Development Of The Algorithm And Technical System Of Genomic Mating For Efficient Three-way Commercial Pig Production

The three-way crossbreeding between Duroc,Landrace and Yorkshire is the mainstream mode of commercial pig production,which can meet 90% of pork supply in our country.This mode mainly determines the optimal breed combination through strictly designed combining ability tests.However,there are also shortcomings in the breeding of synthetic line,such as a complex and lengthy process,high cost,and inability to maximize the heterosis of each boar-sow pairs.As high-throughput sequencing technology continues to advance,genomic information has been used for mating.Genomic mating can upgrade the traditional synthetic line of "breed-level" population mating to "individual-level" precise mating.In this study,a comprehensive system has been developed for precise genomic mating of three-way commercial pigs,including a novel genomic mating algorithm,new software,and an operating procedure.This study is the first to conduct genomic mating for the production of Duroc-Landrace-Yorkshire three-way crossbred commercial pigs.Additionally,the study proposes a new method for rapidly estimating marker effects that significantly reduces computational complexity while maintaining accuracy.The system’s efficacy was evaluated through simulated and real data and genome mating validation experiments.Based on the findings,the following conclusions can be drawn:(1)The optimal mating pair of purebred Duroc boars and Landrace-Yorkshire two-way crossbred sows was selected by genomic mating to maximize the individual heterosis of the three-way commercial pigs.Unlike the traditional breeding programs that primarily focus on maximizing heterosis at the population level,genomic mating can improve production performance at the individual level.(2)Estimating maker effects is a critical step in genomic mating.This study proposes a new method for rapidly estimating marker effect values,which does not require solving the mixed model equation to obtain breeding values in prior and to compute the direct inversion of large matrices.As a result,it is particularly suitable for multirandom effects models that encompass various genetic effects,such as additive and dominance genetic effects.Compared to existing algorithms,this method significantly reduces computation time and memory consumption without sacrificing accuracy and precision in calculations.(3)It is the first study to estimate genetic parameters and marker effects of feed efficiency,growth,carcass traits using the genotype and phenotype from 3573 Duroc-Landrace-Yorkshire three-way crossbred commercial pigs.The genetic contributions of the additive and dominant genetic effects to the production performance of three-way commercial pigs were systematically evaluated.The results showed that the six traits analyzed were medium to low heritability,with additive heritability ranging from 0.20 to 0.33 and dominant heritability ranging from 0.10 to 0.14.(4)This study utilized genotype data from 875 purebred Duroc boars and 350 Landrace-Yorkshire two-way crossbred sows,along with estimated additive and dominant genetic effects,to conduct genomic mating analysis and to evaluate the efficiency of genomic mating.The results showed that the genomic mating based on total genetic values of progeny was more effective than breeding values.Compared to random mating,genomic mating significantly improved the production performances of progeny across different traits,such as feed conversion rate,days from 30 to 120 kg and eye muscle area could be improved by-0.12,-4.58 day and 2.66 cm2,respectively,which were consistent with the real experimental validations.(5)The study also showed that the more available purebred Duroc boars,the richer the genetic diversity,and the more significant the improvement of production performance by genomic mating.The efficiency of genomic mating was influenced by the marker effect estimation model,while different methods of constructing the relationship matrix had little effect on the effectiveness of genomic mating.Genomic mating can maximize the production performance of three-way commercial pigs by allocating the optimal boar-sow pairs.Meanwhile,the combined application of genomic selection and genomic mating can maximize the utilization of favorable gene effects to improve the breeding efficiency.