Changxu Tian

Single Nucleotide Polymorphisms in Growth Hormone Gene and Their Association with Growth Traits in Siniperca chuatsi (Basilewsky)

Growth hormone (GH) has been considered as a candidate gene for growth traits in fish. In this study, polymorphisms of the GH gene were evaluated for associations with growth traits in 282 Siniperca chuatsi individuals. Using directly sequencing, four single nucleotide polymorphisms (SNPs) were identified in GH gene, with two mutations in intron 4 (g.4940A>C, g.4948A>T), one mutation in exon 5 (g.5045T>C) and one in intron 5 (g.5234T>G). Notably, three of them were significantly associated with growth performance, particularly for g.4940A>C which was highly correlated with all the four growth traits. In conclusion, our results demonstrated that these SNPs in GH gene could influence growth performance of S.chuatsi and could be used for marker-assisted selection (MAS) in this species.

Isolation and characterization of fifteen novel microsatellite loci in golden mandarin fish (Siniperca scherzeri) Steindachne

We described the isolation and characterization of 15 new microsatellite loci from golden mandarin fish, Siniperca scherzeri. The analysis of variability was performed in 34 individuals. Allelic diversity ranged from 2 to 7 alleles per locus, with observed and expected heterozygosities ranging from 0.294 to 1.000 and 0.261 to 0.740, respectively. Seven loci deviated significantly from Hardy–Weinberg equilibrium after Bonferroni correction, and no significant linkage disequilibrium were found among 15 pairs of loci following the Bonferroni correction. These are the first microsatellite markers characterized from the S. scherzeri. We expect these microsatellite markers to be useful for population genetic studies in this species.

Population genetic structure of Siniperca chuatsi in the middle reach of the Yangtze River inferred from mitochondrial DNA and microsatellite loci

Abstract The Chinese mandarin fish (Siniperca chuatsi) is currently one of the most important economic freshwater fish in China, whereas the wild resource has declined dramatically in recent years. In this study, we examined the genetic structure and diversity of five populations from the middle reach of the Yangtze River using mitochondrial cytochrome b sequences and microsatellite markers. This research revealed high genetic diversity and low genetic differentiation of S. chuatsi from these regions. The pairwise Fst values of the two markers showed low and no-significant differentiation among populations. AMOVA analysis of two markers and the haplotype genealogy of the Cytb gene confirmed these results. The STRUCTURE analysis of the microsatellite marker implied that the dam upon the tributary of the Yangtze River blocked the gene flow among those regions. This research will be useful in breeding programs and conservation management of this species.

Isolation and Characterization of Novel Genomic and EST-SSR Markers in Coreoperca whiteheadi Boulenger and Cross-Species Amplification

We described and characterized 11 expressed sequence tag (EST)-derived simple sequence repeats (SSR) and seven genomic (G)-derived SSRs in Coreoperca whiteheadi Boulenger. The EST-SSRs comprised 62.2% di-nucleotide repeats, 32.2% tri-nucleotide repeats and 5.5% tetra-nucleotide repeats, whereas the majority of the G-SSRs were tri-nuleotide repeats (81.4%). The number of alleles for the 18 loci ranged from 3 to 6, with a mean of 3.8 alleles per locus. The observed (Ho) and expected heterozygosities (He) values ranged from 0.375 to 1.000, and 0.477 to 0.757, respectively. The polymorphic information content (PIC) values ranged from 0.466 to 0.706. The mean values number of alleles, Ho, He, and PIC of EST-SSRs were higher than those of the G-SSRs. Four microsatellite loci deviated significantly from Hardy-Weinberg equilibrium (HWE) after Bonferroni correction and no significant deviations in linkage disequilibrium (LD) were observed. These loci are the first to be characterized in C. whiteheadi and should be useful in the investigation of a genetic evaluation for conservation. Compared with 11 loci in C. whiteheadi, 37 potential polymorphic EST-SSRs were found in Siniperca chuatsi (Basilewsky), which will provide a valuable tool for mapping studies and molecular breeding programs in S. chuatsi.

Development and characterization of twenty-nine novel polymorphic microsatellite loci in the mandarin fish Siniperca chuatsi

Mandarin fish Siniperca chuatsi (Basilewsky), mainly distributed in the Yangtze and Pearl rivers, is an important commercial freshwater fish species in China (Liang 1996). It has a fast growth rate, but is susceptible to diseases. Compared with S. chuatsi, golden mandarin fish S. scherzeri (Steindachner) has great disease resistance, but grows slowly. Since the hybrid retained desired characteristics such as fast growth rate and great disease resistance from their parents (Mi et al. 2009), breeding a disease-resistant and faster growing strain has been attracting more and more attention from researchers. However, the research mainly focussed on the morphology of the hybrid (Zhao et al. 2008; Mi et al. 2009), very little was known about its genetic variation. Microsatellites, also known as simple sequence repeats (SSRs), have become a useful tool to assess genetic diversity and develop molecular breeding technique in fish because of their codominant nature and high allelic polymorphism (Walter and Epperson 2001; Chen et al. 2005). Nevertheless, only a few microsatellite markers are available for S. chuatsi (Zhang et al. 2006; Kuang et al. 2007a, b, 2009; Liu et al. 2011; Qu et al. 2012) and S. scherzeri (Qu et al. 2012; Yang et al. 2012). The number of available SSRs is grossly inadequate for genetic and mapping studies. These research areas have long suffered from one of the challenges of systematic biology studies, namely the lack of genomic resources such as genome or transcriptome sequences. Hence, there is a need to enhance such resources. With the advent of nextgeneration sequencing technologies, transcriptome sequencing is emerging as a rapid and efficient means for gene discovery and genetic marker development. As hybrid gene

The complete mitochondrial genome of the hybrid of Siniperca chuatsi (♀) × Siniperca scherzeri (♂)

Abstract In this study, we determined the complete mitochondrial DNA sequence of the hybrid of Siniperca chuatsi (♀) × Siniperca scherzeri (♂). The total length of the hybrid mitogenome is 16,497 bp, with the base composition of 28.61% A, 29.16% C, 16.23% G, and 26.00% T. It contains 2 rRNA genes, 13 protein-coding genes, 22 tRNA genes, and 1 control region. The composition and order of these genes are identical to most of other vertebrates. All the protein-coding genes start with ATG, except for COX1 with the initiation codon GTG. Three types of stop codons are used by the coding genes, including complete stop codons (TAA and TAG) and an incomplete stop codon (T). Three conserved domains were observed in the control region. The complete mitogenome of the hybrid of S. chuatsi (♀) × S. scherzeri (♂) could contribute to a better solution of the study in mitochondrial inheritance mechanism.

The complete mitochondrial genome sequence of Coreoperca whiteheadi (Perciformes: Serranidae)

Abstract In this paper, the complete mitochondrial DNA (mtDNA) sequence of Coreoperca whiteheadi was determined. The complete mtDNA genome sequence of C. whiteheadi is 16,483 bp in length. It consists of 13 protein-coding genes, 22 transfer RNA genes, 2 rRNA genes and 2 non-coding regions. Overall base composition of mitogenome is estimated to be 28.30% for A, 29.33% for C, 16.06% for G and 26.32% for T, respectively, with a high A + T content (54.62%). The complete mitogenome of the C. whiteheadi could contribute to basic researches on population history, molecular systematics and phylogeography. It is also helpful to the reasonable utilization and development of rational management strategies for C. whiteheadi resource.

The complete mitochondrial genome sequence of Siniperca undulate (Perciformes: Percichthyidae)

Abstract In this paper, the complete mitochondrial DNA (mtDNA) sequence of Siniperca undulate was determined. The complete mtDNA genome sequence of S. undulate was 16,504 bp in length. It consisted of 13 protein-coding genes, 22 transfer RNA genes, 2 rRNA genes and 2 non-coding regions. Overall base composition of mitogenome was estimated to be 28.38% for A, 29.43% for C, 16.46% for G and 25.73% for T, respectively, with a high A + T content (54.11%). The complete mitogenome of the S. undulate can provide a basic data for the studies on population history, molecular systematics, phylogeography, stock evaluation and conservation genetics. It is also helpful to the reasonable utilization and development of rational management strategies for S. undulate resource.

The complete mitochondrial genome of the hybrid ofSiniperca scherzeri(♀) × Siniperca chuatsi(♂)

Abstract In the present study, the complete mitogenome of the hybrid of Siniperca scherzeri (♀) × Siniperca chuatsi (♂) is determined to be 16,504 bp long and showed a typical vertebrate pattern with 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. The base composition of heave strand in descending order is C (29.61%), A (28.31%), T (25.61%) and G (16.47%), with a slight AT bias of 53.92%. All the protein-coding genes are initiated by typical ATG codon, except for COX1 gene with the initiation codon GTG. Nine genes end with the complete stop codon TAA or TAG, while the COX1, COX2, ND4 and CYTB genes terminate with an incomplete stop codon T. The complete mitogenome of the hybrid of S. scherzeri (♀) × S. chuatsi (♂) could provide an important data set for the study in mitochondrial inheritance mechanism.

The complete mitochondrial genome of the hybrid of Siniperca kneri (♀) × Siniperca chuatsi (♂)

Abstract The complete mitochondrial genome sequence of the hybrid of Siniperca kneri (♀) × Siniperca chuatsi (♂) is described in this study. The 16,488 bp long circular molecule consisted of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region, showed a typical vertebrate pattern. The overall base composition of the heavy strand is 28.59% A, 29.20% C, 16.25% G, and 25.96% T, with a slight AT bias of 54.55%. Except for eight tRNA and ND6 genes, all other mitochondrial genes are encoded on the heavy strand. There are 5 regions of gene overlap totaling 14 bp and 20 intergenic spacer regions totaling 91 bp. The complete mitogenome of the hybrid of S. kneri (♀) × S. chuatsi (♂) could provide an important data set for the study in mitochondrial inheritance mechanism.