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

Muluken Enyew,Tileye Feyissa,Kassahun Tesfaye,Anders S Carlsson,Mulatu Geleta,Cecilia Hammenhag

doi:10.3389/fpls.2021.799482

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.

Highlights

Sorghum [Sorghum bicolor (L.) Moench] is the fifth most important cereal crop in the world next to maize, rice, wheat, and barley in terms of both production and harvested area (FAOSTAT, 2019)
Na = Number of different alleles; Ne = effective number of alleles; I = Shannon’s information index; Ho = observed heterozygosity; He = expected heterozygosity; uHe = unbiased expected heterozygosity; F = fixation index; PPL = percent polymorphic loci; NPA = number of private alleles; NLCA = number of locally common alleles found in 25% or fewer accessions or group of accessions
The present study showed that the genetic diversity of Ethiopian sorghum landrace accessions was more structured along the geographical regions than along the administrative regions or agro-ecological zones

Summary

Introduction

Sorghum [Sorghum bicolor (L.) Moench] is the fifth most important cereal crop in the world next to maize, rice, wheat, and barley in terms of both production and harvested area (FAOSTAT, 2019). It is a major food crop for more than 500 million people across Africa, Asia, and Latin America, for those in the semi-arid tropical regions (Ejeta, 2005). It is grown in drought-prone areas where several other crops cannot reliably grow. In Africa, sorghum is the second most widely cultivated cereal crop, only surpassed by maize (FAOSTAT, 2019)

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