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J Doebley

Publications and source records attributed to J Doebley.

At least 19 recordsLinked to original sources
PubMed2002

Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication.

Crop species experienced strong selective pressure directed at genes controlling traits of agronomic importance during their domestication and subsequent episodes of selective breeding. Consequently, these genes are expected to exhibit the signature of selection. We screened 501 maize genes for the signature of selection using microsatellites or simple sequence repeats (SSRs). We applied the Ewens-Watterson test, which can reveal deviations from a neutral-equilibrium model, as well as two nonequilibrium tests that incorporate the domestication bottleneck. We investigated two classes of SSRs: those known to be polymorphic in maize (Class I) and those previously classified as monomorphic in maize (Class II). Fifteen SSRs exhibited some evidence for selection in maize and 10 showed evidence under stringent criteria. The genes containing nonneutral SSRs are candidates for agronomically important genes. Because demographic factors can bias our tests, further independent tests of these candidates are necessary. We applied such an additional test to one candidate, which encodes a MADS box transcriptional regulator, and confirmed that this gene experienced a selective sweep during maize domestication. Genomic scans for the signature of selection offer a means of identifying new genes of agronomic importance even when gene function and the phenotype of interest are unknown.

Agriculture↗
PubMed2001

Structure of linkage disequilibrium and phenotypic associations in the maize genome.

Association studies based on linkage disequilibrium (LD) can provide high resolution for identifying genes that may contribute to phenotypic variation. We report patterns of local and genome-wide LD in 102 maize inbred lines representing much of the worldwide genetic diversity used in maize breeding, and address its implications for association studies in maize. In a survey of six genes, we found that intragenic LD generally declined rapidly with distance (r(2) < 0.1 within 1500 bp), but rates of decline were highly variable among genes. This rapid decline probably reflects large effective population sizes in maize during its evolution and high levels of recombination within genes. A set of 47 simple sequence repeat (SSR) loci showed stronger evidence of genome-wide LD than did single-nucleotide polymorphisms (SNPs) in candidate genes. LD was greatly reduced but not eliminated by grouping lines into three empirically determined subpopulations. SSR data also supplied evidence that divergent artificial selection on flowering time may have played a role in generating population structure. Provided the effects of population structure are effectively controlled, this research suggests that association studies show great promise for identifying the genetic basis of important traits in maize with very high resolution.

Chromosome Mapping↗
PubMed2001

Dwarf8 polymorphisms associate with variation in flowering time.

Historically, association tests have been used extensively in medical genetics, but have had virtually no application in plant genetics. One obstacle to their application is the structured populations often found in crop plants, which may lead to nonfunctional, spurious associations. In this study, statistical methods to account for population structure were extended for use with quantitative variation and applied to our evaluation of maize flowering time. Mutagenesis and quantitative trait locus (QTL) studies suggested that the maize gene Dwarf8 might affect the quantitative variation of maize flowering time and plant height. The wheat orthologs of this gene contributed to the increased yields seen in the 'Green Revolution' varieties. We used association approaches to evaluate Dwarf8 sequence polymorphisms from 92 maize inbred lines. Population structure was estimated using a Bayesian analysis of 141 simple sequence repeat (SSR) loci. Our results indicate that a suite of polymorphisms associate with differences in flowering time, which include a deletion that may alter a key domain in the coding region. The distribution of nonsynonymous polymorphisms suggests that Dwarf8 has been a target of selection.

Genes, Plant↗
PubMed2001

Molecular evolution of the teosinte branched gene among maize and related grasses.

Several authors have proposed that changes in a small number of regulatory genes may be sufficient for the evolution of novel morphologies. Recent analyses have indicated that teosinte branched1 (tb1), a putative bHLH transcription factor, played such a role during the morphological evolution of maize from its wild ancestor, teosinte. To address whether or not tb1 played a similar role during the evolution of the Andropogoneae, the tribe to which maize belongs, and to examine the rate and pattern of tb1 evolution within this tribe, we analyzed tb1-like sequences from 23 members of the Andropogoneae and five other grasses. Our analysis revealed that the TB1 protein evolves slowly within three conserved domains but rapidly outside these domains. The nonconserved regions of the gene are characterized by both a high nonsynonymous substitution rate and frequent indels. The ratio of nonsynonymous substitutions per nonsynonymous site (d(N)) to synonymous substitutions per synonymous site (d(S)) was not significantly greater than 1.0, providing no evidence for positive selection. However, the d(N)/d(S) ratio varied significantly among lineages and was high compared with those of other plant nuclear genes. Variation in the d(N)/d(S) ratio among the Andropogoneae could be explained by unequal levels of purifying selection among lineages. Consistent with this interpretation, the rate of nonsynonymous substitution differed along several lineages, while the synonymous substitution rate did not differ significantly. Finally, using tb1, we examined phylogenetic relationships within the Andropogoneae. The phylogeny suggests that the tribe underwent a rapid radiation during its early history and that the monoecious Andropogoneae are polyphyletic.

Amino Acid Sequence↗
PubMed2000

Plant genetics. A tomato gene weighs in.

What makes some people big and others small--obviously our genes, but which ones? Working out the complex of genes that control such quantitative traits in animals and plants is one of the big challenges facing geneticists. In his Perspective, Doebley discusses new results that identify the fw2.2 gene as one of the genes determining fruit size in the tomato (Frary et al.).

Alleles↗
PubMed1999

The limits of selection during maize domestication.

The domestication of all major crop plants occurred during a brief period in human history about 10,000 years ago. During this time, ancient agriculturalists selected seed of preferred forms and culled out seed of undesirable types to produce each subsequent generation. Consequently, favoured alleles at genes controlling traits of interest increased in frequency, ultimately reaching fixation. When selection is strong, domestication has the potential to drastically reduce genetic diversity in a crop. To understand the impact of selection during maize domestication, we examined nucleotide polymorphism in teosinte branched1, a gene involved in maize evolution. Here we show that the effects of selection were limited to the gene's regulatory region and cannot be detected in the protein-coding region. Although selection was apparently strong, high rates of recombination and a prolonged domestication period probably limited its effects. Our results help to explain why maize is such a variable crop. They also suggest that maize domestication required hundreds of years, and confirm previous evidence that maize was domesticated from Balsas teosinte of southwestern Mexico.

Agriculture↗
PubMed1999

The TCP domain: a motif found in proteins regulating plant growth and development.

The cycloidea (cyc) and teosinte branched 1 (tb1) genes code for structurally related proteins implicated in the evolution of key morphological traits. However, the biochemical function of CYC and TB1 proteins remains to be demonstrated. To address this problem, we have analysed the predicted secondary structure of regions conserved between CYC and TB1, and looked for related proteins of known function. One of the conserved regions is predicted to form a non-canonical basic-Helix-Loop-Helix (bHLP) structure. This domain is also found in two rice DNA-binding proteins, PCF1 and PCF2, where it has been shown to be involved in DNA-binding and dimerization. This indicates that the conserved domain most probably defines a new family of transcription factors, which we have termed the TCP family after its first characterised members (TB1, CYC and PCFs). Other plant proteins of unknown function also belong to this family. We have studied two of these in Arabidopsis and have shown that they are expressed in rapidly growing floral primordia. This, together with the proposed involvement of cyc and tb1 in influencing meristem growth, suggests that many members of the TCP family may affect cell division. Some of these genes may have been recruited during plant evolution to generate new morphological traits.

Amino Acid Sequence↗
PubMed1998

Of genes and genomes and the origin of maize.

The crop plant maize (corn) is remarkably dissimilar to its recent wild ancestor, teosinte, making it an extremely interesting model for the study of evolution. Investigations into the evolution of maize are currently being performed at the molecular and morphological levels. Three independent lines of research are poised to shed light on the molecular basis of this spectacular transformation: (1) determining the structure and origin of the maize genome; (2) understanding the role of transposable elements in maize evolution; and (3) elucidating the genetic basis for morphological differences between maize and its wild ancestor teosinte.

Biological Evolution↗
PubMed1998

Maize as a model system for investigating the molecular basis of morphological evolution in plants.

The genetic and molecular bases of morphological evolution in plants are largely unknown. To address questions surrounding this issue, my laboratory has been investigating the evolution of maize from its wild ancestor, teosinte. Our research suggests that a few gene changes of large effect were involved in the evolution of several different traits including plant and ear architecture and kernel color. In cases where gene function could be identified, the genes involved in maize evolution were regulatory in nature. Additional evidence suggests that changes in cis regulatory elements of the regulatory genes rather than changes in protein function underlie the evolution of the traits analyzed. Future work with other plant species, especially wild plants, will be required to test the generality of our observations with maize.

Biological Evolution↗
PubMed1997

The evolution of apical dominance in maize.

The domestication of crop plants has often involved an increase in apical dominance (the concentration of resources in the main stem of the plant and a corresponding suppression of axillary branches). A striking example of this phenomenon is seen in maize (Zea mays spp. mays), which exhibits a profound increase in apical dominance compared with its probable wild ancestor, teosinte (Zea mays ssp. parviglumis). Previous research has identified the teosinte branched1 (tb1) gene as a major contributor to this evolutionary change in maize. We have cloned tb1 by transposon tagging and show here that it encodes a protein with homology to the cycloidea gene of snapdragon. The pattern of tb1 expression and the morphology of tb1 mutant plants suggest that tb1 acts both to repress the growth of axillary organs and to enable the formation of female inflorescences. The maize allele of tb1 is expressed at twice the level of the teosinte allele, suggesting that gene regulatory changes underlie the evolutionary divergence of maize from teosinte.

Alleles↗
PubMed1995

teosinte branched1 and the origin of maize: evidence for epistasis and the evolution of dominance.

Two quantitative trait loci (QTL) controlling differences in plant and inflorescence architecture between maize and its progenitor (teosinte) were analyzed. Complementation tests indicate that one of these, which is on chromosome arm 1L, is the locus for the maize mutant teosinte branched1 (tb1). This QTL has effects on inflorescence sex and the number and length of internodes in the lateral branches and inflorescences. This QTL has strong phenotypic effects in teosinte background but reduced effects in maize background. The second QTL, which is on chromosome arm 3L, affects the same traits as the QTL on 1L. We identify two candidate loci for this QTL. The effects of this QTL on several traits are reduced in both maize and teosinte background as compared to a maize-teosinte F2 population. Genetic background appears to affect gene action for both QTL. Analysis of a population in which both QTL were segregating revealed that they interact epistatically. Together, these two QTL substantially transform both plant and inflorescence architecture. We propose that tb1 is involved in the plant's response to local environment to produce either long or short branches and that maize evolution involved a change at this locus to produce short branches under all environments.

Biological Evolution↗
PubMed1993

Evolution of a noncoding region of the chloroplast genome.

The relative rate of occurrence of nucleotide substitutions versus indel (insertion/deletion) events is investigated by comparing complete DNA sequence data from the noncoding portion of the chloroplast genome that maps between the genes rbcL and atp beta. The sequence data are obtained from nine species that represent three tribes of the grass family. Indels could be categorized by those that are deletions or duplications of adjacent or proximal sequences and those that do not appear to be permutations of adjacent sequences. The first category represents 82% of the recorded indels. These indels may also be characterized by being direct duplications of one to several bases usually within runs of As or Ts or by being duplications or deletions of more complex sequences. When viewed from within groups of closely related taxa, indel events appear to occur at an equal or slightly faster rate than do nucleotide substitution events. However, the apparent rate of accumulation of indels in more distantly related species is significantly slower than that of nucleotide substitutions. This difference in apparent accumulation rates between indel events and nucleotide substitutions suggests that the proportion of superimposed changes has been higher among all indel events than among all nucleotide substitution events. Indeed the indels involving more complex sequences were found to be confined across taxa to a number of highly labile sites. Independent, though similar, indel events occur at identical sites in unrelated taxa, yet may not be shared among related taxa, resulting in a type of molecular parallelism. As a result, the phylogenetic tree based on indel events represents an evolutionary hypothesis which is inconsistent with the accepted phylogeny of these grasses. The phylogenetic tree based on nucleotide substitutions is consistent with accepted phylogeny.

Base Sequence↗
PubMed1993

Genetics, development and plant evolution.

The recent mapping of quantitative trait loci in plants indicates that traits are often controlled by relatively few genes, some of which have large effects. Developmental genetics has shown that plant development is often regulated by transcription factors that activate developmental programs in response to internal or environmental signals. These transcription factors are good candidates for the major genes that govern morphological evolution in plants.

Anthocyanins↗
PubMed1993

Inheritance of the morphological differences between maize and teosinte: comparison of results for two F2 populations.

Molecular marker loci (MMLs) were employed to map quantitative trait loci (QTLs) in an F2 population derived from a cross of maize (Zea mays ssp. mays) and its probable progenitor, teosinte (Z. mays ssp. parviglumis). A total of 50 significant associations (putative QTLs) between the MMLs and nine key traits that distinguish maize and teosinte were identified. Results from this analysis are compared with our previous analysis of an F2 population derived from a cross of a different variety of maize and another subspecies of teosinte (Z. mays ssp. mexicana). For traits that measure the architectural differences between maize and teosinte, the two F2 populations possessed similar suites of QTLs. For traits that measure components of yield, substantially different suites of QTLs were identified in the two populations. QTLs that control about 20% or more of the phenotypic variance for a trait in one population were detected in the other population 81% of the time, while QTLs that control less than 10% of the variance in one population were detected in the other population only 28% of the time. In our previously published analysis of the maize x ssp. mexicana population, we identified five regions of the genome that control most of the key morphological differences between maize and teosinte. These same five regions also control most of the differences in the maize x ssp. parviglumis population. Results from both populations support the hypothesis that a relatively small number of loci with large effects were involved in the early evolution of the key traits that distinguish maize and teosinte. It is suggested that loci with large effects on morphology may not be a specific feature of crop evolution, but rather a common phenomenon in plant evolution whenever a species invades a new niche with reduced competition.

Chromosome Mapping↗