A High-Density Integrated DArTseq SNP-Based Genetic Map of Pisum fulvum and Identification of QTLs Controlling Rust Resistance

Abstract

Pisum fulvum, a wild relative of pea is an important source of allelic diversity to improve the genetic resistance of cultivated species against fungal diseases of economic importance like the pea rust caused by Uromyces pisi. To unravel the genetic control underlying resistance to this fungal disease, a recombinant inbred line (RIL) population was generated from a cross between two P. fulvum accessions, IFPI3260 and IFPI3251, and genotyped using Diversity Arrays Technology. A total of 9,569 high-quality DArT-Seq and 8,514 SNPs markers were generated. Finally, a total of 12,058 markers were assembled into seven linkage groups, equivalent to the number of haploid chromosomes of P. fulvum and P. sativum. The newly constructed integrated genetic linkage map of P. fulvum covered an accumulated distance of 1,877.45 cM, an average density of 1.19 markers cM−1 and an average distance between adjacent markers of 1.85 cM. The composite interval mapping revealed three QTLs distributed over two linkage groups that were associated with the percentage of rust disease severity (DS%). QTLs UpDSII and UpDSIV were located in the LGs II and IV respectively and were consistently identified both in adult plants over 3 years at the field (Córdoba, Spain) and in seedling plants under controlled conditions. Whenever they were detected, their contribution to the total phenotypic variance varied between 19.8 and 29.2. A third QTL (UpDSIV.2) was also located in the LGIVand was environmentally specific as was only detected for DS % in seedlings under controlled conditions. It accounted more than 14% of the phenotypic variation studied. Taking together the data obtained in the study, it could be concluded that the expression of resistance to fungal diseases in P. fulvum originates from the resistant parent IFPI3260.

Identification of potential candidate genes controlling pea aphid tolerance in a Pisum fulvum high‐density integrated DArTseq SNP‐based genetic map

“…DNA samples were extracted from leaves of the 84 individuals of the RIL population in F 7 and the parents of the cross, which were sown for this purpose under controlled conditions as described by Barilli et al Twelve days after sowing, 1 g of leaves were cut from the 3rd or 4th node of each seedling and immediately frozen in liquid nitrogen. Genomic DNA was isolated from the fresh and young material using a modified cetyltrimethylammonium bromide (CTAB)/chloroform/isoamyl alcohol method and then it was quantified for the following marker analysis …”

“…The purpose of their inclusion for the construction of the genetic linkage map depends on their well‐known position on the P. sativum chromosomes, acting as a bridge between the two species. So, their positions on our map help us to find the correspondence between the linkage groups of P. fulvum with the P. sativum chromosomes, as ‘anchor’ markers.…”

“…This analysis allowed searching for sequence similarity‐based homology between legume species providing an alternative approach to finding correspondence between linkage groups. The genetic map was constructed as described by Barilli et al, 2018 …”

“…The coefficient of determination (R 2 ) for the marker most tightly linked to a QTL was used to estimate the proportion of the total phenotypic variation explained by the QTL. Broad sense heritability ( h 2 ), that represents the part of genetic variance in the total phenotypic variance, was calculated as described by Barilli et al (2018) …”

“…In such a scenario, Diversity Arrays Technology (DArT) in combination with next‐generation sequencing platforms, known as DArTseq™, offers a good choice as a cost‐effective, high throughput genotyping platform that can detect a relatively large number of polymorphic markers for the construction of dense genetic maps for virtually any genome . DArTseq‐derived markers that are currently used in approximately 500 species (http://www.diversityarrays.com) were recently used in our research group to develop the genetic map of P. fulvum . The aim of this work was to dissect the response of P. fulvum against the PA infestation to allow the first mapping of the genomic regions involved in PA tolerance in a population derived from an intraspecific cross of P. fulvum .…”