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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 F ST 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.

SUBMITTER: Zhang L

PROVIDER: S-EPMC3957079 | biostudies-other | 2014

REPOSITORIES: biostudies-other

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Genome wide screening of candidate genes for improving piglet birth weight using high and low estimated breeding value populations.

Zhang Lifan L Zhou Xiang X Michal Jennifer J JJ Ding Bo B Li Rui R Jiang Zhihua Z

International journal of biological sciences 20140207 3

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 ...[more]

PMID: 24644423

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Project description:The effects of birth weight (BiW; low BiW [LBW] vs. high BiW [HBW]) and estimated breeding value (EBV) for protein deposition (low EBV [LBV] vs. high EBV [HBV]) on N retention, N efficiency, and concentrations of metabolites in plasma and urine related to N efficiency in growing pigs were studied. At an age of 14 wk, 10 LBW-LBV (BiW: 1.07 ± 0.09 [SD] kg; EBV: -2.52 ± 3.97 g/d, compared with an average crossbred pig with a protein deposition of 165 g/d), 10 LBW-HBV (BiW: 1.02 ± 0.13 kg; EBV: 10.47 ± 4.26 g/d), 10 HBW-LBV (BiW: 1.80 ± 0.13 kg; EBV: -2.15 ± 2.28 g/d), and 10 HBW-HBV (BiW: 1.80 ± 0.15 kg; EBV: 11.18 ± 3.68 g/d) male growing pigs were allotted to the experiment. The pigs were individually housed in metabolism cages and were subjected to an N balance study in two sequential periods of 5 d, after an 11-d dietary adaptation period. Pigs were assigned to a protein adequate (A) or protein restricted (R, 70% of A) regime in a change-over design. Pigs were fed 2.8 times the energy requirements for maintenance. Nontargeted metabolomics analyses were performed in urine and blood plasma samples. The N retention (in g/d) was higher in the HBW than in the LBW pigs (P < 0.001). The N retention (in g/[kg metabolic body weight (BW0.75) · d]) and N efficiency, however, were not affected by the BiW of the pigs. The N retention (P = 0.04) and N efficiency (P = 0.04) were higher in HBV than in LVB pigs on the A regime but were not affected by EBV in pigs on the R regime. Restricting the dietary protein supply with 30% decreased the N retention (P < 0.001) but increased the N efficiency (P = 0.003). Nontargeted metabolomics showed that a hexose, free amino acids (AA), and lysophosphatidylcholines were the most important metabolites in plasma for the discrimination between HBV and LBV pigs, whereas metabolites of microbial origin contributed to the discrimination between HBV and LBV pigs in urine. This study shows that BiW does not affect N efficiency in the later life of pigs. Nitrogen efficiency and N retention were higher in HBV than in LBV pigs on the A regime but similar in HBV and LBV pigs on the R regime. In precision feeding concepts aiming to further optimize protein and AA efficiency in pigs, the variation in EBV for protein deposition of pigs should be considered as a factor determining N retention, growth performance, and N efficiency.

Project description:Breeding cassava relies on several selection stages (single row trial-SRT; preliminary; advanced; and uniform yield trials-UYT). This study uses data from 14 years of evaluations. From more than 20,000 genotypes initially evaluated only 114 reached the last stage. The objective was to assess how the data at SRT could be used to predict the probabilities of genotypes reaching the UYT. Phenotypic data from each genotype at SRT was integrated into the selection index (SIN) used by the cassava breeding program. Average SIN from all the progenies derived from each progenitor was then obtained. Average SIN is an approximation of the breeding value of each progenitor. Data clearly suggested that some genotypes were better progenitors than others (e.g., high number of their progenies reaching the UYT), suggesting important variation in breeding values of progenitors. However, regression of average SIN of each parental genotype on the number of their respective progenies reaching UYT resulted in a negligible coefficient of determination (r (2) = 0.05). Breeding value (e.g., average SIN) at SRT was not efficient predicting which genotypes were more likely to reach the UYT stage. Number of families and progenies derived from a given progenitor were more efficient predicting the probabilities of the progeny from a given parent reaching the UYT stage. Large within-family genetic variation tends to mask the true breeding value of each progenitor. The use of partially inbred progenitors (e.g., S1 or S2 genotypes) would reduce the within-family genetic variation thus making the assessment of breeding value more accurate. Moreover, partial inbreeding of progenitors can improve the breeding value of the original (S0) parental material and sharply accelerate genetic gains. For instance, homozygous S1 genotypes for the dominant resistance to cassava mosaic disease (CMD) could be generated and selected. All gametes from these selected S1 genotypes would carry the desirable allele and 100% of their progenies would be resistant. Only half the gametes produced by the heterozygous S0 progenitor would carry the allele of interest. For other characteristics, progenies from the S1 genotypes should be, at worst, similar to those generated by the S0 progenitors.

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Genome wide screening of candidate genes for improving piglet birth weight using high and low estimated breeding value populations.

Publications

Genome wide screening of candidate genes for improving piglet birth weight using high and low estimated breeding value populations.

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