Progress 10/01/07 to 09/30/08

Outputs
OUTPUTS: IDENTIFY GENES UNDERLYING TRAITS OF INTEREST AND TRACE THEIR EVOLUTIONARY HISTORY: 1)We produced a high-resolution map targeting a cluster of yield-related QTLs on the long arm of rice chormosome 9 using a series of NILs derived from backcrossing a Korean japonica cultivar and wild rice O. rufipogon. 2)We identified a mutation in the Rc gene that changes the color of the pericarp from red to white and traced the origin of the mutation. The evolutionary history of this gene implied early contact among Asian people who cultivated the indica and japonica subspecies. 3)We summarized what is known about the evolutionary history of recently cloned domestication genes in O. sativa and inferred that multiple domestications coupled with limited introgression can explain how key domestication alleles were transferred between divergent rice gene pools. 4)We cloned a rice genic male-sterility gene, ms-h, and demonstrated that it has functional roles in both male sterility and the development of a chalky endosperm. Expression analysis and complementation tests confirmed the gene function. Our results suggest that UGPase1 plays a key role in pollen development as well as seed carbohydrate metabolism. DEVELOP STRATEGIES TO UTILIZE GENETIC DIVERSITY FROM WILD AND EXOTIC SOURCES: 1)We summarized published data and proposed a phylogenetic approach to determine which interspecific combinations of parents are most likely to give rise to superior offspring and be useful in a breeding program. CHARACTERIZE THE BACTERIAL BLIGHT PATHOSYSTEM INVOLVING RECESSIVE RESISTANCE: 1)We study the inheritance of xa5 resistance to bacterial blight and explore the relationship between homozygous and heterozygous susceptible lines in promoting disease based on measures of symptom expression and bacterial movement in rice leaves. In a review on this pathosystem, we discuss recent accomplishments in the understanding of recessively inherited R genes and suggest a new model for the function of recessive resistance in plant-bacterial interactions. DEVELOP CONTROLLED VOCABULARIES AND PUBLIC INFORMATION RESOURCES: 1)Working with the Plant Ontology Consortium, we developed simple yet robust and extensible controlled vocabularies that accurately reflect the biology of plant structures and developmental stages. 2)We described a unified gene nomenclature system for rice that outlines standard procedures for describing genes based on DNA, RNA and protein sequence, biochemical function and phenotypic variation. 3)New features, modules, search tools and interfaces were developed for the Gramene database(www.gramene.org) and large amounts of new data were added. OUTREACH AND EDUCATION: 1)We developed a program for students and postdocs to expose them to research and extension activities at the International Rice Research Center in the Philippines. PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
1)At total of seven traits were identified in a single QTL region on rice chromosome 9 in an interspecific backcross population. Higher yielding plants containing an O. rufipogon introgression were also taller and later than controls, suggesting that a single, pleiotropic gene may act as a major regulator of plant development in this region. 2)We demonstrated that the rc mutation leading to white pericarp originated in the japonica subspecies and is shared by 97.9% of rice varieties today. Haplotype analysis showed that approximately 1 Mb of japonica DNA hitchhiked with the rc allele into most indica varieties. 3)Some domestication alleles are found only within one or two subpopulations, while others are common to all cultivated rice varieties. This data is consistent with multiple domestications coupled with significant amounts of gene flow and introgression, particularly from japonica to indica. 4)Cloning of a rice genic male-sterility gene, ms-h, revealed a single nucleotide substitution at the 3'-splice junction of the 14th intron of the UDP-glucose pyrophosphorylase 1 gene. Overexpression of UGPase1 in ms-h mutant plants restored male fertility and the transformants produced T1 seeds that segregated into normal and chalky endosperms. 5)We show that xa5 is inherited in a completely recessive manner and that both resistant indica and japonica plants delay bacterial movement down the leaf. Resistant indica NILs sustain high levels of bacterial populations but suppress symptom expression while resistant japonica NILs lower the level of bacterial populations compared to susceptible lines. 6)We review the fact that these bacterial recessive resistance gene products do not conform to the five commonly described classes of R proteins and suggest that the recessive alleles may be viewed as mutations in dominant susceptibility alleles and may function in a gene-for-gene manner. 7)The current version of the plant ontology integrates over 3500 gene annotations describing the anatomy, morphology and growth stages of Arabidopsis, maize and rice. 8)The gene nomenclature system for rice provides greater clarity in describing the phenotypic consequences of a particular allele in a given genetic background and the biochemical features of a specific gene or gene family. 9)New data in the Gramene database included rice pathways for functional annotation of rice genes; genetic diversity data from rice, maize and wheat; large-scale genome comparisons among Oryza sativa and its wild relatives; and the creation of orthologous gene sets and phylogenetic trees among rice, Arabidopsis thaliana, maize and poplar. We have also improved the web interface and enhanced the search functions. 10)The short-term training course at IRRI exposes an international and interdisciplinary group of students, postdocs and young professionals to the need for improved agricultural productivity and allows them to briefly experience the rewards of working on difficult but important issues in the international arena.

Publications

• Woo, M.-O., Ham, T.-H., Ji, H.-S., Choi, M.-S., Jiang, W., Chu, S.-H., Piao, R., Chin, J.-H., Kim, J.-A., Park, B.S., Seo, H.S., Jwa, N.-S., McCouch, S. and Koh, H.-J. (2008) Inactivation of the UGPase1 gene causes genic male sterility and endosperm chalkiness in rice (Oryza sativa L.). The Plant Journal 54, 190-204.
• Xie, X., Jin, F., Song, M.-H., Suh, J.-P., Hwang, H.-G., Kim, Y.-G., McCouch, S. and Ahn, S.-N. (2008) Fine mapping of a yield-enhancing QTL cluster associated with transgressive variation in an Oryza sativa x O. rufipogon cross. TAG Theoretical and Applied Genetics 116, 613-622.
• Iyer-Pascuzzi, A.S. and McCouch, S.R. (2007) Recessive Resistance Genes and the Oryza sativa-Xanthomonas oryzae pv. oryzae Pathosystem. Molecular Plant-Microbe Interactions 20, 731-739.
• Avraham, S., Tung, C.-W., Ilic, K., Jaiswal, P., Kellogg, E.A., McCouch, S., Pujar, A., Reiser, L., Rhee, S.Y., Sachs, M.M., Schaeffer, M., Stein, L., Stevens, P., Vincent, L., Zapata, F. and Ware, D. (2008) The Plant Ontology Database: A Community Resource for Plant Structure and Developmental Stages, Controlled Vocabulary and Annotations. Nucleic Acids Research 36, D449-D454.
• Iyer-Pascuzzi, A.S., Jiang, H., Huang, J. and McCouch, S. (2008) Genetic and functionals characterization of the rice bacterial blight disease resistance gene xa5. Phytopathology 98, 289-295.
• Kovach, M.J. and McCouch, S.R. (2008) Leveraging natural diversity: back through the bottleneck. Current Opinion in Plant Biology 11, 193-200.
• Kovach, M.J., Sweeney, M.T. and McCouch, S.R. (2007) New insights into the history of rice domestication. Trends in Genetics 23, 578-587.
• Liang, C., Jaiswal, P., Hebbard, C., Avraham, S., Buckler, E.S., Casstevens, T., Hurwitz, B., McCouch, S., Ni, J., Pujar, A., Ravenscroft, D., Ren, L., Spooner, W., Tecle, I., Thomason, J., Tung, C.-w., Wei, X., Yap, I., Youens-Clark, K., Ware, D. and Stein, L. (2008) Gramene: a growing plant comparative genomics resource. Nucleic Acids Research 36, D947-953.
• McCouch, S. and CGSNL (Committee on Gene Symbolization, N.a.L., Rice Genetics Cooperative) (2008) Gene Nomenclature System for Rice. Rice J 1, DOI10.1007/s12284-12008-19004-12289.
• Phillips, R., Magor, N., Shires, D., Leung, H., McCouch, S. and Macintosh, D. (2008) Student Opportunity: Short-Term Exposure to International Agriculture. Rice J 1, DOI10.1007/s12284-12008-19003-12289.
• Sweeney, M., Thomson, M., Cho, Y.-G., Park, Y.-J., Williamson, S., Bustamante, C. and McCouch, S. (2007) Global dissemination of a single mutation conferring white pericarp in rice. PLoS Genetics 3(8): e133. doi: 10.1371/journal.pgen.0030133.

Progress 10/01/06 to 09/30/07

Outputs
We examined genome wide patterns of single nucleotide polymorphism (SNP) at 111 randomly chosen gene fragments in domesticated rice and its wild ancestor and inferred the evolutionary dynamics that led to the origins of rice (Caicedo et al., 2007). We identified regions of high divergence in the sequenced indica and japonica genomes and sequenced genes from these regions in 25 O. sativa cultivars and 35 wild accessions and demonstrated that two, highly divergent haplotypes were consistently identified (Tang et al., 2007). We hypothesized that genes in these regions confer adaptation to different geographical and ecological environments. Genetic diversity was evaluated using 30 SSRs in a collection of 330 traditional and improved rice accessions collected from 21 provinces in Indonesia (Thomson et al., 2007). All of the improved varieties sampled were indica, while tropical japonica comprised the largest proportion of traditional landrace varieties. CHARACTERIZE THE GENETIC ARCHITECTURE OF COMPLEX TRAITS IN RICE : We identified QTL associated with yield, yield components, agronomic characters and physiological nitrogen use efficiency in a recombinant inbred population evaluated over three years and two regions in Korea and identified molecular markers for use in marker-assisted selection (MAS) (Cho et al., 2007a; (Cho et al. 2007b). IDENTIFY GENES UNDERLYING QTLS AND TRACE THEIR EVOLUTIONARY HISTORY: An evolutionary study of the Rc gene for red pericarp showed that a single mutation conferring white pericarp is found in 98% of white rice varieties today and that it originated in japonica and was introgressed into indica (Sweeney et al., 2007). This finding provides evidence of active cultural exchange among ancient farmers during rice domestication. We wrote two reviews on rice domestication, examining evidence for independent domestication of indica and japonica (Sweeney and McCouch, 2007; Kovach et al., 2007). DEVELOP ALLELE-SPECIFIC MARKERS: We developed functional CAPS markers for xa5-mediated resistance in rice (Iyer-Pascuzzi and McCouch, 2007a). These markers provide 100% reliability and are widely used to enhance the efficiency of MAS in Asia. We reviewed the role of recessive resistance genes in plant-bacterial interactions and suggest that they can be viewed as mutations in dominant susceptibility alleles, possibly enhancing the durability of resistance (Iyer-Pascuzzi and McCouch, 2007b). DEVELOP STRATEGIES TO UTILIZE GENETIC DIVERSITY FROM WILD AND EXOTIC SOURCES: We summarized a decade of collaborative research using advanced backcross populations to identify quantitative trait loci (QTL) from an O. rufipogon ancestor that improved the performance of elite cultivars of O. sativa (McCouch et al., 2007). DEVELOP CONTROLLED VOCABULARIES AND PUBLIC INFORMATION RESOURCES: We developed a plant structure ontology, providing a unified vocabulary of anatomy and morphology of flowering plants (Ilic et al., 2007). The ontology and other new querying tools and datasets in the Gramene database (http://www.gramene.org) have improved the functionality of this important information resource.

Impacts
1) Use molecular markers to determine the diversity and population structure of Oryza sativa and O. rufipogon. Use advanced backcross QTL analysis to identify variation from wild and unadapted sources that can be usefully introgressed into elite O. sativa varieties to enhance performance in both favorable and unfavorable environments. 2) Isolate genes underlying specific phenotypes of interest using positional information, candidate genes, biochemical pathways and comparative maps and trace the evolutionary history of those genes. 3) Develop allele-specific markers targeting the functional nucleotide polymorphisms that determine useful phenotypes for use in plant breeding. 4) Develop plant ontologies that can be used to annotate phenotypic variation in a comparative context. 5) Work with software engineers and professional curators to develop a community information resource. 6) Work with graduate and undergraduate students in the university, and with in middle school and highschool students in NY State to engage the population in science-based inquiry and to enhance their understanding of and interest in plant science and agriculture. Non-Technical Summary More than half of the world's population depends on rice as their staple food, and the US is the world's fourth largest exporter of this essential commodity. Rice production must increase dramatically and in a sustainable manner to meet the demands of the 21st century. Population pressure, natural resource limitations, changing climate and globalized markets all contribute to the rapidly evolving landscape of agriculture and underscore the importance of agricultural innovation. Advances in genomic science offer new opportunities to address many of the challenges for the future. The rice genome has been sequenced and efforts to annotate the genome are underway as the basis for applications in plant breeding. Genetic studies aimed at understanding the relationship between DNA sequence (genotype) and whole plant performance (phenotype) are fundamental to improving the productivity and nutritional value of our crops as well as the sustainability of our agricultural system. High through-put genetic evaluation must be coupled with more efficient phenotyping strategies and renewed emphasis on crop management in the face of environmental constraints. We are identifying genes and quantitative trait loci (QTLs) associated with complex traits of importance to rice production, examining the function of these genes and their interaction with other genes in critical pathways, tracing their evolutionary history and developing markers for use in molecular breeding. All information generated in my lab is available to the research community and can be accessed through public databases. We curate and help develop the Gramene Database, a comparative plant genome information resource that provides indepth information about genomes, genes, proteins, pathways, QTLs, phenotypes, germplasm, molecular markers, maps, molecular polymorphisms, ontology terms and literature citations related to flowering plants.

Publications

• Caicedo AL, Williamson SH, Hernandez RD, Boyko A, Fledel-Alon A, York TL, Polato NR, Olsen KM, Nielsen R, McCouch SR, Bustamante CD, Purugganan MD. 2007. Genome-Wide Patterns of Nucleotide Polymorphism in Domesticated Rice. PLoS Genetics 3:e163
• Sweeney M and McCouch S. 2007. The complex history of the domestication of rice. Ann Bot: doi 10.1093/aob/mcm128
• Cho YG, Kang HJ, See JS, Lee YT, Lim SJ, Gaugh H, Eun MY and McCouch SR. 2007a. Identification of quantitative trait loci in rice for yield, yield components, and agronomic traits across years and locations. Crop Sci 47:2403-2417
• Cho Y-I, Jiang W, Chin J-H, Piao Z, Cho YG, McCouch SR, Koh H-J. 2007b. Identification of QTLs associated with physiological nitrogen use efficiency in rice. Molecules and Cells 23: 72-79
• Ilic K, Kellogg EA, Jaiswal P, Zapata F, Stevens PF, Vincent LP, Avraham S, Reiser L, Pujar A, Sachs MM, Whitman NT, McCouch SR, Schaeffer ML, Ware DH, Stein LD, Rhee SY. 2007. The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiol. 143: 587-599
• Tang T, Lu J, Huang J, He J, McCouch SR, Shen Y, Kai Z, Purugganan MD, Shi S, Wu CI. 2007. Genomic variation in rice: genesis of highly polymorphic linkage blocks during domestication. PloS Genet. 2006 Nov 17; 2(11):e199.

Progress 01/01/06 to 12/31/06

Outputs
We summarized a decade of collaborative research using advanced backcross populations to identify QTL from an O. rufipogon ancestor associated with improved performance in elite cultivars of O. sativa (McCouch et al., 2006). This work demonstrated that advanced backcross-QTL analysis was capable of 1. uncovering positive alleles in wild germplasm not obvious in the phenotype, 2. estimating the breeding value of exotic germplasm, 3. generating near isogenic lines useful for the basis of gene isolation and as parents for in a variety development program 4. providing gene-based markers for targeted introgression of alleles using marker-assisted-selection (MAS). We dissected a complex QTL associated with flowering time in which alleles from a late-maturing O. rufipogon ancestor provide earliness when introgressed into an elite O. sativa genetic background (Thomson et al., 2006a). We fine-mapped a QTL associated with enhanced yield where alleles from the low-yielding O. rufipogon donor contributed to enhanced yield in an elite O. sativa genetic background (Xie et al., 2006). We positionally cloned the Rc gene associated with red pericarp in rice and found it corresponded to a basic helix-loop-helix transcription factor (Sweeney et al., 2006). We mapped and characterized a recessive mutation causing seed shattering that mapped very near to the Rc gene and corresponds to a block of domestication genes near the centromere on rice chr. 7 (Ji et al., 2006). We examined the waxy locus on rice chr. 6 and found that a splice donor site mutation in intron 1 played an important role in the origin of low amylose, non glutinous temperate japonica rice varieties (Olsen et al., 2006). Our findings demonstrate that selection pressures associated with crop domestication can exceed by 1-2 orders of magnitude those observed for genes under even strong selection in natural systems. We examined genome-wide genetic diversity in a collection of 330 of traditional and improved rice accessions collected from 21 provinces across the Indonesian archipelago using 30 microsatellite markers (Thomson et al., 2006b). The Plant Ontology Consortium (POC) (www.plantontology.org) is a collaborative effort among experts in plant systematics, botany and genomics. As part of POC, we developed a whole-plant growth-stage ontology for angiosperms and discussed its application in plant biology (Pujar et al., 2006) as well as a plant structure ontology, providing a unified vocabulary (Ilic et al., 2006). These studies provide a network of vocabularies linked by relationships (ontology) to facilitate queries that cut across datasets within a database or between multiple databases. Using the ontology browser, over 3500 gene annotations from three species-specific databases, can now be queried and retrieved. (Jaiswal et al., 2006a). Several new tools in the Gramene database (http://www.gramene.org) facilitate the potential for comparative analysis among the grasses and contribute to understanding the anatomy, development, environmental responses and factors influencing agronomic performance of cereal crops (Jaiswal et al., 2006b).

Impacts
Rice is a staple food for approximately half the world's population. Genetic improvements aimed a increasing productivity, nutritional quality and environmental stability of rice production systems are critical to alleviating hunger and malnutrition.

Publications

• McCouch, S., Sweeney, M., Li, J., Jiang, H., Thomson, M., Septinginsih, E., Edwards, J., Moncada, P., Xiao, J., Garris, A., Tai, T., Martinez, C., Tohme, J., Sugiono, M., McClung, A., Yuan, L. P., Ahn, S. N. 2006. Through the genetic bottleneck: O. rufipogon as a source of trait-enhancing alleles for O. sativa. Euphytica: DOI10.1007/s10681-006-9210-8
• Ilic, K., Kellogg, E., Jaiswal, P., Zapata, F., Stevens, P., Vincent, L., Avraham, S., Reiser, L., Pujar, A., Sachs, M., Whitman, N., McCouch, S., Schaeffer, M., Ware, D., Stein, L., Rhee, S. 2006. Plant Structure Ontology: unified vocabulary of anatomy and morphology of a flowering plant. Pl. Physiol.: DOI:10.1104/10.106.092825
• Jaiswal, P., Avaraham, S., Ilic, K., Kellogg, E., McCouch, S., Pujar, A., Reiser, L., Rhee, S., Sachs, M., Schaeffer, M., Stein, L., Stevens, P., Leszek, V., Ware, D., Zapata, F. 2006. Plant Ontology (PO): A controlled vocabulary of plant structures and growth stages. Comp. Func. Gen. 6:388-397.
• Jaiswal, P., Ni, J., Yap, I., Ware, D., Spooner, W., Youens-Clark, K., Ren, L., Liang, C., Zhao, W., Ratnapu, K., Faga, B., Canaran, P., Fogleman, M., Hebbard, C., Avraham, S., Schmidt, S., Casstevens, T., Buckler, E., Stein, L., McCouch, S. 2006. Gramene: A birds eye view. Nucl. Acids Res. 34:D717-D723; doi:10.1093/nar/gkj154
• Ji, H-S, Chu, S-H., Jiang, W., Cho, Y-I., Hahn, J-H., Eun, M-Y., McCouch, S., Koh, H-J. 2006. Characterization and mapping of a shattering mutant in rice that corresponds to a block of domestication genes. Genetics 173:995-1005.
• Olsen, K., Caicedo, A., Polato, N., McClung, A., McCouch, S., Purugganan, M. 2006. Selection under Domestication: Evidence for a Sweep in the Rice Waxy Genomic Region. Genetics:173:975-983.
• Pujar, A., Jaiswal, P., Kellogg, E., Ilic, K., Vincent, L., Avraham, S., Stevens, P., Zapata, F., Reiser, L., Rhee, S., Sachs, M., Schaeffer, M., Stein, L., Ware, D., McCouch, S. 2006. Whole Plant Growth Stage Ontology for Angiosperms and its Application in Plant Biology. Plant Physiol. Published on August 11, 2006: 10.1104/pp.106.085720
• Sweeney, M., Thomson, M., Pfeil, B., McCouch, S. 2006. Caught Red-Handed: Rc Encodes a Basic Helix-Loop-Helix Protein Conditioning Red Pericarp in Rice. Plant Cell 18:283-294.
• Thomson, M., Edwards, J., Septiningsih, E., Harrington, S., McCouch, S. 2006a. Substitution mapping of dth1.1, a flowering time QTL associated with transgressive variation in rice, reveals a cluster of QTLs. Genetics 172:2501-2514.
• Thomson, M., Septiningsih, E., Suwardjo, F., Santoso, T., Silitonga, T., McCouch, S. 2006b. Genetic diversity analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using microsatellite markers. Theor. Appl. Genet:10.1007/s00122-006-0457-1
• Xie, X., Song, M-H., Jin, F., Suh, J-P., Hwang, H-G., McCouch, S., Ahn, S-N. 2006. Fine mapping of a grain weight quantitative trait locus on rice chromosome 8 using near isogenic lines derived from a cross between Oryza sativa and O. rufipogon. Theor. Appl. Genet. 113:885-894.

Progress 01/01/05 to 12/31/05

Outputs
We evaluated the population sub-structure of three different sets of rice germplasm during 2005. In the first study, we described the population structure of O. sativa using 169 SSR markers and 235 diverse landrace varieties from around the world (Garris et al., 2005). Our results identify five major sub-populations corresponding to the indica, aus, tropical japonica, temperate japonica and aromatic groups..SNPs and indels in the chloroplast genome illustrate the antiquity of the indica-japonica sub-species devide. This work is consistent with morphological, genetic and isozyjme studies and provides a valuable set of markers that can be readily used to identify the sub-population identity of uncharacterized rice accessions. In the second study, we described the population structure of O. glaberrima using a set of 93 SSRs and 198 diverse O. glaberrima landrace varieties from Africa. Our results suggest that there are three sub-populations within O. glaberrima associated with ecologically specialized morphological and growth habits and that admixture with O. sativa is common in rices grown in W. Africa today. Results are summarized in Semon et al. (2005). In the third study, we described the population sub-structure and breeding pattersn of 145 US rice varieties using 169 SSRs and demonstrated that the sub-groups observed in Asian rice are maintained in US cultivars despite 80 years of active plant breeding. In the paper by the International Rice Genome Sequencing Group (2005), we explored the structure, organization and evolution of the rice genome based on the completed draft of the genome sequence. My group contributed the SSR annotation to this study. Using QTL analysis, we report significant associations between marker genotypes and a range of phenotypes associated with domestication and agronomic performance (Lee et al., 2005). As the foundation for identifying QTLs associated with water use efficiently, we optimized a phenotyping procedure for detecting small but significant differences in carbon isotope discrimination in rice (Comstock et al., 2005). As a form of association analysis, we explored the use of disriminant analysis to identify markers associated with agronomic traits in a collection of US rice varieties (Zhange et al., 2005). We contributed plant material and help to select accessions for the development of the Oryza bacterial artificial chromosome library resource (Ammiraju et al., 2005). Finally, in the paper by Xu et al.2005), we evaluated the contributions that rice is making to the integration of genomics techniques in cereal improvement (Xu et al., 2005).

Impacts
Rice is a staple food for approximately half the world's population. Genetic improvements aimed at increasing productivity, nutritional quality and environmental stability of rice production systems are critical to alleviating hunger and malnutrition.

Publications

• International Rice Genome Sequencing Project. 2005. The map-based sequence of the rice genome. Nature 436: 793-800.
• Zhang N, Xu Y, Akash M, McCouch S, Oard J. 2005. Identification of candidate markers associated with agronomic traits in rice using discriminant analysis. Theor Appl Genet 110: 721-729.
• Lee S-J, Oh C-S, Suh J-P, McCouch, S R, Ahn S-N. 2005. Identification of QTLs for domestication-related and agronomic traits in an Oryza sativa x O. rufipogon BC1F7 population. Pl Breed 124: 209-219.
• Lu H, Redus M, Coburn J, Rutger N, McCouch S, Tai T. 2005. Population structure and breeding patterns of 145 U.S. rice cultivars based on SSR marker analysis. Crop Sci 45: 66-76.
• Garris A, Tai T, Coburn J, Kresovich S, McCouch S. 2005. Genetic structure and diversity in Oryza sativa L. Genetics 169:1631-1638 DOI:10.1534/genetics.104.035642
• Ammiraju J, Luo M, Goicoechea JL, Wang W, Kudrna D, Mueller C, Talag J, Kim H, Sisneros NB, Blackmon B, Fang E, Tomkins JB, Brar D, MacKill D, McCouch SR, Kurata N, Lambert G, Galbraith DW, Arumuganathan K, Rao K, Walling JG, Gill N, Yu Y, SanMiguel P, Soderlund C, Jackson S and Wing RA. 2005. The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genomes types of the genus Oryza. Genome Research 16: 140-147.
• Comstock J, McCouch S, Martin B, Tauer C, Vision T, Xu Y, Pausch R. 2005. The effects of resource availability and environmental conditions on genetic ranking for carbon isotope discrimination during growth in tomato and rice. Func Pl Biol 32: 1089-1105.
• Xu Y, McCouch S, Zhang Q. 2005. How can we use genomics to improve cereals with rice as a reference genome? Pl Mol Biol 59: 7-26.

Progress 01/01/04 to 12/31/04

Outputs
Purpose: The rice genome has been sequenced and efforts to annotate the genome are underway. Genetic studies aimed at understanding the relationship between DNA sequence (genotype) and whole plant performance (phenotype) are fundamental to improving agricultural productivity. Information about genes and/or regions of the genome that are associated with complex traits is available and can be accessed through public databases. Objectives: 1) describe the population structure of O. sativa and O. glaberrima and evaluate the relationship between these two cultivated species and their wild ancestors 2) develop ways to efficiently access and manipulate useful genetic diversity in plant breeding 3) understand the function of specific genes, alleles and QTLs in rice 4) understand the structure, organization and evolution of the rice genome 5) develop data information resources that allow biologists to ask novel questions and to easily browse and query diverse domains of information. Approach: 1) Identify SSRs and transposable element (TE) families in the genomic sequence of rice and develop markers for use in genetic studies 2) Use molecular markers to determine the population structure of Oryza sativa and O. glaberrima and evaluate the extent of linkage disequilibrium in different sub-populations. 3) Evaluate and compare levels of genetic diversity in different sub-populations of rice 4) Isolate genes underlying specific phenotypes of interest using positional information, candidate genes, biochemical pathways and comparative maps 5) Work with informatics experts to develop a community resource based on distributed annotation and curation by biologists that accommodates data from multiple domains and supports novel and complex queries. Situation or Problem: Rice is a staple food for approximately half the world's population. Genetic improvements aimed at increasing productivity, nutritional quality and environmental stability of rice production systems are critical to alleviating hunger and malnutrition.

Impacts
Rice is a staple food for approximately half the world's population. Genetic improvements aimed at increasing productivity, nutritional quality and environmental stability of rice production systems are critical to alleviating hunger and malnutrition.

Publications

• Jain S, Jain R, McCouch S. 2004. Genetic analysis of Indian aromatic and quality rice (Oryza sativa L.) germplasm using panels of fluorescently-labeled microsatellite markers. Theor Appl Genet: 109: 965-977 (DOI: 10.1007/s00122-004-1700-2)
• Edwards J, Lee VM, McCouch SR. 2004. Sources and predictors of detectable indel polymorphism using rice as a model. Mol Gen Genomics 271: 298-307
• Moncada P and McCouch S. 2004. Simple Sequence Repeat (SSR) diversity in diploid and tetraploid Coffea species. Genome 47: 501-509
• Xu Y, Beachell H, McCouch SR. 2004. A marker-based approach to broadening the genetic base of rice (Oryza sativa L.) in the U.S. Crop Science 44: 1947-1959
• McCouch S. 2004. Diversifying Selection in Plant Breeding. PLoS Biol 2(10): e347 (DOI: 10.1371/journal.pbio.0020347)
• Cho, Y-I, Park C-W, Kwon, S-W, Chin J-H, Ji, H-S, Park K-J, McCouch S, Koh, H-J. 2004. Key DNA markers for predicting heterosis in F1 hybrids of japonica rice. Breed Sci 54: 389-397
• Li J, Xiao J, Grandillo S, Jiang L, Wan Y, Deng Q, Yuan L, McCouch S. 2004. QTL detection for rice grain quality traits using an interspecific backcross population derived from cultivated Asian (O. sativa L.) and African (O. glaberrima S.) rice. Genome 47: 697-704
• Semon M, Nielsen R, Jones M, McCouch S. 2004. The population structure of African cultivated rice Oryza Glaberrima (Steud.): evidence for elevated levels of LD caused by admixture with O. sativa and ecological adaptation. Genetics: DOI 1010.1534/genetics.104.033175
• Li J, Thomson M, McCouch S. 2004. Fine mapping of a grain weight QTL in the peri-centromeric region of rice chromosome 3. Genetics 168: 2187-2195

Progress 01/01/03 to 12/31/03

Outputs
Purpose The rice genome has been sequenced and efforts to annotate the genome are underway. The information is available and can be accessed through public databases. Genetic studies aimed at understanding the relationship between DNA sequence (genotype) and whole plant performance (phenotype) are fundamental to improving agricultural productivity. Keywords Objectives 1) understand the structure, organization and evolution of the rice genome 2) describe the population structure of rice and compare it to other grasses 3) develop ways to efficiently access and manipulate useful genetic diversity in plant breeding 4) understand the function of specific genes, alleles and QTLs in rice 5) develop user-friendly data information resources that allow biologists to ask novel questions Approach 1) Identify SSRs and transposable element (TE) families in the genomic sequence of rice and develop markers for use in phylogenetic reconstruction and to study the evolutionary history of Oryza 2) Use molecular markers to determine the population structure of Oryza sativa and evaluate the extent of linkage disequilibrium in different sub-populations. 3) Evaluate and compare levels of genetic diversity in different sub-populations of rice 4) Isolate genes underlying specific phenotypes of interest using positional information, candidate genes, biochemical pathways and comparative mapping studies 5) Work with informatics experts to develop a community resource based on distributed annotation and curation by biologists that accommodates data from multiple domains and supports novel and complex queries

Impacts
Rice is a staple food for approximately half the world's population. Genetic improvements aimed at increasing productivity, nutritional quality and environmental stability of rice production systems are critical to alleviating hunger and malnutrition.

Publications

• Blair, M., Garris, A., Iyer, A., Chapman, B., Kresovich, S., McCouch, S. 2003. High resolution genetic mapping and candidate gene identification at the xa5 locus for bacterial blight resistance in rice (Oryza sativa L.). Theor Appl Genet 107:62-73
• Chen, X., Cho, Y., McCouch, S.R. 2002. Sequence divergence of rice microsatellites in Oryza and other plant species. Mol Gen Genet 268:331-343
• Coburn, J., Temnykh, S., Paul, E., McCouch, S.R. 2002. Design and Application of Microsatellite Marker Panels for Semi-automated Genotyping of Rice (Oryza sativa L.). Crop Science 42: 2092-2099
• Jiang, N., Bao, Z., Zhang, X., Hirochika, H., Eddy, McCouch, S.R. and Wessler, S. 2002. An active transposon family in rice. Nature 421:163-167.
• Jiang, N., Bao, Z., Temnykh, S., Cheng, Z., Jiang, J., Wing, R.A., McCouch, S.R., Wessler, S.R. 2002. Dasheng: A recently amplified nonautonomous Ltr elelment that is a major component of pericentromeric regions in rice. Genetics 161: 1293-1305
• McCouch, S., Teytelman, L., Xu, Y., Lobos, K., Clare, K., Walton, M., Fu, B., Maghirang, R., Li, Z., Xing, Y., Zhang, Q., Kono, I., Yano, M., Fjellstrom, R., DeClerck, G., Schneider, D., Cartinhour, S., Ware, D., Stein, L. 2002. Development of 2,240 new SSR markers for rice (Oryza sativa L.) DNA Res.9:199-207
• Septiningsih, E., Prasetiyono, J., Lubis, E., Tai, T.H., Tjubaryat, T., Moeljopawiro, S., McCouch, S.R. 2003a. Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon Theor Appl Genet 107:1419-1432.
• Septiningsih, E., Trijatmiko K.R., Moeljopawiro, S., McCouch, S.R. 2003b. Identification of quantitative trait loci for grain quality in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O.rufipogon. Theor Appl Genet 107:1433-1441.
• Thomson, M., Tai, T., McClung, A., Xai, X-H., Hinga, M., Lobos, K., Xu, Y., Martinez, P., McCouch, S. 2003. Mapping quantitative trait loci for yield, yield components and morphological traits in an advanced backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson. Theor Appl Genet 107:479-493 DOI 10.1007_s00122-003-1270-8
• Ware, D., Jaiswal, P., Ni, J., Yap, I., Pan, X., Clark, K., Teytelman, L., Schmidt, S., Zhao, W., Chang, K., Cartinhour, S., Stein, L., McCouch, S. 2002. Gramene, a tool for Grass Genomics. Pl. Phys. 130: 1606-1613.
• Xu, Y., Beachell, H., McCouch, S.R. 2004. A marker-based approach to broadening the genetic base of rice (Oryza sativa L.) in the U.S. Crop Science (in press)

Progress 01/01/02 to 12/31/02

Outputs
Objectives: 1) understand the structure and organization of the rice genome. 2) compare the genome structure of rice and other grasses. 3) understand the function of specific genes and QTLs in rice. 4) understand the mechanisms that drive allelic diversity in cultivated and wild accessions of rice. 5) develop ways to efficiently access and manipulate useful genetic diversity in plant breeding. 6) understand how structural changes in DNA affect form and function at the organismal level. 7) develop user-friendly data information resources that allow biologists to ask novel questions. Approach: 1) Identify genomic elements based on the availability of genomic sequence information and study their distribution, interspersion and evolution in rice. 2) Compare the organization and evolution of genomic features across the grass family. 3) Isolate genes underlying specific phenotypes of interest using positional information, candidate genes, biochemical pathways and comparative mapping studies. 4) Evaluate the frequency, structural changes and allelic diversity in rice and other organisms. 5) Trigger genome rearrangments, transposition events or other forms of mutation that generate novel genetic variation as the basis for selection. 6) Identify the phenotypic consequences of specific genotypic alterations based on lab and greenhouse analysis. 7) Work with informatics experts to develop a community resource based on distributed annotation and curation by biologists that accomodates data from multiple domains and supports novel and complex queries. Situation or Problem: Rice is a staple food for approximately half the world's population. Genetic improvements aimed at increasing productivity, nutritional quality and environmental stability of rice production systems are critical to alleviating hunger and malnutrition.

Impacts
Sequencing the rice genome continues and the expanding information from this effort is being made publicly available in printed as well as database form as it is discovered. Genetic studies targeting our understanding of the relationship between DNA sequence (genotype) and whole plant performance (phenotype) continue to be fundamental to improving agricultural productivity.

Publications

• McCouch S, Teytelman L, Xu Y, Lobos K, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L. 2002. Development of 2,240 new SSR markers for rice (Oryza sativa L.) DNA Res.9:199-207
• Ware D, Jaiswal P, Ni J, Yap I, Pan X, Clark K, Teytelman L, Schmidt S, Zhao W, Chang K, Cartinhour S, Stein L, McCouch S. 2002. Gramene, a tool for Grass Genomics. Pl. Phys. 130: 1606-1613.
• Jiang N, Bao Z, Zhang X, Hirochika H, Eddy SR, McCouch SR and Wessler SR. 2002. An active transposon family in rice. Nature 421:163-167.
• Chen X, Cho Y, McCouch SR. 2002. Sequence divergence of rice microsatellites in Oryza and other plant species. Mol Gen Genet DOI.1007/s00438-002-0739-5
• Jiang N, Bao Z, Temnykh S, Cheng Z, Jiang J, Wing RA, McCouch SR, Wessler SR. 2002. Dasheng: A recently amplified nonautonomous Ltr element that is a major component of pericentromeric regions in rice. Genetics 161: 1293-1305
• Coburn J., S Temnykh, E Paul, McCouch, SR. 2002. Design and Application of Microsatellite Marker Panels for Semi-automated Genotyping of Rice (Oryza sativa L.). Crop Science 42: 2092-2099
• Ho J, McCouch SR, Smith ME. 2002. Improvement of hybrid yield by advanced backcross QTL analysis in elite maize. Theor Appl Genet DOI 10.1007/s00122-002-0945-x
• Blair MW, V Hedetale and McCouch, SR. 2002. Fluorescent-labeled microsatellite panels useful for detecting allelic diversity in cultivated rice (Oryza sativa L.) Theor Appl Genet DOI 10.1007/s00122-002-0921-5
• Ware D, P Jaiswal, J Ni, X Pan, K Chang, K Clark, L Teytelman, S Schmidt, W Zhao, S Cartinhour, S McCouch and Stein, L. 2002. Gramene: A Resource for Comparative Grass Genomics. Nucl Acids Res 30:103-105
• Jaiswal J, Ware D, Ni J, Chang, K, Zhao W, Schmidt S, Pan X, Clark K, Teytelman L, Cartinhour S, Stein L, McCouch S. 2002. Gramene: development and integration of trait and gene ontologies for rice. Comp Funct Genom 3:132-136 (DOI: 10.1002/cfg.156)

Progress 01/01/01 to 12/31/01

Outputs
The availability of rice genome sequence information opens the door to many applications in genetics, comparative genome analysis and plant breeding. Our goal is to identify, isolate and characterize genes underlying traits of agronomic importance in the cereals and to use genomic information to develop and implement novel molecular breeding strategies. As the biological function of genes is systematically evaluated using model systems, and these functions are increasingly associated with complex biochemical pathways, we take advantage of this information to better understand the genetic components that influence crop performance in agronomically relevant environments. Using interspecific crosses between an elite, cultivated rice variety (Oryza sativa) and a wild ancestor (O. rufipogon), we have identified several quantitative trait loci (QTLs) where introgression from the wild parent enhances performance of the cultivar. Using a positional-candidate gene approach, we have fine mapped the regions containing QTLs for flowering time, plant stature, panicle length and grain weight as the first step toward isolating the genes underlying these QTLs. As the target genes are identified, we evaluate the molecular diversity at the loci to determine the functional nucleotide polymorphism (FNP) that distinguishes the favorable from the unfavorable allele. This information provides the basis for developing high resolution tools that can be used to screen parental material or to select favorable recombinants in a breeding program. It also provides the foundation for in-depth genetic analysis aimed at understanding the molecular and biochemical function of the gene(s) and their relationship to phenotype.

Impacts
Evaluated in a comparative context, our research information can be used to predict the function of similar alleles in related cereal species as well as to look for novel genetic variation in other organisms. Understanding the variety of functional mutations that have evolved in nature offers clues as to the identity of alleles that could prove useful in agriculture as we seek to develop new crop varieties to meet the needs of a changing world.

Publications

• Basu, D., Dehesh. K., Schneider-Poetsch, HJ., Harrington, S.E., McCouch, S.R. and Quail, P.H. 2001. Rice PHYC gene: structure, expression, map position and evolution. Pl Mol Biol 44:27-42.
• McCouch, S.R. 2001. Genomics and Synteny. Plant Physiol 125:152-155,
• Ishii, T., Xu, Y., McCouch, S.R. 2001. Nuclear and chloroplast microsatellite variation in A-genome species of rice. Genome 44:648-666.
• Temnykh, S., DeClerck, G., Lukashova, A., Lipovich, L., Cartinhour, S. and McCouch, S. 2001. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Research 11:1441-1452.