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 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 Korean soybean core collection: Genotypic and phenotypic diversity population structure and genome-wide association study

PLoS ONE ◽  
2019 ◽  
Vol 14 (10) ◽  
pp. e0224074 ◽  
Author(s):  
Namhee Jeong ◽  
Ki-Seung Kim ◽  
Seongmun Jeong ◽  
Jae-Yoon Kim ◽  
Soo-Kwon Park ◽  
...  
Keyword(s):  
Population Structure ◽  
Association Study ◽  
Core Collection ◽  
Genome Wide Association Study ◽  
Phenotypic Diversity ◽  
Genome Wide Association ◽  
Genome Wide

scholarly journals Identification of genes for salt tolerance and yield-related traits in rice plants grown hydroponically and under saline field conditions by genome-wide association study

Rice ◽  
2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Chen Liu ◽  
Kai Chen ◽  
Xiuqin Zhao ◽  
Xiaoqian Wang ◽  
Congcong Shen ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Grain Yield ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Field Conditions ◽  
Genome Wide Association ◽  
Saline Stress ◽  
Rice Breeding ◽  
Genome Wide

Abstract Background Soil salinity is one of the main environmental conditions that affects rice production. Identifying the genetic loci that affect rice salt tolerance (ST)-related traits at the seedling stage, especially under saline field conditions, is crucial for ST rice breeding by pyramiding ST genes that act at different developmental stages. Results Large phenotypic variations were observed in 708 rice accessions, and yield and its related traits were considerably limited when exposed to salt stress. In a genome-wide association study (GWAS), 2255 marker-trait association signals were detected for all measured traits, and the significant SNPs were distributed in 903 genes. Of these, 43 genes processed same functional annotation, and the gene ontology terms “biological processes” and “molecular function” with the known genes responsive to salt stress in rice. Further haplotype analysis detected 15 promising candidates significantly associated with the target traits, including five known genes and 10 novel genes. We identified seven accessions carrying favorable haplotypes of four genes significantly associated with grain yield that performed well under saline stress conditions. Conclusions Using high density SNPs within genes to conduct GWAS is an effective way to identify candidate genes for salt tolerance in rice. Five known genes (OsMYB6, OsGAMYB, OsHKT1;4, OsCTR3, and OsSUT1) and two newly identified genes (LOC_Os02g49700, LOC_Os03g28300) significantly associated with grain yield and its related traits under saline stress conditions were identified. These promising candidates provide valuable resources for validating potential ST-related genes and will facilitate rice breeding for salt tolerance through marker-assisted selection.

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.

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× 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.

scholarly journals Genome-wide association study in New York Phytophthora capsici isolates reveals loci involved in mating type and mefenoxam sensitivity

2020 ◽  
Author(s):  
Gregory Vogel ◽  
Michael A. Gore ◽  
Christine D. Smart
Keyword(s):  
New York ◽  
Population Structure ◽  
Association Study ◽  
Candidate Genes ◽  
Mating Type ◽  
Genome Wide Association Study ◽  
Phytophthora Capsici ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

AbstractPhytophthora capsici is a soilborne oomycete plant pathogen that causes severe vegetable crop losses in New York (NY) State and worldwide. This pathogen is difficult to manage, in part due to its production of long-lasting sexual spores and its tendency to quickly evolve fungicide resistance. We single-nucleotide polymorphism (SNP) genotyped 252 P. capsici isolates, predominantly from NY, in order to conduct a genome-wide association study for mating type and mefenoxam insensitivity. The population structure and extent of chromosomal copy number variation in this collection of isolates were also characterized. Population structure analyses showed isolates largely clustered by the field site where they were collected, with values of FST between pairs of fields ranging from 0.10 to 0.31. Thirty-three isolates were putative aneuploids, demonstrating evidence for having up to four linkage groups present in more than two copies, and an additional two isolates appeared to be genome-wide triploids. Mating type was mapped to a region on scaffold 4, consistent with previous findings, and mefenoxam insensitivity was associated with several SNP markers at a novel locus on scaffold 62. We identified several candidate genes for mefenoxam sensitivity, including a homolog of yeast ribosome synthesis factor Rrp5, but failed to locate near the scaffold 62 locus any subunits of RNA Polymerase I, the enzyme that has been hypothesized to be the target site of phenylamide fungicides in oomycetes. This work expands our knowledge of the population biology of P. capsici and provides a foundation for functional validation of candidate genes associated with epidemiologically important phenotypes.

scholarly journals Linkage Mapping and Genome-Wide Association Study Reveals Conservative QTLs and Candidate Genes for Fusarium Rot Resistance in Maize

2020 ◽  
Author(s):  
Yabin Wu ◽  
Zijian Zhou ◽  
Chaopei Dong ◽  
Jiafa Chen ◽  
Junqiang Ding ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Phenotypic Variation ◽  
Linkage Mapping ◽  
Genome Wide Association Study ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Genome Wide Association ◽  
Ear Rot ◽  
Genome Wide

Abstract Background: Fusarium ear rot (FER) caused by Fusarium verticillioides is a major disease of maize that reduces grain yield and quality globally. However, there have been few reports of major loci for FER were verified and cloned. Result: To gain a comprehensive understanding of the genetic basis of natural variation in FER resistance, a recombinant inbred lines (RIL) population and one panel of inbred lines were used to map quantitative trait loci (QTL) for resistance. As a result, a total of 10 QTL were identified by linkage mapping under four environments, which were located on six chromosomes and explained 1.0%-7.1% of the phenotypic variation. Epistatic mapping detected four pairs of QTL that showed significant epistasis effects, explaining 2.1%-3.0% of the phenotypic variation. Additionally, 18 single nucleotide polymorphisms (SNPs) were identified across the whole genome by genome-wide association study (GWAS) under five environments. Compared linkage and association mapping revealed five common intervals located on chromosomes 3, 4, and 5 associated with FER resistance, four of which were verified in different near-isogenic lines (NILs) populations. GWAS identified three candidate genes in these consistent intervals, which belonged to the Glutaredoxin protein family , actin-depolymerizing factors (ADFs), and AMP-binding proteins. In addition, two verified FER QTL regions were found consistent with Fusarium cob rot (FCR) and Fusarium seed rot (FSR). Conclusions: These results revealed that multi pathways were involved in FER resistance, which was a complex trait that was controlled by multiple genes with minor effects, and provided important QTL and genes, which could be used in molecular breeding for resistance.

scholarly journals Genome-Wide Association Study and Pathway Analysis for Heterophil/Lymphocyte (H/L) Ratio in Chicken

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1005
Author(s):  
Jie Wang ◽  
Bo Zhu ◽  
Jie Wen ◽  
Qinghe Li ◽  
Guiping Zhao
Keyword(s):  
Association Study ◽  
Pathway Analysis ◽  
Phenotypic Variation ◽  
Genome Wide Association Study ◽  
Genetic Regulation ◽  
Genetic Selection ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Genome

Disease control and prevention have been critical factors in the dramatic growth of the poultry industry. Disease resistance in chickens can be improved through genetic selection for immunocompetence. The heterophil/lymphocyte ratio (H/L) in the blood reflects the immune system status of chickens. Our objective was to conduct a genome-wide association study (GWAS) and pathway analysis to identify possible biological mechanisms involved in H/L traits. In this study, GWAS for H/L was performed in 1317 Cobb broilers to identify significant single-nucleotide polymorphisms (SNPs) associated with H/L. Eight SNPs (p < 1/8068) reached a significant level of association. The significant SNP on GGA 19 (chicken chromosome 19) was in the gene for complement C1q binding protein (C1QBP). The wild-type and mutant individuals showed significant differences in H/L at five identified SNPs (p < 0.05). According to the results of pathway analysis, nine associated pathways (p < 0.05) were identified. By combining GWAS with pathway analysis, we found that all SNPs after QC explained 12.4% of the phenotypic variation in H/L, and 52 SNPs associated with H/L explained as much as 9.7% of the phenotypic variation in H/L. Our findings contribute to understanding of the genetic regulation of H/L and provide theoretical support.

Sign in / Sign up

Export Citation Format

Share Document