Networks
McCouch, Susan Rutherford
Cornell Faculty Member
Positions
- Professor, Plant Breeding and Genetics (PB&G), College of Agriculture and Life Sciences (CALS)
- Professor, Plant Biology (BIOPL), College of Agriculture and Life Sciences (CALS)
Susan McCouch is a Professor of Plant Breeding and Genetics and of Plant Biology at Cornell University. She received her PhD from Cornell in 1990 and spent 5 years with the International Rice Research Institute (IRRI) in the Philippines before joining the Cornell faculty in 1995. Her research focuses on rice and includes publication of the first molecular map of the rice genome in 1988, early QTL studies on disease resistance, drought tolerance, maturity and yield, cloning of genes underlying domestication traits, and demonstrating that low-yielding wild and exotic Oryza species harbor genes that can enhance the performance of modern, high-yielding cultivars. Recently, she has used genome wide association studies (GWAS) to demonstrate that the different subpopulations of O. sativa have significantly different genetic architecture underlying complex trait variation, providing new insights into the genetic basis of transgressive variation, and supporting an ancient divergence between cultivated groups. She has trained scores of young scientists throughout the world, was recently elected a fellow of the AAAS and has received numerous research, teaching and faculty awards.
Research Areas
- agricultural biotechnology
- biodiversity
- bioinformatics
- evolution
- genetics
- international agriculture
- molecular genetics
- new life sciences
- plant biology
- plant breeding and genetics
- plant sciences
Websites
- Affiliations
- Research
- Publications
- Teaching
- Service
- Background
- Other
- View All
Affiliations
other Cornell affiliations
Research
research overview
- Susan McCouch is a Professor of Plant Breeding and Genetics and of Plant Biology at Cornell University. She received her PhD from Cornell in 1990 and spent 5 years with the International Rice Research Institute (IRRI) in the Philippines before joining the Cornell faculty in 1995. Her research focuses on rice and includes publication of the first molecular map of the rice genome in 1988, early QTL studies on disease resistance, drought tolerance, maturity and yield, development of the essential repertoire of SSR markers widely used as a genomic resource in rice genetics and breeding, cloning of genes underlying critical traits for rice improvement and studies on the evolutionary history of rice in both Africa and Asia. Her current work focuses on the identification and characterization of genes and quantitative trait loci (QTL) from low-yielding wild and exotic Oryza species that enhance the performance of modern rice cultivars. She has trained scores of young scientists throughout the world and was recently elected a fellow of the AAAS and has received numerous teaching and faculty awards. Current work focuses on using genome-wide association mapping to dissect the genetics of complex traits and to unravel the genetic basis of trangressive variation in rice. Interests include understanding the process of rice domestication, examining how rice diversity is partitioned genetically and distributed geographically, and developing new strategies for recombining genes and quantitative trait loci (QTL) to enhance plant performance in agriculture.
principal investigator on
- CROP WILD RELATIVE GENOMICS: A KEY TO UNLOCKING DIVERSITY awarded by DIRECTORATE FOR BIOLOGICAL SCIENCES NSF 2012 - 2013
- DESIGN AND IMPLEMENTATION OF A "COLLABORATOR'S DATABASE" AS PART OF THE RICE DIVERSITY RESEARCH PLATFORM awarded by INTERNATIONAL RICE RESEARCH INSTITUTE 2011 - 2012
- DEVELOPMENT OF A HIGH RESOLUTION SNP CHIP (400K) AND GENOTYPING OF 500 DIVERSE RICE (ORYZA SP.)ACCESSIONS awarded by NATIONAL INSTITUTE OF FOOD AND AGRICULTURE-USDA 2009 - 2013
- ENHANCING UTILIZATION OF CROP WILD RELATIVES: CAPTURING GENETIC VALUE FROM ANCESTRAL POPULATIONS OF WILD RICE awarded by GLOBAL CROP DIVERSITY TRUST 2011 - 2015
- GENOTYPING OF 1440 RICE SAMPLES USING THE 1M SMP ARRAY DEVELOPED AT CORNELL UNIVERSITY AS PART OF THE RICE SNP CONSORTIUM awarded by INTERNATIONAL RICE RESEARCH INSTITUTE 2010 - 2012
- GEPR: THE GENETIC BASIS OF TRANSGRESSIVE VARIATION IN RICE awarded by DIRECTORATE FOR BIOLOGICAL SCIENCES NSF 2010 - 2014
- TRPGR GRAMENE: A PLATFORM FOR COMPARATIVE PLANT GENOMICS awarded by NATL SCIENCE FOUNDATION 2007 - 2012
co-principal investigator on
- ENHANCING EDUCATION AND RESEARCH BREEDING FOR PLANT DISEASE RESISTANCE awarded by NATIONAL INSTITUTE OF FOOD AND AGRICULTURE-USDA 2010 - 2014
- LINKING CROP GENOTYPES AND PHENOTYPES VIA GENOMICS AND BIOINFORMATICS: PH.D. FELLOWSHIPS FOR PLANT BREEDERS awarded by NATIONAL INSTITUTE OF FOOD AND AGRICULTURE-USDA 2008 - 2013
- PHD FELLOWSHIPS TO TRAIN PLANT BREEDERS FOR THE 21ST CENTURY awarded by NATIONAL INSTITUTE OF FOOD AND AGRICULTURE-USDA 2012 - 2017
area(s) of concentration/expertise
- Agricultural Science Education
- Agriculture Development, Food Systems, Community Development
- Biodiversity Conservation in Working Landscapes
- Bioinformatics
- Biotechnology and Crop Improvement
- Breeding and Genetics (Grapes)
- Conservation
- Crop Physiology
- Diseases of Field Crops
- Evolutionary Biology
- Grain and Oil Crops
- International Agricultural & Rural Development
- International Agriculture/Biotechnology
- Molecular Basis of Disease Resistance and Susceptibility in Plants
- Molecular Genetics of Plant Breeding
- Plant Anatomy
- Plant Biotechnology / Plant Molecular Biology and Genetics
- Plant Breeding
- Plant Genetics
- Plant Genome Structure
- Plant Genomics - Plant Biochem
- Plant Molecular Biology
- Plant Molecular Biology, Genetics & Cell Biology
- Plant Molecular Genetics
- Plant Pathology, Plant Breeding and Genetics, and International Agriculture
- Plant Physiology & Plant Molecular Biology
- Rice Molecular Genetics & Breeding
- Small Grains Breeding and Genetics
- Sustainable Agriculture
- Sustainable Development
- Sustainable agriculture and rural development
- Tropical Crop Systems
- plant
other area(s) of concentration/expertise
- Genetics (Oryza)
keywords
- Database Development and Design
- Gene Discovery
- Molecular Breeding
- Rice Molecular Genetics
geographic focus
-
domestic geographical region
-
transnational region
submitted impact statement
Publications
individual publications
-
academic article
- High-throughput 2D root system phenotyping platform facilitates genetic analysis of root growth and development. . Plant, Cell and Environment. 36:454-466. 2013
- Genomics of gene banks: A case study in rice. American Journal of Botany. 99:407-423. 2012
- Nomenclature report on rice WRKY’s – Conflict regarding gene names and its solution.. RICE. 5:3. 2012
- PICARA, an analytical pipeline providing probabilistic inference about a priori candidate genes underlying genome-wide association QTL in plants.. PLoS One. 7. 2012
- Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nature Biotechnology. 30:105-111. 2012
- Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nature Communications. 2. 2011
- Genetic Architecture of Aluminum Tolerance in Rice (Oryza sativa) Determined through Genome-Wide Association Analysis and QTL Mapping. PLoS Genetics. 7:e1002221. 2011
- Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis. BMC Genomics. 12:142. 2011
- 3-dimensional root phenotyping with a novel imaging and software platform. Plant Physiology. 156:455-465. 2011
- A rice diversity panel evaluated for genetic and agro-morphological diversity between subpopulations and its geographic distribution. Crop Science Journal. 51:2021-2035. 2011
- Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis. BMC Genomics. 12:142. 2011
- Genetic architecture of aluminum tolerance in rice (Oryza sativa) determined through genome-wide association analysis and QTL mapping. PLoS Genetics. 7. 2011
- Genome-wide association mapping reveals rich genetic architecture of complex traits in Oryza sativa. Nature Communications. 2:467. 2011
- Genotype and environment effects on rice (Oryza sativa L.) grain arsenic concentration in Bangladesh. Plant and Soil. 338:367-382. 2011
- Genotype and environment effects on rice (Oryza sativa L.) grain arsenic concentration in Bangladesh. Plant and Soil. 338:367-382. 2011
- Gramene database in 2010: updates and extensions. Nucleic Acids Research. 39. 2011
- Gramene database in 2010: updates and extensions 2011
- High-throughput SNP genotyping for breeding applications in rice using the BeadXpress platform. Molecular Breeding. 29:875-886. 2011
- Three-Dimensional Root Phenotyping with a Novel Imaging and Software Platform. Plant Physiology. 156:455-465. 2011
- Three-dimensional root phenotyping with a novel imaging and software platform. Plant Physiology. 156:455-465. 2011
- ALCHEMY: A Reliable Method for Automated SNP Genotype Calling for Small Batch Sizes and Highly Homozygous Populations. Bioinformatics. 26:2952-2960. 2010
- Development of a research platform for dissecting phenotype-genotype associations in rice (Oryza spp.). Rice. 3:205-217. 2010
- Development of a Novel Aluminum Tolerance Phenotyping Platform Used for Comparisons of Cereal Aluminum Tolerance and Investigations into Rice Aluminum Tolerance Mechanisms. Plant Physiology. 153:1678-1691. 2010
- Development of genome-wide SNP assays for rice. Breeding Science. 60:524-535. 2010
- Genetic analysis of water use efficiency in rice (Oryza sativa; L.) at the leaf level. Rice. 3:72-86. 2010
- Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome. PLoS One. 5. 2010
- Identification of quantitative trait loci for physical and chemical properties of rice grain. Plant Biotechnology Reporter. 4:61-73. 2010
- Inactivation of the CTD phosphatase-like gene OSCPL1 enhances development of the abscission layer and seed shattering in rice. The Plant Journal. 61:96-106. 2010
- The genetic origin of fragrance in NERICA1. Molecular Breeding. . 2010
- A universal core genetic map for rice. Theoretical and Applied Genetics. 120:563-572. 2009
- Analysis of genetic structure in a sample of coffee (Coffea arabica L.) using fluorescent SSR markers. Tree Genetics & Genomes. 5:435-446. 2009
- Dissection of a QTL reveals an adaptive, interacting gene complex associated with transgressive variation for flowering time in rice. Theoretical and Applied Genetics. 120:895-908. 2009
- Evolutionary history of GS3, a gene conferring grain length in rice. Genetics. 182:1323-1334. 2009
- Genetic analysis of water-use efficiency in rice (Oryza sativa L.) at the leaf-level.. Rice J. :9. 2009
- Genetic diversity of isolated populations of Indonesian landraces of rice (Oryza sativa L.) collected in East Kalimantan on the island of Borneo.. Rice J. 2:80-92. 2009
- Gramene QTL database: development, content and applications.. Database: J Biol Databases Curation. 2009. 2009
- Inactivation of the CTD phosphatase-like gene OsCPL1 enhances development of the abscission layer and seed shattering in rice.. Plant Journal. 61:96-106. 2009
- Leaf-level water use efficiency determined by carbon isotope discrimination in rice seedlings: genetic variation associated with population structure and QTL mapping. . Theoretical and Applied Genetics. 118:1065-1081. 2009
- Not just a grain of rice: the quest for quality. Trends in Plant Science. 14:133-139. 2009
- The origin and evolution of fragrance in rice (Oryza sativa L.). Proceedings at the National Academy of Science USA. 106:14444-14449. 2009
- Genetic and functional characterization of the rice bacterial blight disease resistance gene xa5. Phytopathology. 98:289-295. 2008
- Gramene: a growing plant comparative genomics resource.. Nucleic Acids Research. 36. 2008
- Inactivation of the UGPase1 gene causes genic male sterility and endosperm chalkiness in rice (Oryza sativa L.).. The Plant Journal. 54:190-204. 2008
- Leveraging natural diversity: back through the bottleneck.. Current Opinion in Plant Biology. 11:193-200. 2008
- Student Opportunity: Short-Term Exposure to International Agriculture.. Rice Journal. 1:11-15. 2008
- The Plant Ontology Database: A Community Resource for Plant Structure and Developmental Stages, Controlled Vocabulary and Annotations. Nucleic Acids Research. 36. 2008
- Functional markers for xa5-mediated resistance in rice. Molecular Breeding. 19:291-296. 2007
- Genetic diversity analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using microsatellite markers. Theoretical and Applied Genetics. 114:559-568. 2007
- Genome-wide patterns of nucleotide polymorphism in domesticated Asian rice (Oryza sativa). PLoS Genetics. 3:1745-56. 2007
- Genomic variation in rice: genesis of highly polymorphic linkage blocks during domestication. PLOS Genetics. 2. 2007
- Global dissemination of a single mutation conferring white pericarp in rice. PLoS Genetics. 3. 2007
- Identification of QTLs associated with physiological nitrogen use efficiency in rice. Molecules and Cells. 23:72-79. 2007
- Identification of quantitative trait loci in rice for yield, yield components, and agronomic traits across years and locations. Crop Science Journal. 47:2403-2417. 2007
- New insights into the history of rice domestication. Trends Genet. 23:579-587. 2007
- Recessive resistance genes and the Oryza sativa-Xanthomonas oryzae pv. oryzae pathosystem. Molecular Plant - Microbe Interactions. 20:731-739. 2007
- The complex history of the domestication of rice. Annals of Botany. doi 10.1093. 2007
- The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiology. 143:587-599. 2007
- Through the genetic bottleneck: O. rufipogon as a source of trait-enhancing alleles for O. sativa. Euphytica. 154:317-339. 2007
- Caught Red-Handed: Rc Encodes a Basic Helix-Loop-Helix Protein Conditioning Red Pericarp in Rice. Plant Cell. 18:283-294. 2006
- Characterization and mapping of a shattering mutant in rice that corresponds to a block of domestication genes. Genetics. 173:995-1005. 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 Oryza rufipogon. Theoretical and Applied Genetics. 113:885-894. 2006
- Gramene: A bird's eye view of cereal genomes. Nucleic Acids Research. 34. 2006
- Plant Ontology (PO): A controlled vocabulary of plant structures and growth stages. Comp Func Gen. 6:388-397. 2006
- Selection under Domestication: Evidence for a Sweep in the Rice Waxy Genomic Region. Genetics. 173:975-983. 2006
- Substitution mapping of dth1.1, a flowering time QTL associated with transgressive variation in rice, reveals a cluster of QTLs. Genetics. 172:2501-2514. 2006
- The Oryza bacterial artificial chromosome library resource: Construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza. Genome Research. 16:140-147. 2006
- Whole Plant Growth Stage Ontology for Angiosperms and its Application in Plant Biology. Plant Physiology. 14. 2006
- Genetic structure and diversity in Oryza sativa L. Genetics. 169:1631-1658. 2005
- How can we use genomics to improve cereals with rice as a reference genome?. Plant Molecular Biology. 59:7-26. 2005
- Identification of QTLs for domestication-related and agronomic traits in an Oryza sativa x O. rufipogon BC1F7 population. Plant Breeding. 124:209-219. 2005
- Identification of candidate markers associated with agronomic traits in rice using discriminant analysis. Theoretical and Applied Genetics. 110:721-729. 2005
- Population structure and breeding patterns of 145 U.S. rice cultivars based on SSR marker analysis. Crop Science Journal. 45:66-76. 2005
- The effects of resource availability and environmental conditions on genetic ranking for carbon isotope discrimination during growth in tomato and rice. Functional Plant Biology. 32:1089-1105. 2005
- The map-based sequence of the rice genome. Nature. 436:793-800. 2005
- 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. 169:1639-1647. 2005
- A marker-based approach to broadening the genetic base of rice (Oryza sativa L.) in the U.S. Crop Science Journal. 44:1947-1959. 2004
- Diversifying Selection in Plant Breeding. PLoS Biology. 2. 2004
- Fine mapping of a grain weight QTL in the peri-centromeric region of rice chromosome 3. Genetics. 168:2187-2195. 2004
- Genetic analysis of Indian aromatic and quality rice (Oryza sativa L.) germplasm using panels of fluorescently-labeled microsatellite markers.. Theoretical and Applied Genetics. 109:965-977. 2004
- Key DNA markers for predicting heterosis in F1 hybrids of japonica rice. Breed Science. 54:389-397. 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. 2004
- Simple Sequence Repeat (SSR) diversity in diploid and tetraploid Coffea species. Genome. 47:501-509. 2004
- Sources and predictors of resolvable indel polymorphism assessed using rice as a model. Molecular Genetics and Genomics. 271:298-307. 2004
- The Rice Bacterial Blight Resistance Gene xa5 Encodes a Novel Form of Disease Resistance. Molecular Plant-Microbe Interactions. 17:1348-1354. 2004
- A Graph-Theoretic Approach to Comparing and Integrating Genetic, Physical and Sequence-Based Maps. Genetics. 165:2235-2247. 2003
- High resolution genetic mapping and candidate gene identification at the xa5 locus for bacterial blight in rice (oryza sativa L.). Theoretical and Applied Genetics. 107:62-73. 2003
- 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. Theoretical and Applied Genetics. 107:1433-1441. 2003
- 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. Theoretical and Applied Genetics. 107:1419-1432. 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. Theoretical and Applied Genetics. 107:479-493. 2003
- Population structure and its effect on haplotype diversity and linkage disequilibrium surrounding the xa5 locus of rice (Oryza sativa L.). Genetics. 165:759-769. 2003
- An active transposon family in rice. Nature. 421:163-167. 2002
- Dasheng: A recently amplified nonautonomous Ltr elelment that is a major component of pericentromeric regions in rice. Genetics. 161:1293-1305. 2002
- Design and Application of Microsatellite Marker Panels for Semi-automated Genotyping of Rice. Crop Science Journal. 42:2092-2099. 2002
- Development of 2,240 new SSR markers for rice (Oryza sativa L.). DNA Research. 9:199-207. 2002
- Fluorescent-labeled microsatellite panels useful for detecting allelic diversity in cultivated rice (Oryza sativa L.). Theoretical and Applied Genetics. 105:449-457. 2002
- Gramene, a tool for Grass Genomics. Plant Physiology. 130:1606-1613. 2002
- Gramene: A Resource for Comparative Grass Genomics. Nucleic Acids Research. 30:103-105. 2002
- Gramene: development and integration of trait and gene ontologies for rice. Comparative and Functional Genomics. 3:132-136. 2002
- Improvement of hybrid yield by advanced backcross QTL analysis in elite maize. Theoretical and Applied Genetics. 105:440-448. 2002
- Sequence divergence of rice microsatellites in Oryza and other plant species. Molecular & General Genetics. 268:331-343. 2002
- Why finishing the Rice Genome Matters. Science. 296:5. 2002
- Nuclear and chloroplast microsatellite variation in A-genome species of rice. Genome. 44:648-666. 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. 2001
- Genomics and Synteny. Plant Physiology. 125:152-155. 2001
- Quantitative trait loci for yield and yield components in an Oryza sativa x Oryza rufipogon BC2F2 population evaluated in an upland environment. Theoretical and Applied Genetics. 102:41-52. 2001
- Rice PHYC gene: structure, expression, map position and evolution. Plant Molecular Biology. 44:27-42. 2001
- Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theoretical and Applied Genetics. 100:713-722. 2000
- Mapping and genome organization of microsatellite sequences in rice (Oryza sativa. L). Theoretical and Applied Genetics. 100:697-712. 2000
- Mapping quantitative trait loci associated with days to flowering and photoperiod sensitivity in rice (Oryza sativa, L.). Molecular Breeding. 6:145-155. 2000
- Microsatellites and microsynteny in the chloroplast genomes of Oryza and eight other Gramineae species. Theoretical and Applied Genetics. 100:1257-1266. 2000
- Inferences on the genome structure of progenitor maize through comparative analysis of rice, maize, and the domesticated panicoids . Genetics. 153:453-473. 1999
- Inter-simple sequence repeat (ISSR) amplification for analysis of microsatellite frequency and fingerprinting in rice (Oryza sativa L.). Theoretical and Applied Genetics. 98:780-792. 1999
- Molecular characterization of the pdc2 gene and mapping of three pdc genes from rice. Theoretical and Applied Genetics. 98:815-824. 1999
- Molecular mapping of a new genic male-sterility gene causing chalky endosperm in rice (Oryza sativa L.). Euphytica. 105:57-62. 1999
- Production and testing of plants regenerated from protoplasts of photoperiod sensitive genic male sterile rice (Oryza sativa L.). Euphytica. 205:167-172. 1999
- Regeneration of plants from protoplasts of photoperiod sensitive genic male sterile rice (Oryza sativa L.). Euphytica. 205:167-172. 1999
- Anchor Probes for Comparative Mapping of Grass Genera. Theoretical and Applied Genetics. 97:356-369. 1998
- Identification of trait-improving quantitative trait loci alleles from a wild rice relative, O. rufipogon . Genetics. 150:899-909. 1998
- Integrated map of AFLP, SSLP and RFLP markers using a recombinant inbred population of rice (Oryza sativa L.). Theoretical and Applied Genetics. 97:370-380. 1998
- Toward a plant genomics initiative: Thoughts on the value of cross-species and cross-genera comparisons in the grasses. Proceedings of the National Academy of Sciences (PNAS). 95:1983-1985. 1998
- Transgressive segregation of tiller angle caused by complementary action of genes in crosses between indica varieties of rice (Oryza sativa L.). Crop Science Journal. 38:12-19. 1998
- A major QTL for rice yellow mottle virus (RYMV) resistance is lying in a cluster of blast resistance genes on chromosome 12. Phytopathology. 87:1243-1249. 1997
- Chromosomal regions associated with segregation distortion of molecular markers in F2, backcross, doubled haploid, and recombinant inbred populations in rice (Oryza sativa L.). Molecular & General Genetics. 253:535-545. 1997
- Comparative evaluation of within-cultivar variation of rice (Oryza sativa L.) using microsatellite and RFLP markers. Genome. 40:370-378. 1997
- Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). Theoretical and Applied Genetics. 95:553-567. 1997
- Mapping of the starch branching enzyme III (SBEIII) in rice (Oryza sativa L.). Theoretical and Applied Genetics. 94:564-568. 1997
- Microsatellite and sequence tagged site markers diagnostic for the bacterial blight resistance gene, xa-5. Theoretical and Applied Genetics. 95:174-184. 1997
- Microsatellite mapping and applications of SSLP's in rice genetics and breeding. Plant Molecular Biology. 35:89-99. 1997
- RFLP mapping of isozymes, RAPD and QTLs for grain shape, brown planthopper resistance in a doubled haploid rice population. Molecular Breeding. 3:105-113. 1997
- Seed banks and molecular maps: unlocking genetic potential from the wild. Science. 277:1063-1066. 1997
- Transcriptional repression by Oshox1, a novel homeodomain leucine zipper protein from rice. The Plant Journal. 11:263-276. 1997
- Cloning and mapping of variety-specific rice genomic DNA sequences: amplified fragment length polymorphisms (AFLP) from silver stained polyacrylamide gels. Genome. 39:373-378. 1996
- Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Molecular & General Genetics. 252:597-607. 1996
- Genes from wild rice improve yield. Scientific Correspondence - Nature. 384:223-224. 1996
- Genetic diversity and its relationship to hybrid performance and heterosis in rice as revealed by PCR-based markers. Theoretical and Applied Genetics. 92:637-643. 1996
- Molecular Mapping of Resistance to Rice Tungro Spherical Virus and Green Leafhopper. Phytopathology. 86:25-30. 1996
- Molecular mapping of genes for resistance to rice blast (Pyricularia grisea Sacc.). Theoretical and Applied Genetics. 93:859-863. 1996
- Association of Morphological and RFLP Markers in Rice (Oryza sativa L.). Genome. 38:566-574. 1995
- Comparative mapping in grasses. Oat relationships. Molecular & General Genetics. 249:349-356. 1995
- Comparative mapping in grasses. Wheat relationships. Molecular & General Genetics. 248:744-754. 1995
- Frequency of microsatellite sequences in rice (Oryza sativa L.). Genome. 38:1170-1176. 1995
- Genetic diversity and phylogeny analysis of Anabaena azollae based on RFLPs detected in Azolla-Anabaena azollae DNA complexes using nif gene probes. Theoretical and Applied Genetics. 91:589-597. 1995
- Locating genes associated with root morphology and drought avoidance via linkage to molecular markers. Theoretical and Applied Genetics. 90:969-981. 1995
- Molecular analysis of the inheritance of the S-5 locus, conferring wide compatibility in Indica/Japonica hybrids of rice (O. sativa L.). Theoretical and Applied Genetics. 90:182-188. 1995
- Molecular marker facilitated investigation of rice varietal ability to stimulate N2 fixation in the rhizosphere. Theoretical and Applied Genetics. 91:1177-1183. 1995
- Molecular-genetic maps for group 1 chromosomes of Triticeae species and their relation to chromosomes in rice and oat. Genome. 38:45-59. 1995
- QTL mapping in rice. Trends in Genetics. 11:482-487. 1995
- Tagging and combining bacterial blight resistance genes in rice using RAPD and RFLP markers. Molecular Breeding. 1:375-387. 1995
- The semidwarf gene, sd-1, of rice (Oryza sativa L.) II. Molecular mapping and marker-assisted selection. Theoretical and Applied Genetics. 89:54-59. 1994
- Orientation and integration of the classical and molecular genetic maps of chromosome 11 in rice. Euphytica. 76:81-87. 1994
- RFLP mapping of genes conferring complete and partial resistance to blast resistance in a durably resistant rice cultivar. Genetics. 136:1421-1434. 1994
- Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics. 138:1251-1274. 1994
- A protocol for non-radioactive DNA labelling and detection in the RFLP analysis of rice and tomato using single-copy probes. Plant Molecular Biology Reporter. 11:54-59. 1993
- Genetic diversity and phylogeny analysis of Azolla Lam. based on DNA amplification by arbitrary primers. Genome. 36:686-693. 1993
- RiceGenes, an International Genome Database and Bulletin Board for Rice. DNA Link. 3:40-41. 1993
- Genetic and physical analysis of the rice bacterial blight disease resistance locus, Xa21. Mol. Gen. Genet. 236:113-120. 1992
- Molecular mapping of rice chromosomes. Theoretical and Applied Genetics. 76:815-829. 1988
-
article
- SSR Mapping of Minute, a major gene for grain size, on rice chromosome 3 2004
- RiceGenes, an Information System for Rice Research 1995
- A high density molecular map of the rice genome 1992
- Progress in integration of the molecular maps of rice 1992
- Molecular tagging of a recessive gene, xa-5, for resistance to bacterial blight of rice 1991
- RFLP map of rice chromosome 1988
-
booksection
-
chapter
- Chapter 17: Gene Flow and Genetic Isolation in Crop Evolution. Biodiversity in Agriculture: Domestication, Evolution and Sustainability. 2011
- Making rice genomics work for Africa. Realizing Africa’s rice promise. 2011
- Commercialization and the Scientific Research Process: The Example of Plant Breeding. Science and the University. 2007
- DNA-based Markers in Plants, Rice molecular map. Springer. 337-345. 2007
- Molecular Markers for use in Plant Molecular Breeding and Germplasm Evaluation in Marker Assisted Selection (MAS) in Crops, Livestock, Forestry and Fish: Current Status and the Way Forward. Food and Agriculture Organization. 2007
- Naturally Occurring Alleles in Rice Functional Genomics-Challenges, Progress and Prospects, N.M. Springer. 2007
- Marker-assisted evaluation of germplasm resources for plant breeding. Rice Science: Innovations and Impact for Livelihood. 213-290. 2003
- Is Biotechnology an Answer?. Who Will Be Fed In The 21st Century? Challenges for Science and Policy. 29-40. 2001
- Rice Molecular Map. DNA-Based Markers in Plants. 337-347. 2001
- Algorithms for Constructing Comparative Maps. Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and the Evolution of Gene Families. 243-261. 2000
- From Malthus to Molecular Mapping: Prospects for the utilization of genome analysis to enhance world food supply. Molecular analysis of complex traits. 1996
- Genome mapping in temperate grains and grasses in the family Gramineae (Poaceae). Genome Mapping in Plants. 1996
- Mapping blast resistance genes in rice. Rice Blast Disease. 167-186. 1994
- Molecular mapping of blast resistance genes in rice. Rice Blast Disease. 167-186. 1994
- Applications of biotechnology to crop improvement for sustainable agricultural systems. Crop improvement for sustainable agricultural systems. 1992
- Development and use of RFLPs in rice breeding and genetics. Rice Biotechnology. 109-134. 1991
-
conference paper
- Through the genetic bottleneck: discovery and transfer of trait-enhancing alleles from wild species. IRGS Proceedings. 2005
- Molecular Markers for use in Plant Breeding and Germplasm Evaluation. Proceedings of Red Bio. 2004
- Potentials and Limitations of Biotechnology in Rice. Proceedings of the FAO Rice Conference. 2004
- Potentials and Limitations of Biotechnology in Rice. Proceedings of the FAO Rice Conference. 2004
- Advanced backcross analysis for transferring QTLs from O. rufipogon. Advances in rice genetics. Supplement to rice genetics IV. Proceedings of the Fourth International Rice Genetics Symposium, 22-27 October 2000, Los Banos, Philippines. 642. 2003
- DNA fingerprinting and phylogenetic analysis of Indian aromatic High-quality rice germplasm using panels of fluorescent-labeled microsatellite markers. Advances in rice genetics. Supplement to rice genetics IV. Proceedings of the Fourth International Rice Genentics Symposium, 22-27 October 2000, Los Banos, Philippines. 642. 2003
- Evaluation of O. sativa X O. glaberrima-derived lines using microsatellite markers. Advances in rice genetics. Supplement to rice genetics IV. Proceedings of the Fourth International Rice Genentics Symposium, 22-27 October 2000, Los Banos, Philippines. 642. 2003
- RiceGenes 5.0: an online genomic resource for the rice community. Advances in rice genetics. Supplement to rice genetics IV. Proceedings of the Fourth International Rice Genetics Symposium, 22-27 October 2000, Los Banos, Philippines. 642. 2003
- Using new alleles from wild rice Oryza rufipogon to inprive cultivated rice (O. sativa) in Latin America. Advances in rice genetics. Supplement to rice genetics IV. Proceedings of the Fourth International Rice Genetics Symposium, 22-27 October 2000, Los Banos, Philippines. 642. 2003
- Constructing comparative maps with unresolved marker order. Proceedings of the PSB, Jan. 3-7, 2002, Kaua'i, Hawaii. 2002
- Is Biotechnology an Answer?. Who Will Be Fed in the 21st Century? Feb 2000 AAAS Symposium, Washington, DC. 29-40. 2001
- Wild QTLs for Rice Improvement. Proceedings of the Chandler Symposium: Rice Research and Production in the 21st Century. June 15-17, 2000 IRRI, Philippines. 151-169. 2001
- QTL alleles from Oryza rufipogon improve the yield of an elite O. sativa cultivar. Proceedings of workshop on interspecific crossing in rice. Dec. 4-10, 1996. 1997
- Exploring the application of molecular markers for improving resistance to bacterial blight. "Rice Genetics III"; Proc., 3rd International Rice Genetics Symposium. 267-278. 1996
- Molecular mapping of blast resistance genes in rice. Proceedings of the International Symposium on Rice Blast Disease, Aug. 9-13, 1993. Madison, Wisconsin. 1996
- Comparative Mapping in the Gramineae. 1995. Classical and Molecular Cytogenetic Analysis of Cereal Genomes. US-Japan NSF Symp. 1995
- Progress in RFLP mapping of genes controlling root characters in rice. Biotechnology for Aridland Plants. IC2 Institute. The University of Texas at Austin. 153-168. 1994
- Use of molecular markers to evaluate rice genetic variation in associative N2 fixation, N uptake, and N use efficiency. Rice Roots: nutrient and water use. Selected papers from the International Rice Research Conferenc. 1994
- RFLP mapping of major and minor resistance genes in a rice cultivar with durable resistance to blast. "Durability of Disease Resistance", Proc., Symposium on Durability of Disease Resistance. 219-225. 1993
- Progress in RFLP gene tagging and marker-aided selection in rice. Proceedings of the Asia-Pacific Conference on Agricultural Biotechnology, Aug. 20-24, 1992. Beijing, China. 1992
- Development and use of restriction fragment length polymorphism in rice breeding and genetics. Rice Biotechnology. 83-107. 1991
- Recent advances in molecular mapping of the rice genome. Proceedings of the International Symposium on Rice Research: New Frontiers, Nov. 15-18, Hyderabad, India. 1990
- Tagging genes for disease and insect resistance via linkage to RFLP markers. Proceedings of the 2nd International Rice Genetics Symposium, May 1990. IRRI, Los Baños, Philippines. 1990
featured in archived article
- 2010 Einaudi Center seed grants fund projects from malaria research to documentary film
- Cornell-initiated course promotes rice expertise for the developing world
- Faculty panel united by 'the good fight' at Big Apple discussion
- Genetic tools transform 'black box experimentation' to predictive science for designing better rice
- Highly valued rice fragrance has origins in basmati rice, study finds
- New rice course in Philippines attracts host of CU students and is co-taught by Professor Susan McCouch
- Researchers receive $9.4 million from NSF for maize and rice genomics projects
- Today's white rice is mutation spread by early farmers, researchers say
Teaching
teaching overview
- I teach both undergraduate and graduate level courses: 1) PlBr201: Plants, Genes and Global Food Production, is designed to provide students with a basic understanding of the concepts and methods behind genetic improvement of crop plants. Both traditional and biotechnological approaches are discussed. The social and economic context of plant breeding is emphasized and the impact of the field on society is illustrated with specific examples. We trace the evolution of plant improvement from the pre-scientific days of crop domestication through the dawn of Mendelian genetics, to modern applications of biotechnology and genetic engineering. The course offers a blend of biology and social science, and encourages students to synthesize ideas across the traditional boundaries of academic disciplines. 2) BioPl483.1: Concepts and Techniques in Plant, Cell and Molecular Biology (PCMB) is a rapidly-paced, graduate course that is intended to cover the broad spectrum of current techniques and concepts in plant molecular biology & molecular genetics. It is required for all graduate students in the PCMB program and is based on reading and discussion of original research papers in the field. Lectures emphasize critical experimental techniques, approaches, designs and underlying hypotheses that form the basis of Plant Genomics and Plant Biology today.
teaching activities
- BIOPL-7490: Graduate Research in Botany - Spring 2013
- PLBR-5990: Plant Breeding M.P.S. Project Paper - Spring 2013
- PLBR-7900: Graduate-Level Dissertation - Spring 2013
- PLBR-8900: Master's Level Thesis Research - Spring 2013
- PLBR-9900: Doctoral-Level Dissertation Research - Spring 2013
- BIOPL-7420: Current Papers in Plant Biology - Fall 2012
- BIOPL-7490: Graduate Research in Botany - Fall 2012
- PLBR-2010: Plants, Genes, and Global Food Production - Fall 2012
- PLBR-5990: Plant Breeding M.P.S. Project Paper - Fall 2012
- PLBR-7900: Graduate-Level Dissertation - Fall 2012
- PLBR-8900: Master's Level Thesis Research - Fall 2012
- PLBR-9900: Doctoral-Level Dissertation Research - Fall 2012
- BIOPL-7490: Graduate Research in Botany - Spring 2012
- PLBR-5990: Plant Breeding M.P.S. Project Paper - Spring 2012
- PLBR-7900: Graduate-Level Dissertation - Spring 2012
- PLBR-8900: Master's Level Thesis Research - Spring 2012
- PLBR-9900: Doctoral-Level Dissertation Research - Spring 2012
- BIOPL-7490: Graduate Research in Botany - Fall 2011
- PLBR-2010: Plants, Genes, and Global Food Production - Fall 2011
- PLBR-5990: Plant Breeding MPS Project Paper - Fall 2011
- PLBR-7900: Graduate-Level Dissertation - Fall 2011
- PLBR-8900: Master's-Level Thesis Research - Fall 2011
- PLBR-9900: Doctoral-Level Dissertation Research - Fall 2011
advisees
Service
outreach overview
- 1) The primary focus of my outreach activities is on providing middle and high school students with an opportunity to participate in basic, hands-on laboratory experiments involving plant molecular genetics and to think about how research in the plant sciences contributes to addressing problems of global food production, human nutrition and environmental sustainability. 2) In collaboration with scientists at Cold Spring Harbor Lab, my group also develops and curates a large, publicly available comparative plant genome database that integrates knowledge from many different disciplines and allows students and researchers to link molecular genetic information with knowledge about the way plants grow and develop in diverse environments. This offers plant breeders an opportunity to better utilize the vast amounts of information emerging from genomics to develop improved varieties of plants to meet the need for food, fuel and fiber of the growing human population. 3) The third focus of our outreach activities is the development of a 3-week course entitled "Rice: Research to Production" that is taught at the International Rice Research Institute in the Philippines. It is designed to give students and young professionals the opportunity to become familiar with rice in its center of diversity and to establish international research collaborations early in their careers. The long term goal is to create a new generation of plant scientists that understand the importance of addressing global problems in agriculture, energy and the environment.
service to the profession
- Rice Genetics Cooperative, Sub-committee on Gene Nomenclature Committee Member 2005 -
- American Association for the Advancement of Science Faculty Fellow 2004 -
- Genetics Society of America Member 2002 -
- Life Sciences Campaign speaker’s Bureau Member 2002 -
- American Association for the Advancement of Science Chairperson 2012 - 2015
- AI-SPER-0203DF692AB00010819 Co-organizer 2009
- Scientific Advisory committee for USDA-funded RiceCAPS project Committee Member 2005 - 2009
reviewer or editor for
Background
education and training
- Ph.D. in Plant Breeding & Genetics, Cornell University 1990
- M.S. in Plant Pathology, University of Massachusetts 1982
- B.A. in Hispanic Studies, Smith College 1975
awards and honors
- Golden Sickle Award, 2007
- Outstanding Faculty Award, 2006
- AAAS Fellow, 2004
- Outstanding Mentor, Siemens Westinghouse Competition, 2003
- Outstanding Educator, 2002
- Honorary Scientist Award, 1998
- M.S. Swaminathan Outstanding Research Award, 1997
- CALS Young Faculty Teaching Excellence Award, 1996
- Richard Bradfield Award for Outstanding PhD Thesis, 1990
Other
college
- CALS
research keyword
- Database Development and Design
- Gene Discovery
- Molecular Breeding
- Rice Molecular Genetics
name prefix
- Dr.