Han-Ping Wang

Molecular players involved in temperature-dependent sex determination and sex differentiation in Teleost fish

The molecular mechanisms that underlie sex determination and differentiation are conserved and diversified. In fish species, temperature-dependent sex determination and differentiation seem to be ubiquitous and molecular players involved in these mechanisms may be conserved. Although how the ambient temperature transduces signals to the undifferentiated gonads remains to be elucidated, the genes downstream in the sex differentiation pathway are shared between sex-determining mechanisms. In this paper, we review recent advances on the molecular players that participate in the sex determination and differentiation in fish species, by putting emphasis on temperature-dependent sex determination and differentiation, which include temperature-dependent sex determination and genetic sex determination plus temperature effects. Application of temperature-dependent sex differentiation in farmed fish and the consequences of temperature-induced sex reversal are discussed.

Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research

Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships. In addition, it is also important to understand the mechanisms of regulation and evolutionary conservation at the levels of genome, transcriptome, proteome, epigenome, and systems biology. With genomic information and information between the genomes and phenomes, technologies for marker/causal mutation-assisted selection, genome selection, and genome editing can be developed for applications in aquaculture. A set of genomic tools and resources must be made available including reference genome sequences and their annotations (including coding and non-coding regulatory elements), genome-wide polymorphic markers, efficient genotyping platforms, high-density and high-resolution linkage maps, and transcriptome resources including non-coding transcripts. Genomic and genetic control of important performance and production traits, such as disease resistance, feed conversion efficiency, growth rate, processing yield, behaviour, reproductive characteristics, and tolerance to environmental stressors like low dissolved oxygen, high or low water temperature and salinity, must be understood. QTL need to be identified, validated across strains, lines and populations, and their mechanisms of control understood. Causal gene(s) need to be identified. Genetic and epigenetic regulation of important aquaculture traits need to be determined, and technologies for marker-assisted selection, causal gene/mutation-assisted selection, genome selection, and genome editing using CRISPR and other technologies must be developed, demonstrated with applicability, and application to aquaculture industries. Major progress has been made in aquaculture genomics for dozens of fish and shellfish species including the development of genetic linkage maps, physical maps, microarrays, single nucleotide polymorphism (SNP) arrays, transcriptome databases and various stages of genome reference sequences. This paper provides a general review of the current status, challenges and future research needs of aquaculture genomics, genetics, and breeding, with a focus on major aquaculture species in the United States: catfish, rainbow trout, Atlantic salmon, tilapia, striped bass, oysters, and shrimp. While the overall research priorities and the practical goals are similar across various aquaculture species, the current status in each species should dictate the next priority areas within the species. This paper is an output of the USDA Workshop for Aquaculture Genomics, Genetics, and Breeding held in late March 2016 in Auburn, Alabama, with participants from all parts of the United States.Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships. In addition, it is also important to understand the mechanisms of regulation and evolutionary conservation at the levels of genome, transcriptome, proteome, epigenome, and systems biology. With genomic information and information between the genomes and phenomes, technologies for marker/causal mutation-assisted selection, genome selection, and genome editing can be developed for applications in aquaculture. A set of genomic tools and resources must be made available including reference genome sequences and their annotations (including coding and non-coding regulatory elements), genome-wide polymorphic markers, efficient genotyping platforms, high-density and high-resolution linkage maps, and transcriptome resources including non-coding transcripts. Genomic and genetic control of important performance and production traits, such as disease resistance, feed conversion efficiency, growth rate, processing yield, behaviour, reproductive characteristics, and tolerance to environmental stressors like low dissolved oxygen, high or low water temperature and salinity, must be understood. QTL need to be identified, validated across strains, lines and populations, and their mechanisms of control understood. Causal gene(s) need to be identified. Genetic and epigenetic regulation of important aquaculture traits need to be determined, and technologies for marker-assisted selection, causal gene/mutation-assisted selection, genome selection, and genome editing using CRISPR and other technologies must be developed, demonstrated with applicability, and application to aquaculture industries.Major progress has been made in aquaculture genomics for dozens of fish and shellfish species including the development of genetic linkage maps, physical maps, microarrays, single nucleotide polymorphism (SNP) arrays, transcriptome databases and various stages of genome reference sequences. This paper provides a general review of the current status, challenges and future research needs of aquaculture genomics, genetics, and breeding, with a focus on major aquaculture species in the United States: catfish, rainbow trout, Atlantic salmon, tilapia, striped bass, oysters, and shrimp. While the overall research priorities and the practical goals are similar across various aquaculture species, the current status in each species should dictate the next priority areas within the species. This paper is an output of the USDA Workshop for Aquaculture Genomics, Genetics, and Breeding held in late March 2016 in Auburn, Alabama, with participants from all parts of the United States.

The Effects of Size Grading on Production Efficiency and Growth Performance of Yellow Perch in Earthen Ponds

Abstract The culture of yellow perch Perca flavescens has received considerable interest in the Midwest and elsewhere in the USA as a result of the decline of wild populations and their high market demand. In this study, the effects of size-grading on the production efficiency and growth performance of food-sized yellow perch were determined in six 0.1-ha ponds by grading fingerlings into three size-groups (mean initial size): small (5.3 g), large (18.3 g), and unsorted (11.3 g). The mean percentage of marketable production from large-group ponds was significantly greater than that from the small- and ungraded-group ponds. The final biomass of large size-groups was 77% and 27% greater than that of small and ungraded groups, respectively, although no significant differences in total production were detected among the three size-groups. Size-sorting of fingerling yellow perch did not result in improved growth of the small-fish group. No significant differences in growth rates among the three groups were det...

Inherent Growth Capacity and Social Costs of Bluegill and Hybrids of Bluegill and Green Sunfish: Which Fish Really Grows Faster?

Abstract There is interest in knowing whether the bluegill Lepomis macrochirus or a hybrid of bluegill and green sunfish L. cyanellus (F1: male bluegill × female green sunfish; hereafter called B × G hybrids) can be grown faster to food market size (225–340 g). The predominant view is that the hybrid grows faster. In this study, the inherent growth capacities (IGCs) of age-1 bluegills and B × G hybrids were determined over four successive 25-d periods (May–August 2000) by holding them individually at 22°C and feeding them to apparent satiation three times daily. The hybrids IGC was greater during period 1 but fell to only 33% of the bluegills over the three subsequent periods; the consumption and gross growth efficiency (GGE) of the hybrid showed similar declining patterns. The growth-in-weight trajectory of bluegills crossed above that of the hybrids at about 30 g. Gonadosomatic index values suggested that hybrid growth rates declined below those of the bluegill because the former invested more energy ...

Physiological Stress Response of Yellow Perch Subjected to Repeated Handlings and Salt Treatments at Different Temperatures

Abstract Yellow Perch Perca flavescens were subjected to handling stress and salt treatments at different temperatures to determine their physiological changes. Yellow Perch, held at 8–10°C, were divided into three groups with four replicates and subjected to water temperatures of 14, 20, and 26°C to acclimate. Then they were subjected to acute handling twice within separate intervals, in addition to a salt treatment at a salinity of 5‰ for each of the fish groups. Plasma cortisol was used as a stress indicator, and blood samples were taken periodically for plasma cortisol concentration analysis. An increase in plasma cortisol after handling occurred in all groups, but the lowest level of plasma cortisol was in fish subjected to 20°C. We concluded that the optimum water temperature for handling Yellow Perch that results in minimal stress may be 20°C. Salt treatment after handling further stimulated the stress response and increased plasma cortisol levels. Research is needed to identify the optimal salinit...

Isolation and Characterization of Novel Microsatellite Markers for Yellow Perch (Perca flavescens)

To perform whole genome scanning for complex trait analysis, we isolated and characterized a total of 21 novel genomic-SSRs and EST-SSRs for yellow perch (Perca flavescens), using the methods of construction of SSR-enrichment libraries and EST database mining of a related species P. fluviatilis. Of 16 genomic-SSR primer pairs examined, eight successfully amplified scorable products. The number of alleles at these informative loci varied from 3 – 14 with an average of 8.5 alleles per locus. When tested on wild perch from a population in Pennsylvania, observed and expected heterozygosities ranged from 0.07 – 0.81 and from 0.37 – 0.95, respectively. Of 2,226 EST sequences examined, only 110 (4.93%) contained microsatellites and for those, 13 markers were tested, 12 of which exhibited polymorphism. Compared with genomic-SSRs, EST-SSRs exhibited a lower level of genetic variability with the number of alleles of averaging only 2.6 alleles per locus. Cross-species utility indicated that three of the genomic-SSRs and eight of the EST-SSRs successfully cross-amplified in a related species, the walleye (Sander vitreus).

Evaluation of 1-stage and 2-stage selection in yellow perch I: Genetic and phenotypic parameters for body weight of F1 fish reared in ponds using microsatellite parentage assignment1

Two selection methods, 1-stage selection (OSS) and 2-stage selection (TSS), for improving efficiency and profitability of selective breeding of yellow perch were evaluated, through examining the genetic and phenotypic parameters for BW of F(1) fish using microsatellite parentage assignment in this study. Approximately 94% of the sampled yellow perch progeny were assigned to single parental pairs using 8 microsatellite markers, which confirmed the applicability of the communal rearing technique in yellow perch breeding. Within OSS, the genetic correlation between 1-yr-BW and 2-yr-BW was high (0.98), indicating that the growth of yellow perch recorded at yr 1 could predict their growth for yr 2. Also mean family BW and family EBV for BW between yr 1 and 2 were found to be significantly correlated, suggesting yr 1 fast-growing yellow perch families continued to be the fast growing families in yr 2. Two-year random fish undergoing TSS were significantly heavier (P < 0.01) than those undergoing OSS. In addition, top males and females with TSS were heavier (P < 0.01) than those with OSS. Based on these results we concluded that the TSS was more desirable and effective for yellow perch breeding compared with OSS in terms of improving selection efficiency and reducing costs.

Comparative and evolutionary analysis in natural diploid and tetraploid weather loach Misgurnus anguillicaudatus based on cytochrome b sequence data in central China

To obtain the phylogenetic relationship between diploid and tetraploid Misgurnus anguillicaudatus, the mitochondrial cyt b gene in the diploid and tetraploid weather loach were isolated and sequenced. The DNA sequences were analyzed using MEGA 3.0 software to determine the phylogenetic relationship. Forty-five variable sites among cyt b gene sequences and 18 amino acid substitutions occurred within the diploid and tetraploid loaches as deduced from the nucleotide sequences analysis of the cyt b gene. The nucleotide pairwise distance between diploid and tetraploid loach ranged from 0.001 to 0.025. Phylogenetic analysis revealed evolutionary relationships between diploid and tetraploid loach. Our results indicated a significant difference between diploid and tetraploid loach about the cyt b gene. AMOVA analysis indicated that there were no significant genetic variations within diploid loaches (Fst = 0.2529, P > 0.05) and within tetraploid loaches (Fst = 0.0564, P > 0.05), neither. However, significant genetic differences were found between diploid and tetraploid loaches (Fst = 0.7634, P < 0.05). Thus, it is concluded that no reproductive isolation was found within the same cytotypes of different localities, but there was reproductive isolation between these two cytotypes. The diploid loach existed before the tetraploid loach in nature. The present study is the first to describe the phylogenetic relationships of natural polyploidy weather loach using mtDNA cyt b gene.

Establishment of mostly male groups of bluegills by grading selection and evaluation of their growth performance.

Abstract Concerns over the economic feasibility of commercial aquaculture production of bluegills Lepomis macrochirus have heightened the need for strategies to enhance growth. Recent studies have shown that individually reared bluegill males can grow twice as fast as females; such studies have generated increased interest in development of mostly male or all-male populations. In this study, we developed a practical procedure to establish mostly male bluegill groups through grading selection and we tested their growth against that of a normal population. A single cohort of bluegill juveniles was cultured in a pond for 1 year; when the fish reached a mean weight of 30.1 g, the cohort was graded and divided into two mostly male groups (top 25% and top 50% of fish by total length) and a mixed-sex control group. The percentage of males in each group was as follows: 50.0% in the mixed control group, 75.4% in the top 25% group, and 69.7% in the top 50% group. Weight gain per fish in the top 25% group was signif...

De novo transcriptome sequencing and analysis of male, pseudo-male and female yellow perch, Perca flavescens

Transcriptome sequencing could facilitate discovery of sex-biased genes, biological pathways and molecular markers, which could help clarify the molecular mechanism of sex determination and sexual dimorphism, and assist with selective breeding in aquaculture. Yellow perch has unique gonad system and sexual dimorphism and is an alternative model to study mechanism of sex determination, sexual dimorphism and sexual selection. In this study, we performed the de novo assembly of yellow perch gonads and muscle transcriptomes by high throughput Illumina sequencing. A total of 212,180 contigs were obtained, ranging from 127 to 64,876 bp, and N50 of 1,066 bp. The assembly RNA-Seq contigs (≥200bp) were then used for subsequent analyses, including annotation, pathway analysis, and microsatellites discovery. No female- and pseudo-male-biased genes were involved in any pathways while male-biased genes were involved in 29 pathways, and neuroactive ligand receptor interaction and enzyme of trypsin (enzyme code, EC: 3.4.21.4) was highly involved. Pyruvate kinase (enzyme code, EC: 2.7.1.40), which plays important roles in cell proliferation, was highly expressed in muscles. In addition, a total of 183,939 SNPs, 11,286 InDels and 41,479 microsatellites were identified. This study is the first report on transcriptome information in Percids, and provides rich resources for conducting further studies on understanding the molecular basis of sex determinations, sexual dimorphism, and sexual selection in fish, and for population studies and marker-assisted selection in Percids.