Molecular and functional diversity of maize
Edward S Buckler1,Brandon S Gaut2and Michael D McMullen3
Over the past10000years,man has ud the rich genetic
diversity of the maize genome as the raw material for
domestication and subquent crop improvement.Recent
rearch efforts have made tremendous strides toward
characterizing this diversity:structural diversity appears to be
largely mediated by helitron transposable elements,patterns of
diversity are yielding insights into the number and type of genes
involved in maize domestication and improvement,and
functional diversity experiments are leading to allele mining for
future crop improvement.The development of genome
quence and germplasm resources are likely to further
accelerate this progress.
Address
1USDA-ARS;Department of Plant Breeding&Genetics,Cornell
University,Ithaca,New York14853,USA
2Department of Ecology and Evolutionary Biology,University of
California,Irvine,California92697,USA
3USDA-ARS;Department of Agronomy,University of Missouri,
Columbia,Missouri65211,USA
Corresponding author:Buckler,Edward S(esb33@cornell.edu)
Current Opinion in Plant Biology2006,9:172–176
This review comes from a themed issue on
Genome studies and molecular genetics
Edited by Susan R Wessler
Available online3rd February2006
1369-5266/$–e front matter
#2006Elvier Ltd.All rights rerved.
DOI10.1016/j.pbi.2006.01.013
Introduction
The maize genome is a source of tremendous phenotypic
and molecular diversity.Indeed,when considering nucleo-
tide polymorphism in genes,two maize lines are on aver-
age as diverged from one another as humans are from
chimpanzees[1,2].Such abundant variation wasfirst ud
by Native Americans for domestication,and continues to
be harnesd today by modern breeders for crop improve-
ment.Here,we discuss recent advances in studies on the
molecular and functional diversity of maize,including
incread understanding of genome rearrangements and
thefirst large-scale identification of the genes that are
involved in domestication and maize improvement.In
addition,we review the advent of positional cloning and
association approaches that allow for the disction of
complex traits down to the gene and nucleotide level.
Molecular diversity
Whether measured by allozymes,microsatellites(or sim-
ple quence repeats[SSRs])or DNA quences,maize
has long been known to be genetically diver.On the
DNA quence level,exotic and elite maize genotypes
contain more diversity than humans,Drosophila[2]and
many wild plants[3].It has recently become clear,how-
ever,that such diversity cannot be captured fully by
standard marker systems such as SSRs and single nucleo-
tide polymorphisms(SNPs).For example,Fu and
godaDooner[4]uncovered substantial differences in bacterial
artificial chromosome(BAC)quences from the bronze
(bz)region of two maize inbred lines,B73and McC.One
major difference between the lines was the comple-
ment of retroelements,which differed in number and
location.More surprising was that the two lines appeared
to differ in gene complement.In a region of about150kb,
B73and McC shared six genes but differed in four.Thus,
a B73ÂMcC hybrid would be hemizygous for40%of
genes in the bz genomic region.
The obrvations raid more questions than answers.
Is there something unique about the bz region or is
variation in gene content a genome-wide component of
maize diversity?How are the genes duplicated or moved?
Are the genes functional after they have been moved?
Larger studies of multiple regions have now confirmed
that non-homologies are the standard across the genomes
of maize varieties[5,6];incredibly,more than one-third of
genes or gene fragments were specific to a line.In a
follow-up paper,Dooner and coworkers[7 ]addresd
some of the questions by quencing the bz genomic
region from an additional inbred line(Mo17).They
noticed that inrtions among lines contained subtle
but consistent features,including a50-TC terminus,a
30-CTRR terminus,an inrtion site between the host
nucleotides A and T,and a16–20-bp palindrome near the
30terminus.The are features of helitron transposable
elements—a somewhat mysterious class of mobile DNA
elements that might replicate by a rolling circle mechan-
ism[8]—and they strongly suggest that helitrons are
responsible for capturing and moving genes around the
maize genome.
In a parallel study,Morgante et al.[9 ]confirmed that
helitrons mediate gene movement among maize lines.In
addition,the authors determined that the phenomenon
is not limited to the bz region,becau20%of$21000
genes(or gene fragments)differ in genome locationt top box
between B73and Mo17.Clearly contributing to poly-
morphism among modern maize,helitrons have been
active recently and might still be active.The mechanism
新东方英语四级
by which they capture and move genes,however,remains
unknown.The functional effect of gene movement by
helitrons and other transposon-like
Mutator-like DNA elements)[10]is also unclear.Rather than moving complete genes,helitrons appear to transfer gene fragments.Nevertheless,some of the fragments are expresd[4,11]and could affect function,either by RNA interference or by translation into protein.It ems likely that helitron-induced diversity may contribute to differences in gene expression between lines[12 ], dosage effects[13]and heterosis[4].
Although the non-homologies in maize genomes were surprising whenfirst discovered,such structural diversity is consistent with allelic diversity dating back a couple of million years,and with the prence of very active mobile elements over the past few million years.The B73genome is currently being quenced,so a gene inventory of this line will soon be available.Although the quencing of one individual would be sufficient to identify most of the genes of a particular species,additional lines will be required for maize becau of extensive non-homologies.Thirty per-cent of the gene fragments in maize are non-homologous between two lines;thus,even assuming that90%of the non-homologies are pudogenes,quencing one line will only identify85%of functional genes(Figure1). Domestication and artificial lection in maize Archaeological[14]and molecular[15]evidence indicates that modern maize(Zea mays ssp.mays)was domesticated from teosinte in southern Mexico between6600and9000 years ago.Isozyme[16]and microsatellite[15]data
pin-point the annual Balsas teosinte(Zea mays ssp.parviglu-mis)as the direct progenitor to maize.Dispersal occurred rapidly,with evidence of cultivation in South America more than6000years ago[17].Selection soon followed: favorable alleles at loci controlling plant morphology and kernel nutritional quality werefixed at least4400years ago[18 ],and further lection by Native Americans saw maize adapt to numerous varied environments.More recently,lection by plant breeders has focud on the derivation of inbred lines that are suitable for the production of hybrid maize.In the domestication pha, lection was probably focud on making maize culti-vatable and improving access to the ed,while during the improvement pha,lection focud on yield,grain quality,and agro-ecosystem adaptations.
Maize domestication and subquent lection events necessarily reduced genetic diversity in the maize genome when compared to its progenitor population[19].To estimate the parameters of this genetic loss,Wright et al.
[20 ]compared SNP diversity between maize inbreds and teosintes in774genes.Two class of maize genes were identified:tho consistent with a domestication bottle-neck of moderate intensity,and a cond class that experi-enced a much greater reduction of genetic diversity consistent with artificial lection.If the2–4%of genes belonging to this latter class are reprentative
of the larger genome,approximately1200genes bear a signature of lection that is consistent with being direct targets of lection.Despite the population bottlenecks,however, inbred maize lines exhibit high levels of nucleotide diver-sity,retaining up to60%of the diversity of Zea mays ssp. parviglumis and80%of the diversity of the landraces[2]. To identify the targets of lection and the traits they control,maize rearchers have employed both studies directed at logical candidate genes for differences between teosinte and maize and unbiad genomic screens for lected genes.Quantitative trait locus (QTL)analysis of populations derived from cross of teosinte to maize identifiedfive major domestication QTL[21].A combination of transposon tagging,candi-date-gene testing and map-bad cloning subquently led to the isolation of the genes underlying three of the QTL.The teosinte branched1locus[22]on chromosome1 and the barren stalk1locus[23]on chromosome3interact to control lateral meristem formation,thus converting the lateral branches of teosinte into the maize ear.Selection at the teosinte glume architecture1(tga1)locus[24,25 ]was responsible for transforming the hard cupulate fruitca of teosinte into the uncovered grain of the maize ear,a key step in making teosinte an edible crop.The role of a fourth gene,ramosa1,in shaping maize ear morphology has also been recently identified[26].Confirming the proposal by Doebley and Lukens[27]that targets of lection in the evolution of plant morphology will often be transcription regulators,all four of the genes encode
Molecular and functional diversity of maize Buckler,Gaut and McMullen173 Figure
1
Expected proportion of the functional gene space captured
depending on the number of maize lines quenced.The rough
approximations assume the infinite allele model for the varying levels
of non-homologies between pairs of lines and a total population size
of100lines.Some data suggest that30%of the genes are non-
homologous between two lines,so the3%plot is equivalent to
assuming that10%of the non-homologies are functional and90%
are non-functional.
transcription factors.A direct analysis of maize candidate genes that encode enzymes involved in starch metabo-lism demonstrated that artificial lection on starch qual-ity occurred during crop improvement[28].
Incread u of unbiad genomic screens to identify targets of lection[20 ,29,30 ]has greatly expanded our knowledge of the number and scope of the genes that have been involved in the improvement process.New data suggest that auxin-regulated growth,stress respons, maturation and amino-acid composition are all traits with a history of artificial lection[30 ].Once a comprehensive understanding of lected genes and their corresponding traits is obtained,we can begin to modify plant breeding strategies by reintroducing genetic variation that has been lost to le
ction for key agronomic traits.
Maize functional diversity
In the past few years,maize rearchers have made tremendous strides in the identification of genes and nucleotides that control quantitative variation.Most of the phenotypic variation in a species is controlled by polymorphisms at numerous genes;the polymorphisms are the functional basis of quantitative trait loci(QTL). Most crop improvement relies on lecting the numer-ous QTL.QTL mapping in particular,has been pio-neered in maize over the past two decades,with roughly 100rearch studies published in this area during the past two years alone.Given that the average maize gene hous a couple of hundred common polymorphisms and even20–30amino acid polymorphisms that gregate among a diver collection of lines,geneticists must decipher how all of the genes affect quantitative traits. Three major approaches are being ud to evaluate this tremendous diversity:F2-derived QTL mapping,posi-tional cloning,and association mapping.
Mapping using F2-derived populations continues at a great pace for numerous traits,including developmental traits,physiological respons[31],and biochemical makeup[32].The intermated B73ÂMo17mapping populations[33]rve as an invaluable resource for the studies,improving the r
esolution of QTL mapping3–4 fold.Many more studies will make u of the inter-mated populations in the near future,leading to the disction of numerous QTL,particularly as results are integrated and anchored with the physical map. Rearchers of complex traits have debated whether quantitative variation is the product of numerous small QTL or a wide distribution with both large-and small-effect QTL.F2-derived QTL mapping was ud to gain insight into this basic genetic architecture of maize.In one study,two elite inbred lines were crosd and mapped in a1000-individual population in numerous environments[34 ].In a cond study,the high and low lines derived from70generations of long-term lection were crosd,intermated,and mapped[35 ].Interest-ingly,both of the studies documented numerous QTL of very small effect.As experimental design in both cas included high statistical power and robust innovative analys,numerous QTL of small effect might be the norm for the maize genome.However,both the two pairs of parental lines ud for the populations are probably only tapping a small proportion of maize functional varia-tion:founders of the elite inbred lines were targets of breeding lection for more than50years,a process that might have eliminated all large-effect QTL,whereas the long-term lection founders comprid a single farmer’s field that could have contained little genetic diversity. Additional rearch utilizing more diver maize germ-plasm will be needed to resolve this issue.
The positional cloning of QTL in maize has historically been problematic becau of the genome’s large size and the prence of many retrotransposons[36].With the development of physical maps,however,it is now possi-ble to positionally clone maize QTL.The maize domes-tication gene tga1was thefirst to be positionally cloned, by examining more than3000gregating plants and then mapping to within a1042-bp fragment[25 ].Theflower-ing time locus vegetative to generative transition1(vgt1)has also been positionally cloned,and its position sub-quently confirmed by association mapping([37];Savli et al.,2005Maize Genetics Meeting Abstracts).Once the maize genome is completely quenced,positional clon-ing of QTL should become even more routine.Indeed,as maize boasts a higher centiMorgan to gene ratio than Arabidopsis,the total number of plants and meios needed for positional cloning of QTL will be less in maize than in Arabidopsis.
In contrast to linkage mapping,association mapping relies on surveys of natural variation,exploiting the rich history of alleles and recombination gained through evolution.In the approaches,diversity is evaluated across natural populations,and polymorphisms that correlate with phe-notypic variation are identified.Becau no mapping population need be created,association tests are much faster than alternative linkage methods,and also enjoy higher resolution.This high resolution is dependent
upon the structure of linkage diquilibrium(LD),or the correlation between polymorphic loci within the test population[38].LD dictates experimental design,with the distance over which LD persists determining the number and density of required markers.LD decays rapidly in maize,making this phenomenon an ideal tool for association studies:in landraces and a broad sample of tropical and temperate inbreds,LD often declines to nominal levels within1.5kb[2,39],whereas elite breed-ing material has less rapid decay[40,41].
Although ud extensively to study the genetic basis of human dias,association mapping has only recently
174Genome studies and functional genomics
been applied to maize and other plant populations[42–45].Association mapping has identified the candidate nucleotides that affect starch[46],carotenoid[44],and maysin content[47].Improvements continue to be made to the mapping process itlf,including the development of novel statistical approaches that control for pedigree and population adaptations[48 ],the integration of epistatic interactions in the disction of complex traits [47],and the identification of limitations related to population structure[49].Becau current association analysis in maize is candidate gene driven,how
ever, we are still limited to working with known pathways and genes.To resolve this issue,a nested association mapping(NAM)population is being created for the maize community(www.panzea).In this population, two different scales of LD are created by cross between 27very diver lines.The two scales of LD and large sample size will permit a very high resolution genomic scan.
Conclusions
The future of maize rearch is promising.Advances in experimental design and the incread availability of germplasm resources move us ever clor to discting the molecular and functional diversity of maize.Mapping QTLs to the level of individual genes will provide new insights into the molecular and biochemical basis for quantitative trait variation,and will identify novel targets for crop improvement for the21st century. Acknowledgements
We thank N Stevens for technical editing of this manuscript.This work was supported by the US National Science Foundation(DBI-0320683 and DBI-0321467)and the US Department of Agriculture–Agricultural Rearch Services(USDA-ARS).
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