The Vavilov Method: Utilizing Genetic Diversity

2017 Keynote Speakers

Susan McCouch

Susan McCouch

Susan McCouch, Ph.D.

Barbara McClintock Professor, Plant Breeding and Genetics

Cornell University

Bio: Dr. Susan McCouch is the Barbara McClintock Professor of Plant Breeding and Genetics in the School of Integrated Plant Sciences 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. She is well known for her pioneering studies on molecular mapping in rice and the development of genomics-based platforms to explore the extent, distribution and phenotypic consequences of genetic variation in Oryza. Researchers throughout the world utilize the molecular markers, genotyping platforms, analysis protocols and germplasm resources developed in her lab for genetics research and breeding applications. She has trained scores of young scientists who contribute to rice research nationally and internationally and has a prolific publication record. She is the recipient of numerous teaching and faculty awards, is an elected fellow of AAAS. She has served as scientific advisor on the Global Rice Science Partnership (GRiSP), the NSF Advisory Committee for International Science and Engineering (AC-ISE), and as Chair of the AAAS Section on Agriculture and Natural Resources.


Linking genome wide association studies (GWAS) and genomic selection (GS) to better utilize natural variation in rice

Susan McCouch1, Jen Spindel1, Diane Wang1, Lyza Marón1, Eliana Monteverde1, Chih-Wei Tung1, Hasina Begum2, Mark Wright1, Genevieve DeClerck1, Pavel Korniliev1,3, Anthony Greenberg1,3,6, Namrata Singh1, Hyunjung Kim1, Parminder Virk2,7, Bertrand Collard2, Edilberto Redoña2,8, Janelle Jung1, Randy Clark4,9, Leon Kochian4, Anna McClung5, Georgia Eizenga5, Francisco Agosto-Perez1,3, Deniz Akdemir1, Jason Mezey3, Jean-Luc Jannink1,4

1Dept. Plant Breeding & Genetics, Cornell University, Ithaca, NY, USA 14850
2International Rice Research Institute, Los Baños, Philippines
3Dept. Biological Statistics & Computational Biology, Cornell Univ., Ithaca, NY, USA 14850
4USDA-ARS, Robert W. Holley Center, Ithaca, NY, USA 14850
5USDA ARS, Dale Bumpers National Rice Research Center, Stuttgart, AR, USA 72160
6 Current address: Bayesic Research, LLC.  452 Sheffield Rd., Ithaca, NY  14850
7 Current address: Centro Internacional de Agricultura Tropical, Palmira, Colombia
8 Current address: Delta Research and Extension Center, Stoneville, MS
9 Current address: Pioneer Hybrid, 7000 NW 62nd Ave, Johnston, IA  50131

Abstract: Understanding the relationship between genotypic and phenotypic variation lies at the heart of the study of genetics and is also critically important to applications in plant breeding.  Here we present a genome-wide association study (GWAS) based on genotyping a rice diversity panel with a high-density SNP array and systematically phenotyping the panel for a range of agronomic, physiological and morphological traits.  Seeds conserved in global germplasm repositories, including wild rice ancestors, ancient landrace varieties and modern elite cultivars provide insight into a wide range of natural genetic variation that remains underutilized in modern rice genetics and breeding. Using high throughput sequencing and genotyping technologies, we examine genome-wide patterns of variation and document deep sub-population structure within Oryza sativa. We use GWAS to identify common variants influencing complex traits and demonstrate heterogeneity of genetic architecture across subpopulations and environments. We use genomic selection (GS) in combination with de novo GWAS to predict breeding values and improve the rate of genetic gain. This work establishes an open-source translational research platform for genome-wide association studies and genomic selection in rice that directly links molecular variation in genes and metabolic/regulatory pathways with the germplasm resources needed to accelerate varietal development and crop improvement for diverse environments.


Colin Khoury

Colin Khoury

Colin Khoury, Ph.D.

Crop Diversity Specialist

International Center for Tropical Agriculture (CIAT)
USDA National Laboratory for Genetic Resources Preservation -Ft Collins

Bio: Dr. Colin Khoury is a Crop Diversity Specialist at the International Center for Tropical Agriculture (CIAT), Colombia, and a researcher at the USDA National Laboratory for Genetic Resources Preservation in Fort Collins, Colorado. Colin's interest is in enhancing food security, human health, and the sustainability of agricultural production systems through the conservation and use of crop genetic resources. Most of the time he is researching how we can better conserve the wild relatives of our food crops and trying to understand how changes in diversity in our diets and agricultural production impact food security.


N.I. Vavilov and the geography, conservation, and use of crop diversity

Colin K. Khoury

Research Scientist, International Center for Tropical Agriculture, Cali, Colombia

Abstract: Seventy five years after N.I. Vavilov’s death, the brilliance of his botanical research continues to inspire those charged with making crops more productive, resilient, and nutritious. At the same time, the story of his courageous and ultimately tragic life remains pertinent both to the appreciation for objective science in improving human lives, and to the importance of conservation of crop genetic diversity for our long-term food security. In this presentation I recount a number of the great ironies of Vavilov’s life, and outline the scientific progress since that time in delineating the geographic patterns of crop diversity, globalizing efforts to conserve and share these genetic resources, and employing this diversity in order to respond to changing human health and agricultural production challenges.   


Paul Gepts

Paul Gepts

Paul Gepts, Ph.D.

Distinguished Professor, Plant Sciences

University of California, Davis

Bio: Dr. Paul Gepts is a native of Belgium, where he obtained his “agronomic engineering” degree, equivalent to a MS degree in the U.S. He worked for three years at the Gene Bank of the International Center for Tropical Agriculture (CIAT) in Cali, Colombia, where he led a project emphasizing the genetic resources of Phaseolus beans. His results demonstrated the interest of using runner bean (P. coccineus) and year bean (P. dumosus) as sources of genetic diversity in common bean (P. vulgaris) breeding. His PhD research at the University of Wisconsin-Madison was focused on the domestication and evolution of common bean. Following a postdoc at the University of California, Riverside, Dr. Gepts joined the faculty of the University of California, Davis, where he is now a distinguished professor, bean geneticist, and head of the bean breeding program. During his tenure at UC Davis, he has expanded his research on bean genetics, by developing genetic and genomic tools of beans, including recombinant inbred populations, BAC libraries, and PhaseolusGenes, and a marker database. His research has shown 1) the existence and gene flow in bean species, in spite of the predominant self-pollination and the potential for displacement of genetic diversity of wild beans; 2) the presence of co-evolution between the bean host and some of its fungal and bacterial pathogens based on recruitment of differential resistance specificities from the same disease resistance gene cluster; 3) the role of long-distance dispersal of ancestral bean types in establishing the current distribution of wild beans; 4) the role of farmers in traditional agriculture, including centers of domestication, in generating and maintaining crop diversity, as described in surveys of in situ diversity and molecular diversity of domestication genes. 


The Concept of Vavilovian Centers of Origin as Applied to Phaseolus, a Genus with Multiple Domestications

Paul Gepts

Dept. of Plant Sciences, University of California, Davis

Abstract: The genus Phaseolus includes no less than five domesticated species, two of which have been domesticated at least twice. Thus, this genus provides an interesting experimental model for research on crop domestication and genetic diversity, and applications to genetic conservation. After a brief review of the concept of Vavilovian center over the latest centuries until today, I will discuss this concept in the case of the genus Phaseolus, and more in detail for common bean, the domesticated species that is currently the most important economically in the genus. Following a review of the uses so far of wild beans as a source of genetic diversity, I will present more recent results from a landscape genomics study of the distribution of wild common bean combined with DNA sequence level variation, as a prerequisite to identify both accessions and genome regions potentially involved in temperature and drought tolerance.


Charles Simpson

Charles Simpson

Charles Simpson, Ph.D.

Professor Emeritus, Soil and Crop Sciences

Texas A&M University

Bio: Charles E. Simpson, Professor Emeritus of Texas A&M AgriLife Research, Texas A&M AgriLife Research and Extension Center, Stephenville, TX has been the Project Leader of the Peanut Wild Species Program since 1967 and continues in that position, semi-retired. He has developed several pathways for gene introgression. He and colleagues released the first peanut cultivars with genes introgressed into the cultigen from wild Arachis. The most significant of these was the transfer of resistance to root-knot nematode into cultivated peanut. He has been leader or co-leader and participant on 28 expeditions to collect cultivated and wild Arachis germplasm in South America. The teams have collected more than 1800 accessions of wild peanut, including more than75 new species of Arachis, more than 5000 cultivated land races and more than 500 accessions of Rhizobia. Simpson entered Texas A&M University in 1960, where he earned a BS in Agr. Education in1963. He received a NDEA Graduate Fellowship, whereby he earned a MS in 1966 and his PhD in 1967, in Plant Breeding and Cytogenetics at Texas A&M University. In September 1967 he was employed as Peanut Breeder at the West Cross Timbers Experiment Station at Stephenville, Texas, which was later designated as a Research and Extension Center of the Texas Agricultural Experiment Station. From the very beginning he has been involved in the biodiversity in the genus Arachis. Simpson was promoted to Full Professor in 1984. In 1979 he was appointed to the Graduate Faculty of Texas A&M University.  He has been author or co-author on 20 peanut variety releases and Registrations with Crop Science; he served on the Crop Registration subcommittee for Peanut for more than 30 years; he received the Meyer Medal in 1993 for his work on collection, maintenance, distribution and utilization of Arachis germplasm, and in 2015 he was selected to present the Calvin Sperling Memorial Lecture on Biodiversity at the ASA CSSA SSSA meetings. Simpson is author or co-author on a total of 124 refereed journal articles, author or co-author on 14 book chapters, and he co-translated the Peanut Monograph from Spanish to English. In 1983 Simpson was a PI on the first Peanut CRSP, and has continued activities with that program and its replacement, PMIL, to this day. He trained and helped train 14 different persons in that program. Simpson has served on graduate committees of more than 16 MS and PhD students, serving as co-chair of 7 students. He has also mentored numerous MS and PhD students from Argentina and Brazil.


Collecting, Preserving and Utilizing Genetic Diversity in Arachis

Charles E. Simpson

Texas A&M University

Abstract: The genus Arachis originated on the old Brazilian Shield after a mid-Tertiary uplift of the Shield, probably in the area that is now southwest Brazil or northeast Paraguay. Remnants of the old, eroded Shield are still evident in that area and the two most primitive species, based on morphological classification, continue to reside there today. From that origin of the genus, the species, 81 described to date, have evolved and have been dispersed, mostly by running water to an area as follows: starting at an island in the mouth of the Amazon, westward to north Bolivia, then southward along the eastern Cordillera of the Andes (up to 2000 meters), to northern Argentina; from there, then east to the Rio La Plata and southern Uruguay, then north back to the Amazon. Another 12 to 15 species have been collected and are in various stages of evaluation to be described soon. It is projected that the total number of species will reach 115. There have been nine taxonomic sections described, and the largest number of species has been assigned to the most advanced section Arachis which includes the cultigen, Arachis hypogaea L. The cultivated peanut is a tetraploid with 2n=4x=40 chromosomes, but most all of the wild relatives only have 20, except for one group of the section Rhizomatosae which also has 40, and a group of four species which has just 18. The cultivated peanut is a relatively young species originating about 3500 years ago in the gardens of hunters/gatherers somewhere in the western part of Argentina and/or Peru. Despite significant morphological differences in the two taxonomic sub-species and six botanical varieties of the cultigen, A. hypogaea is recognized as having a narrow genetic base. Numerous useful traits for improvement of the cultigen have been identified within the wild species of Arachis. Some of these traits include: disease resistance, insect resistance and drought tolerance, as well as improved quality traits to enhance the edible condition of peanut. To date, we have introgressed genes for resistance to two root-knot nematode species, early and late leafspot resistance, rust and web-blotch resistance, leaf feeding larva resistance and increased oil content. We are developing introgression pathways for other traits, including drought tolerance and white mold resistance. Our primary objective is to utilize the wild relatives of Arachis to improve peanut cultivars.


L.J. Grauke

L.J. Grauke

L.J. Grauke, Ph.D.


National Collection of Genetic Resources for Pecans and Hickories

Bio: L.J. Grauke is Curator of the National Collection of Genetic Resources for Pecans and Hickories (NCGR-Carya). The collection is the major germplasm repository for the genus Carya in the United States, and is dedicated to the collection, maintenance, evaluation, characterization and distribution of world genetic resources for that genus. He has made collections of pecans and hickories throughout the United States as well as in Mexico, Vietnam, and China, developing and maintaining the living collections that comprise the NCGR -Carya.  He has worked to develop reliable molecular genetic markers to characterize the geographic distribution of genetic diversity across the genus.  Grauke is Research Horticulturist for the USDA-ARS Pecan Breeding & Genetics program. The major objective of that program is the development of improved pecan cultivars and rootstocks for all U.S. production areas. He contributed to the release of several pecan cultivars currently in use by the pecan industry.  In addition to the routine evaluation of selections under test, research is also conducted for the improvement of selection criteria using standard field observations and molecular genetic techniques.


Carya: The Next Generation

LJ Grauke

USDA ARS Pecan Breeding & Genetics

Abstract: The USDA ARS National Collection of Genetic Resources for Carya (NCGR-Carya) has been dramatically impacted by Vavilov’s contributions.  However, the constraints of our genus create unique challenges.  Pecan [Carya illinoinensis] is a large, slow to bear, long-lived, wind-pollinated, out-breeding, deciduous tree species native to North America and Mexico.  The archaeological record of Carya nut use by humans spans over 10,000 years, while pecan cultural development in grafted orchards began in the mid 1800’s. Diverse stands of largely unmanaged native trees compete in the market with nuts from intensively managed orchard systems. Co-evolved insects and diseases exert selection and management pressure and provide targets for improvement through breeding. The USDA Pecan Breeding Program began in 1930, with the goal of producing large crops of high quality nuts for use in regionally diverse, grafted pecan orchards.  Until 1998, the USDA effort was the only pecan breeding program. The cultivars used as parents by the first breeder became the core of the National Clonal Germplasm Repository for Pecans and Hickories when it was designated in 1984. At the first meeting of the ad hoc Crop Germplasm Committee in 1984, a Vavilovian strategy was adopted to collect range wide native populations of pecans to represent variation related to distribution. Since seed does not maintain viability in storage it is necessary to maintain collections as living trees. This provides the opportunity to observe patterns of variation in tree performance related to geographic origin. Repository collections have been the foundation for the development of molecular genetic methods of characterization in Carya, and have been pursued in conjunction with refinement of phenotypic descriptors necessary for selection in the breeding program. The first few microsatellite markers (SSRs) were used for cultivar verification and analysis of the geographic distribution of genetic diversity. Appropriate targets for use as reference genomes were identified and sequencing initiated. Utility of the draft template sequence has engaged a broader team of scientists in the characterization of diversity.  How that diversity can be productively and cooperatively integrated into development of multiple national and international breeding programs, while protecting the diversity and resilience of native populations and producers, is a challenge for the next generation to which Vavilov’s concepts continue to contribute.


Emily Combs

Emily Combs

Emily Combs, Ph.D.

Corn Breeder

DuPont Pioneer

Bio:  Dr. Emily Combs is a Research Scientist for DuPont Pioneer in Mankato, MN. Dr. Combs is a corn breeder whose research focuses on increasing genetic diversity in 95-105 CRM corn. She received her Ph.D. in Applied Plant Sciences for the University of Minnesota -- Twin Cities where she was advised by Dr. Rex Bernardo and researched genome wide selection in corn. She received her Bachelor of Science in Biology with a concentration in genetics and development from Cornell University.


Diversity breeding at DuPont Pioneer

Emily Combs

DuPont Pioneer

Abstract: Breeding with diverse germplasm is an important tool for breeders as we strive to continue improving yields while confronting new environmental conditions and disease pressures.  Introducing diverse germplasm can allow breeders to immediately improve specific traits, to increase overall genetic variation and hence genetic gain, and to hedge against future breeding pressures.  Here two examples of diversity breeding in a commercial program will be presented; one which targets a qualitative disease resistance trait in soybeans and one which targets a quantitative disease resistance trait in canola.  Finally, a reflection on the successes and main challenges faced every day in a commercial corn breeding diversity program.