Genome-wide association study reveals novel loci for litter size and its variability in a Large White pig population

Zhang

J Animal Breeding Genetics

2019

Copy number variation (CNV) is an important source of genetic variability in human or animal genomes and play key roles in phenotypic diversity and disease susceptibility. In the present study, we performed a genome‐wide analysis for CNV detection using SNP genotyping data of 857 Large White pigs. A total of 312 CNV regions (CNVRs) were detected with the PennCNV algorithm, which covered 57.76 Mb of the pig genome and correspond to 2.36% of the genome sequence. The length of the CNVRs on autosomes ranged from 1.77 Kb to 1.76 Mb with an average of 185.11 Kb. Of these, 220 completely or partially overlapped with 1,092 annotated genes, which enriched a wide variety of biological processes. Comparisons with previously reported pig CNVR revealed 92 (29.49%) novel CNVRs. Experimentally, 80% of CNVRs selected randomly were validated by quantitative PCR (qPCR). We also performed an association analysis between some of the CNVRs and reproductive traits, with results demonstrating the potential importance of CNVR61 and CNVR283 associated with litter sizes. Notably, the GPER1 gene located in CNVR61 plays a key role in reproduction. Our study is an important complement to the CNV map in the pig genome and provides valuable information for investigating the association between genomic variation and economic traits.

Section: Discussionmentioning

confidence: 99%

Detection and analysis of genome‐wide copy number variation in the pig genome using an 80 K SNP Beadchip

Zhang

J Animal Breeding Genetics

2019

“…A recent study carried out in the Netherlands was based on boars' observations through their daughters [9]. For a deeper insight into the genetics of litter size and related traits, SNP technology is being widely adapted.…”

Section: Discussionmentioning

confidence: 99%

Maximum number of total born piglets in a parity and individual ranges in litter size expressed as specific characteristics of sows

Freyer

2018

J Anim Sci Technol

Background: The objective of this study was to underline that litter size as a key trait of sows needs new parameters to be evaluated and to target an individual optimum. Large individual variation in litter size affects both production and piglet's survival and health negatively. Therefore, two new traits were suggested and analyzed. Two data sets on 5509 purebred German Landrace sows and 3926 Large White and crossing sows including at least two parental generations and at least five parities were subjected to variance components analysis. Results: The new traits for evaluating litter size were derived from the individual numbers of total born piglets (TBP) per parity: In most cases, sows reach their maximum litter size in their fourth parity. Therefore, data from at least five parities were included. The first observable maximum and minimum of TBP, and the individual variation expressed by the range were targeted. Maximum of TBP being an observable trait in pig breeding and management yielded clearly higher heritability estimates (h 2~0 .3) than those estimates predominantly reported so far. Maximum TBP gets closer to the genetic capacity for litter size than other litter traits. Minimum of TBP is positively correlated with the range of TBP (r p = 0.48, r g > 0.6). The correlation between maximum of TBP and its individually reached frequency was negative in both data sets (r p = − 0.28 and − 0.22, respectively). Estimated heritability coefficients for the range of TBP comprised a span of h 2 = 0.06 to 0.10.

“…2016), litter size (Sell‐Kubiak et al . 2015) and ovulation rate (He et al . 2017), have been conducted, but knowledge about the complex genetic mechanism for reproductive performance still remains insufficient.…”

mentioning

confidence: 99%

Genome‐wide association study for reproductive traits in a Large White pig population

et al. 2018

SummaryUsing the PorcineSNP80 BeadChip, we performed a genome‐wide association study for seven reproductive traits, including total number born, number born alive, litter birth weight, average birth weight, gestation length, age at first service and age at first farrowing, in a population of 1207 Large White pigs. In total, we detected 12 genome‐wide significant and 41 suggestive significant SNPs associated with six reproductive traits. The proportion of phenotypic variance explained by all significant SNPs for each trait ranged from 4.46% (number born alive) to 11.49% (gestation length). Among them, 29 significant SNPs were located within known QTL regions for swine reproductive traits, such as corpus luteum number, stillborn number and litter size, of which one QTL region associated with litter size contained the ALGA0098819 SNP for total number born. Subsequently, we found that 376 functional genes contained or were near these significant SNPs. Of these, 14 genes—BHLHA15, OCM2, IL1B2, GCK, SMAD2, HABP2, PAQR5, GRB10, PRELID2, DMKN, GPI, GPIHBP1, ADCY2 and ACVR2B—were considered important candidates for swine reproductive traits based on their critical roles in embryonic development, energy metabolism and growth development. Our findings contribute to the understanding of the genetic mechanisms for reproductive traits and could have a positive effect on pig breeding programs.