scholarly journals 66 A genome-wide association study for gestation length in swine

2019 ◽  
Vol 97 (Supplement_2) ◽  
pp. 40-40
Author(s):  
Garrett See ◽  
Melanie Trenhaile-Gannemann ◽  
Daniel Ciobanu ◽  
Matthew L Spangler ◽  
Benny Mote
Keyword(s):  
Fixed Effects ◽  
Genome Wide Association Study ◽  
Group Development ◽  
Genome Wide Association ◽  
Gestation Length ◽  
Genome Wide ◽  
A Genome ◽  
University Of Nebraska Lincoln ◽  
Genomic Regions ◽  
The University

Abstract The objective of the current study was to conduct a genome-wide association on gestation length (GL) in different parities in swine. Sows (n = 831) belonging to the University of Nebraska – Lincoln resource population (Landrace X Nebraska Index Line) were utilized. GL was defined as the number of days between the final insemination and farrowing. Four traits, GL at parity 1, 2, 3 and 4 (GL1, GL2, GL3 and GL4, respectively) were investigated. Animals which were induced 24h prior to a farrowing event were removed from the analysis. Sows were genotyped with the Illumina SNP60 BeadArray. A Bayes C model with π=0.995 was implemented with fixed effects of contemporary group, development pen, diet, linear and quadratic terms for age at puberty (GL1; P < 0.01), and linear and quadratic terms for farrowing age (GL2; P < 0.01). Results are posterior means of 55,000 samples.Single marker association analysis (SMA) was performed in R utilizing a linear model on SNP from 1-Mb windows (n = 10) which explained the largest proportion of genetic variation in GL1. Top 10 (0.5% of all windows) 1-Mb windows accounted for a limited proportion of genetic variance, 7.75, 4.66, 3.45 and 2.05% in GL1, GL2, GL3 and GL4, respectively. Posterior mean heritability estimates (posterior SD) for GL1, GL2, GL3 and GL4 were 0.33 (0.06), 0.34 (0.07), 0.32 (0.08) and 0.20 (0.08), respectively. The top SNP (ASGA0017859, SSC4, 7.8 Mb) located in one of the two top common genomic regions associated with GL1, GL2 and GL3 displayed a difference of 1.1d in GL1 between alternate homozygotes (P < 0.01). The top SNP from nine of the ten regions were significant (P < 0.05) in the SMA. Two of these regions were in common with GL2 and GL3 where SNP with potential functional effects were found in ZFAT, MAML2 and CCDC82. Results suggest GL is a largely polygenic trait.

scholarly journals Genome-Wide Association Study and Selection Signatures Detect Genomic Regions Associated with Seed Yield and Oil Quality in Flax

2018 ◽  
Vol 19 (8) ◽  
pp. 2303 ◽  
Author(s):  
Frank You ◽  
Jin Xiao ◽  
Pingchuan Li ◽  
Zhen Yao ◽  
Gaofeng Jia ◽  
...  
Keyword(s):  
Association Study ◽  
Seed Yield ◽  
Phenotypic Variation ◽  
Genome Wide Association Study ◽  
Oil Quality ◽  
Genome Wide Association ◽  
Selection Signatures ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

A genome-wide association study (GWAS) was performed on a set of 260 lines which belong to three different bi-parental flax mapping populations. These lines were sequenced to an averaged genome coverage of 19× using the Illumina Hi-Seq platform. Phenotypic data for 11 seed yield and oil quality traits were collected in eight year/location environments. A total of 17,288 single nucleotide polymorphisms were identified, which explained more than 80% of the phenotypic variation for days to maturity (DTM), iodine value (IOD), palmitic (PAL), stearic, linoleic (LIO) and linolenic (LIN) acid contents. Twenty-three unique genomic regions associated with 33 quantitative trait loci (QTL) for the studied traits were detected, thereby validating four genomic regions previously identified. The 33 QTL explained 48–73% of the phenotypic variation for oil content, IOD, PAL, LIO and LIN but only 8–14% for plant height, DTM and seed yield. A genome-wide selective sweep scan for selection signatures detected 114 genomic regions that accounted for 7.82% of the flax pseudomolecule and overlapped with the 11 GWAS-detected genomic regions associated with 18 QTL for 11 traits. The results demonstrate the utility of GWAS combined with selection signatures for dissection of the genetic structure of traits and for pinpointing genomic regions for breeding improvement.

scholarly journals A Genome-Wide Association Study Identifies SNP Markers for Virulence in Magnaporthe oryzae Isolates from Sub-Saharan Africa

2018 ◽  
Author(s):  
Veena Devi Ganeshan ◽  
Stephen O. Opiyo ◽  
Samuel K. Mutiga ◽  
Felix Rotich ◽  
David M. Thuranira ◽  
...  
Keyword(s):  
Association Study ◽  
Magnaporthe Oryzae ◽  
Genome Wide Association Study ◽  
Significant Snps ◽  
Sub Saharan Africa ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Sub Saharan ◽  
Genomic Regions

ABSTRACTThe fungal phytopathogen Magnaporthe oryzae causes blast disease in cereals such as rice and finger millet worldwide. In this study, we assessed genetic diversity of 160 isolates from nine sub-Saharan Africa (SSA) and other principal rice producing countries and conducted a genome-wide association study (GWAS) to identify the genomic regions associated with virulence of M. oryzae. GBS of isolates provided a large and high-quality 617K single nucleotide polymorphism (SNP) dataset. Disease ratings for each isolate was obtained by inoculating them onto differential lines and locally-adapted rice cultivars. Genome-wide association studies were conducted using the GBS dataset and sixteen disease rating datasets. Principal Component Analysis (PCA) was used an alternative to population structure analysis for studying population stratification from genotypic data. A significant association between disease phenotype and 528 SNPs was observed in six GWA analyses. Homology of sequences encompassing the significant SNPs was determined to predict gene identities and functions. Seventeen genes recurred in six GWA analyses, suggesting a strong association with virulence. Here, the putative genes/genomic regions associated with the significant SNPs are presented.

scholarly journals Genome-Wide Association Study of Root Mealiness and Other Texture-Associated Traits in Cassava

2021 ◽  
Vol 12 ◽  
Author(s):  
Kelechi Uchendu ◽  
Damian Ndubuisi Njoku ◽  
Agre Paterne ◽  
Ismail Yusuf Rabbi ◽  
Daniel Dzidzienyo ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Phenotypic Data ◽  
Genome Wide ◽  
A Genome ◽  
Breeding Programmes ◽  
Vegetables And Fruits ◽  
Genomic Regions

Cassava breeders have made significant progress in developing new genotypes with improved agronomic characteristics such as improved root yield and resistance against biotic and abiotic stresses. However, these new and improved cassava (Manihot esculenta Crantz) varieties in cultivation in Nigeria have undergone little or no improvement in their culinary qualities; hence, there is a paucity of genetic information regarding the texture of boiled cassava, particularly with respect to its mealiness, the principal sensory quality attribute of boiled cassava roots. The current study aimed at identifying genomic regions and polymorphisms associated with natural variation for root mealiness and other texture-related attributes of boiled cassava roots, which includes fibre, adhesiveness (ADH), taste, aroma, colour, and firmness. We performed a genome-wide association (GWAS) analysis using phenotypic data from a panel of 142 accessions obtained from the National Root Crops Research Institute (NRCRI), Umudike, Nigeria, and a set of 59,792 high-quality single nucleotide polymorphisms (SNPs) distributed across the cassava genome. Through genome-wide association mapping, we identified 80 SNPs that were significantly associated with root mealiness, fibre, adhesiveness, taste, aroma, colour and firmness on chromosomes 1, 4, 5, 6, 10, 13, 17 and 18. We also identified relevant candidate genes that are co-located with peak SNPs linked to these traits in M. esculenta. A survey of the cassava reference genome v6.1 positioned the SNPs on chromosome 13 in the vicinity of Manes.13G026900, a gene recognized as being responsible for cell adhesion and for the mealiness or crispness of vegetables and fruits, and also known to play an important role in cooked potato texture. This study provides the first insights into understanding the underlying genetic basis of boiled cassava root texture. After validation, the markers and candidate genes identified in this novel work could provide important genomic resources for use in marker-assisted selection (MAS) and genomic selection (GS) to accelerate genetic improvement of root mealiness and other culinary qualities in cassava breeding programmes in West Africa, especially in Nigeria, where the consumption of boiled and pounded cassava is low.

scholarly journals MULTI-TRAIT MODELS FOR GENOMIC REGIONS ASSOCIATED WITH MAL DE RÍO CUARTO AND BACTERIAL DISEASE IN MAIZE

2021 ◽  
Vol 32 (Issue 1) ◽  
pp. 25-33
Author(s):  
M. Ruiz ◽  
E.A. Rossi ◽  
N.C. Bonamico ◽  
M.G. Balzarini
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Mixed Linear Model ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Bacterial Disease ◽  
Maize Germplasm ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

Maize (Zea Mays L.) production has been greatly benefited from the improvement of inbred lines in regard to the resistance to diseases. However, the absence of resistant genotypes to bacteriosis is remarkable. The aim of the study was to identify genomic regions for resistance to Mal de Río Cuarto (MRC) and to bacterial disease (BD) in a diverse maize germplasm evaluated in the Argentinian region where MRC virus is endemic. A maize diverse population was assessed for both diseases during the 2019-2020 crop season. Incidence and severity of MRC and BD were estimated for each line and a genome wide association study (GWAS) was conducted with 78,376 SNP markers. A multi-trait mixed linear model was used for simultaneous evaluation of resistance to MRC and BD in the scored lines. The germplasm showed high genetic variability for both MRC and BD resistance. No significant genetic correlation was observed between the response to both diseases. Promising genomic regions for resistance to MRC and BD were identified and will be confirmed in further trials. Key words: maize disease; genome wide association study; SNP; multi-trait model

scholarly journals MULTI-TRAIT MODELS FOR GENOMIC REGIONS ASSOCIATED WITH MAL DE RÍO CUARTO AND BACTERIAL DISEASE IN MAIZE

2021 ◽  
Vol 32 (Issue 1) ◽  
pp. 25-33
Author(s):  
M. Ruiz ◽  
E.A. Ross ◽  
N.C. Bonamico ◽  
M.G. Balzarini
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Mixed Linear Model ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Bacterial Disease ◽  
Maize Germplasm ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

Maize (Zea Mays L.) production has been greatly benefited from the improvement of inbred lines in regard to the resistance to diseases. However, the absence of resistant genotypes to bacteriosis is remarkable. The aim of the study was to identify genomic regions for resistance to Mal de Río Cuarto (MRC) and to bacterial disease (BD) in a diverse maize germplasm evaluated in the Argentinian region where MRC virus is endemic. A maize diverse population was assessed for both diseases during the 2019-2020 crop season. Incidence and severity of MRC and BD were estimated for each line and a genome wide association study (GWAS) was conducted with 78,376 SNP markers. A multi-trait mixed linear model was used for simultaneous evaluation of resistance to MRC and BD in the scored lines. The germplasm showed high genetic variability for both MRC and BD resistance. No significant genetic correlation was observed between the response to both diseases. Promising genomic regions for resistance to MRC and BD were identified and will be confirmed in further trials. Key words: maize disease; genome wide association study; SNP; multi-trait model

scholarly journals A Genome-Wide Association Study for Resistance to the Insect Pest Leptocybe invasa in Eucalyptus grandis Reveals Genomic Regions and Positional Candidate Defense Genes

2020 ◽  
Vol 61 (7) ◽  
pp. 1285-1296
Author(s):  
Lorraine Mhoswa ◽  
Marja M O’Neill ◽  
Makobatjatji M Mphahlele ◽  
Caryn N Oates ◽  
Kitt G Payn ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Eucalyptus Grandis ◽  
Nucleotide Binding ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Leptocybe Invasa ◽  
Genomic Regions

Abstract The galling insect, Leptocybe invasa, causes significant losses in plantations of various Eucalyptus species and hybrids, threatening its economic viability. We applied a genome-wide association study (GWAS) to identify single-nucleotide polymorphism (SNP) markers associated with resistance to L. invasa. A total of 563 insect-challenged Eucalyptus grandis trees, from 61 half-sib families, were genotyped using the EUChip60K SNP chip, and we identified 15,445 informative SNP markers in the test population. Multi-locus mixed-model (MLMM) analysis identified 35 SNP markers putatively associated with resistance to L. invasa based on four discreet classes of insect damage scores: (0) not infested, (1) infested showing evidence of oviposition but no gall development, (2) infested with galls on leaves, midribs or petioles and (3) stunting and lethal gall formation. MLMM analysis identified three associated genomic regions on chromosomes 3, 7 and 8 jointly explaining 17.6% of the total phenotypic variation. SNP analysis of a validation population of 494 E. grandis trees confirmed seven SNP markers that were also detected in the initial association analysis. Based on transcriptome profiles of resistant and susceptible genotypes from an independent experiment, we identified several putative candidate genes in associated genomic loci including Nucleotide-binding ARC- domain (NB-ARC) and toll-interleukin-1-receptor-Nucleotide binding signal- Leucine rich repeat (TIR-NBS-LRR) genes. Our results suggest that Leptocybe resistance in E. grandis may be influenced by a few large-effect loci in combination with minor effect loci segregating in our test and validation populations.

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

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.

scholarly journals Genome-wide association study reveals genetic link between diarrhea-associated Entamoeba histolytica infection and inflammatory bowel disease

2017 ◽  
Author(s):  
Genevieve L Wojcik ◽  
Chelsea Marie ◽  
Mayuresh M Abhyankar ◽  
Nobuya Yoshida ◽  
Koji Watanabe ◽  
...  
Keyword(s):  
Inflammatory Bowel Disease ◽  
Association Study ◽  
Entamoeba Histolytica ◽  
Bowel Disease ◽  
Fixed Effects ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Inflammatory Bowel

AbstractDiarrhea is the second leading cause of death for children globally, causing 760,000 deaths each year in children under the age of 5. Amoebic dysentery contributes significantly to this burden, especially in developing countries. We hypothesize that genetic variation contributes to susceptibility to diarrhea-associated Entamoeba histolytica infection in Bangladeshi infants; thus, we conducted a genome-wide association study (GWAS) in two independent birth cohorts of diarrhea-associated E. histolytica infection. Cases were defined as children with at least one diarrheal episode positive for E. histolytica through either PCR or ELISA within the first year of life. Controls were children without any episodes positive for E. histolytica in the same time frame. Meta-analyses under a fixed-effects inverse variance weighting model identified variants in two neighboring genes on chromosome 10: CUL2 (cullin 2) and CREM (cAMP responsive element modulator) associated with E. histolytica infection, with SNP rs58000832 achieving genome-wide significance (Pmeta=4.2x10−10). Each additional risk allele (an intergenic insertion between CREM and CCNY) of rs58000832 conferred 2.5 increased odds of a diarrhea-associated E. histolytica infection. The most associated SNP within a gene was in an intron of CREM (rs58468685, Pmeta=2.3x10−9), which with CUL2, has been implicated as a susceptibility locus for Inflammatory Bowel Disease (IBD) and Crohn’s Disease. Gene expression resources suggest these loci are related to the higher expression of CREM, but not CUL2. Increased CREM expression is also observed in early E. histolytica infection. Further, CREM-/- mice were more susceptible to E. histolytica amebic colitis. These genetic associations reinforce the pathological similarities observed in gut inflammation between E. histolytica infection and IBD.

scholarly journals Genome-Wide Association Study and Selection Signatures Detect Genomic Regions Associated with Seed Yield and Oil Quality in Flax

2018 ◽  
Author(s):  
Frank You ◽  
Jin Xiao ◽  
Pingchuan Li ◽  
Zhen Yao ◽  
Gaofeng Jia ◽  
...  
Keyword(s):  
Association Study ◽  
Seed Yield ◽  
Phenotypic Variation ◽  
Genome Wide Association Study ◽  
Oil Quality ◽  
Genome Wide Association ◽  
Selection Signatures ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

A genome-wide association study (GWAS) was performed on a set of 260 lines which belong to three different bi-parental flax mapping populations. These lines were sequenced to an averaged genome coverage of 19&times; using the Illumina Hi-Seq platform. Phenotypic data for 11 seed yield and oil quality traits were collected in eight year/location environments. A total of 17,288 single nucleotide polymorphisms were identified, which explained more than 80% of the phenotypic variation for days to maturity (DTM), iodine value (IOD), palmitic (PAL), stearic, linoleic (LIO) and linolenic (LIN) acid contents. Twenty-three unique genomic regions associated with 33 QTL for the studied traits were detected, thereby validating four genomic regions previously identified. The 33 QTL explained 48-73% of the phenotypic variation for oil content, IOD, PAL, LIO and LIN but only 8-14% for plant height, DTM and seed yield. A genome-wide selective sweep scan for selection signatures detected 114 genomic regions that accounted for 7.82% of the flax pseudomolecule and overlapped with the 11 GWAS-detected genomic regions associated with 18 QTL for 11 traits. The results demonstrate the utility of GWAS combined with selection signatures for dissection of the genetic structure of traits and for pinpointing genomic regions for breeding improvement.

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