Principles of Plant Genetics and Breeding. George Acquaah

not by variation in the environment. Markers are phenotypes that are linked to genotypes (or precisely genes of interest). Markers are discussed in detail in Chapter 21. They are useful in facilitating the selection process and making it more efficient and cost effective. Molecular (DNA‐based) markers have superseded morphological markers in scale of use in plant breeding. Marker‐assisted selection (MAS) is used to facilitate plant breeding (see Chapter 24).

       Gene mapping

      Gene mapping entails a graphic representation of the arrangement of a gene or a DNA sequence on a chromosome. It can be used to locate and identify the gene (or group of genes) that conditions a trait of interest. It depends on availability of markers. The availability of molecular markers has greatly facilitated gene mapping. Further, genomic DNA sequencing produces the most complete maps for species. Now, QTL (quantitative trait loci) mapping is becoming more widespread. Modern plant breeding is greatly facilitated by genetic maps.

       Genomic selection

      Genomic selection methodology and genome wide techniques are helping to facilitate the improvement of quantitative traits.

2.7 Genome‐wide approaches to crop improvement

      An organism's complete set of DNA is called its genome. The concept of genomics began with the successful sequencing of the genomes of a virus and a mitochondrion by Fred Sanger and his colleagues starting in the 1970s. Previously, researchers were limited to understanding plant structure and function piecemeal (gene‐by‐gene). With the advances in technology, whole genomes of certain species have been sequenced, thereby making all the genes they contain accessible to researchers. Because of the cost of such undertakings, whole genome sequences have so far been limited to the so‐called model organisms, including Arabidopsis, rice, and corn. Through comparative genome analysis, researchers seek to establish correspondence between genes or other genomic features in different organisms, without the need to have whole genome maps of all organisms. In sum, the goal of plant genomics is to understand the genetic and molecular basis of all the relevant biological processes that pertain to a plant species, so that they can be exploited more effectively and efficiently for improving the species. Genomics is hence important in modern plant breeding efforts. Two of the major tools employed in genomics research are microarrays and bioinformatics.

2.8 Bioinformatics and OMICs technologies in crop improvement

      Genomics and other OMICs (transcriptomics, proteomics, metabolomics, phenomics, etc.) programs generate large volumes of data or information that need to be organized and interpreted to increase our understanding of biological processes. Bioinformatics is the discipline that combines mathematical and computational approaches to understand biological processes. Researchers in this area engage in activities that include mapping and analyzing DNA and protein sequences, aligning different DNA and protein sequences for the purpose of comparison, gene finding, protein structure prediction, and prediction of gene expression. Bioinformatics, along with the emerging field of big data will continue to have a major impact on how modern plant breeding is conducted.

2.9 Summary of changes in plant breeding over the last half century

      The foregoing brief review has revealed that plant breeding as a discipline and practice has changed significantly over the years.

      2.9.1 Changes in the science of breeding

      It has been said several times previously that plant breeding is a science and an art. Over the last decade, it has become clear that science is what is going to drive the achievements in plant breeding. More importantly, is it clear that a successful plant breeding program has an interdisciplinary approach, for recent strides in plant breeding have come about because of recent advances in allied disciplines. High‐tech cultivars need an appropriate cultural environment for the desired productivity. Advances in agronomy (tillage systems, irrigation technology, and herbicide technology) have contributed to the expansion of crop production acreage. In other words, plant breeders do not focus on crop improvement in isolation, but consider the importance of the ecosystem and its improvement to their success. Whereas most of the traditional plant breeding schemes and technologies previously discussed are still in use, the tools of biotechnology have been the dominant influence in the science of plant breeding. Paradigm shift in plant breeding is discussed in Chapter 30, where the changes in science and technologies that drive breeding are discussed in detail.

      2.9.2 Changes in laws and policies

      In the US, land grant institutions were established to promote and advance agricultural growth and productivity of the states, among other roles. Much of the efforts of researchers are put in the public domain for free access. The Plant Variety Protection Act of 1970, which provided intellectual property rights to plant breeders, was the major impetus for the proliferation of for‐profit private seed companies, and their domination of the more profitable aspects of the seed market where legal protection and enforcement were clearer and more enforceable (e.g. hybrid seed). Plant breeders' rights legislation was implemented in the 1960s and 1970s in most of Western Europe. Australia and Canada adopted similar legislations much later, in the 1990s. The US Supreme Court ruled in 1980 to allow utility patent protection to be applied to living things. This protection was extended to plants in 1985. The European Patent Office granted such protection to GM cultivars in 1999.

      2.9.3 Changes in breeding objectives

      Breeding objectives depend on the species and the intended use of the cultivar to be developed. Over the years, new (alternative) species have been identified to address some traditional needs in some parts of the world. By the same token the traditional uses of some species have been modified. For example, whereas corn continues to be used for food and feed in many parts of the world, corn has an increasingly industrial role in some industrialized countries (e.g. ethanol production for biofuel). Yield or productivity, adaptation to production environment, and resistance to biotic and abiotic stresses will always be important. However, with time, as they are resolved, breeders shift their emphasis to other quality traits (e.g. oil content, or more specific consumer needs like low linolenic content). Advances in technology (high throughput, low cost, precision, repeatability) have allowed breeders to pursue some of the challenging objectives that once were impractical to do. Biotechnology, especially recombinant DNA technology, has expanded the source of genes for plant breeding in the last half decade. Also, the increasing need to protect the environment from degradation has focused breeders' attention on addressing the perennial problem of agricultural sources of pollution.

      2.9.4 Changes in the creation of variability

      The primary way of creating variability for breeding has been through artificial crossing (hybridization) or mutagenesis (induced mutations). Hybridization is best done between crossable parents. However, sometimes, breeders attempt to cross genetically distant parents, with genetic consequences. There are traditional schemes and techniques to address some of these consequences (e.g. wide cross, embryo rescue). The success of hybridization depends on the ability to select and use the best parents in the cross. Breeders have access to elite lines for use as parents. Further, biotech tools are now available to assist in identifying suitable parents for a cross, and also assist in introgressing genes from exotic sources into adapted lines. Transgenesis (genetic engineering involving gene transfer across natural biological boundaries), and more recently cisgenesis (genetic engineering involving gene transfer among related and crossable species) can be used to assist breeders in creating useful variability for breeding. In the case of mutagenesis, advances in technology have enabled breeders