scholarly journals Genome-wide association study identifies a major gene for beech bark disease resistance in American beech (Fagus grandifolia Ehrh.)

BMC Genomics ◽  
2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Irina Ćalić ◽  
Jennifer Koch ◽  
David Carey ◽  
Charles Addo-Quaye ◽  
John E. Carlson ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Major Gene ◽  
Fagus Grandifolia ◽  
Genome Wide Association ◽  
Beech Bark Disease ◽  
American Beech ◽  
Genome Wide

scholarly journals Genome-Wide Association Study and QTL Mapping Reveal Genomic Loci Associated with Fusarium Ear Rot Resistance in Tropical Maize Germplasm

2016 ◽  
Vol 6 (12) ◽  
pp. 3803-3815 ◽  
Author(s):  
Jiafa Chen ◽  
Rosemary Shrestha ◽  
Junqiang Ding ◽  
Hongjian Zheng ◽  
Chunhua Mu ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Physical Map ◽  
Genome Wide Association ◽  
Fusarium Ear Rot ◽  
Ear Rot ◽  
Tropical Maize ◽  
Genome Wide

Abstract Fusarium ear rot (FER) incited by Fusarium verticillioides is a major disease of maize that reduces grain quality globally. Host resistance is the most suitable strategy for managing the disease. We report the results of genome-wide association study (GWAS) to detect alleles associated with increased resistance to FER in a set of 818 tropical maize inbred lines evaluated in three environments. Association tests performed using 43,424 single-nucleotide polymorphic (SNPs) markers identified 45 SNPs and 15 haplotypes that were significantly associated with FER resistance. Each associated SNP locus had relatively small additive effects on disease resistance and accounted for 1–4% of trait variation. These SNPs and haplotypes were located within or adjacent to 38 candidate genes, 21 of which were candidate genes associated with plant tolerance to stresses, including disease resistance. Linkage mapping in four biparental populations to validate GWAS results identified 15 quantitative trait loci (QTL) associated with F. verticillioides resistance. Integration of GWAS and QTL to the maize physical map showed eight colocated loci on chromosomes 2, 3, 4, 5, 9, and 10. QTL on chromosomes 2 and 9 are new. These results reveal that FER resistance is a complex trait that is conditioned by multiple genes with minor effects. The value of selection on identified markers for improving FER resistance is limited; rather, selection to combine small effect resistance alleles combined with genomic selection for polygenic background for both the target and general adaptation traits might be fruitful for increasing FER resistance in maize.

scholarly journals Genome-Wide Association Study of H/L Traits in Chicken

Animals ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 260 ◽  
Author(s):  
Bo Zhu ◽  
Qinghe Li ◽  
Ranran Liu ◽  
Maiqing Zheng ◽  
Jie Wen ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Association Study ◽  
Genetic Basis ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Gene Annotation ◽  
Immune Defense ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

Presently, the heterophil-to-lymphocyte (H/L) ratio is being studied extensively as a disease resistance trait. Through intricate mechanisms to identify and destroy pathogenic microorganisms, heterophils play a pivotal role in the immune defense systems of avian species. To reveal the genetic basis and molecular mechanisms affecting the H/L ratio, phenotypic and H/L data from 1650 white feather chicken broilers were used in performing a genome-wide association study. A self-developed, chicken-specific 55K chip was used for heterophils, lymphocytes, and H/L classification, according to individual genomic DNA profiles. We identified five significant single nucleotide polymorphisms (SNPs) when the genome-wide significance threshold was set to 5% (p < 2.42 × 10−6). A total of 15 SNPs obtained seemingly significant levels (p < 4.84 × 10−5). Gene annotation indicated that CARD11 (Caspase recruitment domain family member 11), BRIX1 (Biogenesis of ribosomes BRX1), and BANP (BTG3 associated nuclear protein) play a role in H/L-associated cell regulation and potentially constitute candidate gene regions for cellular functions dependent on H/L ratios. These results lay the foundation for revealing the genetic basis of disease resistance and future marker-assisted selection for disease resistance.

scholarly journals Genome wide association study reveals novel candidate genes associated with productivity and disease resistance to Moniliophthora spp. in cacao (Theobroma cacao L.)

2019 ◽  
Author(s):  
Jaime A. Osorio-Guarín ◽  
Jhon A. Berdugo-Cely ◽  
Roberto A. Coronado-Silva ◽  
Eliana Baez ◽  
Yeirme Jaimes ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Association Study ◽  
Theobroma Cacao ◽  
Genome Wide Association Study ◽  
Economic Benefits ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Moniliophthora Perniciosa ◽  
Genome Wide ◽  
A Genome

ABSTRACTCacao (Theobroma cacao L.), the source of chocolate, is one the most important commodity products for farmers to improve their economic benefits. However, diseases such as frosty pod rot (FPRD) caused by Moniliophthora roreri and witches’ broom (WBD) caused by Moniliophthora perniciosa, limits the increase in yields. Molecular tools can help to develop more rapidly cacao varieties with disease resistance. In the present study, we sequenced by genotyping-by-sequencing (GBS), 229 cacao accessions to examine their genetic diversity and population structure. From those accessions, 102 have been evaluated for disease resistance and productivity to conduct a genome-wide association study (GWAS) based on 9,003 and 8,131 SNPs recovered by mapping against to the annotated cacao genomes (Criollo and Matina). Three promissory accessions for productivity and 10 accessions showing good tolerance to the evaluated diseases were found in the phenotypic evaluation. The work presented herein provides the first association mapping study in cacao using SNP markers based on GBS data. The GWAS identified two genes associated to productivity and seven to disease resistance. The results enriched the knowledge of the genetic regions associated to important traits in cacao that can have significant implications for conservation and breeding strategies such as marker-assisted selection (MAS).

A genome-wide association study confirms APOE as the major gene influencing survival in long-lived individuals

2011 ◽  
Vol 132 (6-7) ◽  
pp. 324-330 ◽  
Author(s):  
Almut Nebel ◽  
Rabea Kleindorp ◽  
Amke Caliebe ◽  
Michael Nothnagel ◽  
Hélène Blanché ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Major Gene ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

0327 Genome-wide association study for supernumerary teats in Swiss Brown Swiss Cattle reveals LGR5 as a major gene on chromosome 5

2016 ◽  
Vol 94 (suppl_5) ◽  
pp. 157-157 ◽  
Author(s):  
A. M. Butty ◽  
M. Frischknecht ◽  
B. Gredler ◽  
C. Baes ◽  
S. Neuenschwander ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Major Gene ◽  
Genome Wide Association ◽  
Chromosome 5 ◽  
Brown Swiss ◽  
Genome Wide ◽  
Brown Swiss Cattle

scholarly journals Genome-Wide Association Study of Resistance to Xanthomonas gardneri in the USDA Pepper (Capsicum) Collection

2019 ◽  
Vol 109 (7) ◽  
pp. 1217-1225 ◽  
Author(s):  
Neha Potnis ◽  
Sandra E. Branham ◽  
Jeffery B. Jones ◽  
W. Patrick Wechter
Keyword(s):  
Disease Resistance ◽  
Association Study ◽  
Plant Pathogens ◽  
Genome Wide Association Study ◽  
Gene Pyramiding ◽  
Genome Wide Association ◽  
Bacterial Spot ◽  
Basal Resistance ◽  
Genome Wide ◽  
A Genome

Bacterial spot Xanthomonas species cause significant disease outbreaks on tomato and pepper in tropical and subtropical regions throughout the world. Host resistance has been one of the key components of integrated disease management approaches to mitigate plant pathogens. Although a number of resistance genes have been identified in pepper against bacterial spot xanthomonads, emergence of bacterial spot pathogen variants capable of overcoming these sources and changing pathogen distributions reinforce the importance of identifying novel candidates to incorporate into breeding programs. We conducted a genome-wide association study (GWAS) on a diverse U.S. Department of Agriculture collection of pepper germplasm including different species of Capsicum to identify novel sources of disease resistance against a highly virulent X. gardneri strain isolated from a recent outbreak. GWAS identified highly significant single nucleotide polymorphisms associated with defoliation in response to infection with X. gardneri. Functionally relevant candidate genes encoded products involved in disease resistance/susceptibility, hormone signaling, and basal resistance against multiple pathogens in various host-pathogen systems. The X. gardneri-resistant genotypes and quantitative trait loci identified in this study provide alleles that could be used for a resistance gene pyramiding effort against different species of bacterial spot xanthomonads in pepper.

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