| Copy number variation is a kind of important genome structure variations.Mainly by disrupting genes and dose effect to influence the phenotypic traits of the animal and the change of gene expression. In our lab, 213 CNVRs(copy number variation regions) in whole genome was performed based on the genotyping data by Illumina Porcine SNP 60 k chip taking 120 native pigs of Congjiang-Xiang pig. 7 CNVRs(of 6 CNVR were detected in the chip that have differences between the frequency of copy number variation in high litter sizes and low litter sizes Xiang pig individuals and of one CNVR include the kit gene)were validated by real-time PCR methods in Xiang pig for the research of The Xiang pig genome structure and function. Combining with correlation analysis and functional annotation to research growth regulation mechanism between the copy number variation with the growth of Xiang pig.The main results of this study included:1. In the 6 CNVR, the results showed that the dominant status of CNVR21、CNVR115 、 CNVR137 in Xiang pigs were gain.The main CNV status of CNVR69、CNVR81 was loss. The normal status was majority in CNVR206, but copy number increased proportion is greater than the loss ratio. Via the chi-square test, The Mutation frequency of CNV in high litter sizes and low litter sizes Xiang pigs has no Significant difference(P>0.05) were CNVR21、CNVR81、CNVR206, has Significant difference(P<0.05) were CNVR69.2. An association analysis indicated that the copy number variable of Xiang pig individuals was associated with The later parities,Body height, body length, body width, and chest in CNVR21( r=0.283,0.309,0.286,0.347,0.334) 。 The Correlation coefficient between the CNV115 and the body width, and chest was0.293 and 0.263; and The total number of nipple, the first/second/later parities was0.314, 0.474, 0.255, 0.250. Functional notes found that the two CNVRs contains a number of olfactory gene.A comparison between pigs in CNVR21 indicated the Proportion of CNV gain in the four pigs, in turn, Yorkshire pig(88.46%),Xiang pig(35.71%), Kele pig(30.00%), and Rongchang pig(0%).We included that Olfactory genes in multi copy number phenomenon increases the sensitivity of pigs for food, and that the phenomenon may be adaptive responses of pigs to breed aquatics in field grazing.While, in CNVR115 indicated the Proportion of CNV gain in the four pigs, in turn, Rongchang pig(84.38%), Yorkshire pig(77.27%), Kele pig(75.00%),and Xiang pig(71.43%). Including that the increase of CN was up-regulated the born number.3. The correlation analysis showed that the copy number of CNVR69 and the body width were slightly correlation, the correlation coefficient was 0.283; the copy number of samples in CNVR81 was slightly negative correlation with the body height and body length, the correlation coefficient was-0.264,-0.272.Functional notes found the related gene ANKS1B;SFRS11and LRRC40。The comparison of loss proportion between pig breeds was Rongchang pig >Yorkshire pigs >Kele pig > Xiang pig. We speculation that copy number deletion of the ANKS1 B gene in Xiang pig may be associated with high yield, but also may be a cause of disease resistance in Xiang pig. While, SFRS11, LRRC40, two genes play a negative regulation in the breeding and growth of pigs.4. Correlation analysis, the copy number of samples in CNVR137 and body length, tube circumference were slightly negative correlation, the correlation coefficient was-0.311,-0.278; the Xiang pig copy numbers with The total number of nipple, the first parities in CNVR137 were Mild related(r=0.291 and r=0.294).CNVR206, the correlation of the test sample copy number and the correlation between the body measurements indexes are not related; the correlation of the test sample copy number with the later parities were Mild related(r=0.458). Speculated that CNVR137 may inhibit the growth of pig speed, For CNVR137/206 were the newly discovered copy number variation regions, annotation and interval is notperfect, so the specific mechanism needs further research.5. To investigate the association of various coat color phenotypes and copy number variation(CNV) of KIT gene in pig, four indigenous pig breeds originated from Guizhou province were chosen as samples using quantitative real time PCR(q PCR) method. taking Yorkshire and Rongchang pig as controls. The results showed that the dominant status of KIT CNV were loss in four Guizhou indigenous pig breeds with black/brown coat color, The KIT CNV status in pigs with black and white patch were all lose, while the increasing and normal individuals with brown and white patch were half. The main CNV of KIT gene was gain in Yorkshire pig. However, the normal status was majority in Rongchang pig breed. It confirmed that the duplication of KIT gene was the critical reason for the white coat in Yorkshire pig, but it might be not the case in Rongchang pig breed. In the four Guizhou indigenous pig breeds with black/brown coat, it might be associated with the loss of KIT gene copy. It was interested that the copy numbers of KIT gene in Kele and Xiang pig with white patched coat were detected to lose one or two copies. It suggested that the white patched coat might be unrelated with the copy number changes of KIT gene with another special mechanism in Guizhou indigenous pig breeds. |
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