| Through cross breeding,the cultivation of new breeds or lines with Chinese characteristics and reaching the world level has once again become the theme of the times in China’s pig industry.In order to adapt to this situation,firstly we must find the reasons for the lack of competitiveness of the new pig breeds / lines that have been bred in the past,find out the problems of the classic systematic breeding,and lay the foundation for establishing a new and effective method.Nowadays,the increase in the detection throughput of genomic genetic markers and the significant reduction in detection costs have enabled us to conduct analysis and research based on genomic information systemmaticly.That is,why is the result of cross-breeding based on systematic breeding unsatisfactory? Do the existing breeds and specialized strains have resource value? Can it be complemented by genomic information and cross-breeding? To this end,this study intends to select Lulai black pigs and ’Shennong Ⅰ’,which are based on systematic breeding,and use population structure analysis,selection signal analysis,and introgression analysis to examine the success and failure of traditional methods and source.The specific work is as follows.(1)Lulai black pigs bred from Laiwu pigs and Yorkshire as breeding materials were used as research objects.The 50 K chip platform was used to compare Lulai black pigs(LU,313)and their parent breeds Laiwu pigs(LW,233)and Yorkshire(Y,260)SNP detection,a total of 79739 SNPs were obtained.Population structure analysis showed that the genetic distance between LU and LW was close,and the genetic distance between LU and Y was far,and the LU population was mixed.Selection signal analysis showed that the Fst between LU and LW was less than 0.4.The Fst between LU and Y reached 1.0,which indicating that the direction of artificial selection was biased toward LW.Gene annotation was performed on the SNPs before 1% of the Fst value,and 426 LU-LW significant differential genes and 782 LU-Y significant differential genes were obtained.After digging in the literature,three major genes were found among the significant differences in LU-Y genes: LEPR(related to growth and fat accumulation),SCD(related to meat quality and fatty acid composition)and TBC1D1(related to meat quality).Compared with LW,LU differ in the growth traits and meat & carcass traits,the difference between Y and LU also lies in growth traits and meat & carcass traits.Introgression analysis showed that a total of 26,677,332 bases introgressed from LW with 27 significant segments.The number of significantly infiltrated genes was 229.A total of 16,838,316 bases introgressed from Y.The base has 12 significant segments and 182 genes infiltrated significantly.According to functional enrichment analysis,the fragments infiltrated from Laiwu pigs are mainly related to growth and reproduction,and the fragments infiltrated from big white pigs are mainly related to growth and health.On the basis of the above analysis,in order to improve the accuracy of the analysis,we futher chose the sequencing data obtained from the simplified genome sequencing method developed by our laboratory(GGRS)as a supplement.A total of 190 pigs were sequenced by GGRS,including 38 LU,77 LW and 75 Y.After quality inspection and imputation,375,025 SNPs were obtained.In addition to verifying the analysis results of the chip data,the GGRS data analysis results also found some new results.In the selection signal analysis,gene annotation was performed on the SNPs in the first 1% of the Fst value to obtain 634 significant differences in LU-LW genes and 601 significant differences in LU-Y genes.After digging in the literature,three major genes were found among the significantly different genes in LU-LW,MYPN(related to carcass composition),KIT(related to hair color)and PPARD(related to ear size);Three major genes were found in the significantly different genes in LU-Y,IGF2(related to growth and fat accumulation),FTO(related to growth and fat accumulation),and KIT(related to hair color).Based on the results,it can be concluded that LU have different appearance characteristics compared with LW;LU have larger differences in reproductive characteristics than Y.Introgression analysis showed that a total100,649,934 bases introgressed from LW with 149 significant segments.The number of significantly infiltrated genes was 727,which was mainly related to growth and reproduction.A total 38,666,133 bases were introgressed from Y with 94 significant segments,and 363 genes were significantly infiltrated,mainly related to growth and health.Based on the analysis results of the above two platforms,the following conclusions can be drawn: the genetic distance between LU and LW was relatively close,and the LU population was mixed.LU inherited LW at the same time in terms of growth and meat quality And the characteristics of Y,but there are still differences between the two parents,which makes the growth characteristics of LU better than LW but not as good as Y.The meat quality of carcass is worse than Y but not as good as LW.Although the LU has inherited the advantages of the high litter size of LW,it has not inherited the advantages of good resistance of LWs.It has inherited the advantages of Y in terms of immunity.Therefore,the LU bred by the method of group subsequent breeding combined some of the advantages of the two breeds and had resource value.However,compared with the breeding goal,the breeding effect is not satisfactory.LU need further genetically improved by introducing genomic information and introductive crossing or other methods.(2)"Shennong Ⅰ" pig(SN),which was bred with Landrace(L),Yorkshire(Y)and Erhualian pig(EH)as breeding materials,was taken as the research object to further examine the success or failure of the systematic breeding.Using GGRS sequencing,125 individuals including SN,L,Y,EH were sequenced.After quality inspection and imputation,185,657 SNPs were obtained.Population structure analysis showed that the genetic distance between SN and Y was close,but according to the breeding plan,L should occupy 50% of the SN’s lineage,indicating that problems occurred during the cross-breeding stage between Y and EH.Introgression analysis showed that the number of genes infiltrated from EH was 155,the number of genes infiltrated from L was 811,and the number of genes infiltrated from Y was 1,064..A total 25,719,997 bases introgressed from EH to SN with 3 significant segments,were mainly related to body size,growth and reproductive traits,but the disadvantage of EH was slower growth,and SN inherited this disadvantage.A total 90,579,963 bases introgressed from Y to SN with 37 significant segments,were mainly related to health.A total 88,749,957 bases introgressed from L to SN with 43 significant segments,were mainly related to smell and food intake.SN has inherited the reproductive advantages of EH and feed conversion advantages of L,but has not inherited the disease resistance,meat quality advantages and growth advantages of EH.Based on the results,SN did not form a stable genetic resource,and did not fully inherit the advantages of the parent,thus,the breeding effect was not satisfactory.Based on the population structure analysis,selection signal analysis and introgression analysis of LU and SN with their parents,we preliminarily analyzed the reasons for the unsatisfactory results of systematic breeding.Although the two cultivars are not ideal,they still have resource value.They can be supplemented with genomic information by cross-breeding.The results of this research will provide reference and guidance for promoting the breeding,development and utilization of new pig breeds or strains nationwide. |
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