Qtl mapping of combining ability and heterosis of agronomic. Since lander and botstein proposed the interval mapping method for qtl mapping data analysis in 1989, tremendous progress has been made in the last many years to advance new and powerful statistical methods for qtl analysis. The question of pleiotropy versus tight linkage in these studies should be solved using a largesize population combined with highdensity mapping. Pdf the main objective of this study was to dissect the genetic basis of rice flowering regulated by temperature. Tutorial multipleqtl mapping mqm analysis for rqtl. Lod 0 jlk m f likelihood ratio comparing the hypothesis of a qtl at position 0 versus that of no qtl. Nov 30, 2010 new approach for rice improvement using a pleiotropic qtl gene for lodging resistance and yield. Multiple qtl mapping university of wisconsinmadison. Qtl mapping for thermosensitive heading date in rice article pdf available in euphytica 2051 february 2015 with 91 reads how we measure reads. Association mapping of yield and its components in rice cultivars. In the past, qtl mapping has been regarded as a task of hypothesis testing.
Assessing trait contribution and mapping novel qtl for. In this study, 25 qtl clusters were identified on eight lgs. The male parent r998 is an elite indica restorer line widely used in threeline hybrid rice seed production in china. Metaqtl mqtl analysis 22 is a better method for combining data from. Original article open access dissection and fine mapping of two qtl for grain size linked in a 460kb region on chromosome 1 of rice qing dong1,2, zhenhua zhang1, linlin wang1, yujun zhu1,2, yeyang fan1, tongmin mou2. A linkage map with 65 polymorphic ssr markers was constructed, which covered 1517.
Open access resources for genomewide association mapping in rice. Highresolution qtl mapping for grain appearance traits and colocalization of chalkinessassociated differentially expressed candidate genes in rice likai chen1, weiwei gao1, siping chen1, liping wang1, jiyong zou1,2, yongzhu liu1, hui wang1, zhiqiang chen1 and tao guo1 abstract. Development and mapping of 2240 new ssr markers for rice oryza sativa l. Pdf in the last decade, association mapping am has become a wellestablished method to detect genes and.
Pdf importance of qtl mapping for heading date in rice. Qtl mapping in rice pdf map position, qtgw5 seemed to be the same gene as qsw5, which controls. Pdf mapping qtl for heat tolerance at flowering stage in. In the past 10 years, interest in applying the tools of molecular genetics to the problem of increasing world rice production has resulted in the generation of two highly saturated, molecular linkage maps of rice, and the localization of numerous genes and quantitative trait loci qtls. A common strategy of qtl mapping is to use recombinant inbred lines rils, which are usually established by several generations of inbreeding of an f1 population usually up to f6 or f7 populations. As this inbreeding process involves a large amount of labor, we. Qtl mapping for drought tolerance in rice genomics lab.
A total of seven qtls were identified on four chromosomes, 1, 6, 9, and 12, associated. Ijms free fulltext deciphering genetic architecture of. Qtl mapping of grain weight in rice and the validation of. Qtl mapping, molecular marker, population, methods, environment. The loci were distributed on chromosomes 2, 3, 5, 6, 8 and 10. Experimental populations of rice because rice is a diploid selfpollinating annual species, experimental population structures can be manipulated with relative ease. Qtl mapping of low temperature on germination rate of rice. Qtl mapping, candidate gene analysis, and markerassisted. Inheritance and qtl mapping of salt tolerance in rice 27 lod2. Qtl may contains single or many genes, mapping population in case of a cross pollinated crop, those are dissected by designing new markers taking the because most of cross pollinated crops cannot with stand sequence of qtls linked clone bac clone oftenly in inbreeding depression. The development of successful aerobic rice cultivars could be achieved by combining the. The gramene qtl database includes qtl identified for numerous agronomic traits in rice, maize, barley, oat, sorghum, pearl millet, foxtail millet and wild rice.
Genetic architecture of aluminum tolerance in rice oryza. By working from the phenotype to the genotype, qtl mapping uses statistical techniques to. To identify quantitative trait loci qtl controlling heat tolerance in rice, the progeny of bc1f1 and f2 populations derived from an ir64 n22 cross were exposed to 3824 c for 14 days at the. Current research in am includes methods to combine. The development of quantitative trait loci qtl map. New approach for rice improvement using a pleiotropic qtl. A guide to qtl mapping with rqtl april 23, 2009 springer. Qtl mapping for resistance to strip virus disease in rice baoxiang wang state key laboratory of crop genetics and germplasm enhancement, research center of jiangsu plant gene engineering, nanjing agricultural university, nanjing 210095. Genetic mapping of quantitative trait loci qtls to identify genomic regions controlling grain yield under drought and subsequent utilization of markers linked to the qtls in markerassisted pyramiding of desirable alleles is an effective alternative to breeding high yielding drought resistant rice ashraf, 2010. 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. Abstra ct this study was initiated to identify quantitative trait loci qtl involved in root system development by measuring root. Tutorial multipleqtl mapping mqm analysis for rqtl danny arends, pjotr prins, karl w.
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. Despite the popularity of ngsbsa and the r statistical platform, no r packages are currently available for ngsbsa. Qtl seq to rice recombinant inbred lines and f 2 populations and successfully identi. Japonica varieties were twice as al tolerant as indica and aus varieties. Qtl mapping for thermosensitive heading date in rice. Qtl mapping for yield and yield contributing traits in two. Qtl analysis for rice grain length and fine mapping of an identified qtl with stable and. Here, a brief overview of the principle of qtl mapping, salient requirements. Dissection and finemapping of two qtl for grain size linked. Heat stress is one of the major abiotic threats to rice production, next to drought and salinity stress. A qtl is shown as an interval across a chromosome where the probability of association is plotted for each marker used in the mapping experiment. Rice, panicle blast resistance, qtl, fine mappin g, mas, introgression lines, resistance breeding background rice oryza sativa l. Pdf in the last decade, association mapping am has become a well established method to detect genes and. Rice, quantitative trait, qtl mapping, mapping populations, single marker analysis, interval mapping, composite interval mapping, marker aided selection.
Singlelocus qtl analyses involved composite interval mapping cim for individual traits and multipletrait composite interval mapping mcim for correlated yield traits to detect the pleiotropic qtls. Qtls are mapped by identifying which molecular markers such as snps or aflps correlate with an observed trait. Pdf mapping quantitative trait loci qtl associated with. Mapping curve of qtl controlling color of silk locates on chromosome 10. In this study, quantitative trait loci qtls affecting the concentrations of 16 elements in whole, unmilled rice oryza sativa l. African rice gall midge afrgm is one of the most destructive pests of. Frontiers genetic mapping of quantitative trait loci for. We has determined the inheritance of percentage of grain with chalkiness pgwc using a set of chromosome segment.
Mapping quantitative trait loci qtl qtl underlying genes controlling quantitative traits. Jansen 1 1 wageningen urcentre for biometry, plant research international, po box 16, 6700 aa, wageningen, the netherlands 2 wageningen urdepartment of molecular biology, plant research international, po box 16, 6700 aa, wageningen, the netherlands. Three major stable qtls were detected in all eight environments. Therefore, developing salttolerant and highyielding rice using quantitative trait loci qtls and linkage markers is a priority for molecular breeding. Most of the global rice varieties and diverse mapping populations commonly utilized for identification and mapping of quantitative trait loci qtls. A number of qtl studies reported that one genomic region was associated with several traits, indicating linkage andor pleiotropic effects. Genetic mapping identifies consistent quantitative trait loci. Qtl mapping of grain length in rice oryza sativa l. Pdf mapping qtl associated with root and related traits. It is better to view the problem as one of model selection. In bread wheat, singlelocus and twolocus qtl analyses were conducted for seven yield and yield contributing traits using two different mapping populations p i and p ii. Pdf malnutrition is one of the prevailing health problems worldwide, affecting a large proportion of the populations in riceconsuming.
Open access resources for genomewide association mapping. Pdf genetic mapping and validation of quantitative trait. Saline stress severely affects rice oryza sativa l. Author summary while rice oryza sativa is significantly more al tolerant than other cereals, no genes underlying al tolerance in rice have been reported. Linkage and qtl mapping in related full sib families usda. Qtl mapping in three rice populations uncovers major genomic. Mapping qtls using a novel source of salinity tolerance from hasawi and their interaction with environments in rice m. Nov 15, 20 qtls controlling the concentrations elements in rice grain were identified in two mapping populations. The qtl cluster refers to multiple different traits related to a qtl, and the qtl hotspot refers to multiple qtls of the same trait distributed within the 20 cm region. Genotypingbysequencing based qtl mapping for rice grain yield. Curves in plot indicate the genetic or physical coordinate xaxis and lod score yaxis of detected qtl. Doerge in the past lo years, interest in applying the tools of molecular genetics to the problem of increasing world rice production has resulted in the generation of two highly saturate molecular linkage maps of rice, and the ioculization of numerous genes and quantitative trait loci qtls. Quantitative trait locus qtl mapping 10810, cmb lecture 9 eric xing backcross experiment.
Quantitative trait loci qtl analysis for rice grain width and fine. However, few studies were carried out on qtl mapping of rice biomass and its component traits, and the rela. This character along with grain yield determines the commercial potential of any rice cultivar. Simulation study showed that qtl seq is able to detect qtls over wide ranges of experimental variables, and the. At present, most rice qtlmapping studies are carried out using permanent populations, such as doubled haploid dh and recombinant inbred lines ril. Pdf qtl mapping of rice root traits at different nh4.
The qtls were clustered such that most genomic regions were associated with more than one element. In the past, qtl mapping has been regarded as a task ofhypothesis testing. Plus spectrophotometer biorad, usa as described in the users manual. Pdf genetic mapping of qtl for agronomic traits and grain.
Various factors affecting qtl mapping are number of genes controlling the target traits and their position, heritability of the traits, type and size of mapping population used in qtl mapping, type and number of markers in linkage maps, statistical method used. Yamamoto r, horisue n, ikeda r 1995 rice breeding manual. In the past 10 years, interest in applying the tools of molecular genetics to the problem of increasing world rice production has resulted in the generation of two highly saturated. The chinese mitten crab eriocheir sinensis is the most economically important cultivated crab species in china, and its genome has a high number of chromosomes 2n.
Qtl mapping, candidate gene analysis, and markerassisted backcrossing for improved salinity tolerance in rice salt stress is a major constraint across large riceproducing areas because of the high sensitivity of modern rice varieties. Qtl mapping in mice biostatistics and medical informatics. Chalkiness of rice grain is an important quality component of rice, as it has a profound influence on eating and milling qualities. Identification and mapping of qtls associated with drought. Qtl mapping qtl mapping is the statistical study of the alleles that occur in a locus and the phenotypes physical forms or traits that they produce. Mapping of qtl controlling color of silk in f 2 population and the location of r1. Linkage and qtl mapping in related full sib families a case study in potato. Approaches to qtl mapping traditional qtl mapping utilizes biparental population bp mapping populations from controlled crosses zhu et al. At the end of the chapter, we describe the internal structure of qtl mapping data within rqtl. Qtl mapping pdf basic level, qtl mapping simply involves finding an association between a genetic marker and a phenotype that one can measure fig. Qtl analysis for rice grain length and fine mapping of an identified.
Quantitative trait loci qtl analysis for rice grain width and fine mapping of an. Mapping qtl for biomass yield and its components in rice. Pdf high resolution mapping of qtls for heat tolerance in. Qtl mapping and its applications in crop plants 2 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. The development of quantitative trait loci qtl map ping methods to. Kanbar and others published mapping qtl associated with root and related traits in dh population of rice find, read and cite all the research you need on researchgate. Jansen october 27, 2014 1 1 introduction multiple qtl mapping mqm provides a sensitive approach for mapping quantititive trait loci qtl in experimental populations.
Jun 26, 2012 mesocotyl elongation is an important trait for seedling emergence in directseeding cultivation in rice. Mapping quantitative trait loci qtl associated with cooking quality in rice oryza sativa l. Mapping qtl for agronomic traits in breeding populations. An efficient strategy combining ssr markers and advanced qtl. Qtl mapping in the present experiment was carried out by calculating threshold logarithm of odds lod for each trait by performing test with permutations. Pdf fine mapping of the grain chalkiness qtl qpgwc7 in. Mapping a quantitative trait locus for resistance to.
The power of qtl mapping using a saturated rflp map was demonstrated by box 1. Qtls previously detected in other mapping population structures, eshed and zamir 1995 proposed the use of nils to simultaneously map, verify, and incorporate qtls into adapted, elite genetic backgrounds. For example, if each of the 2 parents has a tgwincreasing or sppincreasing qtl that is tightly linked. Apr 18, 2017 there are several reports on qtl mapping for salt stress by ssr genotyping on whole population in rice but no one has done qtl mapping by bsa approach for salt stress in rice. How to map the drought tolerance traits in rice using the qtl mapping is explained in this video. We performed qtl analyses by using composite interval mapping, as implemented by the zmapqtl program model 6 provided in version 2. Qtl mapping of physiological traits at the booting stage in rice. Inheritance and qtl mapping of salt tolerance in rice.
Fine mapping of a panicle blast resistance gene pbbd1 in. We aim to define a qtl nomenclature system providing the simplest possible naming strategy that would still allow each unique qtl to be distinguished. Mapping quantitative trait loci qtl the single or many genes that underlie quantitative phenotypes might represent an important part of the final synthesis of molecular and quantitative genetics. Identification and validation a major qtl from sea rice. Qtls influencing rice biomass yield and grain yield in different mapping populations, demonstrating a large number of epistatic qtl pairs and a few maineffect qtls associated with these traits. Jan 19, 2016 submergence is a common naturally occurring disaster in rice production in south and southeast asia. Mapping and comparative analysis of qtl for rice plant. Incidence of heat stress at reproductive phase of the crop results in abnormal pollination leading to floret sterility, low seed set. To address the demand, plant breeders seek new sources of genetic variation to enhance the productivity, sustainability and resilience of crop varieties. Here, the indica rice sea rice 86 sr86 seedlings showed higher tolerance than ordinary rice varieties in saline soil, and a dominant effect.
Qtlseq identifies cooked grain elongation qtls near soluble. Ka 1976 laboratory manual for physiological studies of rice, vol 83. Mapping of qtl is important to augment our knowledge of the inheritance. It gives clear picture that qtl mapping effective in identification of tolerant alleles. Multipoint mapping considers all of the linked markers on a chromosome simultaneously, resulting in a single analysis for each chromosome conditional probabilities of qtl genotypes the basic element upon which the formal theory of qtl mapping is built is the conditional probability that the qtl genotype is q k, given the observed marker.
Heading date in rice is one of the most important indices in rice breeding being governed by multiple genes known as quantitative trait loci qtls. Qtl mapping of low temperature on germination rate of rice 95 0 5 10 15 20 25 30 5 15253545 5565758595 germination rate % no. Rice blast, caused by the fungal pathogen magnaporthe oryzae, is one of the. Combining drought resistance with yield and desirable economic traits is the. Qhd10, without highresolution mapping, and the reality of qtls identified by interval mapping. In this study, we identified qtls for ge in rice using bulksegregant analysis bsa and wholegenome sequencing based on an f2 population. Linkage based qtl mapping is a variant of qtl mapping. Qtl mapping with an example css population in rice consisting of 65 nonidealized css lines and 82 chromosome segments indicated that a total of 18 segments on eight of the 12 rice chromosomes harboured qtls a. It is better to view the problem as one ofmodel selection. Mapping and characterization of quantitative trait.
Singleseed descent each plant contributes a single offspring to the next generation 111 lllll111 recombinant inbred lines. Jan 20, 2020 next generation sequencing bulk segregant analysis ngsbsa is efficient in detecting quantitative trait loci qtl. Importance of qtl mapping for heading date in rice. Here we launch a highresolution, openaccess research platform to facilitate genomewide association mapping in rice, a staple food crop. 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. Identification and validation a major qtl from sea rice 86. There are several reports on qtl mapping for salt stress by ssr genotyping on whole population in rice but no one has done qtl mapping by bsa approach for salt stress in rice. Qtl quantitative trait loci mapping is commonly used to identify genetic regions responsible to important phenotype variation. Much of the focus has been on adjusting for test multiplicity. By combining this method with tests of advanced backcross progenies. Here, the indica rice sea rice 86 sr86 seedlings showed higher tolerance than ordinary rice varieties in saline soil, and a dominant effect on salinity sensitivity was demonstrated by genetic analysis. We present qtlseqr, an r package for ngsbsa that identifies qtl using two statistical approaches.
Tolerance for salinity is complex, involving a number of different physiological mechanisms, including. In this study, a backcross inbred line bil population from a cross between kasalath and nipponbare was employed to map quantitative trait loci qtls for mesocotyl elongation. Quantitative trait loci qtl underlying related traits at the seedling stage under two different phosphorus levels was investigated in rice using a population of 76 chromosomal sequence. Qtl mapping for resistance to strip virus disease in rice. A recombinant inbred line ril population bred from a cross between a javanica type cv.
Using genomewide association gwa and biparental qtl mapping, we investigated the genetic architecture of al tolerance in rice. A total of 5 qtls for mesocotyl length were identified on chromosomes 1, 3, 7, 9, and 12 in 2 independent. Qtl mapping using an ultrahighdensity snp map reveals a major. Pdf qtl mapping for thermosensitive heading date in rice. Pdf mapping qtl associated with root and related traits in.
Mapping of qtls associated with cytosolic glutamine. An ultrahigh density binmap for rapid qtl mapping for. Genetic mapping and validation of quantitative trait loci qtl for the grain appearance and quality traits in rice oryza sativa l. We suggest using capital letters for the locus name so that it does not confuse qtl names with other gene nomenclature in rice. The chinese mitten crab eriocheir sinensis is the most economically important cultivated crab species in china, and its genome has a high number of chromosomes 2n 146. The asian pool is dominated by indica varieties and includes diverse kernel size and shape market classes, while u. 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. Qtl mapping for the different traits and their introgression in. Recent research progress has been focused on statistical methods and issues for mapping multiple qtl together. Hb277 rice was used to map seven quantitative trait loci qtls for thousand grain weight tgw. Qtls for rice grain yield under reproductive stage drought stress qdty identified earlier with low density markers have shown linkage drag. Qtl mapping for milling quality in elite western u. This is often an early step in identifying and sequencing the actual genes that cause the trait variation. Qtl a gene or chromosomal region that affects a quantitative trait.
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