Deciphering the Genetic Architecture of Plant Virus Resistance by GWAS, State of the Art and Potential Advances
Abstract
:1. Introduction
2. Mapping QTLs via GWAS Using Historical Recombinations
3. The Pre-GWAS Step: Assembled Diversity Panel That Is Genetically and Phenotypically Diverse
3.1. The GWAS Panel Composition Plays a Major Role in GWAS
3.2. Producing Genetic Variant Array to Enhance Positive Association Detection: A New Deal for GWAS
3.3. Examining Resistance Distributions among Genetic Groups of the Panel
3.4. Phenotyping: Tricky Steps for a Powerful GWAS
4. The GWAS Step: Choosing a Model Tailored for the Datasets
4.1. Linear Mixed Models (LMM) Are the Most Used in GWAS
4.2. Multilocus Models in GWAS: Detecting Markers Hidden by Major Effect QTLs
4.3. Other Models That Are More Tailored to Virus Phenotype Distributions
4.4. Describing QTLs: Significance, Number, Precision, and Allele Frequency
5. The Post-GWAS Step: From QTL Validation for Breeding to Candidate Gene Research
5.1. Inferring QTL Effects and Identifying Favorable Alleles… A Complex Issue
5.2. Inviting QTLs in Breeding Programs
5.3. From QTLs to Causal Genes, a Budding Approach
6. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Species | Latin Name | Virus | Article |
---|---|---|---|
Arabidopsis thaliana | Cucumber mosaic virus (CMV) Turnip mosaic virus (TuMV) (×2) Plum pox virus (PPV) | [28,37,38,39] | |
Apricot | Prunus armeniaca | PPV | [40] |
Chinese cabbage | Brassica rapa | TuMV | [41] |
Pepper | Capsicum annuum | Potato virus Y (PVY) | [42,43] |
Common bean | Phaseolus vulgaris | Bean golden yellow mosaic virus (BGYMV) | [44] |
Watermelon | Citrullus lanatus | Papaya ringspot virus (PRSV) | [36] |
Maize | Zea maize spp Mays | Sugarcane mosaic virus (SCMV) (×5) Maize chlorotic mottle vírus (MCMV) SCMV + MCMV (MCMD) (×3) Mal de Rio cuarto virus (MRCV) Rice black-streaked dwarf virus (RBSDV) (×2) Barley yellow dwarf virus (BYDV) | [5,29,45,46,47,48,49,50,51,52,53,54] |
Oat | Avena sativa L. | BYDV | [55] |
Wheat | Triticum aestivum | BYDV Soil-borne wheat mosaic virus (SBWMV) (×2) Wheat spindle streak mosaic virus (WSSMV) | [30,56,57,58] |
Barley | Hordeum sp. | Barley mild mosaic virus (BaMMV) (×2) Barley yellow mosaic virus (BaYMV) (×2) | [59,60] |
Rice | Oryza sativa L. Oryza glaberrima | Rice yellow mottle vírus (RYMV) RBSDV (×3) | [6,34,61,62] |
Sugarcane | Saccharum officinarum Saccharum spontaneum | Fiji disease virus Sugarcane yellow leaf virus (SCYLV) (×4) | [35,63,64,65,66] |
Soybean | Glycine max | Tomato ringspot virus (TRSV) Peanut mottle virus (PMV) Bean pod mosaic virus (BPMV) Soybean mosaic virus (SMV) (×3) | [33,67,68,69] |
Peanut | Arachis hypogaea L. | Tomato spotted wilt virus (TSWV) | [70] |
Cassava | Manihot esculenta | Cassava mosaic disease (CMD) (×2) Cassava brown streak virus (CBSV) | [71,72,73] |
Yam | Dioscorea rotundata | Yam mosaic virus (YMV) | [74] |
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Monnot, S.; Desaint, H.; Mary-Huard, T.; Moreau, L.; Schurdi-Levraud, V.; Boissot, N. Deciphering the Genetic Architecture of Plant Virus Resistance by GWAS, State of the Art and Potential Advances. Cells 2021, 10, 3080. https://doi.org/10.3390/cells10113080
Monnot S, Desaint H, Mary-Huard T, Moreau L, Schurdi-Levraud V, Boissot N. Deciphering the Genetic Architecture of Plant Virus Resistance by GWAS, State of the Art and Potential Advances. Cells. 2021; 10(11):3080. https://doi.org/10.3390/cells10113080
Chicago/Turabian StyleMonnot, Severine, Henri Desaint, Tristan Mary-Huard, Laurence Moreau, Valerie Schurdi-Levraud, and Nathalie Boissot. 2021. "Deciphering the Genetic Architecture of Plant Virus Resistance by GWAS, State of the Art and Potential Advances" Cells 10, no. 11: 3080. https://doi.org/10.3390/cells10113080
APA StyleMonnot, S., Desaint, H., Mary-Huard, T., Moreau, L., Schurdi-Levraud, V., & Boissot, N. (2021). Deciphering the Genetic Architecture of Plant Virus Resistance by GWAS, State of the Art and Potential Advances. Cells, 10(11), 3080. https://doi.org/10.3390/cells10113080