Insertion/deletion variant characterization and marker development in pecan [Carya illinoinensis (Wangenh.) K. Koch]

Pecan is an economically important tree worldwide. However, limited insertion/deletion (InDel) molecular markers are available for this species, which hinders molecular breeding and genetic improvement. In the present study, 112 publicly available transcriptome datasets corresponding to 784 Gb nucleotides were mapped against pecan reference genome for InDel identification. A total of 27,503 InDel loci were detected and found to be unevenly distributed across 16 chromosomes. Among them, 18,805 were located within genic regions, while the remaining 8,698 were situated at non-genic areas. There were 9,307 InDel-associating genes, accounting for 28.84 % of total genes. Out of the InDel-containing genes, 2,548 showed exon variations, and these genes were over-represented in the pathways of 'defense response' and 'signal transduction'. A total of 275 markers were developed based on the flanking sequences around InDel loci, of which, 197 (71.64 %) produced unambiguous and polymorphic bands when screening eight pecan cultivars. For these polymorphic markers, 34 were selected to reveals the genetic relatedness among 34 pecan accessions. The dendrogram resulting from cluster analysis revealed that genetically close lines were generally grouped together. To rapidly and cost-effectively distinguish pecan collections, four multiplex PCR were conducted using 12 InDel markers. The multiplex PCR products could be resolved by agarose gel electrophoresis and allowed the discrimination of 29 pecan lines. The InDel loci and markers obtained here will help for the effective use of pecan germplasms in the future.