Objective The SNPs, InDels and their located biotic stress resistance genes were investigated in Larix kaempferi to provide molecular markers and candidate genes for the molecular breeding of Larix kaempferi.

Method 158 transcriptome data generated from Larix kaempferi trees grown in China, Japan and the United Kingdom were used to identify SNPs and InDels firstly. Subsequently, the gene expression levels between the active and dormant stage were compared. Finally, the differentially expressed genes with reliable markers were functionally annotated.

Result A total of 515 935 SNPs and 1 056 InDels were identified, and they were located in 35 827 genes. Based on the number of SNP and InDel in the transcriptome from different regions, we speculated that the genetic diversity of Larix kaempferi was high in Japan. There were 6 444 non-synonymous mutant SNPs and 10 InDels in at least 50 transcriptomes, which were located in 3 742 genes, and these markers were reliable and could be used further. After comparing the transcriptomes of the active and dormant periods, a total of 2 569 genes with reliable markers were differentially expressed, and 101 genes of them were associated with plant response to fungus, bacterium, oomycetes, virus, insect and nematode based on GO annotation.

Conclusion These data provide molecular markers for genome-wide association study and genomic selection in Larix kaempferi, as well as candidate genes for genetic breeding by means of transgene and gene editing.