Mining of genic SNPs and diversity evaluation of landraces in loquat

- Genic SNP markers derived from transcriptome sequences were mined from 26 loquat cultivars.
- The characteristics of genic SNP loci obtained were analyzed.
- The genetic diversity of all the experimental individuals was evaluated by using a phylogenetic tree based on genic SNPs.

With the development of next-generation sequencing technologies, the exploitation of single nucleotide polymorphism (SNP) markers from transcriptome sequences has gained more attention and this kind of marker is widely utilized in plant genetic research. In this study, genic SNP markers derived from transcriptome sequences were identified from 26 loquat cultivars. A total length of 4183 bp using 9 sets of primers was sequenced and used for alignments. From this, 103 SNPs, with a frequency of one SNP per 41 bp, were found, which were comprised of 55 transitions, 37 transversions, 8 InDels and 3 other types. Among these SNPs, the percentage of transitions and transversions in A/G, C/T, G/T, A/T, G/C and A/C were 31.1% (32), 22.3% (23), 13.6% (14), 11.7% (12), 6.8% (7) and 3.9% (4), respectively. Of these SNP genotypes, 84 were detected as homozygotes in the 26 loquat cultivars, and 8 heterozygous SNPs were found in some cultivars. Cluster analysis of the 26 loquat cultivars was also carried out using the SNPs data, and a phylogenetic tree constructed showed that all the cultivars were separated well, and clustered into several groups which basically corresponds to the genetic background of them. The newly identified genic SNPs in this study will provide powerful tools in molecular studies for cultivar identification, genetic diversity analyses and marker-assisted selection breeding in loquat.