Genetic insight and mapping of the pod constriction trait in Virginia-type peanut

BACKGROUND: Pod constriction is an important descriptive and agronomic trait of peanut. For the in-shell Virginia marketing-type, this trait has commercial importance as well, since deeply constricted pods have a tendency to break, which makes them unmarketable. Classical genetic studies have indicated that pod constriction in peanut is controlled by one to four genes, depending on the genetic background. In all of those studies, pod constriction was evaluated visually as opposed to quantitatively. Here, we examined the genetic nature of this trait in the Virginia-type background. Our study involved 195 recombinant inbred lines (F(7)RILs) derived from two closely related cultivars that differ in their degree of pod constriction. Pod constriction was evaluated visually and quantitatively in terms of the pod constriction index (PCI), calculated as the average ratio between the pod’s waist and shoulders. RESULTS: ANOVA and genetic parameters for PCI among the F(7)RILs in three blocks showed very significant genotypic effect (p(F) < 0.0001) and high heritability and genetic gain estimates (0.84 and 0.52, respectively). The mean PCI values of the different RILs had a bimodal distribution with an approximate 1:1 ratio between the two curves. Pod constriction was also determined visually (VPC) by grading the degree of each RIL as ‘deep’ or ‘slight’. The χ(2) test was found to not be significantly different from a 1:1 ratio (p = 0.79) as well. SNP-array-based technology was used to map this trait in the RIL population. A major locus for the pod constriction trait was found on chromosome B7, between B07_120,287,958 and B07_120,699,791, and the best-linked SNP explained 32% of the total variation within that region. Some discrepancy was found between the SNPs original location and the genetic mapping of the trait. CONCLUSION: The trait distribution and mapping, together with data from F(1) and F(2) generations indicate that in this background the pod constriction is controlled by a major recessive gene. The identity of loci controlling the pod constriction trait will allow breeders to apply marker-assisted breeding approaches to shift allelic frequencies towards a slighter pod constriction and will facilitate future effort for map-based gene cloning. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12863-018-0674-z) contains supplementary material, which is available to authorized users.