Genome-Wide Patterns of Homozygosity and Relevant Characterizations on the Population Structure in Piétrain Pigs

Genome-Wide Detection for Runs of Homozygosity in Baoshan Pigs Using Whole Genome Resequencing

Baoshan pigs (BS) are a local breed in Yunnan Province that may face inbreeding owing to its limited population size. To accurately evaluate the inbreeding level of the BS pig population, we used whole-genome resequencing to identify runs of homozygosity (ROH) regions in BS pigs, calculated the inbreeding coefficient based on pedigree and ROH, and screened candidate genes with important economic traits from ROH islands. A total of 22,633,391 SNPS were obtained from the whole genome of BS pigs, and 201 ROHs were detected from 532,450 SNPS after quality control. The number of medium-length ROH (1-5 Mb) was the highest (98.43%), the number of long ROH (>5 Mb) was the lowest (1.57%), and the inbreeding of BS pigs mainly occurred in distant generations. The inbreeding coefficient FROH, calculated based on ROH, was 0.018 ± 0.016, and the FPED, calculated based on the pedigree, was 0.027 ± 0.028, which were positively correlated. Forty ROH islands were identified, containing 507 genes and 891 QTLs. Several genes were associated with growth and development (IGFALS, PTN, DLX5, DKK1, WNT2), meat quality traits (MC3R, ACSM3, ECI1, CD36, ROCK1, CACNA2D1), and reproductive traits (NPW, TSHR, BMP7). This study provides a reference for the protection and utilization of BS pigs.

Population genetic structure analysis and identification of backfat thickness loci of Chinese synthetic Yunan pigs

Yunan is a crossed lean meat pig breed in China. Backfat thickness is the gold standard for carcass quality grading. However, over 14 years after breed registration, the backfat of Yunan thickened and the consistency of backfat thickness decreased. Meanwhile, no genetic study has been ever performed on Yunan population. So, in this study we collected all the 120 nucleus individuals of Yunan and recorded six backfat traits of them, carried out population genetic structure analysis, selection signals analysis and genome-wide association study of Yunan pigs with the help of their founder population Duroc and Chinese native Huainan pigs, to determine the genomic loci on backfat of Yunan. Genetic diversity indexes suggested Yunan pigs had no inbreeding risk while population genetic structure showed they had few molecular pedigrees and were stratified. A total of 71 common selection signals affecting growth and fat deposition were detected by F_ST and XP-CLR methods. 34 significant loci associated with six backfat traits were detected, among which a 1.40 Mb region on SSC4 (20.03–21.43 Mb) were outstanding as the strong region underlying backfat. This region was common with the results of selection signature analysis, former reported QTLs for backfat and was common for different kinds of backfat traits at different development stage. ENPP2, EXT1 and SLC30A8 genes around were fat deposition related genes and were of Huainan pig’s origin, among which Type 2 diabetes related gene SLC30A8 was the most reasonable for being in a 193.21 Kb haplotype block of the 1.40 Mb region. Our results had application value for conservation, mating and breeding improvement of backfat thickness of Yunan pigs and provided evidence for a human function gene might be reproduced in pigs.

Genome-wide detection of genetic structure and runs of homozygosity analysis in Anhui indigenous and Western commercial pig breeds using PorcineSNP80k data

Background

Runs of homozygosity (ROH) are continuous homozygous regions typically located in the DNA sequence of diploid organisms. Identifications of ROH that lead to reduced performance can provide valuable insight into the genetic architecture of complex traits. Here, we systematically investigated the population genetic structure of five Anhui indigenous pig breeds (AHIPs), and compared them to those of five Western commercial pig breeds (WECPs). Furthermore, we examined the occurrence and distribution of ROHs in the five AHIPs and estimated the inbreeding coefficients based on the ROHs (F_ROH) and homozygosity (F_HOM). Finally, we identified genomic regions with high frequencies of ROHs and annotated candidate genes contained therein.

Results

The WECPs and AHIPs were clearly differentiated into two separate clades consistent with their geographical origins, as revealed by the population structure and principal component analysis. We identified 13,530 ROHs across all individuals, of which 4,555 and 8,975 ROHs were unique to AHIPs and WECPs, respectively. Most ROHs identified in our study were short (< 10 Mb) or medium (10–20 Mb) in length. WECPs had significantly higher numbers of short ROHs, and AHIPs generally had longer ROHs. F_ROH values were significantly lower in AHIPs than in WECPs, indicating that breed improvement and conservation programmes were successful in AHIPs. On average, F_ROH and F_HOM values were highly correlated (0.952–0.991) in AHIPs and WECPs. A total of 27 regions had a high frequency of ROHs and contained 17 key candidate genes associated with economically important traits in pigs. Among these, nine candidate genes (CCNT2, EGR2, MYL3, CDH13, PROX1, FLVCR1, SETD2, FGF18, and FGF20) found in WECPs were related to muscular and skeletal development, whereas eight candidate genes (CSN1S1, SULT1E1, TJP1, ZNF366, LIPC, MCEE, STAP1, and DUSP) found in AHIPs were associated with health, reproduction, and fatness traits.

Conclusion

Our findings provide a useful reference for the selection and assortative mating of pig breeds, laying the groundwork for future research on the population genetic structures of AHIPs, ultimately helping protect these local varieties.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08583-9.

Investigation of the Genetic Architecture of Pigs Subjected to Breeding Intensification

Pigs are strategically important animals for the agricultural industry. An assessment of genetic differentiation between pigs, undergone and not undergone to selection intensification, is of particular interest. Our research was conducted on two groups of Large White pigs grown on the same farm but in different years. A total of 165 samples were selected with 78 LW_А (n = 78, the Russian selection) and LW_B (n = 87, a commercial livestock). For genotyping, we used GeneSeek^® GGP Porcine HD Genomic Profiler v1 (Illumina Inc, San Diego, CA, USA). To define breeding characteristics of selection, we used smoothing FST and segment identification of HBD (Homozygous-by-Descent). The results of smoothing FST showed 20 areas of a genome with strong ejection regions of the genome located on all chromosomes except SSC2, SSC3, and SSC8. The average realized autozygosity in Large White pigs of native selection was in (LW_A)—0.21, in LW_В—0.29. LW_А showed 13,338 HBD segments, 171 per one animal, and LW_B—15,747 HBD segments, 181 per one animal. The ejections found by the smoothing FST method were partially localized in the HBD regions. In these areas, the genes ((NCBP1, PLPPR1, GRIN3A, NBEA, TRPC4, HS6ST3, NALCN, SMG6, TTC3, KCNJ6, IKZF2, OBSL1, CARD10, ETV6, VWF, CCND2, TSPAN9, CDH13, CEP128, SERPINA11, PIK3CG, COG5, BCAP29, SLC26A4) were defined. The revealed genes can be of special interest for further studying their influence on an organism of an animal since they can act as candidate genes for selection-significant traits.

Genome-Wide Assessment of Runs of Homozygosity and Estimates of Genomic Inbreeding in a Chinese Composite Pig Breed

The primary purpose of the current study was to assess the genetic diversity, runs of homozygosity (ROH) and ROH islands in a Chinese composite pig and explore hotspot regions for traces of selection. First, we estimated the length, number, and frequency of ROH in 262 Xidu black pigs using the Porcine SNP50 BeadChip and compared the estimates of inbreeding coefficients, which were calculated based on ROHs (F_ROH) and homozygosity (F_HOM). Our result shows that a total of 7,248 ROH exceeding 1Mb were detected in 262 pigs. In addition, Sus scrofa chromosome (SSC) 8 and SSC10, respectively, has the highest and lowest chromosome coverage by ROH. These results suggest that inbreeding estimation based on total ROH may be a useful method, especially for crossbreed or composite populations. We also calculated an inbreeding coefficient of 0.077 from the total ROH. Eight ROH islands were found in this study. These ROH islands harbored genes associated with fat deposition, muscular development, reproduction, ear shape, and adaptation, such as TRAF7, IGFBP7, XPO1, SLC26A8, PPARD, and OR1F1. These findings may help to understand the effects of environmental and artificial selection on the genome structure of composite pigs. Our results provide a basis for subsequent genomic selection (GS), and provides a reference for the hybrid utilization of other pig breeds.

Genome-Wide Detection of Runs of Homozygosity in Laiwu Pigs Revealed by Sequencing Data

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.

High-density single nucleotide polymorphism chip-based conservation genetic analysis of indigenous pig breeds from Shandong Province, China

Objective

Shandong indigenous pig breeds are important Chinese pig resources. Their progressive population decline in recent decades has attracted attention towards their conservation. Conservation genetics of these indigenous breeds are essential for developing a conservation and utilization scheme.

Methods

A high-density single nucleotide polymorphism (HD-SNP) chip-based comparative analysis of genetic characteristics was performed for seven Shandong indigenous pig breeds in the context of five Western commercial breeds.

Results

The results showed that Shandong indigenous pig breeds varied greatly in genetic diversity, effective population size, inbreeding level, and genetic distance with the Western commercial breeds. Specifically, Laiwu and Dapulian displayed low genetic diversity, and had a genetically distant relationship with the Western commercial breeds (average F statistics [F_ST] value of 0.3226 and 0.2666, respectively). Contrastingly, the other five breeds (Yantai, Licha, Yimeng, Wulain, and Heigai) displayed high genetic diversity within breed and had some extent of mixture pattern with the Western commercial breeds, especially Duroc and Landrace (F_ST values from 0.1043 to 0.2536). Furthermore, intensive gene flow was discovered among the seven Shandong indigenous breeds, particularly Wulian, Licha, and Heigai, as indicated by the large cluster formed in the principal component analysis scatterplot and small population differentiation (average of 0.1253) among them.

Conclusion

Our study advances the understanding of genetic characteristics of Shandong indigenous breeds and provides essential information for developing an appropriate conservation and utilization scheme for these breeds.