Analysis of expressed sequence tags from Prunus mume flower and fruit and development of simple sequence repeat markers.

BMC Genetics
Xiaoying LiJinggui Fang

Abstract

Expressed Sequence Tag (EST) has been a cost-effective tool in molecular biology and represents an abundant valuable resource for genome annotation, gene expression, and comparative genomics in plants. In this study, we constructed a cDNA library of Prunus mume flower and fruit, sequenced 10,123 clones of the library, and obtained 8,656 expressed sequence tag (EST) sequences with high quality. The ESTs were assembled into 4,473 unigenes composed of 1,492 contigs and 2,981 singletons and that have been deposited in NCBI (accession IDs: GW868575 - GW873047), among which 1,294 unique ESTs were with known or putative functions. Furthermore, we found 1,233 putative simple sequence repeats (SSRs) in the P. mume unigene dataset. We randomly tested 42 pairs of PCR primers flanking potential SSRs, and 14 pairs were identified as true-to-type SSR loci and could amplify polymorphic bands from 20 individual plants of P. mume. We further used the 14 EST-SSR primer pairs to test the transferability on peach and plum. The result showed that nearly 89% of the primer pairs produced target PCR bands in the two species. A high level of marker polymorphism was observed in the plum species (65%) and low in the peach (46%), and the clustering analys...Continue Reading

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Citations

Jul 9, 2016·BMC Research Notes·Karim SorkhehPedro Martínez-Gómez

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Methods Mentioned

BETA
PCR
electrophoresis

Software Mentioned

mume
pc
phd2fasta
NYSYS
CAP3
Perl script
Phred
MISA
Primer3
Oligo6

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