scholarly journals Genome-Wide Association Study of Spot Form of Net Blotch Resistance in the Upper Midwest Barley Breeding Programs

2017 ◽  
Vol 107 (1) ◽  
pp. 100-108 ◽  
Author(s):  
R. R. Burlakoti ◽  
S. Gyawali ◽  
S. Chao ◽  
K. P. Smith ◽  
R. D. Horsley ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
The United States ◽  
Genome Wide Association ◽  
Net Blotch ◽  
Upper Midwest ◽  
Breeding Programs ◽  
Breeding Lines ◽  
Barley Breeding ◽  
Genome Wide

Pyrenophora teres f. maculata, the causal agent of spot form of net blotch (SFNB), is an emerging pathogen of barley in the United States and Australia. Compared with net form of net blotch (NFNB), less is known in the U.S. Upper Midwest barley breeding programs about host resistance and quantitative trait loci (QTL) associated with SFNB in breeding lines. The main objective of this study was to identify QTL associated with SFNB resistance in the Upper Midwest two-rowed and six-rowed barley breeding programs using a genome-wide association study approach. A total of 376 breeding lines of barley were evaluated for SFNB resistance at the seedling stage in the greenhouse in Fargo in 2009. The lines were genotyped with 3,072 single nucleotide polymorphism (SNP) markers. Phenotypic evaluation showed a wide range of variability among populations from the four breeding programs and the two barley-row types. The two-rowed barley lines were more susceptible to SFNB than the six-rowed lines. Continuous distributions of SFNB severity indicate the quantitative nature of SFNB resistance. The mixed linear model (MLM) analysis, which included both population structure and kinship matrices, was used to identify significant SNP-SFNB associations. Principal component analysis was used to control false marker-trait association. The linkage disequilibrium (LD) estimates varied among chromosomes (10 to 20 cM). The MLM analysis identified 10 potential QTL in barley: SFNB-2H-8-10, SFNB-2H-38.03, SFNB-3H-58.64, SFNB-3H-78.53, SFNB-3H-91.88, SFNB-3H-117.1, SFNB-5H-155.3, SFNB-6H-5.4, SFNB-6H-33.74, and SFNB-7H-34.82. Among them, four QTL (SFNB-2H-8-10, SFNB-2H-38.03 SFNB-3H-78.53, and SFNB-3H-117.1) have not previously been published. Identification of SFNB resistant lines and QTL associated with SFNB resistance in this study will be useful in the development of barley genotypes with better SFNB resistance.

A genome-wide association study of malting quality across eight U.S. barley breeding programs

2015 ◽  
Vol 128 (4) ◽  
pp. 705-721 ◽  
Author(s):  
Mohsen Mohammadi ◽  
Thomas K. Blake ◽  
Allen D. Budde ◽  
Shiaoman Chao ◽  
Patrick M. Hayes ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Malting Quality ◽  
Breeding Programs ◽  
Barley Breeding ◽  
Genome Wide ◽  
A Genome

scholarly journals Genome-Wide Association Study of Natural Variation in Arabidopsis Exposed to Acid Mine Drainage Toxicity and Validation of Associated Genes with Reverse Genetics

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 191
Author(s):  
Bandana Ghimire ◽  
Thangasamy Saminathan ◽  
Abiodun Bodunrin ◽  
Venkata Lakshmi Abburi ◽  
Arjun Ojha Kshetry ◽  
...  
Keyword(s):  
Acid Mine Drainage ◽  
Association Study ◽  
Root Length ◽  
Natural Variation ◽  
Genome Wide Association Study ◽  
Mine Drainage ◽  
The United States ◽  
Genome Wide Association ◽  
Acid Mine ◽  
Genome Wide

Acid mine drainage (AMD) is a huge environmental problem in mountain-top mining regions worldwide, including the Appalachian Mountains in the United States. This study applied a genome-wide association study (GWAS) to uncover genomic loci in Arabidopsis associated with tolerance to AMD toxicity. We characterized five major root phenotypes—cumulative root length, average root diameter, root surface area, root volume, and primary root length—in 180 Arabidopsis accessions in response to AMD-supplemented growth medium. GWAS of natural variation in the panel revealed genes associated with tolerance to an acidic environment. Most of these genes were transcription factors, anion/cation transporters, metal transporters, and unknown proteins. Two T-DNA insertion mutants, At1g63005 (miR399b) and At2g05635 (DEAD helicase RAD3), showed enhanced acidity tolerance. Our GWAS and the reverse genetic approach revealed genes involved in conferring tolerance to coal AMD. Our results indicated that proton resistance in hydroponic conditions could be an important index to improve plant growth in acidic soil, at least in acid-sensitive plant species.

scholarly journals Genome-wide association study implicates CHRNA2 in cannabis use disorder

2017 ◽  
Author(s):  
Ditte Demontis ◽  
Veera Manikandan Rajagopal ◽  
Thomas D. Als ◽  
Jakob Grove ◽  
Jonatan Pallesen ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Significant Risk ◽  
The United States ◽  
Cannabis Use ◽  
Genome Wide Association ◽  
Cannabis Use Disorder ◽  
Genome Wide ◽  
Independent Population ◽  
A Genome

Introductory paragraphCannabis is the most frequently used illicit psychoactive substance worldwide1. Life time use has been reported among 35-40% of adults in Denmark2 and the United States3. Cannabis use is increasing in the population4–6 and among users around 9% become dependent7. The genetic risk component is high with heritability estimates of 518–70%9. Here we report the first genome-wide significant risk locus for cannabis use disorder (CUD, P=9.31×10−12) that replicates in an independent population (Preplication=3.27×10−3, Pmetaanalysis=9.09×10−12). The finding is based on a genome-wide association study (GWAS) of 2,387 cases and 48,985 controls followed by replication in 5,501 cases and 301,041 controls. The index SNP (rs56372821) is a strong eQTL for CHRNA2 and analyses of the genetic regulated gene expressions identified significant association of CHRNA2 expression in cerebellum with CUD. This indicates a potential therapeutic use in CUD of compounds with agonistic effect on the neuronal acetylcholine receptor alpha-2 subunit encoded by CHRNA2. At the polygenic level analyses revealed a significant decrease in the risk of CUD with increased load of variants associated with cognitive performance.

scholarly journals Genome Wide Association Study of Seedling and Adult Plant Leaf Rust Resistance in Elite Spring Wheat Breeding Lines

PLoS ONE ◽  
2016 ◽  
Vol 11 (2) ◽  
pp. e0148671 ◽  
Author(s):  
Liangliang Gao ◽  
M. Kathryn Turner ◽  
Shiaoman Chao ◽  
James Kolmer ◽  
James A. Anderson
Keyword(s):  
Association Study ◽  
Spring Wheat ◽  
Rust Resistance ◽  
Genome Wide Association Study ◽  
Leaf Rust Resistance ◽  
Wheat Breeding ◽  
Genome Wide Association ◽  
Adult Plant ◽  
Breeding Lines ◽  
Genome Wide

scholarly journals Genome-wide association study suggests an independent genetic basis of zinc and cadmium concentrations in fresh sweet corn kernels

2021 ◽  
Author(s):  
Matheus Baseggio ◽  
Matthew Murray ◽  
Di Wu ◽  
Gregory Ziegler ◽  
Nicholas Kaczmar ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Sweet Corn ◽  
The United States ◽  
Zinc Homeostasis ◽  
Genome Wide Association ◽  
Association Panel ◽  
Elemental Profile ◽  
Genome Wide ◽  
Corn Kernels

Abstract Despite being one of the most consumed vegetables in the United States, the elemental profile of sweet corn (Zea mays L.) is limited in its dietary contributions. To address this through genetic improvement, a genome-wide association study was conducted for the concentrations of 15 elements in fresh kernels of a sweet corn association panel. In concordance with mapping results from mature maize kernels, we detected a probable pleiotropic association of zinc and iron concentrations with nicotianamine synthase5 (nas5), which purportedly encodes an enzyme involved in synthesis of the metal chelator nicotianamine. Additionally, a pervasive association signal was identified for cadmium concentration within a recombination suppressed region on chromosome 2. The likely causal gene underlying this signal was heavy metal ATPase3 (hma3), whose counterpart in rice, OsHMA3, mediates vacuolar sequestration of cadmium and zinc in roots, whereby regulating zinc homeostasis and cadmium accumulation in grains. In our association panel, hma3 associated with cadmium but not zinc accumulation in fresh kernels. This finding implies that selection for low cadmium will not affect zinc levels in fresh kernels. Although less resolved association signals were detected for boron, nickel, and calcium, all 15 elements were shown to have moderate predictive abilities via whole-genome prediction. Collectively, these results help enhance our genomics-assisted breeding efforts centered on improving the elemental profile of fresh sweet corn kernels.

A genome-wide association study to detect genetic variation for postpartum dysgalactia syndrome in five commercial pig breeding lines

2013 ◽  
Vol 44 (5) ◽  
pp. 502-508 ◽  
Author(s):  
Regine Preissler ◽  
Jens Tetens ◽  
Kerstin Reiners ◽  
Holger Looft ◽  
Nicole Kemper
Keyword(s):  
Genetic Variation ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Breeding Lines ◽  
Genome Wide ◽  
A Genome

scholarly journals Genome-Wide Association Study of Waterlogging Tolerance in Barley (Hordeum vulgare L.) Under Controlled Field Conditions

2021 ◽  
Vol 12 ◽  
Author(s):  
Ana Borrego-Benjumea ◽  
Adam Carter ◽  
Min Zhu ◽  
James R. Tucker ◽  
Meixue Zhou ◽  
...  
Keyword(s):  
Population Structure ◽  
Association Study ◽  
Phenotypic Variation ◽  
Abiotic Stresses ◽  
Genome Wide Association Study ◽  
Field Conditions ◽  
Genome Wide Association ◽  
Waterlogging Tolerance ◽  
Barley Breeding ◽  
Genome Wide

Waterlogging is one of the main abiotic stresses severely reducing barley grain yield. Barley breeding programs focusing on waterlogging tolerance require an understanding of genetic loci and alleles in the current germplasm. In this study, 247 worldwide spring barley genotypes grown under controlled field conditions were genotyped with 35,926 SNPs with minor allele frequency (MAF) > 0.05. Significant phenotypic variation in each trait, including biomass, spikes per plant, grains per plant, kernel weight per plant, plant height and chlorophyll content, was observed. A genome-wide association study (GWAS) based on linkage disequilibrium (LD) for waterlogging tolerance was conducted. Population structure analysis divided the population into three subgroups. A mixed linkage model using both population structure and kinship matrix (Q+K) was performed. We identified 17 genomic regions containing 51 significant waterlogging-tolerance-associated markers for waterlogging tolerance response, accounting for 5.8–11.5% of the phenotypic variation, with a majority of them localized on chromosomes 1H, 2H, 4H, and 5H. Six novel QTL were identified and eight potential candidate genes mediating responses to abiotic stresses were located at QTL associated with waterlogging tolerance. To our awareness, this is the first GWAS for waterlogging tolerance in a worldwide barley collection under controlled field conditions. The marker-trait associations could be used in the marker-assisted selection of waterlogging tolerance and will facilitate barley breeding.

scholarly journals Genetic Diversity and Genome-Wide Association Study of Seed Aspect Ratio Using a High-Density SNP Array in Peanut (Arachis hypogaea L.)

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 2
Author(s):  
Kunyan Zou ◽  
Ki-Seung Kim ◽  
Kipoong Kim ◽  
Dongwoo Kang ◽  
Yu-Hyeon Park ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Aspect Ratio ◽  
Association Study ◽  
Arachis Hypogaea ◽  
Genome Wide Association Study ◽  
Snp Array ◽  
The United States ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Arachis Hypogaea L

Peanut (Arachis hypogaea L.) is one of the important oil crops of the world. In this study, we aimed to evaluate the genetic diversity of 384 peanut germplasms including 100 Korean germplasms and 284 core collections from the United States Department of Agriculture (USDA) using an Axiom_Arachis array with 58K single-nucleotide polymorphisms (SNPs). We evaluated the evolutionary relationships among 384 peanut germplasms using a genome-wide association study (GWAS) of seed aspect ratio data processed by ImageJ software. In total, 14,030 filtered polymorphic SNPs were identified from the peanut 58K SNP array. We identified five SNPs with significant associations to seed aspect ratio on chromosomes Aradu.A09, Aradu.A10, Araip.B08, and Araip.B09. AX-177640219 on chromosome Araip.B08 was the most significantly associated marker in GAPIT and Regularization method. Phosphoenolpyruvate carboxylase (PEPC) was found among the eleven genes within a linkage disequilibrium (LD) of the significant SNPs on Araip.B08 and could have a strong causal effect in determining seed aspect ratio. The results of the present study provide information and methods that are useful for further genetic and genomic studies as well as molecular breeding programs in peanuts.

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