Analysis Of Genetic And Expression Differences Between Longlin Goat And Nubia Goat By High Throughput Sequencing

Long Lin goat is a local variety,and also one of the main breeding species in the south.Its early maturity,resistance to coarse feeding,heat and moisture tolerance,and delicate meat are delicious,but its growth and development are slow,its body size is small,and its lactation performance is poor.Nubian goat has many advantages,such as rapid growth,large meat production,large body size,strong fecundity and good lactation performance.However,after introducing it,it is resistant to rough feeding and poor humidity resistance,and is prone to respiratory diseases and skin diseases.In this study,Longlin goat and Nubian goat were selected as research objects.The phenotypic differences of Longlin goat population,Nubian goat population and Nulong crossbred goat F1 generation were compared.The genome-wide sequencing and transcriptome sequencing data were analyzed.Candidate genes for phenotypic differences between Longlin goat and Nubian goat were screened.The main results were as follows:1.There were significant differences in body shape traits（body weight,body height,body size and chest circumference）,reproductive rate,growth rate,and lactation performance between Long Ling goat and Nubian goat.There was a significant difference in meat quality traits between lamb and Nubian goat in marbling and unsaturated fatty acid content of mutton,and the traits of F1 generation in nulon hybrid were significantly higher than that in Long Ling goat.Goats improved Longlin goats significantly.2.Genome sequencing was performed on 13 goats of three Nulong crossbred families,and clean reads 1,132 Gb was obtained.9,654,970 SNPs were found in Nubian goats,10,263,840 SNPs were found in Longlin goats,and 9,483,012 SNPs were found in Nulong crossbred F1.By setting 1%maximum Z(F_ST)value and 1%minimum Z（H_P）value,239selective evolutionary regions(3.20≤|ZH_P|≤6.28;3.26≤Z(F_ST)≤7.85)were screened out in Longlin goats.176 selective evolutionary regions(3.07≤|ZH_P|≤6.40;3.26≤Z(F_ST)≤7.85)were screened out in Nubian goats,and 137 and 76 selective evolutionary genes were annotated respectively.Eighteen candidate genes related to phenotypic traits were screened by enrichment analysis of GO and KEGG,specifically:candidate genes related to growth and development（UBR4,EMC1,TP53 and FGFR1）;candidate genes related to digestion and metabolism（NR4A3 and SLC26A3）;candidate genes related to reproductive traits（ADAM2,ADAM18,AZIN2 and RAN）;candidate genes related to lactation traits（FGF14 and KDM6B）Candidate genes related to meat production traits（TCF4,ACACA and LPL）and genes related to immune traits（DSG1,FGF2 and TDO2）..3.54 samples of liver,skin,mammary gland,bone,fat,muscle and other 6 tissues of 9Nulong crossbred F1 lambs from three families were sequenced by transcriptome,and a total of clean reads 489.08 Gb was obtained.The allele-specific expression of F1 transcriptome data was analyzed by self-programming based on the genomic SNP information of parents in three families to reflect in the same detail.In intracellular environment,allele differential expression was observed in Longlin goat and Nubian goat,respectively.The results showed that there were 144,127,124,107,97 and 78 specific expressed alleles（ASE）in the liver and six tissues respectively.The 524 specific expressed genes had strong tissue specificity,among which the ASE genome in liver tissue had the highest tissue specificity and the lowest in adipose tissue.4.Combining selection signal with allele-specific expression,38 core candidate genes were obtained.These genes were mainly related to growth and development（PODXL,ACACA,ZFPM1 and KCNQ5）,digestion and metabolism（CYP3A4,CYP3A5,CYP2D6,UGT2B7,CYP8B1,ADH4 and SULT6B1）,lactation（RIMBP2,PRKG1 and HBP1）,immune response（ABCC4,TAP1,EXOC4）.TDO2,BPIFA2,TRIM4,C4A,URGCP and CELF2 were correlated with wet and hot environment adaptability（RPS8,TNXB,OR2AE1 and AOX1）.5.The expression of nine core candidate genes（PODXL,RPS8,HBP1,TNXB,TAP1,ZFPM1,ABCC4,KCNQ5 and ACCA genes）in 36 tissue samples of Nulong crossbred goats was quantitatively studied by real-time quantitative PCR.It was found that the expression levels of mRNA in mammary gland,skin,muscle,fat and bone tissues of Nulong crossbred goats of 3 different months of age were significantly different.In summary,38 core candidate genes for phenotypic differences between Longlin and Nubian goats were identified at genome and transcriptome levels.These genes are related to growth and development,digestion and metabolism,lactation,immune response and adaptation to hot and humid environments.This provides a scientific basis for further elucidating the genetic basis of Longlin goat and Nubian goat in terms of body size,growth,development and adaptability,and has theoretical and practical value.