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some segments from diverse inbreds are recombined into sets of inbreds by a very large number of recombination events, and the plants are compared in ways that allow the roles of individual chromosome segments to be inferred6,7. The chromosome segments are also being defined by their molecular polymorphisms and by the genes they carry, allowing them to be tracked throughout the breeding process. However, a very large number of defined polymorphisms will be required to uniquely mark all alleles. This has recently become possible with whole-genome sequencing technologies1,3.

Integration of the new genomics technolo-gies with traditional breeding strategies will also empower breeders in their efforts to design and select the best combinations of chromosome segments, genes and alleles available in the species to meet commercial

From genomics to crop breedingRichard Flavell

New insights into the maize genome must be incorporated into breeding programs to realize the potential of crop genomics.

A collection of recent papers in Science and PLoS Genetics1–7 represents a landmark in plant biology and an indispensable resource for efforts to improve maize by breeding. The papers include the draft genome sequence of an inbred maize line1; analyses of the chro-mosomal organization of genes, microRNAs and transposable elements1,3; comparisons between the genomes of some agriculturally relevant inbred lines4; and transcriptional profiles of some of the same inbred lines and of hybrids generated from crosses between them2,5. The wealth of information in these reports should accelerate breeding projects aimed at generating superior varieties of corn and other crops.

Over 1 billion people eat maize or meat from maize-fed livestock. Maize also provides the raw materials for manufactured products ranging from coatings for paper and cloth to biodegradable plastics and biofuel. Average maize yields over the past 40 years have doubled in the United States, although not elsewhere. This success was due in part to breeding of better-performing hybrids, which are generated by combining the genomes of inbred plants from different genetic groups. There remains much scope for continuing to improve maize yields by exploiting the yield gain in hybrids relative to their inbred parents, a phenomenon known as heterosis. But to support the world’s growing popula-tion, it will be necessary to enhance the rate of increase in the productivity of maize and other crops, especially in inhospitable cli-mates. This challenge will likely be addressed through better farming, more reliable seed supplies and more stable markets, as well as by the application of genomics technologies to breeding of superior varieties.

As most commercially relevant plant phe-notypes depend on the interactions of large numbers of genes and also on the positions of genes with respect to one another and to sites of recombination, plant breeding is an activity that involves whole genomes. Any plant breeder would like to know, first, how every chromosomal segment, gene or allele—

alone and in combination with others—con-tributes to specific traits, and, second, how to alter the genome to manipulate traits at will. Historically, these goals remained out of reach because knowledge of gene–trait asso-ciations was limited by the need to measure traits in the field and to define their genetic basis by the inadequate trait mapping pro-cedures of classical and statistical genetics (right side of Fig. 1). With the advent of genomics technologies, breeders can char-acterize the allelic content of their particu-lar germplasm in exquisite detail throughout the breeding program and so preserve the most valuable allele combinations (left side of Fig. 1).

Progress in identifying gene–trait asso-ciations for maize is being achieved by con-structing and analyzing “nested association mapping” lines. In this approach, chromo-

Richard Flavell is at Ceres, Inc., Thousand Oaks, California, USA. e-mail: rflavell@ceres.net

Figure 1 A highly simplified scheme illustrating how genomics can contribute to steps in a maize-hybrid breeding pipeline. Plants selected from parent inbred improvement programs are used in crosses to make F1 hybrids that are then evaluated. F1 hybrids with improved performance are then adopted for commercialization. Historically, traits could not be managed efficiently as the causal DNA sequences remained largely unknown and their existence was recognized only through the use of extensive field trials (right side). New genomics technologies to determine complete genomes, DNA polymorphisms, whole genome expression patterns and chromosomal haplotype blocks (reflecting recombination patterns) now make it possible to build detailed gene-trait associations and manage such associations throughout the breeding program, including the selection of combinations of alleles (left side). The combined use of trait assessments in the field and genomics technologies increases the efficiency of crop breeding.

Diverse population ofplants/chromosomes

Gene-trait associations

Selection of potential inbred parents of higher-

yielding hybrids

Crossing of inbredsto make hybrids

Selection and evaluation of heterotic hybrids for commerce

Genome-widegenotyping

Trait analysis infields at multiple

locations

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technology systems) to fully exploit the new genomic information, suggesting that the gap between those who have this capability and those who do not will continue to widen.

Those who stand to benefit especially from these reports1–7 are the breeders in the public sector and small companies that are seeking to provide improved lines for poorer societ-ies. Foremost among them is the Consultative Group on International Agricultural Research and its tropical maize breeding efforts spearheaded by the International Maize and Wheat Improvement Center (Centro Internacional de Mejoramiento de Maíz y Trigo; CIMMYT). CIMMYT has struggled to fully embrace genomics and has lagged behind the leading private sec-tor companies in exploiting genomics in its breeding program, on which so many depend. Let us hope that these publications will prove sufficiently compelling to inspire their government funders and other public-sector breeders to expedite the application of genomics 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).

combinations and hybrids. Vielle-Calzada et al.3 defined >100 regions characterized by low genetic diversity among maize lines. These regions may therefore be associated with traits that contributed to domestica-tion (such as a larger number of kernels that remain attached to the cob and lack a stony casing) and consequently have been selected

in all modern maize breeding programs. Other regions are highly polymorphic and may therefore be associated with adaptation to different geographic regions and sources of variation that breeders select and elabo-rate.

The largest maize-breeding companies have probably already sequenced many corn genomes, or parts of them, and they have much more accurate information on pheno-types of lines in a wide array of environments than the public sector does. Nevertheless, the studies1–7 will provide these companies with much new data and analyses that will be used to drive their breeding programs. Unfortunately, most smaller companies lack the resources (e.g., databases and information

criteria for crop improvement (Fig. 1). The recent papers1–7 will guide selection of par-ents by clarifying the substantial differences in active gene contents between different maize inbreds. Assuming that a major basis of heterosis is the complementation of these differences in inbreds1,2, the new information provides pointers as to which parents should complement well in heterotic hybrids.

Interestingly, the genome-wide expression studies of Swanson-Wagner et al.5 suggest that there is much differential gene expres-sion between alleles in hybrids relative to the inbred parents and that this is driven pri-marily by the paternal allele of trans-acting expression quantitative trait loci—genes that exert their effect by regulating the expres-sion of other genes, often elsewhere in the genome. This provocative finding raises the question of the extent to which heterosis depends also on epigenetic and parent-of-origin imprinting effects, and of whether breeders should therefore focus on these loci, in particular when making crosses in specific directions.

The positions and frequencies of recom-bination events relative to the positions of diverse alleles influence tremendously the efficiencies of improved plant production because they determine how readily new combinations of alleles are created. Gore et al.4 revealed that some 21% of genes lie in low-recombination regions around the centromeres and, thus, that variation in these genes is difficult to exploit in breed-ing, except by means of new chromosome

Soybean is the most recent addition to the rapidly growing list of crops for which a high-

quality draft genome is now available. Writing in Nature, Schmutz et al.1 report that the

1.1-gigabase soybean genome—the largest shotgun-sequenced plant genome—is predicted to encode 46,000 genes. Two genome duplication events are likely

to account for the observation that ~75% of these genes are found in multiple copies. Although the importance of soybean as a source of protein and oil alone testifies to the potential implications of understanding its genetic makeup, this genome will also serve as the reference for ~20,000 leguminous species that play a critical ecological role through their unique ability to fix nitrogen with the help of rhizobial bacteria. Availability of the genome should accelerate the association of quantitative

trait loci of nutritional, economic and ecologically important traits with the causal DNA sequences from soybean in the near future. In the longer term, the genome will likely also be leveraged to improve the way in which a range of leguminous subsistence crops are used to both replenish soil nitrogen through crop rotation and meet the expanding needs of developing nations for protein and energy.Peter Hare

1. Schmutz, J. et al. Nature 463, 178–183 (2010).

Spilling the beans on legume biology

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The wealth of information in these reports should accelerate breeding projects aimed at generating superior varieties of corn and other crops.

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