CNV analysis of Meishan pig by nextgeneration sequencing and effects of AHR gene CNV on pig reproductive traits

Background:Reproductive performance of livestock is an economically important aspect of global food production.The Chinese Meishan pig is a prolific breed,with an average of three to five more piglets per litter than European breeds;however,the genetic basis for this difference is not well understood.Results:In this study,we investigated copy number variations(CNVs)of 32 Meishan pigs and 29 Duroc pigs by nextgeneration sequencing.A genome-wide analysis of 61 pigs revealed 12,668 copy number variable regions(CNVRs)that were further divided into three categories based on copy number(CN)of the whole population,i.e.,gain(n=7,638),and loss(n=5,030)CNVRs.We then compared Meishan and Duroc pigs and identified 17.17Mb of 6,387 CNVRs that only existing in Meishan pigs CNVRs that overlapped the reproduction-related gene encoding the aryl hydrocarbon receptor(AHR)gene.We found that normal AHR CN was more frequent than CN loss in four different pig breeds.An association analysis showed that AHR CN had a positive effect on litter size(P<0.05)and that a higher CN was associated with higher total number born(P<0.05),number born alive(P<0.05),number of weaned piglets,and birth weight.Conclusions:The present study provides comprehensive CNVRs for Meishan and Duroc pigs through large-scale population resequencing.Our results provide a supplement for the high-resolution map of copy number variation in the porcine genome and valuable information for the investigation of genomic structural variation underlying traits of interest in pig.In addition,the association results provide evidence for AHR as a candidate gene associated with reproductive traits that can be used as a genetic marker in pig breeding programs.

Polymorphism of mitochondrial tRNA genes associated with the number of pigs born alive

Background: Mutations in mitochondrial tRNA genes have been widely reported association with human reproductions.It is also important to explore the effect on the number of piglets born alive(NBA).Here,1017 sows were used to investigate the association between polymorphisms in mitochondrial tRNA genes and NBA.Results: In total,16 mutations were found in mitochondrial tRNA genes,of which 13 mutations were significantly associated with NBA(P < 0.05).The reproductions of mutant carriers were significantly greater than that of wild carriers by 0.989 piglets born alive/sow farrowing.To test whether the mutations altered the structure of mitochondrial tRNAs,the secondary and tertiary structures were predicted.In result,C2255 T changed the secondary structure of t RNA-Val by elongating the T stem and shrinking the T loop,and C2255 T and G2259 A in the tRNA-Val gene,C6217 T and T6219 C in the tRNA-Ala gene,and T15283 C in the tRNA-Glu gene altered the tertiary structure of their tRNAs,respectively by changing the folding form of the T arm,and C16487 T in the tRNA-Thr gene changed the tertiary structure of mitochondrial tRNA-Thr by influencing the folding form of the acceptor arm.Conclusions: Results highlight the effect of mitochondrial tRNA genes on the number of piglets born alive,and suggest that polymorphic sites of the tRNA genes be genetic markers for selection of pig reproduction.

Mining Unknown Porcine Protein Isoforms by Tissue-based Map of Proteome Enhances Pig Genome Annotation

A lack of the complete pig proteome has left a gap in our knowledge of the pig genome and has restricted the feasibility of using pigs as a biomedical model.In this study,we developed a tissue-based proteome map using 34 major normal pig tissues.A total of 5841 unknown protein isoforms were identified and systematically characterized,including 2225 novel protein isoforms,669 protein isoforms from 460 genes symbolized beginning with LOC,and 2947 protein isoforms without clear NCBI annotation in the current pig reference genome.These newly identified protein isoforms were functionally annotated through profiling the pig transcriptome with high-throughput RNA sequencing of the same pig tissues,further improving the genome annotation of the corresponding protein-coding genes.Combining the well-annotated genes that have parallel expression pattern and subcellular witness,we predicted the tissue-related subcellular locations and potential functions for these unknown proteins.Finally,we mined 3081 orthologous genes for 52.7% of unknown protein isoforms across multiple species,referring to 68 KEGG pathways as well as 23 disease signaling pathways.These findings provide valuable insights and a rich resource for enhancing studies of pig genomics and biology,as well as biomedical model application to human medicine.