Accessing genetic diversity for crop improvement
Introduction
Genetic resources enable plant breeders to create novel plant gene combinations and select crop varieties more suited to the needs of diverse agricultural systems. A wealth of germplasm is accessible worldwide, with about 6 million accessions held in over 1400 gene banks [1]. Yet the collections are barely tapped (less than 1%) [2] by breeders, owing to the scarcity of information on accessions other than their taxonomic status and geographical origin.
Genome analysis tools provide access to thousands of polymorphisms, thus considerably broadening our capacity to monitor genetic diversity. Our whole approach to ecology and biological adaptation has been enriched [3, 4]. Arabidopsis thaliana – the first plant with a sequenced genome – was used to develop and explore innovative applications including high-density array re-sequencing and genome-wide association mapping [5, 6, 7, 8•]. Given their economic importance, major crops have also benefited from early investment in genomics. However, crops are not like wild plants in natural populations, that is, they have undergone and are still undergoing domestication. This is a complex anthropogenic process caused by numerous human populations with specific habits and needs [9•].
Over the past five years, an increasing number of studies have been carried out on the molecular diversity of crop plants and their wild relatives, illustrating various facets of the domestication process and suggesting ways of devising targeted approaches to access the diversity conserved in ex situ germplasm collections. Soon it will be possible to determine and compare the whole sequence of hundreds of accessions. We therefore advocate identification of a common set of reference materials to help R.E.A.D. (Represent existing diversity – Enter the whole collection – Assess phenotypic variation – Dissect trait–gene associations) germplasm through concerted efforts within the research community.
Section snippets
Unraveling the drivers of crop evolution
Over the past 12 000 years, humans have sampled, selected, cultivated, travelled through, and colonized new environments, thus inducing a plethora of bottlenecks, drifts, and selection. Plant breeders have accelerated the whole process by selecting preferred genotypes. Meanwhile, evolution was progressing, some genomes were being reshuffled and genes occasionally mutated. Overall, plant domestication tailored plant development and adaptation to meet the needs of human populations [10, 11, 12, 13•
Organizing access to diversity
Access to genetic diversity contained in large germplasm collections continues to be a significant challenge. The core collection concept [52] was developed 25 years ago to facilitate access to the diversity available in these large collections. The idea is to identify a representative manageable sample upon which analysis will be concentrated before re-exploring broader ranging materials. The rationale underlying core collections has been thoroughly discussed [53•] and for many species has led
Conclusion
Genome studies applied to crop germplasm shed light on the role of selection, foundations, migrations, and introgressions on population patterns, genomic associations, and genic diversity. Thanks to the sharply declining cost of genotyping technologies, it is now possible to make surveys that can be equally broad and whole-genome oriented [67•], or targeted on specific genes of suspected function. The history and diversity of crops can then be analyzed as are those of human populations [68, 69•
References and recommended reading
Papers of particular interest, published within the annual period of review, have been highlighted as:
• of special interest
•• of outstanding interest
Acknowledgements
The authors are thankful to the Generation Challenge Programme (JCG, HDU, RKV), the Agropolis Foundation, France (JCG), the Indian Council of Agricultural Research (ICAR), and the Department of Biotechnology, Government of India (RKV) for sponsoring research on genetic diversity in their laboratories. Thanks are also due to Andreas Graner of the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany, for useful suggestions and discussion on this manuscript.
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