High-Density Genetic Linkage Maps Provide Novel Insights Into ZW/ZZ Sex Determination System and Growth Performance in Mud Crab (Scylla paramamosain).

Abstract:

:Mud crab, Scylla paramamosain is one of the most important crustacean species in global aquaculture. To determine the genetic basis of sex and growth-related traits in S. paramamosain, a high-density genetic linkage map with 16,701 single nucleotide polymorphisms (SNPs) was constructed using SLAF-seq and a full-sib family. The consensus map has 49 linkage groups, spanning 5,996.66 cM with an average marker-interval of 0.81 cM. A total of 516 SNP markers, including 8 female-specific SNPs segregated in two quantitative trait loci (QTLs) for phenotypic sex were located on LG32. The presence of female-specific SNP markers only on female linkage map, their segregation patterns and lower female: male recombination rate strongly suggest the conformation of a ZW/ZZ sex determination system in S. paramamosain. The QTLs of most (90%) growth-related traits were found within a small interval (25.18-33.74 cM) on LG46, highlighting the potential involvement of LG46 in growth. Four markers on LG46 were significantly associated with 10-16 growth-related traits. BW was only associated with marker 3846. Based on the annotation of transcriptome data, 11 and 2 candidate genes were identified within the QTL regions of sex and growth-related traits, respectively. The newly constructed high-density genetic linkage map with sex-specific SNPs, and the identified QTLs of sex- and growth-related traits serve as a valuable genetic resource and solid foundation for marker-assisted selection and genetic improvement of crustaceans.

journal_name

Front Genet

journal_title

Frontiers in genetics

authors

Waiho K,Shi X,Fazhan H,Li S,Zhang Y,Zheng H,Liu W,Fang S,Ikhwanuddin M,Ma H

doi

10.3389/fgene.2019.00298

subject

Has Abstract

pub_date

2019-04-05 00:00:00

pages

298

issn

1664-8021

journal_volume

10

pub_type

杂志文章
  • Three Medicago MtFUL genes have distinct and overlapping expression patterns during vegetative and reproductive development and 35S:MtFULb accelerates flowering and causes a terminal flower phenotype in Arabidopsis.

    abstract::The timing of the transition to flowering is carefully controlled by plants in order to optimize sexual reproduction and the ensuing production of seeds, grains, and fruits. The genetic networks that regulate floral induction are best characterized in the temperate eudicot Arabidopsis in which the florigen gene FT pla...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2015.00050

    authors: Jaudal M,Zhang L,Che C,Putterill J

    更新日期:2015-02-19 00:00:00

  • Draft Genome and Complete Hox-Cluster Characterization of the Sterlet (Acipenser ruthenus).

    abstract::Background: Sturgeons (Chondrostei: Acipenseridae) are a group of "living fossil" fishes at a basal position among Actinopteri. They have raised great public interest due to their special evolutionary position, species conservation challenges, as well as their highly-prized eggs (caviar). The sterlet, Acipenser ruthen...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2019.00776

    authors: Cheng P,Huang Y,Du H,Li C,Lv Y,Ruan R,Ye H,Bian C,You X,Xu J,Liang X,Shi Q,Wei Q

    更新日期:2019-09-05 00:00:00

  • Reproducibility of Methods to Detect Differentially Expressed Genes from Single-Cell RNA Sequencing.

    abstract::Detection of differentially expressed genes is a common task in single-cell RNA-seq (scRNA-seq) studies. Various methods based on both bulk-cell and single-cell approaches are in current use. Due to the unique distributional characteristics of single-cell data, it is important to compare these methods with rigorous st...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2019.01331

    authors: Mou T,Deng W,Gu F,Pawitan Y,Vu TN

    更新日期:2020-01-17 00:00:00

  • Accuracy of Genomic Evaluations of Juvenile Growth Rate in Common Carp (Cyprinus carpio) Using Genotyping by Sequencing.

    abstract::Cyprinids are the most important group of farmed fish globally in terms of production volume, with common carp (Cyprinus carpio) being one of the most valuable species of the group. The use of modern selective breeding methods in carp is at a formative stage, implying a large scope for genetic improvement of key produ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2018.00082

    authors: Palaiokostas C,Kocour M,Prchal M,Houston RD

    更新日期:2018-03-13 00:00:00

  • Severe Phenotype in a Patient With Homozygous 15q21.2 Microdeletion Involving BCL2L10, GNB5, and MYO5C Genes, Resembling Infantile Developmental Disorder With Cardiac Arrhythmias (IDDCA).

    abstract::Homozygous and compound heterozygous mutations in GNB5 gene have been associated with a wide spectrum of clinical presentations, ranging from neurodevelopmental issues with or without cardiac arrhythmia (LADCI) to severe developmental delay with epileptic encephalopathy, retinal dystrophy, and heart rhythm abnormaliti...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.00399

    authors: Sciacca FL,Ciaccio C,Fontana F,Strano C,Gilardoni F,Pantaleoni C,D'Arrigo S

    更新日期:2020-05-13 00:00:00

  • A Comparative Genome-Wide Analysis of the R2R3-MYB Gene Family Among Four Gossypium Species and Their Sequence Variation and Association With Fiber Quality Traits in an Interspecific G. hirsutum × G. barbadense Population.

    abstract::Cotton (Gossypium spp.) is the most important natural fiber crop in the world. The R2R3-MYB gene family is a large gene family involved in many plant functions including cotton fiber development. Although previous studies have reported its phylogenetic relationships, gene structures, and expression patterns in tetrapl...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2019.00741

    authors: Wang N,Ma Q,Ma J,Pei W,Liu G,Cui Y,Wu M,Zang X,Zhang J,Yu S,Ma L,Yu J

    更新日期:2019-08-15 00:00:00

  • The Cell Type-Specific Functions of miR-21 in Cardiovascular Diseases.

    abstract::Cardiovascular diseases are one of the prime reasons for disability and death worldwide. Diseases and conditions, such as hypoxia, pressure overload, infection, and hyperglycemia, might initiate cardiac remodeling and dysfunction by inducing hypertrophy or apoptosis in cardiomyocytes and by promoting proliferation in ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2020.563166

    authors: Dai B,Wang F,Nie X,Du H,Zhao Y,Yin Z,Li H,Fan J,Wen Z,Wang DW,Chen C

    更新日期:2020-11-20 00:00:00

  • Genome-Wide Association Studies and Genomic Selection in Pearl Millet: Advances and Prospects.

    abstract::Pearl millet is a climate-resilient, drought-tolerant crop capable of growing in marginal environments of arid and semi-arid regions globally. Pearl millet is a staple food for more than 90 million people living in poverty and can address the triple burden of malnutrition substantially. It remained a neglected crop un...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2019.01389

    authors: Srivastava RK,Singh RB,Pujarula VL,Bollam S,Pusuluri M,Chellapilla TS,Yadav RS,Gupta R

    更新日期:2020-02-28 00:00:00

  • Employing MCMC under the PPL framework to analyze sequence data in large pedigrees.

    abstract::The increased feasibility of whole-genome (or whole-exome) sequencing has led to renewed interest in using family data to find disease mutations. For clinical phenotypes that lend themselves to study in large families, this approach can be particularly effective, because it may be possible to obtain strong evidence of...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2013.00059

    authors: Huang Y,Thomas A,Vieland VJ

    更新日期:2013-04-19 00:00:00

  • Drosophila melanogaster as a Model to Study the Multiple Phenotypes, Related to Genome Stability of the Fragile-X Syndrome.

    abstract::Fragile-X syndrome is one of the most common forms of inherited mental retardation and autistic behaviors. The reduction/absence of the functional FMRP protein, coded by the X-linked Fmr1 gene in humans, is responsible for the syndrome. Patients exhibit a variety of symptoms predominantly linked to the function of FMR...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2019.00010

    authors: Specchia V,Puricella A,D'Attis S,Massari S,Giangrande A,Bozzetti MP

    更新日期:2019-02-13 00:00:00

  • Endoplasmic Reticulum Stress Activation in Alport Syndrome Varies Between Genotype and Cell Type.

    abstract::Alport syndrome is a hereditary progressive chronic kidney disease caused by mutations in type IV collagen genes COL4A3/4/5. X-linked Alport syndrome (XLAS) is caused by mutations in the COL4A5 gene and is the most common form of Alport syndrome. A strong correlation between the type of COL4A5 mutation and the age dev...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.00036

    authors: Wang C,Liang S,Xing S,Xu K,Xiao H,Deng H,Wang X,Chen L,Ding J,Wang F

    更新日期:2020-02-10 00:00:00

  • Comparative Transcriptome Analysis Reveals Molecular Basis Underlying Fast Growth of the Selectively Bred Pacific Oyster, Crassostrea gigas.

    abstract::Fast growth is one of the most desired traits for all food animals, which affects the profitability of animal production. The Pacific oyster, Crassostrea gigas, is an important aquaculture shellfish around the world with the largest annual production. Growth of the Pacific oyster has been greatly improved by artificia...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2019.00610

    authors: Zhang F,Hu B,Fu H,Jiao Z,Li Q,Liu S

    更新日期:2019-06-28 00:00:00

  • Genome-Wide Association Mapping and Genomic Prediction of Anther Extrusion in CIMMYT Hybrid Wheat Breeding Program via Modeling Pedigree, Genomic Relationship, and Interaction With the Environment.

    abstract::Anther extrusion (AE) is the most important male floral trait for hybrid wheat seed production. AE is a complex quantitative trait that is difficult to phenotype reliably in field experiments not only due to high genotype-by-environment effects but also due to the short expression window in the field condition. In thi...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.586687

    authors: Adhikari A,Basnet BR,Crossa J,Dreisigacker S,Camarillo F,Bhati PK,Jarquin D,Manes Y,Ibrahim AMH

    更新日期:2020-12-08 00:00:00

  • Comparative Analysis of Genomic Island Prediction Tools.

    abstract::Tools for genomic island prediction use strategies for genomic comparison analysis and sequence composition analysis. The goal of comparative analysis is to identify unique regions in the genomes of related organisms, whereas sequence composition analysis evaluates and relates the composition of specific regions with ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2018.00619

    authors: da Silva Filho AC,Raittz RT,Guizelini D,De Pierri CR,Augusto DW,Dos Santos-Weiss ICR,Marchaukoski JN

    更新日期:2018-12-12 00:00:00

  • Winning the Tug-of-War Between Effector Gene Design and Pathogen Evolution in Vector Population Replacement Strategies.

    abstract::While efforts to control malaria with available tools have stagnated, and arbovirus outbreaks persist around the globe, the advent of clustered regularly interspaced short palindromic repeat (CRISPR)-based gene editing has provided exciting new opportunities for genetics-based strategies to control these diseases. In ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2019.01072

    authors: Marshall JM,Raban RR,Kandul NP,Edula JR,León TM,Akbari OS

    更新日期:2019-10-30 00:00:00

  • Bacterial SET domain proteins and their role in eukaryotic chromatin modification.

    abstract::It has been shown by many researchers that SET-domain containing proteins modify chromatin structure and, as expected, genes coding for SET-domain containing proteins have been found in all eukaryotic genomes sequenced to date. However, during the last years, a great number of bacterial genomes have been sequenced and...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2014.00065

    authors: Alvarez-Venegas R

    更新日期:2014-04-02 00:00:00

  • Estimating the Intra-taxa Diversity, Population Genetic Structure, and Evolutionary Pathways of Cryptococcus neoformans and Cryptococcus gattii.

    abstract::Members of the Cryptococcus complex, includes Cryptococcus neoformans (most common fungal infection of the brain) and Cryptococcus gattii (high-impact emerging pathogen worldwide). Currently, the fungal multilocus sequence typing database (Fungal MLST Database) constitutes a valuable data repository of the genes used ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2018.00148

    authors: Muñoz M,Camargo M,Ramírez JD

    更新日期:2018-04-24 00:00:00

  • MPPED2 Polymorphism Is Associated With Altered Systemic Inflammation and Adverse Trauma Outcomes.

    abstract::Trauma is a leading cause of morbidity and mortality. It is unclear why some trauma victims follow a complicated clinical course and die, while others, with apparently similar injury characteristics, do not. Interpatient genomic differences, in the form of single nucleotide polymorphisms (SNPs), have been associated p...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2019.01115

    authors: Schimunek L,Namas RA,Yin J,Barclay D,Liu D,El-Dehaibi F,Abboud A,Cohen M,Zamora R,Billiar TR,Vodovotz Y

    更新日期:2019-11-08 00:00:00

  • Coding or Noncoding, the Converging Concepts of RNAs.

    abstract::Technological advances over the past decade have unraveled the remarkable complexity of RNA. The identification of small peptides encoded by long non-coding RNAs (lncRNAs) as well as regulatory functions mediated by non-coding regions of mRNAs have further complicated our understanding of the multifaceted functions of...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2019.00496

    authors: Li J,Liu C

    更新日期:2019-05-22 00:00:00

  • DNA methyltransferases and TETs in the regulation of differentiation and invasiveness of extra-villous trophoblasts.

    abstract::Specialized cell types of trophoblast cells form the placenta in which each cell type has particular properties of proliferation and invasion. The placenta sustains the growth of the fetus throughout pregnancy and any aberrant trophoblast differentiation or invasion potentially affects the future health of the child a...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2013.00265

    authors: Logan PC,Mitchell MD,Lobie PE

    更新日期:2013-12-04 00:00:00

  • Investigating Causal Relations Between Sleep-Related Traits and Risk of Type 2 Diabetes Mellitus: A Mendelian Randomization Study.

    abstract:Objective:Extensive literature put forward the link between sleep and type 2 diabetes mellitus (T2DM), however, little is known about the underlying causality of the associations. Here we aim to assess the causal relationships between five major sleep-related traits and T2DM. Design Setting and Participants:Two-sample...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.607865

    authors: Gao X,Sun H,Zhang Y,Liu L,Wang J,Wang T

    更新日期:2020-12-15 00:00:00

  • Functional Analyses of a Novel Splice Variant in the CHD7 Gene, Found by Next Generation Sequencing, Confirm Its Pathogenicity in a Spanish Patient and Diagnose Him with CHARGE Syndrome.

    abstract::Mutations in CHD7 have been shown to be a major cause of CHARGE syndrome, which presents many symptoms and features common to other syndromes making its diagnosis difficult. Next generation sequencing (NGS) of a panel of intellectual disability related genes was performed in an adult patient without molecular diagnosi...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2018.00007

    authors: Villate O,Ibarluzea N,Fraile-Bethencourt E,Valenzuela A,Velasco EA,Grozeva D,Raymond FL,Botella MP,Tejada MI

    更新日期:2018-01-26 00:00:00

  • Expanded Carrier Screening in Chinese Population - A Survey on Views and Acceptance of Pregnant and Non-Pregnant Women.

    abstract:Objective:Recessive genetic diseases impose physical and psychological impacts to both newborns and parents who may not be aware of being carriers. Expanded carrier screening (ECS) allows screening for multiple genetic conditions at the same time. Whether or not such non-targeted panethnic approach of genetic carrier s...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.594091

    authors: Cheng HYH,Wong GCY,Chan YK,Lee CP,Tang MHY,Ng EH,Kan AS

    更新日期:2020-11-16 00:00:00

  • The Genomic Health of Human Pluripotent Stem Cells: Genomic Instability and the Consequences on Nuclear Organization.

    abstract::Human pluripotent stem cells (hPSCs) are increasingly used for cell-based regenerative therapies worldwide, with embryonic and induced pluripotent stem cells as potential treatments for debilitating and chronic conditions, such as age-related macular degeneration, Parkinson's disease, spinal cord injuries, and type 1 ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2018.00623

    authors: Henry MP,Hawkins JR,Boyle J,Bridger JM

    更新日期:2019-01-21 00:00:00

  • A Review of Pathway-Based Analysis Tools That Visualize Genetic Variants.

    abstract::Pathway analysis is a powerful method for data analysis in genomics, most often applied to gene expression analysis. It is also promising for single-nucleotide polymorphism (SNP) data analysis, such as genome-wide association study data, because it allows the interpretation of variants with respect to the biological p...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2017.00174

    authors: Cirillo E,Parnell LD,Evelo CT

    更新日期:2017-11-07 00:00:00

  • Frequent Mutations of VHL Gene and the Clinical Phenotypes in the Largest Chinese Cohort With Von Hippel-Lindau Disease.

    abstract::Von Hippel-Lindau (VHL) disease is a rare autosomal-dominant inherited tumor syndrome. We aimed to analyze the correlations between frequent VHL mutations and phenotypes in Chinese VHL families. We screened 540 patients from 187 unrelated Chinese VHL families for 19 frequent VHL mutations. The penetrance and mean age ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2019.00867

    authors: Hong B,Ma K,Zhou J,Zhang J,Wang J,Liu S,Zhang Z,Cai L,Zhang N,Gong K

    更新日期:2019-09-18 00:00:00

  • Recent Advances of Deep Learning in Bioinformatics and Computational Biology.

    abstract::Extracting inherent valuable knowledge from omics big data remains as a daunting problem in bioinformatics and computational biology. Deep learning, as an emerging branch from machine learning, has exhibited unprecedented performance in quite a few applications from academia and industry. We highlight the difference a...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2019.00214

    authors: Tang B,Pan Z,Yin K,Khateeb A

    更新日期:2019-03-26 00:00:00

  • The Missing lnc(RNA) between the pancreatic β-cell and diabetes.

    abstract::Diabetes mellitus represents a group of complex metabolic diseases that result in impaired glucose homeostasis, which includes destruction of β-cells or the failure of these insulin-secreting cells to compensate for increased metabolic demand. Despite a strong interest in characterizing the transcriptome of the differ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2014.00200

    authors: Kameswaran V,Kaestner KH

    更新日期:2014-07-01 00:00:00

  • Transcriptome Analysis of the Breast Muscle of Xichuan Black-Bone Chickens Under Tyrosine Supplementation Revealed the Mechanism of Tyrosine-Induced Melanin Deposition.

    abstract::The Xichuan black-bone chicken, which is a rare local chicken species in China, is an important genetic resource of black-bone chickens. Tyrosine can affect melanin production, but the molecular mechanism underlying tyrosine-induced melanin deposition in Xichuan black-bone chickens is poorly understood. Here, the blac...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2019.00457

    authors: Li D,Wang X,Fu Y,Zhang C,Cao Y,Wang J,Zhang Y,Li Y,Chen Y,Li Z,Li W,Jiang R,Sun G,Tian Y,Li G,Kang X

    更新日期:2019-05-15 00:00:00

  • Understanding Dietary Intervention-Mediated Epigenetic Modifications in Metabolic Diseases.

    abstract::The global prevalence of metabolic disorders, such as obesity, diabetes and fatty liver disease, is dramatically increasing. Both genetic and environmental factors are well-known contributors to the development of these diseases and therefore, the study of epigenetics can provide additional mechanistic insight. Dietar...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2020.590369

    authors: Asif S,Morrow NM,Mulvihill EE,Kim KH

    更新日期:2020-10-15 00:00:00