1
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Xing L, Lu X, Zhang W, Wang Q, Zhang W. Genetic Structure and Genome-Wide Association Analysis of Growth and Reproductive Traits in Fengjing Pigs. Animals (Basel) 2024; 14:2449. [PMID: 39272234 PMCID: PMC11394163 DOI: 10.3390/ani14172449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 08/15/2024] [Accepted: 08/20/2024] [Indexed: 09/15/2024] Open
Abstract
The Fengjing pig is one of the local pig breed resources in China and has many excellent germplasm characteristics. However, research on its genome is lacking. To explore the degree of genetic diversity of the Fengjing pig and to deeply explore its excellent traits, this study took Fengjing pigs as the research object and used the Beadchip Array Infinium iSelect-96|XT KPS_PorcineBreedingChipV2 for genotyping. We analyzed the genetic diversity, relatedness, inbreeding coefficient, and population structure within the Fengjing pig population. Our findings revealed that the proportion of polymorphic markers (PN) was 0.469, and the effective population size was 6.8. The observed and expected heterozygosity were 0.301 and 0.287, respectively. The G-matrix results indicated moderate relatedness within the population, with certain individuals exhibiting closer genetic relationships. The NJ evolutionary tree classified Fengjing boars into five family lines. The average inbreeding coefficient based on ROH was 0.318, indicating a high level of inbreeding. GWAS identified twenty SNPs significantly associated with growth traits (WW, 2W, and 4W) and reproductive traits (TNB and AWB). Notably, WNT8B, RAD21, and HAO1 emerged as candidate genes influencing 2W, 4W, and TNB, respectively. Genes such as WNT8B were verified by querying the PigBiobank database. In conclusion, this study provides a foundational reference for the conservation and utilization of Fengjing pig germplasm resources and offers insights for future molecular breeding efforts in Fengjing pigs.
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Affiliation(s)
- Lei Xing
- Shanghai Animal Disease Control Center, Shanghai 201103, China
| | - Xuelin Lu
- Shanghai Animal Disease Control Center, Shanghai 201103, China
| | - Wengang Zhang
- Shanghai Animal Disease Control Center, Shanghai 201103, China
| | - Qishan Wang
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou 310030, China
| | - Weijian Zhang
- Shanghai Animal Disease Control Center, Shanghai 201103, China
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2
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Xiao Z, Li Y, Yang L, Cui M, Wang Z, Sun W, Wang J, Chen S, Lai S, Jia X. Genome-Wide Association Studies of Growth Trait Heterosis in Crossbred Meat Rabbits. Animals (Basel) 2024; 14:2096. [PMID: 39061558 PMCID: PMC11273820 DOI: 10.3390/ani14142096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/07/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
The application of heterosis can not only effectively improve the disease resistance and meat quality of livestock, but also significantly enhance the reproduction and growth of livestock and poultry. We conducted genome-wide association studies using data from F2 crossbred meat rabbits to screen out candidate genes with significant dominant effects associated with economic trait variation. High-throughput sequencing technology was used to obtain SNPs covering the whole genome to evaluate the homozygosity of the population genome, and analyze the number, length, frequency, and distribution of ROHs in the population. Candidate genes related to economic traits of meat rabbits were searched based on high-frequency ROH regions. After quality control filtering of genotype data, 380 F2 crossbred rabbits were identified with 78,579 SNPs and 42,018 ROHs on the autosomes. The fitting of the Logistic growth curve model showed that 49-day-old rabbits were a growth inflection point. Then, through genome-wide association studies, 10 SNP loci and seven growth trait candidate genes were found to be significantly related to body weight in meat rabbits at 84 days of age. In addition, we revealed the functional roles and locations of 20 candidate genes in the high-frequency ROH region associated with economic traits in meat rabbits. This study identified potential genes associated with growth and development in the high-frequency ROH region of meat rabbits. In this study, the identified candidate genes can be used as molecular markers for assisted selection in meat rabbits. At the same time, the inbreeding situation based on ROH assessment can provide reference for breeding and breeding preservation of meat rabbits.
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Affiliation(s)
- Zhanjun Xiao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (Z.X.); (M.C.); (Z.W.); (W.S.); (S.C.); (S.L.)
| | - Yuchao Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 610000, China; (Y.L.); (L.Y.); (J.W.)
| | - Li Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 610000, China; (Y.L.); (L.Y.); (J.W.)
| | - Mingyan Cui
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (Z.X.); (M.C.); (Z.W.); (W.S.); (S.C.); (S.L.)
| | - Zicheng Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (Z.X.); (M.C.); (Z.W.); (W.S.); (S.C.); (S.L.)
| | - Wenqiang Sun
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (Z.X.); (M.C.); (Z.W.); (W.S.); (S.C.); (S.L.)
| | - Jie Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 610000, China; (Y.L.); (L.Y.); (J.W.)
| | - Shiyi Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (Z.X.); (M.C.); (Z.W.); (W.S.); (S.C.); (S.L.)
| | - Songjia Lai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (Z.X.); (M.C.); (Z.W.); (W.S.); (S.C.); (S.L.)
| | - Xianbo Jia
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (Z.X.); (M.C.); (Z.W.); (W.S.); (S.C.); (S.L.)
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3
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Farhangi S, Gòdia M, Derks MFL, Harlizius B, Dibbits B, González-Prendes R, Crooijmans RPMA, Madsen O, Groenen MAM. Expression genome-wide association study identifies key regulatory variants enriched with metabolic and immune functions in four porcine tissues. BMC Genomics 2024; 25:684. [PMID: 38992576 PMCID: PMC11238464 DOI: 10.1186/s12864-024-10583-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND Integration of high throughput DNA genotyping and RNA-sequencing data enables the discovery of genomic regions that regulate gene expression, known as expression quantitative trait loci (eQTL). In pigs, efforts to date have been mainly focused on purebred lines for traits with commercial relevance as such growth and meat quality. However, little is known on genetic variants and mechanisms associated with the robustness of an animal, thus its overall health status. Here, the liver, lung, spleen, and muscle transcriptomes of 100 three-way crossbred female finishers were studied, with the aim of identifying novel eQTL regulatory regions and transcription factors (TFs) associated with regulation of porcine metabolism and health-related traits. RESULTS An expression genome-wide association study with 535,896 genotypes and the expression of 12,680 genes in liver, 13,310 genes in lung, 12,650 genes in spleen, and 12,595 genes in muscle resulted in 4,293, 10,630, 4,533, and 6,871 eQTL regions for each of these tissues, respectively. Although only a small fraction of the eQTLs were annotated as cis-eQTLs, these presented a higher number of polymorphisms per region and significantly stronger associations with their target gene compared to trans-eQTLs. Between 20 and 115 eQTL hotspots were identified across the four tissues. Interestingly, these were all enriched for immune-related biological processes. In spleen, two TFs were identified: ERF and ZNF45, with key roles in regulation of gene expression. CONCLUSIONS This study provides a comprehensive analysis with more than 26,000 eQTL regions identified that are now publicly available. The genomic regions and their variants were mostly associated with tissue-specific regulatory roles. However, some shared regions provide new insights into the complex regulation of genes and their interactions that are involved with important traits related to metabolism and immunity.
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Affiliation(s)
- Samin Farhangi
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Marta Gòdia
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands.
| | - Martijn F L Derks
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
- Topigs Norsvin Research Center, 's-Hertogenbosch, The Netherlands
| | | | - Bert Dibbits
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Rayner González-Prendes
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
- Ausnutria BV, Zwolle, The Netherlands
| | | | - Ole Madsen
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
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4
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Bedhiaf-Romdhani S, Baazaoui I, Dodds KG, Brauning R, Anderson RM, Van Stijn TC, McCulloch AF, McEwan JC. Efficiency of genotyping by sequencing in inferring genomic relatedness and molecular insights into fat tail selection in Tunisian sheep. Anim Genet 2023; 54:389-397. [PMID: 36727208 DOI: 10.1111/age.13296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 12/14/2022] [Accepted: 01/12/2023] [Indexed: 02/03/2023]
Abstract
In developing countries, the use of simple and cost-efficient molecular technology is crucial for genetic characterization of local animal resources and better development of conservation strategies. The genotyping by sequencing (GBS) technique, also called restriction enzyme- reduced representational sequencing, is an efficient, cost-effective method for simultaneous discovery and genotyping of many markers. In the present study, we applied a two-enzyme GBS protocol (PstI/MspI) to discover and genotype SNP markers among 197 Tunisian sheep samples. A total of 100 333 bi-allelic SNPs were discovered and genotyped with an SNP call rate of 0.69 and mean sample depth 3.33. The genomic relatedness between 183 samples grouped the samples perfectly to their populations and pointed out a high genetic relatedness of inbred subpopulation reflecting the current adopted reproductive strategies. The genome-wide association study contrasting fat vs. thin-tailed breeds detected 41 significant variants including a peak positioned on OAR20. We identified FOXC1, GMDS, VEGFA, OXCT1, VRTN and BMP2 as the most promising for sheep tail-type trait. The GBS data have been useful to assess the population structure and improve our understanding of the genomic architecture of distinctive characteristics shaped by selection pressure in local sheep breeds. This study successfully investigates a cost-efficient method to discover genotypes, assign populations and understand insights into sheep adaptation to arid area. GBS could be of potential utility in livestock species in developing/emerging countries.
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Affiliation(s)
- Sonia Bedhiaf-Romdhani
- Laboratoire des Productions Animales et Fourragères, INRA-Tunisie, Université de Carthage, Tunis, Tunisia
| | - Imen Baazaoui
- Faculty of Sciences of Bizerte, University of Carthage, Bizerte, Tunisia
| | - Ken G Dodds
- AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Rudiger Brauning
- AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Rayna M Anderson
- AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand
| | | | - Alan F McCulloch
- AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - John Colin McEwan
- AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand
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5
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Wang X, Wang L, Shi L, Zhang P, Li Y, Li M, Tian J, Wang L, Zhao F. GWAS of Reproductive Traits in Large White Pigs on Chip and Imputed Whole-Genome Sequencing Data. Int J Mol Sci 2022; 23:13338. [PMID: 36362120 PMCID: PMC9656588 DOI: 10.3390/ijms232113338] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 12/09/2023] Open
Abstract
Total number born (TNB), number of stillborn (NSB), and gestation length (GL) are economically important traits in pig production, and disentangling the molecular mechanisms associated with traits can provide valuable insights into their genetic structure. Genotype imputation can be used as a practical tool to improve the marker density of single-nucleotide polymorphism (SNP) chips based on sequence data, thereby dramatically improving the power of genome-wide association studies (GWAS). In this study, we applied Beagle software to impute the 50 K chip data to the whole-genome sequencing (WGS) data with average imputation accuracy (R2) of 0.876. The target pigs, 2655 Large White pigs introduced from Canadian and French lines, were genotyped by a GeneSeek Porcine 50K chip. The 30 Large White reference pigs were the key ancestral individuals sequenced by whole-genome resequencing. To avoid population stratification, we identified genetic variants associated with reproductive traits by performing within-population GWAS and cross-population meta-analyses with data before and after imputation. Finally, several genes were detected and regarded as potential candidate genes for each of the traits: for the TNB trait: NOTCH2, KLF3, PLXDC2, NDUFV1, TLR10, CDC14A, EPC2, ORC4, ACVR2A, and GSC; for the NSB trait: NUB1, TGFBR3, ZDHHC14, FGF14, BAIAP2L1, EVI5, TAF1B, and BCAR3; for the GL trait: PPP2R2B, AMBP, MALRD1, HOXA11, and BICC1. In conclusion, expanding the size of the reference population and finding an optimal imputation strategy to ensure that more loci are obtained for GWAS under high imputation accuracy will contribute to the identification of causal mutations in pig breeding.
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Affiliation(s)
- Xiaoqing Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ligang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Liangyu Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Laboratory of Genetic Breeding, Reproduction and Precision Livestock Farming, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Pengfei Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yang Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Mianyan Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jingjing Tian
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lixian Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fuping Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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6
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Chang Wu Z, Wang Y, Huang X, Wu S, Bao W. A genome-wide association study of important reproduction traits in large white pigs. Gene 2022; 838:146702. [PMID: 35772658 DOI: 10.1016/j.gene.2022.146702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/13/2022] [Accepted: 06/24/2022] [Indexed: 11/04/2022]
Abstract
Augmenting the reproductive efficiency of sows remains the predominant challenge in the swine industry. This work was aimed at scrutinizing vital genetic markers for reproductive traits in this animal. This entailed probing of the records of vital attributes of Large White pigs (n = 695) inclusive of the total number of born (TNB), number of born alive (NBA), number of weaned pigs (NWP), number of healthy births (NHS), total litter weight of piglets born alive (BALWT), weaning litter weight (WNWT), and corrected litter weight at 21 days (W21). A genome-wide association study (GWAS) for the four litter traits and three traits of litter weight in the Denmark Large White population then ensued. We discovered seven significantly related SNPs and eleven potential candidate genes (e.g., TUSC3, THRB for TNB; STT3B for NBA). The subsequent functional enrichment analysis of these genes showed that the significant gene were associated with steroid hormone receptor activity. Our findings indicated that the genes TUSC3, THRB and STT3B probably contribute to litter traits in this population. This work reveals genetic mechanisms of reproduction traits and also supports ensuing genetic improvement employing marker-assisted selection in Large White pigs.
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Affiliation(s)
- Zheng Chang Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P. R. China; College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, P. R. China.
| | - Yifu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P. R. China.
| | - Xiaoguo Huang
- Jiangsu Engineering Research Centre for Molecular Breeding of Pig, Changzhou 215000, Jiangsu Province, China.
| | - Shenglong Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P. R. China.
| | - Wenbin Bao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P. R. China.
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7
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An M, Zhou G, Li Y, Xiang T, Ma Y, Liu X, Li X, Zhao S, Zhu M. Characterization of genetic fundamentals for piglet mortality at birth in Yorkshire, Landrace, and Duroc sows. Anim Genet 2021; 53:142-145. [PMID: 34897732 DOI: 10.1111/age.13162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2021] [Indexed: 11/29/2022]
Abstract
Piglet mortality is an economically important complex trait that impacts sow prolificacy. Genetic analyses for piglet mortality at weaning have been reported in dozens of studies, but not for piglet mortality at birth. In this study, we used multi-breed data sets from Yorkshire, Landrace, and Duroc sows to characterize the genetic fundamentals of piglet mortality at birth. The heritabilities from parity I to III were estimated to be 0.0630, 0.1031, and 0.1140 respectively. By using a combined strategy, a total of 21 SNPs were detected in three parities, of which six were observed in parity I, five in parity II and 10 in parity III. Genome annotation revealed that these SNPs were harbored within or close to 19 candidate genes. The candidate genes were found to associate with the reproductive system and embryonic development in the tissue expression database, which are reasonably related to piglet mortality. These findings are expected to provide much information for understanding the genetic and genomic fundamentals of farrowing mortality.
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Affiliation(s)
- M An
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - G Zhou
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Y Li
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - T Xiang
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070, China
| | - Y Ma
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070, China
| | - X Liu
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070, China
| | - X Li
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070, China
| | - S Zhao
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070, China
| | - M Zhu
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070, China
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8
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Ding R, Qiu Y, Zhuang Z, Ruan D, Wu J, Zhou S, Ye J, Cao L, Hong L, Xu Z, Zheng E, Li Z, Wu Z, Yang J. Genome-wide association studies reveals polygenic genetic architecture of litter traits in Duroc pigs. Theriogenology 2021; 173:269-278. [PMID: 34403972 DOI: 10.1016/j.theriogenology.2021.08.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/08/2021] [Accepted: 08/09/2021] [Indexed: 01/02/2023]
Abstract
With continuous improvement of sow litter size, breeders are gradually paying more attention to the quality of litter traits that directly impact the production efficiency of pig companies, such as the rate of piglets born alive (RBA) and the rate of healthy births (RHB). The objectives of this study are to dissect the genetic basis of litter traits in pig and to identify valuable genes and genetic markers, especially pleiotropic, for pig breeding. Herein, 1140 Duroc pigs and 2046 reproduction records, 5 litter traits, including the number of healthy births (NHB), number of deformed fetuses (NDF), number of stillborn (NSB), RBA, and RHB, were used in this study. Subsequently, a genome-wide association study (GWAS) was performed for the five litter traits in the first two parities from two Duroc populations. A total of 76 significantly related SNPs and 10 potential candidate genes (CAV1, DAB2, FGF12, FHOD3, DYNC2H1, GRHL1, TCTN3, PYROXD2, MMP8, MMP13, and PGR) were detected, including 13 pleiotropic SNPs that affected more than one litter trait. Finally, the functional enrichment analysis of functional genes that were closest to these significant SNPs indicated that most of the significant pathways were associated with hormone secretion and embryo and organ development. This study advances our understanding of the genetic mechanisms of litter traits, especially the survival rate of piglets born, and provides an opportunity to increase the quality of litter using marker-assisted selection or genomic selection in pigs.
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Affiliation(s)
- Rongrong Ding
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China; Guangdong Wens Breeding Swine Technology Co., Ltd., Guangdong, 527400, PR China
| | - Yibin Qiu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China
| | - Zhanwei Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China
| | - Donglin Ruan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China
| | - Jie Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China
| | - Shenping Zhou
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China
| | - Jian Ye
- Guangdong Wens Breeding Swine Technology Co., Ltd., Guangdong, 527400, PR China
| | - Lu Cao
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China
| | - Linjun Hong
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China
| | - Zheng Xu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, PR China
| | - Zicong Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, PR China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China; Guangdong Wens Breeding Swine Technology Co., Ltd., Guangdong, 527400, PR China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, PR China.
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, PR China.
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9
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Sanglard LP, Mote BE, Willson P, Harding JCS, Plastow GS, Dekkers JCM, Serão NVL. Genomic Analysis of IgG Antibody Response to Common Pathogens in Commercial Sows in Health-Challenged Herds. Front Genet 2020; 11:593804. [PMID: 33193739 PMCID: PMC7646516 DOI: 10.3389/fgene.2020.593804] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/25/2020] [Indexed: 11/13/2022] Open
Abstract
Losses due to infectious diseases are one of the main factors affecting productivity in the swine industry, motivating the investigation of disease resilience-related traits for genetic selection. However, these traits are not expected to be expressed in the nucleus herds, where selection is performed. One alternative is to use information from the commercial level to identify and select nucleus animals genetically superior for coping with pathogen challenges. In this study, we analyzed the genetic basis of antibody (Ab) response to common infectious pathogens in health-challenged commercial swine herds as potential indicator traits for disease resilience, including Ab response to influenza A virus of swine (IAV), Mycoplasma hyopneumoniae (MH), porcine circovirus (PCV2), and Actinobacillus pleuropneumoniae (APP; different serotypes). Ab response was measured in blood at entry into gilt rearing, post-acclimation (∼40 days after entering the commercial herd), and parities 1 and 2. Heritability estimates for Ab response to IAV, MH, and PCV2 ranged from 0 to 0.76. Ab response to APP ranged from 0 to 0.40. The genetic correlation (r G ) of Ab response to IAV with MH, PCV2, PRRSV, and APPmean (average Ab responses for all serotypes of APP) were positive (>0.29) at entry. APPmean was negatively correlated with PCV2 and MH at entry and parity 2 but positively correlated with MH at post-acclimation and parity 1. Genomic regions associated with Ab response to different APP serotypes were identified on 13 chromosomes. The region on chromosome 14 (2 Mb) was associated with several serotypes of APP, explaining up to 4.3% of the genetic variance of Ab to APP7 at entry. In general, genomic prediction accuracies for Ab response were low to moderate, except average Ab response to all infectious pathogens evaluated. These results suggest that genetic selection of Ab response in commercial sows is possible, but with variable success depending on the trait and the time-point of collection. Future work is needed to determine genetic correlations of Ab response with disease resilience, reproductive performance, and other production traits.
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Affiliation(s)
- Leticia P Sanglard
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | | | - Benny E Mote
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Philip Willson
- Canadian Centre for Health and Safety in Agriculture, University of Saskatchewan, Saskatoon, SK, Canada
| | - John C S Harding
- Department of Large Animal Clinical Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Graham S Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Jack C M Dekkers
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Nick V L Serão
- Department of Animal Science, Iowa State University, Ames, IA, United States
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Chen Z, Ye S, Teng J, Diao S, Yuan X, Chen Z, Zhang H, Li J, Zhang Z. Genome-wide association studies for the number of animals born alive and dead in duroc pigs. Theriogenology 2019; 139:36-42. [PMID: 31362194 DOI: 10.1016/j.theriogenology.2019.07.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/12/2019] [Accepted: 07/16/2019] [Indexed: 11/15/2022]
Abstract
Litter size is one of the most important economic traits for pig production as it is directly related to the production efficiency. As an important litter size trait in pigs, the number of piglets born alive at birth (NBA) receives widespread interests in the pig industry. However, traits of piglets born dead, including the number of stillborn piglets (NS) and the piglets mummified at birth (NM) should be noted to explain the loss of reproduction. Herein, in the present study, a total of 803 producing sows were sampled and 2807 farrowing records for NBA, NM, and NS traits were collected in a Duroc swine population. Subsequently, a genome-wide association study (GWAS) was performed for NBA, NS and NM in parity groups 1 to 5. In total, 10 putative regions were found associated with these traits. After stepwise conditional analyses around the putative regions, eight independent signals were ultimately identified for NBA, NS, and NM, and there were seven promising candidate genes related to these traits, including ARID1A, RXRG, NFATC4, ABTB2, GRAMD1B, NDRG1, and APC. Our findings contribute to the understanding of the significant genetic causes of piglets born alive and dead, and could have a positive effect on pig production efficiency and economic profits.
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Affiliation(s)
- Zitao Chen
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Shaopan Ye
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Jinyan Teng
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Shuqi Diao
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaolong Yuan
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Zanmou Chen
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Hao Zhang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Jiaqi Li
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Zhe Zhang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
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