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ARS Home » Pacific West Area » Davis, California » Crops Pathology and Genetics Research » Research » Research Project #437733

Research Project: Integrated Conventional and Genomic Approaches to Almond Rootstock Development-HORT 16

Location: Crops Pathology and Genetics Research

Project Number: 2032-22000-016-074-T
Project Type: Trust Fund Cooperative Agreement

Start Date: Oct 1, 2019
End Date: Dec 31, 2020

1) Produce genetically diverse interspecific hybrids involving Prunus spp. that are known to be potential donors of resistance to soil borne diseases. 2) Perform disease resistance screening of rootstock hybrids produced in obj. 1 to identify resistant hybrids based on high quality disease resistance data. 3) Genotype experimental rootstocks to facilitate association analysis and genomic prediction to develop efficient marker assisted selection (MAS) strategies and to estimate genetic worth of hybrids. 4)Propagate and bud/graft scion cultivars on to disease resistant rootstocks identified in obj. 2 for use in preliminary field trials.

1) Produce 30-40 interspecific hybrid combinations, each with several thousand pollinations. Hybridization in Prunus is laborious as we have to emasculate flowers followed by two-three rounds of pollination with each successfully pollinated flower yielding a single seed. In these situations, the embryos need to be harvested/rescued at an immature stage before the embryo aborts so they can be placed into our in vitro micropropagate pipeline. 2) 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 ordinal/categorical 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 and genomic prediction analyses. 3) The DNA from ~200 interspecific hybrids collected in the summer of 2018 will be used in genomic library preparation. We will construct barcoded genomic libraries for each sample using Illumina's Nextera DNA Library Prep kit and barcoded adapters. The genomic libraries will be pooled equally and sequenced at paired-end 100 (PE100) on four lanes of an Illumina HiSeq 4000 sequencer generating a minimum of 50 Gb per lane. 4) This objective will be performed as we select promising disease resistant hybrids. Typically, hybrids are identified as resistant/tolerant after going through at a two-year evaluation cycle for all the three diseases (PHY/CG/NEM). Promising hybrids will be propagated and scions grafted for replicated field trials. At this stage, the rootstocks will be evaluated for tolerance to biotic and abiotic factors and important horticultural traits such as scion control, precocity, yield, suckering, graft compatibility etc.