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ARS Home » Plains Area » Stillwater, Oklahoma » Wheat, Peanut, and Other Field Crops Research » Research » Research Project #430142

Research Project: Development of a Transcriptome-Based GBS System for Peanut Breeding

Location: Wheat, Peanut, and Other Field Crops Research

Project Number: 3072-21220-008-12-N
Project Type: Non-Funded Cooperative Agreement

Start Date: Jan 1, 2016
End Date: Dec 31, 2020

Our central hypothesis is that it is possible to use SNP polymorphism data to develop a simple, flexible, cost-effective system for marker analysis, suitable to the needs of breeders. Genotype-by-sequencing offers the possibility of identifying a large number of SNPs for a limited number of individuals at a cost far lower than in the past. However, problems of sequence representation and cost ($50/sample) still make this infeasible for large breeding populations, and a further modification of sequencing methods is needed. The goal is to reduce the cost per plant sample to $10. Here, we propose to use SNPs originally identified by transcriptome (RNA-Seq) and reduced representation genome sequencing (RAD-Seq) in a targeted resequencing effort to develop medium-density (200-1000 SNP) genetic marker maps that can be used for selection of QTLs in a breeding population, and far more inexpensively than can be done using previous sequencing methods. The work will have the following five objectives: 1. Develop B genome and tetraploid populations 2. Develop primers for B-genome and tetraploid mapping populations, and screen against parents and other breeding lines in the southwest 3. Map markers on the population 4. Map QTLs for greenhouse-derived data 5. Release data to Peanutbase

Need for SNPs: Single-nucleotide polymorphisms offer a power of detection and speed far in excess of other marker technologies used in peanut. It has been estimated that there are more than 3.1 million SNPs in the human genome. SSR mapping has typically required test scoring of hundreds or thousands of SSRs to identify a number barely sufficient for genetic analysis. The time and labor cost for marker analysis of a population is very high, both in cost of time (years) and reagents. Use of SNP-based markers can reduce time for genotyping to a matter of days. In chicken, using 3072 SNPs, 2396 genotypes were scored in this manner in 3 months. In barley, SNP markers were mapped on 3 populations in this manner and more recently, a transcriptome-based resequencing system has been developed for barley, representing most of the genes in that species. In addition, the quick turnaround for marker-assisted selection is important for making selections in the time frame of a breeding program, which typically may have a window of a few weeks for DNA isolation, analysis, and selection.