scholarly journals Identification of novel sources of resistance to ascochyta blight in a collection of wild Cicer accessions

2020 ◽  
Author(s):  
Toby E. Newman ◽  
Silke Jacques ◽  
Christy Grime ◽  
Fiona L. Kamphuis ◽  
Robert C. Lee ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Ascochyta Blight ◽  
Ascochyta Rabiei ◽  
Sources Of Resistance ◽  
Highly Pathogenic ◽  
Cicer Echinospermum ◽  
Genome Wide ◽  
A Genome ◽  
The Impact ◽  
Chickpea Cultivars

Chickpea production is constrained worldwide by the necrotrophic fungal pathogen Ascochyta rabiei, the causal agent of ascochyta blight (AB). In order to reduce the impact of this disease, novel sources of resistance are required in chickpea cultivars. Here, we screened a new collection of wild Cicer accessions for AB resistance and identified accessions resistant to multiple, highly pathogenic isolates. In addition to this, analyses demonstrated that some collection sites of Cicer echinospermum harbour predominantly resistant accessions, knowledge that can inform future collection missions. Furthermore, a genome-wide association study identified regions of the Cicer reticulatum genome associated with AB resistance and investigation of these regions identified candidate resistance genes. Taken together, these results can be utilised to enhance the resistance of chickpea cultivars to this globally yield-limiting disease.

scholarly journals Identification of QTLs/Defense Genes Effective at Seedling Stage Against Prevailing Races of Wheat Stripe Rust in India

2020 ◽  
Vol 11 ◽  
Author(s):  
Anjan Kumar Pradhan ◽  
Sundeep Kumar ◽  
Amit Kumar Singh ◽  
Neeraj Budhlakoti ◽  
Dwijesh C. Mishra ◽  
...  
Keyword(s):  
Stripe Rust ◽  
Genome Wide Association Study ◽  
Durable Resistance ◽  
Winter Season ◽  
Seedling Stage ◽  
Wheat Cultivars ◽  
Sources Of Resistance ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Locations

Resistance in modern wheat cultivars for stripe rust is not long lasting due to the narrow genetic base and periodical evolution of new pathogenic races. Though nearly 83 Yr genes conferring resistance to stripe rust have been cataloged so far, few of them have been mapped and utilized in breeding programs. Characterization of wheat germplasm for novel sources of resistance and their incorporation into elite cultivars is required to achieve durable resistance and thus to minimize the yield losses. Here, a genome-wide association study (GWAS) was performed on a set of 391 germplasm lines with the aim to identify quantitative trait loci (QTL) using 35K Axiom® array. Phenotypic evaluation disease severity against four stripe rust pathotypes, i.e., 46S119, 110S119, 238S119, and 47S103 (T) at the seedling stage in a greenhouse providing optimal conditions was carried out consecutively for 2 years (2018 and 2019 winter season). We identified, a total of 17 promising QTl which passed FDR criteria. Moreover these 17 QTL identified in the current study were mapped at different genomic locations i.e. 1B, 2A, 2B, 2D, 3A, 3B, 3D, 4B, 5B and 6B. These 17 QTLs identified in the present study might play a key role in marker-assisted breeding for developing stripe rust resistant wheat cultivars.

scholarly journals Genome-Wide Association Mapping of Resistance to Fusarium Head Blight Spread and Deoxynivalenol Accumulation in Chinese Elite Wheat Germplasm

2019 ◽  
Vol 109 (7) ◽  
pp. 1208-1216 ◽  
Author(s):  
Lei Wu ◽  
Yu Zhang ◽  
Yi He ◽  
Peng Jiang ◽  
Xu Zhang ◽  
...  
Keyword(s):  
Fusarium Head Blight ◽  
Genome Wide Association Study ◽  
Snp Array ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Head Blight ◽  
Sources Of Resistance ◽  
Wheat Germplasm ◽  
Genome Wide ◽  
A Genome

Improving resistance to Fusarium head blight (FHB) in wheat is crucial in the integrated management of the disease and prevention of deoxynivalenol (DON) contamination in grains. To identify novel sources of resistance, a genome-wide association study (GWAS) was performed using a panel of 213 accessions of elite wheat germplasm of China. The panel was evaluated for FHB severity in four environments and DON content in grains in two environments. High correlations across environments and high heritability were observed for FHB severity and DON content in grains. The panel was also genotyped with the 90K Illumina iSelect single nucleotide polymorphism (SNP) array and 11,461 SNP markers were obtained. The GWAS revealed a total of six and three loci significantly associated with resistance to fungal spread and DON accumulation in at least two environments, respectively. QFHB-2BL.1 tagged by IWB52433 and QFHB-3A tagged by IWB50548 were responsible for resistance to both fungal spread and DON accumulation. In summary, this study provided an overview of FHB resistance resources in elite Chinese wheat germplasm and identified novel resistance loci that could be used for wheat improvement.

scholarly journals Sequenced-based paternity analysis to improve breeding and identify self-incompatibility loci in intermediate wheatgrass (Thinopyrum intermedium)

2020 ◽  
Vol 133 (11) ◽  
pp. 3217-3233
Author(s):  
Jared Crain ◽  
Steve Larson ◽  
Kevin Dorn ◽  
Traci Hagedorn ◽  
Lee DeHaan ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Diversity Index ◽  
Genome Wide Association ◽  
Pollen Parent ◽  
Self Incompatibility ◽  
Thinopyrum Intermedium ◽  
Intermediate Wheatgrass ◽  
Genome Wide ◽  
A Genome ◽  
The Impact

Abstract Key Message Paternity assignment and genome-wide association analyses for fertility were applied to aThinopyrum intermediumbreeding program. A lack of progeny between combinations of parents was associated with loci near self-incompatibility genes. Abstract In outcrossing species such as intermediate wheatgrass (IWG, Thinopyrum intermedium), polycrossing is often used to generate novel recombinants through each cycle of selection, but it cannot track pollen-parent pedigrees and it is unknown how self-incompatibility (SI) genes may limit the number of unique crosses obtained. This study investigated the potential of using next-generation sequencing to assign paternity and identify putative SI loci in IWG. Using a reference population of 380 individuals made from controlled crosses of 64 parents, paternity was assigned with 92% agreement using Cervus software. Using this approach, 80% of 4158 progeny (n = 3342) from a polycross of 89 parents were assigned paternity. Of the 89 pollen parents, 82 (92%) were represented with 1633 unique full-sib families representing 42% of all potential crosses. The number of progeny per successful pollen parent ranged from 1 to 123, with number of inflorescences per pollen parent significantly correlated to the number of progeny (r = 0.54, p < 0.001). Shannon’s diversity index, assessing the total number and representation of families, was 7.33 compared to a theoretical maximum of 8.98. To test our hypothesis on the impact of SI genes, a genome-wide association study of the number of progeny observed from the 89 parents identified genetic effects related to non-random mating, including marker loci located near putative SI genes. Paternity testing of polycross progeny can impact future breeding gains by being incorporated in breeding programs to optimize polycross methodology, maintain genetic diversity, and reveal genetic architecture of mating patterns.

scholarly journals Deciphering the Impact of Common Genetic Variation on Lung Cancer Risk: A Genome-Wide Association Study

2009 ◽  
Vol 69 (16) ◽  
pp. 6633-6641 ◽  
Author(s):  
Peter Broderick ◽  
Yufei Wang ◽  
Jayaram Vijayakrishnan ◽  
Athena Matakidou ◽  
Margaret R. Spitz ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Genetic Variation ◽  
Cancer Risk ◽  
Genome Wide Association Study ◽  
Lung Cancer Risk ◽  
Genome Wide Association ◽  
Common Genetic Variation ◽  
Genome Wide ◽  
A Genome ◽  
The Impact

scholarly journals Genome-wide associations reveal human-mouse genetic convergence and modifiers of myogenesis,CPNE1andSTC2

2018 ◽  
Author(s):  
Ana I. Hernandez Cordero ◽  
Natalia M. Gonzales ◽  
Clarissa C. Parker ◽  
Greta Sokoloff ◽  
David J. Vandenbergh ◽  
...  
Keyword(s):  
Muscle Mass ◽  
Genome Wide Association Study ◽  
Inbred Strains ◽  
Muscle Loss ◽  
Healthy Humans ◽  
Genome Wide ◽  
A Genome ◽  
The Uk ◽  
The Impact

AbstractMuscle bulk in adult healthy humans is highly variable even after accounting for height, age and sex. Low muscle mass, due to fewer and/or smaller constituent muscle fibers, would exacerbate the impact of muscle loss occurring in aging or disease. Genetic variability substantially influences muscle mass differences, but causative genes remain largely unknown. In a genome-wide association study (GWAS) on appendicular lean mass (ALM) in a population of 85,750 middle-age (38-49 years) individuals from the UK Biobank (UKB) we found 182 loci associated with ALM (P<5×10−8). We replicated associations for 78% of these loci (P<5×10−8) with ALM in a population of 181,862 elderly (60-74 years) individuals from UKB. We also conducted a GWAS on hindlimb skeletal muscle mass of 1,867 mice from an advanced intercross between two inbred strains (LG/J and SM/J) which identified 23 quantitative trait loci. 38 positional candidates distributed across 5 loci overlapped between the two species.In vitrostudies of positional candidates confirmedCPNE1andSTC2as modifiers of myogenesis. Collectively, these findings shed light on the genetics of muscle mass variability in humans and identify targets for the development of interventions for treatment of muscle loss. The overlapping results between humans and the mouse model GWAS point to shared genetic mechanisms across species.

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