Genome-wide Copy Number Variation Detection And Their Association With The Lengths Of Five Limb Bones In Bama Pigs

Copy number variation(CNV)is a kind of structural variation.It is heritable,stable and heterogeneous,and it covers the entire pig genome in several manners.Previous studies showed that CNV was associated with the health status and production performance of livestock and poultry.Pig is a very important farm animals,and it is meaningful to detect CNV and identify the association between CNV and production performance in pigs.Until now,most researches detecting CNV were based on Illumina Porcine SNP60 BeadChip.Because the marker density was relatively low and the distance between adjacent SNPs was long in the 60 K SNP chip,the CNV detection rate was poor.In this study,PennCNV and R-GADA were used detecting CNV based on 1.4M SNP genotypes in a Bama(a Chinese indigenous pig breed)population.The CNV region(CNVR)was the region covering by overlapping CNVs.A total of 6237 CNVs were detected by PennCNV,and they belonged to 795 CNVRs.R-GADA detected 3489 CNVs within 340 CNVRs,of which 226 CNVRs were also identified by PennCNV.The effect of marker density on the CNV detection rate was also investigated in this study.The results showed that the CNV detection rate was improved with the marker density increased,and it indicated that 1.4M SNPs were not saturated to detect CNV,further density markers could improve the CNV detection rate.The association between CNVR and five limb bone lengths were also tested in this study.There were 22 CNVR significantly(P < 0.05)associated with limb bone lengths on chromosomes 2,5,7 and so on.In conclusion,CNV detection was carried out by two methods using 1.4M SNPchip data in Bama pigs,and a profile of CNV was figured out in this population.Even based on 1.4M SNPs,adding more markers would increase the CNV detection rate.A total of 18 of CNVRs were identified significantly associated with the lengths of five limb bones.Those results will facilitate the studies on the breed characteristics and molecular breeding for limb bone lengths of Bama.