Mining and characterizing microsatellites from citrus ESTs

• Published in: Theoretical and applied genetics Vol. 112; no. 7; pp. 1248 - 1257
• Main Authors: Chen, C, Zhou, P, Choi, Y.A, Huang, S, Gmitter, F.G. Jr
• Format: Journal Article
• Language: English
• Published: Heidelberg Springer 01-05-2006; Berlin Springer Nature B.V
• Subjects: Alleles; Base Sequence; bioinformatics; Biological and medical sciences; Citroncirus webberi; Citrus - genetics; Citrus fruits; Citrus sinensis; Classical genetics, quantitative genetics, hybrids; computer software; Computers; Crosses, Genetic; DNA primers; DNA, Plant; Expressed Sequence Tags; Fundamental and applied biological sciences. Psychology; gene banks; Genes, Plant; Genetic Markers; genetic polymorphism; Genetics of eukaryotes. Biological and molecular evolution; Genomics; heterozygosity; Heterozygote; Homozygote; loci; Microsatellite Repeats; Mining; oranges; polymerase chain reaction; Polymorphism, Genetic; Poncirus - genetics; Poncirus trifoliata; Pteridophyta, spermatophyta; Software; Software Design; Vegetals; Citrus; Dicotyledones; Microsatellite DNA; Angiospermae; Rutaceae; Genetics; Spermatophyta; Agriculture
• ISSN: 0040-5752; 1432-2242
• DOI: 10.1007/s00122-006-0226-1

Freely available computer programs were arranged in a pipeline to extract microsatellites from public citrus EST sequences, retrieved from the NCBI. In total, 3,278 bi- to hexa-type SSR-containing sequences were identified from 56,199 citrus ESTs. On an average, one SSR was found per 5.2 kb of EST sequence, with the tri-nucleotide motifs as the most abundant. Primer sequences flanking SSR motifs were successfully identified from 2,295 citrus ESTs. Among those, a subset (100 pairs) were synthesized and tested to determine polymorphism and heterozygosity between/within two genera, sweet orange (C. sinensis) and Poncirus (P. trifoliata), which are the parents of the citrus core mapping population selected for an international citrus genomics effort. Eighty-seven pairs of primers gave PCR amplification to the anticipated SSRs, of which 52 and 35 appear to be homozygous and heterozygous, respectively, in sweet orange, and 67 and 20, respectively, in Poncirus. By pairing the loci between the two intergeneric species, it was found that 40 are heterozygous in at least one species with two alleles (9), three alleles (28), or four alleles (3), and the remaining 47 are homozygous in both species with either one allele (31) or two alleles (16). These EST-derived SSRs can be a resource used for understanding of the citrus SSR distribution and frequency, and development of citrus EST-SSR genetic and physical maps. These SSR primer sequences are available upon request.