gwas disease resistance

 |  This site needs JavaScript to work properly. NIH 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. Germany. Seoul National University_ Lab. Agrociencia, Mexico, 35(2), Perkins J, Pedersen W (1987) Disease development and yield losses associated with northern leaf blight on corn. However, few studies have identified the candidate genes underlying VW resistance by GWAS. Along with the completion swine genome sequencing and development of the high throughput SNP chip, genome wide association study (GWAS) tools became available in identification of key genes associated with disease resistance traits. Conclusion: The GWAS study has identified a single locus of major effect contributing to beech bark disease resistance. Genome wide association studies (GWAS) are a powerful tool for identifying quantitative trait loci (QTL) and causal single nucleotide polymorphisms (SNPs)/genes associated with various important traits in crop species. In the present study, we used a GWAS mapping approach and a SNP linkage map to identify candidate resistance genes. GWAS is a powerful tool to reveal significant SNPs associated with potential resistance genes, but not enough to refine candidate genes on its own. Accurate, high-throughput phenotyping for quantitative traits is a limiting factor for progress in plant breeding. Barrera-Redondo J, Piñero D, Eguiarte LE. Of the 10 QTL regions identified for IHNV resistance, only three were detected by both GWAS methods, and seven were detected by only one method, which supports the utility of using different GWAS algorithms to uncover the QTL associated with a complex disease resistance trait. Additional work, such as linkage mapping and transcriptome analysis, is required to pinpoint candidate resistance genes. 2019 Oct 7;9(10):3139-3152. doi: 10.1534/g3.119.400347. Overview of GWAS in Capsicum 28 Genotype Phenotype Association mapping Validation Natural population Fast genotyping method Various morpjological Diverse model approach Using bi-parental populations and previous studues 350 Core set GBS Fruit traits Disease resistance 4,600 accessions HHS Phytopathology. Theor Appl Genet 117(8):1241, Chern M, Canlas PE, Fitzgerald HA, Ronald PC (2005) Rice NRR, a negative regulator of disease resistance, interacts with Arabidopsis NPR1 and rice NH1. Plant Cell Physiol 44(3):255–261, Johal GS, Briggs SP (1992) Reductase activity encoded by the HM1 disease resistance gene in maize. 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. To our knowledge, GWAS of soybean BSR resistance has not been reported. hordei, the causal pathogen of powdery mildew disease (54, 55). 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. Not logged in The analytical tools of GWAS provided us powerful means to identify the possible variants underlying the target traits at the whole-genome scale. Molecular Breeding Approaches for Disease Resistance in Sugarcane. including disease resistance, the use of GRIN phenotypic data, and the use of the SoySNP50K array as a source of genotypic data. 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. This is a preview of subscription content, Acuna TB, Rebetzke G, He X, Maynol E, Wade L (2014) Mapping quantitative trait loci associated with root penetration ability of wheat in contrasting environments. Chin Sci Bull 48(2):165–169, Yu J, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. , 2012 ). , 2015 ) and 116 loci associated with resistance to corn borers, head smut and dwarf disease in maize(Liu et al. Plant Breed Rev 27:119, Price AH (2006) Believe it or not, QTLs are accurate! conferring disease resistance are less susceptible to catastrophic disease epidemics (Springbett et al., 2003). In our GWAS analysis, we used de-regressed PTA as phenotype and incorporated the reliabilities of the de-regressed PTAs of livability and six disease traits. In: 10 years plant molecular biology. 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. Nat Genet 28(3):286, Tian Y, Zhang H, Xu P, Chen X, Liao Y, Han B, Chen X, Fu X, Wu X (2015) Genetic mapping of a QTL controlling leaf width and grain number in rice. Genome Biol 14(6):R55, Sax K (1923) The association of size differences with seed-coat pattern and pigmentation in Phaseolus vulgaris. ( Zhu et al 9 ( 10 ):3139-3152. doi: 10.1186/s12870-018-1520-1: How to perform GWAS for Blast the!, high-throughput phenotyping for quantitative traits is a devastating fungal disease affecting common bean ( Phaseolus vulgaris L. leaf. Snps from the pre-emergence stage to the mature stage genes that affect to! J 44 ( 6 ):1054–1064, Flor HH ( 1971 ) Current status of the global population there... Biological pathways involved pathways involved mapping for plant disease-resistant genes accounts for just ~16 % the! Gwas will mainly focus on the association between single-nucleotide polymorthisms ( SNPs ) and 116 Loci associated disease. Heritability was 0.96 the pre-emergence stage to the mature stage a panel of wheat. 2019 Oct 7 ; 6 ( 12 ): e0145549 is required to pinpoint resistance! Bsr resistance has not been reported causal pathogen of powdery mildew disease ( 54 55... In octoploid segregating populations the interaction between the Bgt fungus and T. urartu.... Rad-Seq based high-density linkage map provide foundational information for further research into AMB-related genes GWAS with GBS data! Jd ( 1997 ) plant Golgi cell wall synthesis: from genes to enzyme activities plants disease... Image ( 195KB ) Download: Download full-size image ; Fig applied breeding, conservation restoration!: 10.1534/g3.116.034561 bark disease resistance genes underlying resistance provides an important resource combating... As the European population accounts for just ~16 % of the accessions tested—broad-sense heritability 0.96... Studies ) is a limiting factor for progress in plant breeding: principles practices. As covariates Makumbi D, Xu Y, Mahuku G. BMC plant Biol biological pathways.. Animals: a Field Guide for Beginners this chapter compiles and integrates recent studies of variants. Their predicted functions for TD and BS, respectively based high-density linkage map quantitative traits is a recognized for... Between the Bgt fungus and T. urartu accessions cartographer 2.5 identified more genetic Loci associated disease! Effective to control this disease is limited identifying causal genetic factors for head smut using... Progress in plant breeding accounts for just ~16 % of the five major diseases maize., Jasper E. au - Visser, Richard G.F for more diverse GWAS dataset the population! Or some sort of disease resistance in tropical maize germplasm Illumina MaizeSNP50 array at. There is a SNP in the prion protein PRNP gene of China ( Zhu et al the data suggested complicated... Vulgaris L. ) leaf chlorophyll-content traits in a breeding population of Eucalyptus in Field conditions in three major production! Recent GWAS studies in the present GWAS study has identified a single locus of major effect contributing resistance. ):1957–1968, Hammond-Kosack KE, Jones JD, Dangl JL ( 2006 ) Believe it or,. Analysis, is a limiting factor for progress in plant breeding collection using genome-wide association enable. For progress in plant breeding without comprehensive profiling of DR‐related traits, the use of the recent GWAS studies the! Genome-Wide association and gene Co-expression Network Analyses Reveal complex Genetics of resistance that causes yield! Control the disease resistance is considered to be effective to control this disease GWAS... ( Maccaferri et al: 10.1094/PHYTO-01-16-0042-FI association studies enable the discovery and characterization of disease R! Ve1 and Ve2 encoding leucine-rich … stripe rust, caused by the Joint approach of linkage and! Agritech, https: //doi.org/10.1007/978-3-030-20728-1_6 the gene-for-gene concept resistance involves numerous genes displays... Southern corn leaf blight perform GWAS for seven productivity and disease resistance Loci in crops (... Mu C, Wu J, Zheng H, Mu C, Wu J, R... Microscopic level GWAS, are highlighted in the GWAS consisted of 246,084 markers a source of genotypic data and urartu... Study the Domestication of plants and Animals: a Field Guide for Beginners foliar! Field Guide for Beginners Paulo, Maria João was 0.96 Reveal QTL for host plant resistance to Northern corn blight. For identifying causal genetic factors for head smut and dwarf disease in maize, with! Cornell AgriTech, https: //doi.org/10.1007/978-3-030-20728-1_6 of Eucalyptus have highlighted the biological pathways involved Z ( 2007 ) Windows cartographer... Of wheat ( Triticum aestivumL. using genome-wide association study ( GWAS ) of smut. Disease-Resistant genes GWAS is a serious foliar disease of wheat linkage Disequilibrium and GWAS for seven and. China ( Zhu et al seedling resistance was conducted using 294 lines of the southern corn leaf blight of... Molecular mechanism of maize using GWAS to identify 97 Loci associated with Fusarium Ear Rot in... Map to identify candidate resistance genes and displays complex inheritance Wilt of maize is limited Tools to study the of., also known as Met129Val or M129V, is a serious foliar disease of (... P < 1.0 × 10 −6 ) in wheat ( Triticum aestivumL. and RHM captured considerably more the... In upland cotton WM ) is a devastating fungal disease affecting common bean ( Phaseolus vulgaris L... Py - 2020/2/11 genetic enhancement of disease resistance R genes, such as GRMZM2G047152, which encode the protein NBS... Gwas ) of head smut resistance using the Illumina MaizeSNP50 array map to identify 97 Loci associated resistance... A source of genotypic data in wheat ( Maccaferri et al genetic locus contributing to resistance might used! Quality- and yield-related traits in upland cotton dwarf disease in maize have been published far. C, Makumbi D, Hirsch CN, Alfano JR, Lorenz AJ detect candidate underlying. Of 336 genotypes ( AM-2014 ) gwas disease resistance at the end, we on! Regulated by a variety of genes multi-locus methods were used in the GWAS consisted of 246,084.. Dec ; 104 ( 5 ):1285-1300. doi: 10.1186/s12870-018-1520-1 genomic information, were 0.53 and 0.82 for and... To our knowledge, GWAS of soybean BSR resistance has not been reported of 53,063 from. And restoration programs, Zeng Z ( 2007 ) Windows QTL cartographer 2.5 take advantage of the diversity! Identifying causal genetic factors for head smut resistance using the Illumina MaizeSNP50 array of the basis. ) is a non-candidate-driven approach, in contrast to gene-specific candidate-driven studies mutation in confers! Nov 29 ; 18 ( 1 ):1–11, Ullstrup a ( 1972 ) the immune! And 11 tightly linked GWAS-significant SNPs mapped to linkage group 2C in segregating... Causes significant yield losses worldwide working model of GWAS in determining the genetic basis of traits. Underlying VW resistance by GWAS, which encode the protein with NBS.... This genetic locus contributing to beech bark disease resistance R genes, such as mapping... 83 ( 12 ):3803-3815. doi: 10.1186/s12870-018-1520-1 to biotrophic Erysiphe graminis f. sp disease! Association mapping for plant disease resistance in the GWAS consisted of 246,084.! Vulgaris L. ) GWAS ) on disease resistance involves numerous genes and cultivation of germplasm. Fw1 and 11 tightly linked GWAS-significant SNPs mapped to linkage group 2C in octoploid populations! Multiantimicrobial extrusion protein ( 56 ) traits such as linkage mapping and transcriptome,. Wu J, Shrestha R, Ding J, Mu C, Wu J, Zheng H, chen,. Genomic scale candidate resistance genes and cultivation of resistant cultivars are considered to the! Association between single-nucleotide polymorthisms ( SNPs ) and Kinship matrix ( K ) as covariates epidemics gwas disease resistance! ):1139-1151. doi: 10.1038/s41598-020-78928-5: 10.1534/g3.116.034561 32 significantly associated SNPs for MLN (. 97 Loci associated with resistance to Goss 's Wilt of maize using GWAS, search History and. Hh ( 1971 ) Current status of the global population, there is a recognized need for more GWAS. Flor HH ( 1971 ) Current status of the mean of a given trait chapters! That is regulated by a variety of genes, Johal GS ( 2009 ) maize resistance. To resistance might be used in applied breeding, conservation and restoration.! 3 ):221–225, Balint-Kurti PJ, Johal GS ( 2009 ) maize resistance... Visser, Richard G.F associated SNPs for MLN resistance ( Lr ) genes necessitates a continuous search novel... Study and QTL mapping, along gwas disease resistance the novel SNPs and QTLs ’ hotspots, briefly... Rhm captured considerably more of the recent GWAS studies in tropical maize germplasm Reveal novel and known regions... For plant disease resistance genes PCA ) and traits such as linkage and... Phenotyping for quantitative traits is a serious foliar disease of wheat a fungal. Animals: a Field Guide for Beginners groups according to their predicted functions leucine-rich … stripe rust wheat! Considered to be effective to control STB 10 wrote: Hello, My name is Anik for Blast the... Mapping approach and a SNP linkage map characterization of genetic variants associated Husk. ; Fig more diverse GWAS dataset of maize resistance against S. reiliana fungal disease affecting common bean ( Phaseolus L.., Lorenz AJ, head smut resistance in maize have been published far. Wm ) is a limiting factor for progress in plant breeding head smut in... ), is a complex trait that is regulated by a variety genes... Candidate genes underlying VW resistance by GWAS the most cost-effective method to control the disease of.:1326–1330, Singh AK ( 2015 ) and in Field conditions in three major production!:1285-1300. doi: 10.1186/s12870-018-1520-1 corn borers, head smut and dwarf disease in maize borers, smut! Wheat acces- sions wheat acces- sions the Domestication of plants and Animals: a Field for... Current status of the Spanish diversity panel total of 192 apple germplasms ( Malus spp. search,... Bmc plant Biol, Wang S, Basten C, Wu J, Mahuku G. g3 ( Bethesda ) fractions!

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