Genetic structure and diversity of wild sorghum populations (Sorghum spp.) from different eco-geographical regions of Kenya

Genetic Diversity and Population Structure of Sorghum (Sorghum bicolor (L.) Moench) Landraces Using DArTseq-Derived Single-Nucleotide Polymorphism (SNP) Markers

Genetic integrity of an accession should be preserved in the conservation of germplasm. Characterization of diverse germplasm based on a molecular basis enhances its conservation and use in breeding programs. The aim of this study was to assess the genetic diversity of 169 sorghum accessions using a total of 6977 SNP markers. The polymorphic information content of the markers was 0.31 which is considered to be moderately high. Structure analysis using ADMIXTURE program revealed a total of 10 subpopulations. Neighbor-joining tree revealed the presence of six main clusters among these subpopulations whereas in principal component analysis, seven clusters were identified. Cluster analysis grouped most populations depending on source of collection although other accessions originating from the same source were grouped under different clusters. Analysis of molecular variance (AMOVA) revealed 30% and 70% of the variation occurred within and among accessions, respectively. Gene flow within the populations was, however, limited indicating high differentiation within the subpopulation. Observed heterozygosity among accessions varied from 0.03 to 0.06 with a mean of 0.05 since sorghum is a self-pollinating crop. High genetic diversity among the subpopulations can be further explored for superior genes to develop new sorghum varieties.

Variation for Photoperiod and Temperature Sensitivity in the Global Mini Core Collection of Sorghum

Information on photoperiod and temperature sensitivity of sorghum germplasm is important to identify appropriate sources for developing cultivars with a broad adaptation. The sorghum mini core collection consisting of 242 accessions along with three control cultivars were evaluated for days to 50% flowering (DFL) and plant height in two long-day rainy and two short-day post-rainy seasons, and for grain yield and 100-seed weight in the two post-rainy seasons. Differences in DFL and cumulative growing degree days (CGDD) in the rainy and post-rainy seasons were used to classify the accessions for photoperiod and temperature sensitivity. Results revealed 18 mini core landraces as photoperiod and temperature insensitive (PTINS), 205 as photoperiod sensitive and temperature insensitive (PSTINS), and 19 as photoperiod and temperature-sensitive (PTS) sources. The 19 PTS sources and 80 PSTINS sources took less DFL in the long-day rainy seasons than in the short-day post-rainy season indicating their adaptation to the rainy season and a possible different mechanism than that trigger flowering in the short-day sorghums. In all three groups, several accessions with desirable combinations of agronomic traits were identified for use in the breeding programs to develop climate-resilient cultivars and for genomic studies to identify genes responsible for the photoperiod and temperature responses.

The Road to Sorghum Domestication: Evidence From Nucleotide Diversity and Gene Expression Patterns

Native African cereals (sorghum, millets) ensure food security to millions of low-income people from low fertility and drought-prone regions of Africa and Asia. In spite of their agronomic importance, the genetic bases of their phenotype and adaptations are still not well-understood. Here we focus on Sorghum bicolor, which is the fifth cereal worldwide for grain production and constitutes the staple food for around 500 million people. We leverage transcriptomic resources to address the adaptive consequences of the domestication process. Gene expression and nucleotide variability were analyzed in 11 domesticated and nine wild accessions. We documented a downregulation of expression and a reduction of diversity both in nucleotide polymorphism (30%) and gene expression levels (18%) in domesticated sorghum. These findings at the genome-wide level support the occurrence of a global reduction of diversity during the domestication process, although several genes also showed patterns consistent with the action of selection. Nine hundred and forty-nine genes were significantly differentially expressed between wild and domesticated gene pools. Their functional annotation points to metabolic pathways most likely contributing to the sorghum domestication syndrome, such as photosynthesis and auxin metabolism. Coexpression network analyzes revealed 21 clusters of genes sharing similar expression patterns. Four clusters (totaling 2,449 genes) were significantly enriched in differentially expressed genes between the wild and domesticated pools and two were also enriched in domestication and improvement genes previously identified in sorghum. These findings reinforce the evidence that the combined and intricated effects of the domestication and improvement processes do not only affect the behaviors of a few genes but led to a large rewiring of the transcriptome. Overall, these analyzes pave the way toward the identification of key domestication genes valuable for genetic resources characterization and breeding purposes.