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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

2018 Annual Report


1a. Objectives (from AD-416):
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.


1b. Approach (from AD-416):
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.


3. Progress Report:
In FY 2018, three selections were identified for release as new pecan cultivars (Objective 1): 1996-01-0295 [Pawnee X Waco]; 1997-34-0017 [NC2B X NC4]; and 2000-01-0027 [91986-03-0319 X NC4]. The release process is being coordinated with the national pecan industry. Cooperation with plant pathologists in Georgia led to recognition of a new fungal disease (Neofusicoccum spp.) present in both Georgia and Texas (Objective 1). ARS collections were screened for that disease; 'Pawnee' and 'Waco' were identified as the most susceptible cultivars in our collections, necessitating coordinated evaluation in relation to the new pathogen. Increased attention focused on Xylella fastidiosa in FY 2018 influenced evaluation of controlled cross progenies in cooperator orchards in Alabama, highlighting the need for genomic methods currently under development (Objective 3). 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 made in FY 2017, and measured and planted in FY 2018 (Objective 1). Open-pollinated progeny of individuals in rootstock screening at Uvalde, Texas, were subjected to genotyping by sequencing (GBS) analysis in cooperation with Texas A&M AgriLife Research to determine the extent that pollen parent contributes to observed patterns of seedling growth, thus exploring questions of heterosis (hybrid vigor) at the population level (Objective 2). An individual genotype (87MX4-5.5, originated from Repository collections made in Hidalgo, Mexico) was identified for release as an open-pollinated seedstock. In FY 2018 work, cooperative research with a team of researchers from New Mexico State University, the HudsonAlpha Genome Sequencing Center, Texas A&M University, and the University of Georgia, developed reference genome sequences of 'Pawnee', 'Lakota', 'Elliott', and 87MX3-2.11 (Objective 3). Particular focus was on improving resolution of the first to be released reference genome sequences (87MX3-2.11) using consensus linkage analysis developed from the ARS mapping population ('VC1-68' X 'Elliott'), and the University of Georgia mapping population ('Pawnee' X 'Elliott'). Chloroplast sequences of 'Lakota' and 87MX3-2.11 were also aligned and interpreted, confirming accuracy and positions of 3 previously developed plastid microsatellite markers. Over the life of this project, major advances were made in the development of genomic tools to facilitate evaluation of Carya (pecan) germplasm. This significantly increased the participation of domestic and international cooperative programs in coordinated, strategic efforts for genomic analysis. This project expired in FY 2018 and was replaced by 3091-22000-039-00D which is continuing and expanding upon the work.


4. Accomplishments
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 scientists at College Station, Texas, working with colleagues at the HudsonAlpha Genome Sequencing Center, Texas A&M University, the University of Georgia, and New Mexico State University used consensus linkage analysis based on GBS of previously developed mapping populations in Texas and Georgia to refine sequence resolution of the first reference genome for pecan, 87MX3-2.11. This work is foundational to the use of modern molecular and genomic techniques to develop new, more productive, more disease resistant pecan types for U.S. farmers.