Gene banks Challenges for the future

Susan McCouch Dept. Plant Breeding & Genetic Cornell University Grand Challenges

• Population & income growth • Land & water resources • Climate change

• Nutrition, Health, Biosafety • Sustainability Gene Banks

• Gene banks exist to conserve the genetic diversity of wild and domesticated organisms that humans depend on for food, fiber, medicine & energy. • Over 7 million plant germplasm accessions are housed in ~1,750 national and international gene banks. • Most accessions are poorly characterized; few are ever used. • Gene banks manage both genetic resources and information about those resources. • Diverse genetic resources are essential to improving the productivity, nutritional quality and sustainability of agricultural systems. • Rapid scientific/ technological developments have changed the way scientists explore and understand natural variation. • Gene bank managers must stay abreast of scientific developments to fulfill their responsibilities to the public. We are standing at the threshold of a genomics revolution within our gene banks….

• Genomics impacts every aspect of gene bank activities: – Collection and conservation – Documentation, characterization, evaluation – Distribution and dissemination

• The creation of “Digital Gene Banks” based on DNA fingerprints will help gene banks become more efficient, cost‐effective, & informative as collectors, conservers, and providers of germplasm and information DNA fingerprints

– Provide a unique genetic “bar‐code” for each accession – Facilitate tracking of accessions in & out of the gene bank – Assess genetic similarity within and between accessions – Identify potential duplicates within and across collections – Evaluate population structure – Classify types of admixture and introgression – Find novel alleles and genome‐wide archetypes – Understand genotype ‐ phenotype relationships – Create databases for cross‐species comparisons – Develop new querying tools and on‐line ordering system A FEW EXAMPLES FROM MY OWN WORK Basmati rice is genetically more closely related to Chinese japonica than to Indian indica

indica Basmati has long tropical japonica slender grain

Morphologically, it looks more like indica than its closer japonica relatives.

In the scientific

temperate literature and in aus japonica legend, it is referred to as indica rice Basmati Garris et al. (2005) Genetics The Silk Road is key to understanding the genetics Sub‐population structure of O. glaberrima • Single domestication from African O. barthii ancestor •3 cryptic domesticated groups plus admixture with O. sativa •Groups not defined geographically (no “isolation by distance”) •Genetic groups associated with ecology (Portères, 1970)

• floating • non‐floating • upland

Nigeria sativa

O. ‐

Semon et al. (2005) The population structure of African cultivated rice Oryza glaberrima. Genetics 169:1639‐1647 New insights into how to utilize hidden variation

• It has irrevocably altered our understanding of the genetic potential of wild & exotic germplasm in plant improvement

O. glaberrima NERICA O. sativa

6.3% O. glaberrima (93.7% O. sativa) Genomics is changing the face of plant breeding

using genomics & information technology QUESTIONS FOR GENE BANK MANAGERS HOW SHOULD WE MANAGE SPECIALIZED GENETIC STOCKS?

• Mapping populations, mutants and diversity panels are widely used for quantitative genetic analysis, gene discovery, and germplasm characterization; all require careful management, tracking and dissemination to maintain their utility.

• Should gene banks extend their activities by collaborating with the research community and participating in this process?

• Should “genetic stocks” be be put into short‐medium term storage, while other gene bank accessions are of long‐term interest? Use of gene bank holdings

• How will the availability of whole genome sequence change the way recommendations are made or accessions are selected by gene bank managers? • How will users interact with the progressive accumulation of genomic information about the genetic resources housed in ex situ collections? • Will the growing body of genomic information impact the type of germplasm to be maintained in gene banks in the future? • Will it ultimately expand the utilization of gene bank holdings? How will users interact with the data?

• Databases are needed to track, store, analyze and distribute genotypic and phenotypic data connected to genetic resources • Common standards must be adopted for acquiring, indexing, defining, organizing, and sharing genotypic and phenotypic data across laboratories and disciplines • A coordinated, distributed network of statisticians, computational biologists, population geneticists, and computer programmers must be added to the team of gene bank scientists to help analyze and interpret genomic data Conserving and utilizing diversity

• Gene banks conserve living samples that bridge the past and the future

• They complement investments in in situ conservation => conserve complex communities of locally adapted organisms living in dynamic ecological equilibrium

• Genomics, if used wisely, can help us make better use of gene bank collections as we seed to address the grand challenges of the future