Abstract
BackgroundImprovement 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).ResultsPopulation 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.ConclusionApplication 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.
Highlights
Improvement of tuber yield and tolerance to viruses are priority objectives in white Guinea yam breeding programs
tuber yield per plant (TYP) Tuber yield per plant, YMV yam mosaic virus (AUDPC value)
Population structure and linkage disequilibrium The DArT genotyping of 406 white Guinea yam clones detected the highest number of Single nucleotide polymorphism (SNP) (637) mapped on chromosome 5 and the lowest of 123 on chromosome 11 (Supplementary Fig. 1A)
Summary
Improvement of tuber yield and tolerance to viruses are priority objectives in white Guinea yam breeding programs. 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). The global estimated mean annual yam production and gross values are approximately 73 million tons and 14 billion US dollars, respectively, with West Africa accounting for 92% of the total yam production [4, 5]. White Guinea yam (D. rotundata), indigenous to Africa, is the most produced and consumed among cultivated species, supporting the livelihood of over 300 million people [2]. Yam is important in many key life ceremonies in the major producing areas of West Africa [7]
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