Optimized breeding strategies to harness genetic resources with different performance levels. 16:6. doi: 10.1186/s12870-015-0686-z, Tyler, B. M., Tripathy, S., Zhang, X., Dehal, P., Jiang, R. H., Aerts, A., et al. To match this requirement, two innovations were suggested for GWAS: first grouping tightly linked sequential SNPs into linkage disequilibrium blocks (SNPLDBs) to form markers with multi-allelic haplotypes, and second utilizing two-stage association analysis for QTL identification, where the markers were preselected by single-locus model followed by multi-locus multi-allele model stepwise regression. Bi-Phenotypic Trait May Be Conferred by Multiple Alleles in a Germplasm Population. Chang. The Plant Gen. 7, 1–13. Effects are demonstrated for thousand kernel weight (TKW), grain protein (GRNPRO), Alveograph W (ALVW) and P/L (ALVPL), and loaf volume (LOFVOL) traits. By using a GWA mapping method previously developed for human bacterial pathogens and that takes into account both core and pan-genome while controlling for population structure (Sheppard et al., 2013; Pascoe et al., 2015; Yahara et al., 2017), the authors found that the T3SS effectors hopQ1 and hopD1 have probably shaped the adaptation of the ubiquitous plant pathogenic bacterium P. syringae to crops. In the last decade the World Health Organization (WHO) reported more than 300 newly infectious diseases that have emerged as threat for human (Jones et al., 2008). A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica). doi: 10.1073/pnas.1010894108, Power, R. A., Parkhill, J., and Oliveira, T. (2017). In particular, multiple crop epidemics were caused by multiple introductions pathogen populations from restricted geographic regions, as reported for the worldwide spread of kiwifruit bacterial canker caused by the bacterium Pseudomonas syringae pv. 2015 Oct;66(20):6311-25. doi: 10.1093/jxb/erv342. An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton. Glob. The remaining GWAS were conducted on the two model plant species A. thaliana (~33%) and M. truncatula (~3%). New approaches to population stratification in genome-wide association studies. The previous genome-wide association studies (GWAS) have been concentrated on finding a handful of major quantitative trait loci (QTL), but plant breeders are interested in revealing the whole-genome QTL-allele constitution in breeding materials/germplasm (in which tremendous historical allelic variation has been accumulated) for genome-wide improvement. doi: 10.1038/emi.2013.5, Evans, N., Baierl, A., Semenov, M. A., Gladders, P., and Fitt, B. D. L. (2008). Genotyping-by-sequencing-based genome-wide association studies on Verticillium wilt resistance in autotetraploid alfalfa (Medicago sativa L.). Trends Plant Sci. The polyploid offspring of two diploid progenitors tend to be more vigorous and healthier than either of the diploid parents. doi: 10.7554/eLife.01123, Bartoli, C., Lamichhane, J.-R., Berge, O., Varvaro, L., and Morris, C. E. (2015). Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. Sci. 119, 111–156. Using the CSGP marker information, simulation studies demonstrated that RTM-GWAS achieved the highest QTL detection power and efficiency compared with the previous procedures, especially under large sample size and high trait heritability conditions. This problem is also common in crop and animal breeding where many individuals are only evaluated for a single year and large but unbalanced datasets can be generated over multiple years. Bread wheat: a role model for plant domestication and breeding. Plant Sci. doi: 10.1094/MPMI-07-16-0129-TA, Lambrechts, L. (2010). Stat. Mol. Get the latest research from NIH: https://www.nih.gov/coronavirus. Kim KS, Vuong TD, Qiu D, Robbins RT, Grover Shannon J, Li Z, Nguyen HT. Adeyanju, A., Little, C., Yu, J., and Tesso, T. (2015). doi: 10.1111/mpp.12340, Karasov, T. L., Kniskern, J. M., Gao, L., Deyoung, B. J., Ding, J., Dubiella, U., et al. doi: 10.1111/mpp.12190, Kang, H. M., Sul, J. H., Service, S. K., Zaitlen, N. A., Kong, S. Y., Freimer, N. B., et al. BMC Genomics 17:124. doi: 10.1186/s12864-016-2429-4, Deslandes, L., Olivier, J., Theulieres, F., Hirsch, J., Feng, D. X., Bittner-Eddy, P., et al. For the purposes of this review, we highlight in more detail three areas where plant breeding can benefit from evolutionary insights: ... and GWAS. GWAS has been widely used in plant breeding for crop improvement. GWAS has been performed in nearly all economically important crops, such as maize, sorghum, millet, and rice, for the selection and improvement of desirable traits. doi: 10.1038/nature08800, Barret, M., Briand, M., Bonneau, S., Préveaux, A., Valière, S., Bouchez, O., et al. 12:56. doi: 10.1186/1471-2229-12-56, Wang, Z., Hou, W., and Wu, R. (2006). In addition, comparative genomics is mainly employed to detect phenotypic differences that are based on the presence/absence of genes, thereby strongly limiting the potential for identifying SNPs associated with natural variation of virulence/aggressiveness among microbial pathogenic populations. small region of DNA sequences variation). Perspectives on the transition from bacterial phytopathogen genomics studies to applications enhancing disease management : from promise to practice. Generating of polyploids provides plant breeders with more options for developing novel plants and improving existing cultivated varieties. (2016), 119 isolates of the fungal pathogen F. graminearum collected in Germany were phenotyped for aggressiveness on wheat under field conditions in two locations over 2 years (Talas et al., 2016). (2009). 2015. New statistical methods must be developed with the challenge of performing joint GWA mapping by taking into account simultaneously the information provided by the genome sequences of the plant and the pathogen (Roux and Bergelson, 2016). Genome-wide association study of Arabidopsis thaliana leaf microbial community. doi: 10.1111/mpp.12298, Desgroux, A., L'Anthoëne, V., Roux-duparque, M., Rivière, J., Aubert, G., Tayeh, N., et al. However, the environment where the pathogenic populations evolve is of fundamental importance for triggering the evolution of new traits increasing aggressiveness in a pathogen.

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