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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETICS AND GENETIC IMPROVEMENT OF DISEASE RESISTANCE AND QUALITY TRAITS IN WATERMELON, BROCCOLI, AND LEAFY GREEN BRASSICAS

Location: Vegetable Research

Title: Identification of SNP Haplotypes and Prospects of Association Mapping in Watermelon

Authors
item Nimmakayala, P -
item Tomason, Y -
item Vajja, G -
item Abburi, L -
item Pegadaraju, V -
item Wijeratne, A -
item Levi, Amnon
item Reddy, U -

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: December 25, 2011
Publication Date: N/A

Technical Abstract: Watermelon is the fifth most economically important vegetable crop cultivated world-wide. Implementing Single Nucleotide Polymorphism (SNP) marker technology in watermelon breeding and germplasm evaluation programs holds a key to improve horticulturally important traits. Next-generation sequencing strategies coupled with the high-density genotyping platforms offer an opportunity to discover SNP markers and use them in routine genotyping projects in a cost effective manner. We discovered a large number of SNPs (>10,000) using Restriction site Associated DNA (RAD) protocol and Illumina/Solexa paired-end sequencing. Genomic DNAs of mapping parents (PI 244018 of var. citroides and PI270306 of var. lanatus) were used for SNP discovery. A subset of 384 SNPs with high ADT(Assay Design Tool) design scores were idenitfied for Illumina golden gate genotyping. Genotyping experiments were carried using the Illumina BeadExpress platform on the genomic DNAs of a mapping population (94 progenies) and 288 genbank accessions containing 273, 9 and 6 accessions of var. lanatus (Citrullus lanatus var. lanatus), citroides (Citrullus lanatus var. citroides) and colocynthis (Citrullus colocynthis) respectively. A genetic map was constructed by integrating SNP data with the previously mapped 120 microsatellite markers. Molecular diversity data was further used to analyze the population structure and LD blocks. We identified SNP haplotypes within the cultivated watermelon. Fruit quality data obtained from the field evaluation of 40 cultivated watermelons provided preliminary insights into the use of SNP data for association mapping strategies.

Last Modified: 4/20/2014
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