scholarly journals Genome-wide association mapping identifies yellow rust resistance loci in Ethiopian durum wheat germplasm

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0243675
Author(s):  
Sisay Kidane Alemu ◽  
Ayele Badebo Huluka ◽  
Kassahun Tesfaye ◽  
Teklehaimanot Haileselassie ◽  
Cristobal Uauy
Keyword(s):  
Disease Resistance ◽  
Association Study ◽  
Durum Wheat ◽  
Rust Resistance ◽  
Yellow Rust ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Population Structure Analysis ◽  
A Genome ◽  
Yellow Rust Resistance

Durum wheat is an important cereal grown in Ethiopia, a country which is also its center for genetic diversity. Yellow (stripe) rust caused by Puccinia striiformis fsp tritici is one of the most devastating diseases threatening Ethiopian wheat production. To identify sources of genetic resistance and combat this pathogen, we conducted a genome wide association study of yellow rust resistance on 300 durum wheat accessions comprising 261 landraces and 39 cultivars. The accessions were evaluated for their field resistance using a modified Cobb scale at Meraro, Kulumsa and Chefe Donsa in the 2015 and 2016 main growing seasons. Analysis of the 35K Axiom Array genotyping data of the panel resulted in a total of 8,797 polymorphic SNPs of which 7,093 were used in subsequent analyses. Population structure analysis suggested two groups in which the cultivars clearly stood out separately from the landraces. Eleven SNPs significantly associated with yellow rust resistance were identified on four chromosomes (1A, 1B, 2B, and 5A) which defined at least five genomic loci. Six of the SNPs were consistently identified on chromosome 1B singly at each and combined overall environments which explained 62.6–64.0% of the phenotypic variation (R2). Resistant allele frequency ranged from 14.0–71.0%; Zooming in to the identified resistance loci revealed the presence of disease resistance related genes involved in the plant defense system such as the ABC transporter gene family, disease resistance protein RPM1 (NBS-LRR class), Receptor kinases and Protein kinases. This study has provided SNPs for tracking the loci associated with yellow rust resistance and a diversity panel which can be used for association study of other agriculturally important traits in durum wheat.

scholarly journals Genome-wide association mapping identifies Yellow Rust resistance locus in Ethiopian Durum Wheat germplasm

2020 ◽  
Author(s):  
Sisay Kidane Alemu ◽  
Ayele Badebo Huluka ◽  
Kassahun Tesfaye Geletu ◽  
Cristobal Uauy
Keyword(s):  
Durum Wheat ◽  
Rust Resistance ◽  
Yellow Rust ◽  
Genome Wide Association ◽  
Lattice Design ◽  
Genome Wide ◽  
Population Structure Analysis ◽  
Significant Difference ◽  
Yellow Rust Resistance ◽  
Improvement Programs

AbstractDurum wheat is an important cereal grown in Ethiopia, a country which is also its center for genetic diversity. Yellow (stripe) rust caused by Puccinia striiformis fsp tritici is one of the most devastating diseases threatening Ethiopian wheat production. To identify sources of genetic resistance to combat this pathogen, we conducted a genome wide association study of yellow rust resistance on 300 durum wheat accessions comprising 261 landraces and 39 cultivars. The accessions were evaluated for their field resistance in an alpha lattice design (10 × 30) in two replications at Meraro, Kulumsa and Chefe-Donsa in the 2015 and 2016 main growing seasons. Disease Scoring was carried out using a modified Cobb scale and then converted to Coefficient of Infection (CI). Analysis of the 35K Axiom Array genotyping data resulted in a total of 8,797 polymorphic SNPs of which 7,093 were used in subsequent analyses. Population structure analysis suggested two groups in which the cultivars clearly stood out separately from the landraces. We identified twelve SNPs significantly associated with yellow rust resistance across four chromosomes (1A, 1B, 2B, and 7B). Six of the SNPs (AX-95171339, AX-94436448, AX-95238778, AX-95096041, AX-94730403 & AX-94427201), were consistently identified on chromosome 1B at the three field locations and combined across the six environments. The phenotypic variation (R2) explained by all six SNPs on chromosome 1B ranged from 63.7 – 65.4%. Locus-based analysis of phenotypic values between resistant and susceptible allele resulted in a significant difference at (p < 0.001). Further investigation across the genomic interval encompassing the identified loci indicated the presence of disease resistance protein (NBS-LRR class) family and RPM1 in the vicinity of the loci. This study provides SNPs for tracking the QTL associated with yellow rust resistance in durum wheat improvement programs.

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).

scholarly journals A Genome-Wide Association Study of Highly Heritable Agronomic Traits in Durum Wheat

2019 ◽  
Vol 10 ◽  
Author(s):  
Shubin Wang ◽  
Steven Xu ◽  
Shiaoman Chao ◽  
Qun Sun ◽  
Shuwei Liu ◽  
...  
Keyword(s):  
Association Study ◽  
Durum Wheat ◽  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

scholarly journals Genome-Wide Association Study in Wheat Identifies Resistance to the Cereal Cyst Nematode Heterodera filipjevi

2016 ◽  
Vol 106 (10) ◽  
pp. 1128-1138 ◽  
Author(s):  
Shree R. Pariyar ◽  
Abdelfattah A. Dababat ◽  
Wiebke Sannemann ◽  
Gul Erginbas-Orakci ◽  
Abdelnaser Elashry ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Phenotypic Diversity ◽  
Cyst Nematode ◽  
Genome Wide Association ◽  
Cyst Nematodes ◽  
Genome Wide ◽  
Population Structure Analysis ◽  
A Genome ◽  
Heterodera Filipjevi

The cyst nematode Heterodera filipjevi is a plant parasite causing substantial yield loss in wheat. Resistant cultivars are the preferred method of controlling cyst nematodes. Association mapping is a powerful approach to detect associations between phenotypic variation and genetic polymorphisms; in this way favorable traits such as resistance to pathogens can be located. Therefore, a genome-wide association study of 161 winter wheat accessions was performed with a 90K iSelect single nucleotide polymorphism (SNP) chip. Population structure analysis grouped into two major subgroups and first principal component accounted 6.16% for phenotypic diversity. The genome-wide linkage disequilibrium across wheat was 3 cM. Eleven quantitative trait loci (QTLs) on chromosomes 1AL, 2AS, 2BL, 3AL, 3BL, 4AS, 4AL, 5BL, and 7BL were identified using a mixed linear model false discovery rate of P < 0.01 that explained 43% of total genetic variation. This is the first report of QTLs conferring resistance to H. filipjevi in wheat. Eight QTLs on chromosomes 1AL, 2AS, 2BL, 3AL, 4AL, and 5BL were linked to putative genes known to be involved in plant−pathogen interactions. Two other QTLs on 3BL and one QTL on 7BL linked to putative genes known to be involved in abiotic stress.

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.

scholarly journals Genome-Wide Association Study Reveals Novel Candidate Genes Associated with Productivity and Disease Resistance to Moniliophthora spp. in Cacao (Theobroma cacao L.)

2020 ◽  
Vol 10 (5) ◽  
pp. 1713-1725 ◽  
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 ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Moniliophthora Perniciosa ◽  
Genome Wide ◽  
A Genome ◽  
Frosty Pod Rot

Cacao (Theobroma cacao L.), the source of chocolate, is one of the most important commodity products worldwide that helps improve the economic livelihood of farmers. Diseases like frosty pod rot caused by Moniliophthora roreri and witches’ broom caused by Moniliophthora perniciosa limit the cacao productivity, this can be solved by using resistant varieties. In the current study, we sequenced 229 cacao accessions using genotyping-by-sequencing to examine the genetic diversity and population structure employing 9,003 and 8,131 single nucleotide polymorphisms recovered by mapping against two cacao genomes (Criollo B97-61/B2 v2 and Matina 1-6 v1.1). In the phenotypic evaluation, three promising accessions for productivity and 10 with good tolerance to the frosty pod rot and witches’ broom diseases were found. A genome-wide association study was performed on 102 accessions, discovering two genes associated with productivity and seven to disease resistance. The results enriched the knowledge of the genetic regions associated with important cacao traits that can have significant implications for conservation and breeding strategies like marker-assisted selection.

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