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Improved Detection and Characterization of Copy Number Variations Among Diverse Pig Breeds by Array CGH.

Wang J, Jiang J, Wang H, Kang H, Zhang Q, Liu JF - G3 (Bethesda) (2015)

Bottom Line: Of the total porcine genes, 1295 genes were completely or partially overlapped with the identified CNVRs, which enriched in the terms related to sensory perception of the environment, neurodevelopmental processes, response to external stimuli, and immunity.Further probing the potential functions of these genes, we also found a suite of genes related important traits, which make them a promising resource for exploring the genetic basis of phenotype differences among diverse pig breeds.CNVs detected in diverse populations herein are essentially complementary to the CNV map in the pig genome, which would be helpful for understanding the pig genome variants and investigating the associations between various phenotypes and CNVs.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China.

No MeSH data available.


Related in: MedlinePlus

Numbers of CNVs (length) overlapped among different platforms.
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fig5: Numbers of CNVs (length) overlapped among different platforms.

Mentions: CNVRs identified herein were compared with those previously reported in other studies (Fadista et al. 2008; Ramayo-Caldas et al. 2010; Chen et al. 2012; Li et al. 2012; Rubin et al. 2012; Wang et al. 2012; Paudel Y et al. 2013; Wang et al. 2013; Wang et al. 2014; Jiang et al. 2014). As shown in Table 3 and Table S9, the CNVR number and length overlapped with the 10 previous studies vary greatly, ranging from 0.13% to 61.61% in count percentage (0.02%–63.06% in length). After merging the comparison results, a total of 526 CNVRs overlap with previously reported ones, indicating 69.39% of CNVRs identified in the study can be validated by previous studies and the other ones were first detected in our study. Furthermore, we performed an exhaustive comparison with our previous studies using 2.1M NimbleGen (Wang et al. 2014) and read depth (RD) method (Jiang et al. 2014), whereby the same samples were collected in CNV detection. As shown in Figure 5, among the three types of platforms, RD detects the most CNVRs in number or the largest polymorphic sequence in total length, whereas NimbleGen detects more CNVRs in number than Agilent but nearly equal total length. There were 253 CNVRs (length of 17.31 Mb) detected by all three platforms, whereas 261 CNVRs (length of 13.65 Mb) were identified only in the present study.


Improved Detection and Characterization of Copy Number Variations Among Diverse Pig Breeds by Array CGH.

Wang J, Jiang J, Wang H, Kang H, Zhang Q, Liu JF - G3 (Bethesda) (2015)

Numbers of CNVs (length) overlapped among different platforms.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4478553&req=5

fig5: Numbers of CNVs (length) overlapped among different platforms.
Mentions: CNVRs identified herein were compared with those previously reported in other studies (Fadista et al. 2008; Ramayo-Caldas et al. 2010; Chen et al. 2012; Li et al. 2012; Rubin et al. 2012; Wang et al. 2012; Paudel Y et al. 2013; Wang et al. 2013; Wang et al. 2014; Jiang et al. 2014). As shown in Table 3 and Table S9, the CNVR number and length overlapped with the 10 previous studies vary greatly, ranging from 0.13% to 61.61% in count percentage (0.02%–63.06% in length). After merging the comparison results, a total of 526 CNVRs overlap with previously reported ones, indicating 69.39% of CNVRs identified in the study can be validated by previous studies and the other ones were first detected in our study. Furthermore, we performed an exhaustive comparison with our previous studies using 2.1M NimbleGen (Wang et al. 2014) and read depth (RD) method (Jiang et al. 2014), whereby the same samples were collected in CNV detection. As shown in Figure 5, among the three types of platforms, RD detects the most CNVRs in number or the largest polymorphic sequence in total length, whereas NimbleGen detects more CNVRs in number than Agilent but nearly equal total length. There were 253 CNVRs (length of 17.31 Mb) detected by all three platforms, whereas 261 CNVRs (length of 13.65 Mb) were identified only in the present study.

Bottom Line: Of the total porcine genes, 1295 genes were completely or partially overlapped with the identified CNVRs, which enriched in the terms related to sensory perception of the environment, neurodevelopmental processes, response to external stimuli, and immunity.Further probing the potential functions of these genes, we also found a suite of genes related important traits, which make them a promising resource for exploring the genetic basis of phenotype differences among diverse pig breeds.CNVs detected in diverse populations herein are essentially complementary to the CNV map in the pig genome, which would be helpful for understanding the pig genome variants and investigating the associations between various phenotypes and CNVs.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China.

No MeSH data available.


Related in: MedlinePlus