Published in Probe Volume 6 (Final): July 1996
Andrew H. Paterson
Department of Soil and Crop Sciences
College of Agriculture and Life Sciences
Texas A&M University
College Station, Texas
An important component of the USDA Plant Genome Research Program has been comparative mapping, the alignment of the chromosomes of related crop species based on genetic mapping of common DNA markers. Comparative mapping affords many benefits to crop genome analysis, including greater utility of existing DNA probes, effectively increasing the density of genetic markers in many species simultaneously. In addition, comparative mapping offers new opportunities for investigating plant evolution.
Detailed comparative maps are being assembled for several plant families, such as the (1) Solanaceae, (2) Poaceae, Fabaceae (N. D. Young, pers. comm.), (3) Brassicaceae, and (4) Malvaceae, which include many of the crops that feed and clothe humankind. (5) In one particularly well-studied plant family, the Poaceae, extensive conservation of gene repertoire and gene order along the chromosomes has led to the suggestion that the cultivated cereals might be treated as essentially a single genetic system.
Comparative mapping of quantitative trait loci
Recent resuls suggest that comparative mapping may have even greater utility than previously envisioned, reaching directly into the molecular dissection of complex traits that are the basis of agricultural productivity. (6) A collaborative research project involving Andrew Paterson, James Stansel, and James Irvine at Texas A&M University, together with USDA-ARS researchers Keith Schertz (College Station, Texas), Shannon Pinson (Beaumont, Texas), and John Doebley at the University of Minnesota was formed. The results of this collaborative effort revealed that quantitative trait loci (QTL) associated with domestication of sorghum, rice, and maize frequently fall at corresponding genetic map locations.
Specifically, close correspondence appears to occur among QTL affecting traits such as seed size; shattering of the inflorescence; and short-day flowering of sorghum, sugarcane, maize, and rice. This correspondence is mirrored by (7) a companion study in which 185 genes and QTL reported by many independent investigators to affect height and flowering of maize and other species were collated with each other and with a new map of the genes associated with height and flowering in sorghum. (8) An independent study of a smaller set of QTL in maize and sorghum reinforces this theme of correspondence. While correspondence of QTL in different species of the plant genera (9) Lycopersicon and (10) Vigna had previously been reported, such correspondence spans relatively short periods of genetic divergence, and in fact the relative promiscuity of plant species makes it difficult to preclude the possibility of recent gene flow.
Correspondence between QTL has been suggested, not only between different taxa, but also between duplicated chromosome segments within a particular species, indicating that chromosome duplication may contribute to polygenic inheritance. Specifically, (6) pairs of loci affecting shattering of the maize inflorescence, (7) maize height and flowering, and sorghum height, fall on chromosome segments that appear to correspond, based on genetic mapping of duplicated DNA markers. While only a subset of QTL appear to be associated with chromosome duplication, it is offered as one of many mechanisms by which quantitative traits might evolve.
Implications of corresponding QTL for life sciences research
The suggestion that mutations in corresponding genes may account for phenotypic variation in species such as sorghum, maize, and rice, reproductively isolated for an estimated 65 million years, has widespread implications. Perhaps first and foremost, QTL analysis in one taxon may be predictive of results in other taxa. Such predictive value would afford broader utility of QTL mapping results than was previously envisioned, enabling research on easy systems to be extrapolated to more difficult systems, and minimizing redundancy.
For example, recent results describe a set of QTL largely responsible for rhizomatousness of johnsongrass, one of the worlds most important agricultural weeds (11). Such research is difficult to conduct, as rhizomes grow underground, and are very laborious to measure accurately. Rhizomatous forms of both sgarcane and rice harbor genes of potential value to agriculture but cannot be grown in the United States for fear of introducing new weed species to these crops.
Comparative mapping may afford the means to breed rhizomatousness out of these weedy relatives, affording safe access to valuable genes held in these exotic gene pools. On the flip side, aggressive rhizomes contribute to productivity of many forage and turf grasses, essential to the U.S. agroecosystem both for animal fodder and in erosion control. Research in progress seeks to determine whether growth enhancement of several forage and turf species may derive from use of DNA markers closely linked to rhizomatousness in sorghum.
Correspondence of QTL across diverse taxa also provides a strong empirical foundation in support of model systems research on complex phenotypes. For example, the ease of genetic analysis possible in rodents and agricultural mammals has permitted mapping of genes associated with diabetes, hypertension, obesity, alcohol/drug addiction, and other medically important phenotypes. The inherent difficulties associated with mapping complex traits in humans are partly ameliorated by the possibility of cloning QTL in mouse (for example) that account for phenotypic variation in humans. In a like manner, crop plants that grow particular plant organs of extraordinary size, such as the enlarged root of turnip, inflorescence (curd) of cauliflower, or fruit of tomato, might be used to identify developmentally important genes in which genetic variants impair survival or reproduction in other species.
Maximizing the value of future genome mapping results
Many investigators are enhancing the value of their results to the scientific community by making an extra effort to facilitate comparative analysis. There is growing awareness that once a gene has been mapped by any of a wide range of DNA-based techniques now available, it is important that the diagnostic marker(s) be linked to a comprehensive genetic map (or previously mapped DNA clones) that affords integration with related taxa. Genetic maps based on conserved DNA sequences are becoming increasingly prevalent, mapped DNA markers are widely available, and few, if any, genetic mapping labs can resist the opportunity to "put one more marker on the map," especially one linked to an important phenotype. By using the fortuitous tools that nature offers us for comparative analysis of plant chromosomes, an ever larger and more complex body of genetic data on major crops can be integrated into a more coherent and therefore more useful information base, valuable for improving the long-term productivity and sustainability of U.S. agriculture.
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