A major quantitative trait locus affecting resistance to Tilapia lake virus in farmed Nile tilapia (Oreochromis niloticus)

AbstractEnhancing host resistance to infectious disease has received increasing attention in recent years as a major goal of farm animal breeding programs. Combining field data with genomic tools can provide opportunities to understand the genetic architecture of disease resistance, leading to new opportunities for disease control. In the current study, a genome-wide association study was performed to assess resistance to the Tilapia lake virus (TiLV), one of the biggest threats affecting Nile tilapia (Oreochromis niloticus); a key aquaculture species globally. A pond outbreak of TiLV in a pedigreed population of the GIFT strain was observed, with 950 fish classified as either survivor or mortality, and genotyped using a 65 K SNP array. A significant QTL of large effect was identified on chromosome Oni22. The average mortality rate of tilapia homozygous for the resistance allele at the most significant SNP (P value = 4.51E−10) was 11%, compared to 43% for tilapia homozygous for the susceptibility allele. Several candidate genes related to host response to viral infection were identified within this QTL, including lgals17, vps52, and trim29. These results provide a rare example of a major QTL affecting a trait of major importance to a farmed animal. Genetic markers from the QTL region have potential in marker-assisted selection to improve host resistance, providing a genetic solution to an infectious disease where few other control or mitigation options currently exist.

Download Full-text

Genome-Wide Analyses Identifies Known and New Markers Responsible of Chicken Plumage Color

Animals ◽

10.3390/ani10030493 ◽

2020 ◽

Vol 10 (3) ◽

pp. 493

Author(s):

Salvatore Mastrangelo ◽

Filippo Cendron ◽

Gianluca Sottile ◽

Giovanni Niero ◽

Baldassare Portolano ◽

...

Keyword(s):

Genome Wide Association Study ◽

Snp Array ◽

Fixation Index ◽

Phenotypic Traits ◽

Plumage Color ◽

Phenotypic Marker ◽

Genome Wide ◽

A Genome ◽

The Difference ◽

Genomic Regions

Through the development of the high-throughput genotyping arrays, molecular markers and genes related to phenotypic traits have been identified in livestock species. In poultry, plumage color is an important qualitative trait that can be used as phenotypic marker for breed identification. In order to assess sources of genetic variation related to the Polverara chicken breed plumage colour (black vs. white), we carried out a genome-wide association study (GWAS) and a genome-wide fixation index (FST) scan to uncover the genomic regions involved. A total of 37 animals (17 white and 20 black) were genotyped with the Affymetrix 600 K Chicken single nucleotide polymorphism (SNP) Array. The combination of results from GWAS and FST revealed a total of 40 significant markers distributed on GGA 01, 03, 08, 12 and 21, and located within or near known genes. In addition to the well-known TYR, other candidate genes have been identified in this study, such as GRM5, RAB38 and NOTCH2. All these genes could explain the difference between the two Polverara breeds. Therefore, this study provides the basis for further investigation of the genetic mechanisms involved in plumage color in chicken.

Download Full-text

Fine Mapping Using Whole-Genome Sequencing Confirms Anti-Müllerian Hormone as a Major Gene for Sex Determination in Farmed Nile Tilapia (Oreochromis niloticus L.)

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.400297 ◽

2019 ◽

Vol 9 (10) ◽

pp. 3213-3223 ◽

Cited By ~ 8

Author(s):

Giovanna Cáceres ◽

María E. López ◽

María I. Cádiz ◽

Grazyella M. Yoshida ◽

Ana Jedlicki ◽

...

Keyword(s):

Sex Determination ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Oreochromis Niloticus ◽

Nile Tilapia ◽

Major Gene ◽

Whole Genome ◽

Important Species ◽

Genome Wide ◽

A Genome

Nile tilapia (Oreochromis niloticus) is one of the most cultivated and economically important species in world aquaculture. Intensive production promotes the use of monosex animals, due to an important dimorphism that favors male growth. Currently, the main mechanism to obtain all-male populations is the use of hormones in feeding during larval and fry phases. Identifying genomic regions associated with sex determination in Nile tilapia is a research topic of great interest. The objective of this study was to identify genomic variants associated with sex determination in three commercial populations of Nile tilapia. Whole-genome sequencing of 326 individuals was performed, and a total of 2.4 million high-quality bi-allelic single nucleotide polymorphisms (SNPs) were identified after quality control. A genome-wide association study (GWAS) was conducted to identify markers associated with the binary sex trait (males = 1; females = 0). A mixed logistic regression GWAS model was fitted and a genome-wide significant signal comprising 36 SNPs, spanning a genomic region of 536 kb in chromosome 23 was identified. Ten out of these 36 genetic variants intercept the anti-Müllerian (Amh) hormone gene. Other significant SNPs were located in the neighboring Amh gene region. This gene has been strongly associated with sex determination in several vertebrate species, playing an essential role in the differentiation of male and female reproductive tissue in early stages of development. This finding provides useful information to better understand the genetic mechanisms underlying sex determination in Nile tilapia.

Download Full-text

Genome-wide association study identifies loci and candidate genes for internal organ weights in Simmental beef cattle

Physiological Genomics ◽

10.1152/physiolgenomics.00022.2018 ◽

2018 ◽

Vol 50 (7) ◽

pp. 523-531 ◽

Cited By ~ 8

Author(s):

Bingxing An ◽

Jiangwei Xia ◽

Tianpeng Chang ◽

Xiaoqiao Wang ◽

Jian Miao ◽

...

Keyword(s):

Beef Cattle ◽

Association Study ◽

Genome Wide Association Study ◽

Snp Array ◽

Genome Wide Association ◽

Heart Weight ◽

Spleen Weight ◽

Internal Organs ◽

Genome Wide ◽

A Genome

Cattle internal organs as accessible raw materials have a long history of being widely used in beef processing, feed and pharmaceutical industry. These traits not only are of economic interest to breeders, but they are intrinsically linked to many valuable traits, such as growth, health, and productivity. Using the Illumina Bovine HD 770K SNP array, we performed a genome-wide association study for heart weight, liver weight, spleen weight, lung weight, and kidney weight in 1,217 Simmental cattle. In our research, 38 significant single nucleotide polymorphisms (SNPs) ( P < 1.49 × 10−6) were identified for five internal organ weight traits. These SNPs are within or near 13 genes, and some of them have been reported previously, including NDUFAF4, LCORL, BT.94996, SLIT2, FAM184B, LAP3, BBS12, MECOM, CD300LF, HSD17B3, TLR4, MXI1, and MB21D2. In addition, we detected four haplotype blocks on BTA6 containing 18 significant SNPs associated with spleen weight. Our results offer worthy insights into understanding the genetic mechanisms of internal organs' development, with potential application in breeding programs of Simmental beef cattle.

Download Full-text

TCF7L2 lncRNA: a link between bipolar disorder and body mass index through glucocorticoid signaling

Molecular Psychiatry ◽

10.1038/s41380-021-01274-z ◽

2021 ◽

Author(s):

Duan Liu ◽

Thanh Thanh Le Nguyen ◽

Huanyao Gao ◽

Huaizhi Huang ◽

Daniel C. Kim ◽

...

Keyword(s):

Body Mass Index ◽

Bipolar Disorder ◽

Body Mass ◽

Genome Wide Association Study ◽

Induced Pluripotent Stem Cell ◽

Sequencing Data ◽

Peripheral Tissues ◽

Genome Wide ◽

A Genome ◽

Trait Locus

AbstractBipolar disorder (BD) and obesity are highly comorbid. We previously performed a genome-wide association study (GWAS) for BD risk accounting for the effect of body mass index (BMI), which identified a genome-wide significant single-nucleotide polymorphism (SNP) in the gene encoding the transcription factor 7 like 2 (TCF7L2). However, the molecular function of TCF7L2 in the central nervous system (CNS) and its possible role in the BD and BMI interaction remained unclear. In the present study, we demonstrated by studying human induced pluripotent stem cell (hiPSC)-derived astrocytes, cells that highly express TCF7L2 in the CNS, that the BD-BMI GWAS risk SNP is associated with glucocorticoid-dependent repression of the expression of a previously uncharacterized TCF7L2 transcript variant. That transcript is a long non-coding RNA (lncRNA-TCF7L2) that is highly expressed in the CNS but not in peripheral tissues such as the liver and pancreas that are involved in metabolism. In astrocytes, knockdown of the lncRNA-TCF7L2 resulted in decreased expression of the parent gene, TCF7L2, as well as alterations in the expression of a series of genes involved in insulin signaling and diabetes. We also studied the function of TCF7L2 in hiPSC-derived astrocytes by integrating RNA sequencing data after TCF7L2 knockdown with TCF7L2 chromatin-immunoprecipitation sequencing (ChIP-seq) data. Those studies showed that TCF7L2 directly regulated a series of BD risk genes. In summary, these results support the existence of a CNS-based mechanism underlying BD-BMI genetic risk, a mechanism based on a glucocorticoid-dependent expression quantitative trait locus that regulates the expression of a novel TCF7L2 non-coding transcript.

Download Full-text

Transcriptomic and Genome-wide Association Study Reveal Long Noncoding RNAs Responding to Nitrogen Deficiency in Maize

10.21203/rs.3.rs-104831/v1 ◽

2020 ◽

Author(s):

PENG MA ◽

Xiao Zhang ◽

Bowen Luo ◽

Zhen Chen ◽

Xuan He ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Nitrogen Deficiency ◽

Snp Array ◽

Noncoding Rnas ◽

Long Noncoding Rnas ◽

Genome Wide Association ◽

Rna Seq ◽

Genome Wide ◽

A Genome

Abstract Background: Long noncoding RNAs (lncRNAs) play important roles in essential biological processes. However, our understanding of lncRNAs as competing endogenous RNAs (ceRNAs) and their responses to nitrogen stress is still limited.Results: Here, we surveyed the lncRNAs and miRNAs in maize inbred line P178 leaves and roots at the seedling stage under high-nitrogen and low-nitrogen conditions using lncRNA-Seq and small RNA-Seq. A total of 894 differentially expressed lncRNAs and 38 different miRNAs were identified. Co-expression analysis found two lncRNAs and four lncRNA-targets could competitively combine with ZmmiR159 and ZmmiR164, respectively. To dissect the genetic regulatory by which lncRNAs might enable adaptation to limited nitrogen availability. An association mapping panel containing a high-density single–nucleotide polymorphism (SNP) array (56,110 SNPs) combined with variable LN resistance-related phenotypes obtained from hydroponics was used for a genome-wide association study (GWAS). By combining GWAS and RNA-Seq, 170 differently expressed lncRNAs within the range of significant markers were screened. Moreover, 40 consistently LN-responsive genes including those involved in glutamine biosynthesis and nitrogen acquisition in root were identified. Transient expression assays in Nicotiana benthamiana demonstrated LNC_002923 could inhabit ZmmiR159-guided cleavage of Zm00001d015521. Conclusions: These lncRNAs containing trait-associated significant SNPs could consider to be related to root development and nutrient utilization. Taken together, the results of our study can provide new insights into the potential regulatory roles of lncRNAs in response to LN stress, and give valuable information for further screening of candidates as well as the improvement of maize regarding LN-responsive resistance.

Download Full-text

A genome-wide association study for host resistance to Ostreid Herpesvirus in Pacific oysters (Crassostrea gigas)

10.1101/223032 ◽

2017 ◽

Author(s):

Alejandro P. Gutierrez ◽

Tim P. Bearf ◽

Chantelle Hooped ◽

Craig A. Stentort ◽

Matthew B. Sanders ◽

...

Keyword(s):

Host Resistance ◽

Selective Breeding ◽

Genome Wide Association Study ◽

Pacific Oyster ◽

Genetic Resistance ◽

Genome Wide Association ◽

Genotype Data ◽

Oyster Aquaculture ◽

Genome Wide ◽

A Genome

AbstractOstreid herpesvirus (OsHV) can cause mass mortality events in Pacific oyster aquaculture. While various factors impact on the severity of outbreaks, it is clear that genetic resistance of the host is an important determinant of mortality levels. This raises the possibility of selective breeding strategies to improve the genetic resistance of farmed oyster stocks, thereby contributing to disease control. Traditional selective breeding can be augmented by use of genetic markers, either via marker-assisted or genomic selection. The aim of the current study was to investigate the genetic architecture of resistance to OsHV in Pacific oyster, to identify genomic regions containing putative resistance genes, and to inform the use of genomics to enhance efforts to breed for resistance. To achieve this, a population of ~1,000 juvenile oysters were experimentally challenged with a virulent form of OsHV, with samples taken from mortalities and survivors for genotyping and qPCR measurement of viral load. The samples were genotyped using a recently-developed SNP array, and the genotype data were used to reconstruct the pedigree. Using these pedigree and genotype data, the first high density linkage map was constructed for Pacific oyster, containing 20,353 SNPs mapped to the ten pairs of chromosomes. Genetic parameters for resistance to OsHV were estimated, indicating a significant but low heritability for the binary trait of survival and also for viral load measures (h2 0.12 – 0.25). A genome-wide association study highlighted a region of linkage group 6 containing a significant QTL affecting host resistance. These results are an important step towards identification of genes underlying resistance to OsHV in oyster, and a step towards applying genomic data to enhance selective breeding for disease resistance in oyster aquaculture.

Download Full-text

Genome-Wide association study identifies new elements on the genetic basis of quality-related traits in wheat across multiple environments

10.21203/rs.3.rs-99775/v1 ◽

2020 ◽

Author(s):

Zhien Pu ◽

Xueling Ye ◽

Yang Li ◽

Zehou Liu ◽

Bingxin Shi ◽

...

Keyword(s):

Association Study ◽

Complex Traits ◽

Genome Wide Association Study ◽

Snp Array ◽

Mixed Linear Model ◽

Genome Wide Association ◽

Phenotypic Analysis ◽

Genome Wide ◽

A Genome ◽

Genomic Regions

Abstract Backgrounds: Grain protein concentration (GPC), grain starch concentration (GSC), and wet gluten concentration (WGC) are complex traits that determine nutrient concentration, end-use quality, and yield in wheat. To identify the elite and stable loci or genomic regions conferring high GPC, GSC, and WGC, a genome-wide association study (GWAS) based on a mixed linear model (MLM) was performed using 55K single nucleotide polymorphism (SNP) array in a panel of 236 wheat accessions, including 160 commercial varieties and 76 landraces, derived from Sichuan Province, China. The panel was evaluated for GPC, GSC, and WGC at four different fields. Results: Phenotypic analysis showed variation in GPC, GSC, and WGC among the different genotypes and environments. GWAS identified 12 quantitative trait loci (QTL) (-log10(P) > 2.5) associated with these three quality traits in at least two environments and located on chromosomes 1B, 1D, 2A, 2B, 2D, 3B, 3D, 5D, and 7D; the phenotypic variation explained (PVE) by these QTL ranged from 4.2% to 10.7%. Among these, three, seven, and two QTL are associated with GPC, GSC, and WGC, respectively; five QTL (QGsc.sicau-1BL, QGsc.sicau-1DS, QGsc.sicau-2DL.1, QGsc.sicau-2DL.2, QWgc.sicau-5DL) were defined potentially novel Compared with the previously reported QTLs/genes by linkage or association mapping, 5 QTLs (QGsc.sicau-1BL, QGsc.sicau-1DS, QGsc.sicau-2DL.1, QGsc.sicau-2DL.2, QWgc.sicau-5DL) were potentially novel. Furthermore, 21 presumptive candidate genes, which are involved in the metabolism or transportation of all kinds of carbohydrates, photosynthesis, programmed cell death, the balance of abscisic acid and ethylene, within these potentially novel genomic regions were predicted. Conclusions: This study provided new genetic resources and valuable genetic information of nutritional quality to broaden the genetic background and laid the molecular foundation for marker-assisted selection in wheat quality breeding.

Download Full-text

Transcriptomic and genome-wide association study reveal long noncoding RNAs responding to nitrogen deficiency in maize

BMC Plant Biology ◽

10.1186/s12870-021-02847-4 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Peng Ma ◽

Xiao Zhang ◽

Bowen Luo ◽

Zhen Chen ◽

Xuan He ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Nitrogen Deficiency ◽

Snp Array ◽

Noncoding Rnas ◽

Long Noncoding Rnas ◽

Genome Wide Association ◽

Rna Seq ◽

Genome Wide ◽

A Genome

Abstract Background Long noncoding RNAs (lncRNAs) play important roles in essential biological processes. However, our understanding of lncRNAs as competing endogenous RNAs (ceRNAs) and their responses to nitrogen stress is still limited. Results Here, we surveyed the lncRNAs and miRNAs in maize inbred line P178 leaves and roots at the seedling stage under high-nitrogen (HN) and low-nitrogen (LN) conditions using lncRNA-Seq and small RNA-Seq. A total of 894 differentially expressed lncRNAs and 38 different miRNAs were identified. Co-expression analysis found that two lncRNAs and four lncRNA-targets could competitively combine with ZmmiR159 and ZmmiR164, respectively. To dissect the genetic regulatory by which lncRNAs might enable adaptation to limited nitrogen availability, an association mapping panel containing a high-density single–nucleotide polymorphism (SNP) array (56,110 SNPs) combined with variable LN tolerant-related phenotypes obtained from hydroponics was used for a genome-wide association study (GWAS). By combining GWAS and RNA-Seq, 170 differently expressed lncRNAs within the range of significant markers were screened. Moreover, 40 consistently LN-responsive genes including those involved in glutamine biosynthesis and nitrogen acquisition in root were identified. Transient expression assays in Nicotiana benthamiana demonstrated that LNC_002923 could inhabit ZmmiR159-guided cleavage of Zm00001d015521. Conclusions These lncRNAs containing trait-associated significant SNPs could consider to be related to root development and nutrient utilization. Taken together, the results of our study can provide new insights into the potential regulatory roles of lncRNAs in response to LN stress, and give valuable information for further screening of candidates as well as the improvement of maize resistance to LN stress.

Download Full-text

Genome-Wide Association Mapping of Resistance to Fusarium Head Blight Spread and Deoxynivalenol Accumulation in Chinese Elite Wheat Germplasm

Phytopathology ◽

10.1094/phyto-12-18-0484-r ◽

2019 ◽

Vol 109 (7) ◽

pp. 1208-1216 ◽

Cited By ~ 7

Author(s):

Lei Wu ◽

Yu Zhang ◽

Yi He ◽

Peng Jiang ◽

Xu Zhang ◽

...

Keyword(s):

Fusarium Head Blight ◽

Genome Wide Association Study ◽

Snp Array ◽

Snp Markers ◽

Genome Wide Association ◽

Head Blight ◽

Sources Of Resistance ◽

Wheat Germplasm ◽

Genome Wide ◽

A Genome

Improving resistance to Fusarium head blight (FHB) in wheat is crucial in the integrated management of the disease and prevention of deoxynivalenol (DON) contamination in grains. To identify novel sources of resistance, a genome-wide association study (GWAS) was performed using a panel of 213 accessions of elite wheat germplasm of China. The panel was evaluated for FHB severity in four environments and DON content in grains in two environments. High correlations across environments and high heritability were observed for FHB severity and DON content in grains. The panel was also genotyped with the 90K Illumina iSelect single nucleotide polymorphism (SNP) array and 11,461 SNP markers were obtained. The GWAS revealed a total of six and three loci significantly associated with resistance to fungal spread and DON accumulation in at least two environments, respectively. QFHB-2BL.1 tagged by IWB52433 and QFHB-3A tagged by IWB50548 were responsible for resistance to both fungal spread and DON accumulation. In summary, this study provided an overview of FHB resistance resources in elite Chinese wheat germplasm and identified novel resistance loci that could be used for wheat improvement.

Download Full-text

SNPs and GVHD prediction: where to next?

Blood ◽

10.1182/blood-2012-03-409078 ◽

2012 ◽

Vol 119 (22) ◽

pp. 5066-5068 ◽

Cited By ~ 6

Author(s):

Anne M. Dickinson

Keyword(s):

Genome Wide Association Study ◽

Snp Array ◽

Candidate Snps ◽

Cell Transplant ◽

Nucleotide Polymorphisms ◽

Hematopoietic Stem ◽

Novel Approach ◽

Genome Wide ◽

Impute Data ◽

A Genome

The article by Chien at al in this issue of Blood uses a novel approach to assess the role of single nucleotide polymorphisms (SNPs) in acute graft-versus-host disease (GVHD). Using a genome-wide association study (GWAS) employing an Affymetrix GeneChip Genome-Wide Human 500 000 SNP array, they screened 1298 allogeneic hematopoietic stem cell transplant donors and recipients and tested whether the results from 40 previously reported candidate SNPs could be replicated. They also used a novel approach to impute data using IMPUTE software (http://nathgen.stats-ox.ac.uk/impute/impute.html) where the genotyping data were not available.1

Download Full-text