Genotyping‐by‐Sequencing Analysis for Determining Population Structure of Finger Millet Germplasm of Diverse Origins

Abstract

Finger millet [Eleusine coracana (L.) Gaertn.] is grown mainly by subsistence farmers in arid and semiarid regions of the world. To broaden its genetic base and to boost its production, it is of paramount importance to characterize and genotype the diverse gene pool of this important food and nutritional security crop. However, as a result of nonavailability of the genome sequence of finger millet, the progress could not be made in realizing the molecular basis of unique qualities of the crop. In the present investigation, attempts have been made to characterize the genetically diverse collection of 113 finger millet accessions through whole-genome genotyping-by-sequencing (GBS), which resulted in a genome-wide set of 23,000 single-nucleotide polymorphisms (SNPs) segregating across the entire collection and several thousand SNPs segregating within every accession. A model-based population structure analysis reveals the presence of three subpopulations among the finger millet accessions, which are in parallel with the results of phylogenetic analysis. The observed population structure is consistent with the hypothesis that finger millet was domesticated first in Africa, and from there it was introduced to India some 3000 yr ago. A total of 1128 gene ontology (GO) terms were assigned to SNP-carrying genes for three main categories: biological process, cellular component, and molecular function. Facilitated access to high-throughput genotyping and sequencing technologies are likely to improve the breeding process in developing countries, and as such, this data will be very useful to breeders who are working for the genetic improvement of finger millet. The genus Eleusine comprises 10 annual or perennial grasses growing commonly in the warm regions of the old world particularly in South Asia and eastern and central Africa. Finger millet (2n = 4x = 36), subsp. coracana, belongs to the family Poaceae, genus Eleusine in the tribe Eragrostideae. It is believed that Ethiopia or a neighboring region (Uganda) is the center of origin of finger millet, but in India, it was introduced probably over 3000 yr ago. The crop is grown mainly by subsistence farmers and serves as a food security crop because of high nutritional value and excellent storage qualities (Dida et al., 2007). Calcium content in Finger millet grains apparently can be 5 to 30 times more than in most cereals. Grain calcium contents as high as 450 mg 100 Abbreviations: GBS, genotyping-by-sequencing; GO, gene ontology; MAF, minimum allele frequency; MDS, multidimensional scaling; PCA, principal components analysis; SNP, single-nucleotide polymorphism. Core Ideas• GBS analysis generated 33 GB of data with 160 million raw reads.• Population structure analysis revealed three subpopulations among the finger millet accessions.• A total of 1128 GO terms were assigned to SNP carrying genes.• GBS analysis would be useful for future markerassisted breeding applications.

Calcium Biofortification: Three Pronged Molecular Approaches for Dissecting Complex Trait of Calcium Nutrition in Finger Millet (Eleusine coracana) for Devising Strategies of Enrichment of Food Crops

“…Further, the crop is productive in wide range of environments and growing conditions from Karnataka in South India to foothills and middle hills of Himalayas in North India and Nepal, and throughout the middle-elevation areas of Eastern and Southern Africa (Kumar et al, 2016). Finger millet being a promising source of micronutrients and protein (Malleshi and Klopfenstein, 1998), can play a significant role in alleviation of micronutrient and protein malnutrition, which affects more than one half of the world’s population, especially women and preschool children in most countries of South-east Asia and Africa (Underwood, 2000).…”

“…Recently, an effort has been also made to study the genetic make of diverse world finger millet collection and population structure analysis of 113 finger millet accessions using genotyping by sequencing (GBS) (Kumar et al, 2016). This resulted in a genome wide set of 23000 Single Nucleotide Polymorphisms (SNPs) segregating across the entire collection and several thousand SNPs segregating within every accession.…”

Gene Discovery and Advances in Finger Millet [Eleusine coracana (L.) Gaertn.] Genomics—An Important Nutri-Cereal of Future

“…Kumar et al (2016b) identified 23,000 SNPs through genotyping by sequencing (GBS) of 113 diverse finger millet genotypes. Similarly, 23285 SNPs were generated using next-generation sequencing of two cultivated finger millet genotypes, and 92 SNP markers were validated further for genetic diversity in cultivated and wild species of finger millet (Gimode et al, 2016).…”

“…Single nucleotide polymorphism (SNP) in candidate genes, therefore, remains a possible cause of variation in grain calcium contents among finger millet genotypes. Hence, a step forward toward GBS analysis of finger millet genotypes for identification of high density SNP markers linked to grain calcium content was recently taken up by Kumar et al (2016b), and 23,000 SNPs were identified from 33 GB of sequencing data. In future, these SNPs could be further analyzed to identify useful marker(s) associated with grain calcium and protein content.…”

“…Recently, population structure analysis using the SNPs showed three distinctive clusters of accessions, and the population subgroups corresponded largely to geographic regions of accessions with some notable exceptions (Kumar et al, 2016b). Thus, based on structure analysis using molecular markers, clearly finger millet gene pool has 2–4 sub-populations where the Indian and exotic genotypes are separated in different sub-populations with few exceptions, and Eleusine coracana subsp.…”