Predictive genotype-phenotype relations using genetic diversity in African yam bean (Sphenostylis stenocarpa (Hochst. ex. A. Rich) Harms)

Rate of double reduction and genetic variability in yield, quality, and senescence related traits in tetraploid potato (Solanum tuberosum L.)

The amount of genetic variability is the foundation for genetic change in any plant breeding program, and the amount of double reduction can influence genetic gain and the amount of future genetic diversity in polyploid species. Our study investigates these factors using variance components analysis on a dataset comprising 13,131 potato breeding lines and phenotypic data from Scandinavian environments spanning 17 years (2003 to 2021). Pedigree information was used in quantitative genetic models to estimate additive genetic variance and the relative importance of additive and non-additive genetic variance. We used two models, a baseline model (M1) without effects due to specific combining ability (SCA) and M2 (including SCA due to interaction between parental genomes). Two cross-validation (CV) schemes [5-Fold and leave-one-breeding-cycle-out (LBCO)] were used to evaluate the prediction ability (PA) of each model. We estimated the rate of double reduction phenomenon (DRP) by determining the rate best fitting the data using a marginal likelihood approach. Our findings showed a wide range of variation in different traits, with very large proportion of additive genetic variance in dry matter content (DMC), but intermediate additive genetic variance for relative yield (RY), germination (GR), and withering (WNG). All traits showed modest non-additive genetic variance. Furthermore, genotype x environment interaction played a significant role in trait variability but is still much smaller than the additive genetic variance. After using different DRP rates, we found that a model with a 0.05 DRP rate provided the best fit to the data. Heritability estimates indicated a strong genetic basis for DMC, while other traits showed more moderate heritability, which shows contributions from both additive and interaction factors. Model comparison by 5-Fold CV and LBCO and the log likelihood ratio test (LRT) highlighted the importance of considering SCA when capturing trait variability. In 5-Fold CV, PA ranged from 0.296 to 0.812 in M1 and 0.300 to 0.813 in M2. Under LBCO CV, PA ranged from 0.180 to 0.726 in M1 and 0.180 to 0.728 in M2. However, an increase in PA in Model 2, which incorporates SCA, compared to Model 1, can be attributed to the inclusion of SCA effects. Furthermore, the LRT results indicated a highly significant difference between the models. CV and LRT suggest the need for genetic models that account for both additive and SCA effects. Our analysis also showed that genotype x environment interactions should be accounted for in order to maximize the accuracy of predicted breeding values of tetraploid potato clones. The rate of double reductions was small and insignificant.

Exploiting genetic and genomic resources to enhance productivity and abiotic stress adaptation of underutilized pulses

Underutilized pulses and their wild relatives are typically stress tolerant and their seeds are packed with protein, fibers, minerals, vitamins, and phytochemicals. The consumption of such nutritionally dense legumes together with cereal-based food may promote global food and nutritional security. However, such species are deficient in a few or several desirable domestication traits thereby reducing their agronomic value, requiring further genetic enhancement for developing productive, nutritionally dense, and climate resilient cultivars. This review article considers 13 underutilized pulses and focuses on their germplasm holdings, diversity, crop-wild-crop gene flow, genome sequencing, syntenic relationships, the potential for breeding and transgenic manipulation, and the genetics of agronomic and stress tolerance traits. Recent progress has shown the potential for crop improvement and food security, for example, the genetic basis of stem determinacy and fragrance in moth bean and rice bean, multiple abiotic stress tolerant traits in horse gram and tepary bean, bruchid resistance in lima bean, low neurotoxin in grass pea, and photoperiod induced flowering and anthocyanin accumulation in adzuki bean have been investigated. Advances in introgression breeding to develop elite genetic stocks of grass pea with low β-ODAP (neurotoxin compound), resistance to Mungbean yellow mosaic India virus in black gram using rice bean, and abiotic stress adaptation in common bean, using genes from tepary bean have been carried out. This highlights their potential in wider breeding programs to introduce such traits in locally adapted cultivars. The potential of de-domestication or feralization in the evolution of new variants in these crops are also highlighted.

Genetic diversity and population structure of an African yam bean (Sphenostylis stenocarpa) collection from IITA GenBank

African yam bean, AYB (Sphenostylisstenocarpa), is an underutilized legume of tropical Africa. AYB can boost food and nutritional security in sub-Saharan Africa through its nutrient-rich seeds and tubers. However, inadequate information on germplasm with desirable agro-morphological traits, including insufficient data at the genomic level, has prevented the full exploitation of its food and breeding potentials. Notably, assessing the genetic diversity and population structure in a species is a prerequisite for improvement and eventual successful exploitation. The present study evaluated the population structure and genetic diversity of 169 accessions from the International Institute of Tropical Agriculture (IITA) collection using 26 phenotypic characters and 1789 single nucleotide polymorphism (SNP) markers. The phenotypic traits and SNP markers revealed their usefulness in uniquely distinguishing each AYB accession. The hierarchical cluster of phenotypes grouped accessions into three sub-populations; SNPs analysis also clustered the accessions into three sub-populations. The genetic differentiation (F_ST) among the three sub-populations was sufficiently high (0.14–0.39) and significant at P = 0.001. The combined analysis revealed three sub-populations; accessions in sub-population 1 were high yielding, members in sub-population 2 showed high polymorphic loci and heterozygosity. This study provides essential information for the breeding and genetic improvement of AYB.