Gene-Mapping Techniques and Applications

Lawrence B. Schook, Lawrence B. Schook

• Publisher: CRC Press
• Year: 2020
• ISBN:
  9781000147841
• Edition: 1
• Topic: Biological Sciences
• Subtopic: Biology
• Index: Biological Sciences

This book explains current strategies for mapping genomes of higher organisms and explores applications of gene mapping to agriculturally important species of plants and animals. It also explores the experimental techniques used for genetic and physical mapping of genes.

APPLICATIONS OF GENE MAPPING

10
Genomic Genetics and Plant Genetic Improvement

Jacques S. Beckmann

The Volcani Center Bet Dagan, Israel

Contribution from the Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel, No. 2832-E, 1989 series.

INTRODUCTION

The ability to generate complete genetic maps includes the capacity to evaluate the entire genome (hence the term “genomic genetics”), to dissect complex genetic traits into their individual mendelian entities, and to channel all this information into breeding programs. This is what renders marker-based methodologies so powerful. The progress to date in plant genetics will be reviewed and the limitations outlined.

Mapping techniques require still further refinement. For some plants, polymorphism is abundant and easy to uncover. For others, as well as for specific narrow crosses, the opposite situation prevails; informative markers are also required in these situations. Possible strategies to uncover such markers will be discussed.

The search for additional useful markers can be complemented by the design of more efficient mapping schemes. One design, which has remarkable qualities both for the identification and evaluation of single trait loci of economic importance (ETL) and for precise ordering of loci on the chromosome map will be presented. This will enable markers to be placed within realistic “chromosome” walking distances of the ETL, allowing for the molecular cloning of these loci by reverse genetics.

Thus genomic markers, besides serving as specific “tags” to monitor for the presence of ETL in breeding programs, can also serve as reference points toward the cloning of genes of interest. In this way, genomic genetics can provide a solution to two seemingly unrelated problems—the molecular cloning of genes of agricultural interest and the more effective utilization, by classical breeding techniques, of existing genetic variation within a species—and become an intrinsic component of modern breeding methodologies.

Genetic improvement is an area in which new technologies are often slowly assimilated. The latest newcomer in the breeder’s armamentarium is recombinant DNA technology, which provides greatly increased genetic resolution. Indeed, it is now possible to uncover large numbers of genetic polymorphisms, to locate them accurately on the genetic map, and to use them as markers for the evaluation and utilization of the genetic basis for observed phenotypic variability. This is done by uncovering genetic variation directly at the DNA level, in the form of genomic markers. The capacity to relate directly to genomic variation rather than having to infer genotypes from phenotypic observations (the classical mendelian paradigm) led to proposal of the term “genomic genetics” (Beckmann, 1988).

DNA sequence variation is usually equated with restriction fragment length polymorphism (RFLP). The latter, however, is only one of a number of means that can be utilized to uncover genomic variation (we might say, by analogy with computers, that we have already seen several generations of genomic markers). Our purpose is not to review this evolution. The emphasis lies instead on markers in general, rather than on the exact type of markers utilized, and on the fact that genomic markers (whose convenient and attractive properties were reviewed in Beckmann and Soller, 1986) can be used by breeders to deal with the problems posed by traits under the control of a complex of polygenic genetic factors—the quantitative trait loci. These principles will be illustrated with some examples taken from plant studies.

MARKER-BASED METHODOLOGIES

The detailed interrelationships between markers or markers and trait loci need to be determined. But even before this goal is reached, the availability of a battery of markers, per se, lends itself to some immediate and important potential applications (Table 1), such as the assignment of breeding lines to heterotic groups for the prediction of single cross performances (e.g., Kahler and Wehrhahn, 1986; Lee et al., 1989) or the demonstration of the distinctiveness of newly released varieties, a central issue in varietal protection. In fact, genomic markers are the most adequate tool available today to estimate minimum genetic distance between lines that can often be morphologically and agronomically similar. These markers are, therefore, gradually becoming recognized by courts in litigations in plant breeding over misappropriated proprietary germplasm. Genomic markers have indeed the necessary attributes required for these tasks: they provide an adequate sampling of the genome, they are overall the most sensitive probes available for polymorphisms, they are both genetically and environmentally stable, they act in a codominant manner, and they can reproducibly be measured. In addition to the utilization of the existing genetic variation, genomic markers can also be generated do novo: a foreign segment of DNA, once it is stably inserted into the genome, constitutes an easily scorable tag (e.g., Beckmann and Bar-Joseph, 1986).

Table 1 Applications of Marker-Based Methodologies

In conventional breeding Short-range applications Parentage identification Protection of breeder’s rights Assignment of inbred lines to heterotic groups Line and hybrid purity testing Long-range applications Analytical path Mapping and evaluation of effects of single ETL Exploration of homologous loci in other species or genera Germplasm evaluation (diversity, classification, and phylogeny) Synthetic path Introgression of desired traits among cultivars or from resource strain to cultivar Preselection of superior genotypes Prediction of expected phenotypes In transgenic breeding Precise mapping, a first step toward the cloning of ETL and their manipulation through genetic engineering techniques (transgenics)

But the foremost application of genomic markers is elucidation of the historic, genetic, and functional architecture of a genome. It is their enhanced genetic resolution power which is at the basis of “marker-based methodologies.” The latter will enable the analysis of related genomes, the establishment of taxonomical inferences, such as chromosomal duplications or alloploidy formation (see, for instance, Song et al., 1988), the tracing of the evolution of specific cultivars and thus, the verification of the validity of pedigree data. In this manner markers can provide important clues on germplasm diversity in the relatives of domesticated plants. More importantly, marker-based methodologies should make it possible to examine intragenomic relationships, namely, the analysis of the genome into its individual functional components, the mendelian entities, leading to a precise evaluation and understanding of their effects (Beckmann and Soller, 1986) and, eventually, to the molecular cloning of the loci involved and to transgenic manipulations (Table 1).

When considering marker-based methodologies, it is opportune to remember that there are two facets. The first—the subject of this discussion—is analytical: the identification and evaluation of the individual genetic factors—the economic trait loci (ETL)—governing both simple and polygenic traits, allowing for exploration of the entire species gene pool for a search for beneficial alleles. The second is synthetic: integration of all the information gathered on relative breeding values of the characterized loci, allowing predictions to be made as to the overall phenotype to be expected upon combining various alleles and providing the necessary markers for the controlled and efficient introgression of defined chromosomal segments into desired genetic backgrounds. This can replace the less accurate and often difficult scoring of the trait itself (phenotypic selection). Progeny bearing the selected markers (genomic selection) will be enriched for the desired trait; this will be equivalent to selection with a heritability of close to 1.0. Even for easily scorable traits, marker-assisted selection can, in special circumstances, provide an attractive alternative; for instance, wherever there are constraints on the introduction of undesirable pathogens, selection for resistant genotypes could still be pursued without colonization.

TOWARD SATURATED MAPS

The rationale of marker-based methodologies lies in the capacity to distinguish allelic pairs of markers and to assess the phenotypic value of the associated chromosomal segments. By following marker alleles, it is possible to recognize which of the alternative chromosomal regions defined by a give...