Cloning and identification of a female-specific DNA marker in Paramisgurnus dabryanus

Identification of sex-specific markers using genome re-sequencing in the blunt snout bream (Megalobrama amblycephala)

BACKGROUND

The blunt snout bream (Megalobrama amblycephala) is an important economic freshwater fish in China with tender flesh and high nutritional value. With the cultivation of superior new varieties and the expansion of breeding scale, it becomes imperative to employ sex-control technology to cultivate monosexual populations of M. amblycephala, thereby preventing the deterioration of desirable traits. The development of specific markers capable of accurately identifying the sex of M. amblycephala would facilitate the determination of the genetic sex of the breeding population before gonad maturation, thereby expediting the processes of sex-controlled breeding of M. amblycephala.

RESULTS

A whole-genome re-sequencing was performed for 116 females and 141 males M. amblycephala collected from nine populations. Seven candidate male-specific sequences were identified through comparative analysis of male and female genomes, which were further compared with the sequencing data of 257 individuals, and finally three male-specific sequences were generated. These three sequences were further validated by PCR amplification in 32 males and 32 females to confirm their potential as male-specific molecular markers for M. amblycephala. One of these markers showed potential applicability in M. pellegrini as well, enabling males to be identified using this specific molecular marker.

CONCLUSIONS

The study provides a high-efficiency and cost-effective approach for the genetic sex identification in two species of Megalobrama. The developed markers in this study have great potential in facilitating sex-controlled breeding of M. amblycephala and M. pellegrini, while also contributing valuable insights into the underlying mechanisms of fish sex determination.

Exploration of an XX/XY Sex Determination System and Development of PCR-Based Sex-specific Markers in Procambarus clarkii Based on Next-Generation Sequencing Data

Many economic crustacean species have sex dimorphisms during their growth. Exploring the sex determination system and developing sex-specific molecular marker(s) are very helpful for carrying out sex control breeding, and next-generation sequencing has been used as an efficient way to explore them in recent years. In this study, first, the genetic sex determination system of P. clarkii was explored as an XX/XY system by analyzing the 2b-RAD sequencing data. Furthermore, DNA samples of male and female individuals from a P. clarkii family were pooled separately for whole-genome resequencing. Based on the data of whole-genome resequencing, the 9,163 male- and female-specific bias sites with higher feasibility were obtained based on the assumption of the XX/XY sex determination system, and four sites were selected to design the sex-specific marker primers. One efficient sex-specific marker was identified with a sex discrimination rate of 99.49% (195/196) when applied to five different geographical groups with 196 individuals. The results of this study would provide a foundation for the realization of P. clarkii sex control and could provide some reference for investigating the sex determination system and sex molecular marker(s) of other crustacean species based on next-generation sequencing data.

Assessing the risk of insecticides to Actinopterygii in the combination of ecological planting and rearing

In order to study the co-existing environment of pests and economic animals, the toxicity of 15 insecticides to Plutella xylostella, Monopterus albus, and Paramisgurnus dabryanus was tested. Combined with the recommended maximum doses in the field and bioassay, the results showed that for the three insecticides that were of relatively low toxicity to M. albus and P. dabryanus, spinetoram showed the best control effect on P. xylostella, followed by chlorfenapyr and chlorantraniliprole. However, P. xylostella showed a relatively high resistance to chlorfenapyr. Therefore, the best insecticide suitable for the fields with the cauliflower-finless eel or cauliflower-loach planting and rearing combination was spinetoram, followed by chlorantraniliprole and chlorfenapyr. Other insecticides such as emamectin benzoate, Bacillus thuringiensis (Bt), matrine, and so on were effective against the diamondback moth, but they were not suitable for use because of their high toxicity to the finless eel and loach.

An effective live attenuated vaccine against Aeromonas veronii infection in the loach (Misgurnus anguillicaudatus)

Aeromonas veronii is a major pathogenic bacterium in humans and animals. When it causes outbreaks, there are enormous economic losses to the aquaculture industry. An effective live attenuated vaccine strain, ΔhisJ, was obtained in our previous studies by gene knockout in Aeromonas veronii TH0426 using the suicide vector pRE112. Here, we evaluated whether the live attenuated vaccine ΔhisJ was suitable for prevention of Aeromonas veronii infection by injection and immersion in loaches. Compared with that of the TH0426 wild-type strain, the virulence of the live vaccine was significantly weakened. Vaccine safety assessment results also indicated that 1 × 10⁷ CFU/mL live vaccine was safe and did not induce clinical symptoms or obvious pathological changes. Additionally, after challenging loaches with Aeromonas veronii TH0426, the relative percent survival of the IN3 injection group was 65.66%, and that of the IM group was 50.78%. Our data show that the live attenuated vaccine ΔhisJ can improve the immune protection rate of loaches. Furthermore, increased enzyme activity parameters (SOD, LZM, ACP, and AKP) in the skin mucus, increased enzyme activity parameters (SOD, LZM, ACP, AKP, and GPx) in the serum, increased specific IgM antibodies and cytokine IL-1β contents in the serum, and increased cytokine (IL-15, pIgR, IL-1β, and TNF-α) expression in the liver and spleen were observed. These data are the first to indicate that the live attenuated vaccine ΔhisJ is suitable for the development of a safe and effective vaccine against Aeromonas veronii infection in loach aquaculture.

The growth performance and nonspecific immunity of loach Paramisgurnus dabryanus as affected by dietary β-1,3-glucan

Four diets supplemented with three different levels of β-1,3-glucan (0.5, 1, and 2 g kg^-1) were formulated and tested for growth, intestine digestive-enzyme activities, PO, SOD and GPx activities and erythrocytes number, phagocytic percentage of erythrocytes and lysozyme activity and resistance to Aeromonas hydrophila of loach Paramisgurnus dabryanus. A diet without any β-1,3-glucan served as the control. After 60 days of feeding, the growth performance, intestine digestive-enzyme activities, nonspecific immunity, and resistance to Aeromonas hydrophila of P. dabryanus were higher than those of the control when the loaches P. dabryanus were fed with β-1,3-glucan-containing diets. Results revealed that dietary β-1,3-glucan can improve the growth performance, intestine digestive-enzyme activities, PO, SOD and GPx activities and erythrocytes number, phagocytic percentage of erythrocytes and lysozyme activity and resistance of loaches P. dabryanus and can thus be used as their diet supplement.

Identification of Sex-Specific Markers Reveals Male Heterogametic Sex Determination in Pseudobagrus ussuriensis

Comprehending sex determination mechanism is a first step for developing sex control breeding biotechnologies in fish. Pseudobagrus ussuriensis, one of bagrid catfishes in Bagridae, had been observed to have about threefold size dimorphism between males and females, but its sex determination mechanism had been unknown. In this study, we firstly used the amplified fragment length polymorphism (AFLP)-based screening approach to isolate a male-specific DNA fragment and thereby identified a 10,569 bp of male-specific sequence and a 10,365 bp of female-related sequence by genome walking in the bagrid catfish, in which a substantial genetic differentiation with 96.35 % nucleotide identity was revealed between them. Subsequently, a high differentiating region of 650 bp with only 70.26 % nucleotide identity was found from the corresponding two sequences, and three primer pairs of male-specific marker, male and female-shared marker with different length products in male and female genomes, and female-related marker were designed. Significantly, when these markers were used to identify genetic sex of the bagrid catfish, only male individuals was detected to amplify the male-specific marker fragment, and female-related marker was discovered to produce dosage association in females and in males. Our current data provide significant genetic evidence that P. ussuriensis has heterogametic XY sex chromosomes in males and homogametic XX sex chromosomes in females. Therefore, sex determination mechanism of P. ussuriensis is male heterogametic XX/XY system.

Mitochondrial genome sequence of Paramisgurnus dabryanus from the Yellow River estuary: implication for Cobitidae phylogeny

Paramisgurnus dabryanus Sauvage (Cobitidae, Cypriniformes) is a native large-scale loach widely distributed in main inland freshwater systems of China. The complete mitochondrial genome sequence of P. dabryanus from the Yellow River (YR) estuary was characterized in the present study. The circular mitogenome is 16 570 bp in size and contains two ribosomal RNA genes, 22 transfer RNA genes, and 13 protein-coding genes. The overall A + T content is 56.64% in the range of other Cobitidae studied. The mitogenome of P. dabryanus YR has an overall nucleotide sequence identity of 96.9% with that from Zhejiang, and 89.2% with that from Hubei. All the Misgurnus and Paramisgurnus species were clustered into two Misgurnus/Paramisgurnus complex clades with high bootstrap values based on the whole mitogenome sequences. The mitochondrial phylogenomic analysis indicates that the relationships in Cobitidae are inconsistent with the current classification system and taxonomic revision is required on the basis of molecular phylogeny and morphology.

A transcriptome derived female-specific marker from the invasive Western mosquitofish (Gambusia affinis)

Sex-specific markers are a prerequisite for understanding reproductive biology, genetic factors involved in sex differences, mechanisms of sex determination, and ultimately the evolution of sex chromosomes. The Western mosquitofish, Gambusia affinis, may be considered a model species for sex-chromosome evolution, as it displays female heterogamety (ZW/ZZ), and is also ecologically interesting as a worldwide invasive species. Here, de novo RNA-sequencing on the gonads of sexually mature G. affinis was used to identify contigs that were highly transcribed in females but not in males (i.e., transcripts with ovary-specific expression). Subsequently, 129 primer pairs spanning 79 contigs were tested by PCR to identify sex-specific transcripts. Of those primer pairs, one female-specific DNA marker was identified, Sanger sequenced and subsequently validated in 115 fish. Sequence analyses revealed a high similarity between the identified sex-specific marker and the 3´ UTR of the aminomethyl transferase (amt) gene of the closely related platyfish (Xiphophorus maculatus). This is the first time that RNA-seq has been used to successfully characterize a sex-specific marker in a fish species in the absence of a genome map. Additionally, the identified sex-specific marker represents one of only a handful of such markers in fishes.

Effects of dietary selenium on the pathological changes and oxidative stress in loach (Paramisgurnus dabryanus)

In this study, loach (Paramisgurnus dabryanus) were fed artificial diets containing 0.31 (control), 0.39, 0.48, 0.50 and 0.62 mg kg(-1) of selenium (Se) for 60 days, respectively. Liver histopathology, hepatocyte ultrastructure, blood indices, biochemical parameters of liver functions and oxidative stress in the Se-treated loach were then assayed. The results showed the following: histopathological and ultrastructural lesions in liver were only observed in loach fed the 0.62 mg Se kg(-1) diet; Haemoglobin and total protein were significantly increased in the 0.50 mg Se kg(-1) group; albumin and high-density lipoprotein were increased significantly in the 0.48-0.50 mg Se kg(-1) groups. However, white blood cell count was significantly decreased in the 0.48 mg Se kg(-1) group; alanine aminotransferase, aspartate aminotransferase and lactate dehydrogenase were decreased in the 0.39-0.50 mg Se kg(-1) groups. In liver tissue, the content of hydrogen peroxide was lower than that of controls in the 0.48-0.50 mg Se kg(-1) groups, and the malondialdehyde level was lowest in the 0.48 mg Se kg(-1) group. The activities of superoxide dismutase and glutathione peroxidase were significantly increased in the 0.50 mg Se kg(-1) group; catalase and total antioxidant capacity were markedly increased in the 0.48-0.50 mg Se kg(-1) group. These present results indicated that the dietary Se requirement for loach is 0.48-0.50 mg Se kg(-1) diet.

Genetic differentiation and efficient sex-specific marker development of a pair of Y- and X-linked markers in yellow catfish

Pf62-Y and Pf62-X is a pair of allelic Y chromosome-linked and X chromosome-linked markers, and have been used to identify YY super-males, XY males and XX females for commercial production of all-male populations in yellow catfish (Pelteobagrus fulvidraco). However, the SCAR primers used previously have only two nucleotide difference, which restricts the wide utility because of nucleotide polymorphism. In this study, a continuous 8102 bp Pf62-Y sequence and a 5362 bp Pf62-X sequence have been cloned by genome walking, and significant genetic differentiation has been revealed between the corresponding X and Y chromosome allele sequences. Moreover, three pairs of primers were designed to efficiently identify YY super-males, XY males and XX females in an artificial breeding population, and to distinguish XY males and XX females in various wild populations. Together, the three new sex-specific genetic markers develop a highly stable and efficient method for genetic sex identification and sex control application in sustainable aquaculture of all-male yellow catfish.

An AFLP-based approach for the identification of sex-linked markers in blunt snout bream, Megalobrama amblycephala (Cyprinidae)

Sex-specific DNA markers are useful for studying sex-determination mechanisms and establishment of monosex populations. Three widely spaced geographical populations (Liangzi, Poyang and Yuni Lakes in China) of blunt snout bream (Megalobrama amblycephala) were screened with AFLPs to search for sex-linked markers. Female and male pools (10 individuals in each pool) from each population were screened using 64 different primer combinations. A total of 4789 genomic fragments were produced, with a mean frequency of 75 bands per primer pair. Three different primer combinations produced putative sex-associated amplifications and were selected for individual screening in the three populations. However, none showed sex specificity when we converted these three markers into sequence characterized amplified region markers and evaluated all the individuals from the three populations.