MultiGWAS: An integrative tool for Genome Wide Association Studies in tetraploid organisms

Garreta, Luis; Cerón‐Souza, Ivania; Palacio, Manfred Ricardo; Reyes-Herrera, Paula H.

doi:10.1002/ece3.7572

Cited by 4 publications

(3 citation statements)

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“…FarmCPU is consider the best multi locus GWAS approach and it controls both false positives and false negatives ( Kaler et al., 2020 ). There are some challenges in the GWAS for polyploidy species ( Garreta et al., 2021 ). To overcome these challenges only few software packages like GWASpoly and SHEsis ( Rosyara et al., 2016 ; Shen et al., 2016 ) that accept only polyploidy genomic data were developed.…”

Section: Statistical Tools For Gwas Analysismentioning

confidence: 99%

“…To overcome these challenges only few software packages like GWASpoly and SHEsis ( Rosyara et al., 2016 ; Shen et al., 2016 ) that accept only polyploidy genomic data were developed. In addition, to tackle these challenges, a multi GWAS tool is being developed that runs GWAS analysis for both diploid and tetraploid species simultaneously utilizing four software packages ( Garreta et al., 2021 ). Development of improved model to reduce the challenges like population structure and relatedness is continuing to be an important research topic.…”

Section: Statistical Tools For Gwas Analysismentioning

confidence: 99%

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Two decades of association mapping: Insights on disease resistance in major crops

et al. 2022

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Climate change across the globe has an impact on the occurrence, prevalence, and severity of plant diseases. About 30% of yield losses in major crops are due to plant diseases; emerging diseases are likely to worsen the sustainable production in the coming years. Plant diseases have led to increased hunger and mass migration of human populations in the past, thus a serious threat to global food security. Equipping the modern varieties/hybrids with enhanced genetic resistance is the most economic, sustainable and environmentally friendly solution. Plant geneticists have done tremendous work in identifying stable resistance in primary genepools and many times other than primary genepools to breed resistant varieties in different major crops. Over the last two decades, the availability of crop and pathogen genomes due to advances in next generation sequencing technologies improved our understanding of trait genetics using different approaches. Genome-wide association studies have been effectively used to identify candidate genes and map loci associated with different diseases in crop plants. In this review, we highlight successful examples for the discovery of resistance genes to many important diseases. In addition, major developments in association studies, statistical models and bioinformatic tools that improve the power, resolution and the efficiency of identifying marker-trait associations. Overall this review provides comprehensive insights into the two decades of advances in GWAS studies and discusses the challenges and opportunities this research area provides for breeding resistant varieties.

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Section: Statistical Tools For Gwas Analysismentioning

confidence: 99%

Section: Statistical Tools For Gwas Analysismentioning

confidence: 99%

Two decades of association mapping: Insights on disease resistance in major crops

et al. 2022

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“…Economically important traits include agronomic and yield associated traits (reviewed by [14] as well as biotic [15][16][17] and abiotic stress tolerance [18][19][20][21] have been mapped using GWAS in wheat. Conventionally, GWAS was performed using a single-locus mixed linear model (SL-MLM) [22]. In the last few years, multilocus mixed linear models (ML-GWAS) have been developed, as they have higher power to detect significant marker-trait associations for complex traits than conventional SL-MLM methods [23,24], 2018, [25][26][27][28].…”

Section: Introductionmentioning

confidence: 99%

Unlocking the molecular basis of wheat straw composition and morphological traits through multi-locus GWAS

et al. 2022

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Background Rapid reductions in emissions from fossil fuel burning are needed to curb global climate change. Biofuel production from crop residues can contribute to reducing the energy crisis and environmental deterioration. Wheat is a renewable source for biofuels owing to the low cost and high availability of its residues. Thus, identifying candidate genes controlling these traits is pivotal for efficient biofuel production. Here, six multi-locus genome-wide association (ML-GWAS) models were applied using 185 tetraploid wheat accessions to detect quantitative trait nucleotides (QTNs) for fifteen traits associated with biomass composition. Results Among the 470 QTNs, only 72 identified by at least two models were considered as reliable. Among these latter, 16 also showed a significant effect on the corresponding trait (p.value < 0.05). Candidate genes survey carried out within 4 Mb flanking the QTNs, revealed putative biological functions associated with lipid transfer and metabolism, cell wall modifications, cell cycle, and photosynthesis. Four genes encoded as Cellulose Synthase (CeSa), Anaphase promoting complex (APC/C), Glucoronoxylan 4-O Methyltransferase (GXM) and HYPONASTIC LEAVES1 (HYL1) might be responsible for an increase in cellulose, and natural and acid detergent fiber (NDF and ADF) content in tetraploid wheat. In addition, the SNP marker RFL_Contig3228_2154 associated with the variation in stem solidness (Q.Scsb-3B) was validated through two molecular methods (High resolution melting; HRM and RNase H2-dependent PCR; rhAMP). Conclusions The study provides new insights into the genetic basis of biomass composition traits on tetraploid wheat. The application of six ML-GWAS models on a panel of diverse wheat genotypes represents an efficient approach to dissect complex traits with low heritability such as wheat straw composition. The discovery of genes/genomic regions associated with biomass production and straw quality parameters is expected to accelerate the development of high-yielding wheat varieties useful for biofuel production.

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The United States Potato Genebank Holding of cv. Desiree is a Somatic Mutant of cv. Urgenta

2022

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MultiGWAS: An integrative tool for Genome Wide Association Studies in tetraploid organisms

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 4 publications

References 60 publications

Two decades of association mapping: Insights on disease resistance in major crops

Two decades of association mapping: Insights on disease resistance in major crops

Unlocking the molecular basis of wheat straw composition and morphological traits through multi-locus GWAS

The United States Potato Genebank Holding of cv. Desiree is a Somatic Mutant of cv. Urgenta

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