Novel GBS-Based SNP Markers for Finger Millet and Their Use in Genetic Diversity Analyses

Abstract

Eleusine coracana (L.) Gaertn., commonly known as finger millet, is a multipurpose crop used for food and feed. Genomic tools are required for the characterization of crop gene pools and their genomics-led breeding. High-throughput sequencing-based characterization of finger millet germplasm representing diverse agro-ecologies was considered an effective method for determining its genetic diversity, thereby suggesting potential candidates for breeding. In this study, the genotyping-by-sequencing (GBS) method was used to simultaneously identify novel single nucleotide polymorphism (SNP) markers and genotype 288 finger millet accessions collected from Ethiopia and Zimbabwe. The accessions were characterized at individual and group levels using 5,226 bi-allelic SNPs, with a minimum allele frequency (MAF) of above 0.05, distributed across 2,500 scaffolds of the finger millet reference genome. The polymorphism information content (PIC) of the SNPs was 0.23 on average, and a quarter of them have PIC values over 0.32, making them highly informative. The grouping of the 288 accessions into seven populations based on geographic proximity and the potential for germplasm exchange revealed a narrow range of observed heterozygosity (Ho; 0.09–0.11) and expected heterozygosity (He) that ranged over twofold, from 0.11 to 0.26. Alleles unique to the different groups were also identified, which merit further investigation for their potential association with desirable traits. The analysis of molecular variance (AMOVA) revealed a highly significant genetic differentiation among groups of accessions classified based on the geographic region, country of origin, days to flowering, panicle type, and Al tolerance (p < 0.01). The high genetic differentiation between Ethiopian and Zimbabwean accessions was evident in the AMOVA, cluster, principal coordinate, and population structure analyses. The level of genetic diversity of finger millet accessions varies moderately among locations within Ethiopia, with accessions from the northern region having the lowest level. In the neighbor-joining cluster analysis, most of the improved cultivars included in this study were closely clustered, probably because they were developed using genetically less diverse germplasm and/or selected for similar traits, such as grain yield. The recombination of alleles via crossbreeding genetically distinct accessions from different regions of the two countries can potentially lead to the development of superior cultivars.

Finger millet RNA-seq reveals differential gene expression associated with tolerance to aluminum toxicity and provides novel genomic resources

“…As revealed through cluster and principal component analyses conducted based on randomly selected SNPs as well as SNPs within DEGs, there was high genetic variation among the finger millet genotypes, particularly among the Al-susceptible genotypes. The result is in line with previous SSR and SNP marker based studies on Finger millet (Brhane et al, 2021;Brhane et al, 2022). Despite the small number of samples, the fact that more genetic variation was detected in Alsusceptible genotypes than in Al-tolerant genotypes suggests that there is limited diversity in Al-tolerant finger millet.…”

“…These are accessions 215836 (from Gojjam), 215845 (from Bahir dar), 229722 (from Metekel), 212462 (from Hararge), 215804 (from Wellega), and 238323 (from Tigray). They were selected for sampling their representative genotypes based on the results of a preliminary hydroponic experiment, which was carried out as described in (Brhane et al, 2022). The results showed that the first three accessions (215836, 215845, and 229722) could be regarded as Al-tolerant whereas, the other three (212462, 215804, and 238323) are Al-susceptible.…”

“…For this study, the germination of the seeds sampled from the selected accessions followed by the exposure of their seedlings to Al-toxicity was carried out as described in Brhane et al (2022). After germination, the seedlings were transferred to a nutrient solution containing 500 mM KNO 3 , 500 mM CaCl 2 , 500 mM NH 4 NO 3 , 150 mM MgSO 4 .7H 2 O, 10 mM KH 2 PO 4 , 2 mM FeCl 3 , and 100 mM Al 2 (SO 4 ) 3 .18H 2 O, which was prepared according to Zhou et al (2013).…”

“…Transcriptome sequencing generates a large amount of sequence data, which can be used as a source of SSRs to enrich genomic resources of crops for various applications. SNPs are the most recent and popular codominant markers extensively used for diversity analysis, genomewide association studies, and genetic linkage mapping in various crops including finger millet (Enyew et al, 2021;Brhane et al, 2022). By utilizing high-throughput sequencing technology, RNAseq provides a platform for the development and utilization of SSRs and SNPs for species lacking genomic information at a fast, accurate, and affordable scale.…”

Development of a new AgriSeq 4K mid-density SNP genotyping panel and its utility in pearl millet breeding

“…While comparing the genetic differentiation, rice showed PhiPT value of 0.130 between the indica and japonica groups ( Luong et al., 2021 ), and the Ethiopian sorghum group showed 0.252 between B- and R-lines ( Mindaye et al., 2015 ). Finger millet revealed a moderate genetic differentiation (Fst = 0.352) among seven population sub-groups ( Brhane et al., 2022 ). Pearl millet demonstrated genetic differentiation at a PhiPT value of 0.130 for the chosen genotypes, similar to those studies.…”