Enhancements in reproductive cold tolerance of sorghum are essential to expand growing areas into both high-latitude temperate areas and tropical high-altitude environments. Here we present first insights into the genetic architecture of this trait via genome-wide association studies in a broad genetic diversity set (n = 330) phenotyped in multi-location field trials including high-altitude tropical (Mexico) and high-latitude temperate (Germany) environments. We observed a high degree of phenotypic variation and identified several novel, temperate-adapted accessions with superior and environmentally stable cold tolerance. Good heritability indicates strong potential for implementation of reproductive cold tolerance in breeding. Although the trait was found to be strongly quantitative, promising genomic regions with multiple-trait associations were found, including hotspots on chromosomes 3 and 10 which contain candidate genes implicated in different developmental and survival processes under abiotic stress conditions.
Background The Plant Genetic Resources Centre at the Uganda National Gene Bank houses has over 3000 genetically diverse landraces and wild relatives of Sorghum bicolor accessions. This genetic diversity resource is untapped, under-utilized, and has not been systematically incorporated into sorghum breeding programs. In this study, we characterized the germplasm collection using whole-genome SNP markers (DArTseq). Discriminant analysis of principal components (DAPC) was implemented to study the racial ancestry of the accessions in comparison to a global sorghum diversity set and characterize the sub-groups present in the Ugandan (UG) germplasm. Results Population structure and phylogenetic analysis revealed the presence of five subgroups among the Ugandan accessions. The samples from the highlands of the southwestern region were genetically distinct as compared to the rest of the population. This subset was predominated by the caudatum race and unique in comparison to the other sub-populations. In this study, we detected QTL for juvenile cold tolerance by genome-wide association studies (GWAS) resulting in the identification of 4 markers associated (−log10p > 3) to survival under cold stress under both field and climate chamber conditions, located on 3 chromosomes (02, 06, 09). To our best knowledge, the QTL on Sb09 with the strongest association was discovered for the first time. Conclusion This study demonstrates how genebank genomics can potentially facilitate effective and efficient usage of valuable, untapped germplasm collections for agronomic trait evaluation and subsequent allele mining. In face of adverse climate change, identification of genomic regions potentially involved in the adaptation of Ugandan sorghum accessions to cooler climatic conditions would be of interest for the expansion of sorghum production into temperate latitudes.
The National Genebank of Uganda houses a diverse and rich Sorghum bicolor germplasm collection. This genetic diversity resource is untapped, under-utilized, and has not been systematically incorporated into sorghum breeding programs. In this study, we characterized the germplasm collection using whole-genome SNP markers. Discriminant analysis of principal components (DAPC) was implemented to study racial ancestry of the accessions in comparison to a global sorghum diversity set and characterize sub-groups and admixture in the Ugandan germplasm. Genetic structure and phylogenetic analysis were conducted to identify distinct genotypes in the Ugandan collection and relationships among groups. Furthermore, in a case study for the identification of potentially useful adaptive trait variation for breeding, we performed genome-wide association studies for juvenile cold tolerance. Genomic regions potentially involved in the adaptation of Ugandan sorghum varieties to cooler climatic conditions were identified that could be of interest for expansion of sorghum production into temperate latitudes. The study demonstrates how genebank genomics can potentially facilitate effective and efficient usage of valuable, untapped germplasm collections for agronomic trait evaluation and subsequent allele mining.
The Uganda National GeneBank is a key reservoir of genetic diversity for sorghum (Sorghum bicolor (L.) Moench), with over 3333 accessions which are predominantly landraces (96.48%), but also includes the weedy accessions (0.63%), breeding lines (2.5%) and released varieties (0.39%). This genetic resource from the primary center of sorghum diversity and domestication is important for broadening the genetic diversity of elite cultivars through breeding. However, due to the large size of the collection, we aimed to select a core set that captures the maximum genetic and phenotypic diversity, in order to facilitate detailed genetic and phenotypic evaluation at a reduced cost. To achieve this, we genotyped the entire collection in 2020 using Diversity Array Technology sequencing (DArTseq). A total of 27,560 SNPs were used to select a core collection of 310 accessions using the GenoCore software. A comparison of core set and the whole collection based on the polymorphism information content, observed heterozygosity, expected heterozygosity and minor allele frequency showed no significant difference between the two sets, indicating that the core collection adequately captures the genetic diversity and allelic richness present in the whole collection. The core collection captures all the five major sorghum races and the 10 intermediate hybrids. The most strongly represented race is guinea (24.5%), while caudatum-bicolor is least frequent (0.69%). Landraces account for 92.2% of the core collection, whereas breeder’s lines, weedy accessions and released varieties contribute 2.2%, 3.5% and 1.9%, respectively.
This chapter reviews germplasm sources for and new developments in the identification and implementation of useful genetic diversity for temperate climate adaptation, along with genomics-based methods for breeding of complex, low-heritability traits like abiotic stress tolerance in sorghum.
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