Abstract
Laiwu pigs, distinguished by their high intramuscular fat of 7–9%, is an indigenous pig breed of China, and recent studies also found that Laiwu pigs showed high resistance to Porcine circovirus type 2. However, with the introduction of commercial varieties, the population of Laiwu pigs has declined, and some lineages have disappeared, which could result in inbreeding. Runs of homozygosity (ROH) can be used as a good measure of individual inbreeding status and is also normally used to detect selection signatures so as to map the candidate genes associated with economically important traits. In this study, we used data from Genotyping by Genome Reducing and Sequencing to investigate the number, length, coverage, and distribution patterns of ROH in 93 Chinese Laiwu pigs and identified genomic regions with a high ROH frequency. The average inbreeding coefficient calculated by pedigree was 0.021, whereas that estimated by all detected ROH segments was 0.133. Covering 13.4% of the whole genome, a total of 7,508 ROH segments longer than 1 Mb were detected, whose average length was 3.76 Mb, and short segments (1–5 Mb) dominated. For individuals, the coverage was in the range between 0.56 and 36.86%. For chromosomes, SSC6 had the largest number (n = 688), and the number of ROH in SSC12 was the lowest (n = 215). Thirteen ROH islands were detected in our study, and 86 genes were found within those regions. Some of these genes were correlated with economically important traits, such as meat quality (ECI1, LRP12, NDUFA4L2, GIL1, and LYZ), immunity capacity (IL23A, STAT2, STAT6, TBK1, IFNG, and ITH2), production (DCSTAMP, RDH16, and GDF11), and reproduction (ODF1 and CDK2). A total of six significant Gene Ontology terms and nine significant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified, most of which were correlated with disease resistance and biosynthesis processes, and one KEGG pathway was related to lipid metabolism. In addition, we aligned all of the ROH islands to the pig quantitative trait loci (QTL) database and finally found eight QTL related to the intramuscular fat trait. These results may help us understand the characteristics of Laiwu pigs and provide insight for future breeding strategies.
Highlights
Laiwu pigs, a precious Chinese indigenous pig breed, are mainly distributed in Shandong Province, China
Where LROH is defined as the total length of the genome covered by all Runs of homozygosity (ROH) segments for each individual, and Lauto is the length of the sequenced genome, which equaled 2.26 Gb in this research
It has been reported that a lower limit of ROH length of 1 Mb has a genetic distance of 1 cM
Summary
A precious Chinese indigenous pig breed, are mainly distributed in Shandong Province, China They are distinguished by a good meat quality, especially a high intramuscular fat (IMF) content of 9–12%, compared with the major commercial lean pig breeds (Yang et al, 2015). Recent studies have found that Laiwu pigs showed high resistance to certain infectious diseases, such as Porcine circovirus type 2 (PCV2) (Li et al, 2016). These breed-specific features of Laiwu pigs are the consequences of natural and human-mediated selection. During the last 40 years, with the introduction of western pig breeds such as Duroc and Large White pigs, the Laiwu pig population has shrunk, and some lineages have disappeared. Monitoring the genetic inbreeding levels within populations is of great importance in the genetic protection and improvement of Laiwu pigs
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