QTL IciMapping:Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations

QTL Ici Mapping is freely available public software capable of building high-density linkage maps and mapping quantitative trait loci(QTL) in biparental populations. Eight functionalities are integrated in this software package:(1) BIN: binning of redundant markers;(2) MAP: construction of linkage maps in biparental populations;(3) CMP: consensus map construction from multiple linkage maps sharing common markers;(4) SDL: mapping of segregation distortion loci;(5) BIP: mapping of additive, dominant, and digenic epistasis genes;(6) MET: QTL-by-environment interaction analysis;(7) CSL: mapping of additive and digenic epistasis genes with chromosome segment substitution lines; and(8) NAM: QTL mapping in NAM populations. Input files can be arranged in plain text, MS Excel 2003, or MS Excel 2007 formats. Output files have the same prefix name as the input but with different extensions. As examples, there are two output files in BIN, one for summarizing the identified bin groups and deleted markers in each bin, and the other for using the MAP functionality. Eight output files are generated by MAP, including summary of the completed linkage maps, Mendelian ratio test of individual markers, estimates of recombination frequencies, LOD scores, and genetic distances, and the input files for using the BIP, SDL,and MET functionalities. More than 30 output files are generated by BIP, including results at all scanning positions, identified QTL, permutation tests, and detection powers for up to six mapping methods. Three supplementary tools have also been developed to display completed genetic linkage maps, to estimate recombination frequency between two loci,and to perform analysis of variance for multi-environmental trials.

Linkage analysis and integrated software GAPL for pure-line populations derived from four-way and eight-way crosses

Pure lines derived from multiple parents provide abundant variation for genetic study.However,efficient genetic analysis methods and user-friendly software are still lacking.In this study, we developed linkage analysis methods and integrated analysis software for pure-line populations derived from four-way and eight-way crosses.First, polymorphic markers are classified into different categories according to the number of identifiable alleles in the inbred parents.Expected genotypic probability is then derived for each pair of complete markers, and based on them a maximum likelihood estimate(MLE) of recombination frequency is calculated.An EM algorithm is proposed for calculating recombination frequencies in scenarios that at least one marker is incomplete.A linkage map can thus be constructed using estimated recombination frequencies.We describe a software package called GAPL for recombination frequency estimation and linkage map construction in multi-parental pure-line populations.Both simulation studies and results from a reported four-way cross recombinant inbred line population demonstrate that the proposed method and software can build more accurate linkage maps in shorter times than other published software packages.The GAPL software is freely available from www.isbreeding.net and can also be used for QTL mapping in multi-parental populations.

Ordering of high-density markers by the k-Optimal algorithm for the traveling-salesman problem

Construction of accurate and high-density linkage maps is a key research area of genetics.We investigated the efficiency of genetic map construction(MAP)using modifications of the k-Optimal(k-Opt)algorithm for solving the traveling-salesman problem(TSP).For TSP,different initial routes resulted in different optimal solutions.The most optimal solution could be found only by use of as many initial routes as possible.But for MAP,a large number of initial routes resulted in one optimal order.k-Opt using open route length gave a slightly higher proportion of correct orders than the method of adding one virtual marker and using closed route length.Recombination frequency(REC)and logarithm of odds(LOD)score gave similar proportions of correct order,higher than that given by genetic distance.Both missing markers and genotyping error reduced ordering accuracy,but the best order was still achieved with high probability by comparison of the optimal orders from multiple initial routes.Computation time increased rapidly with marker number,and 2-Opt took much less time than 3-Opt.The 2-Opt algorithm was compared with ordering methods used in two other software packages.The best method was 2-Opt using open route length as the criterion to identify the optimal order and using REC or LOD as the measure of distance between markers.We describe a unified software interface for using k-Opt in high-density linkage map construction for a wide range of genetic populations.

Modeling and simulation of recurrent phenotypic and genomic selections in plant breeding under the presence of epistasis

Recurrent selection is an important breeding method for population improvement and selecting elite inbreds or fixed lines from the improved germplasm.Recently,a computer simulation tool called QuMARS has been developed,which allows the simulation and optimization of various recurrent selection strategies.Our major objective in this study was to use the QuMARS tool to compare phenotypic recurrent,marker-assisted recurrent,and genomic selections(abbreviated respectively as PS,MARS and GS)for both short-and long-termbreeding procedures.ForMARS,twomarker selection models were considered,i.e.,stepwise(Rstep)and forward regressions(Forward).For GS,three prediction models were considered,i.e.,genomic best linear unbiased predictors(GBLUP),ridge regression(Ridge),and regression by Moore-Penrose general inverse(InverseMP).To generate genotypes and phenotypes for a given individual during simulation,one additive and two epistasis genetic models were considered with three levels of heritability.Results demonstrated that selection responses from GBLUP-based GS and MARS(Forward)were consistently greater than those from PS under the additive model,particularly in early selection cycles.In contrast,selection response from PS was consistently superior over MARS and GS under epistatic models.For the two epistasis models,total genetic variance and the additive variance component were increased in some cases after selection.Through simulation,we concluded that GS and PS were effective recurrent selection methods for improved breeding of targeted traits controlled by additive and epistatic quantitative trait loci(QTL).QuMARS provides an opportunity for breeders to compare,optimize and integrate new technology into their conventional breeding programs.

Degradation Pathway of Benzothiazole and Microbial Community Structure in Microbial Electrolysis Cells

In this study, benzothiazole was entirely mineralized by an up-flow internal circulation microbial electrolysis reactor. The bioelectrochemical system was operated at ambient temperature under continuous-flow mode. The analysis of metabolite which was extracted by HPLC-MS from the bioreactor indicated that benzothiazole derivative ( BTH ) was firstly converted into 2-hydroxybenzothiazole in the microbial electrolysis cell (MEC) and then mineralized within three steps, i.e., the fracture of thiazole-ring through a series of oxidation and hydrolysis, the deamination and hydroxylation of 2-aminobenzenesulfonic acid, and the mineralization of various carboxylic acids to CO2 and H2O. Bacterial community analysis indicated that the applied electric field could selectively enrich certain species and the dominate bacteria on the electrodes belonged to Proteobacteria, Bacteroidetes, and Firmicutes. Results show that MEC can improve the degradation efficiency of BTH in wastewater, enable the microbiological reactor to satisfy the requirements of high loading rate, thereby fulfilling the scale-up of whole process in the future.

The Statistical Power of Inclusive Composite Interval Mapping in Detecting Digenic Epistasis Showing Common F_2 Segregation Ratios

Epistasis is a commonly observed genetic phenomenon and an important source of variation of complex traits, which could maintain additive variance and therefore assure the long-term genetic gain in breeding. Inclusive composite interval mapping （ICIM） is able to identify epistatic quantitative trait loci （QTLs） no matter whether the two interacting QTLs have any additive effects. In this article, we conducted a simulation study to evaluate detection power and false discovery rate （FDR） of ICIM epistatic mapping, by considering F2 and doubled haploid （DH） populations, different F2 segregation ratios and population sizes. Results indicated that estimations of QTL locations and effects were unbiased, and the detection power of epistatic mapping was largely affected by population size, heritability of epistasis, and the amount and distribution of genetic effects. When the same likelihood of odd （LOD） threshold was used, detection power of QTL was higher in F2 population than power in DH population; meanwhile FDR in F2 was also higher than that in DH. The increase of marker density from 10 cM to 5 cM led to similar detection power but higher FDR. In simulated populations, ICIM achieved better mapping results than multiple interval mapping （MIM） in estimation of QTL positions and effect. At the end, we gave epistatic mapping results of ICIM in one actual population in rice （Oryza sativa L.）.

Quantitative trait locus mapping with background control in genetic populations of clonal F_1 and double cross

In this study, we considered five categories of molecular markers in clonal F1 and double cross populations, based on the number of distinguishable alleles and the number of distinguishable genotypes at the marker locus. Using the completed linkage maps, incomplete and missing markers were imputed as fully informative markers in order to simplify the linkage mapping approaches of quantitative trait genes. Under the condition of fully informative markers, we demonstrated that dominance effect between the female and male parents in clonal F1 and double cross populations can cause the interactions between markers. We then developed an inclusive linear model that includes marker variables and marker interactions so as to completely control additive effects of the female and male parents, as well as the dominance effect between the female and male parents. The linear model was finally used for background control in inclusive composite interval mapping （ICIM） of quantitative trait locus （QTL）. The efficiency of ICIM was demonstrated by extensive simulations and by comparisons with simple interval mapping, multiple-QTLmodels and composite interval mapping. Finally, ICIM was applied in one actual double cross population to identify QTL on days to silking in maize.

Dissecting and Enhancing the Contributions of High-Molecular-Weight Glutenin Subunits to Dough Functionality and Bread Quality

Dear Editor,Seed storage proteins （SSPs） are frequently important determinants of crop quality traits （Shewry and Casey, 1999）. Dissecting and enhancing the genetic contributions of individual SSPs to their target traits are essential for effectively improving crop quality attributes. However, such a task is often difficult to accomplish, because SSPs are frequently expressed from multigene families and exhibit strong allelic variation. Consequently, detailed knowledge of the function of individual SSPs in crop quality trait is still limited. This scenario is well illustrated by high-molecular-weight glutenin subunits （HMW- GSs）, a complex family of SSPs that are involved in wheat enduse quality through affecting dough functionality （Bek6s, 2012; Rasheed et al., 2014）.