Genetic Diversity and Population Structure of Sorghum [Sorghum Bicolor (L.) Moench] Accessions as Revealed by Single Nucleotide Polymorphism Markers

Abstract

Ethiopia is the center of origin for sorghum [Sorghum bicolor (L.) Moench], where the distinct agro-ecological zones significantly contributed to the genetic diversity of the crops. A large number of sorghum landrace accessions have been conserved ex situ. Molecular characterization of this diverse germplasm can contribute to its efficient conservation and utilization in the breeding programs. This study aimed to investigate the genetic diversity of Ethiopian sorghum using gene-based single nucleotide polymorphism (SNP) markers. In total, 359 individuals representing 24 landrace accessions were genotyped using 3,001 SNP markers. The SNP markers had moderately high polymorphism information content (PIC = 0.24) and gene diversity (H = 0.29), on average. This study revealed 48 SNP loci that were significantly deviated from Hardy–Weinberg equilibrium with excess heterozygosity and 13 loci presumed to be under selection (P < 0.01). The analysis of molecular variance (AMOVA) determined that 35.5% of the total variation occurred within and 64.5% among the accessions. Similarly, significant differentiations were observed among geographic regions and peduncle shape-based groups. In the latter case, accessions with bent peduncles had higher genetic variation than those with erect peduncles. More alleles that are private were found in the eastern region than in the other regions of the country, suggesting a good in situ conservation status in the east. Cluster, principal coordinates (PCoA), and STRUCTURE analyses revealed distinct accession clusters. Hence, crossbreeding genotypes from different clusters and evaluating their progenies for desirable traits is advantageous. The exceptionally high heterozygosity observed in accession SB4 and SB21 from the western geographic region is an intriguing finding of this study, which merits further investigation.

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

“…According to the result of site-frequency spectrum analysis, there is substantial genetic diversity among the seven finger millet populations, as evidenced by variation in minor allele frequency distributions between them. However, individual accessions in different populations generally bear minor alleles at fewer loci compared to results obtained in a similar study in sorghum ( Enyew et al, 2021 ). More than 50% of individuals in Pop-5 and over 20% of individuals in Pop-6 had minor alleles in at least 10% of the SNP loci, as opposed to the other populations with minor alleles in less than 8% of the loci.…”

“…In line with the expectation, the mean He value (0.28) was higher than the mean Ho value (0.10) in the present study. A recent study in sorghum (a self-pollinating cereal crop) using 3001 SNP markers reported mean He and Ho values of 0.10 and 0.06 ( Enyew et al, 2021 ). The lower values in the latter case are most likely because most of the SNP markers used were located within genes ( Enyew et al, 2021 ) and hence are expected to be less diverse than GBS-based SNP markers.…”

“…A recent study in sorghum (a self-pollinating cereal crop) using 3001 SNP markers reported mean He and Ho values of 0.10 and 0.06 ( Enyew et al, 2021 ). The lower values in the latter case are most likely because most of the SNP markers used were located within genes ( Enyew et al, 2021 ) and hence are expected to be less diverse than GBS-based SNP markers. Similar bi-allelic SNP-based studies in noug ( Guizotia abyssinica ; Tsehay et al, 2020 ) and red clover ( Trifolium pratense ; Osterman et al, 2021 ) reported Ho values of 0.24 and 0.22, respectively.…”

Genome-wide identification and expression analysis of the U-box E3 ubiquitin ligase gene family related to salt tolerance in sorghum (Sorghum bicolor L.)

“…Sorghum (Sorghum bicolor L.) is the fth most important crop in the world; it originated in Africa and is the most widely utilized C4 model crop [27][28][29]. In addition, sorghum is one of the most important food crops worldwide, especially in developing countries and areas with more drought and salinity [30,31].…”

DeepVariant calling provides insights into race diversity and its implication for sorghum breeding

“…Such variations range from single nucleotides to large-scale structural variations. However, most studies in the past have only used single nucleotide variations (Afolayan et al ., 2019; Enyew et al ., 2022) ignoring other structural variations such as insertion-deletions (indels) and presence-absence variations (PAV) (Saxena et al ., 2014). PAVs are present in some individuals but absent in others, making them perfect for detecting major differences among multiple genomes.…”