Development of Transcriptome-Based Single Nucleotide Polymorphism Markers for Pear Skin Color
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Breeding efficiency in new pear cultivar is considerably low due to long juvenility and self-incompatibility. Therefore, it is necessary to develop early selection markers to screen seedlings with target traits and to increase breeding efficiency. For the comparison of transcription profiles in pear cultivars with different skin color, two cDNA libraries were constructed. Differences in gene expression between red-skinned ‘Rosired Bartlett’ and green-skinned ‘Bartlett’ were investigated by NGS. EST of clones from two cultivars was selected for nucleotide sequence determination and homology searches. MYB10, CHI, and F3H were more predominantly expressed in the red-skinned cultivar rather than the green- skinned cultivar by qRT-PCR. Putative SNPs were screened from pear EST contigs by HRM analysis between ‘Rosired Bartlett’ and ‘Bartlett’. All 21 pairs of SNPs were discriminated and the HRM profiles of amplicons were established. In this study, we report an efficient way to develop two SNP markers for distinguishing between red- and green-skinned pear cultivars by HRM analysis. These SNP markers would be useful for pear marker assisted breeding and provide a good reference for relevant research on molecular mechanisms of color variation in pear cultivars.
Abstract
Breeding efficiency in new pear cultivar is considerably low due to long juvenility and self-incompatibility. Therefore, it is necessary to develop early selection markers to screen seedlings with target traits and to increase breeding efficiency. For the comparison of transcription profiles in pear cultivars with different skin color, two cDNA libraries were constructed. Differences in gene expression between red-skinned ‘Rosired Bartlett’ and green-skinned ‘Bartlett’ were investigated by NGS. EST of clones from two cultivars was selected for nucleotide sequence determination and homology searches. MYB10, CHI, and F3H were more predominantly expressed in the red-skinned cultivar rather than the green- skinned cultivar by qRT-PCR. Putative SNPs were screened from pear EST contigs by HRM analysis between ‘Rosired Bartlett’ and ‘Bartlett’. All 21 pairs of SNPs were discriminated and the HRM profiles of amplicons were established. In this study, we report an efficient way to develop two SNP markers for distinguishing between red- and green-skinned pear cultivars by HRM analysis. These SNP markers would be useful for pear marker assisted breeding and provide a good reference for relevant research on molecular mechanisms of color variation in pear cultivars.