Characterization of Potential Molecular Markers in Lac Insect Kerria lacca (Kerr) Responsible for Lac Production

SIMPLE SUMMARY: Lac insect Kerria lacca (Hemiptera, Kerriidae) is widely used to produce lac in tropical and subtropical areas. This species is genomically understudied and there is no information present on single-nucleotide polymorphisms and insertions and deletions of lac insects. This study involves distribution and characterization of molecular markers in K. lacca. Nucleotide substitution frequency and transition to transversion ratio were highest at the late adult stage. The maximum numbers of SNPs and InDels were distributed on chromosome 8 and 1, respectively. Most variants at low frequencies were detected in InDels compared to SNPs. Gene function analysis showed several gene variations, and candidate SNPs that were involved in lac synthesis. This work paves the way to determining further mechanisms involved in increased lac production. ABSTRACT: Kerria lacca (Kerr) is an important lac insect extensively used in industrial products in the form of resin, wax and dye. The scarce knowledge on molecular markers for K. lacca is a barrier in elucidating genetic information. Our study identified a total of 16,921 single-nucleotide polymorphisms (SNPs), and 6231 insertions and deletions (InDels)—of which, intergenic variation accounted for 41.22% and 56.30%, and exonic variation accounted for 39.10% and 17.46%, of SNPs and InDels, respectively. Observation of SNPs suggested that nucleotide substitution frequency and transition to transversion (Ts/Tv) ratio were highest at the late adult stage, 3.97, compared to at the other stages, with a genome-wide Ts/Tv ratio of 2.95. The maximum number of SNPs, 2853 (16.86%), was identified in chromosome 8, while the lowest, 1126 (6.65%), was identified in chromosome 7. The maximum and minimum numbers of InDels were located on chromosome 1 and 7, with 834 (13.38%) and 519 (8.33%), respectively. Annotation showed that highest numbers of exonic and intergenic SNPs were present at the late adult stage, whereas the maximum number of InDels was found at the larval stage. On the basis of gene function, 47 gene variations were screened and 23 candidate genes were identified in associations with lac production. Concluding work will enhance knowledge on molecular markers to facilitate an increase in lac production in K. lacca as well as other lac insects.