Genomics-based assembly of a sorghum bicolor (L.) moench core collection in the Uganda national genebank as a genetic resource for sustainable sorghum breeding

Abstract

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.

Morphological responses of six sorghum varieties on cadmium-contaminated soil

“…The six sorghum varieties were classified as adaptive until the end of the observation. Most morphological traits in sorghum are linked to one or more economically important traits and will aid in selecting high-yielding sorghum genotypes (Mufumbo et al 2022). Plants suitable for phytoremediation must have several characteristics, including the capability of accumulating heavy metals above ground, tolerance to metal accumulation, fast growth and high biomass, branched root system, and ease of harvest (Eapen and D'Souza 2005;Sarma 2011;Muro-González et al 2020), easy cultivation and quick harvest (Takahashi et al 2021), not consumed by humans (Jia et al 2016;Martiwi et al 2020;Muro-González et al 2020), has rejection of herbivores to avoid contamination of the food chain (Huang et al 2020), has several economic interests (Abdel-Sabour et al 2000;Almodares and Darany 2006;Angelova et al 2011;Liu et al 2020;Saleem et al 2020).…”

Potato soup: analysis of cultivated potato gene bank populations reveals high diversity and little structure

“…Core collections are an essential tool for empowering efficient screening of genebank material for use in breeding ( Haupt and Schmid, 2020 ; Sokolkova et al., 2020 ; Phogat et al., 2021 ; Mufumbo et al., 2023 ; Santos et al., 2023 ; Shigita et al., 2023 ). The goal is to maximize the number of alleles evaluated while minimizing the number of individuals that must be screened.…”

“…The goal is to maximize the number of alleles evaluated while minimizing the number of individuals that must be screened. Such collections have been developed for a wide variety of crops using both morphological ( Phogat et al., 2021 ; Santos et al., 2023 ) and genetic ( Haupt and Schmid, 2020 ; Mufumbo et al., 2023 ; Shigita et al., 2023 ) data. While core subsets based on morphology and traits emphasized by breeders have advantages for use in prediction ( Corak et al., 2019 ), they rely on the curators to foresee the total set of potentially relevant traits.…”