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ARS Home » Pacific West Area » Davis, California » Crops Pathology and Genetics Research » Research » Research Project #434776

Research Project: Integrated Conventional and Genomic Approaches to Almond Rootstock Development (2018-2019)

Location: Crops Pathology and Genetics Research

Project Number: 2032-22000-016-049-T
Project Type: Trust Fund Cooperative Agreement

Start Date: Oct 1, 2018
End Date: Jul 31, 2020

Objective:
Objective 1: Produce genetically diverse interspecific F1 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: Disease testing of experimental rootstocks to produce high quality disease phenotype data. Objective 3: high-density genotyping of experimental rootstocks to perform association analysis to develop efficient marker assisted selection strategies.

Approach:
Objective 1: Produce genetically diverse interspecific F1 hybrids involving Prunus spp. that are potential donors of disease resistance to enlarge diversity among hybrids to improve selection response and genetic gains. During the spring, 2018, we so far have completed 16 cross combinations involving about a dozen species and hybrids. We are planning several more utilizing some late peach genotypes in the USDA collection including a few P. cerasifera x wild almond species crosses. These hybrids will be sent to Sierra Gold Nurseries for embryo rescue/culture and clonal multiplication. Objective 2: Disease testing of experimental rootstocks to produce high quality disease phenotype data. Interspecific hybrids produced in the project are screened for resistance to all three major soil borne diseases, Crown Gall, Phytophthora root and crow rotes, and namatodes. 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 3: high-density genotyping of experimental rootstocks to perform association analysis to develop efficient marker assisted selection strategies. High-density genotype data along with the disease evaluation data will permit establishing association of marker genotypes with disease phenotype. This correlation upon validation will become the indirect selection criterion 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. During 2018, we will be developing DNA libraries of hybrid genotypes as we collate the phenotypic data on disease resistance. We will go for a second round of single nucleotide polymorphism discovery and genotyping through low-depth sequencing of hybrids. Subsequently, we will be augmenting genotypic and diseases phenotypic data for another round of genome-wide association analysis to identify marker linked to potential disease resistance genes, validation and developing of marker assisted selection 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. Association mapping analysis will be performed with a mixed-model implemented in TASSEL by integrating the marker-inferred population structure and the pair-wise co-ancestry or using Efficient Mixed-Model Association (EMMA), a R statistical computer software for association mapping using mixed-models.