Advances in molecular breeding of blackberries in the Arkansas fruit breeding program

M. Worthington, T.M. Chizk, C.A. Johns, L.D. Nelson, A. Silva, C. Godwin, J.R. Clark
The global blackberry (Rubus subgenus Rubus) industry has experienced rapid growth and change during the past 20 years, driven by increased consumer demand, new cultivars, advanced production methods, and year-round product availability. Despite their growing economic importance, the implementation of molecular breeding in blackberry has been delayed by complications, including polyploidy and multisomic inheritance. Recent advances in computational tools for mapping and QTL analyses in polyploids and availability of genomic resources for Rubus crops have removed many of these barriers. Over the past four years, the Arkansas Fruit Breeding team has led initiatives to develop a chromosome-scale genome assembly and annotation of a diploid blackberry and conduct genome-wide association studies (GWAS) to identify genetic regions associated with key traits of economic importance in fresh-market blackberries. The new genome assembly and annotation of R. argutus ‘Hillquist’ is a valuable resource for research in Rubus biology, genetics, and genomics. The R. argutus assembly was used to design 35,054 custom Capture-Seq probes concentrated in genic regions. A large collection of fresh-market cultivars and Arkansas fruit breeding selections were genotyped with these Capture-Seq probes and phenotyped for several horticultural and fruit quality traits between 2019 and 2021. Association analyses revealed significant marker-trait associations for all measured traits. Future molecular breeding priorities include studies to identify the main drivers of consumer preference and the genetic control of key aromatics in blackberry and the development and implementation of diagnostic single nucleotide polymorphism (SNP) markers for simply inherited traits and genomic selection models for medium and low heritability traits.
Worthington, M., Chizk, T.M., Johns, C.A., Nelson, L.D., Silva, A., Godwin, C. and Clark, J.R. (2024). Advances in molecular breeding of blackberries in the Arkansas fruit breeding program. Acta Hortic. 1388, 85-92
DOI: 10.17660/ActaHortic.2024.1388.12
Rubus subgenus Rubus, polyploidy, reference genome, Rubus argutus, genome-wide association studies

Acta Horticulturae