Software Tools to Assist Breeding Decisions

Software Tools to Assist Breeding Decisions

DOI: 10.4018/978-1-7998-4312-2.ch010
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Abstract

Plant breeders are usually faced with the problem of predicting the performance of new individuals with untested gene combinations. Therefore, it is important to follow an integrated breeding approach by combining molecular tools, molecular mapping, and MAS. It is also required to develop tools for modeling and simulation analysis by utilizing all pre-existing and newly generated data. Several software tools have been developed that integrates breeding simulations and phenotype prediction models using genomic information. Reliable phenotype prediction models for the simulation were constructed from actual genotype and phenotype data. Such simulation-based genome-assisted approach to breeding will help optimize plant breeding in all important agricultural crops. Software tools have also been developed for designing target sites or evaluating the outcome of genome/gene editing system. This chapter provides an overview of the key software support tools that will assist the plant breeders in decision making during the process of conducting various breeding program.
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Introduction

Important steps involved in molecular breeding include: identification and selection of beneficial genetic variations and utilization of such variations more effectively and efficiently for crop improvement. Marker-assisted selection (MAS) has been recognized as a reliable identification tool and thus has lot of potential for its utilization in crop breeding. To achieve the desired goal, MAS has to be combined with other advanced techniques such as genome scans, advanced biometrical analysis and quantitative genetics modeling that will require complex software. Effective molecular breeding procedure will depend on the following parameters (Singh et al. 2010).

  • 1.

    Identification of new sources of variation and development of strong marker-trait associations.

  • 2.

    Management of large numbers of genotypes and manipulation of genotype, phenotype and pedigree data.

  • 3.

    Selection of desirable recombinants by combining genotypic and phenotypic information.

  • 4.

    Development of breeding systems to minimize population size, number of generations and overall cost, but to maximize genetic gain for traditional and novel traits.

Supporting tools are required to manage and optimize various components of plant molecular breeding procedures. Many of these tools come in the form of software. Some of the important software having applications in molecular plant breeding can be obtained from the sites: http://linkage.rockefeller.edu/soft/list.html.

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Management And Evaluation Of Germplasm

With the increase in the size of germplasm collections, genebank curators find it difficult to manage and provide required information to the breeders and researchers. MAGE (marker-assisted germplasm evaluation) has played an important role in the process of acquisition, maintenance, distribution, and use of germplasm in the gene banks. For efficient management of the various activities of the gene bank through MAGE it is important to have the following resources in place (Xu 2014).

  • 1.

    Characterization of suitable genetic markers for large number alleles, polymorphic information content (PIC value), size and range of the alleles, signal strength, working conditions and information for multiplexing,

  • 2.

    Generate high-density molecular maps for selection of markers evenly spread over the entire genome or densely spread over the specific region of interest,

  • 3.

    Establishment of association of the marker and the trait of agronomical importance,

  • 4.

    Establishment of high-throughput genotyping system, and

  • 5.

    Establishment of an efficient data management and analysis system.

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