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Increase viability and efficiency in the design and development of new plant varieties through molecular assisted breeding in the postgenomic era

Plant breeding is an applied science of design where constantly new designs are performed to solve specific problems, such as productivity, resistance to biotic and abiotic stresses, fruit quality, postharvest performance and sensorial attributes. At this moment, the treating of breeding as science of design supposes to consider this activity closer to software development or the pharmaceutical industry than biology. The requirement of these new designs demands each time more complicated mechanisms to choose parental for crossing and select the new descendants. In addition, genetic transformation to develop GMOs (Genetically Modified Organisms), including CRISPR (clustered regularly interspaced short palindromic repeats) application, is at this moment a far option from a consumer point of view. Classical plant breeding is a long and tedious process involving the generation of large populations through controlled crosses of previously selected progenitors and the final selection of top individuals, the future new varieties. This process can take between 5 years in the case of horticultural crops to 15 years in the case of perennial fruit crops or 25 years in forest species. The management, phenotyping and selection process of progenitors and seedlings are the main factors limiting the generation of new cultivars. In order to improve efficiency and viability of breeding programs in relation to parent and seedling selection, the implementation of molecular tools is an essential requirement, including development of new Marker Assisted Selection (MAS) strategies based on the molecular knowledge of the determination of the phenotypic traits. Molecular effort should be oriented in the analysis of the molecular basis of the target traits and the implementation of molecular tools to be incorporated together with the classical activity of the visual selection of good descendants. In this context, at this moment in the present Postgenomic era we are facing a new molecular-biological perspective based on new methodologies that are affecting the molecular analysis. This new molecular perspective opens new possibilities to improve the use of molecular tools in new more efficient and viable plant breeding.

Design of new plant varieties: an increasingly complicated task

We can consider plant breeding as an applied science of design which requires empirical support based on observation and experimentation. At the same time, plant breeding is a design science, as it comes up with models to meet aims that expand human possibilities. In fact, the design of new varieties involves applied knowledge, because the models proposed have a practical dimension: they seek to solve specific problems (in the short, medium or long term). This activity has a link with technology since it can lead to innovation, an achievement produced by the creative transformation of reality. This can lead, for example, to the creation of a new plant variety, which is a desired transformation.

Tto develop suitable new cultivars, we need to know the relevant variables that influence our knowledge of the possible future in the success of new cultivars. It is thus necessary to examine the internal and external variables influencing the phenomenon in question. Both types of variable must be subjected to scientific evaluation (Fig. 1). The first internal variables to consider in any almond breeding program are derived from plant traits that are considered as objectives. The knowledge of these internal variables of genetic type will indicate their suitability with respect to the proposed design objectives. Secondly, internal variables also include the current methodologies available for use in the selection of individuals. These methodologies are closely related to the level of knowledge available at the molecular levels especially in relation to the development and application of new markers for the selection of individuals and will give us an idea of the efficacy and feasibility of new designs or cultivars. Finally, we can include various economic factors within the production framework, i.e., the goals, processes and outcomes. The effectiveness and viability of the improvement program will depend on these methodological developments dedicated to the evaluation. These two terms (effectiveness and viability) are related in the economic context to the relationship between science and economics. The evaluation of this feasibility, effectiveness and feasibility can lead to the abandonment of the new design if it were not feasible or to its production. We would have to proceed with the design of a new variety with new crosses and new variables to evaluate within the program. In any case, this evaluation process is continuous.

On the other hand, in plant breeding, it is necessary to consider a number of external variables including biotic and abiotic stress and interactions with the environment over a period of several years (Fig. 1). There are many characteristics such as flowering time and floral compatibility which must be evaluated for at least three years, when trees produce the first flowers. Due to drawbacks, the use of molecular marker-assisted selection methods is of particular interest in breeding programs. These drawbacks make the use of methods of assisted selection by molecular markers already discussed. These environmental conditions will determine the feasibility of the objectives and the new variety in a given environment. The adaptation of new designs or new cultivars to specific climatic conditions is fundamentally conditioned by their winter cold needs for lethargy and by their adaptation to different soil conditions in the case of rootstocks. Its capacity for production depends largely on this character and on its interaction with the environment considered as an external variable. In addition, the knowledge of these external variables related to possible biotic stresses (pest and disease) will indicate their feasibility with respect to the proposed design objectives. The feasibility of developments is another important issue to consider. The technological feasibility will also depend on the existence of germplasm with the desired genes for resistance to different biotic or abiotic stresses.

Molecular assisted breeding to increase viability and efficiency in the development of new design in the postgenomic era

At this moment, more than 550 plant species have sequenced and their reference genomes are available including the most important crops in the world (, accessed 1st July 2020). This whole sequenced work started in 2002 with the development of the reference genome of the rice. Last years for instance, several important crops were sequenced including hazelnut, mulberry, pistachio, poplar or almond in 2019. The development of complete genomes is making any organism accessible and amenable for many kinds of studies which will allow a precise reference of the molecular results obtained, and the development of high-throughput methods for genomic analysis involving the most abundant genetic variation and transcriptomic analysis at differential gene expression (DEG) level in a new postgenomic perspective. At this moment, the new Big Data Biology harboring the development of DNA  high-throughput sequencing technologies together with bioinformatics analysis as well as the creation of databases with billions of data has made possible to access genetics knowledge at the level of each nucleotide. This new methodological perspective where millions of sequences are available in one single experiment with the detailed information of complete genomes (defined as the DNA organized into separate chromosomes inside the nucleus of a cell) and transcriptomes (described as the complete list of all types of RNA molecules). Several authors have even characterized this data-intensive biology as a new kind of science, a science of information management, different from traditional biology. Big data science is now being introduced in the development of molecular markers to assist breeding selection methodologies.

This new postgenomic perspective integrating available reference genomes and new sequencing and bioinformatic methodologies will allow the implementation of new Marker Assisted Selection (MAS) to accelerate breeding process. The application of these molecular tools will increase the viability and efficiency in the development of the new planned design. In this context, high-throughput sequencing technologies resulted in a great advance in the development and application of MAS strategies.

This situation does mean that MAS will replace conventional breeding; other ways is a necessary complement. The practical learning that conventional breeding gives is unparalleled with the molecular support. In this context, there has been a significant shift of conventional breeders to molecular breeding aspects. However, in this enjoyed strategy (conventional and molecular) the target must be well defined in a complete integrated work plan. While the ability of breeders to generate large new breeding populations is almost unlimited, the evaluation and selection of these promising seedlings is the main limiting factors due to the cost and time-consuming. In this context, genomic studies at DNA level are especially useful for the development of MAS strategies. In addition, proteomic (proteins and enzymes), transcriptomic (RNA) and epigenetic (DNA Methylation and histone modifications) studies are being applied to breeding programs. Finally, these strategies at genomic, epigenetic, transcriptomic and proteomic level should be all integrated for a better understanding of the molecular mechanisms involved in the most important plant breeding aspects, which will facilitate the development and optimization of molecular markers to apply in the field exploitation of the new varieties, offering and integrating complete technological offers.

Figure 1. Internal and external variables affecting the viability and establishment of a plant breeding programs based on the realization of genetically diverse crosses and subsequent selection of elite individuals. Application of molecular (DNA, RNA and epigenetic) markers could affect feasibility, efficiency and viability of these breeding programs.

Picture 1. New apricot release from the CEBAS-CSIC breeding program in Murcia (Spain).

Picture 2. General view of the molecular laboratory associated to the CEBAS-CSIC breeding programs (apricot, almond and plum) in Murcia (Spain).


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Written By

Pedro Martínez-Gómez

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Department of Plant Breeding

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