Genome-Wide Association Analyses Reveal Genomic Regions Controlling Canopy Wilting in Soybean

Drought stress causes the greatest soybean [Glycine max (L.) Merr.] yield losses among the abiotic stresses in rain-fed U.S. growing areas. Because less than 10% of U.S. soybean hectares are irrigated, combating this stress requires soybean plants which possess physiological mechanisms to tolerate drought for a period of time. Phenotyping for these mechanisms is challenging, and the genetic architecture for these traits is poorly understood. A morphological trait, slow or delayed canopy wilting, has been observed in a few exotic plant introductions (PIs), and may lead to yield improvement in drought stressed fields. In this study, we visually scored wilting during stress for a panel of 162 genetically diverse maturity group VI-VIII soybean lines genotyped with the SoySNP50K iSelect BeadChip. Field evaluation of canopy wilting was conducted under rain-fed conditions at two locations (Athens, GA and Salina, KS) in 2015 and 2016. Substantial variation in canopy wilting was observed among the genotypes. Using a genome-wide association mapping approach, 45 unique SNPs that tagged 44 loci were associated with canopy wilting in at least one environment with one region identified in a single environment and data from across all environments. Several new soybean accessions were identified with canopy wilting superior to those of check genotypes. The germplasm and genomic regions identified can be used to better understand the slow canopy wilting trait and be incorporated into elite germplasm to improve drought tolerance in soybean.

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

International Journal of Molecular Sciences ◽

10.3390/ijms19082303 ◽

2018 ◽

Vol 19 (8) ◽

pp. 2303 ◽

Cited By ~ 18

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.

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P1.08 Identification of Three Genomic Regions with Multiple Consecutive Prostate Cancer Susceptibility Loci Through a Genome-Wide Association Study in ARAB Population

Annals of Oncology ◽

10.1016/s0923-7534(20)31299-0 ◽

2012 ◽

Vol 23 ◽

pp. v14

Author(s):

L. Chouchane ◽

S. Shan ◽

K. al-Rumaihi ◽

I. al-Bozom ◽

S. al-Said ◽

...

Keyword(s):

Prostate Cancer ◽

Genome Wide Association Study ◽

Cancer Susceptibility ◽

Genome Wide Association ◽

Susceptibility Loci ◽

Arab Population ◽

Prostate Cancer Susceptibility ◽

Genome Wide ◽

A Genome ◽

Genomic Regions

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

10.1101/418509 ◽

2018 ◽

Cited By ~ 1

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.

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

Frontiers in Plant Science ◽

10.3389/fpls.2021.770434 ◽

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.

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Genome-wide Association Study of Anxiety and Stress-related Disorders in the iPSYCH Cohort

10.1101/263855 ◽

2018 ◽

Cited By ~ 9

Author(s):

Sandra M. Meier ◽

Kalevi Trontti ◽

Thomas Damm Als ◽

Mikaela Laine ◽

Marianne Giørtz Pedersen ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Common Mental Disorders ◽

Twin Studies ◽

Genome Wide Association ◽

Sensitivity Analyses ◽

Association Analyses ◽

Genome Wide ◽

A Genome ◽

Wide Range

AbstractAnxiety and stress-related disorders (ASRD) are among the most common mental disorders with the majority of patients suffering from additional disorders. Family and twin studies indicate that genetic and environmental factors are underlying their etiology. As ASRD are likely to configure various expressions of abnormalities in the basic stress-response system, we conducted a genome-wide association study including 12,655 cases with various anxiety and stress-related diagnoses and 19,225 controls. Standard association analyses were performed supplemented by a framework of sensitivity analyses. Variants in PDE4B showed consistent association with ASRD across a wide range of our analyses. In mice models, alternations in PDE4B expression were observed in those mice displaying anxious behavior after exposure to chronic stress. We also showed that 28% of the variance in ASRD was accounted for by common variants and that the genetic signature of ASRD overlapped with psychiatric traits, educational outcomes, obesity-related phenotypes, smoking, and reproductive success.

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

Journal of Basic and Applied Genetics ◽

10.35407/bag.2021.32.01.03 ◽

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

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

Journal of Basic and Applied Genetics ◽

10.35407/bag.2020.32.01.03 ◽

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

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

Plant and Cell Physiology ◽

10.1093/pcp/pcaa057 ◽

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.

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Genome-wide association study (GWAS) for morphological and yield-related traits in an oil palm hybrid (Elaeis oleifera x Elaeis guineensis) population

BMC Plant Biology ◽

10.1186/s12870-019-2153-8 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 3

Author(s):

Jaime A. Osorio-Guarín ◽

Gina A. Garzón-Martínez ◽

Paola Delgadillo-Duran ◽

Silvio Bastidas ◽

Leidy P. Moreno ◽

...

Keyword(s):

Candidate Genes ◽

Oil Palm ◽

Elaeis Guineensis ◽

Genome Wide Association ◽

Hybrid Population ◽

Potential Candidate ◽

Elaeis Oleifera ◽

Genome Wide ◽

A Genome ◽

Genomic Regions

Abstract Background The genus Elaeis has two species of economic importance for the oil palm agroindustry: Elaeis oleifera (O), native to the Americas, and Elaeis guineensis (G), native to Africa. This work provides to our knowledge, the first association mapping study in an interspecific OxG oil palm population, which shows tolerance to pests and diseases, high oil quality, and acceptable fruit bunch production. Results Using genotyping-by-sequencing (GBS), we identified a total of 3776 single nucleotide polymorphisms (SNPs) that were used to perform a genome-wide association analysis (GWAS) in 378 OxG hybrid population for 10 agronomic traits. Twelve genomic regions (SNPs) were located near candidate genes implicated in multiple functional categories, such as tissue growth, cellular trafficking, and physiological processes. Conclusions We provide new insights on genomic regions that mapped on candidate genes involved in plant architecture and yield. These potential candidate genes need to be confirmed for future targeted functional analyses. Associated markers to the traits of interest may be valuable resources for the development of marker-assisted selection in oil palm breeding.

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Genome-wide association and transcriptome analysis suggests total serum ghrelin to be linked with GFRAL

Acta Endocrinologica ◽

10.1530/eje-20-1220 ◽

2021 ◽

Author(s):

Dirk Alexander Wittekind ◽

Markus Scholz ◽

Jürgen Kratzsch ◽

Markus Löffler ◽

Katrin Horn ◽

...

Keyword(s):

Association Study ◽

Energy Homeostasis ◽

Genome Wide Association Study ◽

Statistical Tests ◽

Genome Wide Association ◽

Total Serum ◽

Association Analyses ◽

Genome Wide ◽

A Genome ◽

Serum Ghrelin

Objective: Ghrelin is an orexigenic peptide hormone involved in the regulation of energy homeostasis, food intake and glucose metabolism. Serum levels increase anticipating a meal and fall afterwards. Underlying genetic mechanisms of the ghrelin secretion are unknown. Methods: Total serum ghrelin was measured in 1501 subjects selected from the population-based LIFE-ADULT-sample after an overnight fast. A genome-wide association study (GWAS) was performed. Gene-based expression association analyses (transcriptome-wide association study (TWAS)) are statistical tests associating genetically predicted expression to a certain trait and were done using MetaXcan. Results: In the GWAS, three loci reached genome-wide significance: the WW-domain containing the oxidoreductase-gene (WWOX; p=1.80E-10) on chromosome 16q23.3-24.1 (SNP: rs76823993); the Contactin-Associated Protein-Like 2 gene (CNTNAP2; p=9.0E-9) on chromosome 7q35-q36 (SNP: rs192092592) and the Ghrelin And Obestatin Prepropeptide gene (GHRL; p=2.72E-8) on chromosome 3p25.3 (SNP: rs143729751). In the TWAS, the three genes where expression was strongest associated with serum ghrelin levels was the Ribosomal Protein L36 (RPL36; p=1.3E-06, FDR=0.011, positively correlated), AP1B1 (p=1.1E-5, FDR=0.048, negatively correlated) and the GDNF Family Receptor Alpha Like (GFRAL), receptor of the anorexigenic Growth Differentiation Factor-15 (GDF15), (p=1.8E-05, FDR=0.15, also negatively correlated). Conclusions: The three genome-wide significant genetic loci from the GWA and the genes identified in the TWA are functionally plausible and should initiate further research.

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