Abstract
Key messageWe have constructed a densely populated, saturated genetic linkage map of black raspberry and successfully placed a locus for aphid resistance.Black raspberry (Rubus occidentalis L.) is a high-value crop in the Pacific Northwest of North America with an international marketplace. Few genetic resources are readily available and little improvement has been achieved through breeding efforts to address production challenges involved in growing this crop. Contributing to its lack of improvement is low genetic diversity in elite cultivars and an untapped reservoir of genetic diversity from wild germplasm. In the Pacific Northwest, where most production is centered, the current standard commercial cultivar is highly susceptible to the aphid Amphorophora agathonica Hottes, which is a vector for the Raspberry mosaic virus complex. Infection with the virus complex leads to a rapid decline in plant health resulting in field replacement after only 3–4 growing seasons. Sources of aphid resistance have been identified in wild germplasm and are used to develop mapping populations to study the inheritance of these valuable traits. We have constructed a genetic linkage map using single-nucleotide polymorphism and transferable (primarily simple sequence repeat) markers for F1 population ORUS 4305 consisting of 115 progeny that segregate for aphid resistance. Our linkage map of seven linkage groups representing the seven haploid chromosomes of black raspberry consists of 274 markers on the maternal map and 292 markers on the paternal map including a morphological locus for aphid resistance. This is the first linkage map of black raspberry and will aid in developing markers for marker-assisted breeding, comparative mapping with other Rubus species, and enhancing the black raspberry genome assembly.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-015-2541-x) contains supplementary material, which is available to authorized users.
Highlights
Genetic linkage map construction of rosaceous crops has been used to understand genetics and as a precursor to enabling molecular breeding for about 20 years
To construct the linkage map for ORUS 3021-2, five Genotyping by sequencing (GBS)-generated single-nucleotide polymorphic (SNP) markers were removed for skewed segregation ratios, four were removed for creating double recombination events within a distance of 10 cM or less, and one was removed due to unsuccessful linkage phase determination
Of the 222 GBS SNP markers used for map construction, 200 (90 %) segregated as expected, either 1:1 or 1:2:1; two loci (1 %) varied from expected at a significance level of 0.01, 11 loci (5 %) varied from expected at a significance level of 0.05, and nine loci (4 %) varied from expected at a significance level of 0.1
Summary
Genetic linkage map construction of rosaceous crops has been used to understand genetics and as a precursor to enabling molecular breeding for about 20 years. Additional technological advances in high-throughput detection of single-nucleotide polymorphic (SNP) loci using arrays, or genotyping by sequencing (GBS), and the associated improvement of data analysis have made SNP markers increasingly useful for genetic map construction. Genetic linkage maps have been constructed for tetraploid blackberry (Castro et al 2013), diploid red raspberry (Sargent et al 2007; Ward et al 2013; Woodhead et al 2010), and an interspecific cross between diploid red raspberry and diploid black raspberry (Bushakra et al 2012). While blackberry and red raspberry are highly heterozygous, black raspberry, R. occidentalis, is highly homozygous (Dossett et al 2012b). Genetic improvement of blackberry and red raspberry through breeding has been a continual process for decades. Black raspberry figures prominently in the pedigrees of many of the red raspberry cultivars released between
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