Jiří Korecký

Comparison of genetic parameters from marker-based relationship, sibship, and combined models in Scots pine multi-site open-pollinated tests

Nine microsatellite DNA markers (simple sequence repeats, SSRs) were used to estimate pairwise relationships among 597 Scots pine (Pinus sylvestris) trees as well as to generate a sibship structure for quantitative genetic parameters’ estimation comparison. The studied trees were part of an open-pollinated progeny test of 102 first-generation parents. Three methods were used to estimate variance components and heritabilities, namely, structured pedigree (half- and full-sib), marker-based pairwise relationships (four pairwise estimators), and a combined pedigree and marker-based relationship. In each of the three methods, the same animal model was used to compute variances except when marker-based relationship was used wherein we substituted the average numerator relationship matrix (i.e., pedigree-based matrix) with that computed based on markers’ pairwise relationships. Our results showed a high correlation in estimated breeding values between the pedigree (full-sib) and the combined marker-pedigree estimates. The marker-based relationship method produced high correlations when individual site data were analyzed. In contrast, the marker-based relationship method resulted in a significant decrease in both variance estimation and their standard errors which were in concordance with earlier published results; however, no estimates were produced when across-site analyses were attempted. We concluded that the combined pedigree method is the best approach as it represents the historical (pairwise) and contemporary (pedigree) relationships among the tested individuals, a situation that cannot be attained by any of the used methods individually. This method is dependent on the number and informativeness of the markers used.

Expansion of the minimum-inbreeding seed orchard design to operational scale

The minimum-inbreeding (MI) seed orchard layout, formulated originally as a global quadratic assignment problem, was expanded into realistic problem sizes that are often encountered in operational forestry, where two modifications were tested: (1) the merging algorithm of independent MI’s solutions (i.e., smaller blocks) and (2) the extended global (genetic-tabu) algorithm. Extending the global heuristic algorithm of the quadratic assignment problem seems to be the most efficient strategy. The reported minimum-inbreeding distance of the extended MI scheme was the lowest in comparison to the completely randomized and the randomized, replicated, staggered clonal-row (R2SCR) seed orchard design schemes. These conclusions also hold for more complex scenarios when added relatedness among orchard’s parents or unequal deployment was considered. This improved MI scheme is suitable to large and complex advanced-generation seed orchards, where many practical constraints have to be jointly considered.

Congruence between theory and practice: reduced contamination rate following phenotypic pre-selection within the Breeding without Breeding framework

Wind-pollinated seed orchards are often subjected to pollen intrusion from outside pollen sources. When wind-pollinated seed orchards seed are used to establish progeny trials, the offspring is expected to harbour varying proportion sired by outside sources. Theoretically the magnitude of selection differential between the orchards population and the contaminant pollen sources will affect the proportion of offspring resulting from outside pollen sources matings. If phenotypic pre-selection is implemented through selecting the top phenotypically ranked individuals from these progeny trials, then it is expected that the proportion of individuals sired by outside pollen sources will be lower within the pre-selected vs. unselected individuals. Here, we present empirical data from two Scots pine progeny trials supporting these theoretical expectations. The observed reduced contamination rate among fingerprinted elite offspring was 3.9 and 4.2%, suggesting a significant reduction in comparison to reported contamination rates between 21 and 70% in Scots pine. Results provide support to the proposed phenotypic pre-selection during the implementation of Breeding without Breeding scheme.

Temporal quantification of mating system parameters in a coastal Douglas-fir seed orchard under manipulated pollination environment

Seed orchards main function is delivering breeding programs’ gains in the form of genetically improved seedlings. They are unique experimental populations, perfectly suited for studying various pollination environments (natural or otherwise), affecting their mating system parameters. Here, under different pollination environment (natural and intrusive (pollen augmentation and/or bloom-delay)), the mating system of a second generation, wind-pollinated, coastal Douglas-fir (Pseudotsuga menziesii var. menziesii (Mirb.) Franco) seed orchard was evaluated over four years. Using DNA microsatellite markers and bulk seed samples, we conducted pedigree reconstruction to assign each seed’s male and female parents, followed by determining the extent of pollen contamination (external gene flow), selfing rate, and, parental gametic contribution for each year. Overall, external pollen contamination rates ranged between 10 and 28%, selfing rate varied between 12 and 17%, and 80% of the seed crops were produced by 37–64% of the orchard’s parents. Pollination environment and seed crop size substantially influenced the observed results, particularly for small crops as pollen contamination was high in natural (28%) vs. intrusive pollination (10%). Generally, irrespective of the crop size, seed produced under natural pollination had higher pollen contamination, confirming the role of pollination environment manipulation in improving seed crops’ genetic quality.

Innovative multiplex and its evaluation for effective genotyping of wild cherry

Trees from the family Rosaceae play an important role in forest and agricultural ecosystems. Therefore, they are often an object of interest for both forest and horticultural tree breeders. Here, we present the utilization of an effective microsatellite (SSRs) genotyping method for wild cherry (Prunus avium L.) and verified the discriminatory power of the presented multiplex by genotyping 48 genetically distinctive individuals (plus-trees). Concerned loci were previously proven to be cross-compatible among various cultivars of cherry, hence, the method could have a broader utilization beyond to the field of forestry. Our technique is based on post-PCR processing of 15 polymorphic SSRs loci amplified in three multiplex reactions with fluorescently labeled primers (6-FAM, VIC, PET and NED). All PCR products could be pooled and analyzed simultaneously (pseudo 15-plex). In order to make this approach feasible, we redefined sequences of several primers. Thus, utilizing modified primers provides non-overlapping amplicons of each fluorescent dye.

S-Genotype Diversity in Wild Cherry Populations in the Czech Republic

Abstract Wild cherry (Prunus avium L.) S-genotyping is aimed to uncover and thus make it possible to select appropriate genotypes applicable in establishing commercial plantations and advanced forest tree breeding activities. The general and long-term aim is to increase genetic gain in economically valuable traits while maintaining sufficient genetic variability (represented by diverse S-alleles in population). We genotyped 123 accessions from wild cherry growing areas in the Czech Republic using polymerase chain reaction based length polymorphisms detection of S-RNase and SFB genes. The studied plant material revealed 18 different S-haplotypes, 54 S-genotypes corresponded to 25 defined incompatibility groups of cultivated sweet cherry. Eighteen unique S-genotypes were designated to group ‘0’ as a universal pollinator. Eleven new incompatibility groups were found out, of which four were cross-compatible with sweet cherry cultivars. The most frequent was a new incompatibility group S14S21 followed by the group S12S14. The haplotypes S14 (13%) and S1 (10%) were the most frequent whereas S20 was less frequent in the wild populations of cherry. The present study of S-genotyping in the wild cherry population reveals the genetic diversity structure of natural populations and hopefully will help define the breeding strategy including more accurate planning activities such as the optimal seed design of orchards.