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QTLmappingin rice
R i c e (Oryza sativa) is grown on more than 148 million hectares 1 and feeds 50% of the world population. Increasing world rice production could make a major contribution to meeting the dietary demands of a growing global population. Although rice is grown in a wide range of environments, including dry uplands, the most productive rice-growing environments are irrigated lowlands. Environmental and health concerns about the overuse of pesticides, and the inefficiencies of irrigation and fertilizer practices in rice paddies have raised serious questions about the long-term sustainability of modem production systems. How to ensure a reliable and wholesome food supply on the planet is a topic of much discussion. This review focuses on quantitative trait loci (QTLs) analyses in rice, a strategy that has the potential to identify and manipulate genes involved in the complex characters that condition crop performance. The ideas described below are part of a broad-based scheme to apply biotechnology to the problem of ensuring a stable, world food supply. Analytical approaches The first attempts to study individual determinants of quantitatively inherited characters in plants date back to Sax2. Thoday3 pointed out that the study of quantitative variation suffered from a lack of precision because of the lack of complete genetic maps. This limitation was overcome with the advent of DNA markers, detected as restriction fragment length polymorphisms (RFLPs) 4. The power of QTL mapping using a saturated RFLP map was demonstrated by

SUSAN R. McCOUCHAND REBECCAW. DOERGE

In the past lO years, interest in applying the tools of moleculargenetics to the problem of increasing world rice production has resulted in the generation of two highly saturate~ molecular linkage maps of rice, and the Ioculization of numerous genes and quantitative trait loci (QTLs). Primary studies have idenHfledQTLs associated with disease resistance, abiotic stress tolerance and yteld potential of rice in a range of ecosystems. The ability to identify, manipulate and potentta~y clone individual genes involved in quantitaHvely inherited characters, combined with the demonstrated conservaHon of numerous linkage blocks among members of the grass family, emphasizes the contribution of map.based genetlc ana{Fses both to applied and to basic crop research.
Paterson et al. 5 Since then, RFLPs and subsequent PCR-based molecular markers have revolutionized the field of genetic mapping and gene identification both in animals and in plants. The US Department of Agriculture and National Agricultural Library provides access to a wide variety of plant genome databases through a World Wide Web server (located at http://probe.nalusda.gov:8000). The basis of all QTL detection, regardless of the crop to which it is applied, is the identification of association between genetically determined phenotypes and specific genetic markers. Any measurable phenotype is, in principle, amenable to QTL analysis. Typical singlemarker-analysis methods do not use information from the order of markers on a map. They divide the population into classes based on the genotype at each marker locus, and declare a QTL if there is a significant difference in the mean phenotypic score for each of the groups. Single-marker methods tend to be functionally related to each other (i.e. Student's t-test, analysis of variance and regression). Since the advent of complete DNA-based genetic maps, parametric statistical procedures have been developed that use the estimated position of DNA markers on a genetic map to calculate QTL location(s) and effect(s) in experimental populations 6-8. Interval mapping, as made popular by Lander and Botstein 6, has had the largest impact on the identification of single QTLs in backcross and Fx experimental populations through the publicly available computer package MAPMAKER/QTL5,9-n. However, the approach remains limited in its application by not addressing recombinant inbred lines (Box 1; Fig. 1) or other advanced population designs, and by imposing a set of assumptions that are often difficult to meet in practical terms. Recent advances using nonparamettic statistics to map QTLs 12 and to calculate empirical critical (threshold) values for declaring significant QTLs 13 offer a way around some of these problems. New, publicly available software packages will soon provide alternative approaches to QTL analysis (i,e. 'QTL Cartographer' by B.S. Weir, pers. commun, and 'QGene' by J.C. Nelson, pets. commun.). For plant breeding applications, QTL analysis provides a way of selectively manipulating individual

Box 1. Experimental populations of rice

Because rice is a diploid self-pollinating annual species, experimental population structures can be manipulated with relative ease. Early RFLP mapping experiments were conducted on F2 (Refs I5-17) or backctms (BC) populations 18, and Q ~ studies on F2 and F4 families have been repotted33. Doubled haploid lines (DHL)17, and recombinant inbred lines (Rll,$)lg, 20 are stable permanent populations that are genotypically true-breeding or homozygous and well suited to QTL analysis. DHLs are produced through a spontaneous doubling of the chromosome complement of haploid microspores during in vitro culture. RRa take longer to produce, as they are the result of 8-12 generations of inbreeding (Fig. 1). The advantage of DIEs is that homoz,/gosity is achieved in a single step, and there is less chance of inadvertent selection resulting in skewed allele distributions, than in PdIz. However, not all rice genotypes are equally amenable to in v/tro culture, and hence RILs might be the only realistic way to achieve the desired population structure for some cttx~ combinations. Though no information on dominant gene expression can be obtained from these inbred populations, DHLs or RILs can be backcrossed to the respective parents if such information is desired21. Each individual DHL or R1L of rice can produce hundreds of homozygous seeds in a single generation so that unchanging genotypes can be evaluated repeatedly over years and locations, and for multiple waits (phenotypes). The ability to replicate experiments using fixed genotypes offers an elegant way of discriminating between the role of the environment and of genetic factors in the expression of a phenotype.

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genetic components of a complex trait. Along with estimates about the magnitude of the phenotypic effect of different QYIz, the ability to distinguish between variation caused by the environment [genotype-by-environment interaction (GXE)], by the interaction of genes at different loci (epistasis and transgressive variation), or by alleles at the same locus (overdominance) offers plant breeders a way of predicting whether a QTL is likely to be useful in different genetic backgrounds (varieties) and/or diverse environments t4.

Female parent (C039)

~ F1

Male parent (Moroberekan)

1,1111 lll,l,ll,l1111 llll I 1111

Single-seed descent

Rice as a model organism Rice has one of the best devel(each plantcontributesa singleoffspringto the nextgeneration) oped systems for molecular genetic studies in monocots. It is a diploid organism with 12 gametic chromosomes, has the smallest genome of any monocot known (450Mb) 22, has a large collection of cultivated Fa Recombinant inbred lines varieties and wild species (greater than 120000 accessions worldwide), Flc,tr~ 1. The development of a population of recombinant inbred lines (RILs)via can be regenerated from protosingle-seed descent. Rice is especiallyamenable to this population structure because of its plasts, and has a relatively high natural inbreeding habit, relativelyshort generation time (90-140d) and high seed degree of transformation efficiency production capability. relative to other cereal species57, 58 (reviewed in Kothari et al.23). Two, well-saturated molecular linkage maps are avail- The traits we focus on are disease resistance 20, drought ablel8, 24 that together provide rice researchers with a resistance31,32, flowering time21,33 (M. Maheswaran stock of 2000 publicly available mapped molecular et al., pets. commun.) and yield21. These studies were markets, or one marker approximately every 0.9 cM. The based on populations of recombinant inbred lines (Rlks) average DNA:cM ratio is estimated to be approximately and a common RFLP map of rice TM. They were the 250-300kbcM -1, a figure very close to the value for result of international collaboration among researchers Arabidopsis tbaliana. Though the generation time in who specialized in the evaluation of a particular trait rice (90-140d) is significantly longer than in Arabidopsis, or phenotype. it has been proposed as a model plant in the world of monocots, parallel to Arabidopsis in dicots, with the Resistance to rice blast disease The first report of marker-assisted quantitative trait additional emphasis of its value as a major food crop. analysis in rice was for rice blast resistance 2. Rice blast, Rice has also been important in comparative mapcaused by the fungus Pyricularia oryzae, is one of the ping in Gramineae species, such as wheat, barley, rye, oat and maize 25-29. These studies show that large segmost devastating diseases of rice in the world. Though high and stable levels of blast resistance are observed ments of Gramineae chromosomes have been inherited intact from a common ancestor. The identification of in some traditional rice cultivars, the complexity of reaction types and the quantitative nature of the recorresponding chromosome segments in modem crop sistance has made it difficult to transfer into modem varieties suggests that gene mapping in one species could provide clues as to the possible location of varieties. Many modem, high-yielding varieties contain a few major genes that confer complete resistance to orthologous genes in related species25,3. Thus, locating specific races of the pathogen, but resistance is fregenes of agronomic importance in rice can be expected quently overcome by the pathogen 34,35. Combining to have a positive impact on several of the most imporgenes for complete and partial (rate-reducing) resisttant cereal crops in the world. Rice can, likewise, benefit ance has long been advanced as a remedy but it has from research in other crops, especially from the long been nearly impossible to achieve using conventional history of genetic research in wheat and maize. As a whole, the grass family is emerging as a model system selection procedures36,37. The study by Wang et aL 2 outlined both a general for comparative and evolutionary studies in plants. approach to dissecting the genetics of complex disease resistance using an RIL population, and provided a speQTL mapping in rice cific set of markers that could be used to universally In this review, we describe four QTL studies in rice, identify and recombine blast-resistance genes. Many of explain how the results are being applied in agriculture the QTLs associated with resistance in this study were and how they help link the genetics of related species.

111 lllll111

II

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the blast study described above z. Moroberekan, the blast resistant (a) (b) (c) (d) (e) (f) (g) (h) (i) (j) parent, is a drought tolerant, RZ597 upland variety with a long thick root system that allows it to 5cM I RG20 escape drought stress by accessing water in the deep soil layers 41. CO39 is a lowland cultivar with a less well developed root system. RG333 Champoux et al.31 found that RZ562 all of the alleles that exerted a CD0192 positive effect toward stronger RZ323 thicker roots were derived from ii: :i the Moroberekan parent. Over RZ617 RGI034 50% of the putative QTLs associRG978 ated with root characters in the greenhouse study mapped to the RG28 ... same chromosomal locations as QTLs associated with drought resistance in field experiments. RG1 Shoot, rather than root, characCD0464 ters are associated with drought RZ66 / resistance in lowland indica variCD0595 eties, such as CO39. In lowland ecosystems, drought is generally RG136 C] intermittent and tends to be less RZ649 severe than in upland environCD099 ments. Shoot-based drought tolerance can be evaluated as osmotic adjustment (OA) ability and tolerance to desiccation (measured l~Gtm 2. Rice quantitativetrait loci (QTLs). Chromosome 8 of rice is shown as a vertical as lethal osmotic potential), both open bar with mapped markers indicated to the left (Ref. 18 and unpublished). (a) The size and location of a homeologous segment of the wheat chromosome 7A of which allow a plant to survive based on common cDNA markers mapped in wheat and rice27. (b) Leaf rolling short-term drought stress. In a study by Lilley et aLDX, OA was (drought avoidance evaluated in the field)31. (c) Root thickness (evaluated in the greenhouse) 31. (d) Osmotic adjustment (evaluated in the greenhouse)32. evaluated on a subset of the same (e) Lesion number (partial blast resistance)20. (0 Pi-zh (complete blast resistance)39. population of RILs used in the (g) Days to flowering (10 h) (M. Maheswaran, pets. commun.). (h) Days to flowering blast and the root studies de(14 h) (M. Maheswaran, pets. commun.). (i) Days to heading33. (j) Days to heading21. scribed above (Box 2). A single QTLs (b-e,g,h), indicatedwith an asterisk, were based on a common QTL explaining 36% of the phenoRILpopulation and RFLPdata set. QTLs (f,i,j)were mapped in different typic variation for osmotic adjustpopulations but using a common set of mapped RFLPmarkers18. ment was identified on chromosome 8 (Fig. 2). The location of stable over three environments tested. Three of the the putative OA QTL in rice coincided with a QTL marker loci associated with partial resistance in this described by Champoux et al.31 that was associated study had previously been found to be linked to genes both with root parameters (measured in the greenconferring complete resistance in other material38,39 house) and with drought resistance of RILs in the field (Fig. 2). The RILs provide the basis for additional cross- (Fig. 2). The marker alleles associated positively with ing, free mapping, and ultimately cloning aimed at clari- OA in the study by Lilley et al.32 came from the CO39 fying the relationship between polygenes and quali- parent, while those associated with larger, thicker roots tative mutants, and deepening our understanding of came from the Moroberekan parent. These results QTL performance in different genetic backgrounds, in reveal a correlation of traits related to specific 'stratresponse to different races of the pathogen and in egies' of plant adaptation to stressful environments and different environments. suggest that blocks of genes involved in the response of a plant to water stress might have evolved together in Root characters associated with drought avoidance this region of the genome. A saturated genetic map Drought stress aggravates the severity of rice allows us to clarify the linkage relationships between blast 4, and together these two factors impose major shoot and root related QTLs in this region and to deterlimitations on rice production, especially in the up- mine whether useful recombinants can be obtained that land and rain-fed lowland ecosystems that are home combine the positive aspects of these two different to many subsistence rice farmers of the world. drought resistance strategies. Champoux et al.D1 mapped QTLs associated with five It is noteworthy that a single locus putatively associparameters of rice root morphology. They used the ated with OA was previously identified on chromosome same RIL population and the same RFLP data set as in 7A of wheat42 and that the region of rice chromosome 8
k 'k '/r ~r "k "/r

l ll I

DH

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containing the OA QTL32 is homeologous with a segment of wheat chromosome 7A (Ref. 27) (Fig. 2). Homeology 43 is inferred by the fact that the same cDNAs have been mapped in the same order in the two regions of rice and wheat chromosomes, and that rice and wheat are both derived from a common ancestor. With cDNA markers that map both to rice and to wheat from this conserved region, it should be possible to confirm whether the genes controlling OA in these two grass species both map to this region.
Maturity a n d photosensitivity Another basic feature of plant adaptation to the environment involves photosensitivity. Genes that respond to changes in photoperiod regulate the shift from the vegetative to the reproductive phase of plant development. Rice breeders have developed varieties with shortened growth duration by selectively eliminating the photosensitive alleles that prolong the vegetative stage under long (more than 11 h) daylengths. Under modem, high-production systems, this allows farmers to increase the number of generations and, hence, the number of crops, per year. However, photoperiod sensitivity is beneficial in traditional farming systems where farmers do not have control over water supplies, because it ensures that reproduction and grain filling occur simultaneously with the monsoon 45. Comparative mapping studies provide some of the first data suggesting that some of the genes associated with days to flowering can be found in homeologous (conserved) segments of rice, wheat, barley, maize and sorghum genomes and, therefore, that these Gramineae species have inherited this trait from a common ancestor 26,3A6. In rice, QTLs related to flowering and maturity aaits have been reported 21,33. In addition, days to flowering was evaluated on the CO39 Moroberekan RIL population, described above, in relation to the blast and drought studies (M. Maheswaran et al., pets. commun.). Two of the QTLs associated with days to flowering in this population were in the same chromosomal regions as days to maturity QTLs identified in different populations by Li et al.33 and Xiao et al. zl (Fig. 2), suggesting that some of the same loci are active in a range of different genotypes of rice. When the QTLs associated with days to flowering were aligned with those associated with blast resistance in the CO39 Moroberekan RIL population, it became apparent that many of the same chromosomal regions were significantly associated with both traits (Fig. 2). Such a correlation was not observed for QTLs associated with drought and blast resistance. Specifically, blast resistance and late flowering were almost always associated with the Moroberekan marker allele. This observation helps to explain the difficulty, long known to rice breeders, of combining earliness with high levels of blast resistance, especially when the resistance is coming from a traditional cultivar. If the reason for this observation is that the genes for blast resistance are linked with genes for delayed flowering, then marker-based selection might help break the linkage. It is possible that a single locus exerts a pleiotropic effect on both traits, but examples of early blastresistant varieties provide evidence that this is not always the case.

Yield potential Hybrid rice technology has contributed to increasing yields in China by approximately 20% over the past 25 years47. Understanding the genetic basis of heterosis, or hybrid vigor, is of great interest because producing hybrid rice seed is a labor-intensive operation and more efficient systems for obtaining high yields are being sought. The first QTL analysis of yield components associated with heterosis in rice was reported recendy by Xiao et al. 21 Based on a RIL population (9024/LH422) and derived test cross lines, this study identified QTLs associated with nine components of yield in addition to plant height, days to heading and days to maturity. Dominance complementation (interaction of alleles at different loci) rather than overdominance (interaction of alleles at the same locus) appeared to be the major genetic basis of heterosis in this cross combination. These results are similar to those recently reported by Stuber (this issue) where evidence for dominance and pseudo-overdominance (rather than true over-dominance) was reported in maize. The finding suggests the possibility of fixing specific QTLs for yield in rice and raises the question of how markerassisted selection could be most effectively combined with hybrid-rice-breeding efforts to maximize yield potential. The development of nearly isogenic lines containing individual QTLs for yield in an array of agronomically useful backgrounds will help clarify the type of gene action involved and will allow us to evaluate specific QTLs, or combinations of QTLs, both in inbred and in hybrid combinations. One of the most powerful applications of QTL mapping to plant improvement is the ability to dissect the allelic composition of individual segregants that outperform the two parents (Fig. 3). Such transgressive variation results when alleles at different loci are recombined in the progeny. The phenomenon is frequently observed in wide crosses in rice. By identifying QTLs associated with yield potential via linkage to molecular markers and knowing the parental origin of those alleles,

Box 2. Missing data and sample size

Quality and quantity of genetic marker and trait data is an important issue in the estimation of QTL location. Quantitative traits have to be measured as precisely as possible, and limited amounts of missing data can be tolerated 44. The power to resolve the location of QTL (i.e. estimate QTL location) is limited first by sample size and then by genetic marker coverage of the genome. Often, the number of individuals in a sample might appear to be large, but missing data or skewed allele frequencies in the population cause the effective sample size to diminish, thus sacrificing statistical power. In the study by Lilley et al.32, a small population of 52 RILs was used to identify the OA locus on chromosome 8 (Fig. 2). It was necessary to sacrifice population size in favor of data quality, and this trade-off meant that only QTLs with a relatively large effect could be detected. Nonetheless, enough genetic variation was sampled to detect associations between QTL and genetic markers. Marker assisted selection strategies aimed at introgressing desired genes into breeding lines or developing sets of near isogenic lines offer a direct way of testing the validity of these primary studies.

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P1 P2

"6

Yield component
Fmtr~ 3. The phenomenon of transgressive variation, which is common in interspecific and inter-subspecific crosses of rice. The transgressive segregants are the plants with the phenotype outside the range of the two parents (P1 and P2).

transgressive variation can be explained and manipulated 1~,a8. The opportunity to identify and concentrate positive alleles for yield is currently being explored in inter-subspecific and interspecific crosses by our group at Comell in collaboration with an international network of scientists in National Agricultural Research Systems in China, Korea, Indonesia and Brazil, and in International Crop Improvement Centers in Colombia (Centro Intemacional para Agricultura Tropical, CIAT) and in The Philippines (International Rice Research Institute, IRRI).

Futuredirections
The possibility of combining inheritance genetics (based on crossing and segregation analysis) and association genetics (based on documented family relationships) offers a powerful new way of utilizing QTL analysis to directly benefit the field of plant improvemerit. In a crop like rice, reliance on the pedigree method of breeding means that detailed records of genealogy are available for many hundreds of inbred varieties developed over the past 30-50years. Combined with the availability of both RFLP and, more recently, microsatellite marker maps, it is possible to trace the flow of genes (or marker alleles) through a pedigree. Workers at Comell are developing a new generation of graphically based software designed to link the primary molecular marker data acquired in the laboratory with historical pedigree and performance information (E. Paul, pers. commun.). This expands on the model developed by Young and Tanksley 49 and will allow plant breeders to determine which specific regions of chromosomes have been transferred over the course of a breeding program, and to link information about chromosomal regions and performance. Rice offers an excellent model syst,=m for developing this concept. Most rice breeding is done in public institutions throughout the world; the International Rice Germplasm Collection and the International Rice Testing Program at IRRI help to ensure continued public access to rice germplasm. Rice seed can be purified and maintained for long periods of time (more than 50years), and there is continued international interest

in the problem of improving the stability and sustainability of rice production systems. The use of molecular markers to isolate putative QTLs based on their map position is an area of great interest. Primary QTL mapping studies, such as those presented in this review, provide only the first step in understanding the genetics that underlie the expression of quantitative traits. Additional fine mapping and ultimately cloning is required to understand what the genes actually do. Strategies that have been successful in map-based cloning of qualitative mutants are being applied to QTL cloning as well. These include the use of transposable element systemsSO-5z, chromosome walking 53,54, chromosome landing 55, and combinations of structural and positional analysis 56. Cloning of plant genes will not only provide new opportunities for transformation but it will also provide the basis for comparing the structure and function of evolutionarily related genes within and between diverse plant families. Understanding the variety of mutations that alter the functional specificity of genes can be expected to inspire new approaches to improving the performance of agricukural species, with emphasis on designing production systems that allow sustainable use of natural resources. Technically, Thoday's vision about the power of saturated genetic maps to shed light on some of the mysteries of quantitative genetic variation appears to have been realized. The emergence of new, high resolution molecular marker technologies is likely to facilitate large-scale QTL analyses in the future. The dynamic incorporation of biotechnology into rice improvement, coupled with innovative international collaboration, offers exciting new possibilities for helping to ensure the stability of world food production.

Acknowledgements
We gratefully acknowledge the Rockefeller Foundatiofi for financial support that made possible many of the QTL studies reported in this paper. We also thank A. Paterson, C. Nelson, R. Nelson and S. Kowalski for valuable critical reviews, and C. Morehouse for formatting the manuscript.

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48 Rick, C.M. and Smith, P.G. (1953) Am. Nat. 88, 359-373 49 Young, N.D. and Tanksley, S.D. (1989) Theor. Appl. Genet. 77, 95-101 50 Jones, D.A. et al. (1994) Science 266, 789-793 51 Whitham, S. et al. (1994) Cell78, 1101-1115 52 Johal, G.S. and Briggs, S.P. (1992) Science 258, 985 53 Aronclel,V. etal. (1992)Science258, 1353-1355 54 Leung,J. et al. (1994) Science264, 1448-1452 55 Tanksley, S.D., Ganal, M.W. and Martin, G.B. (1995) Trends Genet. 11, 63-68 56 Song, W-Y. et al. Science (in press)

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S.R. McCOUCH AND R . W . DOERGE ARE IN THE DEPARTMENT OF PLANT ~REEDING AND BtOMErRV, CORNELL UNIVERSITY, ITHACA, N ~ 14853, US~" R.W. DOERGE IS CURRENTLYIN THE DEPARTMENT OF STATISTICSAND DEPARTMENT OF AGRONOMY, PUROUEUNn'ERSr~, WESTLAFAYEr~ I N 47907, US#-

Meeting reports i n Tremts in G e n e t i c s

In 1996, T/G will feature regular meeting reports. These will provide highlights of meetings of interest to geneticists and developmental biologists. We will generally cover smaller meetings, although the topics should be of widespread interest. The reports will be around 500 words, and shou!d focus on the surprises, the excitement and the controversies at the meeting rather than attempt to summarize the whole meeting. If you know about a meeting that we should cover, or if you would like to write a report for us, then please get in touch.
Mark Patterson Trends in Genetics,

Elsevier Trends Journals, 68 Hills Road, Cambridge, UK CB2 1LA. Tel: 44 1223 315961, fax: 44 1223 464430, email: TIG@elsevier.co.uk TIG DECEMBER1995 VOL. 11 NO. 12

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