Screening The Indel And Its Association With The Productive Traits In Goats (Capra Hircus)

Goat,as one of the earliest domesticated livestock species,traditionally had a strong influence on the socio-economic life of human populations,especially in rural and less developed regions of the world.Due to the diverse of socio-economic systems and the people's needs for different goat products in China,goat is rich in breeds and genetic resources.China also has a long history of goat raising,which is one of the most important agricultural economic sources for Chinese people.However,at present,the basic research on the growth,reproduction and other important economical traits of goats is very inadequate,and the progressing of goat breeding is very slowly.With the development of high-throughput sequencing technology and molecular biology,it is possible to analyze the genetic mechanism of goat economic traits from the whole genome level.In this study,the whole-genome resequencing results of 12 goat individuals(Dazu black goat,DBG,n=6;Inner Mongolia cashmere goat,IMCG,n=6)were used for calling Insertion and Deletion(Indel)by aligning against goat the reference genome(CHIR1.0).SAMtools tools were used to result in the high quality Indels,which were then used for functional annotation via ANNOVAR software.Comparative analysis of variation was performed via incorporating those same Indels at each group and screen population specific Indels.Three Indels randomly selected were genotyped with KASP method for performing population genetic analysis in three population of DBG(n=36),IMCG(n=65)and Hechuan white goat(HWG,n=74).Furthermore,the association analysis was carried out by using the least square method under SPSS statistics with the phenotypic measurement data such as goat body weight,body height and body length.The results were showed as followings.1.Screening result of Indels.We obatined a total of 334,151 high quality Indels in average thgrough the analysis of 12 goat genomes.The comparative genome revealed that there were 11,486 and 9,125 same Indels between the DBG and IMCG while the specific Indels contained 110 and 100,which were annotated to 38 and 30 genes,respectively.2.Genotyping of candidate Indels.Three candidate sites(specific Indels of DBG: rs668795676 and rs657996810,specific Indel of IMCG: rs669452874)screened from the group's specific Indels were genotyped.The results showed that the insertion(Ins)was the dominant allele of all these three loci among DBG,IMCG and HWG.The homozygous insertion genotype(Ins/Ins)was the dominant genotype,and the 3 candidate-Indels loci displayed low or moderate polymorphism.Only rs669452874 locus was deviated from Hardy-Weinberg slightly in DBG(P=0.0491<0.05).3.Association analysis of candidate Indels with goat productive traits.There was no significance observed neither rs668795676 or rs657996810 with production traits among three goat groups.For rs669452874 locus,the Ins/Del genotype were significantly higher than those of Ins/Ins genotype in body weight(P<0.05)and chest width(P<0.05)in DBG population.The Del/Del genotype were significantly higher than those of Ins/Ins genotype in body height,body length and cannon circumference in the IMCG(P<0.05).In HWGs,the length and heart girth of Del/Del genotype were significantly higher than those of the Ins/Del and Ins/Ins genotypes(P<0.05).In conclusion,the distribution of Indels in the genomes of the two goat breeds and the population genetic structure of three candidate Indels(rs668795676,rs657996810 and rs669452874)in three goat breeds were obtained.It was revealed that the rs669452874 is linkage disequilibrium with goat productive traits,which supplies the foundation for the future study in development the molecular genetic marker for goat selection.