Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025.

Abstract:

:Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step change in technology and analytical approaches available to define, manage and conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR conservation in terms of technological continuity, analytical capacity and integrative methodologies needed to fully exploit new, multidimensional data. The final conference of the ESF Genomic Resources program aimed to address these interdisciplinary problems in an attempt to contribute to the agenda for research and policy development directions during the coming decade. By 2020, according to the Convention on Biodiversity's Aichi Target 13, signatories should ensure that "…the genetic diversity of …farmed and domesticated animals and of wild relatives …is maintained, and strategies have been developed and implemented for minimizing genetic erosion and safeguarding their genetic diversity." However, the real extent of genetic erosion is very difficult to measure using current data. Therefore, this challenging target demands better coverage, understanding and utilization of genomic and environmental data, the development of optimized ways to integrate these data with social and other sciences and policy analysis to enable more flexible, evidence-based models to underpin FAnGR conservation. At the conference, we attempted to identify the most important problems for effective livestock genomic resource conservation during the next decade. Twenty priority questions were identified that could be broadly categorized into challenges related to methodology, analytical approaches, data management and conservation. It should be acknowledged here that while the focus of our meeting was predominantly around genetics, genomics and animal science, many of the practical challenges facing conservation of genomic resources are societal in origin and are predicated on the value (e.g., socio-economic and cultural) of these resources to farmers, rural communities and society as a whole. The overall conclusion is that despite the fact that the livestock sector has been relatively well-organized in the application of genetic methodologies to date, there is still a large gap between the current state-of-the-art in the use of tools to characterize genomic resources and its application to many non-commercial and local breeds, hampering the consistent utilization of genetic and genomic data as indicators of genetic erosion and diversity. The livestock genomic sector therefore needs to make a concerted effort in the coming decade to enable to the democratization of the powerful tools that are now at its disposal, and to ensure that they are applied in the context of breed conservation as well as development.

journal_name

Front Genet

journal_title

Frontiers in genetics

authors

Bruford MW,Ginja C,Hoffmann I,Joost S,Orozco-terWengel P,Alberto FJ,Amaral AJ,Barbato M,Biscarini F,Colli L,Costa M,Curik I,Duruz S,Ferenčaković M,Fischer D,Fitak R,Groeneveld LF,Hall SJ,Hanotte O,Hassan FU,Helsen

doi

10.3389/fgene.2015.00314

subject

Has Abstract

pub_date

2015-10-21 00:00:00

pages

314

issn

1664-8021

journal_volume

6

pub_type

杂志文章
  • Ideal Cereals With Lower Arsenic and Cadmium by Accurately Enhancing Vacuolar Sequestration Capacity.

    abstract::Cereals are a staple food for many people around the world; however, they are also a major dietary source of toxic metal(loid)s. Many agricultural regions throughout the world are contaminated with toxic metal(loid)s, which can accumulate to high levels in the grains of cereals cultivated in these regions, posing seri...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2019.00322

    authors: Deng F,Yu M,Martinoia E,Song WY

    更新日期:2019-04-09 00:00:00

  • Novel Compound Heterozygous Variants of ETHE1 Causing Ethylmalonic Encephalopathy in a Chinese Patient: A Case Report.

    abstract::Ethylmalonic encephalopathy (EE) is a very rare autosomal recessive metabolic disorder that primarily affects children. Less than one hundred EE patients have been diagnosed worldwide. The clinical manifestations include chronic diarrhea, petechiae, orthostatic acrocyanosis, psychomotor delay and regression, seizures,...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.00341

    authors: Chen X,Han L,Yao H

    更新日期:2020-04-17 00:00:00

  • Whole-Genome Resequencing Reveals Loci Associated With Thoracic Vertebrae Number in Sheep.

    abstract::The number of vertebrae, especially thoracic vertebrae, is an important economic trait that may influence carcass length and meat production in animals. However, the genetic basis of vertebrae number in sheep is still poorly understood. To detect the candidate genes, 400 increased number of thoracic vertebrae (T14L6) ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2019.00674

    authors: Li C,Li M,Li X,Ni W,Xu Y,Yao R,Wei B,Zhang M,Li H,Zhao Y,Liu L,Ullah Y,Jiang Y,Hu S

    更新日期:2019-07-18 00:00:00

  • Integrated Analysis of RNA-Binding Proteins Associated With the Prognosis and Immunosuppression in Squamous Cell Carcinoma of Head and Neck.

    abstract::RNA-binding proteins (RBPs) interacting with target RNAs play essential roles in RNA metabolism at the post-transcription level. Perturbations of RBPs can accelerate cancer development and cause dysregulation of the immune cell function and activity leading to evade immune destruction of cancer cells. However, few stu...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.571403

    authors: Hu G,Jiang Q,Liu L,Peng H,Wang Y,Li S,Tang Y,Yu J,Yang J,Liu Z

    更新日期:2021-01-11 00:00:00

  • A Population Genomics Analysis of the Native Irish Galway Sheep Breed.

    abstract::The Galway sheep population is the only native Irish sheep breed and this livestock genetic resource is currently categorised as 'at-risk'. In the present study, comparative population genomics analyses of Galway sheep and other sheep populations of European origin were used to investigate the microevolution and recen...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2019.00927

    authors: McHugo GP,Browett S,Randhawa IAS,Howard DJ,Mullen MP,Richardson IW,Park SDE,Magee DA,Scraggs E,Dover MJ,Correia CN,Hanrahan JP,MacHugh DE

    更新日期:2019-10-08 00:00:00

  • Whole Genome Scan Reveals Molecular Signatures of Divergence and Selection Related to Important Traits in Durum Wheat Germplasm.

    abstract::The first breeding program in the world for durum wheat was conceived in Italy in the early 1900s. Over the decades, pressure exerted by natural and artificial selection could have progressively reduced the genetic diversity of the durum wheat germplasm. In the present study, a large panel of Italian durum wheat acces...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.00217

    authors: Taranto F,D'Agostino N,Rodriguez M,Pavan S,Minervini AP,Pecchioni N,Papa R,De Vita P

    更新日期:2020-04-21 00:00:00

  • Human migration, diversity and disease association: a convergent role of established and emerging DNA markers.

    abstract::With the gradual development of intelligence, human got curious to know his origin and evolutionary background. Historical statements and anthropological findings were his primary tool for solving the puzzles of his own origin, until came the golden era of molecular markers which took no time to prove it's excellence ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2013.00155

    authors: Guha P,Srivastava SK,Bhattacharjee S,Chaudhuri TK

    更新日期:2013-08-09 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

  • 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

  • Genetic Model to Study the Co-Morbid Phenotypes of Increased Alcohol Intake and Prior Stress-Induced Enhanced Fear Memory.

    abstract::Posttraumatic Stress Disorder (PTSD) is a complex illness, frequently co-morbid with depression, caused by both genetics, and the environment. Alcohol Use Disorder (AUD), which also co-occurs with depression, is often co-morbid with PTSD. To date, very few genes have been identified for PTSD and even less for PTSD com...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2018.00566

    authors: Lim PH,Shi G,Wang T,Jenz ST,Mulligan MK,Redei EE,Chen H

    更新日期:2018-11-27 00:00:00

  • Intestinal Lipid Metabolism Genes Regulated by miRNAs.

    abstract::MicroRNAs (miRNAs) crucial roles in translation repression and post-transcriptional adjustments contribute to regulate intestinal lipid metabolism. Even though their actions in different metabolic tissues have been elucidated, their intestinal activity is yet unclear. We aimed to investigate intestinal miRNA-regulated...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.00707

    authors: Ruiz-Roso MB,Gil-Zamorano J,López de Las Hazas MC,Tomé-Carneiro J,Crespo MC,Latasa MJ,Briand O,Sánchez-López D,Ortiz AI,Visioli F,Martínez JA,Dávalos A

    更新日期:2020-07-10 00:00:00

  • Multi-model inference in comparative phylogeography: an integrative approach based on multiple lines of evidence.

    abstract::Comparative phylogeography has its roots in classical biogeography and, historically, relies on a pattern-based approach. Here, we present a model-based framework for comparative phylogeography. Our framework was initially developed for statistical phylogeography based on a multi-model inference approach, by coupling ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2015.00031

    authors: Collevatti RG,Terribile LC,Diniz-Filho JA,Lima-Ribeiro MS

    更新日期:2015-02-17 00:00:00

  • Transposon insertion mapping with PIMMS - Pragmatic Insertional Mutation Mapping System.

    abstract:UNLABELLED:The PIMMS (Pragmatic Insertional Mutation Mapping System) pipeline has been developed for simple conditionally essential genome discovery experiments in bacteria. Capable of using raw sequence data files alongside a FASTA sequence of the reference genome and GFF file, PIMMS will generate a tabulated output o...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2015.00139

    authors: Blanchard AM,Leigh JA,Egan SA,Emes RD

    更新日期:2015-04-09 00:00:00

  • Genetic and Clinical Analyses of 13 Chinese Families With Cystine Urolithiasis and Identification of 15 Novel Pathogenic Variants in SLC3A1 and SLC7A9.

    abstract:Background:Cystinuria is a rare genetic disorder characterized by defective renal reabsorption of cystine, ornithine, arginine, and lysine. The increased urinary excretion of cystine results in the development of cystine urolithiasis (CU). The mutated SLC3A1 and SLC7A9 genes are the cause of CU, a global disorder. Its ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.00074

    authors: Li C,Yang Y,Zheng Y,Shen F,Liu L,Li Y,Li L,Zhao Y

    更新日期:2020-02-18 00:00:00

  • Enrollment of Diverse Populations in the INGENIOUS Pharmacogenetics Clinical Trial.

    abstract::Recruitment of diverse populations and subjects living in Medically Underserved Areas and Populations (MUA/P's) into clinical trials is a considerable challenge. Likewise, representation of African-Americans in pharmacogenetic trials is often inadequate, but critical for identifying genetic variation within and betwee...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.00571

    authors: Shah-Williams E,Levy KD,Zang Y,Holmes AM,Stoughton C,Dexter P,Skaar TC

    更新日期:2020-06-25 00:00:00

  • Impact of Ancestral Differences and Reassessment of the Classification of Previously Reported Pathogenic Variants in Patients With Brugada Syndrome in the Genomic Era: A SADS-TW BrS Registry.

    abstract::Brugada syndrome (BrS) is a heritable disease that results in sudden cardiac death. In the exome/genomic era, certain reported pathogenic variants in some genetic diseases have been reclassified as benign owing to their high frequency in some ancestries. In the present study, we comprehensively reassessed all previous...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2018.00680

    authors: Chen CJ,Lu TP,Lin LY,Liu YB,Ho LT,Huang HC,Lai LP,Hwang JJ,Yeh SS,Wu CK,Juang JJ,Antzelevitch C

    更新日期:2019-01-04 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

  • Proband Whole-Exome Sequencing Identified Genes Responsible for Autosomal Recessive Non-Syndromic Hearing Loss in 33 Chinese Nuclear Families.

    abstract::Autosomal recessive non-syndromic hearing loss (ARNSHL) is a highly heterogeneous disease involving more than 70 pathogenic genes. However, most ARNSHL families have small-sized pedigrees with limited genetic information, rendering challenges for the molecular diagnosis of these patients. Therefore, we attempted to es...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2019.00639

    authors: Sang S,Ling J,Liu X,Mei L,Cai X,Li T,Li W,Li M,Wen J,Liu X,Liu J,Liu Y,Chen H,He C,Feng Y

    更新日期:2019-07-17 00:00:00

  • Kernel Fusion Method for Detecting Cancer Subtypes via Selecting Relevant Expression Data.

    abstract::Recently, cancer has been characterized as a heterogeneous disease composed of many different subtypes. Early diagnosis of cancer subtypes is an important study of cancer research, which can be of tremendous help to patients after treatment. In this paper, we first extract a novel dataset, which contains gene expressi...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.00979

    authors: Li S,Jiang L,Tang J,Gao N,Guo F

    更新日期:2020-09-10 00:00:00

  • A new method for estimating the demographic history from DNA sequences: an importance sampling approach.

    abstract::The effective population size over time (demographic history) can be retraced from a sample of contemporary DNA sequences. In this paper, we propose a novel methodology based on importance sampling (IS) for exploring such demographic histories. Our starting point is the generalized skyline plot with the main differenc...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2015.00259

    authors: Ait Kaci Azzou S,Larribe F,Froda S

    更新日期:2015-08-07 00:00:00

  • The obesity epidemic: from the environment to epigenetics - not simply a response to dietary manipulation in a thermoneutral environment.

    abstract::The prevalence of obesity continues to increase particularly in developed countries. To establish the primary mechanisms involved, relevant animal models which track the developmental pathway to obesity are required. This need is emphasized by the substantial rise in the number of overweight and obese children, of whi...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2011.00024

    authors: Symonds ME,Sebert S,Budge H

    更新日期:2011-05-31 00:00:00

  • A Theory for the Origin of Human Menopause.

    abstract::A complete and compelling evolutionary explanation for the origin of human menopause is wanting. Menopause onset is defined clinically as the final menses, confirmed after 1 year without menstruation. The theory proposed herein explains at multiple levels - ultimately genetic but involving (1) behavioral, (2) life his...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2016.00222

    authors: Takahashi M,Singh RS,Stone J

    更新日期:2017-01-06 00:00:00

  • Pan-Cancer Analysis Reveals the Functional Importance of Protein Lysine Modification in Cancer Development.

    abstract::Large-scale tumor genome sequencing projects have revealed a complex landscape of genomic mutations in multiple cancer types. A major goal of these projects is to characterize somatic mutations and discover cancer drivers, thereby providing important clues to uncover diagnostic or therapeutic targets for clinical trea...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2018.00254

    authors: Chen L,Miao Y,Liu M,Zeng Y,Gao Z,Peng D,Hu B,Li X,Zheng Y,Xue Y,Zuo Z,Xie Y,Ren J

    更新日期:2018-07-17 00:00:00

  • Tools for the Recognition of Sorting Signals and the Prediction of Subcellular Localization of Proteins From Their Amino Acid Sequences.

    abstract::At the time of translation, nascent proteins are thought to be sorted into their final subcellular localization sites, based on the part of their amino acid sequences (i.e., sorting or targeting signals). Thus, it is interesting to computationally recognize these signals from the amino acid sequences of any given prot...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2020.607812

    authors: Imai K,Nakai K

    更新日期:2020-11-25 00:00:00

  • Interaction between oxytocin receptor DNA methylation and genotype is associated with risk of postpartum depression in women without depression in pregnancy.

    abstract::Postpartum depression (PPD) affects up to 19% of women, negatively impacting maternal and infant health. Reductions in plasma oxytocin levels have been associated with PPD and heritability studies have established a genetic contribution. Epigenetic regulation of the oxytocin receptor gene (OXTR) has been demonstrated ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2015.00243

    authors: Bell AF,Carter CS,Steer CD,Golding J,Davis JM,Steffen AD,Rubin LH,Lillard TS,Gregory SP,Harris JC,Connelly JJ

    更新日期:2015-07-21 00:00:00

  • Genome Scan for Parent-of-Origin QTL Effects on Bovine Growth and Carcass Traits.

    abstract::Parent-of-origin effects (POE) such as genomic imprinting influence growth and body composition in livestock, rodents, and humans. Here, we report the results of a genome scan to detect quantitative trait loci (QTL) with POE on growth and carcass traits in Angus × Brahman cattle crossbreds. We identified 24 POE-QTL on...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2011.00044

    authors: Imumorin IG,Kim EH,Lee YM,De Koning DJ,van Arendonk JA,De Donato M,Taylor JF,Kim JJ

    更新日期:2011-07-12 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

  • DNA methylation changes in the postmortem dorsolateral prefrontal cortex of patients with schizophrenia.

    abstract:BACKGROUND:Schizophrenia is a complex psychiatric disorder with a lifetime morbidity rate of 0.5-1.0%. The pathophysiology of schizophrenia still remains obscure. Accumulating evidence indicates that DNA methylation, which is the addition of a methyl group to the cytosine in a CpG dinucleotide, might play an important ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2014.00280

    authors: Numata S,Ye T,Herman M,Lipska BK

    更新日期:2014-08-26 00:00:00

  • The Challenges of Microbial Control of Mosquito-Borne Diseases Due to the Gut Microbiome.

    abstract::Mosquitoes are one of the deadliest animals on earth because of their ability to transmit a wide range of human pathogens. Traditional mosquito control methods use chemical insecticides, but with dwindling long-term effectiveness and negative effects on the environment, microbial forms of control have become common al...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2020.504354

    authors: Dacey DP,Chain FJJ

    更新日期:2020-10-07 00:00:00

  • Redundancy of the genetic code enables translational pausing.

    abstract::The codon redundancy ("degeneracy") found in protein-coding regions of mRNA also prescribes Translational Pausing (TP). When coupled with the appropriate interpreters, multiple meanings and functions are programmed into the same sequence of configurable switch-settings. This additional layer of Ontological Prescriptiv...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2014.00140

    authors: D'Onofrio DJ,Abel DL

    更新日期:2014-05-20 00:00:00