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ARS Home » Pacific West Area » Davis, California » Crops Pathology and Genetics Research » Research » Research Project #413231

Research Project: Integrated Conventional and Genomic Approaches to Almond Rootstock Development

Location: Crops Pathology and Genetics Research

Project Number: 2032-22000-016-37-T
Project Type: Trust Fund Cooperative Agreement

Start Date: Oct 1, 2017
End Date: Jul 31, 2019

Objective:
Objective 1: Produce genetically diverse interspecific hybrids involving Prunus spp. that are potential donors of disease resistance to enlarge diversity among hybrids to improve selection response and genetic gains. Objective 2: Intensify genotyping-by-sequencing (GBS) based high density genotyping of rootstock breeding populations and perform association analysis to develop efficient marker assisted selection strategies. Objective 3: Disease testing of commercial and experimental rootstocks to produce high quality disease phenotype data. Objective 4: Develop and use effective marker assisted selection strategies for rapid development of improved rootstocks.

Approach:
Objective 1: We are planning to infuse plum species germplasm (P. salicina, P. cerasifera, P. americana, P. aungustifolia, and P. spinosa) in cross combinations with peach and almond species. Plums are known to possess nematode and Phytophthora tolerance and complement the rootability and graft compatibility of peach and almond species. Objective 2: We will be developing DNA libraries of hybrid genotypes as we collate phenotypic data on disease resistance. We plan to go for a second round of SNP discovery and genotyping during 2018. Subsequently, we will be augmenting genotypic and diseases phenotypic data from previous years for another round of genome-wide association analysis to identify marker linked to potential disease resistance genes, validation and developing MAS schemes. Perhaps the greatest advantage of effective MAS in tree crops is the ability to select hybrids that possess desirable characteristics at the juvenile stages. This tremendously saves time and resources and permits rapid development of improved rootstocks. GBS is cost-effective as it accomplishes both SNP discovery and genotyping simultaneously (Elshire et al., 2011). GBS permits high density genotyping and flexibility of data for genetic and association mappings. We will be utilizing GBS extensively to genotype commercial and experimental hybrid rootstocks. The SNP genotype data in combination with disease screening data will permit us to analyze for the association of markers with disease resistance loci. Association mapping analysis will be performed with a mixed-model implemented in TASSEL by integrating the marker-inferred population structure at an estimated number of subpopulations (Q-matrix) and the pair-wise co-ancestry or using EMMA (Efficient Mixed-Model Association), a package for the R statistical computer software for association mapping using mixed-models (Kang et al., 2008). Objective 3: Interspecific hybrids produced in the project will be subjected to screening for resistance to all three major soil borne diseases, CG, PHY and NEM. Standard disease screening protocols developed for each of these diseases will be implemented to stringently evaluate the plant response to controlled inoculation. The experiments are generally laid out in a standard statistical design to compute the analysis of variance to compare different experimental rootstocks. The disease response scores either in quantitative or in multistage format will be utilized to analyze the nature of inheritance of disease resistance. The data in combination with the molecular genotypic data will be subjected to association analysis. Objective 4: High density genotype data in combination with the disease data will permit establishing association of marker genotypes with disease phenotype. It is this correlation which upon validation will become the selection criterion called indirect selection. This strategy of indirect selection is called marker assisted selection which permits selecting desirable (resistant/tolerant) genotypes at the seedling and sapling stages without extensive disease testing process thus saving time and resources.