Medical genetics was revolutionized during the 1980s by the application of genetic mapping to locate the genes responsible for simple Mendelian diseases. Most diseases and traits, however, do not follow simple inheritance patterns. Geneticists have thus begun taking up the even greater challenge of the genetic dissection of complex traits. Four major approaches have been developed: linkage analysis, allele-sharing methods, association studies, and polygenic analysis of experimental crosses. This article synthesizes the current state of the genetic dissection of complex traits—describing the methods, limitations, and recent applications to biological problems.

Genetic Dissection of Complex Traits

DNA markers have enormous potential to improve the efficiency and precision of conventional plant breeding via marker-assisted selection (MAS). The large number of quantitative trait loci (QTLs) mapping studies for diverse crops species have provided an abundance of DNA marker–trait associations. In this review, we present an overview of the advantages of MAS and its most widely used applications in plant breeding, providing examples from cereal crops. We also consider reasons why MAS has had only a small impact on plant breeding so far and suggest ways in which the potential of MAS can be realized. Finally, we discuss reasons why the greater adoption of MAS in the future is inevitable, although the extent of its use will depend on available resources, especially for orphan crops, and may be delayed in less-developed countries. Achieving a substantial impact on crop improvement by MAS represents the great challenge for agricultural scientists in the next few decades.

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Marker-assisted selection: an approach for precision plant breeding in the twenty-first century

The volume of publications on the development and to a lesser extent the application of molecular markers in plant breeding has increased dramatically during the last decade. However, most of the publications result from investments from donors with a strategic science quality or biotech advocacy mandate leading to insufficient emphasis on applied value in plant breeding. Converting promising publications into practical applications requires the resolution of many logistical and genetical constraints that are rarely addressed in journal publications. This results in a high proportion of published markers failing at one or more of the translation steps from research arena to application domain. The rate of success is likely to increase due to developments in gene-based marker development, more efficient quantitative trait locus (QTL) mapping procedures, and lower cost genotyping systems. However, some fundamental issues remain to be resolved, particularly regarding complex traits, before marker-assisted selection realizes its full potential in public sector breeding programs. These include the development of high throughput precision phenotyping systems for QTL mapping, improved understanding of genotype by environment interaction and epistasis, and development of publicly available computational tools tailored to the needs of molecular breeding programs.

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Marker-Assisted Selection in Plant Breeding: From Publications to Practice

Random amplified polymorphic DNA (RAPD) markers have been used for numerous applications in plant molecular genetics research despite having disadvantages of poor reproducibility and not generally being associated with gene regions. A novel method for generating plant DNA markers was developed based on the short conserved region flanking the ATG start codon in plant genes. This method uses single 18-mer primers in single primer polymerase chain reaction (PCR) and an annealing temperature of 50°C. PCR amplicons are resolved using standard agarose gel electrophoresis. This method was validated in rice using a genetically diverse set of genotypes and a backcross population. Reproducibility was evaluated by using duplicate samples and conducting PCR on different days. Start codon targeted (SCoT) markers were generally reproducible but exceptions indicated that primer length and annealing temperature are not the sole factors determining reproducibility. SCoT marker PCR amplification profiles indicated dominant marker like RAPD markers. We propose that this method could be used in conjunction with these markers for applications such as genetic analysis, bulked segregant analysis, and quantitative trait loci mapping, especially in laboratories with a preference for agarose gel electrophoresis.

Start Codon Targeted (SCoT) Polymorphism: A Simple, Novel DNA Marker Technique for Generating Gene-Targeted Markers in Plants

The importance of plant genetic diversity (PGD) is now being recognized as a specific area since exploding population with urbanization and decreasing cultivable lands are the critical factors contributing to food insecurity in developing world. Agricultural scientists realized that PGD can be captured and stored in the form of plant genetic resources (PGR) such as gene bank, DNA library, and so forth, in the biorepository which preserve genetic material for long period. However, conserved PGR must be utilized for crop improvement in order to meet future global challenges in relation to food and nutritional security. This paper comprehensively reviews four important areas; (i) the significance of plant genetic diversity (PGD) and PGR especially on agriculturally important crops (mostly field crops); (ii) risk associated with narrowing the genetic base of current commercial cultivars and climate change; (iii) analysis of existing PGD analytical methods in pregenomic and genomic era; and (iv) modern tools available for PGD analysis in postgenomic era. This discussion benefits the plant scientist community in order to use the new methods and technology for better and rapid assessment, for utilization of germplasm from gene banks to their applied breeding programs. With the advent of new biotechnological techniques, this process of genetic manipulation is now being accelerated and carried out with more precision (neglecting environmental effects) and fast-track manner than the classical breeding techniques. It is also to note that gene banks look into several issues in order to improve levels of germplasm distribution and its utilization, duplication of plant identity, and access to database, for prebreeding activities. Since plant breeding research and cultivar development are integral components of improving food production, therefore, availability of and access to diverse genetic sources will ensure that the global food production network becomes more sustainable. The pros and cons of the basic and advanced statistical tools available for measuring genetic diversity are briefly discussed and their source links (mostly) were provided to get easy access; thus, it improves the understanding of tools and its practical applicability to the researchers.

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Importance of Genetic Diversity Assessment in Crop Plants and Its Recent Advances: An Overview of Its Analytical Perspectives

Recognizing the enormous potential of DNA markers in plant breeding, many agricultural research centers and plant breeding institutes have adopted the capacity for marker development and marker-assisted selection (MAS). However, due to rapid developments in marker technology, statistical methodology for identifying quantitative trait loci (QTLs) and the jargon used by molecular biologists, the utility of DNA markers in plant breeding may not be clearly understood by non-molecular biologists. This review provides an introduction to DNA markers and the concept of polymorphism, linkage analysis and map construction, the principles of QTL analysis and how markers may be applied in breeding programs using MAS. This review has been specifically written for readers who have only a basic knowledge of molecular biology and/or plant genetics. Its format is therefore ideal for conventional plant breeders, physiologists, pathologists, other plant scientists and students.

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An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: The basic concepts

A collection of 114 Cicer accessions including 95 wild Cicer accessions from four different species (C. bijugum K. H. Rech., C. echinospermum P. H. Davis, C. pinnatifidum Jaub. & Sp. and C. reticulatum Ladiz.) was screened in glasshouse trials for resistance to ascochyta blight (caused by Ascochyta rabiei (Pass.) Lab.). Resistance was identified in accessions from all four wild Cicer species. There was variation for resistance within accessions of C. echinospermum, C. pinnatifidum and C. reticulatum, with only C. bijugum containing accessions in which all plants were completely resistant. Resistant accessions from C. echinospermum and C. reticulatum may offer accessible sources of resistance because fully fertile hybrids with cultivated chickpea can be readily obtained.

Prospecting for sources of resistance to ascochyta blight in wild Cicer species

The lentil accession ILL7537 was resistant in glasshouse bioassays to isolates of Ascochyta lentis Vassilievsky from a range of Australian pathotype groups, confirming its status as a highly resistant cultivated accession. Two dominant complementary genes were determined to condition the genetic mechanism and mode of inheritance of resistance in ILL7537. Accession ILL7537 was screened with molecular markers that were linked to, and flanking, the major resistance gene AbR
 1 from the accession ILL5588. The absence of all of the markers from the AbR
 1 linkage group indicated that the resistance mechanism in ILL7537 was potentially novel.

A novel source of resistance in lentil (Lens culinaris ssp. culinaris) to ascochyta blight caused by Ascochyta lentis

The ascochyta blight resistance of 14 chickpea cultivars, 29 imported chickpea lines and 38 local breeding lines to four Australian isolates of Ascochyta rabiei was investigated. Each isolate was tested individually on each chickpea genotype. There were no differences between the four isolates in their pathogenicity. However, there were large differences between chickpea genotypes in the expression of disease symptoms. All of the Australian chickpea cultivars tested were susceptible to A. rabiei. Seven imported lines and three local breeding lines were found to be resistant to A. rabiei. The eight isolates of A. rabiei tested in these studies were all the same mating type, i.e. MAT1-1.

J. B. Brouwer

Papers

An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: The basic concepts

Prospecting for sources of resistance to ascochyta blight in wild Cicer species

A novel source of resistance in lentil (Lens culinaris ssp. culinaris) to ascochyta blight caused by Ascochyta lentis

Screening chickpea germplasm for ascochyta blight resistance

Genome-specific sequence tagged microsatellite site (STMS) markers for diversity analysis and genotyping in Pisum species.