Rootstock Genetic Research: Project in Depth
The overall goal of the genetics research of the rootstock working group is to discover the underlying genetic basis of resistance in walnut to crown gall, Phytophthora, lesion nematode, and Armillaria through pathology screening and development of molecular markers to utilize in the development of improved walnut rootstock. Mapping resistance genes and quantitative trait loci (QTL) with molecular markers will allow us to identify markers linked to resistance genes/QTL thus accelerating the development of improved rootstocks at reduced cost.
The group has previously developed, or currently has in development, multiple genetic and genomic resources for J. regia. Resources currently available are single nucleotide polymorphisms (SNPs) located in gene coding regions, a 6K Illumina Infinium SNP assay, a SNP-based genetic map and a physical map for J. regia, bacterial artificial chromosome (BAC) end sequences (BES), gene tags mapped on the physical map, and RNA expression profiles of 20 tissues and/or developmental stages. Currently a whole genome shotgun (WGS) sequence of J. regia ‘Chandler’ is being assembled and WGS sequencing is in preparation for wild species J. microcarpa and J. cathayensis, a separate project funded by the California Walnut Board.
Our specific goals are to 1) complete development of a high resolution English walnut (J. regia) reference genome sequence, which will facilitate marker development and mapping resistance genes, 2) map genes controlling resistance to soil-borne pathogens in wild Juglans mother trees, and 3) develop molecular markers for efficient development of resistant rootstocks.
Approach & Activities
Though technically this phase of the research is just beginning, the group already has numerous resources developed or in development. One foundation for future work is to produce a completed assembly of the J. regia ‘Chandler’ genome sequence. To facilitate completion of the genome assembly we will nanomap the walnut genome, which will aid ordering and orienting the scaffolds onto the physical map and close any gaps between them. Nanomapping of the walnut genome will aid in transforming the currently assembled scaffolds into pseudomolecules, representing the 16 walnut chromosomes, and resulting in a reference genome for J. regia. To better annotate the genome for genes expressed in walnut roots, we will also add four root transcriptomes from rootstocks showing susceptibility or tolerance in response to soil-borne pathogens to the 20 scion tissue and/or developmental stage transcriptomes available from prior work.
Preliminary data supports that resistance is expressed in hybrids of wild Juglans spp. and J. regia, such as the commercially available rootstock RX1 (J. microcarpa x J. regia) that exhibits elevated resistance to Phytopthora spp. (PHY). Our preliminary crown gall (CG) screening demonstrates the ability of wild Juglans spp. and J. regia hybrids to express CG resistance. To utilize disease resistance found in wild species we must first identify mother trees with resistance from half-sib families, which are more efficient to produce in terms of cost, time, and labor. The half-sib family mean resistance of J. microcarpa accessions DJUG31.01 and DJUG31.07 to PHY and CG was significantly higher than the population mean. Likewise, half-sib progeny of J. cathayensis (accession DJUG 11.03) showed a greater degree of resistance to lesion nematode (NEM) than progeny of other mother trees tested. The segregation of resistant progeny in these and several other mother trees where the half-sib family means suggest resistance will be validated in a second round of half-sib evaluations. Mother trees showing significantly higher half-sib family means for resistance than the population mean will be used for gene/QTL mapping of resistance genes using populations of full-sib F1 interspecific hybrids.
- Walnut reference genome sequence.
- Comparative genetic maps densely populated with molecular markers for the discovery and mapping of disease resistance genes.
- Discovery and mapping of genes conferring resistance to soil-borne pathogens.
- Development of markers for selection of resistance genes in segregating populations.
- Knowledge-base and genomic tools for gene discovery and the deployment of marker assisted selection in walnut rootstock breeding.
- Genomic resources for wild relatives of English walnut, which will accelerate biological, agronomic and forestry research.