The development of molecular genetic tools to improve efficiency in raspberry breeding

Abstract

Raspberry growing and trade has expanded over the last 20 years, fueled by the increasing demand for this healthy fruit. At the same time, raspberry breeding is challenged by changes in economics, climate and growing technology. In the following thesis, traits important for raspberry breeding were explored through molecular genetic tools, subsequently using this knowledge to develop molecular genetic tools to aid breeding.

As trueness-to-type is very important for growing and breeding clonally propagated crops, the state of the German raspberry trade was explored by genotyping six cultivars from up to six sources with 16 SSR markers for cultivar mismatches. Out of the 33 samples, nine were not true-to-type, indicating an issue of cultivar mix-ups in the German raspberry trade.

Subsequently, a trait relevant to fruit size and quality, self-compatibility, was studied. For this purpose, the progeny of 16 open pollinated cultivars were genotyped with up to 16 SSR markers to determine if they were self- or cross-fertilized. One cultivar, ‘Rumla’, was found to be highly self-incompatible in both this, and subsequent hand-pollination and topcross experiments. The other 15 cultivars showed more flexibility in tolerating self-fertilization. The existence of self-incompatible cultivars in raspberry, usually considered self-fertile, cautions from using cultivars with unknown self-fertility status as a monoculture in protected growing.

Furthermore, a trait relevant for fungal resistance, waxy bloom, was investigated in an interspecific Rubus occidentalis × R. idaeus population. The trait was mapped to linkage group 2, corresponding to chromosome 2, in R. occidentalis by using SNP markers obtained from Genotyping-by-Sequencing, SSR markers and phenotyping data.

Additionally, the molecular genetic basis of floral development, which is relevant for fruit size and quality traits in raspberry, was studied. First, 82 MADS-box gene candidates were identified in R. occidentalis by Hidden Markov Model search. These results were used in primer development to identify and sequence genes in R. idaeus. First two PISITLLATA homologues, the paralogous genes RidPI1 and RidPI2, then a LEAFY homologue with two alleles, RidLFY-1 and RidLFY-2, were found. RidLFY-2 has a 3.7 Mb transposon inserted into their first intron compared to RidLFY-1, and it correlates with a sepaloid flower mutation occurring in a raspberry population.