Population Genomics And Genome-Wide Association Study Of Major Agro-Morphological Traits Of Tef (Eragrostis Tef) Accessions From Ethiopia

Eragrostis tef is one of the most widely grown cereal crop with significant agricultural importance in Ethiopia and gaining global popularity due to its gluten-free property.Genomic information such as genome-scale SNPs polymorphism and high-resolution molecular markers are powerful methods for unraveling genetic basis of phenotypic variations.However,the application of such molecular tools for breeding and conservation of these species is extremely limited.Therefore,the main objective of this study was to identify genome-wide DNA polymorphism and determine candidate genes for agronomic traits using genome-wide associations study(GWAS).To achieve this,we analyzed the data from agro-morphological,complete plastomes and whole-genome resequencing of E.tef accessions collected from Ethiopia.In this study,we assembled and compared the complete chloroplast genomes of 32 E.tef accessions.The size of the chloroplast genomes ranged from 134,349 to 134,437 bp with similar GC content(~ 38.3%).Genomes annotations revealed 112 individual genes,including 77 Protein-coding,31 tRNA,and four rRNA genes.Comparison among E.tef chloroplast genome revealed a low degree of intraspecific sequence variations and no structural differentiations.We found 34(13 cpSSRs,12 InDels,and nine SNPs)polymorphic sites that can be used as valuable DNA barcodes.The majority(88%)of the polymorphic sites were identified in the noncoding genomic regions,remaining were found in the gene coding regions.Nonsynonymous(ka)and synonymous(ks)substitution analysis showed that all PCGs were under purifying selection(ka/ks < 1).The phylogenetic analysis of the whole chloroplast genome and polymorphic region sequence was able to distinguish the accession from the southern population based on their geographical location,indicating its potential to use as a super-barcode.Agro-morphological traits of 121 accessions were evaluated under two agro-ecology and analyzed using cluster and principal components analysis(PCA).The PCA of accessions was able to determine the traits contributing to the total variation in the population.Cluster analysis provides useful pre-breeding information to assist genotype selection with desirable traits in crop improvement programs.However,the accessions grouping did not in line with accession geographic origin.Mean summary statistics have shown large degree of phenotypic variations in the samples and used in subsequent analysis.Whole-genome resequencing of 93 E.tef accessions was performed,allowing genome wide SNPs discover for population and evolutionary study.After trimming and filtering,5,633,228,310(98.75%)clean reads were produced,with an average of 60.20 million clean reads per accessions.A total of 1,379,234 DNA variants was discovered in the E.tef genome.The most common variant is SNPs that make up 1,154,793(83.72%)of the total followed by 113,615(8.23%)Deletions and 110,826(8%)insertions.We found that the distribution of variants in the chromosome was nonrandom and correlated with the size of the chromosome.Our study also analyzed genetic diversity,population structure and phylogenetic relationships using detected SNPs.Our results showed indistinct and low mean nucleotide diversity among E.tef the accessions.The mean nucleotide diversity(?)of total sites was 0.002 for the whole genome of E.tef accessions.FST values for E.tef sub-populations generally range from –0.001 to 0.007,suggesting poor differentiation among the sub-populations.Phylogenetic relatedness of the accessions was not consistent with their biogeographic distribution,indicating E.tef frequent seed exchange among geographical boundaries.However,the tree has able to provide relatedness among accessions from sub-populations four and partly showing the geographic pattern.Genome-wide association studies were performed to identify candidate genes that controlling agronomic traits in E.tef.Using twelve agro-morphological traits and high-density SNPs markers was used to assess trait-marker associations.The genomic region associated with yield related traits such biomass,seed weight and grain yield were identified.Five significantly associated SNPs were detected for the days to heading on chromosomes one and two.For plant height,the significance threshold level exceeds the P-values in chromosomes two,six,and seven.Furthermore,significant traits-SNPs association were detected on more than one chromosomal locations for all studied traits.Overall,the results of the present study shed light on the genetic architecture of E.tef and provide a baseline for future evolutionary studies and molecular breeding.