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Volume 12 Journal of Molecular and Genetic Medicine
ISSN: 1747-0862
May 21-23, 2018 Barcelona, Spain
&
Integrative Biology
6th International Conference on
Genomics and Molecular Biology
10th International Conference on
Genomics 2018 and Integrative Biology 2018
May 21-23, 2018
JOINT EVENT
Population genomics reveals adaptive divergence in global populations of common carp (Cyprinus
carpio)
Jian Xu1, Zixia Zhao 1, Yanliang Jiang1, Hanyuan Zhang1, Yan Zhang 1, Chuanju Dong2, Ruyu Tai1 and Peng Xu3
1Chinese Academy of Fishery Sciences, Beijing, China
2Henan Nornal University, Xinxiang, China
3Xiamen University, Xiamen, China
The common carp, Cyprinus carpio, is one of the most important cyprinid species cultured in Europe and Asia and globally
accounts for over 70% of freshwater aquaculture production worldwide. Various populations of C. carpio distribute all over
the world and mainly in the Eurasian continent, showing distinct biological characteristics including scale, color, body shape,
etc. However, the genetic mechanism underlying the traits were not very clear yet. Here we present a population genomic
analysis on 14 populations of C. carpio. High throughput SNP genotyping of 2,587 representative individuals from worldwide
14 populations demonstrates different genetic component for C. carpio in two subspecies (C. carpio subsp. haematopterus
and C. carpio subsp. carpio). Quality control of SNPs were conducted with following parameters (call rate>95%, genotype
rate>95%, MAF>5%). A maximum-likelihood tree was constructed with RAxML and displayed with iTOL software (http://
, and all SNPs were used to investigate the PCA with SMARTPCA. Population structure were finished
using STRUCTURE with 2,000 iterations. The resulting structure matrix was plotted using STRCTURE PLOT v2.0. LD (linkage
disequilibrium) block average lengths of 14 populations range from 3.94kb to 36.67kb. We calculated the π distribution for
each linkage group using a sliding window method in VCFTOOLS. The window width was set to 10 kb, and the stepwise
distance was 10 kb. The π values from the main populations were compared, and the ratios were sorted. Fst and Tajima’s D
values were also calculated using VCFTOOLS with the parameters “–weir-fst-pop” and “–TajimaD”, respectively. We identified
the regions with the 5% highest p ratios and the regions with the 5% highest Fst values. Genes within selective sweep regions
were identified by genome scanning among different populations, including gdf6a, grb7, mtnr1ba, tgfbr2, etc. Gene ontology
and KEGG enrichment analyses by DAVID software unveiled potential trait-related GO terms and pathways which were
associated with body shape, scaling patterns and skin color, such as TGF-beta signaling pathway, ECM-receptor interaction
and so on. The population genomics analysis paves the way for better evolutional studies and improved genome-assisted
breeding of C. carpio.
Biography
Jian Xu has completed his PhD from Peking Union Medical School, China. He is an Associate Professor and Vice Director of Center of Aquatic Genomics of
Chinese Academy of Fishery Sciences, Beijing, China. He has published 33 papers in reputed journals and has been serving as an Editorial Board Member of
Frontiers in Genetics.
Jian Xu et al., J Mol Genet Med 2018, Volume 12
DOI: 10.4172/1747-0862-C2-028