George Acquaah - Principles of Plant Genetics and Breeding

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.

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

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.

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.

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.

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 to be more efficient in screening mutants (e.g. by TILLING). Products from mutation breeding, not being transgenic, are more acceptable to consumers who are unfavorably disposed to GM crops.

Identifying and measuring quantitative variability continues to be challenging, even though some progress has been made (e.g. QTLs analysis and mapping). This has been possible because of the new kinds of molecular markers that have been developed and the accompanying throughput technologies. QTLs are more precisely mapped, in addition to the increased precision of linkage maps (marker‐dense). The abundance of molecular markers and availability of more accessible genomic tools has made it easier for researchers to readily characterize biodiversity.

Selection schemes have remained relatively the same for a long time. Here, too, the most significant change over the last half century has been driven by molecular technology. The use of molecular markers in selection (MAS) gained significant attention over the period. Most traits of interest to breeders are quantitatively inherited. The continuing challenge with this approach is the lack of precision (need for more high‐resolution QTL maps) and higher throughput marker technology, among others. Selected genotypes are evaluated across time and space in the same old fashioned way.

The achievements of plant breeders are numerous, but may be grouped into several major areas of impact – yield increase, enhancement of compositional traits, crop adaptation, and the impact on crop production systems.

Yield increaseYield increase in crops has been accomplished in a variety of ways including targeting yield per se or its components, or making plants resistant to economic diseases and insect pests, and breeding for plants that are responsive to the production environment. Yields of major crops (e.g. corn, rice, sorghum, wheat, and soybean) have significantly increased in the USA over the years (Figure 1.1). For example, the yield of corn rose from about 2000 kg ha−1 in the 1940s to about 7000 kg ha−1 in the 1990s. In England, it took only 40 years for wheat yields to rise from 2 metric tons ha−1 to 6 metric tons ha−1. Food and Agriculture Organization (FAO) data comparing crop yield increases between 1961 and 2000 show dramatic changes for different crops in different regions of the of the world. For example, wheat yield increased by 681% in China, 301% in India, 299% in Europe, 235% in Africa, 209% in South America, and 175% in the USA. These yield increases are not totally due to the genetic potential of the new crop cultivars (about 50% is attributed to plant breeding) but also due to the improved agronomic practices (e.g. application of fertilizer, irrigation). Crops have been armed with disease resistance to reduce yield loss. Lodging resistance also reduces yield loss resulting from harvest losses.