Reference genome sequences from many important crops and several model plant species are enabling a number of new applications of crop comparative genomics.
Compared with previous methods, comparative resequencing and high-density SNP genotyping permit much more detailed examination of crop evolutionary history and improve the potential to identify loci that are involved in plant domestication and improvement.
Genome-wide association studies and a new generation of genetic-mapping populations will improve assessment of the genetic basis of trait variation.
Deleterious mutations in individual genomes can be identified and selected against or even repaired.
Genomic selection or genome-wide marker-assisted selection can incorporate prior information on the effects of markers and accelerate plant breeding cycles.
The completion of reference genome sequences for many important crops and the ability to perform high-throughput resequencing are providing opportunities for improving our understanding of the history of plant domestication and to accelerate crop improvement. Crop plant comparative genomics is being transformed by these data and a new generation of experimental and computational approaches. The future of crop improvement will be centred on comparisons of individual plant genomes, and some of the best opportunities may lie in using combinations of new genetic mapping strategies and evolutionary analyses to direct and optimize the discovery and use of genetic variation. Here we review such strategies and insights that are emerging.
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We thank the US Department of Agriculture (USDA)–US National Institute for Food and Agriculture (NIFA) (2011-68002-30029) for partial support for P.L.M., USDA–NIFA (2009-01864) for J.R.-I. and the USDA Agriculture Research Service and the National Science Foundation (NSF)–Plant Genome Research (0820691) and NSF–Division of Biological Infrastructure (0965342) for support to E.S.B. The authors are grateful to J. Gerke, A. Gonzales, M. Hufford, D. Segal, R. Stupar and three anonymous referees for comments on the manuscript.
The authors declare no competing financial interests.
- Genome-wide association studies
(GWASs). Studies that search for a statistical association between a phenotype and a particular allele by screening loci (most commonly by genotyping SNPs) across the entire genome.
Unlike orthologous genes, which trace their common origin to a locus in an ancestral species, paralogous loci consist of gene copies that trace their common origin to a duplication event within a genome.
- Linkage disequilibrium
(LD). Nonrandom association of alleles at two or more loci. The pattern and extent of LD in a genomic region is affected by mutation, recombination, genetic drift, natural selection and demographic history.
A temporary marked reduction in population size.
- Site frequency spectrum
The distribution of allele frequencies in a population: essentially a count of the number of alleles in a population at a given frequency.
- Genetic drift
Fluctuations in allele frequencies that are due to the effects of random sampling.
The mixing of two or more genetically differentiated populations.
The incorporation of genetic material from one population or species into another by hybridization and backcrossing.
The combination of alleles or genetic markers found on a single chromosome of an individual.
- Selective sweeps
Increases in frequency of an allele and closely linked chromosomal segments that are due to positive selection. Sweeps initially reduce variation and subsequently lead to a local excess of rare alleles as new unique mutations accumulate.
- Standing variation
Variation for a locus or trait that is polymorphic in a population.
Otherwise known as 'hybrid vigour', heterosis is the phenomenon whereby progeny of a cross between genetically distinct parents have greater fitness than either of the parental types.
- Purifying selection
Selection against a deleterious allele.
- Ascertainment bias
Sampling bias that arises from how SNPs are chosen for inclusion on SNP arrays; SNPs that are known to be polymorphic in a particular population will have frequencies that are higher than would be expected by random sampling alone.
- Hill–Robertson effect
The reduction in efficacy of selection at a locus owing to selection at linked loci.
- Dobzhansky–Muller effects
Intrinsic reductions in viability or fertility resulting from epistatic interactions between multiple substitutions, typically observed in the offspring of a cross between individuals from genetically distinct populations.
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Morrell, P., Buckler, E. & Ross-Ibarra, J. Crop genomics: advances and applications. Nat Rev Genet 13, 85–96 (2012). https://doi.org/10.1038/nrg3097
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