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Human Genome News Archive Edition

Human Genome News, July 1994; 6(2)

Plant Genome Research Begins a New Voyage of Discovery

Plant Genome II was held January 24-27, 1994 in San Diego. The conference, which attracted 553 participants from 22 countries, featured applications of genome mapping and analysis to solve existing problems and uncover answers to fundamental questions about plant genomes and their evolution.

According to Steven Oliver (University of Manchester, U.K.), the taxonomy of gene function will soon be essential in efficiently identifying new genes. This new age of research, which he compared to another voyage of Darwin's Beagle , will require a multidisciplinary approach with the collaboration of physiologists, geneticists, biochemists, and plant breeders. James Cook [U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), and Cooperative State Research Service] reinforced Oliver's message by pointing out that now is the time to bring plant breeders together with molecular biologists to search for agronomically important genes.

New Insights

The study of plant genome structure and organization can lead to interesting discoveries as highlighted by Richard Flavell (John Innes Institute, U.K.). Understanding the role of epigenetic regulation, gene order, and in situ homology sequence searching will ultimately advance the practical application of biotechnology. As a result of having to protect themselves from foreign DNA, plants have developed strategies--including gene silencing--to cope with transposon- selection pressures. The plant's ancient art of antisense technology may take advantage of gene location to determine epigenetic DNA methylation events, which in turn would regulate gene expression. Flavell pointed out that concerted evolution in the long term helps to maintain high levels of conservation across the chromosome in both sequence and gene order or synteny.

Progress in Rice

Nori Kurata (National Institute of Agrobiological Resources, Japan) described a genetic map of the rice genome with 1400 restriction fragment length polymorphism and random amplified polymorphic DNA markers. Over 7500 clones, of which 1800 are of known function, have been sequenced from callus tissue at different developmental stages. Kurata reported construction of a rice cDNA expression map that includes information on tissue specificity, distribution of isozyme genes, gene families, and such functionally related genes as ribosomal protein genes and the histone gene family.

Physical mapping in the Japanese program will focus on identifying economically important genes. High priority is being given to chromosomes 1, 4, 6, and 11. A number of important resistance genes are known to reside on 6. Mapping data from the Japanese program have been entered into two versions of an internal database called RiceBase, one version containing mostly cDNA information and the other physical map data.

International collaboration in rice mapping was encouraged by an informal workshop held in conjunction with the conference and cochaired by Susan McCouch (Cornell University) and Goufan Hong (Director, Chinese Rice Genome Program). Kurata indicated that the Japanese mapping data should be made public later this year and that 5' sequence data are available for several hundred markers. Over 4000 expressed sequence tag (EST) sequences for rice currently reside in the dbEST and GenBank databases. Pamela Ronald (University of California, Davis) announced the public availability of a variety of libraries, including bacterial artificial chromosomes and cosmids.

Physical Mapping

Physical mapping was highlighted again in the Arabidopsis workshop. Caroline Dean (John Innes Institute, U.K.) and Howard Goodman (Massachusetts General Hospital) reported that chromosomes 4 and 5 are nearing completion in the effort to integrate the two YAC and cosmid maps. A new YAC library developed by David Bouchez (Institut National de la Recherche Agronomique, France) should help in developing the integrated physical map. Michel Delseny (National Scientific Research Center, France) reported that the project on ESTs has sequenced several thousand Arabidopsis cDNAs, which have been deposited in the public database.

QTL Experimental Design

Quantitative trait (QTL) analysis was examined with attention to experimental design. In a discussion of soybean cyst-nematode resistance, Dave Webb (Pioneer Hi-Bred) reported that one soybean introduction was found to have more resistance than any other tested. With the identification of three resistance loci, the effect of population size in detecting traits was tested. Large sample populations (minimum 200) were found to be essential in finding and mapping traits.

The need for large sample populations was emphasized also by Karl Lark (University of Utah, Salt Lake City), who reported that specialized statistical methods and graphing are needed to identify many important loci. Specifically, Lark identified interacting traits in epistasis. One height trait measured individually had no effect but, when interacting with another plant height QTL, could account for 25% of the variation. The basis of Lark's technique is to use large populations and to conduct pairwise comparisons of loci in plants with extreme phenotypes. After the results are graphed, epistatic interactions are identified. According to Thomas Cheesbrough, (South Dakota State University, Brookings), this type of analysis will be essential in studying the genes of such metabolic pathways as oil production because each enzyme is highly dependent on gene products of the entire metabolic chain.

Mapping Technologies

Mapping technologies were featured in several talks and posters throughout the conference. Perry Cregan (USDA, ARS) and others reported continued success with simple sequence repeats, which are small sequence patterns that are repeated at variable lengths. The variable length of the repeats provides a tool needed by crop breeders and geneticists to identify varieties. Amplified fragment length polymorphism (AFLP), a related new technology, was reported by Pieter Vos and Marc Zabeau (KeyGene, Netherlands). AFLP will provide markers for map regions that other markers have not bridged successfully. The AFLP technique has the capacity to exploit multiple forms of variation within the genome. The new technology described by Vos is still a long way from direct application by plant breeders. [Susan McCarthy, USDA]

Plant Genome III will be held January 15-19, 1995, in San Diego. Information or program suggestions: Jerome Miksche or Stephen Heller, USDA/ARS; BARC-W, Bldg. 005, Room 331-C; Beltsville, MD 20705 (Fax: 301/504-6231, Internet: ).

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