Genome sequencing and analysis of Mangalica, a fatty local pig of Hungary

BMC Genomics

Endre Barta¹  Ferenc Marincs¹  Gábor Tóth³  Viktor Stéger¹  Tibor Nagy¹  János Molnár² 

[1] Agricultural Genomics and Bioinformatics Group, Agricultural Biotechnology Institute, NARIC, Gödöllő, Hungary;Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary;Hungarian Scientific Research Fund, Budapest, Hungary

关键词: Gene function;    Breed-specific SNP;    Fatty pig;    Genome sequencing;    Mangalica;   

Others  :  1140917
DOI  :  10.1186/1471-2164-15-761

 received in 2013-09-02, accepted in 2014-09-02,  发布年份 2014

【 摘 要 】

Background

Mangalicas are fatty type local/rare pig breeds with an increasing presence in the niche pork market in Hungary and in other countries. To explore their genetic resources, we have analysed data from next-generation sequencing of an individual male from each of three Mangalica breeds along with a local male Duroc pig. Structural variations, such as SNPs, INDELs and CNVs, were identified and particular genes with SNP variations were analysed with special emphasis on functions related to fat metabolism in pigs.

Results

More than 60 Gb of sequence data were generated for each of the sequenced individuals, resulting in 11× to 19× autosomal median coverage. After stringent filtering, around six million SNPs, of which approximately 10% are novel compared to the dbSNP138 database, were identified in each animal. Several hundred thousands of INDELs and about 1,000 CNV gains were also identified. The functional annotation of genes with exonic, non-synonymous SNPs, which are common in all three Mangalicas but are absent in either the reference genome or the sequenced Duroc of this study, highlighted 52 genes in lipid metabolism processes. Further analysis revealed that 41 of these genes are associated with lipid metabolic or regulatory pathways, 49 are in fat-metabolism and fatness-phenotype QTLs and, with the exception of ACACA, ANKRD23, GM2A, KIT, MOGAT2, MTTP, FASN, SGMS1, SLC27A6 and RETSAT, have not previously been associated with fat-related phenotypes.

Conclusions

Genome analysis of Mangalica breeds revealed that local/rare breeds could be a rich source of sequence variations not present in cosmopolitan/industrial breeds. The identified Mangalica variations may, therefore, be a very useful resource for future studies of agronomically important traits in pigs.

【 授权许可】

   
2014 Molnár et al.; licensee BioMed Central Ltd.

【 图 表 】

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