Genotype × Environment Analysis, and SNP Validation and Trait Association of Rubus spp.
Katie Sheehan-Lust, MS Seminar
(Under the direction of Dr. Gina Fernandez)
Wednesday, July 20, 2022, 1:00pm

Zoom link:  https://ncsu.zoom.us/j/92965960611?pwd=YnVqcVBZYXdZV0RvTFgxMDJ1bmZ3Zz09
Meeting ID: 929 6596 0611
Passcode:  849783

 Sheehan-Lust.Abstr.pdf

Abstract:
Although a very popular fruit in retail and local markets, the diversity of raspberry and blackberry (Rubus spp.) cultivars has been limited by the scant germplasm pool that has been used in breeding programs. North Carolina State University, Cornell University, University of Arkansas, BC Berry Cultivar Development Inc., and the United States Department of Agriculture (USDA) collaborated with Pairwise, and Plant Sciences Inc., in a series of research projects focused on Rubus, the genus that includes blackberries and raspberries.

One component of this collaboration was a genotype × environmental (G × E) study that focused on phenotyping a set of traits on 5 seminal genotypes in 5 geographically distinct locations over two years. The genotypes evaluated included ‘Heritage’, a primocane-fruiting raspberry, ‘Latham’ a floricane-fruiting raspberry, ‘Prime-Ark® 45’, a primocane-fruiting blackberry, ‘Chester Thornless’, a floricane fruiting blackberry, and ‘Bristol’ a black raspberry. Our team at NCSU collated and then analyzed the data from all sites. Floricane fruit size was significantly affected by the interaction of G, E, and harvest date (H). The three-way interaction encouraged further investigation into individual climate variables’ effects on fruit size. An interaction between cultivar and growing degree days (GDD) was found to impact floricane fruit size. The primocane fruit size analysis determined the interaction between G and E to be significant. The primocane blackberry maintained the same fruit size across all E, while the primocane raspberry fruit size differed by E. Floricane fruiting lateral counts were affected by an interaction between G and E. Contrasts indicated that primocane genotypes had higher counts of floricane fruiting laterals. The floricane berries per fruiting lateral analysis also found the same interaction but contrasts indicate the primocane fruiting blackberries produced significantly less fruit per later than the floricane genotypes. The length of dormant primocane and their node densities were also analyzed. No interaction was found, and the main effects of E and G were significant for both. The Arkansas plots produced the longest primocanes and ‘Heritage’ produced significantly shorter canes than other genotypes. Node density evaluations determined a clear separation between blackberry and raspberry. Raspberry genotypes had significantly more nodes per 50 cm segment. In this study G and E were significant sources of variation for most of the traits phenotyped.

The second component of the research at NCSU focused on a SNP validation and trait association. 31 Rubus spp. genotypes sequenced by Pairwise were aligned to the black raspberry (R. occidentalis) genome to identify single nucleotide polymorphisms (SNP). NCSU set out to validate the presence of SNPs correlated with meaningful phenotypes. Traits evaluated valuable to producers include the primocane fruiting and prickle free phenotypes. Primocane fruiting SNPs were identified by comparing nucleotide identity and fruiting phenotype. This yielded SNPs associated with 3 previously annotated genes involved in protein phosphorylation, DNA repair, and RNA splicing. SNPs associated with the presence or absence of prickles were selected after aligning the flanking sequences to red raspberry genes (R. idaeus subsp. strigosus) identified by Cornell to be associated with prickle presence. 3 of these SNPs were found to be associated with prickle presence and within annotated genes determined to produce proteins associated with prickle development in other Rosaceae species. Validating the presence of meaningful SNPs within the population may facilitate the development of KASP markers, and ultimately improve marker assisted selection.