Dataset Information

Survey of SNPs Associated with Total Number Born and Total Number Born Alive in Pig.

ABSTRACT: Reproductive productivity depend on a complex set of characteristics. The number of piglets at birth (Total number born, Litter size, TNB) and the number of alive piglets at birth (Total number born alive, NBA) are the main indicators of the reproductive productivity of sows in pig breeding. Great hopes are pinned on GWAS (Genome-Wide Association Studies) to solve the problems associated with studying the genetic architecture of reproductive traits of pigs. This paper provides an overview of international studies on SNP (Single nucleotide polymorphism) associated with TNB and NBA in pigs presented in PigQTLdb as "Genome map association". Currently on the base of Genome map association results 306 SNPs associated with TNB (218 SNPs) and NBA (88 SNPs) have been identified and presented in the Pig QTLdb database. The results are based on research of pigs such as Large White, Yorkshire, Landrace, Berkshire, Duroc and Erhualian. The presented review shows that most SNPs found in chromosome areas where candidate genes or QTLs (Quantitative trait locus) have been identified. Further research in the given direction will allow to obtain new data that will become an impulse for creating breakthrough breeding technologies and increase the production efficiency in pig farming.

SUBMITTER: Bakoev S

PROVIDER: S-EPMC7291110 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Survey of SNPs Associated with Total Number Born and Total Number Born Alive in Pig.

Bakoev Siroj S Getmantseva Lyubov L Bakoev Faridun F Kolosova Maria M Gabova Valeria V Kolosov Anatoly A Kostyunina Olga O

Genes 20200430 5

Reproductive productivity depend on a complex set of characteristics. The number of piglets at birth (Total number born, Litter size, TNB) and the number of alive piglets at birth (Total number born alive, NBA) are the main indicators of the reproductive productivity of sows in pig breeding. Great hopes are pinned on GWAS (Genome-Wide Association Studies) to solve the problems associated with studying the genetic architecture of reproductive traits of pigs. This paper provides an overview of int ...[more]

PMID: 32365801

Similar Datasets

Project description:BackgroundPiglet pre-weaning mortality (PWM) is one of the biggest problems regarding sow performance and piglet welfare. Recently, PWM has increased in some countries, but it is not known if there are similar increases in other countries, nor whether increased PWM is related to either increased numbers of piglets born alive (PBA) or to sow herd size. So, the objectives of the present study were 1) to explore the trend in PWM in Spanish sow herds over a recent 10-year period, along with related measurements such as PBA, stillborn piglets, herd productivity and herd size; and 2) to examine the relationships between PWM and the related measurements.MethodsHerd-level annual data from 2007 to 2016 for 91 herds in Spain were abstracted from a sow database compiled by a veterinary consultancy firm that asked client producers to mail data files on a regular basis. The database software automatically calculated herd-level PWM (%) as follows: the total number of piglets born alive to a sow completely weaned during a year (TPBA) minus the total number of piglets weaned by the completely weaned sow during the year divided by TPBA × 100. All the statistical analyses were performed by using SAS University Edition. A growth curve model was applied to incorporate correlations for all of the observations arising from the same farm.ResultsOver the 10 years, herd means of PWM (standard deviation) increased from 11.9 (4.1) % to 14.4 (3.2) %, and mean PBA increased by 1.9 pigs. Mean age of piglet death during lactation increased by 3.8 days, and later years were significantly associated with herd size and the number of piglets weaned per sow per year (PSY; P < 0.05). Higher PWM was associated with more PBA, more stillborn piglets and small-to-mid herds (lower than the median size: < 570 sows; P < 0.05). Also, there was a significant interaction between the herd size groups and PBA for PWM (P < 0.05): as PBA increased from 9 to 14 pigs, PWM increased by 9.6% in small-to-mid herds, compared with an increase of only 6.6% in large herds (> 570 sows). Furthermore, as PWM decreased from 18 to 8%, herd productivity measured as PSY increased by 2.2 pigs in large herds, compared with only 0.6 pigs in small-to-mid herds.ConclusionLarge herds were better than small-to-mid herds at alleviating the association between increased PBA and increased PWM. Also, the relationship between decreased PWM and increased herd productivity was improved more in large herds than in small-to-mid herds.

Project description:Background: The use of breed-informative genetic markers, specifically coding Single Nucleotide Polymorphisms (SNPs), is crucial for breed traceability, authentication of meat and dairy products, and the preservation and improvement of pig breeds. By identifying breed informative markers, we aimed to gain insights into the genetic mechanisms that influence production traits, enabling informed decisions in animal management and promoting sustainable pig production to meet the growing demand for animal products. Methods: Our dataset consists of 300 coding SNPs genotyped from three Italian commercial pig populations: Landrace, Yorkshire, and Duroc. Firstly, we analyzed the genetic diversity among the populations. Then, we applied a discriminant analysis of principal components to identify the most informative SNPs for discriminating between these populations. Lastly, we conducted a functional enrichment analysis to identify the most enriched pathways related to the genetic variation observed in the pig populations. Results: The alpha diversity indexes revealed a high genetic diversity within the three breeds. The higher proportion of observed heterozygosity than expected revealed an excess of heterozygotes in the populations that was supported by negative values of the fixation index (FIS) and deviations from the Hardy-Weinberg equilibrium. The Euclidean distance, the pairwise FST, and the pairwise Nei's GST genetic distances revealed that Yorkshire and Landrace breeds are genetically the closest, with distance values of 2.242, 0.029, and 0.033, respectively. Conversely, Landrace and Duroc breeds showed the highest genetic divergence, with distance values of 2.815, 0.048, and 0.052, respectively. We identified 28 significant SNPs that are related to phenotypic traits and these SNPs were able to differentiate between the pig breeds with high accuracy. The Functional Enrichment Analysis of the informative SNPs highlighted biological functions related to DNA packaging, chromatin integrity, and the preparation of DNA into higher-order structures. Conclusion: Our study sheds light on the genetic underpinnings of phenotypic variation among three Italian pig breeds, offering potential insights into the mechanisms driving breed differentiation. By prioritizing breed-specific coding SNPs, our approach enables a more focused analysis of specific genomic regions relevant to the research question compared to analyzing the entire genome.

Project description:OBJECTIVE:The study was designed to perform a genome-wide association (GWA) and partitioning of genome using Illumina's PorcineSNP60 Beadchip in order to identify variants and determine the explained heritability for the total number of teats in Yorkshire pig. METHODS:After screening with the following criteria: minor allele frequency, MAF≤0.01; Hardy-Weinberg equilibrium, HWE≤0.000001, a pair-wise genomic relationship matrix was produced using 42,953 single nucleotide polymorphisms (SNPs). A genome-wide mixed linear model-based association analysis (MLMA) was conducted. And for estimating the explained heritability with genome- or chromosome-wide SNPs the genetic relatedness estimation through maximum likelihood approach was used in our study. RESULTS:The MLMA analysis and false discovery rate p-values identified three significant SNPs on two different chromosomes (rs81476910 and rs81405825 on SSC8; rs81332615 on SSC13) for total number of teats. Besides, we estimated that 30% of variance could be explained by all of the common SNPs on the autosomal chromosomes for the trait. The maximum amount of heritability obtained by partitioning the genome were 0.22±0.05, 0.16±0.05, 0.10±0.03 and 0.08±0.03 on SSC7, SSC13, SSC1, and SSC8, respectively. Of them, SSC7 explained the amount of estimated heritability along with a SNP (rs80805264) identified by genome-wide association studies at the empirical p value significance level of 2.35E-05 in our study. Interestingly, rs80805264 was found in a nearby quantitative trait loci (QTL) on SSC7 for the teat number trait as identified in a recent study. Moreover, all other significant SNPs were found within and/or close to some QTLs related to ovary weight, total number of born alive and age at puberty in pigs. CONCLUSION:The SNPs we identified unquestionably represent some of the important QTL regions as well as genes of interest in the genome for various physiological functions responsible for reproduction in pigs.

Dataset Information

Survey of SNPs Associated with Total Number Born and Total Number Born Alive in Pig.

Publications

Survey of SNPs Associated with Total Number Born and Total Number Born Alive in Pig.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets