Identification of QTLs Controlling Resistance to Anthracnose Disease in Water Yam (Dioscorea alata)

Abstract

Anthracnose disease caused by a fungus Colletotrichum gloeosporioides is the primary cause of yield loss in water yam (Dioscorea alata), the widely cultivated species of yam. Resistance to yam anthracnose disease (YAD) is a prime target in breeding initiatives to develop durable-resistant cultivars for sustainable management of the disease in water yam cultivation. This study aimed at tagging quantitative trait loci (QTL) for anthracnose disease resistance in a bi-parental mapping population of D. alata. Parent genotypes and their recombinant progenies were genotyped using the Genotyping by Sequencing (GBS) platform and phenotyped in two crop cycles for two years. A high-density genetic linkage map was built with 3184 polymorphic Single Nucleotide Polymorphism (NSP) markers well distributed across the genome, covering 1460.94 cM total length. On average, 163 SNP markers were mapped per chromosome with 0.58 genetic distances between SNPs. Four QTL regions related to yam anthracnose disease resistance were identified on three chromosomes. The proportion of phenotypic variance explained by these QTLs ranged from 29.54 to 39.40%. The QTL regions identified showed genes that code for known plant defense responses such as GDSL-like Lipase/Acylhydrolase, Protein kinase domain, and F-box protein. The results from the present study provide valuable insight into the genetic architecture of anthracnose resistance in water yam. The candidate markers identified herewith form a relevant resource to apply marker-assisted selection as an alternative to a conventional labor-intensive screening for anthracnose resistance in water yam.

Chromosome evolution and the genetic basis of agronomically important traits in greater yam

“…While previous studies identified two significant anthracnose QTL using EST-SSRs 25 and three QTL using GBS-SNPs 62 , none of these colocalize with the QTL in our study. This discrepancy (and the variability seen among different years in our work) may be due to differences in the parental yam genotypes, differences in anthracnose strain and/or inoculation rate in these field studies, and possible genotype-by-environment interactions.…”

Genome‐wide dissection of the genetic factors underlying food quality in boiled and pounded white Guinea yam

“…Such analysis has been employed in many crops (including yam) to explore the alleles for enhancing agronomic, flower sex and biotic stress tolerance. 14,23,[52][53][54][55]…”

“…The prediction for the lowest index value refers to the closeness to the ideal genotype and thus indicates the desired quality for BY/PY food product. Such analysis has been employed in many crops (including yam) to explore the alleles for enhancing agronomic, flower sex and biotic stress tolerance 14,23,52‐55 …”

Identification of diagnostic KASP‐SNP markers for routine breeding activities in yam (Dioscorea spp.)

“…• This study is a pioneer that validated kompetitive allele-specific (KASP)-based single nucleotide polymorphism (SNP) assay for quality control (QC) and assurance in yam breeding. Girma et al, 2014Girma et al, , 2015Loko et al, 2017;Siadjeu et al, 2018), evolution of yam domestication (Sugihara et al, 2020), quantitative trait locus identification (Agre et al, 2022;Bhattacharjee et al, 2018;Cormier, Lawac, et al, 2019), and genomic prediction (Norman et al, 2020). Routine breeding activities (assessment of genetic diversity or identification of mislabeled genotypes, pedigree verification, variety tracking, so on), also known as quality control (QC) in crop breeding leveraging molecular breeding tools, have been employed as a routine practice in many breeding and seed programs to harness genetic gain and delivery of quality products to the end users.…”