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Background Improvement of tuber yield and tolerance to viruses are priority objectives in white Guinea yam breeding programs. However, phenotypic selection for these traits is quite challenging due to phenotypic plasticity and cumbersome screening of phenotypic-induced variations. This study assessed quantitative trait nucleotides (QTNs) and the underlying candidate genes related to tuber yield per plant (TYP) and yam mosaic virus (YMV) tolerance in a panel of 406 white Guinea yam ( Dioscorea rotundata ) breeding lines using a genome-wide association study (GWAS). Results Population structure analysis using 5,581 SNPs differentiated the 406 genotypes into seven distinct sub-groups based delta K. Marker-trait association (MTA) analysis using the multi-locus linear model (mrMLM) identified seventeen QTN regions significant for TYP and five for YMV with various effects. The seveteen QTNs were detected on nine chromosomes, while the five QTNs were identified on five chromosomes. We identified variants responsible for predicting higher yield and low virus severity scores in the breeding panel through the marker-effect prediction. Gene annotation for the significant SNP loci identified several essential putative genes associated with the growth and development of tuber yield and those that code for tolerance to mosaic virus. Conclusion Application of different multi-locus models of GWAS identified 22 QTNs. Our results provide valuable insight for marker validation and deployment for tuber yield and mosaic virus tolerance in white yam breeding. The information on SNP variants and genes from the present study would fast-track the application of genomics-informed selection decisions in breeding white Guinea yam for rapid introgression of the targeted traits through markers validation.

White Guinea yam ( Dioscorea rotundata ) is mainly a dioecious tuberous crop that produces flowers of varying sex phenotypes. Agronomic traits in Guinea yam differ according to the sex phenotype, but the precise interaction between the traits and sex phenotype is not clearly understood. This might be due to the high heterozygosity of yam where cultivars with different flowering sex have different genetic backgrounds, which mask the sole effect of sex phenotype on the agronomic traits. This study used F 1 -derived clonal progenies from a bi-parental cross to minimize the impact of different genetic backgrounds among the plants with different sex phenotypes. The impact of plant sex on agronomic traits, specifically tuber yield, was evaluated through field trials conducted for four years. The results showed that only plants with a female genotype exhibited varying sex phenotypes even within the clones of same accession grown in the same experimental field. The significant effects of sex genotype and phenotype on agronomic traits were detected. Our results revealed that the flowering date was delayed in the plants with female genotypes compared to male genotypes, even when compared only among the plants with male phenotypes. The flowering date is the most important reason for the sexual differences in tuber yield. A high tuber yield was obtained when plants with the female phenotype flowered before tuber enlargement. This result can be attributed to the fact that the low flowering intensity in female plants increases the availability of carbon resources for leaf development. Female plants also showed a large negative effect of late flowering on tuber yield owing to resource competition between flowering and tuber enlargement. These findings demonstrate the feasibility of yield improvement by controlling the flowering time, with a higher effectiveness achieved in female than in male plants.

Field trials were conducted in the forest zone of southern Nigeria on three soil series, gravelly loamy sand Ibadan soil (Oxic paleustalf), gravelly sandy loam Egbeda soil (Oxic paleustalf) and sandy loam Alagba soil (Oxic paleustalf). The trials were carried out to study the effects of planting on flat versus various mound sizes and NPK fertilizer on performance of white Guinea yam (Dioscorea rotundata) cultivar Laoko. Mound size appeared to have a more pronounced effect on tuber yield than fertilizer even on land which was in the second and third year of cropping after bush fallow. The average tuber yield for the three locations without fertilizers was 7.83 tons/ha on the flat compared with 9.44 tons/ha on large mound (about 30 cm height). With fertilizer application, tuber yields were 7.43 tons/ha on the flat and 11.30 tons/ha on large mound respectively. Total yield reduction on flat may in part be related to physical soil impedence. Planting on large mounds also resulted in longer tubers and shorter harvesting time.