Webinar: Breeding in a Genomics Era
During this webinar, presented at the 2011 Potato Association of America conference, Dr. David Francis, The Ohio State University, discusses the use of genome-level data for potato breeding, including breeding strategies and genotyping strategies.
Dr. Francis introduces the concept of using genome scale data for crop improvement and reviews equations fundamental to plant breeding and their implications. Specifically, emphasizes the use of marker-assisted selection (MAS) to accelerate the breeding cycle. Other topics also discussed are populations and population structure in the context of academic and breeding programs and appropriate approaches for data analysis; importance of collecting objective, standardized, and quantiative phenotypic data to allow linkage between phenotype and ontology as ontology data can be readily stored in databases and trait heritability can be accurately estimated; and the rapid changes in genotyping technology.
In addition, he stresses that availability of high quality genotypic data should no longer be a limitation for breeding programs. Dr. Francis poses questions to help plant breeders assess how and why they may use genome-wide SNP data and demonstrates use of genome-wide SNP data in tomato. Furthermore, Dr. Francis considers strategies for cost-efficient genotyping of breeding populations depending on intended application of the data.
He also discusses about strategies for integrating genotyping and breeding, including examples from tomato, and standing out the importance of population size and selection strategy with regards to potential for successful integration of genotyping and breeding.
Finally, Dr. Francis demonstrates how to maximize population size with equal resources using an augmented design. Dr. Francis introduces augmented design and a sample analysis pipeline considering genotypes as fixed or random effects.