Ontology engineering

news and views© 2010 Nature America, Inc. All rights reserved.criteria for crop improvement (Fig. 1). Therecent papers 1–7 will guide selection of parentsby clarifying the substantial differencesin active gene contents between differentmaize inbreds. Assuming that a major basisof heterosis is the complementation of thesedifferences in inbreds 1,2 , the new informationprovides pointers as to which parents shouldcomplement well in heterotic hybrids.Interestingly, the genome-wide expressionstudies of Swanson-Wagner et al. 5 suggestthat there is much differential gene expressionbetween alleles in hybrids relative to theinbred parents and that this is driven primarilyby the paternal allele of trans-actingexpression quantitative trait loci—genes thatexert their effect by regulating the expressionof other genes, often elsewhere in thegenome. This provocative finding raises thequestion of the extent to which heterosisdepends also on epigenetic and parent-oforiginimprinting effects, and of whetherbreeders should therefore focus on these loci,in particular when making crosses in specificdirections.The positions and frequencies of recombinationevents relative to the positions ofdiverse alleles influence tremendously theefficiencies of improved plant productionbecause they determine how readily newcombinations of alleles are created. Goreet al. 4 revealed that some 21% of genes liein low-recombination regions around thecentromeres and, thus, that variation inthese genes is difficult to exploit in breeding,except by means of new chromosomecombinations and hybrids. Vielle-Calzadaet al. 3 defined >100 regions characterizedby low genetic diversity among maize lines.These regions may therefore be associatedwith traits that contributed to domestication(such as a larger number of kernels thatremain attached to the cob and lack a stonycasing) and consequently have been selectedThe wealth of information inthese reports should acceleratebreeding projects aimed atgenerating superior varieties ofcorn and other crops.in all modern maize breeding programs.Other regions are highly polymorphic andmay therefore be associated with adaptationto different geographic regions and sourcesof variation that breeders select and elaborate.The largest maize-breeding companieshave probably already sequenced many corngenomes, or parts of them, and they havemuch more accurate information on phenotypesof lines in a wide array of environmentsthan the public sector does. Nevertheless,the studies 1–7 will provide these companieswith much new data and analyses that willbe used to drive their breeding programs.Unfortunately, most smaller companies lackthe resources (e.g., databases and informationtechnology systems) to fully exploit the newgenomic information, suggesting that the gapbetween those who have this capability andthose who do not will continue to widen.Those who stand to benefit especially fromthese reports 1–7 are the breeders in the publicsector and small companies that are seekingto provide improved lines for poorer societies.Foremost among them is the ConsultativeGroup on International AgriculturalResearch and its tropical maize breedingefforts spearheaded by the InternationalMaize and Wheat Improvement Center(Centro Internacional de Mejoramientode Maíz y Trigo; CIMMYT). CIMMYT hasstruggled to fully embrace genomics andhas lagged behind the leading private sectorcompanies in exploiting genomics inits breeding program, on which so manydepend. Let us hope that these publicationswill prove sufficiently compelling to inspiretheir government funders and other publicsectorbreeders to expedite the application ofgenomics in crop breeding.COMPETING INTERESTS STATEMENTThe author declares no competing financial interests.1. Schnable, P.S. et al. Science 326, 1112–1115(2009).2. Springer, N.M. et al. PLoS Genet. 5, e1000734(2009).3. Vielle-Calzada, J.-P. et al. Science 326, 1078 (2009).4. Gore, M.A. et al. Science 326, 1115–1117 (2009).5. Swanson-Wagner, R.A. et al. Science 326, 1118–1120 (2009).6. McMullen, M.D. et al. Science 325, 737–740(2009).7. Buckler, E.S. et al. Science 325, 714–718(2009).Spilling the beans on legume biologySoybean is the most recentaddition to the rapidly growinglist of crops for which a highqualitydraft genome is nowavailable. Writing in Nature,Schmutz et al. 1 report that the1.1-gigabasesoybeangenome—thelargest shotgunsequencedplantgenome—ispredictedto encode46,000 genes.Two genomeduplicationevents are likelyRoy Kaltschmidtto account for the observationthat ~75% of these genesare found in multiple copies.Although the importanceof soybean as a source ofprotein and oil alone testifiesto the potential implicationsof understanding its geneticmakeup, this genome willalso serve as the reference for~20,000 leguminous speciesthat play a critical ecologicalrole through their unique abilityto fix nitrogen with the help ofrhizobial bacteria. Availability ofthe genome should acceleratethe association of quantitativetrait loci of nutritional,economic and ecologicallyimportant traits with the causalDNA sequences from soybeanin the near future. In the longerterm, the genome will likelyalso be leveraged to improvethe way in which a range ofleguminous subsistence cropsare used to both replenish soilnitrogen through crop rotationand meet the expanding needsof developing nations forprotein and energy.Peter Hare1. Schmutz, J. et al. Nature 463, 178–183 (2010).nature biotechnology volume 28 number 2 february 2010 145