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ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Crop Germplasm Research » Research » Research Project #424405

Research Project: Pecan Improvement through Breeding and Genetics

Location: Crop Germplasm Research

2017 Annual Report

The long-term goal of this project is to produce improved scion and rootstock cultivars for the U.S. pecan industry. The project will also elucidate genetic control of important pecan traits using traditional and molecular genetics techniques. Over the next 5 years we will focus on the following objectives: Objective 1: Develop new pecan scion cultivars with high yield, superior nut quality, and improved resistance to diseases and insects. Focus will be on early nut maturity to reduce impact of alternate bearing and improved resistance to pecan scab. Sub-objective 1A: Develop high yielding pecan scion cultivars with early nut maturity, improved nut quality, and superior disease and insect resistance. Sub-objective 1B: Elucidate the genetic control of key horticultural traits in pecan utilizing appropriate qualitative and quantitative techniques. Sub-objective 1C: Characterize kernel composition found in native pecans across the species range. Objective 2: Develop superior rootstocks with outstanding vigor and site adaptation for all pecan growing regions. Sub-objective 2A: Quantify heterosis in pecan. Sub-objective 2B: Screen diverse seedling rootstocks for resistance to the root knot nematode. Sub-objective 2C: Refine recognition of rootstock effects on phenology and nutrient accumulation, impacting regional deployment. Objective 3: Develop genetic markers for use in genotyping diverse Carya breeding lines. Sub-objective 3A: Develop scaffold framework for sequence alignment. Sub-objective 3B: Use Restriction-site Associated DNA sequencing (RADseq) techniques to conduct phylogeographic analysis on populations of native pecans.

Research objectives will be met by basic genetic research and by an intensive cultivar and rootstock selection program. Phenotypic breeding techniques, supplemented with molecular tools, will be used to develop and release new pecan scion cultivars with high yield and quality, exhibiting improved disease and insect resistance. Similar approaches will be utilized to develop superior pecan rootstocks with outstanding vigor and salt tolerance. Qualitative and quantitative techniques, in conjunction with molecular techniques, will be used to elucidate the genetic control of key horticultural traits in pecans. Genetic research conducted by this project will increase our knowledge of the genetic control of yield components, nut maturity, nut quality, tree size, and disease and insect resistance. The scion cultivar development component of the work will produce precocious, high-yielding, regular bearing, disease- and insect-resistant cultivars that also have high nut quality. Rootstock breeding activities will produce new rootstocks with improved vigor, uniformity, salt tolerance, disease and insect resistance, and specific geographical adaptation; and which will ultimately contribute to increased yields of grafted scions.

Progress Report
In FY 2017 work, cooperative research with HudsonAlpha Genome Sequencing Center was continued on the reference genome sequences for two pecan types, 87MX3-2.11 and 'Pawnee', and initiated for reference templates for 'Lakota' and 'Elliott' (Objective 3). Buds, leaves, flowers, and root tissues were collected from multiple inventories of reference genetic types (genotypes) for RNA extraction to be used in genetic studies known as transcriptome analysis. The work was done in cooperation with scientists from Texas A&M University, New Mexico State University, and HudsonAlpha. A diversity panel of over 100 individual pecan types representing controlled crosses and parents with selected diverse relatives was analyzed using a molecular technique known as genotyping by sequencing (GBS); the work identified markers associated with a genetic trait known as heterodichogamy. Project objectives to develop new pecan scion (graft wood) cultivars with the aid of improved genomic methods were addressed through creation of a series of controlled crosses coordinated in conjunction with the pecan researchers at ARS in Byron, Georgia and the University of Georgia (Objective 1). Tissue samples collected from open-pollinated progeny of high performing individuals in rootstock screening at Uvalde, Texas, were subjected to GBS analysis in cooperation with cooperators at Texas A&M AgriLife Research to determine the extent that pollen parent contributes to observed patterns of seedling growth, exploring questions of heterosis (hybrid vigor) at the population level (Objective 2).

1. Molecular methods to accelerate pecan improvement. In order to better understand cultivar characteristics, appreciate regional adaptation, and improve selection in pecan breeding programs, improved genomic tools that are cost-effective and capable of high-throughput screening are necessary. ARS researchers at College Station, Texas, working with Texas A&M University colleagues, characterized a diverse panel of more than 100 pecan cultivars and accessions from the USDA ARS National Collection of Genetic Resources for Pecans and Hickories (NCGR-Carya). These were selected to represent regionally adapted native pecans, controlled cross progeny with both parents, selected wild relatives, and interspecific hybrids between those species. A technique known as genotyping by sequencing (GBS) was used to discover over 87,000 genetic traits known as single nucleotide polymorphisms (SNPs) throughout the pecan genome, by aligning to a draft reference scaffold developed by the project. SNPs were used to develop genomic profiles to confirm, refute, or inform questions of cultivar origin, both in terms of lineage and geography. The work discovered 34 SNPs that are significantly associated with expression of the simply inherited trait controlling flowering type (heterodichogamy). Information, techniques, and resources developed in this research will benefit the pecan community by improving the ability to associate expressed traits with genes, which will reduce breeding time by facilitating more informed and efficient selection of parents and progeny.

Review Publications
Bock, C.H., Grauke, L.J., Conner, P., Burrell, S.L., Hotchkiss, M.W., Boykin, D.L., Wood, B.W. 2016. Scab susceptibility of a provenance collection of pecan in three different seasons in the Southeastern USA. Plant Disease. 100(9):1937-1945.
Medrano, E.G., Grauke, L.J., Thompson, T.E., Stanford, R. 2017. Evidence for the presence of an endosymbiont in the pecan scab pathogen Venturia effusa (basyonym: Fusicladium effusum). Journal of Applied Microbiology. 123:491-497.