Abstract
The eastern Africa region, Ethiopia and its surroundings, is considered as the center of origin and diversity for sorghum, and has contributed to global sorghum genetic improvement. The germplasm from this region harbors enormous genetic variation for various traits but little is known regarding the genetic architecture of most traits. Here, 1425 Ethiopian landrace accessions were phenotyped under field conditions for presence or absence of awns, panicle compactness and shape, panicle exsertion, pericarp color, glume cover, plant height and smut resistance under diverse environmental conditions in Ethiopia. In addition, F1 hybrids obtained from a subset of 1341 accessions crossed to an A1 cytoplasmic male sterile line, ATx623, were scored for fertility/sterility reactions. Subsequently, genotyping-by-sequencing generated a total of 879,407 SNPs from which 72,190 robust SNP markers were selected after stringent quality control (QC). Pairwise distance-based hierarchical clustering identified 11 distinct groups. Of the genotypes assigned to either one of the 11 sub-populations, 65% had high ancestry membership coefficient with the likelihood of more than 0.60 and the remaining 35% represented highly admixed accessions. A genome-wide association study (GWAS) identified loci and SNPs associated with aforementioned traits. GWAS based on compressed mixed linear model (CMLM) identified SNPs with significant association (FDR ≤ 0.05) to the different traits studied. The percentage of total phenotypic variation explained with significant SNPs across traits ranged from 2 to 43%. Candidate genes showing significant association with different traits were identified. The sorghum bHLH transcription factor, ABORTED MICROSPORES was identified as a strong candidate gene conditioning male fertility. Notably, sorghum CLAVATA1 receptor like kinase, known for regulation of plant growth, and the ETHYLENE RESPONSIVE TRANSCRIPTION FACTOR gene RAP2-7, known to suppress transition to flowering, were significantly associated with plant height. In addition, the YELLOW SEED1 like MYB transcription factor and TANNIN1 showed strong association with pericarp color validating previous observations. Overall, the genetic architecture of natural variation representing the complex Ethiopian sorghum germplasm was established. The study contributes to the characterization of genes and alleles controlling agronomic traits, and will serve as a source of markers for molecular breeding.
Highlights
Sorghum [Sorghum bicolor (L.) Moench] is the fifth most important cereal crop following wheat, rice, maize, and barley in both total production and acreage in the world (FAOSTAT, 2018)
The global positioning system (GPS) was not captured at the time of collection but details on locality, agro-climatic information and race classification are included with the phenotype data that have been deposited on Purdue university repository1
Analysis of variance revealed that phenotypic variation due to environment as well as G × E interaction were lower for plant height, with genotypic differences being the primary sources of variation
Summary
Sorghum [Sorghum bicolor (L.) Moench] is the fifth most important cereal crop following wheat, rice, maize, and barley in both total production and acreage in the world (FAOSTAT, 2018). Sorghum is a staple food crop for millions of the most food-insecure poorest people in the semi-arid tropics of Africa, South Asia and Central America (Leff et al, 2004). These regions are often too dry for the cultivation of most of the other important cereal crops. The identification of genomic regions and loci underlying traits of interest in crops were primarily based on evaluation of genetic populations derived from bi-parental crosses This approach has yielded limited genomic resolution and restricted allelic diversity, as only allelic segregates between and among the parents of the particular recombinant progenies can be assayed (Korte and Farlow, 2013)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
