QTL analysis of white blood cell, platelet and red blood cell-related traits in an F2 intercross between Landrace and Korean native pigs

Haematological traits play important roles in disease resistance and defence functions. The objective of this study was to locate quantitative trait loci (QTL) and the associated positional candidate genes influencing haematological traits in an F₂ intercross between Landrace and Korean native pigs. Eight blood‐related traits (six erythrocyte traits, one leucocyte trait and one platelet trait) were measured in 816 F₂ progeny. All experimental animals were genotyped with 173 informative microsatellite markers located throughout the pig genome. We report that nine chromosomes harboured QTL for the baseline blood parameters: genomic regions on SSC 1, 4, 5, 6, 8, 9, 11, 13 and 17. Eight of twenty identified QTL reached genome‐wide significance. In addition, we evaluated the KIT locus, an obvious candidate gene locus affecting variation in blood‐related traits. Using dense single nucleotide polymorphism marker data on SSC 8 and the marker‐assisted association test, the strong association of the KIT locus with blood phenotypes was confirmed. In conclusion, our study identified both previously reported and novel QTL affecting baseline haematological parameters in pigs. Additionally, the positional candidate genes identified here could play an important role in elucidating the genetic architecture of haematological phenotype variation in swine and in humans.     

QTL analysis of clinical-chemical traits in an F₂ intercross between Landrace and Korean native pigs

Clinical-chemical traits are essential when examining the health status of individuals. The aim of this study was to identify quantitative trait loci (QTL) and the associated positional candidate genes affecting clinical-chemical traits in a reciprocal F(2) intercross between Landrace and Korean native pigs. Following an overnight fast, 25 serum phenotypes related to clinical-chemical traits (e.g., hepatic function parameters, renal function parameters, electrolyte, lipids) were measured in >970 F(2) progeny. All experimental samples were subjected to genotyping analysis using 165 microsatellite markers located across the genome. We identified eleven genome-wide significant QTL in six chromosomal regions (SSC 2, 7, 8, 13, 14, and 15) and 59 suggestive QTL in 17 chromosomal regions (SSC 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, and 18). We also observed significant effects of reciprocal crosses on some of the traits, which would seem to result from maternal effect, QTL on sex chromosomes, imprinted genes, or genetic difference in mitochondrial DNA. The role of genomic imprinting in clinical-chemical traits also was investigated. Genome-wide analysis revealed a significant evidence for an imprinted QTL in SSC4 affecting serum amylase levels. Additionally, a series of bivariate linkage analysis provided strong evidence that QTL in SSC 2, 13, 15, and 18 have a pleiotropic effect on clinical-chemical traits. In conclusion, our study detected both novel and previously reported QTL influencing clinical-chemical traits in pigs. The identified QTL together with the positional candidate genes identified here could play an important role in elucidating the genetic structure of clinical-chemical phenotype variation in humans and swine.     

A quantitative trait locus for oleic fatty acid content on Sus scrofa chromosome 7

A partial genome scan using microsatellite markers was conducted to detect quantitative trait loci (QTLs) for 10 fatty acid contents of backfat on 15 chromosomes in a porcine resource population. Two QTLs were discovered on Sus scrofa chromosome 4 (SSC4) and SSC7. The QTL on SSC4 was located between marker loci sw1336 and sw512, and this QTL was detected (P < 0.05) only for linoleic acid. Its position was in proximity of those mapped for linoleic acid content in previous studies. The QTL on SSC7 was mapped between markers swr1343 and sw2155, and it was significant (P < 0.05) only for oleic acid. A novelty of the QTL for oleic acid was suggested because the QTL was located far from any other QTLs previously mapped for fatness traits. The QTL on SSC7 explained 19% of phenotypic variation for oleic acid content. Further studies on fine mapping and positional comparative candidate gene analysis would be the next step toward better understanding of the genetic architecture of fatty acid contents.     

QTL modulating ear size and erectness in pigs

Ear size and erectness are important conformation measurements in pigs. An F(2) population established by crossing European Large White (small, erect ears) with Chinese Meishan (large, flop ears) was used to study the genetic influence of the two ear traits for the first time. A linkage map incorporating 152 markers on 18 autosomal chromosomes was utilised in a genome scan for QTL. Significant QTL were found on SSC1, 5, 7, 9 and 12 for the two traits. The QTL on SSC5 and SSC7 had major effects and were significant at the genome-wide level (P < 0.01). The QTL on SSC1 for ear erectness also had a major effect and was genome-wide significant (P < 0.01). The 95% confidence interval (CI) of the ear size QTL on SSC5 spanned only 4 cM. The QTL on SSC7 for the two ear traits each had a CI of <20 cM, and their positions overlapped with those of the major QTL affecting subcutaneous fat depths on the same chromosome. This study provides insights on the complex genetic influences underlying pig ear traits and will facilitate positional candidate gene analysis to identify causative DNA variants.     

Test for positional candidate genes for body composition on pig chromosome 6

One QTL affecting backfat thickness (BF), intramuscular fat content (IMF) and eye muscle area (MA) was previously localized on porcine chromosome 6 in an F₂ cross between Iberian and Landrace pigs. This work was done to study the effect of two positional candidate genes on these traits: H-FABP and LEPR genes. The QTL mapping analysis was repeated with a regression method using genotypes for seven microsatellites and two PCR-RFLPs in the H-FABP and LEPR genes. H-FABP and LEPR genes were located at 85.4 and 107 cM respectively, by linkage analysis. The effects of the candidate gene polymorphisms were analyzed in two ways. When an animal model was fitted, both genes showed significant effects on fatness traits, the H-FABP polymorphism showed significant effects on IMF and MA, and the LEPR polymorphism on BF and IMF. But when the candidate gene effect was included in a QTL regression analysis these associations were not observed, suggesting that they must not be the causal mutations responsible for the effects found. Differences in the results of both analyses showed the inadequacy of the animal model approach for the evaluation of positional candidate genes in populations with linkage disequilibrium, when the probabilities of the parental origin of the QTL alleles are not included in the model.     

Comparative mapping of a region on chromosome 10 containing QTL for reproduction in swine

Several quantitative trait loci (QTL) for important reproductive traits (age of puberty, ovulation rate, nipple number and plasma FSH) have been identified on the long arm of porcine chromosome 10. Bi-directional chromosome painting has shown that this region is homologous to human chromosome 10p. Because few microsatellite or type I markers have been placed on SSC10, we wanted to increase the density of known ESTs mapped in this region of the porcine genome. Genes were chosen for their position on human chromosome 10, sequence availability from the TIGR pig gene indices, and their potential as a candidate gene. The PCR primers were designed to amplify across introns or 3'-UTR to maximize single nucleotide polymorphism (SNP) discovery. Parents of the mapping population (one sire and seven dams) were amplified and sequenced to find informative markers. The SNPs were genotyped using primer extension and mass spectrometry. These amplification products were also used to probe a BAC library (RPCI-44, Roswell Park Cancer Institute) for positive clones and screened for microsatellites. Six genes from human chromosome 10p (AKR1C2, PRKCQ, ITIH2, ATP5C1, PIP5K2A and GAD2) were mapped in the MARC swine mapping population. Gene order was conserved within these markers from centromere to telomere of porcine chromosome 10q, as compared with human chromosome 10p. Four of these genes (PIP5K2A, ITIH2, GAD2 and AKR1C2), which map under QTL, are potential candidate genes. Identification of porcine homologues near important QTL and development of a comparative map for this chromosome will allow further fine- mapping and positional cloning of candidate genes affecting reproductive traits.     

A genome‐wide association study to detect genetic variation for postpartum dysgalactia syndrome in five commercial pig breeding lines

Postpartum dysgalactia syndrome (PDS) in sows is an important disease after parturition with a relevant economic impact, affecting the health and welfare of both sows and piglets. The genetic background of this disease has been discussed and its heritability estimated, but further genetic analyses are lacking in detail. The aim of the current study was to detect loci affecting the susceptibility to PDS through a genome‐wide association approach. The study was designed as a family‐based association study with matched sampling of affected sows and healthy half‐ or full‐sib control sows on six farms. For the study, 597 sows (322 affected vs. 275 healthy control sows) were genotyped on 62 163 single nucleotide polymorphisms (SNPs) using the Illumina PorcineSNP60 BeadChip. After quality control, 585 sows (314 affected vs. 271 healthy control sows) and 49 740 SNPs remained for further analysis. Statistics were performed mainly with the r package genabel and included a principal component analysis. A statistically significant genome‐wide associated SNP was identified on porcine chromosome (SSC) 17. Further promising results with moderate significance were detected on SSC 13 and on an unplaced scaffold with an older annotation on SSC 15. The PRICKLE2 and NRP2 genes were identified as candidate genes near associated SNPs. Several quantitative trait loci (QTL) have been previously described in these genomic regions, including QTL for mammary gland condition, as teat number and non‐functional nipples QTL, as well as QTL for body temperature and gestation length.     

Four loci differentially expressed in muscle tissue depending on water-holding capacity are associated with meat quality in commercial pig herds

Four genes, VTN, KERA, LYZ, and a non-annotated EST (Affymetrix probe set ID: Ssc.25503.1.S1_at), whose candidacy for traits related to water-holding capacity of meat arises from their trait-dependent differential expression, were selected for candidate gene analysis. Based on in silico analysis SNPs were detected, confirmed by sequencing and used to genotype animals of 4 pig populations including 3 commercial herds of Pietrain (PI), Pietrain × (German Large White × German Landrace) (PIF1), German Landrace (DL) and 1 experimental F₂ population Duroc × Pietrain (DUPI). Comparative and genetic mapping established the location of VTN on SSC12, of LYZ and KERA on SSC5 and of UN on SSC7, coinciding with QTL regions for meat quality traits. VTN showed association with pH1, pH24 and drip loss. LYZ revealed association with conductivity 24, pH1 and drip loss. KERA was associated with pH. UN showed association with pH24 and drip loss, respectively. However, none of the candidate genes showed significant associations for a particular trait across all populations. This may be due to breed specific effects that are related to the differences in meat quality of theses pig breeds. The studies revealed statistic evidence for a link of genetic variation at these loci or close to them and promoted those four candidate genes as functional and/or positional candidate genes for meat quality traits.     

QTL for the heritable inverted teat defect in pigs

The mothering ability of a sow largely depends on the shape and function of the mammary gland. The aim of this study was to identify QTL for the heritable inverted teat defect, a condition characterized by disturbed development of functional teats. A QTL analysis was conducted in a porcine experimental population based on Duroc and Berlin Miniature pigs (DUMI). The significant QTL were confirmed by linkage analysis in commercial pigs according to the affected sib pair design and refined by family-based association test (FBAT). Nonparametric linkage (NPL) analysis revealed five significant and seven suggestive QTL for the inverted teat defect in the porcine experimental population. In commercial dam lines five significant NPL values were detected. QTL regions in overlapping marker intervals or close proximity in both populations were found on SSC3, SSC4, SSC6, and SSC11. SSC6 revealed QTL in both populations at different positions, indicating the segregation of at least two QTL. The results confirm the previously proposed polygenic inheritance of the inverted teat defect and, for the first time, point to genomic regions harboring relevant genes. The investigation revealed variation of the importance of QTL in the various populations due to either differences in allele frequencies and statistical power or differences in the genetic background that modulates the impact of the liability loci on the expression of the disease. The QTL study enabled us to name a number of plausible positional candidate genes. The correspondence of QTL regions for the inverted teat defect and previously mapped QTL for teat number are in line with the etiologic relationship of these traits.     

A genome-wide association study for feed efficiency-related traits in a crossbred pig population

Feed efficiency (FE) is one of the most important traits in pig production. However, it is difficult and costly to measure it, limiting the collection of large amount of data for an accurate selection for better FE. Therefore, the identification of single-nucleotide polymorphisms (SNPs) associated with FE-related traits to be used in the genetic evaluation is of great interest of pig breeding programs for increasing the prediction accuracy and the genetic progress of these traits. The objective of this study was to identify SNPs significantly associated with FE-related traits: average daily gain (ADG), average daily feed intake (ADFI) and feed conversion ratio (FCR). We also aimed to identify potential candidate genes for these traits. Phenotypic information recorded on a population of 2386 three-way crossbreed pigs that were genotyped for 51 468 SNPs was used. We identified three loci of quantitative trait (QTL) regions associated with ADG and three QTL regions associated with ADFI; however, no significant association was found for FCR. A false discovery rate (FDR) ≤ 0.005 was used as the threshold for declaring an association as significant. The QTL regions associated with ADG on Sus scrofa chromosome (SSC) 1 were located between 177.01 and 185.47 Mb, which overlaps with the QTL regions for ADFI on SSC1 (173.26 and 185.47 Mb). The other QTL region for ADG was located on SSC12 (2.87 and 3.22 Mb). The most significant SNPs in these QTL regions explained up to 3.26% of the phenotypic variance of these traits. The non-identification of genomic regions associated with FCR can be explained by the complexity of this trait, which is a ratio between ADG and ADFI. Finally, the genes CDH19, CDH7, RNF152, MC4R, PMAIP1, FEM1B and GAA were the candidate genes found in the 1 Mb window around the QTL regions identified in this study. Among them, the MC4R gene (SSC1) has a well-known function related to ADG and ADFI. In this study, we identified three QTL regions for ADG (SSC1 and SSC12) and three for ADFI (SSC1). These regions were previously described in purebred pig populations; however, to our knowledge, this is the first study to confirm the relevance of these QTL regions in a crossbred pig population. The potential use of the SNPs and genes identified in this study in prediction models that combine genomic selection and marker-assisted selection should be evaluated for increasing the prediction accuracy of these traits in this population.     

Quantitative trait loci for organ weights and adipose fat composition in Jersey and Limousin back‐cross cattle finished on pasture or feedlot

A QTL study of live animal and carcass traits in beef cattle was carried out in New Zealand and Australia. Back‐cross calves (385 heifers and 398 steers) were generated, with Jersey and Limousin backgrounds. This paper reports on weights of eight organs (heart, liver, lungs, kidneys, spleen, gastro‐intestinal tract, fat, and rumen contents) and 12 fat composition traits (fatty acid (FA) percentages, saturated and monounsaturated FA subtotals, and fat melting point). The New Zealand cattle were reared and finished on pasture, whilst Australian cattle were reared on grass and finished on grain for at least 180 days. For organ weights and fat composition traits, 10 and 12 significant QTL locations (P < 0.05), respectively, were detected on a genome‐wide basis, in combined‐sire or within‐sire analyses. Seven QTL significant for organ weights were found at the proximal end of chromosome 2. This chromosome carries a variant myostatin allele (F94L), segregating from the Limousin ancestry, and this is a positional candidate for the QTL. Ten significant QTL for fat composition were found on chromosomes 19 and 26. Fatty acid synthase and stearoyl‐CoA desaturase (SCD1), respectively, are positional candidate genes for these QTL. Two FA QTL found to be common to sire groups in both populations were for percentages of C14:0 and C14:1 (relative to all FAs) on chromosome 26, near the SCD1 candidate gene.     

Genes with expression levels correlating to drip loss prove association of their polymorphism with water holding capacity of pork

Six genes that were known to exhibit expression levels that are correlated to drip loss BVES, SLC3A2, ZDHHC5, CS, COQ9, and EGFR have been for candidate gene analysis. Based on in silico analysis SNPs were detected, confirmed by sequencing, and used for genotyping. The SNPs were genotyped in about 1,800 animals from six pig populations including commercial herds of Pietrain (PI) and German Landrace (DL), different commercial herds of Pietrain × (German Large White × German Landrace) (PIF1(a/b/c)), and one experimental F₂-population Duroc × Pietrain (DUPI). Comparative and genetic mapping established the location of BVES on SSC1, of SLC3A2 and ZDHHC5 on SSC2, of CS on SSC5, of COQ9 on SSC6 and of EGFR on SSC9, respectively, coinciding with QTL regions for carcass and meat quality traits. BVES, SLC3A2, and CS revealed association at least with drip loss and with several other measures of water holding capacity (WHC). Moreover, COQ9 and EGFR were associated with several meat quality traits such as meat color and/or thawing loss. This study reveals statistic evidence in addition to the functional relationship of these genes to WHC previously evidenced by expression analysis. This study reveals positional and genetic statistical evidence for a link of genetic variation at these loci or close to them and promotes those six candidate genes as functional and/or positional candidate genes for meat quality traits.     

Cytogenetic mapping of<Emphasis Type="Italic">DGAT1, PPARA,ADIPOR1</Emphasis> and<Emphasis Type="Italic">CREB</Emphasis> genes in the pig

In the present study we show FISH localization of 4 porcine BAC clones harbouring potential candidate genes for fatness traits: DGAT1 (SSC4p15), PPARA (SSC5p15), ADIPOR1 (SSC10p13) and CREB (SSC15q24). Until now the CREB and ADIPOR1 genes are considered to be monomorphic, DGAT1 is highly polymorphic, while for the PPARA gene only 1 SNP was identified. Assignment of the studied genes in relation to QTL chromosome regions for meat quality in pig chromosomes SSC4, SSC5, SSC10 and SSC15 is discussed.     

Comparative mapping of human chromosome 10 to pig chromosomes 10 and 14

Identification of predictive markers in QTL regions that impact production traits in commercial populations of swine is dependent on construction of dense comparative maps with human and mouse genomes. Chromosomal painting in swine suggests that large genomic blocks are conserved between pig and human, while mapping of individual genes reveals that gene order can be quite divergent. High-resolution comparative maps in regions affecting traits of interest are necessary for selection of positional candidate genes to evaluate nucleotide variation causing phenotypic differences. The objective of this study was to construct an ordered comparative map of human chromosome 10 and pig chromosomes 10 and 14. As a large portion of both pig chromosomes are represented by HSA10, genes at regularly spaced intervals along this chromosome were targeted for placement in the porcine genome. A total of 29 genes from human chromosome 10 were mapped to porcine chromosomes 10 (SSC10) and 14 (SSC14) averaging about 5 Mb distance of human DNA per marker. Eighteen genes were assigned by linkage in the MARC mapping population, five genes were physically assigned with the IMpRH mapping panel and seven genes were assigned on both maps. Seventeen genes from human 10p mapped to SSC10, and 12 genes from human 10q mapped to SSC14. Comparative maps of mammalian species indicate that chromosomal segments are conserved across several species and represent syntenic blocks with distinct breakpoints. Development of comparative maps containing several species should reveal conserved syntenic blocks that will allow us to better define QTL regions in livestock.     

Quantitative trait loci mapping for fatty acid contents in the backfat on porcine chromosomes 1, 13, and 18

A partial genome scan using microsatellite markers was conducted in order to detect quantitative trait loci (QTLs) for 10 fatty acid contents of the backfat in a pig reference population. Two QTLs were found by studying SSC1, SSC13, and SSC18, where QTLs had already been identified for backfat thickness. A QTL was located between marker loci S0113 and SW974 on chromosome 1; this QTL was only significantly detected (P < 0.05) for linoleic acid. The other QTL was discovered between markers S0062 and S0120 on chromosome 18, and its significance only showed (P < 0.05) for myristic acid. The two QTLs mapped to the same location as the backfat thickness QTL. A third of the phenotypic variation was explained for linoleic acid by the QTL on chromosome 1, and a quarter for myristic acid by the QTL on chromosome 18. Further studies on fine mapping and positional comparative candidate gene analyses will be the next step toward a better understanding of the genetic architecture of fatty acid contents.     

Analysis of candidate genes underlying two epistatic quantitative trait loci on SSC12 affecting litter size in pig

The previous results from a genome scan for total number of piglets born and number of piglets born alive in a F₂ Iberian by Meishan intercross showed several single and epistatic QTL. One of the most interesting results was obtained for SSC12, where two QTL affecting both traits showed epistatic interaction. In this study, we proposed two genes ( SLC9A3R1 and NOS2 ) as biological and potentially positional candidates underlying these QTL. Both cDNAs were characterized and 23 polymorphisms were detected. A chromosome scan was conducted with 12 markers, plus one SNP in SLC9A3R1 and one in NOS2, covering 110 cM of SSC12. The epistatic QTL (QTL1 at 15 cM and QTL2 at 97 cM) were confirmed, and SLC9A3R1 and NOS2 were mapped around the QTL1 and QTL2 regions respectively. Several SNPs in both genes were tested with standard animal model and marker assisted association tests. The most significant results were obtained with the NOS2 haplotype defined by one missense SNP c.2192C > T (Val to Ala) and a 15 bp duplication at the 3'UTR. This duplication seems to include AU-rich elements, and could be a target site for miRNA, therefore there are statistical and biological indications to consider this haplotype as the potential causal mutation underlying QTL2. SLC9A3R1 results were not conclusive. Although the interaction between the SNPs was not significant, we cannot reject the possibility of interaction of the NOS2 haplotype with other polymorphisms closely linked to the SL9A3R1 SNPs analysed.     

QTL detection on porcine chromosome 12 for fatty-acid composition and association analyses of the fatty acid synthase, gastric inhibitory polypeptide and acetyl-coenzyme A carboxylase alpha genes

Refinement of previous QTL on porcine chromosome 12 for fatty-acid composition and a candidate gene association analysis were conducted using an Iberian × Landrace cross. The concentrations of ten fatty acids were assayed in backfat tissue from which four metabolic ratios were calculated for 403 F₂ animals. Linkage analysis identified two significant QTL. The first QTL was associated with the average chain length ratio and the percentages of myristic, palmitic and gadoleic acids. The second QTL was associated with percentages of palmitoleic, stearic and vaccenic acids. Based upon its position on SSC12, fatty acid synthase was tested as a candidate gene for the first QTL and no significant effects were found. Similarly, gastric inhibitory polypeptide ( GIP ) and acetyl-coenzyme A carboxylase alpha ( ACACA ) were tested as candidate genes for the second QTL using three SNPs in GIP and 15 synonymous SNPs in ACACA cDNA sequences. Two missense SNPs in GIP showed significant effects with palmitoleic and stearic fatty-acid concentration. Highly significant associations were found for two SNPs in ACACA with stearic, palmitoleic and vaccenic fatty-acid concentrations. These associations could be due to linkage disequilibrium with the causal mutations.     

Genome-wide QTL analysis of meat quality-related traits in a large F2 intercross between Landrace and Korean native pigs

Background

We conducted a genome-wide linkage analysis to identify quantitative trait loci (QTL) that influence meat quality-related traits in a large F₂ intercross between Landrace and Korean native pigs. Thirteen meat quality-related traits of the m. longissimus lumborum et thoracis were measured in more than 830 F₂ progeny. All these animals were genotyped with 173 microsatellite markers located throughout the pig genome, and the GridQTL program based on the least squares regression model was used to perform the QTL analysis.

Results

We identified 23 genome-wide significant QTL in eight chromosome regions (SSC1, 2, 6, 7, 9, 12, 13, and 16) (SSC for Sus Scrofa) and detected 51 suggestive QTL in the 17 chromosome regions. QTL that affect 10 meat quality traits were detected on SSC12 and were highly significant at the genome-wide level. In particular, the QTL with the largest effect affected crude fat percentage and explained 22.5% of the phenotypic variance (F-ratio = 278.0 under the additive model, nominal P = 5.5 × 10⁻⁵⁵). Interestingly, the QTL on SSC12 that influenced meat quality traits showed an obvious trend for co-localization.

Conclusions

Our results confirm several previously reported QTL. In addition, we identified novel QTL for meat quality traits, which together with the associated positional candidate genes improve the knowledge on the genetic structure that underlies genetic variation for meat quality traits in pigs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-014-0080-6) contains supplementary material, which is available to authorized users.     

Comparative mapping of bovine chromosome 27 with human chromosome 8 near a dairy form QTL in cattle

In the absence of a complete and annotated bovine genome sequence, detailed human-bovine comparative maps are one of the most effective tools for identification of positional candidate genes contributing to quantitative trait loci (QTL) in cattle. In the present study, eight genes from human chromosome 8 were selected for mapping in cattle to improve breakpoint resolution and confirm gene order on the comparative map near the 40 cM region of the BTA27 linkage map where a QTL affecting dairy form had previously been identified. The resulting map identified ADRB3 as a positional candidate gene for the QTL contributing to the dairy form trait based on its estimated position between 40 and 45 cM on the linkage map. It is also a functional candidate gene due to its role in fat metabolism, and polymorphisms in the ADRB3 gene associated with obesity and metabolic disease in humans, as well as, carcass fat in sheep. Further studies are underway to investigate the existence of polymorphisms in the bovine ADRB3 gene and their association with traits related to fat deposition in cattle.     

SNPs associated with body weight and backfat thickness in two pig breeds identified by a genome-wide association study

Growth and fat deposition are important economic traits due to the influence on production in pigs. In this study, a dataset of 1200 pigs with 345,570 SNPs genotyped by sequencing (GBS) was used to conduct a GWAS with single-marker regression method to identify SNPs associated with body weight and backfat thickness (BFT) and to search for candidate genes in Landrace and Yorkshire pigs. A total of 27 and 13 significant SNPs were associated with body weight and BFT, respectively. In the region of 149.85–149.89 Mb on SSC6, the SNP (SSC6: 149876737) for body weight and the SNP (SSC6: 149876507) for BFT were in the same locus region (a gap of 230 bp). Two SNPs were located in the DOCK7 gene, which is a protein-coding gene that plays an important role in pigmentation. Two SNPs located on SSC8: 54567459 and SSC11: 33043081 were found to overlap weight and BFT; however, no candidate gene was found in these regions. In addition, based on other significant SNPs, two positional candidate genes, NSRP1 and CADPS, were proposed to influence weight. In conclusion, this is the first study report using GBS data to identify the significant SNPs for weight and BFT. A total of four particularly interesting SNPs and one potential candidate genes (DOCK7) were found for these traits in domestic pigs. This study improves our knowledge to better understand the complex genetic architecture of weight and BFT, but further validation studies of these candidate loci and genes are recommended in pigs