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Whole‐genome sequencing reveals breed‐differential CNVs between Tongcheng and Large White pigs
Author(s) -
Wu Q.,
Zhou Y.,
Wang Y.,
Zhang Y.,
Shen Y.,
Su Q.,
Gao G.,
Xu H.,
Zhou X.,
Liu B.
Publication year - 2020
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12993
Subject(s) - biology , breed , genetics , genome , copy number variation , whole genome sequencing , candidate gene , white (mutation) , phenotype , gene
Summary Large phenotypic differences have been observed between Tongcheng and Large White pigs. However, little is known about their genetic basis. This study performed a genome‐wide comparison of CNVs between Tongcheng and Large White pigs using genome sequencing data. By combining the advantages of three different strategies (read depth, paired‐end mapping and split read), we detected in total 18 687 CNVs that covered approximately 3.5% of the pig genome length for Tongcheng and Large White pigs. We identified 1864 breed‐stratified CNVs (top 10%) by performing V ST statistics. Functional enrichment analyses for genes located in breed‐stratified CNVs were found to be involved in pigmentation, behavior, immune system and reproductive processes, which coincide with phenotypic differences between the two breeds. Using a systematic analysis of the genome and transcriptome data, we further identified four novel breed‐differential CNVs on the functional genes (disease‐resistant, DCUN1D2 and SPARCL1 ; lipid metabolism, PLEKHA2 and SLCO1A2 ). Subsequent PCR validation confirmed their accurate breakpoint positions in 33 Tongcheng pigs and 33 Large White pigs. This study provides essential information on differential CNVs for further research on the genetic basis of phenotypic differences between Tongcheng and Large White pigs.