Ontology engineering

news and viewsFrom genomics to crop breedingRichard FlavellNew insights into the maize genome must be incorporated into breeding programs to realize the potential of cropgenomics.© 2010 Nature America, Inc. All rights reserved.A collection of recent papers in Science andPLoS Genetics 1–7 represents a landmark inplant biology and an indispensable resourcefor efforts to improve maize by breeding. Thepapers include the draft genome sequence ofan inbred maize line 1 ; analyses of the chromosomalorganization of genes, microRNAsand transposable elements 1,3 ; comparisonsbetween the genomes of some agriculturallyrelevant inbred lines 4 ; and transcriptionalprofiles of some of the same inbred lines andof hybrids generated from crosses betweenthem 2,5 . The wealth of information in thesereports should accelerate breeding projectsaimed at generating superior varieties ofcorn and other crops.Over 1 billion people eat maize or meatfrom maize-fed livestock. Maize also providesthe raw materials for manufactured productsranging from coatings for paper and cloth tobiodegradable plastics and biofuel. Averagemaize yields over the past 40 years havedoubled in the United States, although notelsewhere. This success was due in part tobreeding of better-performing hybrids, whichare generated by combining the genomes ofinbred plants from different genetic groups.There remains much scope for continuingto improve maize yields by exploiting theyield gain in hybrids relative to their inbredparents, a phenomenon known as heterosis.But to support the world’s growing population,it will be necessary to enhance the rateof increase in the productivity of maize andother crops, especially in inhospitable climates.This challenge will likely be addressedthrough better farming, more reliable seedsupplies and more stable markets, as well asby the application of genomics technologiesto breeding of superior varieties.As most commercially relevant plant phenotypesdepend on the interactions of largenumbers of genes and also on the positionsof genes with respect to one another and tosites of recombination, plant breeding is anactivity that involves whole genomes. Anyplant breeder would like to know, first, howevery chromosomal segment, gene or allele—Richard Flavell is at Ceres, Inc., Thousand Oaks,California, USA.e-mail: rflavell@ceres.netalone and in combination with others—contributesto specific traits, and, second, howto alter the genome to manipulate traits atwill. Historically, these goals remained out ofreach because knowledge of gene–trait associationswas limited by the need to measuretraits in the field and to define their geneticbasis by the inadequate trait mapping proceduresof classical and statistical genetics(right side of Fig. 1). With the advent ofgenomics technologies, breeders can characterizethe allelic content of their particulargermplasm in exquisite detail throughoutthe breeding program and so preserve themost valuable allele combinations (left sideof Fig. 1).Progress in identifying gene–trait associationsfor maize is being achieved by constructingand analyzing “nested associationmapping” lines. In this approach, chromo-Genome-widegenotypingDiverse population ofplants/chromosomesGene-trait associationsSelection of potentialinbred parents of higheryieldinghybridsCrossing of inbredsto make hybridsSelection andevaluation of heterotichybrids for commercesome segments from diverse inbreds arerecombined into sets of inbreds by a verylarge number of recombination events, andthe plants are compared in ways that allowthe roles of individual chromosome segmentsto be inferred 6,7 . The chromosome segmentsare also being defined by their molecularpolymorphisms and by the genes they carry,allowing them to be tracked throughoutthe breeding process. However, a very largenumber of defined polymorphisms will berequired to uniquely mark all alleles. Thishas recently become possible with wholegenomesequencing technologies 1,3 .Integration of the new genomics technologieswith traditional breeding strategies willalso empower breeders in their efforts todesign and select the best combinations ofchromosome segments, genes and allelesavailable in the species to meet commercialTrait analysis infields at multiplelocationsFigure 1 A highly simplified scheme illustrating how genomics can contribute to steps in a maize-hybridbreeding pipeline. Plants selected from parent inbred improvement programs are used in crosses tomake F 1 hybrids that are then evaluated. F 1 hybrids with improved performance are then adopted forcommercialization. Historically, traits could not be managed efficiently as the causal DNA sequencesremained largely unknown and their existence was recognized only through the use of extensive fieldtrials (right side). New genomics technologies to determine complete genomes, DNA polymorphisms,whole genome expression patterns and chromosomal haplotype blocks (reflecting recombinationpatterns) now make it possible to build detailed gene-trait associations and manage such associationsthroughout the breeding program, including the selection of combinations of alleles (left side). Thecombined use of trait assessments in the field and genomics technologies increases the efficiency ofcrop breeding.144 volume 28 number 2 february 2010 nature biotechnology