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ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Crop Germplasm Research » Research » Publications at this Location » Publication #310069

Research Project: Management and Characterization of Pecan (Carya) Genetic Resources and Related Wild Populations

Location: Crop Germplasm Research

Title: Towards a reference pecan genome sequence

Author
item Jenkins, Jerry - Hudsonalpha Institute For Biotechnology
item Wilson, Brent - Hudsonalpha Institute For Biotechnology
item Grimwood, Jane - Hudsonalpha Institute For Biotechnology
item Schmutz, Jeremy - Hudsonalpha Institute For Biotechnology
item Grauke, Larry - L J

Submitted to: Acta Horticulturae
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/22/2014
Publication Date: 2/15/2015
Citation: Jenkins, J., Wilson, B., Grimwood, J., Schmutz, J., Grauke, L.J. 2015. Towards a reference pecan genome sequence. Acta Horticulturae. 1070:101-108.

Interpretive Summary: Development of molecular markers for use in pecan has been slow, but cooperative research efforts were initiated to provide tools that can speed further efforts. Two pecan genotypes were sequenced and assembled, providing the first drafts of genomic "maps" for pecan. The draft assemblies have been delivered to researchers who are using them for the development of additional genomic markers. These markers will greatly facilitate ongoing efforts to develop new pecan cultivars for productive and profitable use by U.S. farmers.

Technical Abstract: The cost of generating DNA sequence data has declined dramatically over the previous 15 years as a result of the Human Genome Project and the potential applications of genome sequencing for human medicine. This cost reduction has generated renewed interest among crop breeding scientists in applying sequencing and new genomic tools to accelerate traditional breeding programs by both increasing the specificity of offspring selection and by better understanding the genetic material within a program to reduce breeding cycle times. Pecan (Carya illinoinensis) is an important native tree nut crop with production that averaged over 130 metric tons (t)/y from 2010 to 2012, with farm gate value of over $600 million/y (NASS 2013). Pecan trees have extended periods of juvenility before they begin to bear and the time from initial cross to release has averaged almost 30 years for the 29 pecan cultivars released by the USDA ARS Pecan Breeding Program. In order to assess the feasibility of applying genomic technologies to pecan improvement, we generated low-cost, short-read sequences for two pecan cultivars, the commonly planted cultivar 'Pawnee' and a Mexican derived accession named 87MX3-2.11. We assembled these sequences, and assessed genomic repeat content and polymorphism rate between the two haplotypes for each tree. We also identified SNPs and short indels within each of the two cultivars and between the two cultivars based on comparing this short read data to the reference assembly for 87MX3-2.11. Finally, we suggest a path forward for generating a reference pecan genome sequence as a platform for accelerating crop improvement, taking advantage of current genomic technologies.