Construction of a high-density genetic map and mapping of growth related QTLs in the grass carp (Ctenopharyngodon idellus)

AbstractBackgroundGrass carp (Ctenopharyngodon idellus) are important species in Asian aquaculture. A draft genome for grass carp has already been published in 2015. However, there is still a requirement for a suitable genetic linkage map to arrange scaffolds on chromosomal frameworks. QTL analysis is a powerful tool to detect key locations for quantitative traits, especially in aquaculture. There no growth related QTLs of grass carp have been published yet. Even the growth trait is one of the focuses in grass carp culture.ResultsIn this study, a pair of distantly related parent grass carps and their 100 six-month-old full-sib offspring were used to construct a high-density genetic map with 6429 single nucleotide polymorphisms (SNPs) by 2b-RAD technology. The total length of the consensus map is 5553.43?cM with the average marker interval of 1.92?cM. The map has a good collinearity with both the grass carp draft genome and the zebrafish genome, and it assembled 89.91% of the draft genome to a chromosomal level. Additionally, according to the growth-related traits of progenies, 30 quantitative trait loci (QTLs), including 7 for body weight, 9 for body length, 5 for body height and 9 for total length, were identified in 16 locations on 5 linkage groups. The phenotypic variance explained for these QTLs varies from 13.4 to 21.6%. Finally, 17 genes located in these regions were considered to be growth-related because they either had functional mutations predicted from the resequencing data of the parents.ConclusionA high density genetic linkage map of grass carp was built and it assembled the draft genome to a chromosomal level. Thirty growth related QTLs were detected. After the cross analysis of Parents resequencing data, 17 candidate genes were obtained for further researches.</p

Modeling the Ecological Response of a Temporarily Summer-Stratified Lake to Extreme Heatwaves

Climate extremes, which are steadily increasing in frequency, can have detrimental consequences for lake ecosystems. We used a state-of-the-art, one-dimensional, hydrodynamic-ecosystem model [General Ocean Turbulence Model (GOTM)-framework for aquatic biogeochemical models (FABM)-PCLake] to determine the influence of extreme climate events on a temperate and temporarily summer stratified lake (Lake Bryrup, Denmark). The model was calibrated (eight years data) and validated (two years data), and the modeled variables generally showed good agreement with observations. Then, a span of extreme warming scenarios was designed based on weather data from the heatwave seen over northern Europe in May-July 2018, mimicking situations of extreme warming returning every year, every three years, and every five years in summer and all year round, respectively. We found only modest impacts of the extreme climate events on nutrient levels, which in some scenarios decreased slightly when looking at the annual mean. The most significant impacts were found for phytoplankton, where summer average chlorophyll a concentrations and cyanobacteria biomass peaks were up to 39% and 58% higher than during baseline, respectively. As a result, the phytoplankton to nutrient ratios increased during the heat wave experiments, reflecting an increased productivity and an increased cycling of nutrients in the pelagic. The phytoplankton blooms occurred up to 15 days earlier and lasted for up to half a month longer during heat wave years relative to the baseline. Our extreme scenarios illustrated and quantified the large impacts of a past heat wave (observed 2018) and may be indicative of the future for many temperate lakes

Synergistic toxicity of microcystin-LR and Cu to zebrafish (Danio rerio)

Toxic cyanobacterial blooms often coincide with metal pollution in a freshwater environment because of surface run-off enriched with nutrients and metals. However, the joint toxic effects of cyanobacterial toxins and metals on aquatic animals remain unknown. In this study, single and joint toxic effects and mechanisms of microcystinLR (MCLR) and copper (Cu) were investigated in the early development of zebrafish (Danio rerio). The LC50(72)(-h) values were 2.79 mg/L for MCLR and 3.23 mg/L for Cu. The sublethal concentrations of MCLR (<= 600 mu g/L) did not affect the normal development of zebrafish but increased its hatchability. Strong synergistic toxic effects were observed after co-exposure to MCLR and Cu at environmental concentrations (<= 60 mu g/L). The synergistic toxic effects of these two compounds could be attributed to the increased bioaccumulation of MCLR and Cu, which was mediated by MCLR transporters (e.g., oatp1d1 and oatp2b1) and Cu transporters (e.g., ctr1 and atp7a), in zebrafish. Such bioaccumulation caused oxidative stress, as suggested by the disrupted gene expression of anti-oxidative enzymes (e.g., Cu/Zn-SOD, Mn-SOD, and CAT). Our results revealed for the first time the synergistic toxic effects and potential toxic mechanism of MCLR-Cu in aquatic animals. These synergistic effects should be considered when assessing the ecological risk of toxic cyanobacterial blooms. (C) 2019 Published by Elsevier B.V

Phylogenetic relationships of three Kudoa spp. with morphologically similar myxospores (K. iwatai, K. lutjanus, and K. bora), with the redescription of K. uncinata and K. petala and description of a new species (K. fujitai n. sp.) in fishes in the South China Sea

Members of the myxozoan genus Kudoa (Myxosporea: Multivalvulida: Kudoidae) are characterized as having four or more shell valves in a myxospore, with a corresponding number of polar capsules. Certain Kudoa spp. are critical pathogens in fish, causing postmortem myoliquefaction, unmarketable fish musculature due to unsightly macroscopic cysts, and reduced aquaculture production due to the outbreaks of neurological symptoms or cardiac diseases. Molecular genetic techniques have enabled the differentiation of Kudoa spp. with morphologically similar myxospores. In the present study, we employed integrated taxonomic approaches on five Kudoa spp. forming cysts between the trunk muscle myofibers (K. bora from Osteomugil perusii and K. lutjanus from Acanthopagrus latus), or cysts in the gallbladder wall (K. petala from Sillago sihama), and pseudocysts in the trunk muscle myofibers (K. uncinata from Nuchequula nuchalis and K. fujitai n. sp. from O. perusii). These four host fishes, which originated in the South China Sea, were purchased in the wet markets in Zhanjiang City, Guangdong Province, China, between August 2016 and April 2018. We have redescribed the four Kudoa spp. (K. bora, K. lutjanus, K. petala, and K. uncinata) on which little data are available after their original descriptions. Particularly, genetic characterization of K. bora and K. lutjanus, which are known to have myxospores morphologically similar to those of K. iwatai, was performed based on the nuclear ribosomal RNA gene and partial mitochondrial DNA genes such as cytochrome c oxidase subunit I and small and large ribosomal genes, demonstrating the validity and independence of these three kudoid species. We also provide description of a new species-K. fujitai n. sp.-in the present study. Application of integrated taxonomic approaches to known species characterized solely based on morphological criteria, as well as unknown species (e.g., K. fujitai n. sp. in the present study), contributes to better understanding of the biodiversity of Kudoa and multivalvulid myxosporeans

Alterations in biomass allocation indicate the adaptation of submersed macrophytes to low-light stress

The decline in submersed macrophytes induced by low-light stress is ubiquitous in mid-lower Yangtze lakes in China. However, the trade-offs among the adaptation mechanisms used by submersed macrophytes to low-light stress remain unclear. Moreover, the experimental period used in most previous studies was relatively short, and plant traits were not monitored multiple throughout the experimental period. In the present study, we examined the growth of a representative submersed macrophyte, Potamogeton maackianus, under four light regimes (2.8%, 7.1%, 17.1% and 39.5% of ambient light) over a course of 12 months and assessed various plant traits at monthly and quarterly intervals. The results showed that P. maackianus exhibited a lower leaf moisture content and a higher stem moisture content under decreased light conditions. Under the lowest light regime, P. maackianus had low soluble carbohydrate (SC) contents in the leaves and low starch contents in the stems at all the seasons. P. maackianus showed different allometric relationships among different treatments reflected different adaption strategies resulting from different light environment. P. maackianus exhibited a relatively stable biomass allocation pattern characterized by a continual increase in the stem mass fraction of total biomass under relatively high light transmittance (17.1% and 39.5%), which is a response of P. maackianus that can ensure a high initial biomass in the next spring season. However, under low light transmittance, the biomass allocation pattern fluctuated early in the experiment, and the amplitude increased with decreases in the light transmittance (2.8% and 7.1%). P. maackianus exhibited trade-offs between the stem (plant height) and leaf mass (leaf area) fractions of the total biomass, which help improve the adaptation of the macrophyte to a low-light environment. Our results can be useful for estimating light-use conditions of P. maackianus according to regression relationships between the leaf/stem mass fractions of the total biomass and time.</p

Species richness and biodiversity significance of alpine micro-waterbody systems in Gaoligong Mountain, Northwest Yunnan, China

Water quality, size, connectivity and other physical properties of hydrological systems might have different functions in the formation and maintenance of biodiversity, but this remains mostly unclear due to the lack of undisturbed sites for experimental modelling. Alpine freshwater habitats such as micro-waterbodies (MWB) represent a kind of natural system suitable for biodiversity research. In order to assess potential linkages between environmental factors, connectivity of MWBs and aquatic species richness, we conducted a pilot study in two separated MWB systems located in Gaoligong Mountain, northwest Yunnan province, China. A total of 27 MWBs have been analyzed, including 22 connected and 5 isolated bodies. 13 conventional environmental factors were tested while all kinds of aquatic macro-organisms were collected and classified. Results showed a high environmental heterogeneity among MWBs and significant differences between the two systems but only a few environmental variables such as the depth of soil bottom, total Nitrogen and altitude were related to species richness and the formation of the community structure. As a benefit from the high environmental heterogeneity, the cascaded MWB systems provided divergent habitats able to support species richness at a higher level than the same number of randomly selected MWBs. This finding supports the idea that habitat connectivity matters also in extremely small aquatic ecosystems. Moreover, although still a preliminary result, a polarization effect within connected chains where edge MWBs host higher taxa and endemic taxa richness as well as larger populations, was detectable. This study gives interesting insights on the spatial processes driving community structure and a new prospective for biodiversity conservation. Since alpine MWBs have significant effects on the maintenance of watershed biodiversity, further research on such small and crucial ecosystems is encouraged.</p

Sequencing and characterization of the macronuclear rDNA minichromosome of the protozoan Tetrahymena pyriformis

Tetrahymena ribosomal DNA (rDNA) is an ideal system for studying eukaryotic DNA replication and gene transcription. In this study, we developed a new method to isolate rDNA from Tetrahymena cells and used it to sequence and annotate the complete 19,670 bp macronudear rDNA minichromosome of Tetrahymena pyriformis, a species that lacks the germ-line micronucleus and is unable to undergo sexual reproduction. The key features of T. pyriformis and Tetrahymena thermophila rDNA sequences were then compared. Our results showed (i) the short inverted repeats (M repeats) essential for formation of rDNA minichromosome palindromic structure during sexual reproduction in Tetrahymena are highly conserved in T. pyriformis; (ii) in contrast to T. thermophila. which has two tandem domains that coordinately regulate rDNA replication, T. pyriformis has only a single domain; (iii) the 35S pre-rRNA precursor has 8025% similarity between the two species; and (iv) the G + C content is higher in the transcribed region than the non-transcribed region in both species, but the GC-skew is more stable in T. pyriformis. The new isolation method and annotated information for the T. pyriformis rDNA minichromosome will provide a useful resource for studying DNA replication and chromosome copy number control in Tetrohymena. (C) 2020 Elsevier B.V. All rights reserved.</p

Environmental Factors and Microbial Diversity and Abundance Jointly Regulate Soil Nitrogen and Carbon Biogeochemical Processes in Tibetan Wetlands

Wetlands have numerous critical ecological functions, some of which are regulated by several nitrogen (N) and carbon (C) biogeochemical processes, such as denitrification, organic matter decomposition, and methane emission. Until now, the underlying pathways of the effects of environmental and biological factors on wetland N and C cycling rates are still not fully understood. Here, we investigated soil potential/net nitrification, potential/unamended denitrification, methane production/oxidation rates in 36 riverine, lacustrine, and palustrine wetland sites on the Tibet Plateau. The results showed that all the measured N and C cycling rates did not differ significantly among the wetland types. Stepwise multiple regression analyses revealed that soil physicochemical properties (e.g., moisture, C and N concentration) explained a large amount of the variance in most of the N and C cycling rates. Microbial abundance and diversity were also important in controlling potential and unamended denitrification rates, respectively. Path analysis further revealed that soil moisture and N and C availability could impact wetland C and N processes both directly and indirectly. For instance, the indirect effect of soil moisture on methane production rates was mainly through the regulating the soil C content and methanogenic community structure. Our findings highlight that many N and C cycling processes in high-altitude and remote Tibetan wetlands are jointly regulated by soil environments and functional microorganisms. Soil properties affecting the N and C cycling rates in wetlands through altering their microbial diversity and abundance represent an important but previously underestimated indirect pathway

鱼类应激应对策略及其在抗逆育种中的应用

发展现代水产种业,引领水产养殖绿色发展,成为未来水产养殖业可持续发展的保障。应鼓励产业选育推广优质、高效、多抗、安全的水产养殖新品种,由单纯高产品种转向适宜生态化、集约化养殖模式的优质高效、节料节药、抗逆性强、适应性广的品种。本文分析了当前水产种业存在的一些问题,剖析了优质、高效、多抗水产养殖品种的耐应激本质,围绕应激反应、应激恢复、应激应对方式在畜禽种业中的应用案例等,提出了环境限制育种理念和未来综合性抗逆育种技术发展方向,助推水产养殖业的可持续发展

Identification and characterization of two mannan-binding lectin associated proteins in lectin complement pathway of grass carp

The lectin pathway of complement activation is an important component of the innate immune response, which must be tightly controlled to maintain immune homeostasis. However, its control mechanisms have not been investigated in detail in bony fish. In this study, we identified and characterized two novel, phylogenetically conserved mannan-binding lectin (MBL)-associated proteins (MAps) of grass carp (Ctenopharyngodon idella), CiMAp27 and CiMAp39, which were truncated, alternatively-spliced forms of grass carp MBL-associated serine proteases (MASPs), CiMASP1 and CiMASP2, respectively. Gene expression profiling showed that both CiMAp27 and CiMAp39 were upregulated by low doses of Aeromonas hydrophila, and inhibited by high doses, which lead to the inference that these genes acted as immune factors in antibacterial defense. Sequence analysis showed that CiMAp27 lack a catalytic domain but retains two domains (CUB1-EGF) involved in the association with MBL, while CiMAp39 retained four domains (CUB1-EGF-CUB2-CCP1). Not only the two CiMASPs but also the CiMAps were detected in grass carp serum. Furthermore, both recombinant CiMASPs (rCiMASPs) and recombinant rCiMAps (rCiMAps) interacted with recombinant MBL and the two CiMAps competed with CiMASPs for binding to MBL, and hence inhibited downstream C4 binding. These results indicated that CiMAps acted as competitive inhibitors in the lectin complement pathway of grass carp