Screening Of Candidate Genes Related To Egg Production Traits Based On Shitou Goose And Analysis Of Polymorphisms Of ESR1 And HSD17B2 Genes

The Shitou goose is a famous large-scale meat goose species in my country.However,the Shitou goose lays only about 30 eggs,which severely restricts its industrial development.In order to screen the candidate genes of Shitou goose egg production traits and analyze its population polymorphism,the whole genome sequence of Shitou Goose and Jilin White Goose were compared in this study with an annual egg production of more than 100 Jilin White Goose as a control.The experiment selected two-year-old adult Shitou goose and 5 Jilin white goose geese each,collected blood and re-sequenced the whole genome for screen the Shitou goose egg-laying-related candidate genes through the sequencing results.On this basis,the polymorphism analysis of candidate genes ESR1 and HSD17B2 were performed on the SNP loci of200 individual Shitou goose individuals.The test results are as follows:(1)The average coverage depth of the whole genome resequencing of the two varieties is 26X(15X～49X).After filtering the data,a clean sequence of 350.35 Gbp was obtained,of which Q20 and Q30 reach 96.87% and 92.19% respectively.The comparison rate between the sequencing data and the reference gene is between 93.18%and 94.96%,and the average comparison rate is 94.15%,indicating that the amount of data in all samples is sufficient and the sequencing quality is qualified.The GC content of the sequencing data is between 43.67% and 45.64%,the distribution is normal,and the database is successfully constructed and sequenced.(2)The SNP loci of Shitou goose and Jilin White Goose were mainly distributed in introns,accounting for 54.91% and 55.76% respectively.The genome-wide heterozygosity ratios of SNPs in the two populations were similar(Shitou goose:57.698%,Jilin White Goose: 61.276%).The number and distribution of Indel mutations in Shitou goose and Jilin White Goose are similar to the reference genome.They are mainly distributed in introns,accounting for 52.12% and 54.18%,respectively.Indel loci are the least distributed in the exon region.A total of 51962 structural variants(SV)were detected in the data,and the lengths of the variants were mainly distributed in four intervals of 100～200bp,200～300bp,300～400bp and 1 200 bp.A total of 1154 copy number variations(CNV)were found in the data,including 1 146 insertions(99.31%)and 8 deletions(0.69%).(3)Through GO,KEGG screened 11 128 variant genes,these variant genes are distributed in 17 cell components,20 molecular functions,23 biological processes and253 metabolic pathways.Further analysis and screening of Gn RH signaling pathway,prolactin signaling pathway,estrogen signaling pathway,oxytocin signaling pathway,and progesterone-mediated oocyte maturation pathways were five pathways related to egg production.(4)The principal component analysis of the SNP of Shitou goose Goose and Jilin White Goose populations shows that the two populations were effectively separated,which indicates that the two geese have greater differences at the SNP level.Through variation comparison analysis,25 SNP differential genes,10 Indel differential genes and20 SV differential genes related to reproduction were screened out.(5)Gene polymorphism analysis found that there are SNP mutation sites in the ESR1 and HSD17B2 genes in the Shitou geese population,which proves that the sequencing results are accurate.In addition,the SNP mutation sites of the ESR1 and HSD17B2 genes comply with the Hardy-Weinberg balance,indicating During the genetic process of Shitou goose population,genetic performance remained relatively stable.