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Development of new genomic resources and tools for molecular breeding in blackberry

Worthington Margaret L., Aryal R., Bassil N. V., Mead D., Fernandez G. E., Clark J. R., Fernandez-Fernandez F., Finn C. E., Hummer K. E., H. Ashrafi
Acta horticulturae 2020 v. no.1277 pp. 39-46
Rubus argutus, Rubus inermis, blackberries, breeding programs, crops, diploidy, flow cytometry, fresh market, fruiting, genome, genomics, genotyping, heterozygosity, inheritance (genetics), plant breeding, polyploidy, primocanes, quantitative trait loci, thornless varieties
The application of molecular breeding in blackberry is a complex problem due to polyploidy, multisomic inheritance, and heterozygosity. However, recent advances in computational tools for mapping and quantitative trait loci analyses in polyploids and development of genomic resources for Rubus crops have removed many of these barriers. The objective of this project was to develop high-quality draft genomes for two diploid blackberry accessions and a polyploid resequencing panel. The diploid accessions chosen for reference genome development, 'Burbank Thornless' (R. ulmifolius inermis, PI 554060) and 'Hillquist' (R. argutus, PI 553951), represented important sources of thornlessness and primocane fruiting in fresh-market blackberry breeding programs. The genome sizes were estimated to be 405 Mb in 'Burbank Thornless' and 376 Mb in 'Hillquist' using nuclear flow cytometry. Single-Molecule Real-Time (SMRT) sequencing technology generated ~80X genome coverage for each genome. The reads were assembled using Falcon-unzip and Purge Haplotigs into a 341 Mb genome with contig N50 of 1.19 Mb for 'Burbank Thornless' and a 297 Mb genome with contig N50 of 650 Kb for 'Hillquist'. Chromosome-level assemblies for both accessions are being developed using 10X genomic and Hi-C scaffolding tools. Genome annotation will be performed using diverse tissue samples collected from 'Hillquist' and 'Burbank Thornless'. Breeders can use these resources in combination with new computational tools and genotyping strategies for polyploid crops to develop effective molecular breeding strategies for blackberry.