Genome Wide Screening of Candidate Genes for Improving Piglet Birth Weight Using High and Low Estimated Breeding Value Populations

Abstract

Birth weight is an economically important trait in pig production because it directly impacts piglet growth and survival rate. In the present study, we performed a genome wide survey of candidate genes and pathways associated with individual birth weight (IBW) using the Illumina PorcineSNP60 BeadChip on 24 high (HEBV) and 24 low estimated breeding value (LEBV) animals. These animals were selected from a reference population of 522 individuals produced by three sires and six dam lines, which were crossbreds with multiple breeds. After quality-control, 43,257 SNPs (single nucleotide polymorphisms), including 42,243 autosomal SNPs and 1,014 SNPs on chromosome X, were used in the data analysis. A total of 27 differentially selected regions (DSRs), including 1 on Sus scrofa chromosome 1 (SSC1), 1 on SSC4, 2 on SSC5, 4 on SSC6, 2 on SSC7, 5 on SSC8, 3 on SSC9, 1 on SSC14, 3 on SSC18, and 5 on SSCX, were identified to show the genome wide separations between the HEBV and LEBV groups for IBW in piglets. A DSR with the most number of significant SNPs (including 7 top 0.1% and 31 top 5% SNPs) was located on SSC6, while another DSR with the largest genetic differences in FST was found on SSC18. These regions harbor known functionally important genes involved in growth and development, such as TNFRSF9 (tumor necrosis factor receptor superfamily member 9), CA6 (carbonic anhydrase VI) and MDFIC (MyoD family inhibitor domain containing). A DSR rich in imprinting genes appeared on SSC9, which included PEG10 (paternally expressed 10), SGCE (sarcoglycan, epsilon), PPP1R9A (protein phosphatase 1, regulatory subunit 9A) and ASB4 (ankyrin repeat and SOCS box containing 4). More importantly, our present study provided evidence to support six quantitative trait loci (QTL) regions for pig birth weight, six QTL regions for average birth weight (ABW) and three QTL regions for litter birth weight (LBW) reported previously by other groups. Furthermore, gene ontology analysis with 183 genes harbored in these 27 DSRs suggested that protein, metal, ion and ATP binding, viral process and innate immune response present important pathways for deciphering their roles in fetal growth or development. Overall, our study provides useful information on candidate genes and pathways for regulating birth weight in piglets, thus improving our understanding of the genetic mechanisms involved in porcine embryonic or fetal development.

Conservation Genomic Analysis of the Croatian Indigenous Black Slavonian and Turopolje Pig Breeds

“…Additional selection signature has been identified in PEBP4 gene region (placed on SSC14) in Turopolje breed as significant signals were obtained by eROHi and iHS analyses. Assuming that the necessary data become available, future work may wish to take a more comprehensive approach, at least for the relatively large Black Slavonian population, by estimating breeding values for traits of conservation interest and combining those estimates with F ST values to detect conservation-relevant SNPs (Zhang et al, 2014).…”

A genome‐wide association study suggests several novel candidate genes for carcass traits in Chinese Simmental beef cattle

“…WDFY3 ( WD repeat and FYVE domain containing 3 ) has been identified to be associated with birth weight in piglets and might be involved in embryonic or fetal development in pigs (Zhang et al . ). FER1L6 ( fer‐1 like family member 6 ), which was found to affect the pattern of marble marbling score in Korean cattle, also has been suggested as a candidate gene affecting beef quality (Ryu & Lee ).…”

Genome-Wide Association Study and Fine Mapping Reveals Candidate Genes for Birth Weight of Yorkshire and Landrace Pigs

“…With the widespread use of customized single nucleotide polymorphism (SNP) arrays, an increasing number of potential markers have been identified by genome-wide association study (GWAS). Wang X. et al (2016) found over two hundred SNPs associated with birth weight by using first parity sows whose offspring had extreme birth weights; Zhang et al (2018) identified 17 genomic regions associated with birth weight; Wang et al (2017) found 12 SNPs that were significantly associated with piglet uniformity; and 27 differentially selected regions associated with the birth weight of piglets were detected by Zhang et al (2014). However, a birth weight GWAS of Large white pigs by Wang et al (2018) was unable to determine any significant loci.…”