Inheritance Of Horn And Economic Traits In Inner Mongolia Cashmere Goat And Screening And Identification Of Candidate Genes

China has the most abundant genetic resources of cashmere goats in the world.The number of cashmere goats,cashmere production and quality are all ranked first in the world.Among them,the Inner Mongolia cashmere goat is an excellent local breed in China.Understanding the genetic structure of phenotypic variation in natural populations is a basic goal of evolutionary genetics.Horn traits of Inner Mongolia cashmere goats has genetic polymorphisms in both sexes.In this population,horn size is different or polledness,indicating genetic variation of horn trait in Inner Mongolia cashmere goats.Determining the genetic basis of horn traits will provide an important basis for understanding the maintenance of different morphologies in natural selection.There are no reports on the analysis of horn trait variation in cashmere goats.Therefore,we studied genetic diversity of horn traits in Inner Mongolia cashmere goats to understand the genetic mechanism of horn traits with quantitative genetics,genomics,transcriptomics,and bioinformatics approaches.The relationship of horn and other traits,the genetic characters of horns and the mechanism of the genetic variation of horn traits,and the screening of candidate genes related to horn traits in our results greatly improve the understanding of the genetic mechanism of mammalian horn traits.This study first estimated genetic parameters to reveal the genetic characters of relationships between horn-type traits and other traits.Then,1920 Inner Mongolia cashmere goats were genotyped using 70 K SNP chip,and the genome-wide association analysis of horn-type traits was performed to discover and validate related.Then,transcriptome sequencing was performed for both horned and hornless cashmere goats to identify candidate genes regulating horn-type traits from the transcriptome level.Finally,significant SNP loci and candidate genes were validated by q RT-PCR.This study provides new theoretical basis and genomic genetic resources for breeding hornless Inner Mongolia cashmere goats.Main results are as follows:1.Based on the pedigree and production performance records of Inner Mongolia cashmere goats measured and accumulated by the research group from 2018 to 2021,genetic parameters of horn traits and other traits were evaluated by Wombat.We discovered that heritability of horn length,horn base interval and horn base circumference are 0.35,0.27 and0.17,respectively.The genetic correlations of horn base interval with both horn length and horn base circumference are-0.21 and-0.26,and the phenotypic correlation is-0.12 and-0.32 respectively.The genetic correlation of horn length and horn base base circumference is 0.54,and the phenotypic correlation is 0.61.The repetitive force of horn base interval,horn length,and horn base circumference are 0.29,0.59,and 0.68,respectively.The heritability of wool length,cashmere yield,cashmere length,body weight of fleecing,birth weight and weaning weight are 0.29 and 0.21,0.11,0.18,0.15 and 0.12,respectively.Genetic correlations between horn length and economic traits is between 0.03 and-0.53,and the phenotypic correlation is between-0.41 and-0.68.The genetic correlation between base circumference and economic traits is between 0.01 and 0.34,and the phenotypic correlation is between-0.47 and 0.39.Genetic correlations between horn base interval and economic traits is between-0.08 and 0.10,and the phenotypic correlation is between-0.41 and-0.68.Horn length and horn base circumference traits belong to medium heritability and are positively genetically related to the production of cashmere.Among them,horn length trait and the weight after fleeing are strongly genetically and phenotypically related,indicating that individuals with long and thick horns may be selected at the same time.Cashmere production and body weight of fleecing were selected,and the genetic correlation and phenotypic correlation between the two traits were both weakly correlated.2.Based on the 70 K SNP chip,the genotypes of 1920 Inner Mongolia cashmere goats was identified,and the genome-wide association analysis was performed on the three traits of Inner Mongolia cashmere goat,horn length,horn spacing and horn base perimeterare.Eight significant SNPs were discovered at the genome level,20 significant SNPs were identified at the chromosome level.RXFP2,NRDC,NBEA,STARD13,FOXO1,KIAA1429,UNC79,ATG2 B and LOC102178917 were identified as important candidate genes for Inner Mongolia cashmere goat horn type,which can be further anlyzed in the following work.3.We anlyzed three hornless Inner Mongolia cashmere goats and three horned Inner Mongolia cashmere goats using transcriptome sequencing technology and obtained a total of 55.88 G filtered bases,31,574 transcripts after data quality control.There are 891 differential genes between hornless goats and horned cashmere goats,including 167 upregulated genes and 724 down-regulated genes,e.g.,TWIST1?CDH23?HOXD8?HOXD9?HOXD10?HOXD11?DCN?RORA?NXN?MYL2?RNF220?SSH2 and GSN.KEGG enrichment analysis indicates that these genes are closely correlated to cytokine-cytokine receptor Body interaction,osteoclast differentiation and cell adhesion molecules and other pathways related to bones and immunity.4.We selected the six SNP loci identified in whole genome association analysis of horn type traits in the second study and used sanger sequencing to genotype extreme phenotypes(96 individuals for each trait)and performed chi-square test.The candidate genes DCN,RORA,NXN and MYL2 of Inner Mongolia cashmere goat horns identified in Study 3 were also analyzed by real-time fluorescent quantitative PCR technology(q RT-PCR).We found that:(1)Sanger sequencing and genotyping statistics of candidate gene loci showed that the genes NRDC(26352836,C?T)and RXFP2(57445295,A?C)were significantly related to horny traits.(2)In this study,the relative expression levels of candidate genes DCN and MYL2 were significantly higher in horned individuals than in non-horned individuals(P<0.05).It is speculated that DCN and MYL2 are important candidate genes for horn-type traits in Inner Mongolia cashmere goats.This verifies the relationships between the target gene and the horn-type traits of Inner Mongolia cashmere goats and confirms that the expression of DCN and MYL2 genes play an important role in the regulation of horn formation.In summary,this study discovered signal pathways closely related to the horn growth and development of Inner Mongolia cashmere goat,constructed the analysis model of horn traits of Inner Mongolia cashmere goat,and identified relevant candidate genes.These findings provide a reference for exploring the genetic mechanism of horn trait variation of Inner Mongolia cashmere goat and lay the foundation for the breeding of new breeds of Inner Mongolia cashmere goats(polledness type)in the future.