Genome-wide association analysis reveals genetic loci and candidate genes for feeding behavior and eating efficiency in Duroc boars

Ding, Rongrong; Quan, Jianping; Yang, Ming; Wang, Xingwang; Zheng, Enqin; Yang, Huaqiang; Fu, Disheng; Yang, Yang; Yang, Linhua; Li, Zicong; Liu, Dewu; Cai, Guangyan; Wu, Zhenfang; Yang, Jie

doi:10.1371/journal.pone.0183244

Cited by 31 publications

(29 citation statements)

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“…Interestingly, the strongest differentiation signal in this region is obtained close to TCF7 , which, as LEF1 , is a main downstream effector of a signalling pathway (i.e., Wnt/β catenin) and both genes have recently been found to be involved in a regulatory feedback loop controlling taste cell renewal in the circumvallate papilla epithelium and loss of gustatory nerve fibres in mice (Gaillard et al, ). Similarly, a SNP proximal to LEF1 is also associated with feeding behaviour and eating efficiency in Duroc pigs (Ding et al, ).…”

Section: Discussionmentioning

confidence: 99%

A genomic map of climate adaptation in Mediterranean cattle breeds

et al. 2019

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Domestic species such as cattle (Bos taurus taurus and B. t. indicus) represent attractive biological models to characterize the genetic basis of short‐term evolutionary response to climate pressure induced by their post‐domestication history. Here, using newly generated dense SNP genotyping data, we assessed the structuring of genetic diversity of 21 autochtonous cattle breeds from the whole Mediterranean basin and performed genome‐wide association analyses with covariables discriminating the different Mediterranean climate subtypes. This provided insights into both the demographic and adaptive histories of Mediterranean cattle. In particular, a detailed functional annotation of genes surrounding variants associated with climate variations highlighted several biological functions involved in Mediterranean climate adaptation such as thermotolerance, UV protection, pathogen resistance or metabolism with strong candidate genes identified (e.g., NDUFB3, FBN1, METTL3, LEF1, ANTXR2 and TCF7). Accordingly, our results suggest that main selective pressures affecting cattle in Mediterranean area may have been related to variation in heat and UV exposure, in food resources availability and in exposure to pathogens, such as anthrax bacteria (Bacillus anthracis). Furthermore, the observed contribution of the three main bovine ancestries (indicine, European and African taurine) in these different populations suggested that adaptation to local climate conditions may have either relied on standing genomic variation of taurine origin, or adaptive introgression from indicine origin, depending on the local breed origins. Taken together, our results highlight the genetic uniqueness of local Mediterranean cattle breeds and strongly support conservation of these populations.

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Section: Discussionmentioning

confidence: 99%

A genomic map of climate adaptation in Mediterranean cattle breeds

et al. 2019

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“…During the period of 2013–2016, phenotypic data were collected for Duroc pigs ( n = 1,008) from the Guangdong Wen’s Foodstuffs Group, Co., Ltd. (Guangdong, China) using the Osborne FIRE Pig Performance Testing System (Osborne, KS, United States) as previously described ( Ding et al, 2017 ). Briefly, pigs were subjected to uniform feeding conditions for measurement of traits during the fattening period (approximately 11 weeks) from 30 to 100 kg live weight.…”

Section: Methodsmentioning

confidence: 99%

“…Duroc pig population is widely used as the terminal male parent of the DLY (Duroc × Landrace × Yorkshire) commercial pigs thanks to its excellent performance on growth traits. In previous studies, several single nucleotide polymorphisms (SNPs) that were significantly associated with FCR were detected on SSC 12 in a Canadian Duroc population by genome-wide association study (GWAS) ( Ding et al, 2017 ). However, due to the limited sample size (<400), we detected only a few significant SNPs for feeding behavior and feed efficiency traits.…”

Section: Introductionmentioning

confidence: 99%

Genetic Architecture of Feeding Behavior and Feed Efficiency in a Duroc Pig Population

et al. 2018

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Increasing feed efficiency is a major goal of breeders as it can reduce production cost and energy consumption. However, the genetic architecture of feeding behavior and feed efficiency traits remains elusive. To investigate the genetic architecture of feed efficiency in pigs, three feeding behavior traits (daily feed intake, number of daily visits to feeder, and duration of each visit) and two feed efficiency traits (feed conversion ratio and residual feed intake) were considered. We performed genome-wide association studies (GWASs) of the five traits using a population of 1,008 Duroc pigs genotyped with an Illumina Porcine SNP50K BeadChip. A total of 9 genome-wide (P < 1.54E-06) and 35 suggestive (P < 3.08E-05) single nucleotide polymorphisms (SNPs) were detected. Two pleiotropic quantitative trait loci (QTLs) on SSC 1 and SSC 7 were found to affect more than one trait. Markers WU_10.2_7_18377044 and DRGA0001676 are two key SNPs for these two pleiotropic QTLs. Marker WU_10.2_7_18377044 on SSC 7 contributed 2.16 and 2.37% of the observed phenotypic variance for DFI and RFI, respectively. The other SNP DRGA0001676 on SSC 1 explained 3.22 and 5.46% of the observed phenotypic variance for FCR and RFI, respectively. Finally, functions of candidate genes and gene set enrichment analysis indicate that most of the significant pathways are associated with hormonal and digestive gland secretion during feeding. This study advances our understanding of the genetic mechanisms of feeding behavior and feed efficiency traits and provide an opportunity for increasing feeding efficiency using marker-assisted selection or genomic selection in pigs.

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“…These findings shed light on the different interactions underlying the genomic regulation in several traits. Although, a large number of GWAS studies for feed efficiency and feeding behavior traits in pigs have been reported (Ding et al, 2017;Reyer et al, 2017b;Ding et al, 2018;Zhang et al, 2018), the epistatic effects over these traits are still not explored. By using 88 microsatellite markers in pigs, (Duthie et al, 2011b) epistatic QTLs (Quantitative Trait Loci) for growth, feed intake and chemical body composition at different stages of growth have been reported.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Epistatic Interaction Networks Affecting Feed Efficiency in Duroc and Landrace Pigs

2020

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Interactions among genomic loci have often been overlooked in genome-wide association studies, revealing the combinatorial effects of variants on phenotype or disease manifestation. Unexplained genetic variance, interactions among causal genes of small effects, and biological pathways could be identified using a network biology approach. The main objective of this study was to determine the genome-wide epistatic variants affecting feed efficiency traits [feed conversion ratio (FCR) and residual feed intake (RFI)] based on weighted interaction SNP hub (WISH-R) method. Herein, we detected highly interconnected epistatic SNP modules, pathways, and potential biomarkers for the FCR and RFI in Duroc and Landrace purebreds considering the whole population, and separately for low and high feed efficient groups. Highly interacting SNP modules in Duroc (1,247 SNPs) and Landrace (1,215 SNPs) across the population and for low feed efficient (Duroc-80 SNPs, Landrace-146 SNPs) and high feed efficient group (Duroc-198 SNPs, Landrace-232 SNPs) for FCR and RFI were identified. Gene and pathway analyses identified ABL1, MAP3K4, MAP3K5, SEMA6A, KITLG, and KAT2B from chromosomes 1, 2, 5, and 13 underlying ErbB, Ras, Rap1, thyroid hormone, axon guidance pathways in Duroc. GABBR2, GNA12, and PRKCG genes from chromosomes 1, 3, and 6 pointed towards thyroid hormone, cGMP-PKG and cAMP pathways in Landrace. From Duroc low feed efficient group, the TPK1 gene was found involved with thiamine metabolism, whereas PARD6G, DLG2, CRB1 were involved with the hippo signaling pathway in high feed efficient group. PLOD1 and SETD7 genes were involved with lysine degradation in low feed efficient group in Landrace, while high feed efficient group pointed to genes underpinning valine, leucine, isoleucine degradation, and fatty acid elongation. Some SNPs and genes identified are known for their association with feed efficiency, others are novel and potentially provide new avenues for further research. Further validation of epistatic SNPs and genes identified here in a larger cohort would help to establish a framework for modelling epistatic variance in future methods of genomic prediction, increasing the accuracy of estimated genetic merit for FE and helping the pig breeding industry.

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Genome-wide association analysis reveals genetic loci and candidate genes for feeding behavior and eating efficiency in Duroc boars

Cited by 31 publications

References 50 publications

A genomic map of climate adaptation in Mediterranean cattle breeds

A genomic map of climate adaptation in Mediterranean cattle breeds

Genetic Architecture of Feeding Behavior and Feed Efficiency in a Duroc Pig Population

Genome-Wide Epistatic Interaction Networks Affecting Feed Efficiency in Duroc and Landrace Pigs

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