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

Authors: WORTHINGTON, MARGARET - University Of Arkansas; ARYAL, RISHI - North Carolina State University; Bassil, Nahla; MEAD, DAN - Wellcome Trust Sanger Institute; FERNANDEZ, GINA - North Carolina State University; CLARK, JOHN - University Of Arkansas; FERNANDEZ-FERNANDEZ, FELICIDAD - National Institute Of Agricultural Botany (NIAB); Finn, Chad; Hummer, Kim; ASHRAFI, HAMID - North Carolina State University

Submitted to: Acta Horticulturae
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/4/2020
Publication Date: 7/1/2020
Publication URL: https://handle.nal.usda.gov/10113/7071194
Citation: Worthington, M.I., Aryal, R., Bassil, N.V., Mead, D., Fernandez, G.E., Clark, J.R., Fernandez-Fernandez, F., Finn, C.E., Hummer, K.E., Ashrafi, H. 2020. Development of new genomic resources and tools for molecular breeding in blackberry. Acta Horticulturae. 1277:39-46. https://doi.org/10.17660/ActaHortic.2020.1277.6.
DOI: https://doi.org/10.17660/ActaHortic.2020.1277.6

Interpretive Summary: The application of molecular breeding in blackberry is a complex problem due to many chromosomes and complex genetics. However, recent advances in computational tools for mapping and quantitative trait loci analyses in plants with high numbers of chromosomes and development of genomic resources for bramble species and crops have removed many of these barriers. The objective of this project was to develop high-quality draft genomes for two blackberry cultivars and some with higher number of chromosomes. The diploid accessions chosen for reference genome development, ‘Burbank Thornless’ (PI 554060) and ‘Hillquist’ (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. A technique called Single-Molecule Real-Time (SMRT) sequencing technology was able to determine good coverage of sequences for each cultivar. The sections of sequences were assembled using Falcon-unzip and Purge Haplotigs into 1.19 Mb for ‘Burbank Thornless’ and 650 Kb for ‘Hillquist’. Chromosome-level assemblies for both cultivars are being developed using some specific DNA building block tools. The sequences will be annotates with gene locations by collecting and analyzing tissue samples from ‘Hillquist’ and ‘Burbank Thornless’. Plant breeders can use these resources in combination with new computational tools and to develop new blackberry cultivars more rapidly than before.

Technical Abstract: 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.