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ARS Home » Pacific West Area » Davis, California » Nat'l Clonal Germplasm Rep - Tree Fruit & Nut Crops & Grapes » Research » Research Project #434841

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

Location: Nat'l Clonal Germplasm Rep - Tree Fruit & Nut Crops & Grapes

Project Number: 2032-21000-024-08-T
Project Type: Trust Fund Cooperative Agreement

Start Date: Apr 1, 2018
End Date: Jun 30, 2019

Objective:
Objective 1: Produce genetically diverse pistachio interspecific hybrids involving diverse species that are potential donors of resistance to soil borne pathogens and pests, and use embryo rescue/culture and micropropagate clonal plants. Objective 2: Evaluate experimental rootstocks for tolerance to Verticillium wilt, Phytophthora root and crown rot, and Nematodes to produce high quality disease phenotype data. Objective 3: Develop and use genomic tools to characterize pistachio wild gene pools and rootstock breeding populations to decipher genetic basis for rootstock traits. Objective 4: Develop and implement effective marker assisted selection strategies for rapid development of improved rootstocks.

Approach:
We have produced several pistachio interspecific hybrids, which are in micropropagation and more are produced as we implement the project. Major focus will be on the sect. Eu Terebinthus comprising P. khinjuk, P. integerrima, P. palaestina, P. terebinthus, and P. vera. Pistacia spp. are rich in polyphenols and tannins, which interfere with embryo culture and standardization of protocols is critical for successful embryo rescue and clonal propagation of interspecific hybrids. Immature embryos are germinated in vitro, shoots multiplied, and rooted in presence of auxin in darkness to produce clonal plants for disease testing and field evaluations. We use well-tested disease evaluation protocols for screening interspecific hybrids for the major soil borne diseases; Verticillium wilt (VERT; Verticillium dahliae), Phytophthora crown rot (PHY; Phytophthora spp.) and root knot, lesion, and ring nematodes (NEM). Three plant pathologists; two specialized in Phytophthora crown and root rot diseases and the other in Verticillium wilt, are the CoPIs in this project. They will be screening important germplasm and breeding populations developed at the National Clonal Germplasm Respository (NCGR)to produce disease phenotype data. In cooperation with a Nematologist, at UC Riverside, Kearney Ag. Center, we will evaluate rootstocks generated in the project for tolerance to nematodes. A professor at the UC Davis Plant Sciences Department will be developing the molecular and genomic resources to assay and analyze pistachio wild gene pools and breeding populations to decipher the genetic basis for biotic and abiotic traits and genomic prediction of rootstock performance in the genetic improvement of rootstocks. An ARS scientist will perform embryo rescue, tissue culture, and horticultural phenotyping of hybrids. The wild species of the sect. Eu Terebinthus constitute the association mapping population (AMP) as well as used for interspecific hybridization. SNP discovery and genotyping of AMP are accomplished by the RAD-Seq strategy. AMP is evaluated for tolerance to Verticillium wilt, Phytophthora root and crown rots, and Nematodes. The genotype and disease phenotype data are subjected to association analysis to identify SNPs linked to disease resistance. We infer population structure and the pair-wise coefficient of co-ancestry using appropriate statistical methods. Association analysis is performed with a mixed linear model by integrating the marker-inferred population structure and the pairwise co-ancestry. Independent association analysis using general linear, stepwise, and mixed regression models with population structure and coancestry as covariates is performed using SAS to compare results. After validation of associations, marker assisted selection strategies will be developed and implemented in ongoing pistachio rootstock breeding efforts.