Joint mapping of quantitative trait loci using F2 populations

In this paper, the theory of joint mapping of quantitative trait loci is extended to F₂ populations. Two independent regression equations, related to the additive and dominance effects respectively, are derived. Therefore, there are three alternative strategies for mapping QTLs, called additive-based mapping (ABM), dominance-based mapping (DBM) and additive-dominance-based mapping (ADBM). Simulation results have shown that ADBM is the most appropriate in most situations.     

The effect of parental divergence on F2 heterosis in winter wheat crosses

Summary In winter wheat (Triticum aestivum L.), the development of a methodology to estimate genetic divergence between parental lines, when combined with knowledge of parental performance, could be beneficial in the prediction of bulk progeny performance. The objective of this study was to relate F₂ heterosis for grain yield and its components in 116 crosses to two independent estimates of genetic divergence among 28 parental genotypes of diverse origins. Genetic divergence between parents was estimated from (a) pedigree relationships (coefficients of kinship) determined without experimentation, and (b) quantitative traits measured in two years of field experimentation in Kansas and North Carolina, USA. These distances, designated (1 -r) and G, respectively, provided ample differentiation among the parents. The 116 F₂ bulks were evaluated at four locations in Kansas and North Carolina in one year. Significant rank correlations of 0.46 (P = 0.01) and 0.44 (P = 0.01) were observed between G and grain yield and kernel number heterosis, respectively. Although (1 -r) was poorly associated with grain yield heterosis, G and midparent performance combined to account for 50% of the variation in F₂ yields among crosses when (1 -r) was above the median value, whereas they accounted for only 9% of the variation among crosses when (1-r) was below the median. Midparent and (1 -r) had equal effects on F₂ grain yield (R ²= 0.40) when G was greater than the median value. A breeding strategy is proposed whereby parents are first selected on the basis of performance per se and, subsequently, crosses are made between genetically divergent parents that have both large quantitative (G) and pedigree divergence (1 -r).Paper No. 12162 of the Journal Series of the North Carolina Agricultural Research Service, Raleigh, NC 27695-7643, and Contribution No. 89-396-J of the Kansas Agricultural Experiment Station, Manhattan, KS 66506     

Effects of missing marker and segregation distortion on QTL mapping in F2 populations

Missing marker and segregation distortion are commonly encountered in actual quantitative trait locus (QTL) mapping populations. Our objective in this study was to investigate the impact of the two factors on QTL mapping through computer simulations. Results indicate that detection power decreases with increasing levels of missing markers, and the false discovery rate increases. Missing markers have greater effects on smaller effect QTL and smaller size populations. The effect of missing markers can be quantified by a population with a reduced size similar to the marker missing rate. As for segregation distortion, if the distorted marker is not closely linked with any QTL, it will not have significant impact on QTL mapping; otherwise, the impact of the distortion will depend on the degree of dominance of QTL, frequencies of the three marker types, the linkage distance between the distorted marker and QTL, and the mapping population size. Sometimes, the distortion can result in a higher genetic variance than that of non-distortion, and therefore benefits the detection of linked QTL. A formula of the ratio of genetic variance explained by QTL under distortion and non-distortion was given in this study, so as to easily determine whether the segregation distortion marker (SDM) increases or decreases the QTL detection power. The effect of SDM decreases rapidly as its linkage relationship with QTL becomes looser. In general, distorted markers will not have a great effect on the position and effect estimations of QTL, and their effects can be ignored in large-size mapping populations.     

Multiple regression for molecular-marker,quantitative trait data from large F2 populations

Molecular marker-quantitative trait associations are important for breeders to recognize and understand to allow application in selection. This work was done to provide simple, intuitive explanations of trait-marker regression for large samples from an F₂ and to examine the properties of the regression estimators. Beginning with a(- 1,0,1) coding of marker classes and expected frequencies in the F₂, expected values, variances, and covariances of marker variables were calculated. Simple linear regression and regression of trait values on two markers were computed. The sum of coefficient estimates for the flanking-marker regression is asymptotically unbiased for an included additive effect with complete interference, and is only slightly biased with no interference and moderately close (15 cM) marker spacing. The variance of the sum of regression coefficients is much more stable for small recombination distances than variances of individual coefficients. Multiple regression of trait variables on coded marker variables can be interpreted as the product of the inverse of the marker correlation matrix R and the vector a of simple linear regression estimators for each marker. For no interference, elements of the correlation matrix R can be written as products of correlations between adjacent markers. The inverse of R is displayed and used to illustrate the solution vector. Only markers immediately flanking trait loci are expected to have non-zero values and, with at least two marker loci between each trait locus, the solution vector is expected to be the sum of solutions for each trait locus. Results of this work should allow breeders to test for intervals in which trait loci are located and to better interpret results of the trait-marker regression.     

Detection of quantitative trait loci in outbred populations with incomplete marker data.

Augmentation of marker genotypes for ungenotyped individuals is implemented in a Bayesian approach via the use of Markov chain Monte Carlo techniques. Marker data on relatives and phenotypes are combined to compute conditional posterior probabilities for marker genotypes of ungenotyped individuals. The presented procedure allows the analysis of complex pedigrees with ungenotyped individuals to detect segregating quantitative trait loci (QTL). Allelic effects at the QTL were assumed to follow a normal distribution with a covariance matrix based on known QTL position and identity by descent probabilities derived from flanking markers. The Bayesian approach estimates variance due to the single QTL, together with polygenic and residual variance. The method was empirically tested through analyzing simulated data from a complex granddaughter design. Ungenotyped dams were related to one or more sons or grandsires in the design. Heterozygosity of the marker loci and size of QTL were varied. Simulation results indicated a significant increase in power when ungenotyped dams were included in the analysis.     

Quantitative trait loci mapping of dark-induced senescence in winter wheat (Triticum aestivum)

In order to explore the genetics of dark-induced senescence in winter wheat(Triticum aestivum L.),a quantitative trait loci(QTL)analysis was carried out in a doubled haploid population developed from a cross between the varieties Hanxuan 10(HX)and Lumai 14(LM).The senescence parameters chlorophyll content(Chl a+b,Chl a,and Chl b),original fluorescence(Fo),maximum fluorescence level(Fm),maximum photochemical efficiency(Fv/Fm),and ratio of variable fluorescence to original fluorescence(Fv/Fo)were evaluated in the second leaf of whole three-leaf seedlings subjected to 7 d of darkness.A total of 43 QTLs were identified that were associated with dark-induced senescence using composite interval mapping.These QTLs were mapped to 20 loci distributed on 11 chromosomes:1B,1D,2A,2B,3B,3D,5D,6A,6B,7A,and 7B.The phenotypic variation explained by each QTL ranged from 7.5% to 19.4%.Eleven loci coincided with two or more of the analyzed parameters.In addition,14 loci co-located or were linked with previously reported QTLs regulating flag leaf senescence,tolerance to high light stress,and grain protein content(Gpc),separately.     

Identification of quantitative trait loci and associated candidate genes for low-temperature tolerance in cold-hardy winter wheat

Low-temperature (LT) tolerance is an important economic trait in winter wheat (Triticum aestivum L.) that determines the plants’ ability to cope with below freezing temperatures. Essential elements of the LT tolerance mechanism are associated with the winter growth habit controlled by the vernalization loci (Vrn-1) on the group 5 chromosomes. To identify genomic regions, which in addition to vrn-1 determine the level of LT tolerance in hexaploid wheat, two doubled haploid (DH) mapping populations were produced using parents with winter growth habit (vrn-A1, vrn-B1, and vrn-D1) but showing different LT tolerance levels. A total of 107 DH lines were analyzed by genetic mapping to produce a consensus map of 2,873 cM. The LT tolerance levels for the Norstar (LT₅₀=−20.7°C) × Winter Manitou (LT₅₀=−14.3°C) mapping population ranged from −12.0 to −22.0°C. Single marker analysis and interval mapping of phenotyped lines revealed a major quantitative trait locus (QTL) on chromosome 5A and a weaker QTL on chromosome 1D. The 5A QTL located 46 cM proximal to the vrn-A1 locus explained 40% of the LT tolerance variance. Two C-repeat Binding Factor (CBF) genes expressed during cold acclimation in Norstar were located at the peak of the 5A QTL.     

Genome inheritance in populations derived from hexaploid/tetraploid and tetraploid/hexaploid wheat crosses

Hexaploid/tetraploid and tetraploid/hexaploid wheat hybrids were established using the hexaploid (Triticum aestivum L.) bread wheat LRC2010-150 and the tetraploid durum wheat (T. turgidum spp. durum) WID802. Thirty F₂ progeny from each cross were characterised using Diversity Arrays Technology (DArTseq?) markers to determine whether there are differences between the crosses in the proportion of A, B and D genomic material inherited from each parent. Inheritance of the A and B genome from the tetraploid durum parent varied from 32 to 63% among the 60 lines assessed, and results indicated significant differences between the two F₂ populations in the mean overall proportion of chromosomes A and B inherited from each parent. Significant differences were also observed between the crosses in the proportion of chromosomal segments on 2B, 3A, 3B and 4A inherited from the tetraploid parent. The F₂ populations also showed significant differences in the average retention of D chromosomes per line with the tetraploid/hexaploid cross retaining a mean of 2.83 chromosomes while the reciprocal cross retained a mean of 1.8 chromosomes per line. A strong negative correlation was observed in individual lines from both populations between the proportion of the A and B genome inherited from the tetraploid durum parent and the retention of the D genome. The implication of these results for the design of efficient crossing strategies between hexaploid and tetraploid wheats is discussed.     

Inferring linkage disequilibrium between a polymorphic marker locus and a trait locus in natural populations

Three approaches are proposed in this study for detecting or estimating linkage disequilibrium between a polymorphic marker locus and a locus affecting quantitative genetic variation using the sample from random mating populations. It is shown that the disequilibrium over a wide range of circumstances may be detected with a power of 80% by using phenotypic records and marker genotypes of a few hundred individuals. Comparison of ANOVA and regression methods in this article to the transmission disequilibrium test (TDT) shows that, given the genetic variance explained by the trait locus, the power of TDT depends on the trait allele frequency, whereas the power of ANOVA and regression analyses is relatively independent from the allelic frequency. The TDT method is more powerful when the trait allele frequency is low, but much less powerful when it is high. The likelihood analysis provides reliable estimation of the model parameters when the QTL variance is at least 10% of the phenotypic variance and the sample size of a few hundred is used. Potential use of these estimates in mapping the trait locus is also discussed.     

Inheritance of resistance to Fusarium head blight in three European winter wheat populations

Fusarium head blight (FHB) resistance is of particular importance in wheat breeding programmes due to the detrimental effects of this fungal disease on human and animal health, yield and grain quality. Segregation for FHB resistance in three European winter wheat populations enabled the identification of resistance loci in well-adapted germplasm. Populations obtained from crosses of resistant cultivars Apache, History and Romanus with susceptible semi-dwarfs Biscay, Rubens and Pirat, respectively, were mapped and analysed to identify quantitative trait loci (QTL) for FHB severity, ear emergence time and plant height. The results of the present study together with previous studies in UK winter wheat indicated that the semi-dwarfing allele Rht-D1b seems to be the major source for FHB susceptibility in European winter wheat. The high resistance level of the cultivars Romanus and History was conditioned by several minor resistance QTL interacting with the environment and the absence of Rht-D1b. In contrast, the semi-dwarf parents contributed resistance alleles of major effects apparently compensating the negative effects of Rht-D1b on FHB reaction. The moderately resistant cultivar Apache contributed a major QTL on chromosome 6A in a genome region previously shown to carry resistance loci to FHB. A total of 18 genomic regions were repeatedly associated with FHB resistance. The results indicate that common resistance-associated genes or genomic regions are present in European winter wheats.     

Changes in the variability of quantitative characters in M2 induced in einkorn wheat by N-nitroso-N-methylurea and X-rays

Changes in the variability of quantitative characters (number of fertile stems, length of the stem and of the spike, number of spikelets in the spike, number of seeds in the spike and in the spikelet) in M₂ induced with 0·1 mM, 0·2 mM and 0·3 mM N-nitroso-N-methylurea (MNH) and with 5000r and 10 000 r of X-rays inTriticum monococcum L. var.sofianum Körn. were evaluated. The mean of the populations remained practically unchanged by the mutagens whereas the variability increased considerably with increasing concentration or dose. Changes in the variability were more pronounced in the values for the first stem than in the values for the first three stems. When changes in the population mean were found (with some of the most elevated concentrations and doses), these changes were shown to be mostly due to a repetition of the cultivation, whereas the changes in the variability were mostly due to the action of the mutagens. In all experimental populations, mutations in quantitative characters were successfully induced.     

Dynamic of black-grass populations depending on the sowing time of winter wheat

Currently, economic, agronomic and environmental concerns, lead to reduce use of herbicides. This reduction can be help by cultural measures like delay of the sowing date. Four sowing dates of winter wheat from 15th of October to 26th of November were tested. Dynamic of black-grass (Alopecurus myosuroides Huds.) populations and their reproduction rate were assessed as well as dynamic of winter wheat for each date. Delay of sowing could significantly reduce reproduction rate of black-grass. It was shown that the emergence rate (pl/m2), but also number of ears per plant and number of seeds per ear of black-grass decreased significantly with the sowing date. This reduction of seeds production already is from sixty per cent for a delay of two weeks sowing.     

M145F/F146M突变对光受体蛋白细菌视紫红质和古紫质4光循环的影响 *

古紫质4(archaerhodopsin 4,aR4)与细菌视紫质(bacteriorhodopsin,bR)同属于盐杆菌科,同源性59%,均为光驱质子泵。其功能是在光照条件下将质子由胞内泵到胞外形成跨膜质子梯度,该梯度差被膜上另外一种蛋白ATP合成酶用于ATP的合成,从而完成光能向生物能的转化。aR4和bR具有相似的光循环过程,但质子传递时序不同,aR4是先从胞内吸收质子再将质子释放到胞外,而bR恰好相反。甲硫氨酸-145是位于bR视黄醛发色团键合区的一个重要残基,对其光循环有着重要的影响,而在aR4中处在相应位置上的苯丙氨酸-146是其视黄醛键合区与bR唯一不相同的残基。因此通过定点突变,采用紫外可见吸收光谱、动力学光谱、质子泵功能检测、低温透射红外光谱等手段对比分析研究M145F和F146M单点突变对bR和aR4光循环造成的影响,有助于深入理解aR4结构与功能的关系。研究结果表明,M145F突变造成了bR光循环L的丢失和质子泵功能的减弱,而F146M突变并未对aR4的光循环造成显著影响,且突变后aR4质子释放时序没有反转,表明该位置上的残基在两个体系中的作用不尽相同。     

Temporal and spatial changes in aphid and parasitoid populations following applications of deltamethrin in winter wheat

The spatial and temporal effects of the pyrethroid insecticide, deltamethrin, on populations of cereal aphids and their primary parasitoids and hyperparasitoids were investigated in a large scale field experiment in winter wheat. Four hectare plots were treated at the recommended field concentration or a reduced concentration representing one twentieth of field rate. A control plot was left unsprayed. Invertebrate populations were sampled at sites within a grid layout covering the whole plots, enabling the use of geostatistical analysis. Hymenopteran populations were monitored using transparent sticky traps and suction sampling. Aphid populations were recorded by visual counts. Monitoring continued for 36 days after treatment. The full rate deltamethrin treatment resulted in initial reductions of aphid populations by 78%. Primary parasitoid and hyperparasitoid populations were reduced in suction samples by 90% and 47% respectively, when corrected for control fluctuations. The reduced deltamethrin concentration caused reductions of aphid, primary parasitoid and hyperparasitoid populations of 40, 60 and 54% respectively. Aphid population recovery over the full rate plot occurred slowly and in a patchy manner following treatment. No significant reinvasion gradients were detected. Aphid population density recovered more rapidly in the reduced rate treatment; with initial evidence for increased densities at the plot centre. Significant patterns of reinvasion were initially detected for both groups of Hymenoptera in the full rate treatment, suggesting that reinvasion of the sprayed area was taking place from untreated surrounding reservoirs. It was concluded that experiments that examine pesticide impacts within small plots will lead to underestimates of effects on dispersive groups including parasitic Hymenoptera.     

Use of winter wheat x Triticum tauschii backcross populations for germplasm evaluation

The wild diploid goatgrass, Triticum tauschii (Coss.) Schmal., is an important source of genes for resistance to both diseases and insects in common wheat (Triticum aestivum L.) We have evaluated grain yield, kernel weight, protein concentration, and kernel hardness of 641 BC₂ F₁-derived families from direct crosses involving four T. aestivum cultivars and 13 T. tauschii accessions over 2 years and at two Kansas, USA, locations. On average, T. tauschii germplasm depressed grain yield and increased protein concentration, whereas kernel weight was affected either positively or negatively, depending on the T. tauschii parent. Three T. tauschii parents produced a large proportion of families with very soft endosperm. Some variation among progeny of different T. tauschii parents resulted from the segregation of genes for resistance to leaf rust (caused by Puccinia recondita Rob. ex Desm.). This study confirmed that random BC₂-derived families can be used to evaluate the effects of T. tauschii genes in the field. This methodology, although laborious, can provide useful information which is not obtainable by the screening of T. tauschii accessions themselves.Joint contribution of USDA-ARS, the Kansas Agricultural Experiment Station, and the Wheat Genetics Resource Center. Contribution no. 94-242-J. Mention of a proprietary name in the article does not imply approval to the exclusion of other suitable products     

Estimating linkage disequilibrium between a polymorphic marker locus and a trait locus in natural populations.

Positional cloning of gene(s) underlying a complex trait requires a high-resolution linkage map between the trait locus and genetic marker loci. Recent research has shown that this may be achieved through appropriately modeling and screening linkage disequilibrium between the candidate marker locus and the major trait locus. A quantitative genetics model was developed in the present study to estimate the coefficient of linkage disequilibrium between a polymorphic genetic marker locus and a locus underlying a quantitative trait as well as the relevant genetic parameters using the sample from randomly mating populations. Asymptotic covariances of the maximum-likelihood estimates of the parameters were formulated. Convergence of the EM-based statistical algorithm for calculating the maximum-likelihood estimates was confirmed and its utility to analyze practical data was exploited by use of extensive Monte-Carlo simulations. Appropriateness of calculating the asymptotic covariance matrix in the present model was investigated for three different approaches. Numerical analyses based on simulation data indicated that accurate estimation of the genetic parameters may be achieved if a sample size of 500 is used and if segregation at the trait locus explains not less than a quarter of phenotypic variation of the trait, but the study reveals difficulties in predicting the asymptotic variances of these maximum-likelihood estimates. A comparison was made between the statistical powers of the maximum-likelihood analysis and the previously proposed regression analysis for detecting the disequilibrium.     

Broad-spectrum resistance loci for three quantitatively inherited diseases in two winter wheat populations

Septoria tritici blotch (STB), caused by S. tritici, Stagonospora glume blotch (SGB), caused by S. nodorum, and Fusarium head blight (FHB), caused by F. graminearum and F. culmorum, are the most important diseases of wheat (Triticum aestivum L.) in temperate growing areas. The main goals of this study were to detect (1) new quantitative trait loci (QTL) for STB resistance in two adapted European biparental populations (Arina/Forno, History/Rubens) and (2) QTL regions for broad-spectrum resistance (BSR) to the above-mentioned diseases during the adult-plant stage in the field. The three resistances were phenotyped across 4–7 field environments and phenotypic data revealed significant (P < 0.01) genotypic differentiation in all cases. Entry-mean heritabilities (h2) ranged from 0.73 to 0.93. For STB resistance, correlations between disease ratings and heading date were significant (P < 0.01), but moderate (r = −0.23 to −0.30) in both populations. Correlations between STB and plant height were higher in Arina/Forno (r = −0.45) and History/Rubens (r = −0.55), the latter population segregating at the Rht-D1 locus. During the initial QTL analysis, 5 QTL were detected for STB resistance in each of the populations, amounting to an explained genotypic variance of 45–63%, thus, showing the same ranges as FHB and SGB resistances in Arina/Forno and FHB resistance in History/Rubens. In total, 7 BSR QTL were found in the meta-analysis with the raw data, including the QTL on chromosome 4D at the Rht-D1 locus. A BSR QTL for all three diseases was not found but several BSR QTL for combinations with two diseases were detected. Combining the BSR QTL detected in the present breeding material by applying marker-assisted selection seems a promising approach.     

The inheritance of a urease-null trait in soybeans

Summary Four soybean seed urease nulls (lacking both the activity and antigen of the embryo-specific urease) were intermated and the F₁ and F₂ seed examined for urease activity. Both generations were without urease activity, and the nulls were therefore considered noncomplementing. In crosses of each null line to cultivars homozygous for the allelic, codominantly inherited urease slow or fast isozyme, the F₁ seed expressed the embryo-specific urease isozyme of the urease-expressing parent. A 3 1 segregation for presence and absence of urease was observed in progeny from F₁ and heterozygous F₂ plants. The F₂ and F₃ from fastXnull combinations revealed that urease-positive seed were all phenotypically urease fast, while the same seed from slowXnull combinations showed a segregation of one seed containing a fast urease, either exclusively or in a heterozygous state with the slow isozyme, for every 69 phenotypic slows. Data pooled from F₂ plants which segregate for both the presence (Sun) and absence (Sun) of urease and for the fast (Eu1-b) or slow (Eu1-a) urease allele indicate that the null lesion (Sun) is linked to Eu1 by approximately one map unit. The evidence is consistent with two models: (1) sun is an allele at the embryo-specific urease isozyme locus (Eu1) and that a high degree of exchange (and/or conversion) within the locus results in a 1% recombination frequency between the null trait and urease allozyme; (2) sun is at a distinct locus which is separated by one map unit from the embryo-specific urease isozyme locus (Eu1) upon which it acts in the cis position. Polyadenylated embryo RNA from one of the null lines, PI 229324, exhibited no urease template activity in vitro. Thus, the lack of urease antigen is due to lack of accumulation of translatable urease mRNA. The availability of soybeans lacking seed urease should be extremely useful to breeders as a trait for linkage studies and to geneticists as a transformation marker.Portions of this work were funded by the Illinois and Missouri Agricultural Experiment Stations, the SOHIO-University of Illinois Center of Excellence in Crop Molecular Genetics and Genetic Engineering and by grants PCM-8219652 from the National Science Foundation and USDA/SEA-CRCR-1-1374 from the USDA Competitive Grants Office