Polymorphisms on SSC15q21-q26 Containing QTL for reproduction in Swine and its association with litter size

Effect of SNPs on Litter Size in Swine

Although sows do not directly enter the market, they play an important role in piglet breeding on farms. They consume large amounts of feed, resulting in a significant environmental burden. Pig farms can increase their income and reduce environmental pollution by increasing the litter size (LS) of swine. PCR-RFLP/SSCP and GWAS are common methods to evaluate single-nucleotide polymorphisms (SNPs) in candidate genes. We conducted a systematic meta-analysis of the effect of SNPs on pig LS. We collected and analysed data published over the past 30 years using traditional and network meta-analyses. Trial sequential analysis (TSA) was used to analyse population data. Gene set enrichment analysis and protein-protein interaction network analysis were used to analyse the GWAS dataset. The results showed that the candidate genes were positively correlated with LS, and defects in PCR-RFLP/SSCP affected the reliability of candidate gene results. However, the genotypes with high and low LSs did not have a significant advantage. Current breeding and management practices for sows should consider increasing the LS while reducing lactation length and minimizing the sows' non-pregnancy period as much as possible.

Positive selection signatures in Anqing six-end-white pig population based on reduced-representation genome sequencing data

Anqing six-end-white (AQ) pig performs well on resistance to coarse fodder and disease, reproduction and meat quality, offering high potential for exploitation. Environmental conditions and strict selections from local farmers have cultivated the AQ pig to be an outstanding and unique local pig breed. Thus we aim to detect genetic positive selection signatures within the AQ pig population to explore underlying genetic mechanisms. A relative extended haplotype homozygosity (REHH) test was performed in the population of 79 AQ pigs to seek evidence demonstrating that selective actions have left an imprint on the whole genome. In total, 430 500 REHH tests were performed on 53 067 core regions with average REHH tests of 8.11, average lengths of 11.50 kb and an overall length of 610.38 Mb which accounted for 26.94% of the whole genome. Finally, a total of 1819 core haplotypes (P < 0.01) and 586 candidate genes were obtained. These genes were mainly related to meat quality (MYOG, SNX19), resistance to disease (CRISPLD2, CD14) and reproduction traits (ERBB2, NRP2). A panel of genes within the 30 top significant REHH tests was mainly categorized to traits of meat quality and disease resistance. Among 13 KEGG pathways, MAPK, GnRH and Oxytocin signaling pathways, associated with the biological processes of crucial economic traits, were noteworthy. The excellent characteristics of the AQ pig benefited from the combination of natural and human factors. We provide a sketch map that shows the distribution of selection footprints on the whole genome of AQ pig and found potential genes for future studies.

Neuropilin-2 rs849563 gene variations and susceptibility to autism in Iranian population: A case-control study

Autism spectrum disorders (ASD) are neurodevelopmental disruptions usually diagnosed in the first three years of child's life that characterized by some impairments in verbal and nonverbal communication, problems in social interactions and repetitive behaviors. The neuropilin-2 (NRP2) gene has been shown to both guide axons and control neuronal migration in the central nervous system (CNS). In this study the association between the NRP2 gene and autism using a cohort of 120 Iranian children (50 cases with autism and 70 control cases) was analyzed. Single nucleotide polymorphism (SNP) was genotyped by the polymerase chain reaction-based restriction fragment length polymorphism (PCR-RFLP) analyses. There was significant difference between the genotype and allele frequency between control and patient groups (P = 0.003 and P = 0.01, respectively). The prevalence of genotype frequencies of TT and TG in autistic children were 40% and 60%, respectively, while in controls were 68.5% and 31.5%, respectively. The heterozyote TG was associated with an increased risk of autism compared with TT genotype (OR = 3.72, 95%CI = 1.53-6.95, P = 0.02). The allele frequencies of T and G in autistic children were 78.5% and 21.4%, respectively and in controls were 84.2% and 15.7%, respectively. The NRP2 G allele conferred a 2.29-fold increased risk to autism relative to the T allele (OR = 2.29, 95%CI = 1.23-4.29, P = 0.009). The results of this study showed that there is a significant association between rs849563 polymorphism and autism in the studied population. However in order to obtain a definitive conclusion larger studies with more samples are required to confirm the results of this study.

Genome-wide genetic structure and differentially selected regions among Landrace, Erhualian, and Meishan pigs using specific-locus amplified fragment sequencing

As typical Chinese indigenous pig breeds, Erhualian and Meishan have been widely used to produce new strain or breed in the world. However, the genetic basis of characteristics of these pig breeds is still limited. Moreover, considering cost and output of sequencing, it is necessary to further develop cost-effective method for pig genome screening. To contribute on this issue, we developed a SLAF-seq (specific-locus amplified fragment sequencing) method for pigs and applied it to analyze the genetic difference among Landrace, Erhualian, and Meishan pigs. A total of 453.75 million reads were produced by SLAF-seq. After quality-control, 165,670 SNPs (single nucleotide polymorphisms) were used in further analysis. The results showed that Landrace had distinct genetic relationship compared to Erhualian (F_ST = 0.5480) and Meishan (F_ST = 0.5800), respectively, while Erhualian and Meishan held the relatively close genetic relationship (F_ST = 0.2335). Furthermore, a genome-wide scanning revealed 268 differentially selected regions (DSRs) with 855 genes and 256 DSRs with 347 genes between Landrace and the two Chinese indigenous pig breeds and between Erhualian and Meishan, respectively. This study provides a new cost-effective method for pig genome study and might contribute to a better understanding on the formation mechanism of genetic difference among pigs with different geographical origins.

Transcriptomic Analysis of Ovaries from Pigs with High And Low Litter Size

Litter size is one of the most important economic traits for pig production as it is directly related to the production efficiency. Litter size is affected by interactions between multiple genes and the environment. While recent studies have identified some genes associated with prolificacy in pigs, transcriptomic studies of specific genes affecting litter size in porcine ovaries are rare. In order to identify candidate genes associated with litter size in swine, we assessed gene expression differences between the ovaries of Yorkshire pigs with extremely high and low litter sizes using the RNA-Seq method. A total of 1 243 differentially expressed genes were identified: 897 genes were upregulated and 346 genes were downregulated in high litter size ovary samples compared with low litter size ovary samples. A large number of these genes related to steroid hormone regulation in animal ovaries, including 59 Gene Ontology terms and 27 Kyoto Encyclopedia of Genes and Genomes pathways involved in steroid biosynthesis and ovarian steroidogenesis. From these differentially expressed genes, we identified a total of 11 genes using a bioinformatics screen that may be associated with high litter size in Yorkshire pigs. These results provide a list of new candidate genes for porcine litter size and prolificacy to be further investigated.