SHAH, T. | Search bioRxiv

bioRxiv2024

Long read sequencing and assembly of wild diploid relatives and cultivars in support of banana breeding programs

Banana is an important fruit and staple crop, which is vital for food and income security in developing countries. A genomics initiative was undertaken as part of the Global Alliance against TR4 (Tropical Race 4 of Fusarium Wilt of Banana) Alliance, with Bayer Crop Science, International Institute of Tropical Agriculture, and University of Queensland to collectively accelerate the breeding efforts in Eastern Africa. The goal of this project is to develop genomics resources to improve banana breeding, productivity, and quality traits amid a changing climate and shifting disease pressures for breeding. Here, we present the PacBio HiFi sequencing, assembly, and comparative analysis of seven genomes of wild and edible diploid banana accessions belonging to subspecies considered important progenitors to cultivated banana varieties and part of breeding programs. This banana genome resource will help power genome editing, a pangenome effort, and conventional breeding programs for germplasm improvement.

genomics↗

bioRxiv2021

A panel of single nucleotide polymorphism (SNP) markers identifies potential duplicates in cassava (Manihot esculenta Crantz) varieties from Cote dIvoire

Accurate identification of varieties is paramount to optimizing efficiencies in the management and conservation of genetic resources. A relatively inexpensive, rapid methodology is required to identify putative duplicates from any collection, when morphological traits give insufficient discrimination. Here we select a panel of 36 SNPs, visualized using the Kompetitive Allele-specific PCR (KASP) system. We used a panel of 95 cassava genotypes from Cote dIvoire to identify varieties that are not duplicates and few potential duplicates which could be put forward for further verification. The genetic variability and population structure of the germplasm is also described. 36 SNPs were polymorphic across the panel of 95 varieties with polymorphic information contents ranging from 0.23 to 0.37. Using these SNPs, we were able to identify 66 unique genotypes from the panel of 95 genotypes, discriminate three sets of known duplicates and identify 11 sets of unknown putative duplicates which can be subjected to further verification using higher density genotyping. As expected in an outcrossing species, both expected heterozygosity (0.46) and observed heterozygosity (0.48) were high with an analysis of molecular variance (AMOVA) indicating that the majority of variation was within individuals. Three statistical approaches i.e., hierarchical ascending clustering, Bayesian analysis and discriminant analysis of principal components were used and all revealed low genetic differentiation between sub-populations, a conclusion that was supported by the low value of the fixation index (0.05). This panel of SNPs can be used to enhance cost-effectiveness and efficiency of germplasm conservation and enhance quality control at various stages in the breeding process through varietal tracking.

plant biology↗