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United States Department of Agriculture

Agricultural Research Service


Location: Crop Germplasm Research

2012 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: Enlist phenotypic breeding techniques, supplemented with molecular tools, to develop and release new pecan scion cultivars with high yield and quality, and improved disease and insect resistance. Sub-objective 1.A: Develop high yielding pecan scion cultivars with early nut maturity, improved nut quality, and superior disease and insect resistance. Sub-objective 1.B: Develop DNA markers to identify genetic variability and enhance the selection of superior scion cultivars. Objective 2: Enlist traditional selection techniques and newly developed molecular tools, to develop superior pecan rootstocks with outstanding vigor and salt tolerance. Sub-objective 2.A: Establish patterns of variation in pecan seedlings as a function of geographic origin. Sub-objective 2.B: Develop additional molecular genetic tools for use in pecan, including markers based on sequences of the chloroplast genome and capable of discriminating between accessions of pecan on the basis of maternal inheritance. Objective 3: Apply qualitative and quantitative techniques, in conjunction with molecular techniques, to elucidate the genetic control of key horticultural traits (such as yield level, nut size, time of nut maturity, salt tolerance, and disease and insect resistance) for pecans. Sub-objective 3.A: Elucidate the genetic control of key horticultural traits in pecan utilizing appropriate qualitative and quantitative techniques. Sub-objective 3.B: Establish families of controlled cross seedling pecans suitable for use in mapping qualitative and quantitative trait loci related to scab disease resistance, and to determine levels of scab resistance within those progenies.

1b. Approach (from AD-416):
Research objectives will be met by basic genetic research and by an intensive cultivar and rootstock selection program. These improvements will be accomplished through several approaches. Phenotypic breeding techniques, supplemented with molecular tools, will be used to develop and release new pecan scion cultivars with high yield and quality, and 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:
The project's pecan breeding program during FY 2012 evaluated more than 8,000 controlled-cross seedlings in the Basic Breeding Program (BBP). Almost 10,000 trees (clones) were evaluated for scab resistance, nut maturity date, nut quality, and yield to select 105 elite clones for further evaluation. In the BBP crossing program, 1,342 pecan clusters were control-crossed utilizing 15 parental clones. Scab resistance screening of clones from crossings done in FY 2010 and FY 2011 was conducted under scab-infected trees (total of 730 clones). Data from 17 NPACTS (National Pecan Advanced Clone Testing System) tests from other sites were added to master databases to provide evaluation data for future pecan variety releases. Graftwood of Lipan, released to growers in 2011, was disseminated to pecan nurseries. The goal of developing additional DNA markers related to scab resistance (and other genetic traits) was pursued in FY 2012 through a newly developed cooperative effort with molecular researchers working on Juglans, a sister genus. Existing markers were used to evaluate a subset of the pecan cultivar collection as well as a core of the provenance collection. The controlled cross mapping population for scab resistance was evaluated in FY 2012, and is currently being sampled for genetic analysis to verify cross integrity. Families from crosses of resistant and susceptible parentage should represent maximum genetic segregation and elucidate genetic control of this important genetic trait. A diverse group of seedstocks, planted in FY 2009 into plots infected with cotton root rot, yielded valuable data in FY 2012; mortality due to the disease was verified and studies on differential response are ongoing. In FY 2012, diverse pecan and hickory seedstocks were established in plots infested with the root knot nematode in an effort to identify sources of resistance to this pest. All seedstocks became infested, with no sources of resistance evident.

4. Accomplishments
1. Circumventing alternate year bearing in pecan. Pecan is an important U.S. nut crop that is primarily grown by small producers, with most commercial pecan orchards being 20 acres or less in size. Profit margins are minimal for most producers, and the alternate bearing problem (profitable crops only every other year) in pecan poses a severe cash flow problem for producers in years of little or no crop. New pecan varieties are needed that will bear good nut crops every year. ARS researchers at College Station, Texas, developed statistical procedures to define year-to-year stability constants applicable to most major yield components evaluated in the pecan breeding program. This Phenotypic Stability Index, or PSI, will help guide the breeding program to more quickly develop new, non-alternate bearing pecan varieties that will enhance producer profitability and price stability from year to year.

Review Publications
Thompson, T.E., Grauke, L.J. 2012. 'Lipan' Pecan. HortScience. 47(1):121-123.

Thompson, T.E., Conner, P.J. 2012. Pecan. In: Badenes, M.L., Byrne, D.H., editors. Handbook of Plant Breeding, 1, Volume 8, Fruit Breeding, Part 4. New York, NY: Springer Publishing. p. 771-801.

Last Modified: 06/25/2017
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