Four genetic loci affecting swine lung lesions identified by whole-genome sequencing-based association studies

Tong, Xinkai; Huang, Tao; Zhang, Mingpeng; Chen, Jiaqi; Zhang, Zhou; Li, Jingquan; Du, Huipeng; Ling, Ziqi; Wu, Zhongzi; Yang, Bin; Xiao, Shijun; Ai, Huashui

doi:10.1007/s11427-020-1826-x

Cited by 4 publications

(3 citation statements)

References 9 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Both the anterior and posterior of lungs from each experimental pig were photographed using a digital camera. Six professionally trained panelists scored the level of lung lesions independently according to the following scoring criteria 39 : (i) A total of 13 sections were scored, including six sections from the anterior lung and seven sections from the posterior lung. The sections of anterior lung included left and right apical lobes, left and right cardiac lobes, and left and right diaphragmatic lobes.…”

Section: Methodsmentioning

confidence: 99%

Characterization of the pig lower respiratory tract antibiotic resistome

Zhou,

Li,

Huang

et al. 2023

Nat Commun

Self Cite

View full text Add to dashboard Cite

Respiratory diseases and its treatments are highly concerned in both the pig industry and human health. However, the composition and distribution of antibiotic resistance genes (ARGs) in swine lower respiratory tract microbiome remain unknown. The relationships of ARGs with mobile genetic elements (MGEs) and lung health are unclear. Here, we characterize antibiotic resistomes of the swine lower respiratory tract microbiome containing 1228 open reading frames belonging to 372 ARGs using 745 metagenomes from 675 experimental pigs. Twelve ARGs conferring resistance to tetracycline are related to an MGE Tn916 family, and multiple types of ARGs are related to a transposase gene tnpA. Most of the linkage complexes between ARGs and MGEs (the Tn916 family and tnpA) are also observed in pig gut microbiomes and human lung microbiomes, suggesting the high risk of these MGEs mediating ARG transfer to both human and pig health. Gammaproteobacteria are the major ARG carriers, within which Escherichia coli harbored >50 ARGs and >10 MGEs. Although the microbial compositions structure the compositions of ARGs, we identify 73 ARGs whose relative abundances are significantly associated with the severity of lung lesions. Our results provide the first overview of ARG profiles in the swine lower respiratory tract microbiome.

show abstract

Section: Methodsmentioning

confidence: 99%

Characterization of the pig lower respiratory tract antibiotic resistome

Zhou,

Li,

Huang

et al. 2023

Nat Commun

Self Cite

View full text Add to dashboard Cite

show abstract

“…For instance, PLAG1 and BMP2 have been identified as strong candidate genes associated with body size 16 – 18 . MUC13 and RNF216 were associated with disease resistance 4 , 19 . In domestic pigs, PLAG1 has been subjected to long-term positive selection 12 , and the favorable allele conferring larger stature has a higher frequency in domestic pigs than in wild boars 20 .…”

Section: Introductionmentioning

confidence: 99%

Accurate haplotype construction and detection of selection signatures enabled by high quality pig genome sequences

Tong,

Chen,

et al. 2023

Nat Commun

Self Cite

View full text Add to dashboard Cite

High-quality whole-genome resequencing in large-scale pig populations with pedigree structure and multiple breeds would enable accurate construction of haplotype and robust selection-signature detection. Here, we sequence 740 pigs, combine with 149 of our previously published resequencing data, retrieve 207 resequencing datasets, and form a panel of worldwide distributed wild boars, aboriginal and highly selected pigs with pedigree structures, amounting to 1096 genomes from 43 breeds. Combining with their haplotype-informative reads and pedigree structure, we accurately construct a panel of 1874 haploid genomes with 41,964,356 genetic variants. We further demonstrate its valuable applications in GWAS by identifying five novel loci for intramuscular fat content, and in genomic selection by increasing the accuracy of estimated breeding value by 36.7%. In evolutionary selection, we detect MUC13 gene under a long-term balancing selection, as well as NPR3 gene under positive selection for pig stature. Our study provides abundant genomic variations for robust selection-signature detection and accurate haplotypes for deciphering complex traits in pigs.

show abstract

“…Thus far, 35,384 QTLs have been identified in pigs according to pigQTLdb, of which 3315 QTLs are associated with reproduction ( , 25 April 2022). In pigs, GWAS has identified numerous SNPs significantly associated with growth traits [ 4 , 5 ], meat quality [ 6 , 7 ], feed efficiency [ 8 , 9 ], semen traits [ 10 , 11 ], coat color [ 12 , 13 ], genetic defects [ 14 , 15 ], disease susceptibility [ 16 , 17 ], and microbial phenotypes [ 18 ]. However, most of them were genotyped based on SNP microarrays, and the density of markers is a key factor affecting GWAS efficiency [ 19 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Study on Reproductive Traits Using Imputation-Based Whole-Genome Sequence Data in Yorkshire Pigs

Sun

Xiao

Jiang

et al. 2023

Genes

View full text Add to dashboard Cite

Reproductive traits have a key impact on production efficiency in the pig industry. It is necessary to identify the genetic structure of potential genes that influence reproductive traits. In this study, a genome-wide association study (GWAS) based on chip and imputed data of five reproductive traits, namely, total number born (TNB), number born alive (NBA), litter birth weight (LBW), gestation length (GL), and number of weaned (NW), was performed in Yorkshire pigs. In total, 272 of 2844 pigs with reproductive records were genotyped using KPS Porcine Breeding SNP Chips, and then chip data were imputed to sequencing data using two online software programs: the Pig Haplotype Reference Panel (PHARP v2) and Swine Imputation Server (SWIM 1.0). After quality control, we performed GWAS based on chip data and the two different imputation databases by using fixed and random model circulating probability unification (FarmCPU) models. We discovered 71 genome-wide significant SNPs and 25 potential candidate genes (e.g., SMAD4, RPS6KA2, CAMK2A, NDST1, and ADCY5). Functional enrichment analysis revealed that these genes are mainly enriched in the calcium signaling pathway, ovarian steroidogenesis, and GnRH signaling pathways. In conclusion, our results help to clarify the genetic basis of porcine reproductive traits and provide molecular markers for genomic selection in pig breeding.

show abstract

Four genetic loci affecting swine lung lesions identified by whole-genome sequencing-based association studies

Cited by 4 publications

References 9 publications

Characterization of the pig lower respiratory tract antibiotic resistome

Characterization of the pig lower respiratory tract antibiotic resistome

Accurate haplotype construction and detection of selection signatures enabled by high quality pig genome sequences

Genome-Wide Association Study on Reproductive Traits Using Imputation-Based Whole-Genome Sequence Data in Yorkshire Pigs

Contact Info

Product

Resources

About