An automatic mistirrigation system, switched by leafwetness measurement. Why qtl mapping qtl mapping is used to offer direct mean to investigate the number of genes influencing the trait, to find out the location of the gene and to know the effect of dosage of these genes on variation of the trait. Inconsistent qtl detection across environments was due primarily to non or. Preliminary qtl maps were made for droughtresponse traits from field droughtscreens at irri 1996 and 1998 and. Slight deviation in qtl locations could be raised due to different handling status in two locations and differences in experimental settings at irri and sri lanka. Eight qtls with logarithm of odds lod values ranging from 2. Conventional breeding for drought resistant dr rice varieties is slow and limited due to the quantitative nature of the dr traits. The development of megavarieties with tolerance conferred by the sub1 gene on chromosome 9 derived from fra that can withstand up to 2 weeks of complete submergence has been one of the best solutions. Here, a brief overview of the principle of qtl mapping, salient requirements for qtl mapping, common statistical tools and techniques employed in qtl analysis. Zeigler, director general, international rice research institute r ice feeds roughly half the planets population and approximately threequarters of a billion of the worlds poorest people depend on the staple to survive. Frontiers qtl identification for cooking and eating quality. Drought is one of the most widespread and damaging of all environmental stresses, affecting 23 million hectares of rainfed rice in south and southeast asia alone. In this study, qtls were identified for ten physicochemical properties related to ceq using 508 f6 magic lines.
Qtl mapping for resistance to and tolerance for the rice. Ghost qtlcomposite interval mappingmouse hypertensionplant data why we need the window mar1 irri and sri lanka in years 2014 and 2017 respectively. Qtl mapping thus represents the foundation of the development of markers for mas. Mapping qtls using a novel source of salinity tolerance from. R system software for microarrray data analysis microarray analysis software has been developed under the r system, which is in the public domain and available at. We also mapped qtls for morphological attributes related to drought tolerance. Tutorial multipleqtl mapping mqm analysis for rqtl. Climate change ready rice international rice research. The process of marker validation is required to determine the reliability of a marker to predict phenotype and this points out the advantages of using. N22 cross were exposed to 3824c for 14 days at the flowering stage, and spikelet fertility was assessed. We performed qtl mapping for four agronomic traits. Linkage based qtl mapping is a variant of qtl mapping. Most of the investigations have identified qtl either in two or three environments paterson et al.
Qtl mapping for resistance to and tolerance for the rice root. Qtls are mapped by identifying which molecular markers such as snps or aflps correlate with an observed trait. Molecular mapping of qtls for drought related traits at. Molecular mapping of qbk1wd, a major qtl for bakanae disease resistance in rice dongsoo park irrc0090.
In drought, snp markers for xylem area were identified on chromosome 4 with total pve of 9. The whole population and eight founder lines were genotyped with 6k. These populations were phenotyped during 2015ds and 2015ws at irri. Linkage analysis and qtl mapping are two closely related aspects of genetic studies but have hitherto been handled by separate software packages tables s2 and s3. Deciphering genetics underlying stable anaerobic germination. Recognizing the enormous potential of dna markers in plant breeding, many agricultural research centers and plant breeding institutes have adopted the capacity for marker development and markerassisted selection mas.
A subset of 142 common rils evaluated in both senegal and tanzania was genotyped at irri, philippines. These were screened at irri in the dry season of 2002. So, high zinc and iron content in the grain are primary targets in rice biofortification breeding. Pdf one hundred twenty six doubledhaploid dh rice lines were evaluated in nine diverse asian.
Over the last 10 years, we have developed integrated software called qtl icimapping. The association analysis identified two and three qtl for ph and. To be more precise about the location of the identified qtl for salt tolerance, interval mapping im and composite interval mapping cim analysis. Rice provides energy and nutrition to more than half of the worlds population. Java project tutorial make login and register form step by step using netbeans and mysql database duration. The spring wheatderived qtl fhb1 was successfully introgressed into triticale and resulted in. Genotypingbysequencing based qtl mapping for rice grain yield. Genetic mapping is the first step to map based cloning.
However, due to rapid developments in marker technology, statistical methodology for identifying quantitative trait loci qtls and the jargon used by molecular biologists, the. Jan 19, 2016 submergence is a common naturally occurring disaster in rice production in south and southeast asia. A carefully focused agenda for continued research on this vital crop is more imperative than ever. It must be polymorphic have allelic variation to have an effect in a population and it must be linked to a polymorphic marker allele to be detected. Feb 12, 2008 this may occur even if genetic distances from a preliminary qtl mapping study indicated tight linkage, because data from a single qtl mapping experiment may not be accurate sharp et al. While the mapping of qtl traits has been reported by several workers, there are not many reports on the identification of the qtl in one mapping population across several environments. A set of 300 f5 rils from international rice research institute irri was used for genotyping in this study.
Genetic mapping of quantitative trait loci for grain yield. At the end of the chapter, we describe the internal structure of qtl mapping data within rqtl. Mapping population this study was conducted using two bc 1f 2. As a whole, the grass family is emerging as a model system for comparative and evolutionary studies in plants. Locations of markers goals identify the or at least one genomic region, called quantitative trait locus qtl, that contributes to variation in the trait. Genetic studies of qtl mapping quantitative trait loci mapping based on finescale linkage maps have greatly increased our understanding of the inheritance of quantitative traits in the last 20 years. To understand the genetic basis of dynamics of grainfilling, quantitative trait locus qtl analysis was conducted using timerelated phenotypic data on grainfilling collected from a population of 155 recombinant inbred lines f 12, derived from a cross between milyang 23 and akihikari. This is often an early step in identifying and sequencing the actual genes that cause the trait variation. Molecular breeding international rice research institute.
The default of 82 allows six missing markers per individual in a. List of major qtl pve 20% for seven droughtresponsive traits identified in earlier studies along with their linked markers, pve, mapping population type, and parental genotypes. Many earlier studies reported big qsaltol for seedling stage salinity tolerance in rice is on short arm of chromosome 1 but none of the qtl in our study was on qsaltol or nearby position, therefore, hasawi. Each ril derived from seeds of a single f4 plant from a cross between ir29 salt sensitive and hasawi salt tolerant were advanced to constitute the phenotyping population f5. Genetic mapping of qtl for agronomic traits and grain mineral.
Drought resistance in upland rice, genetic analysis and varietal. The whole population and eight founder lines were genotyped with 6k illumina infinium hd assay. To identify quantitative trait loci qtl controlling heat tolerance in rice, the progeny of bc 1 f 1 and f 2 populations derived from an ir64. However, due to rapid developments in marker technology, statistical methodology for identifying quantitative trait loci qtls and the. Irc 2018 poster presentation groups and titles presentation slot. Interval mapping by regression it is essentially the same as the method of basic qtl analysis regression on coded marker genotypes except that phenotypes are regressed on qtl genotypes. Assessing trait contribution and mapping novel qtl for. Identification of qtls and possible candidate genes. Frontiers genetic mapping of quantitative trait loci for.
First international rice genetics symposium here at irri. The rootknot nematode meloidogyne graminicola is an. Recent studies at irri and elsewhere suggest the possibilities of detecting stress tolerance qtl in parental sources not known to be tolerant 23,24. Evaluation system ses for rice irri, 2002 detailed. Association mapping using a multiparent advanced generation intercross magic population provides a promising tool in genetic dissection of rice cooking and eating quality ceq. An introduction to markers, quantitative trait loci qtl mapping and. Utilization of molecular markers for pgrfa characterization and prebreeding for climate changes aug. The best flanking markers for this qtl would be q and r. This level of irrigation resulted in a fully aerobic soil profile. However, the recent severe conditions of flooding because of climate change, which has. Linkage mapping edit based on morgans observation that the recombination fraction between two loci increases with the distance between them, alfred sturtevant neglected his homework one evening and constructed the first genetic. To understand the genetic basis of dynamics of grainfilling, quantitative trait locus qtl analysis was conducted using timerelated phenotypic data on grainfilling collected from a population of 155 recombinant inbred lines f 12, derived from a cross between. Introduction to quantitative trait locus qtl mapping.
Information identified by qtl mapping is important for fine gene mapping, mapbased cloning, and efficient use of gene information in molecular breeding. Qtl mapping and successful introgression of the spring wheat. Analysis of environmental effects on expression of root. Mapping qtl for heat tolerance at flowering stage in rice. Qtl mapping was used to determine effects of loci associated with drought tolerance traits. Timerelated mapping of quantitative trait loci controlling.
Breeding rice varieties with the increased levels of bioavailable micronutrients is one of the most sustainable approaches to tackle micronutrient malnutrition. Mapping qtls using a novel source of salinity tolerance. Irc 2018 poster presentation groups and titles presentation. Biotechnology division, international rice research institute irri, dapo box 7777, metro manila, philippines. Qtl mapping of cold tolerance at the seedling stage using.
Sep 07, 2017 java project tutorial make login and register form step by step using netbeans and mysql database duration. Qtl mapping studies have been reported in most crop plants for diverse traits including yield, quality, disease and insect resistance, abiotic stress tolerance, and environmental adaptation. Mapping quantitative trait loci qtl in progeny derived from cross aa x aa. Identification of qtl for growth and grain yieldrelated. Buu2 1cuulong delta rice research institute, viet nam 2institute of agricultural science of southern viet nam, viet nam corresponding authors email. It performs all the operations necessary for qtl mapping analysis. Mapping and functional validation of a quantitative trait. For example, to use mapqtl for qtl mapping, one needs first to use joinmap to build linkage maps. Software for qtl data analysis university of wisconsin. Identification of genes qtlsmarkers associated with dr traits is a prerequisite for. This may occur even if genetic distances from a preliminary qtl mapping study indicated tight linkage, because data from a single qtl mapping experiment may not be accurate sharp et al. The identification of genes and quantitative trait loci qtls and dna markers that are linked to them is accomplished via qtl mapping experiments. A quantitative trait locus qtl is a locus section of dna that correlates with variation of a quantitative trait in the phenotype of a population of organisms.
Dart technology, has also been widely used in qtl mapping 3941. The rootknot nematode meloidogyne graminicola is an obligate biotrophic pathogen considered to. Rice genetics iv books international rice research institute. Pdf mapping qtl for heat tolerance at flowering stage in. Qtl mapping is based on the principle that genes and markers segregate via chromosome recombinationcalledcrossingoverduringmeiosisi. Singh3 1sokoine university of agriculture, department of crop science and production, plant breeding, p. Four winners will get the chance to be an irri scientist for a day. Each position in the genome, one at a time, is posited as the putative qtl. Mendels experimental results on law of segregation and independent assortment presented in 1865 and published in 1866 in the proceedings of the brunn society of natural history has led founding stone in genetical studies in plants and humans. Submergence is a common naturally occurring disaster in rice production in south and southeast asia. Qtl a gene or chromosomal region that affects a quantitative trait. Linkage loci that are close enough together on the same chromosome to deviate from independent assortment are said to display genetic linkage 4. It was observed in multilocus analysis that, if the combined effects of some major qtl qna1.
All approaches used for qtl detection obtained similar results. Mapping additional qtls from fra to increase submergence. Jul 10, 2018 association mapping using a multiparent advanced generation intercross magic population provides a promising tool in genetic dissection of rice cooking and eating quality ceq. Tutorial multiple qtl mapping mqm analysis for r qtl danny arends, pjotr prins, karl w. Pdf on jan 1, 2008, untung susanto and others published qtl mapping of yield, yield components, and morphological traits in rice oryza sativa l. R system software for microarrray data analysis microarray analysis software has been developed under the r system, which is in the public domain and available at present for unix and windows. Grainfilling is a crucial process that determines final grain yield in rice oryza sativa l. Sabrao journal of breeding and genetics 45 3 409421, 20 quantitative trait loci qtls associated with drought tolerance in rice oryza sativa l. List of polymorphic rice microsatellite rm markers used in the qtl mapping.
An introduction to markers, quantitative trait loci qtl. Ppt markers, qtl mapping and markerassisted selection in. Identification of qtl for root anatomical traits may be useful for. Identification of quantitative trait loci for salinity tolerance in rice oryzasativa l. Linkage mapping of qtls involves using linkage behaviour between qtl or major genes with the markers of interest. Frontiers qtl identification for cooking and eating. Users manual of qtl icimapping, the quantitative genetics group.
Pdf genetic mapping and validation of quantitative trait. The rils used for genotyping from the set phenotyped at irri were completely different except for three rils from. Mapping quantitative trait loci qtl qtl underlying genes controlling quantitative traits. Genotypingbysequencing based qtl mapping for rice grain.
Identification of quantitative trait loci for salinity. Drought stress is a constant threat to rice production worldwide. Keeping the foregoing, the present study was initiated with the objective of detecting hidden drought response qtls in mapping population derived from the cross in. Quantitative trait loci qtls associated with drought. Qtl maps for root growth and drought reaction produced including quantification of qtl x environment interaction activity 4.