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1.
The grass genus Zea contains the domesticate maize and several wild taxa indigenous to Central and South America. Here we study the genetic consequences of speciation and domestication in this group by sampling DNA sequences from four taxa-maize (Zea mays ssp. mays), its wild progenitor (Z. mays ssp. parviglumis), a more distant species within the genus (Z. luxurians), and a representative of the sister genus (Tripsacum dactyloides). We sampled a total of 26 sequences from the glb1 locus, which encodes a nonessential seed storage protein. Within the Zea taxa sampled, the progenitor to maize contains the most sequence diversity. Maize contains 60% of the level of genetic diversity of its progenitor, and Z. luxurians contains even less diversity (32% of the level of diversity of Z. mays ssp. parviglumis). Sequence variation within the glb1 locus is consistent with neutral evolution in all four taxa. The glb1 data were combined with adh1 data from a previous study to make inferences about the population genetic histories of these taxa. Comparisons of sequence data between the two morphologically similar wild Zea taxa indicate that the species diverged approximately 700, 000 years ago from a common ancestor of intermediate size to their present populations. Conversely, the domestication of maize was a recent event that could have been based on a very small number of founding individuals. Maize retained a substantial proportion of the genetic variation of its progenitor through this founder event, but diverged rapidly in morphology. 相似文献
2.
Members of the grass family (Poaceae) exhibit a broad range of inflorescence structures and other morphologies, making the grasses an interesting model system for studying the evolution of development. Here we present an analysis of the molecular evolution of FLORICAULA/LEAFY-like genes, which are important developmental regulatory loci known to affect inflorescence development in a wide range of flowering plant species. We have focused on sequences from the Andropogoneae, a tribe within the grass family that includes maize (Zea mays ssp. mays) and Sorghum (Sorghum bicolor). The FLORICAULA/LEAFY gene phylogeny we generated largely agrees with previously published phylogenies for the Andropogoneae using other nuclear genes but is unique in that it includes both members of one of the many duplicate gene sets present in maize. The placement of these sequences in the phylogeny suggests that the duplication of the maize FLORICAULA/LEAFY orthologs, zfl1 and zfl2, is a consequence of a proposed tetraploidy event that occurred in the common ancestor of Zea and a closely related genus, Tripsacum. Our data are consistent with the hypothesis that the transcribed regions of the FLORICAULA/LEAFY-like genes in the Andropogoneae are functionally constrained at both nonsynonymous and synonymous sites and show no evidence of directional selection. We also examined conservation of short noncoding sequences in the first intron, which may play a role in gene regulation. Finally, we investigated the genetic diversity of one of the two maize FLORICAULA/LEAFY orthologs, zfl2, in maize and its wild ancestor, teosinte (Z. mays ssp. parviglumis), and found no evidence for selection pressure resulting from maize domestication within the zfl2-coding region. 相似文献
3.
Genomic screening for artificial selection during domestication and improvement in maize 总被引:1,自引:1,他引:0
BACKGROUND: Artificial selection results in phenotypic evolution. Maize (Zea mays L. ssp. mays) was domesticated from its wild progenitor teosinte (Zea mays subspecies parviglumis) through a single domestication event in southern Mexico between 6000 and 9000 years ago. This domestication event resulted in the original maize landrace varieties. The landraces provided the genetic material for modern plant breeders to select improved varieties and inbred lines by enhancing traits controlling agricultural productivity and performance. Artificial selection during domestication and crop improvement involved selection of specific alleles at genes controlling key morphological and agronomic traits, resulting in reduced genetic diversity relative to unselected genes. SCOPE: This review is a summary of research on the identification and characterization by population genetics approaches of genes affected by artificial selection in maize. CONCLUSIONS: Analysis of DNA sequence diversity at a large number of genes in a sample of teosintes and maize inbred lines indicated that approx. 2 % of maize genes exhibit evidence of artificial selection. The remaining genes give evidence of a population bottleneck associated with domestication and crop improvement. In a second study to efficiently identify selected genes, the genes with zero sequence diversity in maize inbreds were chosen as potential targets of selection and sequenced in diverse maize landraces and teosintes, resulting in about half of candidate genes exhibiting evidence for artificial selection. Extended gene sequencing demonstrated a low false-positive rate in the approach. The selected genes have functions consistent with agronomic selection for plant growth, nutritional quality and maturity. Large-scale screening for artificial selection allows identification of genes of potential agronomic importance even when gene function and the phenotype of interest are unknown. These approaches should also be applicable to other domesticated species if specific demographic conditions during domestication exist. 相似文献
4.
The aim of this paper is to test with genomic in situ hybridization the genomic affinities between maize and its putative progenitor Zea mays subsp. parviglumis. Blocking procedures were applied for the purpose of improving discrimination among chromosome regions. Unlabeled genomic DNA from Z. mays subsp. parviglumis as a blocking agent and labeled genomic DNA from maize were hybridized on maize chromosomes. On the other hand, mitotic metaphases from Z. mays subsp. parviglumis were blocked with unlabeled genomic DNA of maize and hybridized with labeled genomic DNA from Z. mays subsp. parviglumis. Both experiments showed that either maize or Z. mays subsp. parviglumis chromosomes have their own unique sequences. This means an unexpected degree of divergence if Z. mays subsp. parviglumis is the only progenitor of maize, a result that is discussed in relation to our previous genomic in situ hybridization observations and to the different scenarios proposed about the origin of maize. 相似文献
5.
Inheritance of the Morphological Differences between Maize and Teosinte: Comparison of Results for Two F(2) Populations 总被引:8,自引:4,他引:4
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Molecular marker loci (MMLs) were employed to map quantitative trait loci (QTLs) in an F(2) 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 F(2) 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 F(2) 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. 相似文献
6.
The closest wild relatives of maize, Zea mays ssp. mays are various Zea taxa known as "teosinte." Hybrids between maize and the teosinte taxon, Zea mays ssp. mexicana, often occur when the 2 are sympatric in Mexico. Measuring the spontaneous hybridization rate of the 2 taxa would shed light on the mechanisms contributing to the evolution and persistence of these hybrid swarms. We conducted a series of field experiments in Riverside, CA, to measure the natural hybridization rates between maize and 2 teosinte taxa, Z. m. ssp. mexicana and Zea mays ssp. parviglumis. We planted teosinte within and near maize plantations. Hybrids were identified by progeny testing for a maize-specific herbicide resistance allele and a teosinte-specific allozyme allele. Hybridity was confirmed by growing putative hybrid progeny to maturity to evaluate whether they had the characteristic morphology of maize x teosinte hybrids. We found that maize and Z. m. ssp. mexicana naturally hybridize at a low rate (<1%), whereas Z. m. ssp. parviglumis hybridizes with the crop at a high rate (>50%). 相似文献
7.
Plant defense genes are subject to nonneutral evolutionary dynamics. Here we investigate the evolutionary dynamics of the duplicated defense genes hm1 and hm2 in maize and its wild ancestor Zea mays ssp. parviglumis. Both genes have been shown to confer resistance to the fungal pathogen Cochliobolus carbonum race 1, but the effectiveness of resistance differs between loci. The genes also display different population histories. The hm1 locus has the highest nucleotide diversity of any gene yet sampled in the wild ancestor of maize, and it contains a large number of indel polymorphisms. There is no evidence, however, that high diversity in hm1 is a product of nonneutral evolution. In contrast, hm2 has very low nucleotide diversity in the wild ancestor of maize. The distribution of hm2 polymorphic sites is consistent with nonneutral evolution, as indicated by Tajima's D and other neutrality tests. In addition, one hm2 haplotype is more frequent than expected under the equilibrium neutral model, suggesting hitchhiking selection. Both defense genes retain >80% of the level of genetic variation in maize relative to the wild ancestor, and this level is similar to other maize genes that were not subject to artificial selection during domestication. 相似文献
8.
Two genetic linkage maps of cultivated maize inbred lines and teosinte species were constructed. One population comprised 81 F(2) individuals derived from a cross between maize inbred line B73 and Zea mays ssp parviglumis, while the second consisted of 63 backcross individuals from a cross of maize inbred line B73 with Z. mays ssp diploperennis. In the B73 x Z. mays ssp parviglumis F(2) population, 172 simple sequence repeat (SSR) markers were mapped to 10 chromosomes, which covered 2210.8 cM. In the B73 x Z. mays ssp diploperennis backcross population, 258 SSR markers were mapped to 10 chromosomes, covering 1357.7 cM. Comparison of the two maps revealed that the total map length of Z. mays ssp diploperennis covers 1357.7 cM, which is about 61.4% of that of Z. mays ssp parviglumis (2210.8 cM). Extensive segregation distortion regions were found on chromosomes 1, 2, 3, 5, 6, 7, and 10 in the B73 x Z. mays ssp parviglumis F(2) population and on chromosomes 1-5 and 8-10 in the B73 x Z. mays ssp parviglumis backcross population. Segregation distortion analysis confirmed that the segregation distortion ratio in the interspecific population B73 x Z. mays ssp diploperennis was higher than in B73 x Z. mays ssp parviglumis. We found that the recombination distances are highly variable in these genetic crosses between cultivated and wild species of maize. 相似文献
9.
Plant pathogenesis-related genes (PR genes) code for enzymes, enzyme inhibitors, and other peptides that confer resistance to pathogens and herbivores. Although several PR genes have been the subject of molecular population genetic analyses, a general understanding of their long-term evolutionary dynamics remains incomplete. Here we analyze sequence data from 17 PR genes from two closely related teosinte species of central Mexico. In addition to testing whether patterns of diversity at individual loci depart from expectations under a neutral model, we compared patterns of diversity at defense genes, as a class, to nondefense genes. In Zea diploperennis, the majority of defense genes have patterns of diversity consistent with neutral expectations while at least two genes showed evidence of recent positive selection consistent with arms-race models of antagonistic coevolution. In Zea mays ssp. parviglumis, by contrast, analyses of both defense and nondefense genes revealed strong and consistent departures from the neutral model, suggestive of nonequilibrium population dynamics or population structure. Nevertheless, we found a significant excess of replacement polymorphism in defense genes compared to nondefense genes. Although we cannot exclude relaxed selective constraint as an explanation, our results are consistent with temporally variable (transient or episodic) selection or geographically variable selection acting on parviglumis defense genes. The different patterns of diversity found in the two Zea species may be explained by parviglumis' greater distribution and population structure together with geographic variation in selection. 相似文献
10.
The domestication of maize (Zea mays ssp. mays) from its wild ancestor (Zea mays ssp. parviglumis) led to a loss of genetic diversity both through a population bottleneck and through directional selection at agronomically important genes. In order to discriminate between those effects and to investigate the nature of the domestication bottleneck, we analyzed nucleotide diversity data from 12 chromosome 1 loci in parviglumis. We found an average loss of nucleotide diversity of 38% across genes, but this average was skewed downward by four putatively selected loci (tb1, d8, ts2, and zagl1). To better understand the domestication process, we used the coalescent with recombination to simulate bottlenecks under various lengths and population sizes. For each locus, we determine the likelihood of the observed data using three summary statistics: the number of segregating sites, an estimate of the population recombination parameter, and Tajima's D. Based on the eight neutrally evolving loci, a model with a bottleneck had a significantly higher likelihood than a model without one. The four putatively selected loci had significantly different likelihood optimums than the neutral loci, and this approach confirmed that ts2 and d8 were selected either during domestication or breeding. Overall, the best-fitting models had a bottleneck in which the population size and the bottleneck duration had a ratio of approximately 4- to approximately 5; for example, if the initial domestication event occurred over a 500-year period, the population size was roughly 2,000 to 2,500 individuals. However, this range did vary with the summary statistic used to assess the fit of simulations to data. In this context, Tajima's D performed poorly as a goodness-of-fit statistic, probably because Z. mays ssp. parviglumis has a frequency spectrum that is significantly skewed toward low-frequency variants. Finally, we found that demography is unlikely to account for the previously observed positive correlation between nucleotide diversity and the population-recombination parameter in maize, leaving this observation difficult to interpret. 相似文献
11.
Estimating a nucleotide substitution rate for maize from polymorphism at a major domestication locus
To estimate a rate for single nucleotide substitutions for maize (Zea mays ssp. mays), we have taken advantage of data from genetic and archaeological studies of the domestication of maize from its wild ancestor, teosinte (Z. mays ssp. parviglumis). Genetic studies have shown that the teosinte branched1 (tb1) gene was a major target of human selection during maize domestication, and sequence diversity in the intergenic region 5' to the tb1-coding sequence is extraordinarily low. We show that polymorphism in this region is consistent with new mutation following fixation for a small number of tb1 haplotypes during domestication. Archeological studies suggest that maize was domesticated approximately 6,250-10,000 years ago and subsequently the size of the maize population is thought to have expanded rapidly. Using the observed number of mutations within the region of selection at tb1, the approximate age of maize domestication, and approximations for the maize genealogy, we have derived estimates for the nucleotide substitution rate for the tb1 intergenic region. Using two approaches, one of which is a coalescent approach, we obtain rate estimates of approximately 2.9 x 10(-8) and 3.3 x 10(-8) substitutions per site per year. We also show that the pattern of polymorphism in the tb1 intergenic region appears to have been strongly affected by the mutagenic effect of DNA methylation. Excluding target sites of symmetric DNA methylation (CG and CNG sites) from analysis, the mutation rate estimates are reduced by approximately 50%-60%, while the rates for CG and CNG sites are nearly an order of magnitude higher. We use rate estimates from the tb1 region to estimate the timing of expansion of transposable elements in the maize genome and suggest that this expansion occurred primarily within the last million years. 相似文献
12.
Zea systematics: ribosomal ITS evidence 总被引:10,自引:0,他引:10
Ribosomal internal transcribed spacer (ITS) sequences were used to evaluate
the phylogenetics of Zea and Tripsacum. Maximum likelihood and polymorphism
parsimony were used for phylogenetic reconstructions. Zea ITS nucleotide
diversity was high compared to other plant species, but approximately
equivalent to other maize loci. Coalescence of ITS alleles was rapid
relative to other nuclear loci; however, there was still much diversity
within populations. Zea and Tripsacum form a clade clearly differentiated
from all other Poaceae. Four Zea ITS pseudogenes were identified by
phylogenetic position and nucleotide composition. The phylogenetic position
of Z. mays ssp. huehuetenangensis was clearly established as basal to the
other Z. mays. The ITS phylogeny disfavored a Z. luxurians and Z.
diploperennis clade, which conflicted with some previous studies. The
introgression of Z. mays alleles into Z. perennis and Z. diploperennis was
also established. The ITS data indicated a near contemporary divergence of
domesticated maize and its two closest wild relatives.
相似文献
13.
Molecular DNA analyses of the New World grass (Poaceae) genus Zea, comprising five species, has resolved taxonomic issues including the most likely teosinte progenitor (Zea mays ssp. parviglumis) of maize (Zea mays ssp. mays). However, archaeologically, little is known about the use of teosinte by humans both prior to and after the domestication of maize. One potential line of evidence to explore these relationships is opaline phytoliths produced in teosinte fruit cases. Here we use multidimensional scaling and multiple discriminant analyses to determine if rondel phytolith assemblages from teosinte fruitcases reflect teosinte taxonomy. Our results indicate that rondel phytolith assemblages from the various taxa, including subspecies, can be statistically discriminated. This indicates that it will be possible to investigate the archaeological histories of teosinte use pending the recovery of appropriate samples. 相似文献
14.
Isozyme variation in 94 accessions of Mexican maize (Zea mays ssp. mays) and 37 collections of Mexican annual teosinte (Z. mays ssp. mexicana and var. parviglumis) are compared. Variety parviglumis (a predominantly wild plant) shows a closer genetic relationship to maize than does ssp. mexicana (a weedy teosinte often found in maize fields). The isozyme data suggest that maize and Z. mays var. parviglumis share a more recent common ancestor than either of these taxa share with other members of the genus Zea. In this sense, the isozyme data support the theory that maize is a domesticated form of teosinte. Isozyme data provide no evidence for independent origin of Mexican maize races from different taxa of teosinte. Isozyme analysis suggests that gene flow between maize and ssp. mexicana exists, but that it is highly restricted and more probably goes from weed into crop. Maize and var. parviglumis are isozymically too similar and too variable to allow patterns of gene flow between them (if any) to be discerned. The maize- teosinte complex does not fit a model applied to some other crops in that (I) weedy teosinte (ssp. mexicana) does not appear to be a hybrid of the wild form (var. parviglumis,) and maize and (2) the weedy form does not act as a genetic bridge between wild form and crop. 相似文献
15.
Genetic relationship of a newly discovered teosinte from Nicaragua, Zea nicaraguensis with waterlogging tolerance, was determined based on randomly amplified polymorphic DNA (RAPD) markers and the internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA using 14 accessions from Zea species. RAPD analysis showed that a total of 5,303 fragments were produced by 136 random decamer primers, of which 84.86% bands were polymorphic. RAPD-based UPGMA analysis demonstrated that the genus Zea can be divided into section Luxuriantes including Zea diploperennis, Zea luxurians, Zea perennis and Zea nicaraguensis, and section Zea including Zea mays ssp. mexicana, Zea mays ssp. parviglumis, Zea mays ssp. huehuetenangensis and Zea mays ssp. mays. ITS sequence analysis showed the lengths of the entire ITS region of the 14 taxa in Zea varied from 597 to 605 bp. The average GC content was 67.8%. In addition to the insertion/deletions, 78 variable sites were recorded in the total ITS region with 47 in ITS1, 5 in 5.8S, and 26 in ITS2. Sequences of these taxa were analyzed with neighbor-joining (NJ) and maximum parsimony (MP) methods to construct the phylogenetic trees, selecting Tripsacum dactyloides L. as the outgroup. The phylogenetic relationships of Zea species inferred from the ITS sequences are highly concordant with the RAPD evidence that resolved two major subgenus clades. Both RAPD and ITS sequence analyses indicate that Zea nicaraguensis is more closely related to Zea luxurians than the other teosintes and cultivated maize, which should be regarded as a section Luxuriantes species. 相似文献
16.
Fukunaga K Hill J Vigouroux Y Matsuoka Y Sanchez G J Liu K Buckler ES Doebley J 《Genetics》2005,169(4):2241-2254
The teosintes, the closest wild relatives of maize, are important resources for the study of maize genetics and evolution and for plant breeding. We genotyped 237 individual teosinte plants for 93 microsatellites. Phylogenetic relationships among species and subspecific taxa were largely consistent with prior analyses for other types of molecular markers. Plants of all species formed monophyletic clades, although relationships among species were not fully resolved. Phylogenetic analysis indicated that the Mexican annual teosintes divide into two clusters that largely correspond to the previously defined subspecies, Z. mays ssp. parviglumis and ssp. mexicana, although there are a few samples that represent either evolutionary intermediates or hybrids between these two subspecies. The Mexican annual teosintes show genetic substructuring along geographic lines. Hybridization or introgression between some teosintes and maize occurs at a low level and appears most common with Z. mays ssp. mexicana. Phylogeographic and phylogenetic analyses of the Mexican annual teosintes indicated that ssp. parviglumis diversified in the eastern part of its distribution and spread from east to west and that ssp. mexicana diversified in the Central Plateau of Mexico and spread along multiple paths to the north and east. We defined core sets of collections of Z. mays ssp. mexicana and ssp. parviglumis that attempt to capture the maximum number of microsatellite alleles for given sample sizes. 相似文献
17.
Fang Z Pyhäjärvi T Weber AL Dawe RK Glaubitz JC González Jde J Ross-Ibarra C Doebley J Morrell PL Ross-Ibarra J 《Genetics》2012,191(3):883-894
Chromosomal inversions are thought to play a special role in local adaptation, through dramatic suppression of recombination, which favors the maintenance of locally adapted alleles. However, relatively few inversions have been characterized in population genomic data. On the basis of single-nucleotide polymorphism (SNP) genotyping across a large panel of Zea mays, we have identified an ~50-Mb region on the short arm of chromosome 1 where patterns of polymorphism are highly consistent with a polymorphic paracentric inversion that captures >700 genes. Comparison to other taxa in Zea and Tripsacum suggests that the derived, inverted state is present only in the wild Z. mays subspecies parviglumis and mexicana and is completely absent in domesticated maize. Patterns of polymorphism suggest that the inversion is ancient and geographically widespread in parviglumis. Cytological screens find little evidence for inversion loops, suggesting that inversion heterozygotes may suffer few crossover-induced fitness consequences. The inversion polymorphism shows evidence of adaptive evolution, including a strong altitudinal cline, a statistical association with environmental variables and phenotypic traits, and a skewed haplotype frequency spectrum for inverted alleles. 相似文献
18.
Landraces of maize (Zea mays ssp. mays) and its wild teosinte relatives (Zea mays spp. parviglumis and mexicana) were surveyed for sensitivity to fumonisin B(1), a phytotoxin produced by the maize pathogen Gibberella moniliformis. Only two of 42 Z. mays samples were highly insensitive to FB(1) (ED(50) = ca. 200 microM). The teosintes and 76% of the maize landraces were moderately or highly sensitive to FB(1) (ED(50) < or = 30 microM), which indicates that FB(1) sensitivity is likely to be an ancestral trait in Z. mays. F(1) generations derived from crosses between FB(1)-sensitive maize inbred B73 and insensitive landraces were significantly less sensitive than B73. Thus, our data indicate that FB(1)-insensitivity is a relatively rare but heritable trait in maize. We also report the sensitivity of maize to other Gibberella toxins - beauvericin, diacetoxyscirpenol, and moniliformin. 相似文献
19.
Indirect two-generation analysis of pollen flow has proven to be an effective alternative to exhaustive paternity analysis in numerous plant populations. In this investigation, the method is extended to an annual wild maize species, Zea mays ssp. parviglumis (Poaceae). Our analysis of mating system in parviglumis revealed high levels of outcrossing and higher biparental inbreeding than typically observed in grasses. Pollen dispersal analysis suggested low levels of long-distance dispersal. Given previous evidence for intrapopulation genetic structure in parviglumis populations, we explored the impact of cryptic population structure on estimates of mating system and pollen flow. Subpopulations inferred through spatially explicit Bayesian assignment showed markedly different values for both mating system parameters and pollen flow than the entire population. Finally, a novel method of pollen haplotype assignment revealed nonrandom mating consistent with intrapopulation structure. These results indicate parviglumis could be particularly susceptible to habitat fragmentation currently occurring throughout Mexico due to recent changes in land use. 相似文献
20.
Despite numerous quantitative trait loci and association mapping studies, our understanding of the extent to which natural allelic series contribute to the variation for complex traits is limited. In this study, we investigate the occurrence of a natural allelic series for complex traits at the teosinte branched1 (tb1) gene in natural populations of teosinte (Zea mays ssp. parviglumis, Z. mays ssp. mexicana, and Z. diploperennis). Previously, tb1 was shown to confer large effects on both plant architecture and ear morphology between domesticated maize and teosinte; however, the effect of tb1 on trait variation in natural populations of teosinte has not been investigated. We compare the effects of nine teosinte alleles of tb1 that were introgressed into an isogenic maize inbred background. Our results provide evidence for a natural allelic series at tb1 for several complex morphological traits. The teosinte introgressions separate into three distinct phenotypic classes, which correspond to the taxonomic origin of the alleles. The effects of the three allelic classes also correspond to known morphological differences between the teosinte taxa. Our results suggest that tb1 contributed to the morphological diversification of teosinte taxa as well as to the domestication of maize. 相似文献