Dataset Information

A second generation SNP and SSR integrated linkage map and QTL mapping for the Chinese mitten crab Eriocheir sinensis.

ABSTRACT: The Chinese mitten crab Eriocheir sinensis is the most economically important cultivated crab species in China, and its genome has a high number of chromosomes (2n?=?146). To obtain sufficient markers for construction of a dense genetic map for this species, we employed the recently developed specific-locus amplified fragment sequencing (SLAF-seq) method for large-scale SNPs screening and genotyping in a F1 full-sib family of 149 individuals. SLAF-seq generated 127,677 polymorphic SNP markers, of which 20,803 valid markers were assigned into five segregation types and were used together with previous SSR markers for linkage map construction. The final integrated genetic map included 17,680 SNP and 629 SSR markers on the 73 linkage groups (LG), and spanned 14,894.9?cM with an average marker interval of 0.81?cM. QTL mapping localized three significant growth-related QTL to a 1.2?cM region in LG53 as well as 146 sex-linked markers in LG48. Genome-wide QTL-association analysis further identified four growth-related QTL genes named LNX2, PAK2, FMRFamide and octopamine receptors. These genes are involved in a variety of different signaling pathways including cell proliferation and growth. The map and SNP markers described here will be a valuable resource for the E. sinensis genome project and selective breeding programs.

SUBMITTER: Qiu GF

PROVIDER: S-EPMC5206627 | biostudies-literature | 2017 Jan

REPOSITORIES: biostudies-literature

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Publications

A second generation SNP and SSR integrated linkage map and QTL mapping for the Chinese mitten crab Eriocheir sinensis.

Qiu Gao-Feng GF Xiong Liang-Wei LW Han Zhi-Ke ZK Liu Zhi-Qiang ZQ Feng Jian-Bin JB Wu Xu-Gan XG Yan Yin-Long YL Shen Hong H Huang Long L Chen Li L

Scientific reports 20170103

The Chinese mitten crab Eriocheir sinensis is the most economically important cultivated crab species in China, and its genome has a high number of chromosomes (2n = 146). To obtain sufficient markers for construction of a dense genetic map for this species, we employed the recently developed specific-locus amplified fragment sequencing (SLAF-seq) method for large-scale SNPs screening and genotyping in a F1 full-sib family of 149 individuals. SLAF-seq generated 127,677 polymorphic SNP markers, o ...[more]

PMID: 28045132

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Project description:Environmental hypoxia represents a major physiological challenge for Eriocheir sinensis and Palaemonetes sinensis and is a severe problem in aquaculture. Therefore, understanding the metabolic response mechanisms of E. sinensis and P. sinensis, which are economically important species, to environmental hypoxia and reoxygenation is essential. However, little is known about the intrinsic mechanisms by which E. sinensis and P. sinensis cope with environmental hypoxia at the metabolic level. Hypoxia-reoxygenation represents an important physiological challenge for their culture. In this study, respiratory metabolism and respiratory metabolic enzymes of E. sinensis and P. sinensis were evaluated after different hypoxia and reoxygenation times. The results showed that environmental hypoxia had a dramatic influence on the respiratory metabolism and activities of related enzymes. The oxygen consumption rates (OCR) significantly increased as hypoxia time increased, while the ammonia excretion rate (AER) was significantly lower than that in the control group after 8 h hypoxia. The oxygen to nitrogen ratio (O:N) in the control group was <16, indicating that all the energy substrates were proteins. After environmental hypoxia, the O:N significantly increased, and the energy substrate shifted from protein to a protein-lipid mixture. The OCR, AER, and O:N did not restore to initial levels after 2 h or 12 h reoxygenation and was still the same as after 8 h hypoxia. As environmental hypoxia time increased, succinate dehydrogenase (SDH) gradually decreased and lactate dehydrogenase (LDH) gradually increased. Both SDH and LDH were gradually restored to normal levels after reoxygenation. Therefore, environmental hypoxia should be avoided as much as possible during aquaculture breeding of E. sinensis and P. sinensis. Further, since OCR will significantly increase after a short period of reoxygenation, secondary environmental hypoxia due to rapid consumption of oxygen should also be avoided in aquaculture.

Project description:Dopamine (DA) plays a modulatory role in numerous physiological processes such as light adaptation and food intake, and exerts these functions through DA receptors (DARs). This study presents, for the first time, isolation and characterization of the dopamine receptor 2(DA2 receptor) cDNA from the intestinal tissue of Eriocheir sinensis, an economically important freshwater aquaculture species in China. The DA2 receptor cDNA sequence, which was obtained by rapid amplification of cDNA ends, is 2369bp long, encode peptide of 589 amino acid, and is highly homologous to related sequences in crustaceans. Analysis of the deduced amino acid sequence and the structure of the DA2 indicated that this receptor is a member of the family of G protein-coupled receptors (GPCRs), as it contains seven transmembrane domains and other common signatures of GPCRs. RT-PCR showed that the expression of the DA2 receptor gene was distributed in various tissues, and high expression levels were observed in the cranial ganglia and the thoracic ganglia. Further study of the effect of photoperiod on DA2 expression showed that constant darkness induced a significant increase in DA2 expression in the cranial ganglia. Finally, analysis of DA2 receptor expression under different feeding statuses showed that there was significantly greater expression in the hepatopancreas and intestines after feeding than before feeding, but there were no differences in expression between the before feeding and during feeding periods in either tissue. Our results indicate that the DA2 receptor structurally belongs to the family of G protein-coupled receptors, and that the cranial ganglia are the main tissues in which the DA2 receptor participates in light adaptation during dark hours. In addition, the DA2 receptor in E. sinensis may be involved in the physiological regulation of the hepatopancreas and digestive tract after the ingestion of food. This study provides a foundation for further exploration of the light adaptation and digestive functions of the DA2 receptor in decapods.

Dataset Information

A second generation SNP and SSR integrated linkage map and QTL mapping for the Chinese mitten crab Eriocheir sinensis.

Publications

A second generation SNP and SSR integrated linkage map and QTL mapping for the Chinese mitten crab Eriocheir sinensis.

Similar Datasets

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