| Pig feed efficiency is an important economic trait, so it has been one of the key content of pig breeding work. The feed efficiency of pigs was commonly evaluated by the used feed conversion ratio(FCR), i.e., the ratio of feed to weight or the ratio of feed to weight ratio. The FCR is a ratio trait influenced by feed intake and weight,whose heritability is unstable, so it is not suitable as direct selection traits in the breeding process, but can be a target traits to reflect different groups of feed efficiency. In the past ten years,many large enterprises in Europe and America start using a new selection traits- residual feed intake(residual feed intake, RFI) as a selective trait to improve the feed efficiency of livestock, and RFI has the largest weight in the whole breeding program. Residual feed intake is defined as the difference between actual feed intake and estimated feed intake. The pig who has high RFI value has low feed efficiency;the pig who has low RFI value has high feed efficiency. RFI can reflect the difference of maintenance requirement of different pigs, which is the main reason for the difference in feed efficiency. And RFI has low genetic correlation with daily gain(ADG) and back fat thickness(BF), so we can select individuals with high feed efficiency by selecting RFI. This study start from 2013 to now, make high and low differentiation selection in Junmu No. 1 white pig breeding core group depending on RFI, establish a feed efficiency differentiation system, and select individuals with extreme differences in feed efficiency to carry out the whole genome association analysis. The purpose of this study is to find the SNP combination group closely related to the feed efficiency, lay the foundation for the early selection of the pig breeding; meanwhile we can deepen our understanding of the genetic basis of the feed efficiency by the analysis of the main metabolic pathways associated with feed efficiency.This study selected three generations continuously in junmu No. 1 white core group, and totally measured 574 backup pigs(40-110Kg), among which there are 222 boars. We measured RFI, ADFI, ADG, FCR and BF(110Kg), and partly calculated breeding value of RFI, ADG and BF. We divide the population into two groups with the RFI as the main characters, the ADG and BF as constraints depending on the comprehensive breeding value : I=-0.7EBVRFI+0.2 EBVADG-0.1EBVBF,and we continued for 3 generations(G0, G1 and G2) of the two-way selection, obtained two groups of high and low significantly differentiation feed efficiency. From the 3 generation we choose 101 individuals with extreme difference in feed efficiency, for genotype of Illumina Porcine SNP60 K genome SNP microarray. RFI, ADFI, ADG, BF and FCR were analyzed by PLINK software after genotyping. Then the pathway analysis of the genes in the SNP range of the significant 1M loci was carried out. Experimental results:1. Completed 3 generations of differentiation and selection, the high and low feed efficiency differentiation group of RFI respectively were 0.051±0.180 kg/d and 0.224kg±0.059 kg/d, heritability h2=0.15; ADG respectively were 0.855±0.159 kg/d and 0.895±0.157 kg/d, heritability h2=0.22; BF respectively were 18.82±3.456 mm and 20.6±3.071 mm, heritability h2=0.28; ADFI respectively were 2.645±0.239 kg/d and 2.655±0.313 kg/d; FCR respectively were 3.14±0.66 and 3.03±0.653. RFI, ADG, BF, ADFI, FCR in H-RFI group have higher standard deviation of 0.55-0.32,-1.262, 2.585, 0.118 than these traits in L-RFI group.2. We conducted GWAS for 101 individuals with comprehensive breeding value of extreme differences, and acquire final 49375 genotype data per individual after screening. And then,through the association analysis of RFI, ADFI, ADG, BF and FCR, we found that: RFI was significantly associated(p<0.00001) with the 22 sites focused on 2, 5, 13, 15 chromosome; ADFI was significantly related(p<0.00005) to the 18 sites mainly concentrated in 1,2,7 chromosome; ADG was significantly related(p<0.00074) to the 32 sites mainly concentrated in the 7, 8, 10, 11 chromosome; BF was significantly associated(p<0.0000001) with 23 sites concentrated in 2, 13, 18 chromosomes; and FCR was significantly related(p<0.0000001) to the 19 site focused on 1, 4, 11, 13 chromosomes.3. By comparison with the NCBI Sus scrofa, animal genome database, Ensembl, GEO, KEGG and so on bioinformatics analysis, we located the SNPs and select the genes in the upstream and downstream 1M as the candidate genes for the traits. Then according to the DAVID, GO and KEGG pathway analysis database, the main role of candidate genes or mainly related pathway were found: the candidate genes related to RFI were mainly involved in the ligand receptor interaction of neural activity; the candidate genes related to ADFI were mainly involved in pathway of vascular smooth muscle contraction; the candidate genes related to ADG were mainly involved in mitochondrial biogenesis; the candidate genes related to BF were involved in Toll like receptor signal pathway; the candidate genes related to FCR were mainly involved in SKI family gene transcriptional regulation pathway.Conclusion: The residual feed intake is an effective selection of feed efficiency traits and we selected differentiated product line with a significant difference in feed efficiency. We found 114 SNPs related to feed efficiency, which can be used in combination of low density chips and make preliminary judgment that the ligand receptor interaction of neural activity pathway、vascular smooth muscle contraction pathway、mitochondrial biogenesis pathway、Toll like receptor signal pathway and SKI family gene transcriptional regulation pathway were related to feed efficiency in pigs. |
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