Screening Genes From Whole Genomic Sequencing And Their Association With Economic Traits In The Goat (Capra Hircus) "Phenotypic And Genotypic Characterization Of Some Chinese Goat Breeds"

This research was designed to figure out some basic knowledge about domestication,adaptation,and immigration of goat breeds,with a spotlight on goat breeds in the southwest of China along with recognizing their role in the livestock production industry with a special focus on the position adaptive selection in view of the new high technologies of investigating genome and building of selective comparison between goat breeds.In addition,a presentation of the results on recent genomic studies on goats are listed in logic and sequential fashion.Also,important statistical methods of measuring genetic differences are included in order to furnish the necessary foundation stone to explore the genome of goats.This study consisted of four parts: 1)investigate the body measurements and formulate body indices.2)Evaluate the morphological traits and physiological variables for the studied goat breeds.3)Assessment of hair and cashmere properties,and 4)perform the genome sequencing and predict some candidate genes influencing economic traits.Experiment 1: Body measurements and body indices This part of the research was carried out on several goat breeds: Saanen milk goat(SMG),Black Boer x Dazu black goat(BBx DBG),Hechuan white goat(HWG),Dazu black goat(DBG),Inner Mongolia cashmere goat(IMCG),IMCGx DBG cross(F1)and F1 x F1 double cross(F2)residents of different regions of China but raised in Southwest China to describe the body measurements,body indexes,and the correlations among them.Data were collected on adult males and females all of the same age(36.50±0.75 months).Results showed that the DBG,BBx DBG,F1 and F2 were heavier than other breeds.The mean live body weight of DBG,BBx DBG,F1 and F2 were 60.80,59.00,62.75 and 63.08 kg,respectively,while of HWG,SMG,and IMCG were 57.00,43.42,and 57.15 kg.Meanwhile,SMG,BBx DBG,IMCG,F1 and F2 had longer bodies than other breeds,recording 77.00,73.83,72.50,65.17 and 67.17 cm respectively.As for wither height SMG,BBx DBG,DBG,IMCG and F1 recorded 75.33,68.33,68.33,66.67 and 66.17 cm respectively.Breed differences were significant(P<0.05).The results revealed variable estimates of correlation coefficients among body measurements.Most body indices showed significant differences between breeds along with crosses(P<0.05).According to the current results,SMG was more suitable for milk production with good thoracic development,while BBx DBG and DBG were more compatible with meat production with a firm morphological structure.On the other side,the large bone structure and large flat body of IMCG and its crosses provide superior potentials of these breeds for cashmere production.Experiment 2: Evaluation of morphological traits and physiological variables To evaluate the morphological traits of the studied goat breeds raised in southwest China,several goat breeds were used: Dazu black goat(DBG),Saanen milk goat(SMG),Black Boer x Dazu black goat(BBx DBG),Hechuan white goat(HWG),Inner Mongolia Cashmere goat(IMCG),IMCGx DBG(F1),and F1XF1(F2).All goats were adults and of the same age(36.50±0.75 months).Twenty morphological and production traits: body condition score(BCS),testicle measurements,coat colour,fibre traits,skin colour,horn colour,horn shape,horn orientation,wattles,front hair,beard,ear shape,ear size,rump angle,hind leg angulation and physiological variables were analysed.BBx DBG and DBG had dark coat colour,while SMG,HWG and IMCG had light colour,whilst F1 and F2 had a coat colour range from light to dark.Concerning BCS,the breeds BBx DBG and DBG were characterized as fat goats,while SMG,HWG,F1 and F2 were average,whilst IMCG was a thin breed.The highest testicle measurements were recorded for BBx DBG,SMG and DBG.For fibre,IMCG,F1 and F2 had the best characteristics.BBx DBG and DBG males had high fertility parameters.The highest values for rectal temperature,skin temperature and breath rate were recorded for SMG.These findings revealed the presence of wide range of morphological differences among studied goat breeds.Such diversity in the performance of goat breeds raised in Southwest China is crucial to implement reliable selection strategies for breeding goats in this area.Experiment 3: Assessment of hair and cashmere properties This experiment was designed to compare the properties and quality characteristics of hair and cashmere fibres of two pure goat breeds raised in Southwest China,namely Inner Mongolia cashmere goat(IMCG),Dazu black goat(DBG)and their first cross(F1)using totals of 5219,2130 and 2981 fibre samples,from the three breeds respectively prior to shearing at 32.5±01.25 months of age from four body sites: shoulder,side-portion,abdomen and leg.Breed effects on most hair and cashmere properties were significant(P<0.01).IMCG and F1 hair length was longer(P<0.001)but had less variable lengths than DBG.Shoulder hair diameter of the three breeds were not different(P>0.05)but of the side-portion and abdomen sites for DBG were thicker(P>0.01),however,the thickest(P<0.001)hair diameter was recorded for the leg site of F1 and the thinnest(P>0.01)for IMCG.IMCG recorded the longest cashmere length followed by DBG,while F1 recorded the lowest(P= 0.001),whilst F1 recorded the thickest(P= 0.001)diameter,whereas no differences existed between parents breeds.The cortical cell lengths of IMCG and DBG were 94.57 and 86.85 μm without a significant difference detected between breeds.Differences between hair length and diameter of different body sites of the studied goat breeds were significant unlike whiteness,cashmere diameter and diameter of cortical cells were not.Sex had no significant effect on all hair/ cashmere properties.However,quality characteristics of cashmere fibres from IMCG and F1 were better(P<0.001)than from DBG.Leg hair diameter,curl recovery rate and cashmere diameter were superior in the crossbred F1 compared to purebred parents,and DBG was superior to IMCG for fibre elasticity and intensity traits.FGF-5 gene was detected as a candidate gene for hair and cashmere traits in IMCG breed.Whilst,KIT gene was found to be associated with coat colour in the studied breeds.More investigations are needed to examine cashmere goat breeds and compare them to detect genetic diversity in cashmere production locally in comparison to the worldwide cashmere industry.Experiment/Investigation 4: Genetic differentiation of economic traits Indigenous goat breeds usually develop specific genomic properties through adaptation to local management regions or environments over long periods of time.Most of the studied goat breeds are particularly productive in commercial terms,and have abilities to survive in harsh environments and are tolerant of prevalent diseases.Their adaptive characteristics play an essential role in being resources for genetic improvement of commercial breeds.This is what greatly motivated research to explore the genetic background of the studied breeds.1)The genomes of IMCG and DBG were analyzed,2)genes associated with economic traits were screened from WGS and generated a total of 192.747 Gb of raw data and about 5.03 million SNPs.The selective sweep analysis uncovered several promising candidate genes and many pathways associated with productive or reproductive traits.This provides a crucial resource for future QTL mapping of goat breeds.3)Screening the Indels as related to economic traits was carried out on the two breeds.4)The candidate Indels and their association with body dimensions of DBG,IMCG and HWG were investigated,where,Del/Del genotype of rs669452874 locus could be used as a candidate molecular marker related to the body dimensions in the studied goat breeds.5)Several candidate genes were examined,such as a)Kit gene and its association with coat colour in DBG,IMCG and F1,where,the non-synonymous mutation g.68354798G>A(rs647214940 site)led to 765glutamic(Glu)/765glycine(Gly)(off white to light brown coat colour)in F1,while was 765Glu/765Glu(white coat colour)in IMCG,and was 765Gly/765Gly(black coat colour)in DBG,b)EGLN-1 gene and its association with the adaption in DBG and IMCG,where,the frequency of the allele(A)in IMCG breed was significantly higher(0.64)than that of DBG(0.37)also,the findings of biological information(BI)showed that there was a mutation taking place in the rs659097694 locus ’’219th position’’,thus that led to converting: Serine to Leucine in IMCG breed.The superiority of IMCG breed for adaptation to high-altitude areas,hypoxic environment and high aerobic capacity is strong probably due to this mutation,and differentiation in the genotyping of EGLN-1 gene among both studied goat breeds.c)FGF-5 gene and its association with hair/ cashmere traits,where,FGF-5 gene was found as a candidate gene in IMCG breed,with high significant effects on several of hair/cashmere properties and quality characteristics.