Genome-wide association studies enable the discovery and characterization of genetic variants associated with disease. In this study, we sought to detect candidate genes that affect resistance to AMB using a GWAS with GBS SNP data. A GWAS identified a total of 243 significant SNPs (P > 1.08 × 10 −6) that were associated with 35 traits including agronomic, disease resistance, and grain quality traits, (Figure 2, Tables 1 and S3). GWAS (Genome-wide association studies) is a common study when you want to check genetic variability in a genomic scale. Plant J 43(5):623–635, Clements M, Maragos C, Pataky J, White D (2004) Sources of resistance to fumonisin accumulation in grain and Fusarium ear and kernel rot of corn. Head smut, caused by the fungus Sphacelotheca reiliana (Kühn) Clint, is a devastating global disease in maize, leading to severe quality and yield loss each year. Septoria tritici blotch (STB) disease caused by Zymoseptoria tritici is one of the most damaging diseases of wheat causing significant yield losses worldwide. •Disease resistance is NOT correlated with population structure late flowering early flowering. Sequencing studies of rare variants have highlighted the biological pathways involved. Y1 - 2020/2/11 Proc Natl Acad Sci U S A 102(6):1815–1816, Ding J-Q, Wang X-M, Chander S, Yan J-B, Li J-S (2008) QTL mapping of resistance to Fusarium ear rot using a RIL population in maize. Heritabilities for resistance to IPNV estimated using genomic information, were 0.53 and 0.82 for TD and BS, respectively. Knowledge of this genetic locus contributing to resistance might be used in applied breeding, conservation and restoration programs. GWAS for many diseases and disorders have not yet been performed and the large majority (79%) of participants in GWAS to-date are of European ancestry. Theor Appl Genet 82(4):393–398, Broman KW, Wu H, Sen Ś, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. NIH To our knowledge, GWAS of soybean BSR resistance has not been reported. The GWAS (based on 2‐yr entry means) identified 16 significant (p < 0.001) single nucleotide polymorphisms (SNPs) associated with disease traits on multiple chromosomes. resistance, indicating the advantages of GWAS in determining the genetic basis of complex traits in cotton (Zhao et al., 2014). The economically important diseases in maize, along with the novel SNPs and QTLs’ hotspots, are highlighted in the chapter. This chapter compiles and integrates recent studies of the five major diseases of maize using GWAS. Drought resistance (DR) is a complex trait that is regulated by a variety of genes. Disease-resistant genetically modified animals C.B.A. 2.9 years ago by. Over the last 50 years, soybean germplasm has been phenotyped for resistance to many pathogens, resulting in the development of disease-resistant elite breeding lines and commercial cultivars. GWA studies identify SNPs and other variants in DNA associated with a disease, but they cannot on their own specify which genes are causal. A genome-wide association study (GWAS) was performed using the phenotypes time to death (TD) and binary survival (BS), along with the genotypes of the challenged fish using a Bayesian model (Bayes C). Nat Genet 38(8):904, Pring DR, Lonsdale DM (1989) Cytoplasmic male sterility and maternal inheritance of disease susceptibility in maize. The first successful GWAS published in … To provide an insight into the genomic basis of MAS disease resistance, in this study, we conducted a genome-wide association study (GWAS) to identify quantitative trait loci (QTL). Denser Markers and Advanced Statistical Method Identified More Genetic Loci Associated with Husk Traits in Maize. Genome-wide dissection of hybridization for fiber quality- and yield-related traits in upland cotton. pp 113-130 | A more precise location of previously identified resistance genes underlying the QTL on chromosome 16 In: Handbook of maize: its biology. The short-lived nature of leaf rust resistance (Lr) genes necessitates a continuous search for novel sources of resistance. A total of 56 QTLs associated with blast resistance to the three isolates were detected in the rice genome (−Log 10 P ≥ 4.0) (Fig. , 2012 ). Proc Natl Acad Sci 108(17):6893–6898, Pratt RC, Gordon SG (2006) Breeding for resistance to maize foliar pathogens. BMC Genomics. As the European population accounts for just ~16% of the global population, there is a recognized need for more diverse GWAS dataset. I am new to this website. Germany. White mold (WM) is a devastating fungal disease affecting common bean (Phaseolus vulgaris L.). Mehzabin Rahman, Sabira Sultana, Deepshikha Nath, Surya Kalita, Dhiresh Chakravarty, Sahil Mehta et al. Pages 131-155. 2016 Dec 7;6(12):3803-3815. doi: 10.1534/g3.116.034561. Analysis of Linkage Disequilibrium and GWAS for Blast Resistance The SNP panel used in the GWAS consisted of 246,084 markers. Higher SB severity, 82.3 ± 13.5 (mean ± SD), was recorded at the Banaras Hindu University (BHU) … Department of statistics. 2016 Oct;106(10):1139-1151. doi: 10.1094/PHYTO-01-16-0042-FI. COVID-19 is an emerging, rapidly evolving situation. GWAS will mainly focus on the association between single-nucleotide polymorthisms (SNPs) and traits such as herbicide resistance or some sort of disease. PLoS Genet 12(2):e1005767, Lu X, Brewbaker J (1999) Molecular mapping of QTLs conferring resistance to Sphacelotheca reiliana (Kühn) Clint. We developed an automated image analysis to measure quantitative resistance to septoria tritici blotch (STB), a globally important wheat disease, enabling identification of small chromosome intervals containing plausible candidate genes for STB resistance. Annu Rev Genet 37(1):579–609, Nordborg M, Tavaré S (2002) Linkage disequilibrium: what history has to tell us. AU - Prodhomme, Charlotte. Field Crop Res 106(2):148–155, Liu X, Huang M, Fan B, Buckler ES, Zhang Z (2016) Iterative usage of fixed and random effect models for powerful and efficient genome-wide association studies. The present GWAS study revealed 18 candidate genes that could be classified into three groups according to their predicted functions. Genome-wide association studies in tropical maize germplasm reveal novel and known genomic regions for resistance to Northern corn leaf blight. Thus, there is a need to bridge the gap between genomics and phenomics. anikduttapotol • 10. However, a general review and compilation of the recent GWAS studies in the disease resistance of maize is limited. Molecular Breeding Approaches for Disease Resistance in Sugarcane. Combined linkage and association mapping reveal QTL for host plant resistance to common rust (Puccinia sorghi) in tropical maize. The country of origin and infection type of T. urartu accessions. 2 ). To identify genomic regions that are associated with blast resistance to the three isolates, we performed a GWAS using the disease scores and the 700 K SNP genotypes of the inoculated cultivars. The economically important diseases in maize, along with the novel SNPs and QTLs’ hotspots, are highlighted in the chapter. 157.230.241.103. BMC Genomics 16(1):916, Martin GB, Brommonschenkel SH, Chunwongse J, Frary A, Ganal MW, Spivey R, Wu T, Earle ED, Tanksley SD (1993) Map-based cloning of a protein kinase gene conferring disease resistance in tomato. J Exp Bot 53(377):2089–2098, Causse M, Duffe P, Gomez M, Buret M, Damidaux R, Zamir D, Gur A, Chevalier C, Lemaire-Chamley M, Rothan C (2004) A genetic map of candidate genes and QTLs involved in tomato fruit size and composition. The most significant SNP explained 85% of the phenotypic variability and predicted resistance in 97% of the accessions tested—broad-sense heritability was 0.96. Pages 113-130. Phytopathology 83(12):1326–1330, Singh B, Singh AK (2015) Marker-assisted plant breeding: principles and practices. GWAS is a powerful tool to reveal significant SNPs associated with potential resistance genes, but not enough to refine candidate genes on its own. Since 2007, GWAS have identified nearly 100 genetic variants associated with coronary artery disease, some near genes with known roles in lipid metabolism and others related to blood pressure. AU - Vossen, Jack H. AU - van Eck, Herman J. PY - 2020/2/11. Download : Download high-res image (195KB) Download : Download full-size image; Fig. 24 Seoul National University Byoung-Cheorl Kang . Science 325(5941):737–740, Nimchuk Z, Eulgem T, Holt Iii BF, Dangl JL (2003) Recognition and response in the plant immune system. The data suggested a complicated molecular mechanism of maize resistance against S. reiliana. Springer, New York, pp 229–250, Balint-Kurti P, Zwonitzer JC, Wisser RJ, Carson M, Oropeza-Rosas MA, Holland JB, Szalma SJ (2007) Precise mapping of quantitative trait loci for resistance to southern leaf blight, caused by Cochliobolus heterostrophus race O, and flowering time using advanced intercross maize lines. Several review papers and chapters on QTL mapping of disease resistance in maize have been published so far. Genomic heritabilities accounted for large fractions of narrow-sense heritabilities and RHM captured considerably more of the genomic heritability than GWAS. Triticum urartu, a diploid wild wheat and progenitor of the A genome of bread wheat, is an important resource for resistance to powdery mildew fungus caused by Blumeria graminis f. sp. Plant Genome 1(1):5–20, Zila CT, Samayoa LF, Santiago R, Butrón A, Holland JB (2013) A genome-wide association study reveals genes associated with Fusarium ear rot resistance in a maize core diversity panel. Additional work, such as linkage mapping and transcriptome analysis, is required to pinpoint candidate resistance genes. After filtering for callrate (>95%) and minor al- lele frequency (>5%) the final set included 37,423 SNPs, with an average value of 3119 markers/chromosome. Out of 45,868 single nucleotide polymorphisms in a panel of 144 inbred lines, 18 novel candidate genes were associated with head smut resistance in maize. Genetics 176(1):645–657, Bent AF, Kunkel BN, Dahlbeck D, Brown KL, Schmidt R, Giraudat J, Leung J, Staskawicz BJ (1994) RPS2 of Arabidopsis thaliana: a leucine-rich repeat class of plant disease resistance genes. Other aspects of HIV biology and disease have been investigated by GWAS including the role of the X chromosome, the role of the HIV-associated HLA locus in CD4:CD8 T lymphocyte ratios and genetic factors that may influence mother to child transmission. GWAS has been successfully used to study various traits in wheat such as grain yield (Sukumaran et al., 2018), eyespot disease resistance (Zanke et al., 2017), pre-harvest sprouting resistance (Zhou et al., 2017), 36 agro-morphological traits (Sheoran et al., 2019) and so on. Identification and employment of resistant germplasm is the most cost-effective method to control STB. Published by Elsevier Ireland Ltd. All rights reserved. In: 10 years plant molecular biology. rs1799990, also known as Met129Val or M129V, is a SNP in the prion protein PRNP gene. Theor Appl Genet 89(6):794–800, Ray J, Yu L, McCouch S, Champoux M, Wang G, Nguyen H (1996) Mapping quantitative trait loci associated with root penetration ability in rice (Oryza sativa L.). Singh A, Li G, Brohammer AB, Jarquin D, Hirsch CN, Alfano JR, Lorenz AJ. This service is more advanced with JavaScript available, Disease Resistance in Crop Plants Coronary artery disease. Genetics 178(3):1709–1723, Kump KL, Bradbury PJ, Wisser RJ, Buckler ES, Belcher AR, Oropeza-Rosas MA, Zwonitzer JC, Kresovich S, McMullen MD, Ware D (2011) Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Characterization of Disease Resistance Loci in the USDA Soybean Germplasm Collection Using Genome-Wide Association Studies. Euphytica 124(2):147–156, Paterson AH, Lander ES, Hewitt JD, Peterson S, Lincoln SE, Tanksley SD (1988) Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms. The mixed linear model was employed in TASSEL using principal component analysis (PCA) and Kinship matrix (K) as covariates. Part of Springer Nature. With the reduction in the genotyping cost of the sequencing technique, improved statistical methods, and increased computational efficiency, association mapping, especially genome wide association study (GWAS), is widely used to dissect the architecture of the several complex traits. Crown Copyright © 2012. The GWAS study has identified a single locus of major effect contributing to beech bark disease resistance. To our knowledge, GWAS of soybean BSR resistance has not been reported. rice, bakanae disease, GWAS, resistance loci Bakanae disease is one of the most serious and oldest problems of rice production, caused by one or more seed-borne Fusarium species, mainly F. fujikuroi. 2. Plant J 44(6):1054–1064, Flor HH (1971) Current status of the gene-for-gene concept. Karnal Bunt (KB) disease in wheat through a genome-wide association study (GWAS) on a set of 179 pre-breeding lines (PBLs). North Carolina state university, Raleigh, Wang M, Yan J, Zhao J, Song W, Zhang X, Xiao Y, Zheng Y (2012) Genome-wide association study (GWAS) of resistance to head smut in maize. 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