The Association of an SNP in the EXOC4 Gene and Reproductive Traits Suggests Its Use as a Breeding Marker in Pigs

He, Yingting; Zhou, Xiaofeng; Zheng, Rongrong; Jiang, Yao; Yao, Zhixiang; Wang, Xilong; Zhang, Zhe; Zhang, Hao; Li, Jiaqi; Yuan, Xiaolong

doi:10.3390/ani11020521

Cited by 7 publications

(4 citation statements)

References 38 publications

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“…However, 10 QTL were found for the trait "Piglet Mortality". There was also no trait in the database defined as "Total litter weight within 3 weeks" (LW3W), but 1 QTL was listed for "Total litter weight at weaning" (He et al, 2021). There was also no QTL listed for Body Condition Score (BCS) or Shoulder Lesions (SHL).…”

Section: Genetic Architecturementioning

confidence: 99%

Accuracy of genomic prediction of maternal traits in pigs using Bayesian variable selection methods

Kjetså

Gjuvsland

Nordbø

et al. 2022

J Animal Breeding Genetics

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The aim of this study was to compare three methods of genomic prediction: GBLUP, BayesC and BayesGC for genomic prediction of six maternal traits in Landrace sows using a panel of 660 K SNPs. The effects of different priors for the Bayesian methods were also investigated. GBLUP does not take the genetic architecture into account as all SNPs are assumed to have equally sized effects and relies heavily on the relationships between the animals for accurate predictions. Bayesian approaches rely on both fitting SNPs that describe relationships between animals in addition to fitting single SNP effects directly. Both the relationship between the animals and single SNP effects are important for accurate predictions. Maternal traits in sows are often more difficult to record and have lower heritabilities. BayesGC was generally the method with the higher accuracy, although its accuracy was for some traits matched by that of GBLUP and for others by that of BayesC. For piglet mortality within 3 weeks, BayesGC achieved up to 9.2% higher accuracy. For many of the traits, however, the methods did not show significant differences in accuracies.

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Section: Genetic Architecturementioning

confidence: 99%

Accuracy of genomic prediction of maternal traits in pigs using Bayesian variable selection methods

Kjetså

Gjuvsland

Nordbø

et al. 2022

J Animal Breeding Genetics

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“…Moreover, several studies have reported that SNPs in intron were found relevant to production traits in pigs (such as litter size, backfat thickness, etc. ), which provided theoretical support and potential direction for further research [ 72 – 74 ]. This locus can predict the intramuscular fat content of pigs in an early, rapid, low-cost, and effective way, which could be used as a useful molecular marker for genetic breeding improvement of pigs.…”

Section: Discussionmentioning

confidence: 99%

Integrated analysis strategy of genome-wide functional gene mining reveals DKK2 gene underlying meat quality in Shaziling synthesized pigs

He,

Wang,

Luo

et al. 2024

BMC Genomics

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Background Shaziling pig is a well-known indigenous breed in China who has superior meat quality traits. However, the genetic mechanism and genomic evidence underlying meat quality characteristics of Shaziling pigs are still unclear. To explore and investigate the germplasm characteristics of Shaziling pigs, we totally analyzed 67 individual’s whole genome sequencing data for the first time (20 Shaziling pigs [S], 20 Dabasha pigs [DBS], 11 Yorkshire pigs [Y], 10 Berkshire pigs [BKX], 5 Basha pigs [BS] and 1 Warthog). Results A total of 2,538,577 SNPs with high quality were detected and 9 candidate genes which was specifically selected in S and shared in S to DBS were precisely mined and screened using an integrated analysis strategy of identity-by-descent (IBD) and selective sweep. Of them, dickkopf WNT signaling pathway inhibitor 2 (DKK2), the antagonist of Wnt signaling pathway, was the most promising candidate gene which was not only identified an association of palmitic acid and palmitoleic acid quantitative trait locus in PigQTLdb, but also specifically selected in S compared to other 48 Chinese local pigs of 12 populations and 39 foreign pigs of 4 populations. Subsequently, a mutation at 12,726-bp of DKK2 intron 1 (g.114874954 A > C) was identified associated with intramuscular fat content using method of PCR–RFLP in 21 different pig populations. We observed DKK2 specifically expressed in adipose tissues. Overexpression of DKK2 decreased the content of triglyceride, fatty acid synthase and expression of relevant genes of adipogenic and Wnt signaling pathway, while interference of DKK2 got contrary effect during adipogenesis differentiation of porcine preadipocytes and 3T3-L1 cells. Conclusions Our findings provide an analysis strategy for mining functional genes of important economic traits and provide fundamental data and molecular evidence for improving pig meat quality traits and molecular breeding.

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“…Recent development of sequencing and genotyping tools for pigs have permitted the investigation of genomic evidence of selection and the discovery of potential genes linked with desired traits (He et al, 2021). For example, the bone morphogenetic protein receptor type 1B (BMPR-1B) gene in sheep may have foremost effect on their reproduction (Qi et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Novel polymorphisms in GPX5 gene and their association with reproductive and productive traits in Lumsniang (Hampshire x Niang Megha) pigs under subtropical hilly region of Meghalaya

Kumar¹,

Kadirvel²,

Khargharia³

et al. 2022

JEB

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Aim: To detect genetic variants of GPX5 gene and their associations with reproductive and productive traits in the Lumsniang (Hampshire x Niang Megha) pigs. Methodology: In this study, a total of 87 Lumsniang pigs were selected for collecting blood samples (3-5 ml) from Nucleus Pig Breeding Farm of ICAR Research Complex for North Eastern Hilly region, Umiam, Meghalaya. Genomic DNA was extracted from the blood leukocytes using the Qiagen DNeasy Blood and tissue kits and diluted to working concentration (50 ng μl-1) and stored at -20°C, which were used as templates for association of GPX5 variants with polymerase chain reaction. The data for reproductive and productive traits were recorded from all the animals taken in this study. The reproductive and productive traits were analyzed using a general linear model (GLM) procedure of SPSS Version 16.0. Results: Polymorphisms at Intron 1 of the GPX5 gene was determined by PCR-RFLP with HinfI restriction enzyme and DNA sequencing analyses. Two alleles and three genotypes were identified by HinfI digestion of the GPX5 gene. In the SNP-HinfI (g.1896A>G) locus, significant associations were found between GPX5 genotypes and litter size at birth. The genotype AA demonstrated significantly (P<0.05) superior litter size at birth as compared to AG and GG genotypes at the SNP-HinfI locus in Lumsniang pig. Interpretation: The study reported probable associations of GPX5 variants with reproduction and production traits in Lumsniang pig. The genotype AA at locus SNP-HinfI improved the litter size at birth in the studied population. The GPX5 gene may be considered as a DNA marker for marker-assisted selection after validation in a large pig population.

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The Association of an SNP in the EXOC4 Gene and Reproductive Traits Suggests Its Use as a Breeding Marker in Pigs

Cited by 7 publications

References 38 publications

Accuracy of genomic prediction of maternal traits in pigs using Bayesian variable selection methods

Accuracy of genomic prediction of maternal traits in pigs using Bayesian variable selection methods

Integrated analysis strategy of genome-wide functional gene mining reveals DKK2 gene underlying meat quality in Shaziling synthesized pigs

Novel polymorphisms in GPX5 gene and their association with reproductive and productive traits in Lumsniang (Hampshire x Niang Megha) pigs under subtropical hilly region of Meghalaya

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