Investigation Of Feed Intake Behavior,Feed Conversion Ratio And Reproduction Failure In Swine:Precise Determination Of Trait And Genetic Dissection

First Part:A large proportion of gilts and sows are culled from the reproduction population because of anestrus and pubertal reproductive failure.Selecting early onset of puberty gilts has a favorable effect on sows’ reproductivity.However,age at puberty is hard to be routinely measured in commercial herds.With molecular genetic predictors,identifying individuals that have a propensity for early onset of puberty can be simplified.We previously performed genome scanning and genome-wide association study for puberty in an F2 resource population using 183 microsatellites and 62125 SNPs,respectively.The detection power and resolution of identified quantitative trait loci were very low.Herein,we re-sequenced 19 founders of the F2 resource population in high coverage and whole genome sequences of F2 individuals were imputed to perform association study for reproductive traits.A total of 2339 SNPs associated with pubertal reproductive failure were identified in the region of 30.94 to 40.74 Mb on SSC7,with the top one positioned at 33.36 Mb.The proportion of phenotypic variances explained by the top SNP was 16%.We improved the significance of P-value about 10e5～10e7 magnitude using whole genome sequence than using low/middle density markers in previous studies,and we narrowed down the QTL confidence interval to 5.25Mb.Combining the annotation of gene function,RAB23 and BAK1 were perceived as the most compelling candidate genes.The identified loci may be useful in culling sows failing to show estrus by marker-assisted selection to increase reproductive efficiency of swine herds.Second Part:In this study,we used electronic feeding station observations in pigs to investigate their growth performance and feed behavior.These pigs were raised in Xinda Livestock Limited Company in Henan,China and following the Chinese directive for the protection of farm animals.Electronic feeding station is often used in pigs breeding and identifying loci associated with feed consumption,meanwhile it can also provide much valuable information of pig behavior that could be directly used to improve production efficiency.This study involves three different pig populations’ feeding intake data of 383 Yorkshire,243 Landrace,and 197 Duroc to investigate their growth performance and feed behavior.Similar patterns of growth performance(slow-fast-slow)was observed for the three breeds,while the Duroc have a slightly faster average growth rate during the whole testing periods.Study on the number of visits over 24 hours detected two peaks of feeding intake activities at 8:00-09:00 am and 14:00-15:00 pm.During these two feeding peak times,lower feed intake and less occupation time were observed implicating fiercer competition at these time periods.The effective intake time for Duroc,Landrace and Yorkshire population was 19 mins,16mins,19mins respectively,suggesting that the ultimate feed intake time for each individual can be set up to 20 mins for each visit.Studies on ADFI(average daily feed intake)showed significant difference(P-value=0.000009)between seasons and consistent pattern on three breeds.The present study provided a detailed survey on the pig feed intake behaviors cross different populations and feeding seasons.Third Part:Feed conversion ratio is one of the most important measurements of the ability of converting feed into live body weight.In pig production,the feed cost takes account for about 60%～70%of the production cost and feed conversion ratio is the most important factors that affect the feed consumption and the profit of pig production.Improving feed conversion ratio is becoming more and more important in pig breeding and can greatly benefit the overall profit.In present study,we collected the feed conversion ratio using electronic feeding station in the pure Duroc sires and all individuals were genotyped using Illumina PorcineSNP60 Beadchip and then imputed from the low density markers to whole genome sequence,heritability of feed conversion ratio was calculated and genome wide association studies were performed based on 60K genotyped data and whole genome sequence,respectively.According to the results,the average accuracy of imputation achieved 0.9,higher heritability(h2=0.38)were captured using whole genome sequence than using 60K genotype data(h2=0.20),but we did not find the significant associations between feed conversion and the variants.The genomic predictions were studied using 60K genotype data and whole genome sequence and two cross-validation patterns were used to investigate the accuracy of the genomic prediction:(Ⅰ)spliting the data into 5 parts evenly,one of them was uasd as testing set and the other parts were used as training set;(Ⅱ)single individual was masked and recycled until all individuals got a predicted genomic breeding value.According to the results,we found the correlation between the estimated genomic breeding values and feed conversion ratio based on 60K genotype data and whole genome sequence were 0.70 and 0.63,the correlation decreased 10%.Two cross-validation patterns were used to investigate the accuracy of genomic prediction.The first pattern:the accuracy of genomic prediction based on 60K data and whole genome sequence were 0.14 and 0.17,the accuracy was improved about 21.4%by using whole genome sequence.The correlations between predicted genomic breeding value and estimated genomic breeding value based on 60K data and whole genome sequence data were 0.66 and 0.74,respectively.The correlation increased 12.1%.The second pattern:the correlation between predicted genomic breeding value and estimated genomic breeding value based on 60K genotype data were 0.83,the correlation increased 25.8%compared to the correlation based on 60K data in the first pattern based on 60K data;the accuracy of genomic prediction was 0.34,the accuracy increased 142.8%compared to the accuracy based on 60K data in the first pattern.Our results showed that using denser marker across whole genome can improve the accuracy of genomic prediction and increased the accuracy of prediction and the correlation between predicted genomic breeding value and estimated breeding value.Our study would benefit the improvement of the feed conversion ratio in pig production.