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Results for “QTL mapping”

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PubMed2002

Genetic dissection of a modern sugarcane cultivar ( Saccharum spp.).II. Detection of QTLs for yield components.

The genetics of current sugarcane cultivars ( Saccharum spp.) is outstandingly complex, due to a high ploidy level and an interspecific origin which leads to the presence of numerous chromosomes belonging to two ancestral genomes. In order to analyse the inheritance of quantitative traits, we have undertaken an extensive Quantitative Trait Allele (QTA) mapping study based on a population of 295 progenies derived from the selfing of cultivar R570, using about 1,000 AFLP markers scattered on about half of the genome. The population was evaluated in a replicated trial for four basic yield components, plant height, stalk number, stalk diameter and brix, in two successive crop-cycles. Forty putative QTAs were found for the four traits at P = 5 x 10(-3), of which five appeared in both years. Their individual size ranged between 3 and 7% of the whole variation. The stability across years was improved when limiting threshold stringency. All these results depict the presence in the genome of numerous QTAs, with little effects, fluctuating slightly across cycles, on the verge to being perceptible given the experimental resolution. Epistatic interactions were also explored and 41 independent di-genic interactions were found at P = (5 x 10(-3))(2). Altogether the putative genetic factors revealed here explain from 30 to 55% of the total phenotypic variance depending on the trait. The tentative assignment of some QTAs to the ancestral genomes showed a small majority of contributions as expected from the ancestral phenotypes. This is the first extensive QTL mapping study performed in cultivated sugarcane.

Journal Article↗

PubMed2026

Integrated analysis uncovers exogenous induction and molecular regulation of erinacine A accumulation in Hericium erinaceus.

Erinacine A, a cyathane-type diterpenoid mainly from Hericium erinaceus mycelia, exhibits prominent neurotrophic and neuroprotective activities, making it a promising candidate for managing neurodegenerative diseases. However, its low abundance and unclear genetic regulatory mechanisms hinder its application as a nutraceutical. This study aimed to decipher its regulatory mechanisms and enhance production. Four exogenous inducers were screened, with salicylic acid (SA) and ergosterol (ERG) significantly increasing erinacine A content by 62.21% and 146.70% at 20 days, respectively. Transcriptome and WGCNA of inducer-treated sample identified darkorange and magenta modules associated with erinacine A biosynthesis, with the eri gene cluster enriched in the darkorange module and eriG and eriF as hub genes. Forward genetic analysis via QTL mapping of the HeD127 dikaryon population revealed significant phenotypic variation in erinacine A content (0.341-13.085 mg/g) and identified two loci (erA-1 and erA-2) explaining 18.63% of phenotypic variation. Integrating these forward and reverse genetic analyses revealed that salicylic acid and ergosterol synergistically regulate core carbon metabolic pathways to augment acetyl-CoA supply for the mevalonate pathway, suppressed competitive metabolism, enhanced diterpene skeleton construction and structural modification. These results deepen our understanding of the genetic and molecular basis governing accumulation of erinacine A, and facilitate its application in neuroprotective pharmaceuticals.

Diterpenes↗

PubMed2005

Bayesian shrinkage estimation of quantitative trait loci parameters.

Mapping multiple QTL is a typical problem of variable selection in an oversaturated model because the potential number of QTL can be substantially larger than the sample size. Currently, model selection is still the most effective approach to mapping multiple QTL, although further research is needed. An alternative approach to analyzing an oversaturated model is the shrinkage estimation in which all candidate variables are included in the model but their estimated effects are forced to shrink toward zero. In contrast to the usual shrinkage estimation where all model effects are shrunk by the same factor, we develop a Bayesian method that allows the shrinkage factor to vary across different effects. The new shrinkage method forces marker intervals that contain no QTL to have estimated effects close to zero whereas intervals containing notable QTL have estimated effects subject to virtually no shrinkage. We demonstrate the method using both simulated and real data for QTL mapping. A simulation experiment with 500 backcross (BC) individuals showed that the method can localize closely linked QTL and QTL with effects as small as 1% of the phenotypic variance of the trait. The method was also used to map QTL responsible for wound healing in a family of a (MRL/MPJ x SJL/J) cross with 633 F(2) mice derived from two inbred lines.

Animals↗

PubMed2002

Mapping of the QTL (quantitative trait locus) conferring partial resistance to leaf blast in rice cultivar Chubu 32.

The rice cultivar Chubu 32 possesses a high level of partial resistance to leaf blast. The number and chromosomal location of genes conferring this resistance were detected by restriction fragment length polymorphism (RFLP) linkage mapping and quantitative trait locus (QTL) analysis. For the mapping, 149 F(3) lines derived from the cross between rice cultivar Norin 29, with a low level of partial resistance, and Chubu 32 were used, and their partial resistance to leaf blast was assessed in upland nurseries. A linkage map covering six chromosomes and consisting of 36 RFLP markers was constructed. In the map, only one significant QTL (LOD>2.0) for partial resistance was detected on chromosome 11. This QTL explained 45.6% of the phenotypic variation. The segregation ratio of the F3 lines was 3:1 for partial resistance to susceptibility. These results suggest that the partial resistance in Chubu 32 is controlled by a major gene.

Journal Article↗

PubMed2005

A genome-wide search for quantitative trait Loci that influence antisocial drug dependence in adolescence.

BACKGROUND: Among adolescents, externalizing problem behavior and substance use disorders are often comorbid. Familial influences, including shared genetic risk factors, may account for part of this comorbidity. Previously we reported 2 chromosomal regions (3q24-3q25 and 9q34) likely to contain genes that influence substance dependence vulnerability (DV) in adolescence. OBJECTIVES: To identify quantitative trait loci (QTLs) that influence externalizing problem behavior in adolescence and to determine whether any identified QTL overlap chromosomal regions that influence DV. DESIGN: Regression-based QTL mapping procedures designed for selected sibling pair samples. SETTING: Patient probands were drawn from consecutive admissions to residential and outpatient (milieu-type) treatment facilities for substance abuse and delinquency operated by the University of Colorado; most of these patients were referred for treatment by juvenile justice or social service agencies. PATIENTS: A total of 249 proband-sibling pairs from 191 families were selected for the study. Patient probands were 13 to 19 years of age; siblings of the probands ranged in age from 12 to 25 years. MAIN OUTCOME MEASURES: A community-based sample of 4493 adolescents and young adults was used to define clinically significant, heritable, age- and sex-normed indexes of DV, conduct disorder symptoms (CDS), and a composite index of antisocial substance dependence (DV + CDS). Siblings and parents were genotyped for 374 microsatellite markers distributed across the 22 autosomes (mean intermarker distance, 9.2 centimorgans). RESULTS: For both DV and CDS, there was evidence of linkage to the same region on chromosome 9q34, as well as to 3q24-3q25 for DV, and a novel region on chromosome 17q12 for CDS. Our composite index (DV + CDS) yielded the strongest evidence for linkage (logarithm of odds = 2.65) to the chromosome 9q34 region. CONCLUSION: These results provide the first evidence of a potential molecular genetic basis for the comorbidity between DV and antisocial behavior.

Adolescent↗

PubMed1999

Genetics and evolution of insect resistance in Arabidopsis.

The genetic and molecular tools available in Arabidopsis allow identification of insect resistance genes. Many functional aspects of pest recognition and signal transduction are conserved in the defensive physiology of a broad range of plant species. Therefore, studies of insect resistance in Arabidopsis may be extended to functional genomics studies in many plant species of agricultural and ecological importance. Because of public concerns for field release of genetically modified organisms, naturally occurring genetic variation for resistance to insect herbivores will be valuable in plant breeding. Combined studies employing QTL mapping and candidate resistance genes are necessary to find and understand the genes responsible for variation in resistance. We review experiments showing that plant populations contain high levels of genetic variation for defensive physiology and disease and insect resistance, and that this variation can be manipulated to alter resistance and its components in a predictable fashion. In Arabidopsis, we can map the genes controlling physiological variation, and estimate the importance of regulatory or enzyme-encoding loci. Finally, we review functional genomics approaches for identification of insect resistance genes in Arabidopsis.

Animals↗

PubMed2007

Detection of novel quantitative trait loci for cutaneous melanoma by genome-wide scan in the MeLiM swine model.

Human cutaneous melanoma is a complex trait inherited in about 10% of cases. Although 2 high-risk genes, CDKN2A and CDK4, and 1 low risk gene, MC1R, have been identified, susceptibility genes remain to be discovered. Here, we attempted to determine new genomic regions linked to melanoma using the pig MeLiM strain, which develops hereditary cutaneous melanomas. We applied quantitative trait loci (QTL) mapping method to a significant genome-wide scan performed on 331 backcross pigs derived from this strain. QTLs were detected at chromosome-wide level for a melanoma synthetic trait corresponding to the development of melanoma. The peak positions on Sus scrofa chromosomes (SSC) were at 49.4 and 88.0 cM (SSC1), 56.0 cM (SSC13), 86.5 cM (SSC15) and 39.8 cM (SSC17), and, on SSC2, at 16.9 cM, in families derived from F1 males only (p < 0.05, except for SSC13, p < 0.01). Analysis of 7 precise specific traits revealed highly significant QTLs on SSC10 (ulceration), on SSC12 (presence of melanoma at birth), on SSC13 (lesion type), and on SSC16 and SSC17 (number of aggressive melanomas) at the respective positions 42.0, 95.6, 81.0, 45.3 and 44.8 cM (p < 0.001 and p < 0.05 respectively at the chromosome- and genome-wide levels). We also showed that MeLiM MC1R*2 allele, which determines black coat colour in pigs, predisposes significantly to melanoma. Interactions were observed between MC1R and markers located on SSC1 (p < 0.05). Taken together, these results indicate that MeLiM swine is a model for human multigenic diseases. Comparative mapping revealed human regions of interest to search for new melanoma susceptibility candidates.

Alleles↗

PubMed2007

Allelopathy in crop/weed interactions--an update.

Since varietal differences in allelopathy of crops against weeds were discovered in the 1970s, much research has documented the potential that allelopathic crops offer for integrated weed management with substantially reduced herbicide rates. Research groups worldwide have identified several crop species possessing potent allelopathic interference mediated by root exudation of allelochemicals. Rice, wheat, barley and sorghum have attracted most attention. Past research focused on germplasm screening for elite allelopathic cultivars and the identification of the allelochemicals involved. Based on this, traditional breeding efforts were initiated in rice and wheat to breed agronomically acceptable, weed-suppressive cultivars with improved allelopathic interference. Promising suppressive crosses are under investigation. Molecular approaches have elucidated the genetics of allelopathy by QTL mapping which associated the trait in rice and wheat with several chromosomes and suggested the involvement of several allelochemicals. Potentially important compounds that are constitutively secreted from roots have been identified in all crop species under investigation. Biosynthesis and exudation of these metabolites follow a distinct temporal pattern and can be induced by biotic and abiotic factors. The current state of knowledge suggests that allelopathy involves fluctuating mixtures of allelochemicals and their metabolites as regulated by genotype and developmental stage of the producing plant, environment, cultivation and signalling effects, as well as the chemical or microbial turnover of compounds in the rhizosphere. Functional genomics is being applied to identify genes involved in biosynthesis of several identified allelochemicals, providing the potential to improve allelopathy by molecular breeding. The dynamics of crop allelopathy, inducible processes and plant signalling is gaining growing attention; however, future research should also consider allelochemical release mechanisms, persistence, selectivity and modes of action, as well as consequences of improved crop allelopathy on plant physiology, the environment and management strategies. Creation of weed-suppressive cultivars with improved allelopathic interference is still a challenge, but traditional breeding or biotechnology should pave the way.

Breeding↗

PubMed2002

Lactuca saligna, a non-host for lettuce downy mildew ( Bremia lactucae), harbors a new race-specific Dm gene and three QTLs for resistance.

Lactuca sativa (lettuce) is susceptible to Bremia lactucae (downy mildew). In cultivated and wild Lactuca species, Dm genes have been identified that confer race-specific resistance. However, these genes were soon rendered ineffective by adaptation of the pathogen. Lactuca saligna (wild lettuce) is resistant to all downy mildew races and can be considered as a non-host. Therefore, L. saligna might be an alternative source for a more-durable resistance to downy mildew in lettuce. In order to analyze this resistance, we have developed an F(2) population based on a resistant L. saligna x susceptible L. sativa cross. This F(2) population was fingerprinted with AFLP markers and tested for resistance to two Bremia races NL14 and NL16. The F(2) population showed a wide and continuous range of resistance levels from completely resistant to completely susceptible. By comparison of disease tests, we observed a quantitative resistance against both Bremia races as well as a race-specific resistance to Bremia race NL16 and not to NL14. QTL mapping revealed a qualitative gene ( R39) involved in the race-specific resistance and three QTLs ( RBQ1, RBQ2 and RBQ3) involved in the quantitative resistance. The qualitative gene R39 is a dominant gene that gives nearly complete resistance to race NL16 in L. saligna CGN 5271 and therefore it showed features similar to Dm genes. The three QTLs explained 51% of the quantitative resistance against NL14, which indicated that probably only the major QTLs have been detected in this F(2) population. The perspectives for breeding for durable resistance are discussed.

Journal Article↗

PubMed2002

Detection of Fusarium head blight resistance QTL in a wheat population using bulked segregant analysis.

A population of 218 recombinant inbred lines (RILs) was developed from the cross of two wheat (Triticum aestivum L.) cultivars, 'Ning 894037' and 'Alondra'. Ning 894037 has resistance to Fusarium head blight (FHB) and Alondra is moderately susceptible. Response of the RILs and their parental lines to FHB infection was evaluated with point inoculation in four experiments both in greenhouse and in field conditions. Distribution of disease severity in the population is continuous, indicating quantitative inheritance of resistance to FHB. Bulked segregant analysis and QTL mapping based on simple sequence repeat (SSR) markers revealed three chromosome regions that are responsible for FHB resistance. A chromosome region on 3BS accounted for 42.5% of the phenotypic variation for FHB resistance. Additional QTLs were located on chromosomes 2D and 6B. These three QTLs jointly accounted for 51.6% of the phenotypic variation. SSR markers linked to the QTLs influencing resistance to FHB have potential for use in breeding programs.

Analysis of Variance↗

PubMed2003

Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and two testcross populations.

To understand the types of gene action controlling seven quantitative traits in rice, QTL mapping was performed to dissect the main effect (M-QTLs) and digenic epistatic (E-QTLs) QTLs responsible for the trait performance of 254 recombinant inbred lines (RILs) of "Lemont/Teqing", and two testcross (TC) F(1) populations derived from these RILs. The correlation analyses reveal a general pattern, i.e. trait heritability in the RILs was negatively correlated to trait heterosis in the TC hybrids. A large number of M-QTLs and E-QTLs affecting seven traits, including heading date (HD), plant height (PH), flag leaf length (FLL), flag leaf width (FLW), panicle length (PL), spikelet number per panicle (SN) and spikelet fertility (SF), were identified and could be classified into two predominant groups, additive QTLs detected primarily in the RILs, and overdominant QTLs identified exclusively in the TC populations. There is little overlap between QTLs identified in the RILs and in the TC populations. This result implied that additive gene action is largely independent from non-additive gene action in the genetic control of quantitative traits of rice. The detected E-QTLs collectively explained a much greater portion of the total phenotypic variation than the M-QTLs, supporting prior findings that epistasis has played an important role in the genetic control of quantitative traits in rice. The implications of these results to the development of inbred and hybrid cultivars were discussed.

Crosses, Genetic↗

PubMed2003

QTLs for Na+ and K+ uptake of the shoots and roots controlling rice salt tolerance.

An F2 and an equivalent F3 population derived from a cross between a high salt-tolerance indica variety, Nona Bokra, and a susceptible elite japonica variety, Koshihikari, were produced. We performed QTL mapping for physiological traits related to rice salt-tolerance. Three QTLs for survival days of seedlings (SDSs) under salt stress were detected on chromosomes 1, 6 and 7, respectively, and explained 13.9% to 18.0% of the total phenotypic variance. Based on the correlations between SDSs and other physiological traits, it was considered that damage of leaves was attributed to accumulation of Na+ in the shoot by transport of Na+ from the root to the shoot in external high concentration. We found eight QTLs including three for three traits of the shoots, and five for four traits of the roots at five chromosomal regions, controlled complex physiological traits related to rice salt-tolerance under salt stress. Of these QTLs, the two major QTLs with the very large effect, qSNC-7 for shoot Na+ concentration and qSKC-1 for shoot K+ concentration, explained 48.5% and 40.1% of the total phenotypic variance, respectively. The QTLs detected between the shoots and the roots almost did not share the same map locations, suggesting that the genes controlling the transport of Na+ and K+ between the shoots and the roots may be different.

DNA, Plant↗

PubMed2004

Advanced backcross QTL analysis of a Lycopersicon esculentum x L. pennellii cross and identification of possible orthologs in the Solanaceae.

In this study, the advanced backcross QTL (AB-QTL) mapping strategy was used to identify loci for yield, processing and fruit quality traits in a population derived from the interspecific cross Lycopersicon esculentum E6203 x Lycopersicon pennellii accession LA1657. A total of 175 BC(2) plants were genotyped with 150 molecular markers and BC(2)F(1) plots were grown and phenotyped for 25 traits in three locations in Israel and California, U.S.A. A total of 84 different QTLs were identified, 45% of which have been possibly identified in other wild-species-derived populations of tomato. Moreover, three fruit-weight/size and shape QTLs ( fsz2b.1, fw3.1/ fsz3.1 and fs8.1) appear to have putative orthologs in the related solanaceous species, pepper and eggplant. For the 23 traits for which allelic effects could be deemed as favorable or unfavorable, 26% of the identified loci had L. pennellii alleles that enhanced the performance of the elite parent. Alleles that could be targeted for further introgression into cultivated tomato were also identified.

Alleles↗

PubMed2003

Construction of a genetic map for arabica coffee.

We have used AFLPs to construct a genetic linkage map on a pseudo-F(2) population of arabica coffee ( Coffea arabica L.) derived from a cross between the cultivars Mokka hybrid and Catimor. Sixty trees from this population were selected on the basis of plant height distribution to construct a linkage map. A total of 456 dominant markers and eight co-dominant markers were generated from 288 AFLP primer combinations. Of the total number of markers generated, 68% were from cv. Catimor, 30% from cv. Mokka hybrid, and 2% were co-dominant. This distribution suggests that the heterozygosity within the cv. Catimor sub-genomes was twice that within the cv. Mokka hybrid sub-genomes. Linkage groups were constructed using MAPMAKER version 3.0, resulting in 16 major linkage groups containing 4-21 markers, and 15 small linkage groups consisting of 2-3 linked markers each. The total length of the map was 1,802.8 cM, with an average distance of 10.2 cM between adjacent markers. This genetic map will serve as the framework for mapping QTL controlling source-sink traits in the same population.

Coffee↗

PubMed2004

Marker-evaluated selection in rice: shifts in allele frequency among bulks selected in contrasting agricultural environments identify genomic regions of importance to rice adaptation and breeding.

Conventional methods for quantitative trait locus (QTL) mapping require the selection of particular traits to be measured based on assumptions as to their importance. We have tested an alternative approach for the location of QTLs-marker-evaluated selection-that makes no prior assumptions as to which traits are important. The results of phenotype selection were evaluated in the products of modified bulk-population breeding that was replicated across a range of rice ecosystems. Selection was carried out in close collaboration with farmers in bulk populations that were all derived from a cross between an Indian upland variety (Kalinga III) and a high-yielding semi-dwarf variety (IR64).Twenty-seven diverse bulks were produced that were screened with molecular markers in order to determine whether shifts could be detected in marker allele frequency as a result of selection and if such changes varied by genomic region across ecosystems. Marker loci linked to important traits for adaptation to specific environments were identified without making any prior assumptions about which traits might be important. Genomic regions from Kalinga III were strongly selected in the upland environments and regions from IR64 in the lowland ones.However, exceptions occurred where the upland parent contributed positively to lowland adaptation and vice versa. The results can be used as a basis for the development of second-cycle varieties, using marker-assisted selection to produce genotypic ideotypes for specific target environments. The very strong selection for genomic regions from the adapted parents of the wide(upland x lowland) cross indicates that, in non-marker-assisted breeding, where genetically distant parents have been used, modified backcross breeding should be efficient. A single backcross to the adapted parent for aspecific ecosystem will result in a higher frequency of segregants with the desired high genetic contribution from the adapted parent.

Acclimatization↗

PubMed2006

Stability over genetic backgrounds, generations and years of quantitative trait locus (QTLs) for organoleptic quality in tomato.

The efficiency of marker-assisted backcross for the introgression of a quantitative trait locus (QTL) from a donor line into a recipient line depends on the stability of QTL expression. QTLs for six quality traits in tomato (fruit weight, firmness, locule number, soluble solid content, sugar content and titratable acidity) were studied in order to investigate their individual effect and their stability over years, generations and genetic backgrounds. Five chromosome regions carrying fruit quality QTLs were transferred following a marker-assisted backcross scheme from a cherry tomato line into three modern lines with larger fruits. Three sets of genotypes corresponding to three generations were compared: (1) an RIL population, which contained 50% of each parental genome, (2) three BC3S1 populations which segregated simultaneously for the five regions of interest but were almost fully homozygous for the recipient genome on the eight chromosomes carrying no QTL and (3) three sets of QTL-NILs (BC3S3 lines) which differed from the recipient line only in one of the five regions. QTL detection was performed in each generation, in each genetic background and during 2 successive years for QTL-NILs. About half of the QTLs detected in QTL-NILs were detected in both years. Eight of the ten QTLs detected in RILs were recovered in the QTL-NILs with the genetic background used for the initial QTL mapping experiment, with the exception of two QTLs for fruit firmness. Several new QTLs were detected. In the two other genetic backgrounds, the number of QTLs in common with the RILs was lower, but several new QTLs were also detected in advanced generations.

Fruit↗

PubMed2006

Quantitative trait loci analysis of phenotypic traits and principal components of maize tassel inflorescence architecture.

Maize tassel inflorescence architecture is relevant to efficient production of F(1) seed and yield performance of F(1) hybrids. The objectives of this study were to identify genetic relationships among seven measured tassel inflorescence architecture traits and six calculated traits in a maize backcross population derived from two lines with differing tassel architectures, and identify Quantitative Trait Loci (QTL) involved in the inheritance of those tassel inflorescence architecture traits. A Principal Component (PC) analysis was performed to examine relationships among correlated traits. Traits with high loadings for PC1 were branch number and branch number density, for PC2 were spikelet density on central spike and primary branch, and for PC3 were lengths of tassel and central spike. We detected 45 QTL for individual architecture traits and eight QTL for the three PCs. For control of inflorescence architecture, important QTL were found in bins 7.02 and 9.02. The interval phi034-ramosa1 (ral) in bin 7.02 was associated with six individual architecture trait QTL and explained the largest amount of phenotypic variation (17.3%) for PC1. Interval bnlg344-phi027 in bin 9.02 explained the largest amount of phenotypic variation (14.6%) for PC2. Inflorescence architecture QTL were detected in regions with candidate genes fasciated ear2, thick tassel dwarf1, and ral. However, the vast majority of QTL mapped to regions without known candidate genes, indicating positional cloning efforts will be necessary to identify these genes.

Chromosome Mapping↗

PubMed2025

Identifying canopy wilting QTLs and evaluating remote sensing approaches for selecting drought-tolerant soybean.

Drought is the most damaging abiotic stress for soybean yield; cultivars with improved drought tolerance are needed to sustain and increase crop production. PI 603535 previously was identified as an ultra-slow canopy wilting (CW) line in a genome-wide association study but the quantitative trait loci (QTLs) underlying this phenotype have not been determined. In this study, a recombinant inbred line (RIL) population derived from Benning × PI 603535 was evaluated for three years under rain-fed conditions. CW was rated following extended periods of drought when CW variation was present. Aerial multispectral and thermal imagery was also captured in conjunction with visual ratings to explore the feasibility of implementing remote sensing to improve the efficiency and objectivity of drought evaluations. The normalized difference vegetation index (NDVI) and green-based NDVI (GNDVI) exhibited strong, significant correlations (|r|= 0.42-0.44) with CW across years. CW scores and the remote sensing traits were used as phenotypes for QTL mapping. Seven CW QTLs were identified across six chromosomes in the combined analysis, with NDVI and GNDVI QTLs generally colocalizing with the CW QTLs with the highest percentage of variation explained (PVE). The QTLs were not consistently identified among individual years, highlighting the complex genetics and gene expression of drought tolerance. The instability and low additive effect estimates of individual QTLs imply challenges of improving drought tolerance through the selection of a few QTLs. However, the slow CW RILs developed in this study can serve as valuable breeding stocks for future drought improvement breeding efforts and genetic studies.

Quantitative Trait Loci↗