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

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

doi:10.1371/journal.pone.0183244

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

PLoS One. 2017 Aug 16;12(8):e0183244. doi: 10.1371/journal.pone.0183244. eCollection 2017.

Authors

Rongrong Ding¹, Jianping Quan¹, Ming Yang², Xingwang Wang¹, Enqin Zheng¹, Huaqiang Yang¹, Disheng Fu¹, Yang Yang¹, Linxue Yang¹, Zicong Li¹, Dewu Liu¹, Gengyuan Cai^{1

2}, Zhenfang Wu^{1

2}, Jie Yang¹

Affiliations

¹ College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China.
² National Engineering Research Center for Breeding Swine Industry, Guangdong Wens Foodstuffs Group Co., Ltd, Guangdong, P.R. China.

Abstract

Efficient use of feed resources is a challenge in the pork industry because the largest variability in expenditure is attributed to the cost of fodder. Efficiency of feeding is directly related to feeding behavior. In order to identify genomic regions controlling feeding behavior and eating efficiency traits, 338 Duroc boars were used in this study. The Illumina Porcine SNP60K BeadChip was used for genotyping. Data pertaining to individual daily feed intake (DFI), total daily time spent in feeder (TPD), number of daily visits to feeder (NVD), average duration of each visit (TPV), mean feed intake per visit (FPV), mean feed intake rate (FR), and feed conversion ratio (FCR) were collected for these pigs. Despite the limited sample size, the genome-wide association study was acceptable to detect candidate regions association with feeding behavior and eating efficiency traits in pigs. We detected three genome-wide (P < 1.40E-06) and 11 suggestive (P < 2.79E-05) single nucleotide polymorphism (SNP)-trait associations. Six SNPs were located in genomic regions where quantitative trait loci (QTLs) have previously been reported for feeding behavior and eating efficiency traits in pigs. Five candidate genes (SERPINA3, MYC, LEF1, PITX2, and MAP3K14) with biochemical and physiological roles that were relevant to feeding behavior and eating efficiency were discovered proximal to significant or suggestive markers. Gene ontology analysis indicated that most of the candidate genes were involved in the development of the hypothalamus (GO:0021854, P < 0.0398). Our results provide new insights into the genetic basis of feeding behavior and eating efficiency in pigs. Furthermore, some significant SNPs identified in this study could be incorporated into artificial selection programs for Duroc-related pigs to select for increased feeding efficiency.

MeSH terms

Animals
Eating / physiology*
Feeding Behavior / physiology
Genome-Wide Association Study / methods*
Genotype
Hypothalamus / metabolism
Lymphoid Enhancer-Binding Factor 1 / genetics
Lymphoid Enhancer-Binding Factor 1 / metabolism
Male
Polymorphism, Single Nucleotide / genetics
Protein Serine-Threonine Kinases / genetics
Protein Serine-Threonine Kinases / metabolism
Quantitative Trait Loci / genetics
Serpins / genetics
Serpins / metabolism
Swine
Transcription Factors / genetics
Transcription Factors / metabolism

Substances

Lymphoid Enhancer-Binding Factor 1
Serpins
Transcription Factors
Protein Serine-Threonine Kinases

Grants and funding

The authors appreciate the financial support from the Natural Science Foundation of China (31601912), the Natural Science Foundation of Guangdong Province (2016A030310447), and the Applied Science and Technology Research and Development of Special Funds of Guangdong Province (2015B020231010). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.