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ARS Home » Southeast Area » Byron, Georgia » Fruit and Tree Nut Research » Research » Publications at this Location » Publication #307199

Research Project: Breeding Stone Fruit Adapted to the Production Environment of the Southeastern United States

Location: Fruit and Tree Nut Research

Title: Expressed haplotypes and polymorphisms in prunus species

item Chen, Chunxian
item JUNG, SOOK - Washington State University
item MAIN, DORRIE - Washington State University

Submitted to: International Plant and Animal Genome IX Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/11/2013
Publication Date: 1/11/2014
Publication URL:
Citation: Chen, C., Jung, S., Main, D. 2014. Expressed haplotypes and polymorphisms in prunus species. International Plant and Animal Genome IX Conference. 22:222.

Interpretive Summary: Expressed sequences are redundant transcripts of genes that usually contain two same or different versions in a diploid genotype, called alleles (or haplotypes). Nucleotide discrepancies or polymorphisms between the two alleles, if affecting the protein sequence and function, may cause phenotype changes in crops. Identification of these gene-derived polymorphisms will greatly facilitate marker based linkage analysis and genetic association studies, and thereby enhances selection efficiency of trait-targeted breeding.

Technical Abstract: Expressed sequence tags (ESTs) represent collective and redundant gene transcripts that contain alleles and paralogs of genes expressed in various genotypes, tissues, developmental stages, and environmental conditions. The former are primarily responsible for distinct individual phenotypes in a segregating manner, and the latter may additionally contribute to functional and phenotypic diversification. In this study, genome-wide analysis was performed to identify expressed haplotypes harboring simple sequence repeat (SSR) polymorphisms, single nucleotide polymorphisms (SNP), short insertions / deletions, introns, coding degeneracy statuses (non-synonymous vs. synonymous), and other genomic features, using ESTs from all Prunus species and the peach reference genome. In addition, some unigenes containing a single haplotype but sharing high identities among them likely are paralogous functional members in a same gene family. The distribution of all polymorphic haplotypes on the peach reference genome was also determined to facilitate selective use of these expressed allelic polymorphisms and genomic features in many genetic studies, such as mapping of whole genomes, tagging of important traits, comparison of genome evolution, classification of diverse clades, and many rapidly developing areas such as pharmacogenomics and functional proteomics.