Inheritance of Phytophthora root rot resistance in red raspberry determined by generation means and molecular linkage analysis

Abstract

Classical and molecular methodologies were used to determine the inheritance of Phytophthora root rot (PRR) resistance in red raspberry. The varieties 'Latham' and 'Titan,' resistant and susceptible, respectively, were used to create F(1), F(2), B(1), B(2), and S(1) populations for analysis. Generational means analysis was used to calculate the components of genetic variation and estimates of narrow and broad sense heritability for the plant disease index and the incidence of petiole lesions. The plant disease index showed additive genetic variation with additional significant interactions, but the incidence of petiole lesions was non-additive. A dominant, two-gene model was shown to be the best fit for the observed segregation ratios when classification for resistance was based on a combination of all criteria measured. Molecular linkage maps were generated from the segregating B(2) population. Linkage maps of both parents were constructed from amplified fragment length polymorphism (AFLP), Random amplified polymorphic DNA (RAPD), and uncharacterized resistant gene analog polymorphism (RGAP) markers with seven linkage groups each totaling 440 and 370 cM of genetic distance, respectively. An analysis of the distributional extremes of the B(2) population identified several RAPD markers clustered on two linkage groups associated with PRR resistance. QTL analysis identified two similar genomic regions on each map that explained significant percentages of phenotypic variation observed for the disease assessment criteria. Genetic mapping supports the dominant two-gene model developed from generational means analysis. The results reconcile conflicting reports on inheritance of PRR resistance, provide a basis for further investigation of durable resistance to Phytophthora caused diseases, and indicates that recurrent selection is the appropriate approach for the development of new resistant cultivars.

Isolation and linkage mapping of NBS-LRR resistance gene analogs in red raspberry (Rubus idaeus L.) and classification among 270 Rosaceae NBS-LRR genes

“…Genomic DNA from newly expanded leaves from the resistant cultivar 'Latham' was extracted for RGA amplification using the cetyl trimethylammonium bromide method as described by Pattison et al (2007). PCRs were carried out in a total volume of 50 μl with a 100-ng template DNA and 0.4 μM of each primer in 49.3 mM Tris-HCl (pH=8.3), 2.5 mM MgCl 2 , 1 mM tartrazine, 1.5% Ficoll, 125 μM deoxynucleotide triphosphates, and 0.5 U Taq polymerase.…”

“…Mapping of markers derived from RGAs was performed using 68 individuals from a B 1 population previously screened for PRR resistance (Pattison et al 2007). Identified polymorphisms were mapped using JoinMap 3.0® (Van Oijen and Voorrips 2001) with linkage groups assigned at a minimum logarithm of the odds of 3.0.…”

“…Specific primers were designed for each RGA sequence (Table 2) to identify polymorphic markers that could be placed on a red raspberry genetic linkage map (Pattison et al 2007). The map was developed using a segregating B 1 population that was screened for resistance to P. fragariae var.…”

“…The oligonucleotides were synthesized by MWG-Biotech (High Point, NC, USA). Each primer pair was tested with genomic DNA from 'Titan', 'Latham', and the F 1 parent from the previously mapped B 1 population (Pattison et al 2007) to identify polymorphisms. Amplification was performed under the same conditions already described, only with an annealing temperature of 62°C instead of 50°C.…”

“…Analysis of the distributional extremes and quantitative trait loci (QTL) mapping of a backcross population (B 1 ) [('Titan' × 'Latham') × 'Titan'] using RAPD, AFLP, CAPS, and SCAR markers revealed two major genomic regions associated with PRR resistance in red raspberry (Pattison et al 2007). A collection of RGA sequences from red raspberry would be an effective tool for the characterization of these regions and other disease-related genes (Leister et al 1996(Leister et al , 1998Yu et al 1996).…”