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PubMed2002

QTL mapping for growth and carcass traits in an Iberian by Landrace pig intercross: additive, dominant and epistatic effects.

Results from a QTL experiment on growth and carcass traits in an experimental F2 cross between Iberian and Landrace pigs are reported. Phenotypic data for growth, length of carcass and muscle mass, fat deposition and carcass composition traits from 321 individuals corresponding to 58 families were recorded. Animals were genotyped for 92 markers covering the 18 porcine autosomes (SSC). The results from the genomic scan show genomewide significant QTL in SSC2 (longissimus muscle area and backfat thickness), SSC4 (length of carcass, backfat thickness, loin, shoulder and belly bacon weights) and SSC6 (longissimus muscle area, backfat thickness, loin, shoulder and belly bacon weights). Suggestive QTL were also found on SSC1, SSC5, SSC7, SSC8, SSC9, SSC13, SCC14, SSC16 and SSC17. A bidimensional genomic scan every 10 cM was performed to detect interaction between QTL. The joint action of two suggestive QTL in SSC2 and SSC17 led to a genome-wide significant effect in live weight. The results of the bidimensional genomic scan showed that the genetic architecture was mainly additive or the experimental set-up did not have enough power to detect epistatic interactions.

Adipose Tissue↗

PubMed2004

QTL mapping of ten agronomic traits on the soybean ( Glycine max L. Merr.) genetic map and their association with EST markers.

A set of 184 recombinant inbred lines (RILs) derived from soybean vars. Kefeng No.1 x Nannong 1138-2 was used to construct a genetic linkage map. The two parents exhibit contrasting characteristics for most of the traits that were mapped. Using restricted fragment length polymorphisms (RFLPs), simple sequence repeats (SSRs) and expressed sequence tags (ESTs), we mapped 452 markers onto 21 linkage groups and covered 3595.9 cM of the soybean genome. All of the linkage groups except linkage group F were consistent with those of the consensus map of Cregan et al. (1999). Linkage group F was divided into two linkage groups, F1 and F2. The map consisted of 189 RFLPs, 219 SSRs, 40 ESTs, three R gene loci and one phenotype marker. Ten agronomic traits-days to flowering, days to maturity, plant height, number of nodes on main stem, lodging, number of pods per node, protein content, oil content, 100-seed weight, and plot yield-were studied. Using winqtlcart, we detected 63 quantitative trait loci (QTLs) that had LOD>3 for nine of the agronomic traits (only exception being seed oil content) and mapped these on 12 linkage groups. Most of the QTLs were clustered, especially on groups B1 and C2. Some QTLs were mapped to the same loci. This pleiotropism was common for most of the QTLs, and one QTL could influence at most five traits. Seven EST markers were found to be linked closely with or located at the same loci as the QTLs. EST marker GmKF059a, encoding a repressor protein and mapped on group C2, accounted for about 20% of the total variation of days to flowering, plant height, lodging and nodes on the main stem, respectively.

Agriculture↗

PubMed2024

QTL mapping for seed vigor-related traits under artificial aging in common wheat in two introgression line (IL) populations.

BACKGROUND: Seed vigor recognized as a quantitative trait is of particular importance for agricultural production. However, limited knowledge is available for understanding genetic basis of wheat seed vigor. METHODS: The aim of this study was to identify quantitative trait loci (QTL) responsible for 10 seed vigor-related traits representing multiple aspects of seed-vigor dynamics during artificial aging with 6 different treatment times (0, 24, 36, 48, 60, and 72 h) under controlled conditions (48 °C, 95% humidity, and dark). The mapping populations were two wheat introgression lines (IL-1 and IL-2) derived from recipient parent (Lumai 14) and donor parent (Shaanhan 8675 or Jing 411). RESULTS: A total of 26 additive QTLs and 72 pairs of epistatic QTLs were detected for wheat seed-vigor traits. Importantly, chromosomes 1B and 7B contained several co-located QTLs, and chromosome 2A had a QTL-rich region near the marker Xwmc667, indicating that these QTLs may affect wheat seed vigor with pleiotropic effects. Furthermore, several possible consistent QTLs (hot-spot regions) were examined by comparison analysis of QTLs detected in this study and reported previously. Finally, a set of candidate genes for wheat seed vigor were predicted to be involved in transcription regulation, carbohydrate and lipid metabolism. CONCLUSION: The present findings lay new insights into the mechanism underlying wheat seed vigor, providing valuable information for wheat genetic improvement especially marker-assisted breeding to increase seed vigor and consequently achieve high grain yield despite of further investigation required.

Triticum↗

PubMed2005

An application of Bayesian QTL mapping to early development in double haploid lines of rainbow trout including environmental effects.

A Bayesian model and variable dimensional parameter estimation based on Markov chain Monte Carlo was applied to map quantitative trait loci (QTLs) in a doubled haploid mapping population of rainbow trout. To increase power, the analysis was performed using the multiple-QTL model, which simultaneously accounted for all the environmental and genetic main effects that influence the expression of early development life history traits. By doing so we obtained the posterior estimated effects for the environmental factors as well as the number, positions, and the effects for the QTLs. The analyses revealed QTLs for time at hatching, embryonic length and weight at swim-up stage. The posterior expectation of the number of QTLs in different linkage groups shows that at least four QTLs are needed to explain the observed differences in early development between the clonal lines. The Bayesian method effectively combined all the information available to accurately position these QTLs in the rainbow trout genome.

Animals↗

PubMedDate not supplied

The effect of mixed selected and unselected samples on the power of QTL mapping.

It is known from previous work that selection by truncation can lead to substantial loss of power to detect linkage with a QTL We examine the effect of mixed selected and unselected samples. We show that even if a modest proportion of the sample originates from an unselected population, this loss of power is quite effectively neutralized. Moreover, we reach the unexpected conclusion that if the selection intensity in the selected subpopulation is high, the power to detect QTL may actually increase.

Animals↗

PubMed1994

QTL mapping of naturally-occurring variation in flowering time of Arabidopsis thaliana.

A segregating F2 population of Arabidopsis thaliana derived from a cross between the late-flowering ecotype Hannover/Münden (HM) and the early-flowering ectoype Wassilewskija (WS) was analyzed for flowering time and other morphological traits. Two unlinked quantitative trait loci (QTLs) affecting days to first flower (DFF-a and DFF-b) mapped to chromosome 5. QTLs which affect node number (NN), leaf length at flowering (LLF), and lead length at 35 days (LL35) also mapped to chromosome 5; LLF-a, LL35-a, NN-a map to the same region of chromosome 5 as DFF-a; LLF-b and LL35-bmap to the same region of chromosome 5 as DFF-b. Another QTL affecting leaf length at flowering (LLF-c) maps to chromosome 3. The proximity of DFF-a, LLF-a, LL35-a and NN-a, as well as the similarity in gene action among these QTLs (additivity), suggest that they may be pleiotropic consequences of a single gene at this locus. Similarly, LL35-b and LLF-b map near each other and both display recessive gene action, again suggesting the possibility of pleiotropy. DFF-b, which also maps near LL35-b and LLF-b, displays largely additive gene action (although recessive gene action could not be ruled out). This suggests that DFF-b may represent a different gene from LL35-b and/or LLF-b. DFF-a maps near two previously identified mutants: co (which also affects flowering time and displays gene action consistent with additivity) and flc.(ABSTRACT TRUNCATED AT 250 WORDS)

Arabidopsis↗

PubMed2005

Identification of candidate genes for drought stress tolerance in rice by the integration of a genetic (QTL) map with the rice genome physical map.

Genetic improvement for drought stress tolerance in rice involves the quantitative nature of the trait, which reflects the additive effects of several genetic loci throughout the genome. Yield components and related traits under stressed and well-water conditions were assayed in mapping populations derived from crosses of AzucenaxIR64 and AzucenaxBala. To find the candidate rice genes underlying Quantitative Trait Loci (QTL) in these populations, we conducted in silico analysis of a candidate region flanked by the genetic markers RM212 and RM319 on chromosome 1, proximal to the semi-dwarf (sd1) locus. A total of 175 annotated genes were identified from this region. These included 48 genes annotated by functional homology to known genes, 23 pseudogenes, 24 ab initio predicted genes supported by an alignment match to an EST (Expressed sequence tag) of unknown function, and 80 hypothetical genes predicted solely by ab initio means. Among these, 16 candidate genes could potentially be involved in drought stress response.

Disasters↗

PubMed2002

QTL mapping and introgression of yield-related traits from Oryza glumaepatula to cultivated rice ( Oryza sativa) using microsatellite markers.

Rice ( Oryza sativa) cultivar development currently faces the task of overcoming yield plateaus, which is difficult due to the narrow genetic base of breeding programs. Oryza glumaepatula is a diploid wild relative of cultivated rice, native to Central and South America, and is therefore a potential source of alleles of agronomic importance to rice breeding programs. We studied 11 agronomic traits in BC(2)F(2) families of the interspecific cross Oryza sativa x O. glumaepatula. Transgressive lines which are almost isogenic to the elite recurrent O. sativa parent were identified for most of these traits. Quantitative trait locus (QTL) analysis was performed by single-point and interval mapping using a molecular map based on 157 microsatellite and STS markers. Marker regions accounting for 14.5 to 72.9% of a phenotypic variation trait were identified in 9 of the 12 rice chromosomes. Positive QTL effects from O. glumaepatula were observed in chromosomal regions associated with tillering and panicle-number traits.

Journal Article↗

PubMed2006

Identification of informative strains and provisional QTL mapping of amphetamine (AMPH)-induced locomotion in recombinant congenic strains (RCS) of mice.

Amphetamine (AMPH)-induced locomotor activity is a rodent behavioral trait that reflects mesolimbic dopaminergic activity. To identify potential quantitative trait loci (QTL) associated with this behavior, we used 34 recombinant congenic strains (RCSs) of mice derived from A/J (A strains) and C57BL/6J (B strains) and measured AMPH-induced total distance traveled (AMPH-TDIST). Two strains in the A panel (A52 and A63) showed significantly elevated AMPH-TDIST compared to the parental A/J strain and behaved similarly to C57BL/6J. Simple sequence length polymorphism (SSLP) markers on chromosomes 1, 2, 3, 5, 6, 8, 9, 10 and 20 were significantly associated with AMPH-TDIST in the A strains. Within the B panel, two strains (B81 and B74) had significantly higher and two strains (B69 and B75) had significantly lower AMPH-TDIST than C57BL/6J. Markers associated with AMPH-TDIST in the B strains appeared on chromosomes 5, 17 and 20. Combining data from this approach and other genetic (mapping data in humans) and functional (cDNA expression) sources may help to identify suitable candidate genes relevant to human disorders where mesolimbic dopamine dysregulation has been postulated.

Amphetamine↗

PubMed2002

Mapping QTL for popping expansion volume in popcorn with simple sequence repeat markers.

Popping expansion volume is the most important quality trait in popcorn ( Zea mays L.), but its genetics is not well understood. The objectives of this study were to map quantitative trait loci (QTLs) responsible for popping expansion volume in a popcorn x dent corn cross, and to compare the predicted efficiencies of phenotypic selection, marker-based selection, and marker-assisted selection for popping expansion volume. Of 259 simple sequence repeat (SSR) primer pairs screened, 83 pairs were polymorphic between the H123 (dent corn) and AG19 (popcorn) parental inbreds. Popping test data were obtained for 160 S(1) families developed from the [AG19(H123 x AG19)] BC(1) population. The heritability ( h(2)) for popping expansion volume on an S(1) family mean basis was 0.73. The presence of the gametophyte factor Ga1(s) in popcorn complicates the analysis of popcorn x dent corn crosses. But, from a practical perspective, the linkage between a favorable QTL allele and Ga1(s) in popcorn will lead to selection for the favorable QTL allele. Four QTLs, on chromosomes 1S, 3S, 5S and 5L, jointly explained 45% of the phenotypic variation. Marker-based selection for popping expansion volume would require less time and work than phenotypic selection. But due to the high h(2) of popping expansion volume, marker-based selection was predicted to be only 92% as efficient as phenotypic selection. Marker-assisted selection, which comprises index selection on phenotypic and marker scores, was predicted to be 106% as efficient as phenotypic selection. Overall, our results suggest that phenotypic selection will remain the preferred method for selection in popcorn x dent corn crosses.

Chromosome Mapping↗

PubMed2005

QTL mapping of resistance to Sclerotinia midstalk rot in RIL of sunflower population NDBLOSsel x CM625.

Midstalk rot caused by Sclerotinia sclerotiorum is an important disease of sunflower in its main areas of cultivation. The objectives of this study were to (1) verify quantitative trait loci (QTL) for midstalk-rot resistance found in F3 families of the NDBLOSsel x CM625 population in recombinant inbred lines (RIL) derived from the same cross; (2) re-estimate their position and genetic effects; (3) draw inferences about the predictive quality of QTL for midstalk-rot resistance identified in the F3 families as compared to those in the RIL. Phenotypic data for three resistance (leaf lesion, stem lesion, and speed of fungal growth) and two morphological traits (leaf length and leaf length with petiole) were obtained from 317 RIL following artificial infection in field experiments across two environments. For genotyping the 248 RIL, we selected 41 simple sequence repeat (SSR) markers based on their association with QTL for Sclerotinia midstalk-rot resistance in an earlier study. The resistance traits showed intermediate to high heritabilities (0.51 < h2 <0.79) and were significantly correlated with each other (0.45 < rg < 0.78). Genotypic correlations between F3 families and the RIL were highly significant and ranged between 0.50 for leaf length and 0.64 for stem lesion. For stem lesion, two genomic regions on linkage group (LG) 8 and LG16 explaining 26.5% of the genotypic variance for Sclerotinia midstalk-rot resistance were consistent across generations. For this trait, the genotypic correlation between the observed performance and its prediction based on QTL positions and effects in F3 families was surprisingly high (rg(MiF3, YiRIL). The genetic effects and predictive quality of these two QTL are promising for application in marker-assisted selection to Sclerotinia midstalk-rot resistance.

Ascomycota↗

PubMed2006

Mapping QTL for dollar spot resistance in creeping bentgrass (Agrostis stolonifera L.).

Dollar spot caused by Sclerotinia homoeocarpa F. T. Bennett is the most economically important turf disease on golf courses in North America. Dollar spot resistance in a creeping bentgrass cultivar would greatly reduce the frequency, costs, and environmental impacts of fungicide application. Little work has been done to understand the genetics of resistance to dollar spot in creeping bentgrass. Therefore, QTL analysis was used to determine the location, number and effects of genomic regions associated with dollar spot resistance in the field. To meet this objective, field inoculations using a single isolate were performed over 2 years and multiple locations using progeny of a full sib mapping population '549 x 372'. Dollar spot resistance seems to be inherited quantitatively and broad sense heritability for resistance was estimated to be 0.88. We have detected one QTL with large effect on linkage group 7.1 with LOD values ranging from 3.4 to 8.6 and explaining 14-36% of the phenotypic variance. Several smaller effect QTL specific to rating dates, locations and years were also detected. The association of the tightly linked markers with the LG 7.1 QTL based on 106 progeny was further examined by single marker analysis on all 697 progeny. The high significance of the QTL on LG 7.1 at a sample size of 697 (P < 0.0001), along with its consistency across locations, years and ratings dates, indicated that it was stable over environments. Markers tightly linked to the QTL can be utilized for marker-assisted selection in future bentgrass breeding programs.

Agrostis↗

PubMed1996

Confidence intervals in QTL mapping by bootstrapping.

The determination of empirical confidence intervals for the location of quantitative trait loci (QTLs) was investigated using simulation. Empirical confidence intervals were calculated using a bootstrap resampling method for a backcross population derived from inbred lines. Sample sizes were either 200 or 500 individuals, and the QTL explained 1, 5, or 10% of the phenotypic variance. The method worked well in that the proportion of empirical confidence intervals that contained the simulated QTL was close to expectation. In general, the confidence intervals were slightly conservatively biased. Correlations between the test statistic and the width of the confidence interval were strongly negative, so that the stronger the evidence for a QTL segregating, the smaller the empirical confidence interval for its location. The size of the average confidence interval depended heavily on the population size and the effect of the QTL. Marker spacing had only a small effect on the average empirical confidence interval. The LOD drop-off method to calculate empirical support intervals gave confidence intervals that generally were too small, in particular if confidence intervals were calculated only for samples above a certain significance threshold. The bootstrap method is easy to implement and is useful in the analysis of experimental data.

Animals↗

PubMed2004

Mapping QTL associated with resistance to Fusarium head blight in the Nanda2419 x Wangshuibai population. I. Type II resistance.

Scab disease caused by Fusarium spp. has been a major concern for both wheat producers and consumers. Deployment of scab-resistant varieties is the major strategy to curb this disease. To identify the scab resistance genes in wheat cv. Wangshuibai, we produced a F(6:7) recombinant inbred line (RIL) population by crossing Wangshuibai with the scab-susceptible cultivar Nanda2419. The RILs were evaluated for scab resistance in the field by single floret inoculation in two replicates in 2002 and one replicate in 2003. The number of diseased spikelets (NDS) and the length of diseased rachides (LDR) were investigated to reflect the Type II resistance. Among 654 simple sequence repeat (SSR) markers surveyed, 326 were found to be polymorphic between the parents. A partial molecular map was constructed with these markers that covered over 2,210 cM of the wheat genome. Six chromosome regions showed association with both NDS and LDR in a one-way anova analysis, even though the variation explained by them varied between the two traits. Eight intervals were detected for their association with Type II resistance through interval mapping, five of which were not identified in single-point analysis. The quantitative trait loci (QTL) with large effects were the ones in the interval of Xgwm533-3-Xgwm533-1 on chromosome 3B and in the interval of Xwmc539-Xbarc024 on chromosome 6B, whose alleles favoring resistance originate from Wangshuibai. In addition, a QTL whose resistance allele originated from Nanda2419 was consistently detected in the interval of Xs1021m-Xgwm47-1 on chromosome 2B. These results suggest that Wangshuibai is the major source for Type II resistance in this population. The markers associated with these QTL would facilitate the use of scab-resistant genes of Wangshuibai in scab resistance breeding programs of wheat.

Chromosome Mapping↗

PubMed2004

QTL mapping of grain quality traits from the interspecific cross Oryza sativa x O. glaberrima.

International rice export markets are increasing demands for rapid improvements in grain quality characteristics. The African rice Oryza glaberrima is a new potential source of genes that will enhance the eating, cooking, and milling properties of the rice grain. The objective of this research was to identify and characterize quantitative trait loci (QTLs) among 312 doubled haploid lines derived from the BC3F1 of an interspecific cross of O. sativa x O. glaberrima. Genetic material was planted in replicated plots and evaluated for ten grain quality traits in 2001 in Colombia. A linkage map was constructed with 100 polymorphic microsatellite markers using the mapdisto software program to adjust for segregation distortion. Transgressive segregation was observed for all traits. Interval and composite interval analyses identified 27 QTLs for nine characters located on 11/12 chromosomes. The chromosomal positions of QTLs for percentage amylose, alkali-spreading score, and percentage protein were in agreement with data reported by others, whereas QTL markers for percentage head rice, percentage milled rice, percentage protein, and percentage brown rice were different in our mapping population. Five major QTLs were found to be associated with improved percentage rice bran, percentage amylose, and alkali-spreading score. Seven QTLs for improved percentage rice bran, percentage milled rice, alkali-spreading score, percentage protein, and grain length/width ratio were derived from the O. glaberrima accession. Three new QTLs for percentage rice bran are reported here for the first time. Results from this study suggest that the African rice might be a valuable new source for introgression and improvement of several traits that affect quality traits demanded by the different rice export markets.

Chromosome Mapping↗

PubMed2005

Mapping QTL associated with resistance to Fusarium head blight in the Nanda2419 x Wangshuibai population. II: type I resistance.

Fusarium head blight (FHB) is a serious disease in wheat and barley affecting both yield and quality. To identify genes for resistance to infection, the RIL population derived from 'Nanda2419' x 'Wangshuibai' and the parents were evaluated for percentage of infected spikes (PIS) in four different environments. Using a 2,960 cM marker framework map constructed for this population, ten chromosome regions were detected for their association with type I resistance through interval mapping with Mapmaker/QTL, among which QTLs mapped in the intervals of Xwmc349--Xgwm149 on chromosome 4B, of Xwmc96--Xgwm304 on chromosome 5A and of Xgwm408--Xbarc140 on chromosome 5B were revealed in at least three environments and have Wangshuibai as the source of resistance alleles. Qfhi.nau-4B and Qfhi.nau-5A had larger effects and explained up to 17.5 and 27.0% of the phenotypic variance, respectively. To detect epistasis QTLs, two-locus interactions were examined by whole genome scan. Interactions of five locus pairs were found to have significant effects on type I resistance with the LOD score ranging 3.8-6.5 and four of them conferred resistance in parental phase. The one with the most significant effect was Xcfd42--Xgwm469 (6D)/Xwmc390-2--Xbd04 (2A) pair. No QTL x E interaction was detected for PIS. It was found that flowering time did not have significant effects on PIS in this population. Our studies indicated that Wangshuibai is useful for breeding for both type I and type II scab resistance and the markers associated with the QTLs could be used in marker-assisted selection and isolation of scab-resistance QTLs.

Chromosome Mapping↗

PubMed2006

Mapping QTL for biomass yield and its components in rice (Oryza sativa L.).

Additive effects, additive by additive epistatic effects, and their environmental interactions of QTLs are important genetic components of quantitative traits. Genetic architecture underlying rice biomass yield and its two component traits (straw yield and grain yield) were analyzed for a population of 125 DH lines from an inter-subspecific cross of IR64/Azucena. The mixed-model based composite interval mapping approach (MCIM) was used to detect QTLs, There were 12 QTLs detected with additive main effects, 27 QTLs involved in digenic interaction with aa and/or aae effects, and 18 QTLs affected by environments with ae and/or aae effects. It was revealed that epistatic effects and QE interaction effects existed on biomass yield and its component traits in rice. In addition, the genetic basis of relationships among these traits were investigated. Four QTLs and one pair of epistatic QTLs were detected to be responsible for the positive correlation between biomass yield and straw yield. Three QTLs might be responsible for the negative correlation between straw yield and grain yield. This result could partially explain the genetic basis of correlation among the three traits, and provide useful information for genetic improvement of these traits by marker-assisted selection.

Biomass↗

PubMed2004

QTL mapping for European corn borer resistance ( Ostrinia nubilalis Hb.), agronomic and forage quality traits of testcross progenies in early-maturing European maize ( Zea mays L.) germplasm.

In hybrid breeding the performance of lines in hybrid combinations is more important than their performance per se. Little information is available on the correlation between individual line and testcross (TC) performances for the resistance to European corn borer (ECB, Ostrinia nubilalis Hb.) in maize ( Zea mays L.). Marker assisted selection (MAS) will be successful only if quantitative trait loci (QTL) found in F(2) derived lines for ECB resistance are still expressed in hybrid combinations. The objectives of our study were: (1) to identify and characterize QTL for ECB resistance as well as agronomic and forage quality traits in a population of testcrossed F(2:3) families; (2) to evaluate the consistency of QTL for per se and TC performances; and (3) to determine the association between per se and TC performances of F(2:3) lines for these traits. Two hundred and four F(2:3) lines were derived from the cross between maize lines D06 (resistant) and D408 (susceptible). These lines were crossed to D171 and the TC progenies were evaluated for ECB resistance and agronomic performance in two locations in 2000 and 2001. Using these TC progenies, six QTL for stalk damage rating (SDR) were found. These QTL explained 27.4% of the genotypic variance in a simultaneous fit. Three QTL for SDR were detected consistently for per se and TC performance. Phenotypic and genotypic correlations were low for per se and TC performance for SDR. Correlations between SDR and quality traits were not significant. Based on these results, we conclude that MAS will not be an efficient method for improving SDR. However, new molecular tools might provide the opportunity to use QTL data as a first step to identify genes involved in ECB resistance. Efficient MAS procedures might then be based on markers designed to trace and to combine specific genes and their alleles in elite maize breeding germplasm.

Alleles↗