An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.

Shifting the limits in wheat research and breeding using a fully annotated reference genome

https://www.iro.umontreal.ca/~ferland/Seminars/Local_search/Pisinger,Ropke_ALNS_2007.pdf

A general heuristic for vehicle routing problems

We investigated the genetic and statistical properties of the nested association mapping (NAM) design currently being implemented in maize (26 diverse founders and 5000 distinct immortal genotypes) to dissect the genetic basis of complex quantitative traits. The NAM design simultaneously exploits the advantages of both linkage analysis and association mapping. We demonstrated the power of NAM for high-power cost-effective genome scans through computer simulations based on empirical marker data and simulated traits with different complexities. With common-parent-specific (CPS) markers genotyped for the founders and the progenies, the inheritance of chromosome segments nested within two adjacent CPS markers was inferred through linkage. Genotyping the founders with additional high-density markers enabled the projection of genetic information, capturing linkage disequilibrium information, from founders to progenies. With 5000 genotypes, 30-79% of the simulated quantitative trait loci (QTL) were precisely identified. By integrating genetic design, natural diversity, and genomics technologies, this new complex trait dissection strategy should greatly facilitate endeavors to link molecular variation with phenotypic variation for various complex traits.

/pdf/genetic-design-and-statistical-power-of-nested-association-6pmd14fv34.pdf

Genetic Design and Statistical Power of Nested Association Mapping in Maize

The Vehicle Routing Problem (VRP) was introduced 50 years ago by Dantzig and Ramser under the title “The Truck Dispatching Problem.” The study of the VRP has given rise to major developments in the fields of exact algorithms and heuristics. In particular, highly sophisticated exact mathematical programming decomposition algorithms and powerful metaheuristics for the VRP have been put forward in recent years. The purpose of this article is to provide a brief account of this development.

Fifty Years of Vehicle Routing

Active guided evolution strategies for large-scale vehicle routing problems with time windows

Active-guided evolution strategies for large-scale capacitated vehicle routing problems

This article is devoted to the problem of ordering in linkage groups with many dozens or even hundreds of markers. The ordering problem belongs to the field of discrete optimization on a set of all possible orders, amounting to n!/2 for n loci; hence it is considered an NP-hard problem. Several authors attempted to employ the methods developed in the well-known traveling salesman problem (TSP) for multilocus ordering, using the assumption that for a set of linked loci the true order will be the one that minimizes the total length of the linkage group. A novel, fast, and reliable algorithm developed for the TSP and based on evolution-strategy discrete optimization was applied in this study for multilocus ordering on the basis of pairwise recombination frequencies. The quality of derived maps under various complications (dominant vs. codominant markers, marker misclassification, negative and positive interference, and missing data) was analyzed using simulated data with approximately 50-400 markers. High performance of the employed algorithm allows systematic treatment of the problem of verification of the obtained multilocus orders on the basis of computing-intensive bootstrap and/or jackknife approaches for detecting and removing questionable marker scores, thereby stabilizing the resulting maps. Parallel calculation technology can easily be adopted for further acceleration of the proposed algorithm. Real data analysis (on maize chromosome 1 with 230 markers) is provided to illustrate the proposed methodology.

https://www.genetics.org/content/genetics/165/4/2269.full.pdf

Constructing large-scale genetic maps using an evolutionary strategy algorithm

A new genetic map of maize, ISU–IBM Map4, that integrates 2029 existing markers with 1329 new indel polymorphism (IDP) markers has been developed using intermated recombinant inbred lines (IRILs) from the intermated B73 × Mo17 (IBM) population. The website http://magi.plantgenomics.iastate.edu provides access to IDP primer sequences, sequences from which IDP primers were designed, optimized marker-specific PCR conditions, and polymorphism data for all IDP markers. This new gene-based genetic map will facilitate a wide variety of genetic and genomic research projects, including map-based genome sequencing and gene cloning. The mosaic structures of the genomes of 91 IRILs, an important resource for identifying and mapping QTL and eQTL, were defined. Analyses of segregation data associated with markers genotyped in three B73/Mo17-derived mapping populations (F2, Syn5, and IBM) demonstrate that allele frequencies were significantly altered during the development of the IBM IRILs. The observations that two segregation distortion regions overlap with maize flowering-time QTL suggest that the altered allele frequencies were a consequence of inadvertent selection. Detection of two-locus gamete disequilibrium provides another means to extract functional genomic data from well-characterized plant RILs.

/pdf/genetic-dissection-of-intermated-recombinant-inbred-lines-3d1ilwhnet.pdf

Genetic Dissection of Intermated Recombinant Inbred Lines Using a New Genetic Map of Maize

This paper presents a new deterministic annealing metaheuristic for the fleet size and mix vehicle-routing problem with time windows. The objective is to service, at minimal total cost, a set of customers within their time windows by a heterogeneous capacitated vehicle fleet. First, we motivate and define the problem. We then give a mathematical formulation of the most studied variant in the literature in the form of a mixed-integer linear program. We also suggest an industrially relevant, alternative definition that leads to a linear mixed-integer formulation. The suggested metaheuristic solution method solves both problem variants and comprises three phases. In Phase 1, high-quality initial solutions are generated by means of a savings-based heuristic that combines diversification strategies with learning mechanisms. In Phase 2, an attempt is made to reduce the number of routes in the initial solution with a new local search procedure. In Phase 3, the solution from Phase 2 is further improved by a set of four local search operators that are embedded in a deterministic annealing framework to guide the improvement process. Some new implementation strategies are also suggested for efficient time window feasibility checks. Extensive computational experiments on the 168 benchmark instances have shown that the suggested method outperforms the previously published results and found 167 best-known solutions. Experimental results are also given for the new problem variant.

David Mester

Papers

Active guided evolution strategies for large-scale vehicle routing problems with time windows

Active-guided evolution strategies for large-scale capacitated vehicle routing problems

Constructing large-scale genetic maps using an evolutionary strategy algorithm

Genetic Dissection of Intermated Recombinant Inbred Lines Using a New Genetic Map of Maize

An Effective Multirestart Deterministic Annealing Metaheuristic for the Fleet Size and Mix Vehicle-Routing Problem with Time Windows