Articles
TOWARDS A REFERENCE PECAN GENOME SEQUENCE
Article number
1070_11
Pages
101 – 108
Language
English
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.
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.
Authors
J. Jenkins, B. Wilson, J. Grimwood , J. Schmutz, L.J. Grauke
Keywords
pecan, genome sequencing, polymorphism, SNPs
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