DEVELOPMENT OF SNP MARKERS FOR MARKER-ASSISTED SELECTION IN PEAR

Abstract

Single-nucleotide polymorphisms (SNPs) are desirable DNA markers for marker-assisted selection because of their high abundance, codominant inheritance, locus specificity and potential for automated high-throughput analysis. The average number of SNPs in introns has been reported to be several times higher than that in exons in many organisms. Potential intron polymorphism (PIP) markers, designed from expressed sequence tag (EST) sequences (exon regions), could amplify potential flanking intron regions without requiring genome sequence information. In this study, we used PIP markers designed from apple (Malus × domestica) ESTs to identify intron regions and to detect SNPs in pear (Pyrus spp.). We evaluated 170 PIP markers for Japanese pear P. pyrifolia cultivar 'Housui' and the European pear P. communis cultivar 'Bartlett'. Of the 170 PIP markers, 142 markers amplified fragments in both cultivars. The fragment size was larger than the size predicted from the apple EST sequences, suggesting the existence of introns in the amplified fragments. We sequenced the amplified fragments and detected candidate bi-allelic SNPs in intron regions of both cultivars. The genome sequences obtained from pear were aligned to the apple EST sequences, revealing that the sequences included donor and acceptor sites, and contained deduced exons and flanking introns in pear. SNP analysis showed that 55 and 54 markers were mapped on the genetic linkage maps of 'Bartlett' and 'Housui', respectively. The PIP markers designed from apple ESTs were applicable in pear and could be used to detect SNPs in intron regions and to develop SNP markers in pear. The PIP markers will facilitate marker-assisted selection for disease resistance and other important traits in pear breeding programs.