Genetic studies of qtl mapping quantitative trait loci mapping based on. Icim was first proposed for qtl mapping in biparental populations and has been widely applied in qtl mapping researches, for example, in wheat zhu et al. Introduction to quantitative trait locus qtl mapping. Utilization of molecular markers for pgrfa characterization and prebreeding for climate changes aug. Qtl mapping of nnms of soybean with cim and icim methods across 8 years. Linkage qtl, mapping populations and markerassistedselection. The inclusive composite interval mapping icim method in icimapping v3.
Environment qtl method linkage group lod additive r 2 startposition bp endposition bp 2008hrb qnnms021 cim gm02 3. Qtl mapping was done using a simple sequence repeat ssr map combined with speci. Rqtl r package for qtl mapping suitable for mediumsized data other tools. Nov 27, 2017 the reliability of the linkage map for qtl mapping. 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. Quantitative trait loci mapping and genetic dissection for lint. Information identified by qtl mapping is important for fine gene mapping, mapbased cloning, and efficient use of gene information in molecular breeding. Each qtl mapping method sma, imadd, icimadd, sgm, imepi, or icimepi has three kinds of output, denoted as q for significant qtl, r for results at all scan positions, and t for permutation tests. Strategy of qtl mapping with multiple models proposed by su et al 2010b was adopted. Qtl analysis of head splitting resistance in cabbage. Frontiers qtl mapping of grain zn and fe concentrations in. In this study, a doubled haploid dh population derived from an intracross between head splittingsusceptible inbred cabbage line 79156 and resistant line 96100 was obtained and used to analyze inheritance and. By using icim, a total of 34 qtls with additive effects aqtls were identified.
A negative effect size suggested that the enhancing allele at the qtl was derived from the female parentyumai 18. Epistatic qtl can be identified by icim, no matter whether the two interacting qtl have any additive effects. Linkage qtl, mapping populations and markerassisted. Qtl mapping of soybean node numbers on the main stem and. Qtl mapping and candidate gene mining for soybean seed. The download package also contains a manual and sample datasets. Inclusive composite interval mapping icim was accordingly. Qtl mapping of soybean node numbers on the main stem and meta. Considering t he number of markers is always g reater than the number of qtl. This parameter is for all the figure files, including.
Oct 01, 2008 the proposed linear model is the theoretical basis for inclusive compositeinterval qtl mapping icim for f2 populations, which consists of two steps. Frontiers qtl analysis and nested association mapping for. Qtl mapping of physiological traits at the booting stage in rice. Nov 26, 2019 two novel midge resistance qtl were mapped to a 4. In this study, we used a mapping population derived from a cross between a chromosome segment substitution line cssl3228 donor.
Each qtl mapping method sma, imadd, icim add, sgm, imepi, or icim epi has three kinds of output, denoted as q for significant qtl, r for results at all scan positions, and t for permutation tests. Inclusive composite interval mapping of qtl by environment. Jul 19, 2017 icim was first proposed for qtl mapping in biparental populations and has been widely applied in qtl mapping researches, for example, in wheat zhu et al. Relatively small sample size in many qtl mapping experiments adds to the challenge. Oct 18, 2017 the icim method applies a strategy in which a stepwise regression is firstly made, so markers with significant effect on qtl are selected, and then follows an interval mapping step, where the phenotypic values are adjusted by the selected marker variables, except for the two markers that flank the scanning position at each mapping step for. Mapping quantitative trait loci qtl qtl underlying genes controlling quantitative traits. In this study, icim was extended to qtl by environment interaction qei mapping for multienvironmental trials, where the qtl average effect and qei effects could be properly estimated. Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations lei meng1, huihui li1, luyan zhang1, jiankang wang. A tool for improvement in crop plants shaukeen khan department of plant breeding and genetics, mpuat, udaipur, rajasthan 301, india available online at. Relatively small sample size in many qtl mapping experiments adds to. In order to detect owbm resistance genes and quantitative trait loci qtl for wheat breeding, two recombinant inbred line ril populations were.
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. Qtl mapping was performed using inclusive composite interval mapping of additive icimadd and epistatic qtl icimepi functions in qtl icimapping version 3. In icim algorithm, use all marker information wh e n construct model 4. Before using genotype data, you should clean the data bad markers, monomorphic etc this will be in appendix process 1. Locations of markers goals identify the or at least one genomic region, called quantitative trait locus qtl, that contributes to variation in the trait. Genomewide association study and qtl mapping reveal genomic.
Inclusive composite interval mapping icim was accordingly developed and proved to be more efficient for background con trol via a twostep mapping strategy 3,11,12. The progeny of 234 f2 plants and the two parents were planted in. Construction of a highdensity genetic map and qtl mapping of. Once a highdensity linkage map is developed using highthroughput snp markers, we are not sure how accurate is the linkage map regarding marker. Qtl mapping and candidate gene mining for soybean seed weight. Linkage, qtl, mapping populations and markerassistedselection dave douches, allen van deynze and dave francis paa solcap workshop. Combining qtlseq and linkage mapping to fine map a wild. In order to detect owbm resistance genes and quantitative trait loci qtl for wheat breeding, two recombinant inbred line ril populations were established and. Q1660 was identified as a qtl for five leaf traits, and three significant qtls q91, q1866 and q1873 associated with plant growth were detected at least twice. Therefore, qtl mapping is considered to be the best method to study the.
A significant logarithm of odds lod threshold was determined using. The icim method applies a strategy in which a stepwise regression is firstly made, so markers with significant effect on qtl are selected, and then follows an interval mapping step, where the phenotypic values are adjusted by the selected marker variables, except for the two markers that flank the scanning position at each mapping step for. Review of statistical methods for qtl mapping in experimental crosses karl w. Dec 01, 2016 the inclusive composite interval mapping icim method in icimapping v3. Qtl analysis for seven quality traits of ril population in. Icim was first proposed for qtl mapping in biparental populations and has been widely applied in qtl mapping researches, for example, in wheat zhu. Ici mapping manual quantitative trait locus genetic. In statistical genetics, inclusive composite interval mapping icim has been proposed as an approach to qtl quantitative trait locus mapping for populations derived from biparental crosses. Qtl a gene or chromosomal region that affects a quantitative trait. Jan 14, 2016 technical development of qtl icimapping.
However, in zengs algorithm, qtl effect at the current testing position and regression coef. Inclusive composite interval mapping icim for digenic epistasis of quantitative traits in biparental populations huihui li. The reliability of the linkage map for qtl mapping. Genomewide association study and qtl mapping reveal. 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. Qtl detection and mapping methods part 1 by vikas mangal.
Jul 27, 2017 lod contours for quantitative trait loci qtl to powdery mildew on chromosomes 1bl, 1dl, 4bl, and 5bl identified by inclusive composite interval mapping icim in the avocet. Inclusive composite interval mapping icim for additive and dominance qtl zhang, l. Pdf qtl icimapping is freely available public software capable of building high density linkage. The proposed linear model is the theoretical basis for inclusive compositeinterval qtl mapping icim for f2 populations, which consists of two steps. Sep 07, 2017 qtl editing for crop improvement in rice. Icim has been proven to be an efficient qtl mapping method and widely used in biparental e. Qtl mapping is based on genetic linkage map and phenotypic data and attempts to locate individual genetic factors on chromosomes and to estimate their. Plant height ph is an important agronomic trait and is closely related to yield in soybean glycine max l. Orange wheat blossom midge owbm is a devastating insect pest affecting wheat production. Simulated populations and one barley doubled haploids dh population were used to demonstrate the efficiency of icim in mapping both additive qtl and digenic interactions. Qtl mapping was conducted by using the inclusive composite interval mapping icim method in the qtl icimapping 4. Whole genome resequencing reveals agronomically important loci in rice using mutmap and qtl seq duration.
Pdf robust icim for qtl analysis by minimum betadivergence. Review of statistical methods for qtl mapping in experimental. Simulation studies and application in a cowpea magic population in this. Head splitting resistance hsr in cabbage is an important trait closely related to both quality and yield of head. By combining qtls with the qtl physical locations, two qtl intervals located in the. Interactions between markers can be caused by the dominance effect of qtl. Due to the complex genetic background of ph in soybean, there are few reports on its fine mapping. Conduct multiple quantitative trait loci qtl mapping under the. 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. Qtl mapping of kernel traits and validation of a major qtl for.
Some interacting qtl could be in linkage, and some may even have little or no main effect. A positive effect size was defined by the enhancing allele of the qtl derived from the male parent pi277012. Qtl mapping is based on genetic linkage map and phenotypic data and attempts to locate individual genetic factors on chromosomes and to estimate their genetic effects. Here, a brief overview of the principle of qtl mapping, salient requirements for qtl mapping, common statistical tools and techniques employed in qtl analysis. Interactions between markers can be caused by the dominance.
However, the genetic control of this trait remains unclear. At the end of the chapter, we describe the internal structure of qtl mapping data within rqtl. Inclusive composite interval mapping icim for digenic. Inclusive composite interval mapping icim was accordingly developed and proved to be. These qtl were also detected by icim, and therefore, should preferentially be used for marker assisted. The difficulty mainly lies in the biological complexity of epistasis of quantitative trait loci qtl. Linkage loci that are close enough together on the same chromosome to deviate from independent assortment are said to display genetic linkage 4. Genetic mapping with background control for quantitative. Qtls are mapped by identifying which molecular markers such as snps or aflps correlate with an observed trait.
Inclusive composite interval mapping icim has been proposed for additive, dominant and epistatic qtl mapping in biparental populations for single environment. Mapping quantitative trait loci for plant adaptation and. Quantitative trait locus qtl analysis was conducted using gacd software with the inclusive composite interval mapping icim method. Qtl mapping was performed using inclusive composite interval mapping of additive icim add and epistatic qtl icim epi functions in qtl icimapping version 3.
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