marker of choice but still SSRs seem to be largely useful for estimating diversity, defining heterotic groups and DNA fingerprinting.…”

Identifying Anti-Oxidant Biosynthesis Genes in Pearl Millet [Pennisetum glaucum (L.) R. Br.] Using Genome—Wide Association Analysis

“…Interestingly, our results corroborate with earlier studies; for example, Sehgal et al (2015) reported that there were six subpopulations within these PMiGAP by using 345 entries of the PMiGAP and 37 SSR markers. Similarly, population genomic analysis was carried out by Kanfany et al (2020) and reported that the pearl millet inbred lines derived from diverse geographic and agroecological features possessed five subgroups mostly following pedigree differences with different levels of admixture. They have also stated that high genetic diversity prevails 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.…”