Jahn Davik
Seniorforsker (pensjonistavtale)
Sammendrag
High-throughput and reproducible genotyping platforms are critical for advancing genetic research and breeding in horticultural crops. Here, the development and validation of a custom single nucleotide polymorphism (SNP) panel using the Flex-Seq genotyping platform for red raspberry (Rubus idaeus L.) is described. SNPs were derived from existing linkage maps and RNA-seq data, resulting in a panel of 5,639 high-confidence, bi-allelic markers distributed across the seven chromosomes of the R. idaeus ‘Malling Jewel’ reference genome. The panel was used to genotype 457 red raspberry accessions including 161 individuals from a bi-parental mapping population (Paris×486), enabling the construction of high-density linkage maps and the identification of quantitative trait loci (QTL) for fruit size, leaf colour, plant vigour, and thorn density. Genome-wide association studies (GWAS) identified a major QTL for thornlessness on chromosome 4, co-locating with a candidate HOX3 gene, and multiple QTLs associated with anthocyanin biosynthesis genes for leaf colour. The SNP panel demonstrated utility for linkage mapping and trait association analyses, offering a powerful resource for marker-assisted selection and genetic improvement in red raspberry.
Sammendrag
Background The soil-borne oomycete Phytophthora cactorum causes crown rot, a major disease of the allo-octoploid strawberry (Fragaria × ananassa Duch., 2n = 8× = 56) that limits cultivation worldwide. Resistance to P. cactorum is a highly desirable trait but is typically quantitative and moderately heritable. A better understanding of the genetic basis of resistance to crown rot is essential for developing durable crown rot-resistant cultivars. Results We conducted a genome-wide association study (GWAS) using multi-locus models on 100 wild strawberry accessions from South and North America. The accessions were genotyped using the Axiom™ 50 K strawberry SNP array and mapped to the F. × ananassa cv. Royal Royce v. 1.0 reference genome. Testing for resistance to P. cactorum revealed a wide range of phenotypes. A single genetic marker, AX-184528282, located on chromosome 7B, was strongly associated with resistance to P. cactorum and explained 53% of the observed phenotypic variation. This marker was present in several highly resistant exotic Fragaria accessions that represent potential donors for introgression of favorable alleles into modern strawberry cultivars. In addition, several strong candidate resistance genes were identified within the 2 Mb genomic region surrounding the significant marker. Conclusions This study advances understanding of resistance to P. cactorum in strawberry and identifies genetic resources that can accelerate the development of crown rot-resistant cultivars through marker-assisted breeding.
Sammendrag
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