Screening Of Candidate Genes Related To Litter Size Traits In Guanzhong Dairy Goats Based On Whole-genome Resequencing

Guanzhong dairy goat is a well-known and excellent dairy goat breed in China.It has strong adaptability,rough feeding resistance,high disease resistance,stable milk production performance and high milk yield.However,the problems of backward breeding technology and slow breeding progress have led to the decline of their fertility and production level,which seriously restricted the healthy development of the dairy goat industry.With the improvement of the technology flux and the reduction of cost,the use of modern breeding technology to improve the breeding and improvement of goat goats can greatly improve the genetic progress,and then promote the development of dairy goat industry.At present,the main genes that regulate the litter size traits of Guanzhong dairy goats are still unclear,and there are few studies on the gene screening of litter size traits.Therefore,in this study,the genome variation of Guanzhong dairy goat ewes was identified by whole-genome resequencing technology,and the selection and elimination analysis of different litter size groups was carried out to screen the related candidate genes and molecular markers affecting the litter size traits of Guanzhong dairy goats,in order to provide corresponding theoretical support for the protection and breeding of goat genetic resources.The main results of this study are as follows:1.Through whole-genome resequencing of Guanzhong dairy goats,a large number of genetic variations were identified,including 20,496,195 SNPs,2,239,766 In Dels,598,774 SVs,and 598,774 CNVs,of which SNPs and In Dels were mostly mutated at the ends of chromosomes,and most of the variation is located in intergenic regions,followed by regions such as introns.After annotation and functional enrichment of SNP nonsynonymous mutations and In Del frameshift mutations,more reproduction-related genes and pathways were found,such as FSHR,AMH,EGFR,PLA2G4 D,PLK4,SMAD1 and SMAD9 and other genes and oxytocin signaling pathway,oocyte meiosis and PI3K-Akt signaling pathway,etc.,suggesting that these genes and signaling pathways may be involved in the evolutionary selection of litter size traits in Guanzhong dairy goats.2.By analyzing the population genetic diversity and genomic variation pattern of Guanzhong dairy goats,it was found that Guanzhong dairy goat populations with different litter sizes had a certain degree of differentiation.By selective elimination analysis of different litter size populations,65 genes that may be related to litter size traits were screened,which including PLCD3,KPNA1,PIWIL2,PDS5 B,PUM2,SOX17,PXT1,ALKBH5,HERC5,STRA8,SP1,PHB,LLGL1,SGK,SMAD9,E2F1,AMHR2,NR4A1,BCL2,ADIPOQ,FIGLA and IQCH etc.Based on the analysis method of Fst and θπ,437 genes were annotated in 1754 selection windows of the high fecundity group,and 230 genes were annotated in 865 selection windows of the low fecundity group,and both groups were significantly enriched to the lower fecundity group.There are many pathways related to reproductive regulation,such as estrogen signaling pathway,TGF-β signaling pathway,NFκB signaling pathway,Hippo signaling pathway,etc.,suggesting that these genes and signaling pathways may be involved in the regulation of reproductive processes such as follicle formation,growth and development in Guanzhong dairy goats,which in turn affects the litter size.3.PCR was performed on 6 variant sites of g.61909419A>G,g.61909434G>A,g.61922756C>A,g.61922864C>T,g.61929226G>T and g.61929514C>T in the exon of SMAD9 gene Amplification,Sanger sequencing and population genetic analysis showed that the 6 SNP variant sites all contained three genotypes: wild type,heterozygous type and mutant type.Meanwhile,the three mutation sites g.61909419A>G,g.61909434G>A and g.61922864C>T showed moderate polymorphism(0.25 < PIC < 0.5).In addition,except for g.61922756C>A,the other five sites were in Harder-Weinberg equilibrium(P > 0.05).Through further correlation analysis between the 6 mutation sites and the litter size,it was found that there was no significant correlation between the 6 mutation sites and the first litter size of Guanzhong dairy goats(P > 0.05),but the CC of g.61922756C>A the genotype had the largest average litter size(1.86±0.34),and its litter size was 0.29 and 0.28 more than the CA and AA genotypes,respectively,indicated that the genotype could be used as a potential marker for the selection of high fecity individuals in Guanzhong dairy goats.In conclusion,this study identified a large number of genetic variations in the Guanzhong dairy goat genome by whole-genome resequencing,and preliminarily screened out candidate genes that may affect their litter size traits,such as PLCD3,KPNA1,PIWIL2,PDS5 B,PUM2,SOX17,PXT1,ALKBH5 and SMAD9,etc.,and explored the relationship between the SMAD9 gene exon mutation and the litter size of Guanzhong dairy goats,and found that the CC genotype of g.61922756C>A had the largest average litter size.Therefore,this study can provide a certain theoretical basis for the selection and breeding of excellent individuals of Guanzhong dairy goats.