Discovery of single nucleotide polymorphisms in bone morphogenetic protein (

Abstract

Context Two native goat breeds from Kerala, Malabari and Attappady Black, differ significantly in prolificacy (i.e. no. of kids born/kidding). Prolificacy is an important economic trait and the subject of genetic research showing that bone morphogenetic protein (BMP) genes have a significant effect. Double digest restriction-site associated DNA sequencing (ddRADseq) is a highly efficient and low cost technology for high density discovery of single nucleotide polymorphisms (SNPs), which could serve as predictive markers for animal breeding programs. Aims The study was aimed at discovering SNPs in BMP genes that affect prolificacy, using ddRADseq followed by validation of selected SNP. Methods Blood DNA samples of 10 highly prolific Malabari and 10 less prolific Attappady Black goats were pooled by group and subjected to ddRADseq. SNPs observed in BMP genes were investigated and compared between groups. A validation study was done for the c.614–32789C>T variant in 100 Malabari and 50 Attappady Black goats by using PCR-RFLP. Key results In total, 6333 variants were identified by ddRADseq. Three variants were identified in BMP genes, which included two intronic variants c.614–32789C>T and c.490+6793T>C, in genes BMP6 and BMP5 and a downstream gene variant near the BMPR1B gene. According to ddRADseq data, variants in BMP5 and BMP6 differed in allelic distribution between Malabari and Attappady Black goats. For c.490+6793T>C in BMP5, the CC genotype was predominant in the highly prolific Malabari whereas TC was present in the Attappady Black group. The variant c.614–32789C>T in BMP6 was genotyped as TC in Malabari and CC in Attappady Black goats by ddRADseq. This variant was predicted to have an effect on splicing, according to the tool SplicePort. On the basis of bioinformatics analysis and the role of BMP6 gene in follicular dynamics, the variant in BMP6 was selected for further validation studies. All three genotypes were identified by PCR-RFLP; the C allele was the rare allele in the population with an allele frequency of 0.36. Presence of both alleles C and T and the three genotypes CC, TC and TT in this larger population substantiated the robustness of ddRADseq technique. Conclusions The technique discovered high confidence SNPs, which could be used for further validation and association studies to develop markers for selection of animals and for genetic improvement of this complex trait. Implications Techniques such as ddRADseq provide a large number of SNPs, and investigation of those polymorphisms found across the genome will help to identify new loci affecting traits of interest. This, in turn, will aid in exploring genetically complex traits in a faster and cheaper manner.