Breeding

Plant breeding is undergoing a major change in methodology with the application of DNA-based markers for selection. Little has been done to quantify the efficiency of apple breeding, or indeed tree fruit breeding, with or without the new technology. This study aims to investigate the impact on different optimization criteria of alternative designs for an evaluation of selection candidates established in phase 2 field trials of the Washington State University Apple Breeding (WABP) program using two metrics. Acceptance probability, an extension of the least significance difference (LSD) common in statistics, has been used to evaluate alternative trial designs. Acceptance probability expresses the observed percentage difference a candidate must have when compared to a standard(s) to reject the hypothesis that the mean of the candidate is equal to the mean of the standard(s). Response to selection was also used to compare alternative designs which differ in trial size. This is because variation in numbers of candidates may affect both variation of predicted cultivar mean (similar to the account in LSD and acceptance probability) and the intensity of selection. Apple breeding is a costly and long-term investment (18 years minimum from cross to release), for which improvements in efficiency have huge positive repercussions. Opportunities for improvement identified in the WABP can then be adopted by other tree fruit breeding programs, resulting in faster development of new varieties.

Apple breeding populations are valuable resources in genomic, physiological and genetic research. They help to reveal unique traits, assess characteristics of distantly related Malus species and generate useful materials for elucidating components of fruit quality and plant morphology. The germplasm resources within breeding programs allow the comparison of traits across a host of harvest times and genetic backgrounds. Using cultivars as both a maternal and paternal parent often yield differences in trait expression in these reciprocal crosses. This presentation will provide a “behind the scenes” look at unexpected traits found within progenies. The purpose of the cross will be provided, including parental attributes, followed by images of traits, which deviate from expectations. Variants in tree architecture, fruit cuticle attributes, fruit size and shape and postharvest attributes will be explained. Different types of genetic dwarfs will be described, along with variants for leaf morphology. This presentation seeks to foster further discussions on such resources within breeding programs and how best to leverage them for studying traits of importance.

Verticillium wilt is a major obstacle to U.S. strawberry production. Our current and ongoing investigations include defining new sources of resistance in cultivated and wild strawberry germplasm, and advancing genetic studies on the basis of resistance/susceptibility. We screened 26 octoploid, 1 decaploid, and 23 diploid strawberry genotypes for response to root-dip inoculation with Verticillium dahliae isolate V1. Inoculated plants were individually rated at eight weeks post-inoculation using a categorical scale: 1=healthy; 1.5=slightly symptomatic; 2=moderately symptomatic; 2.5=very symptomatic; 3=dead. Qualitative classifications were assigned to genotypes on the basis of their respective mean disease resistance ratings. The rating ranges and corresponding classifications (in parentheses) were: 1.0-1.3 (very resistant = VR), 1.4-1.7 (moderately resistant = MR), 1.8-2.2 (intermediate = I), 2.3-2.6 (moderately susceptible = MS), and 2.7-3.0 (very susceptible = VS). Considerable variability in inoculation response existed within and between species at both the diploid and octoploid levels. VR or MR genotypes were found within each of the following species: diploids F. vesca, F. iinumae, and F. nipponica); and octoploids F. chiloensis, F. virginiana, and F. ×ananassa. MS and VS genotypes were documented within F. vesca, within each octoploid species, and in a genotype of decaploid F. cascadensis. We compared our screening results to those of previous studies and constructed a pedigree of the evaluated and related octoploid cultigens for visualization. We also made resistant × susceptible crosses at both the diploid and octoploid levels as a step toward genetic analysis of wilt resistance/susceptibility and resistance gene identification in strawberry.

Rapid development of single nucleotide polymorphism (SNP) markers and their automation have resulted in SNPs becoming the molecular markers of choice in high throughput genotyping of a wide variety of plant species. Advantages of SNPs include prolificacy of polymorphism in any genome, ease of their development, low error rate of genotype calling, and the possibility of finding polymorphism within genes of interest. SNP genotyping platforms provide low cost and high throughput capabilities resulting in a dramatic reduction in cost efficiency. This cost reduction has made the application of marker-assisted breeding technology affordable for even the smallest plant breeding programs.

We will describe how the combination of High Marker Throughput (HMT) and High Sample Throughput (HST) platforms implemented at BioDiagnostics, Inc. (BDI) has been used to assist breeding programs. This combination can be used to optimize the value of breeding projects’ funds by increasing success and reducing cost and time to market of new varieties. We will explain how BDI can reduce the time between developing useful trait markers and implementing them in your breeding programs, using association mapping studies. Advantage of genomic selection in plant breeding with practical examples and also in tree fruit breeding will be discussed. We will also provide examples of projects that have been conducted at BDI to assist breeding programs in the new genomics era.