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

Abstract

BACKGROUND Pea (Pisum sativum) is one of the most important temperate grain legumes in the world, and its production is severely constrained by the pea aphid (Acyrthosiphon pisum). Wild relatives, such as P. fulvum, are valuable sources of allelic diversity to improve the genetic resistance of cultivated pea species against A. pisum attack. To unravel the genetic control underlying resistance to the pea aphid attack, a quantitative trait loci (QTL) analysis was performed using the previously developed high density integrated genetic linkage map originated from an intraspecific recombinant inbred line (RIL) population (P. fulvum: IFPI3260 × IFPI3251). RESULTS We accurately evaluated specific resistance responses to pea aphid that allowed the identification, for the first time, of genomic regions that control plant damage and aphid reproduction. Eight QTLs associated with tolerance to pea aphid were identified in LGs I, II, III, IV and V, which individually explained from 17.0% to 51.2% of the phenotypic variation depending on the trait scored, and as a whole from 17.0% to 88.6%. The high density integrated genetic linkage map also allowed the identification of potential candidate genes co‐located with the QTLs identified. CONCLUSIONS Our work shows how the survival of P. fulvum after the pea aphid attack depends on the triggering of a multi‐component protection strategy that implies a quantitative tolerance. The genomic regions associated with the tolerance responses of P. fulvum during A. pisum infestation have provided six potential candidate genes that could be useful in marker‐assisted selection (MAS) and genomic assisted breeding (GAB) after functional validation in the future. © 2019 Society of Chemical Industry

Breeding for Biotic Stress Resistance in Pea

“…It results from a combination of antixenosis and antibiosis resistance mechanisms [129][130][131][132]. QTLs associated with tolerance to aphid damage have been reported in a RIL population derived from two P. fulvum accessions [133]. Further genetic studies have enabled the identification of a major-effect quantitative trait locus, ApRVII, on Chr7LGVII, associated with resistance against different adapted and non-adapted biotypes of pea aphids [131].…”

“…This, together with proper phenotyping, is allowing the identification of trait associations through QTL mapping or GWAS. As a result, markers associated with resistance genes/QTLs have been identified for resistance against ascochyta blight [7,8,119], powdery mildew [22,30,182,183], downy mildew [41], rust [44][45][46]184], fusarium root rot [67][68][69][70], fusarium wilt [60,185], aphanomyces root rot [73][74][75][76][77][78][79], broomrape [101][102][103], bacterial blight [110][111][112], several viruses [114,115,118,121], weevil [128], and aphid [131][132][133]. Earlier reported markers were often not close enough for precise utilization in MAS.…”

Unraveling the Genetic Basis of Key Agronomic Traits of Wrinkled Vining Pea (Pisum sativum L.) for Sustainable Production

“…The DArT discovered the other method of high-throughput genotyping, which is combining GBS with the next-generation sequencing platforms called NGS-DArTseq, or simply DArTseq. This approach can generate SNP markers with higher numbers covering the plants’ whole genome ( Akbari et al, 2006 ; Raman et al, 2014 ; Barilli et al, 2020 ) and is successfully used in several crops, including pea ( Aznar-Fernández et al, 2020 ). The DArTseq method reduces the complexity of the genome through digestion with restriction enzymes followed by sequencing of short reads, predominantly corresponding to the active genes ( Tomkowiak et al, 2021 ).…”

Pea Breeding for Resistance to Rhizospheric Pathogens

“…This led to the discovery of extensive single-nucleotide polymorphic (SNPs) markers [ 265 ] with a huge potential for pea improvements [ 233 ]. These novel platforms have already guided the identification of heritable QTLs contributing to phenotypic variance in pea resistance breeding [ 102 , 266 , 267 , 268 ]. These high-throughput techniques also enabled the quantitative elucidation of nematode population composition [ 269 ], and pea genetic diversity studies [ 270 , 271 ].…”