Speciation and domestication in maize and its wild relatives: evidence from the globulin-1 gene

Adaptive and maladaptive introgression in grapevine domestication

Domesticated grapevines spread to Europe around 3,000 years ago. Previous studies have revealed genomic signals of introgression from wild to cultivated grapes in Europe, but the time, mode, genomic pattern, and biological effects of these introgression events have not been investigated. Here, we studied resequencing data from 345 samples spanning the distributional range of wild (Vitis vinifera ssp. sylvestris) and cultivated (V. vinifera ssp. vinifera) grapes. Based on machine learning-based population genetic analyses, we detected evidence for a single domestication of grapevine, followed by continuous gene flow between European wild grapes (EU) and cultivated grapes over the past ~2,000 y, especially from EU to wine grapes. We also inferred that soft-selective sweeps were the dominant signals of artificial selection. Gene pathways associated with the synthesis of aromatic compounds were enriched in regions that were both selected and introgressed, suggesting EU wild grapes were an important resource for improving the flavor of cultivated grapes. Despite the potential benefits of introgression in grape improvement, the introgressed fragments introduced a higher deleterious burden, with most deleterious SNPs and structural variants hidden in a heterozygous state. Cultivated wine grapes have benefited from adaptive introgression with wild grapes, but introgression has also increased the genetic load. In general, our study of beneficial and harmful effects of introgression is critical for genomic breeding of grapevine to take advantage of wild resources.

Large haplotypes highlight a complex age structure within the maize pan-genome

The genomes of maize and other eukaryotes contain stable haplotypes in regions of low recombination. These regions, including centromeres, long heterochromatic blocks, and rDNA arrays, have been difficult to analyze with respect to their diversity and origin. Greatly improved genome assemblies are now available that enable comparative genomics over these and other nongenic spaces. Using 26 complete maize genomes, we developed methods to align intergenic sequences while excluding genes and regulatory regions. The centromere haplotypes (cenhaps) extend for megabases on either side of the functional centromere regions and appear as evolutionary strata, with haplotype divergence/coalescence times dating as far back as 450 thousand years ago (kya). Application of the same methods to other low recombination regions (heterochromatic knobs and rDNA) and all intergenic spaces revealed that deep coalescence times are ubiquitous across the maize pan-genome. Divergence estimates vary over a broad timescale with peaks at ∼16 and 300 kya, reflecting a complex history of gene flow among diverging populations and changes in population size associated with domestication. Cenhaps and other long haplotypes provide vivid displays of this ancient diversity.

Genome sequencing reveals evidence of adaptive variation in the genus Zea

Maize is a globally valuable commodity and one of the most extensively studied genetic model organisms. However, we know surprisingly little about the extent and potential utility of the genetic variation found in wild relatives of maize. Here, we characterize a high-density genomic variation map from 744 genomes encompassing maize and all wild taxa of the genus Zea, identifying over 70 million single-nucleotide polymorphisms. The variation map reveals evidence of selection within taxa displaying novel adaptations. We focus on adaptive alleles in highland teosinte and temperate maize, highlighting the key role of flowering-time-related pathways in their adaptation. To show the utility of variants in these data, we generate mutant alleles for two flowering-time candidate genes. This work provides an extensive sampling of the genetic diversity of Zea, resolving questions on evolution and identifying adaptive variants for direct use in modern breeding.

Computational approaches for the classification of seed storage proteins

Seed storage proteins comprise a major part of the protein content of the seed and have an important role on the quality of the seed. These storage proteins are important because they determine the total protein content and have an effect on the nutritional quality and functional properties for food processing. Transgenic plants are being used to develop improved lines for incorporation into plant breeding programs and the nutrient composition of seeds is a major target of molecular breeding programs. Hence, classification of these proteins is crucial for the development of superior varieties with improved nutritional quality. In this study we have applied machine learning algorithms for classification of seed storage proteins. We have presented an algorithm based on nearest neighbor approach for classification of seed storage proteins and compared its performance with decision tree J48, multilayer perceptron neural (MLP) network and support vector machine (SVM) libSVM. The model based on our algorithm has been able to give higher classification accuracy in comparison to the other methods.

Pleistocene climate change and the origin of two desert plant species, Pugionium cornutum and Pugionium dolabratum (Brassicaceae), in northwest China

Pleistocene climate change has had an important effect in shaping intraspecific genetic variation in many species; however, its role in driving speciation is less clear. We examined the possibility of a Pleistocene origin of the only two representatives of the genus Pugionium (Brassicaceae), Pugionium cornutum and Pugionium dolabratum, which occupy different desert habitats in northwest China. We surveyed sequence variation for internal transcribed spacer (ITS), three chloroplast (cp) DNA fragments, and eight low-copy nuclear genes among individuals sampled from 11 populations of each species across their geographic ranges. One ITS mutation distinguished the two species, whereas mutations in cpDNA and the eight low-copy nuclear gene sequences were not species-specific. Although interspecific divergence varied greatly among nuclear gene sequences, in each case divergence was estimated to have occurred within the Pleistocene when deserts expanded in northwest China. Our findings point to the importance of Pleistocene climate change, in this case an increase in aridity, as a cause of speciation in Pugionium as a result of divergence in different habitats that formed in association with the expansion of deserts in China.

Genetic diversity and molecular evolution of Chinese waxy maize germplasm

Waxy maize (Zea mays L. var. certaina Kulesh), with many excellent characters in terms of starch composition and economic value, has grown in China for a long history and its production has increased dramatically in recent decades. However, the evolution and origin of waxy maize still remains unclear. We studied the genetic diversity of Chinese waxy maize including typical landraces and inbred lines by SSR analysis and the results showed a wide genetic diversity in the Chinese waxy maize germplasm. We analyzed the origin and evolution of waxy maize by sequencing 108 samples, and downloading 52 sequences from GenBank for the waxy locus in a number of accessions from genus Zea. A sharp reduction of nucleotide diversity and significant neutrality tests (Tajima's D and Fu and Li's F*) were observed at the waxy locus in Chinese waxy maize but not in nonglutinous maize. Phylogenetic analysis indicated that Chinese waxy maize originated from the cultivated flint maize and most of the modern waxy maize inbred lines showed a distinct independent origin and evolution process compared with the germplasm from Southwest China. The results indicated that an agronomic trait can be quickly improved to meet production demand by selection.

Grande retrotransposons contain an accessory gene in the unusually long 3'-internal region that encodes a nuclear protein transcribed from its own promoter

LTR retrotransposons are major components of plant genomes playing important roles in the evolution of their host genomes, for example, generating new genes or providing new promoters to existing genes. The Grande family of retrotransposons is present in Zea species and is characterized by an unusually long internal region due to the presence of a 7-kbp region between the gag-pol coding region and the 3'LTR. We demonstrate here that such unusual sequence is present in the great majority of Grande copies in maize genome. This region contains a gene, gene23, which is transcribed from its own promoter in antisense orientation to the gag-pol genes. The expression of gene23 is ubiquitous, and its promoter contains all the putative consensus sequences typical of eukaryotic promoters, being able to direct GUS expression in different plant species and organs. The coding region of gene23 is conserved in most Grande copies and encodes a protein rich in glycine, serine, and acidic amino acids that shows no significant similarity with any protein of known function. Nevertheless, the C- and N-terminal parts are rich in basic amino acids, and these are interspersed with other amino acids in its C-terminus, compatible with a putative DNA-binding function. It contains a nuclear localization signal KRKR motif in the N-terminus. Fusions to GFP demonstrate that this protein localizes in the nucleus. We discuss the possible origin of gene23 and the potential function of its encoded protein.

Dynamic evolution of bz orthologous regions in the Andropogoneae and other grasses

Genome structure exhibits remarkable plasticity within Zea mays. To examine how haplotype structure has evolved within the Andropogoneae tribe, we have analyzed the bz gene-rich region of maize (Zea mays), the Zea teosintes mays ssp. mexicana, luxurians and diploperennis, Tripsacum dactyloides, Coix lacryma-jobi and Sorghum propinquum. We sequenced and annotated BAC clones from these species and re-annotated the orthologous Sorghum bicolor region. Gene colinearity in the region is well conserved within the genus Zea. However, the orthologous regions of Coix and Sorghum exhibited several micro-rearrangements relative to Zea, including addition, truncation and deletion of genes. The stc1 gene, involved in the production of a terpenoid insect defense signal, is evolving particularly fast, and its progressive disappearance from some species is occurring by microhomology-mediated recombination. LTR retrotransposons are the main contributors to the dynamic evolution of the bz region. Common transposon insertion sites occur among haplotypes from different Zea mays sub-species, but not outside the species. As in Zea, different patterns of interspersion between genes and retrotransposons are observed in Sorghum. We estimate that the mean divergence times between maize and Tripsacum, Coix and Sorghum are 8.5, 12.1 and 12.4 million years ago, respectively, and that between Coix and Sorghum is 9.3 million years ago. A comparison of the bz orthologous regions of Zea, Sorghum and Coix with those of Brachypodium, Setaria and Oryza allows us to infer how the region has evolved by addition and deletion of genes in the approximately 50 million years since these genera diverged from a common progenitor.

Phylogeny and evolutionary history of the silkworm

The silkworm, Bombyx mori, played an important role in the old Silk Road that connected ancient Asia and Europe. However, to date, there have been few studies of the origins and domestication of this species using molecular methods. In this study, DNA sequences of mitochondrial and nuclear loci were used to infer the phylogeny and evolutionary history of the domesticated silkworm and its relatives. All of the phylogenetic analyses indicated a close relationship between the domesticated silkworm and the Chinese wild silkworm. Domestication was estimated to have occurred about 4100 years ago (ya), and the radiation of the different geographic strains of B. mori about 2000 ya. The Chinese wild silkworm and the Japanese wild silkworm split about 23600 ya. These estimates are in good agreement with the fossil evidence and historical records. In addition, we show that the domesticated silkworm experienced a population expansion around 1000 ya. The divergence times and the population dynamics of silkworms presented in this study will be useful for studies of lepidopteran phylogenetics, in the genetic analysis of domestic animals, and for understanding the spread of human civilizations.

Evidence of selection at melanin synthesis pathway loci during silkworm domestication

The domesticated silkworm (Bombyx mori) was domesticated from wild silkworm (Bombyx mandarina) more than 5,000 years ago. During domestication, body color between B. mandarina and B. mori changed dramatically. However, the molecular mechanism of the silkworm body color transition is not known. In the present study, we examined within- and between-species nucleotide diversity for eight silkworm melanin synthesis pathway genes, which play a key role in cuticular pigmentation of insects. Our results showed that the genetic diversity of B. mori was significantly lower than that of B. mandarina and 40.7% of the genetic diversity of wild silkworm was lost in domesticated silkworm. We also examined whether position effect exists among melanin synthesis pathway genes in B. mandarina and B. mori. We found that the upstream genes have significantly lower levels of genetic diversity than the downstream genes, supporting a functional constraint hypothesis (FCH) of metabolic pathway, that is, upstream enzymes are under greater selective constraint than downstream enzymes because upstream enzymes participate in biosynthesis of a number of metabolites. We also investigated whether some of the melanin synthesis pathway genes experienced selection during domestication. Neutrality test, coalescent simulation, as well as network and phylogenetic analyses showed that tyrosine hydroxylase (TH) gene was a domestication locus. Sequence analysis further suggested that a putative expression enhancer (Abd-B-binding site) in the intron of TH gene might be disrupted during domestication. TH is the rate-limiting enzyme of melanin synthesis pathway in insects. Real-time polymerase chain reaction assay did show that the relative expression levels of TH gene in B. mori were significantly lower than that in B. mandarina at three different developmental stages, which is consistent with light body color of domesticated silkworm relative to wild silkworm. Therefore, we speculated that expression change of TH gene may contribute to the body color transition from B. mandarina to B. mori. Our results emphasize the exceptional role of gene expression regulation in morphological transition of domesticated animals.

MADS-box genes of maize: frequent targets of selection during domestication

MADS-box genes encode transcription factors that are key regulators of plant inflorescence and flower development. We examined DNA sequence variation in 32 maize MADS-box genes and 32 randomly chosen maize loci and investigated their involvement in maize domestication and improvement. Using neutrality tests and a test based on coalescent simulation of a bottleneck model, we identified eight MADS-box genes as putative targets of the artificial selection associated with domestication. According to neutrality tests, one additional MADS-box gene appears to have been under selection during modern agricultural improvement of maize. For random loci, two genes were indicated as targets of selection during domestication and four additional genes were indicated to be candidate-selected loci for maize improvement. These results suggest that MADS-box genes were more frequent targets of selection during domestication than genes chosen at random from the genome.

Molecular characterization of global maize breeding germplasm based on genome-wide single nucleotide polymorphisms

Characterization of genetic diversity is of great value to assist breeders in parental line selection and breeding system design. We screened 770 maize inbred lines with 1,034 single nucleotide polymorphism (SNP) markers and identified 449 high-quality markers with no germplasm-specific biasing effects. Pairwise comparisons across three distinct sets of germplasm, CIMMYT (394), China (282), and Brazil (94), showed that the elite lines from these diverse breeding pools have been developed with only limited utilization of genetic diversity existing in the center of origin. Temperate and tropical/subtropical germplasm clearly clustered into two separate groups. The temperate germplasm could be further divided into six groups consistent with known heterotic patterns. The greatest genetic divergence was observed between temperate and tropical/subtropical lines, followed by the divergence between yellow and white kernel lines, whereas the least divergence was observed between dent and flint lines. Long-term selection for hybrid performance has contributed to significant allele differentiation between heterotic groups at 20% of the SNP loci. There appeared to be substantial levels of genetic variation between different breeding pools as revealed by missing and unique alleles. Two SNPs developed from the same candidate gene were associated with the divergence between two opposite Chinese heterotic groups. Associated allele frequency change at two SNPs and their allele missing in Brazilian germplasm indicated a linkage disequilibrium block of 142 kb. These results confirm the power of SNP markers for diversity analysis and provide a feasible approach to unique allele discovery and use in maize breeding programs.

Tracking footprints of maize domestication and evidence for a massive selective sweep on chromosome 10

Maize domestication is one of the greatest feats of artificial selection and evolution, wherein a weedy plant in Central Mexico was converted through human-mediated selection into the most productive crop in the world. In fact, the changes were so astounding that it took much of the last century to identify modern maize's true ancestor. Through modern genetic studies, the molecular basis of this evolution is being unraveled. Maize's new morphology and adaptation to diverse environments required selection at thousands of loci, and we are beginning to understand the magnitude and rates of these genetic changes. Most of the known major genes have experienced strong selection, but only small regions surrounding the selected genes exhibit substantially reduced genetic diversity. Here, we report the discovery of a large region on chromosome 10 involved in adaptation or domestication that has been the target of strong selection during maize domestication. Unlike previously described regions in the maize genome, 1.1 Mb and >15 genes lost genetic diversity during selection at this region. Finally, the prospects of a detailed understanding of maize evolution are discussed with consideration of both top-down and bottom-up approaches.

SNP deserts of Asian cultivated rice: genomic regions under domestication

When performing a genome-wide comparison between indica (93-11) and japonica (Nipponbare), we find 8% of the genome, which have an extremely low SNP rate (< 1 SNP/kb). Inside these 'SNP deserts', experimentally confirmed genes show increased K(a)/K(s) that indicate adaptive selection. To further elucidate this connection, we survey the level and pattern of genetic variation in both cultivated and wild rice groups, using 155 noncoding regions located within SNP deserts. The results suggest that cultivated rice has greatly reduced genetic variation within SNP deserts as compared to either the nondesert or corresponding genomic regions in wild rice. Consistent with this reduction in genetic variation, we find a biased distribution of derived allele frequency in the cultivated group, indicative of positive selection. Furthermore, over half of the confirmed, domestication-related genes are found within SNP deserts, also suggesting that SNP deserts are strongly related to domestication, and might be the key sites in the process of domestication.

Historical divergence and gene flow in the genus Zea

Gene flow plays a fundamental role in plant evolutionary history, yet its role in population divergence--and ultimately speciation--remains poorly understood. We investigated gene flow and the modalities of divergence in the domesticated Zea mays ssp. mays and three wild Zea taxa using sequence polymorphism data from 26 nuclear loci. We described diversity across loci and assessed evidence for adaptive and purifying selection at nonsynonymous sites. For each of three divergence events in the history of these taxa, we used approximate Bayesian simulation to estimate population sizes and divergence times and explicitly compare among alternative models of divergence. Our estimates of divergence times are surprisingly consistent with previous data from other markers and suggest rapid diversification of lineages within Zea in the last approximately 150,000 years. We found widespread evidence of historical gene flow, including evidence for divergence in the face of gene flow. We speculate that cultivated maize may serve as a bridge for gene flow among otherwise allopatric wild taxa.

Globulins are the main seed storage proteins in Brachypodium distachyon

Brachypodium distachyon is being developed as a model system to study temperate cereals and forage grasses. We have begun to investigate its utility to understand seed development and grain filling by identifying the major seed storage proteins in a diploid accession Bd21. With the use of ID SDS-PAGE and mass spectrometry we detected seven major storage protein bands, six of which were identified as globulins. A subset of the major seed proteins isolated from three hexaploid accessions, Bd4, Bd14 and Bd17 were also identified as globulins. Several Brachypodium cDNAs clones encoding globulin were completely sequenced. Two types of globulin genes were identified, Bd.glo1 and Bd.glo2, which are similar to maize 7S and oat 12S globulins, respectively. The derived polypeptide sequences of the globulins contain a typical signal peptide sequence in their polypeptide N-termini and two cupin domains. Bd.glo1 is encoded by a single copy gene, whereas, Bd.glo2 belongs to a gene family.

The role of regulatory genes during maize domestication: evidence from nucleotide polymorphism and gene expression

We investigated DNA sequence variation in 72 candidate genes in maize landraces and the wild ancestor of maize, teosinte. The candidate genes were chosen because they exhibit very low sequence diversity among maize inbreds and have sequence homology to known regulatory genes. We observed signatures of selection in 17 candidate genes, indicating that they were potential targets of artificial selection during domestication. In addition, 21 candidate genes were identified as potential targets of natural selection in teosinte. A comparison of the proportion of selected genes between our regulatory genes and genes unfiltered for their potential function (but also with very low sequence diversity among maize inbreds) provided some weak evidence that regulatory genes are overrepresented among selected genes. We detected no significant association between the positions of genes identified as potential targets of selection during domestication and quantitative trait loci (QTL) responsible for maize domestication traits. However, a subset of these genes, those identified by sequence homology as kinase/phosphatase genes, significantly cluster with the domestication QTL. We also analyzed expression profiles of genes in distinct maize tissues and observed that domestication genes are expressed on average at a significantly higher level than neutral genes in reproductive organs, including kernels.

Genomic screening for artificial selection during domestication and improvement in maize

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.

Population structure and its effects on patterns of nucleotide polymorphism in teosinte (Zea mays ssp. parviglumis)

Surveys of nucleotide diversity in the wild ancestor of maize, Zea mays ssp. parviglumis, have revealed genomewide departures from the standard neutral equilibrium (NE) model. Here we investigate the degree to which population structure may account for the excess of rare polymorphisms frequently observed in species-wide samples. On the basis of sequence data from five nuclear and two chloroplast loci, we found significant population genetic structure among seven subpopulations from two geographic regions. Comparisons of estimates of population genetic parameters from species-wide samples and subpopulation-specific samples showed that population genetic subdivision influenced observed patterns of nucleotide polymorphism. In particular, Tajima's D was significantly higher (closer to zero) in subpopulation-specific samples relative to species-wide samples, and therefore more closely corresponded to NE expectations. In spite of these overall patterns, the extent to which levels and patterns of polymorphism within subpopulations differed from species-wide samples and NE expectations depended strongly on the geographic region (Jalisco vs. Balsas) from which subpopulations were sampled. This may be due to the demographic history of subpopulations in those regions. Overall, these results suggest that explicitly accounting for population structure may be important for studies examining the genetic basis of ecologically and agronomically important traits as well as for identifying loci that have been the targets of selection.

Plant domestication, a unique opportunity to identify the genetic basis of adaptation

Despite the fundamental role of plant domestication in human history and the critical importance of a relatively small number of crop plants to modern societies, we still know little about adaptation under domestication. Here we focus on efforts to identify the genes responsible for adaptation to domestication. We start from a historical perspective, arguing that Darwin's conceptualization of domestication and unconscious selection provides valuable insight into the evolutionary history of crops and also provides a framework to evaluate modern methods used to decipher the genetic mechanisms underlying phenotypic change. We then review these methods, framing the discussion in terms of the phenotype-genotype hierarchy. Top-down approaches, such as quantitative trait locus and linkage disequilibrium mapping, start with a phenotype of interest and use genetic analysis to identify candidate genes. Bottom-up approaches, alternatively, use population genetic analyses to identify potentially adaptive genes and then rely on standard bioinformatics and reverse genetic tools to connect selected genes to a phenotype. We discuss the successes, advantages, and challenges of each, but we conclude that bottom-up approaches to understanding domestication as an adaptive process hold greater promise both for the study of adaptation and as a means to identify genes that contribute to agronomically important traits.

Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice

Varying degrees of reduction of genetic diversity in crops relative to their wild progenitors occurred during the process of domestication. Such information, however, has not been available for the Asian cultivated rice (Oryza sativa) despite its importance as a staple food and a model organism. To reveal levels and patterns of nucleotide diversity and to elucidate the genetic relationship and demographic history of O. sativa and its close relatives (Oryza rufipogon and Oryza nivara), we investigated nucleotide diversity data from 10 unlinked nuclear loci in species-wide samples of these species. The results indicated that O. rufipogon and O. nivara possessed comparable levels of nucleotide variation ((sil) = 0.0077 approximately 0.0095) compared with the relatives of other crops. In contrast, nucleotide diversity of O. sativa was as low as (sil) = 0.0024 and even lower ((sil) = 0.0021 for indica and 0.0011 for japonica), if we consider the 2 subspecies separately. Overall, only 20-10% of the diversity in the wild species was retained in 2 subspecies of the cultivated rice (indica and japonica), respectively. Because statistic tests did not reject the assumption of neutrality for all 10 loci, we further used coalescent to simulate bottlenecks under various lengths and population sizes to better understand the domestication process. Consistent with the dramatic reduction in nucleotide diversity, we detected a severe domestication bottleneck and demonstrated that the sequence diversity currently found in the rice genome could be explained by a founding population of 1,500 individuals if the initial domestication event occurred over a 3,000-year period. Phylogenetic analyses revealed close genetic relationships and ambiguous species boundary of O. rufipogon and O. nivara, providing additional evidence to treat them as 2 ecotypes of a single species. Lowest linkage disequilibrium (LD) was found in the perennial O. rufipogon where the r(2) value dropped to a negligible level within 400 bp, and the highest in the japonica rice where LD extended to the entirely sequenced region ( approximately 900 bp), implying that LD mapping by genome scans may not be feasible in wild rice due to the high density of markers needed.

Integrase diversity and transcription of the maize retrotransposon Grande

Grande is an abundant gypsy-like retrotransposon present in the genera Zea and Tripsacum. Related retro transposon families can be found in sorghum, rice, and barley, but not in wheat or rye. We have amplified and sequenced several copies of part of the integrase domain derived from the Zea mays, Zea diploperennis, and Tripsacum dactyloides genomes. There are no significant differences in divergence or clustering between the integrase sequences of these species. The substitution rate for synonimous sites was found to be higher than those of non-synomymous sites; this indicates that Grande integrase has been under purifying selection for function. Grande is transcribed in leaves. The transcripts show sequence diversity similar to that of genomic sequences, but belong to restricted clades; this indicates that only some evolutionary branches of Grande have retained transcriptional competence.

The maize Ab10 meiotic drive system maps to supernumerary sequences in a large complex haplotype

The meiotic drive system on maize abnormal chromosome 10 (Ab10) is contained within a terminal domain of chromatin that extends the long arm of Ab10 to approximately 1.3 times the size of normal chromosome 10L. Ab10 type I (Ab10-I) does not recombine with normal chromosome 10 (N10) over an approximately 32-cM terminal region of the long arm. Comparative RFLP mapping demonstrates that multiple independent rearrangements are responsible for the current organization of Ab10-I, including a set of nested inversions and at least one long supernumerary segment at the end of the chromosome. Four major meiotic drive functions, i.e., the recombination effect, smd3, 180-bp neocentromere activity, and the distal tip function, all map to the distal supernumerary segment. TR-1-mediated neocentromere activity (the fifth known drive function) is nonessential in the type II variant of Ab10 and maps to a central region that may include a second supernumerary insertion. Both neocentromere activity and the recombination effect behave as dominant gain-of-function mutations, consistent with the view that meiotic drive involves new or alien gene products. These and other data suggest that the Ab10 meiotic drive system was initially acquired from a related species and that a complex haplotype evolved around it.

Domestication history in the Medicago sativa species complex: inferences from nuclear sequence polymorphism

DNA sequence polymorphism carries genealogical information and allows for testing hypotheses on selection and population history, especially through coalescent-based analysis. Understanding the evolutionary forces at work in plant domestication and subsequent selection is of critical importance for the management of genetic resources. In this study, we surveyed DNA sequence diversity at two assumed neutral nuclear loci in the wild-domesticated species complex of alfalfa (Medicago sativa L.). A high level of polymorphism was detected. The domesticated pool contains on average 31% less diversity than the wild pool, but with a high heterogeneity among loci. Coalescent simulations of the domestication process showed that this result cannot be explained by assuming a constant population size but is rather consistent with a demographic bottleneck during domestication. A very low level of divergence was detected between the wild and the domesticated forms as well as between the related subspecies of the M. sativa species complex. However, the originality of the Spanish wild populations, already observed based on mitochondrial DNA polymorphism, was confirmed. These results, together with patterns of intrapopulation polymorphism, suggest that nuclear sequence polymorphism could be a promising tool, complementary to mitochondrial DNA and phenotypic evaluations, to investigate historical demographic and evolutionary processes.

Retroelement genome painting: cytological visualization of retroelement expansions in the genera Zea and Tripsacum

Divergence of abundant genomic elements among the Zea and Tripsacum genera was examined cytologically and a tool kit established for subsequent studies. The LTR regions from the CRM, Huck, Grande, Prem1, Prem2/Ji, Opie, Cinful-1, and Tekay retroelement families were used as FISH probes on mitotic chromosome spreads from a "trispecies" hybrid containing chromosomes from each of three species: Zea mays (2n = 20), Z. diploperennis (2n = 20), and Tripsacum dactyloides (2n = 36). Except for Tekay, which painted both Zea and Tripsacum chromosomes with nearly equal intensity, the retroelement probes hybridized strongly to the Zea chromosomes, allowing them to be distinguished from those of Tripsacum. Huck and Grande hybridized more intensely to maize than to Z. diploperennis chromosomes. Tripsacum genomic clones containing retroelement sequences were isolated that specifically paint Tripsacum chromosomes. The retroelement paints proved effective for distinguishing different genomes in interspecific hybrids and visualizing alien chromatin from T. dactyloides introgressed into maize lines. Other FISH probes (180-bp knob, TR-1, 5S, NOR, Cent4, CentC, rp1, rp3, and alpha-ZeinA) could be simultaneously visualized with the retroelement probes, emphasizing the value of the retroelement probes for cytogenetic studies of Zea and Tripsacum.

Documenting domestication: the intersection of genetics and archaeology

Domestication, a process of increasing mutual dependence between human societies and the plant and animal populations they target, has long been an area of interest in genetics and archaeology. Geneticists seek out markers of domestication in the genomes of domesticated species, both past and present day. Archaeologists examine the archaeological record for complementary markers--evidence of the human behavior patterns that cause the genetic changes associated with domestication, and the morphological changes in target species that result from them. In this article, we summarize the recent advances in genetics and archaeology in documenting plant and animal domestication, and highlight several promising areas where the complementary perspectives of both disciplines provide reciprocal illumination.

An antifungal peptide from the coconut

A chromatographic procedure consisting of ion exchange chromatography on DEAE-cellulose, affinity chromatography on Affi-gel blue gel, ion exchange chromatography on CM-cellulose, and gel filtration by fast performance liquid chromatography on Supedex 75 was utilized to isolate a 10 kDa antifungal peptide from coconut flesh. The peptide was unadsorbed on DEAE-cellulose, but adsorbed on Affi-gel blue gel and CM-cellulose. It displayed antifungal activity against Fusarium oxysporum, Mycosphaerella arachidicola and Physalospora piricola. The IC50 values of its inhibitory activities on mycelial growth in M. arachidicola and HIV-1 reverse transcriptase activity were respectively 1.2 and 52.5 microM.

A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement

Maize (Zea mays subsp mays) was domesticated from teosinte (Z. mays subsp 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, which were spread throughout the Americas by Native Americans and adapted to a wide range of environmental conditions. Starting with landraces, 20th century plant breeders selected inbred lines of maize for use in hybrid maize production. Both 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. Here, we sequenced 1095 maize genes from a sample of 14 inbred lines and chose 35 genes with zero sequence diversity as potential targets of selection. These 35 genes were then sequenced in a sample of diverse maize landraces and teosintes and tested for selection. Using two statistical tests, we identified eight candidate genes. Extended gene sequencing of these eight candidate loci confirmed that six were selected throughout the gene, and the remaining two exhibited evidence of selection in the 3' portion of each gene. The selected genes have functions consistent with agronomic selection for nutritional quality, maturity, and productivity. Our large-scale screen for artificial selection allows identification of genes of potential agronomic importance even when gene function and the phenotype of interest are unknown.

A comparative study of retrotransposons in the centromeric regions of A and B chromosomes of maize

Bacterial Artificial Chromosomes (BACs) derived from the B chromosome, based on homology with the B specific sequence, were subcloned and sequenced. Analysis of DNA sequence data indicated the presence of 23 common retroelements, as well as novel sequences of B chromosome origin. Generally, where the same retrotransposon type was observed in both A and B chromosomes, there were more copies per unit of sequence in the B centromeric region (the major site of B repeat) than in the A centromere, except for Huck-1. Based on previous estimates of the age of the major burst of transposition into the maize genome, the oldest retrotransposons (Ji-6 and Tekay, approximately 5.0 and 5.2 million years ago, respectively) were found in the B centromere region only, while the next two oldest (Huck-1 and Opie-1) were found in both the A and B sequences. Phylogenetic analysis of Opie retroelements from both A and B centromeres indicated that some of the B Opie centromeric sequences share a more recent common ancestor with A Opie retroelements than they do with other B Opie centromeric sequences. These results imply that the supernumerary maize B chromosome has coexisted with the A chromosomes during that period of transposition. They also support the hypothesis that the B chromosome had its origins from A chromosome elements, or that alternative origins, such as being donated to the maize genome in a wide species cross, preceded six million years ago, because the spectrum of retrotransposons in the two chromosomes is quite similar.

Genetic diversity and the evolutionary history of plant immunity genes in two species of Zea

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.

The effects of artificial selection on the maize genome

Domestication promotes rapid phenotypic evolution through artificial selection. We investigated the genetic history by which the wild grass teosinte (Zea mays ssp. parviglumis) was domesticated into modern maize (Z. mays ssp. mays). Analysis of single-nucleotide polymorphisms in 774 genes indicates that 2 to 4% of these genes experienced artificial selection. The remaining genes retain evidence of a population bottleneck associated with domestication. Candidate selected genes with putative function in plant growth are clustered near quantitative trait loci that contribute to phenotypic differences between maize and teosinte. If we assume that our sample of genes is representative, approximately 1200 genes throughout the maize genome have been affected by artificial selection.

Sequence polymorphism in polyploid wheat and their d-genome diploid ancestor

Sequencing was used to investigate the origin of the D genome of the allopolyploid species Triticum aestivum and Aegilops cylindrica. A 247-bp region of the wheat D-genome Xwye838 locus, encoding ADP-glucopyrophosphorylase, and a 326-bp region of the wheat D-genome Gss locus, encoding granule-bound starch synthase, were sequenced in a total 564 lines of hexaploid wheat (T. aestivum, genome AABBDD) involving all its subspecies and 203 lines of Aegilops tauschii, the diploid source of the wheat D genome. In Ae. tauschii, two SNP variants were detected at the Xwye838 locus and 11 haplotypes at the Gss locus. Two haplotypes with contrasting frequencies were found at each locus in wheat. Both wheat Xwye838 variants, but only one of the Gss haplotypes seen in wheat, were found among the Ae. tauschii lines. The other wheat Gss haplotype was not found in either Ae. tauschii or 70 lines of tetraploid Ae. cylindrica (genomes CCDD), which is known to hybridize with wheat. It is concluded that both T. aestivum and Ae. cylindrica originated recurrently, with at least two genetically distinct progenitors contributing to the formation of the D genome in both species.

The genetics of maize evolution

Maize and its closest wild relatives, the teosintes, differ strikingly in the morphology of their female inflorescences or ears. Despite their divergent morphologies, several studies indicate that some varieties of teosinte are cytologically indistinguishable from maize and capable of forming fully fertile hybrids with maize. Molecular analyses identified one form of teosinte (Zea mays ssp. parviglumis) as the progenitor of maize. Analyses of the inheritance of the morphological traits that distinguish maize and teosinte indicates that they are under the control of multiple genes and exhibit quantitative inheritance. Nevertheless, these analyses have also identified a few loci of large effect that appear to represent key innovations during maize domestication. Remaining challenges are to identify additional major and minor effect genes, the polymorphisms within these genes that control the phenotypes, and how the combination of the individual and epistatic effects of these genes transformed teosinte into maize.

Comparative evolutionary histories of chitinase genes in the Genus zea and Family poaceae

Patterns of DNA sequence diversity vary widely among genes encoding proteins that protect plants against pathogens and herbivores. Comparative studies may help determine whether these differences are due to the strength of selection acting on different types of defense, in different evolutionary lineages, or both. I analyzed sequence diversity at three chitinases, a well-studied component of defense, in two species of Zea and several Poaceae taxa. Although the Zea species are closely related and these genes code for proteins with similar biochemical function, patterns of diversity vary widely within and among species. Intraspecific diversity at chiB, chiI, and Z. mays ssp. parviglumis chiA are consistent with a neutral-equilibrium model whereas chiA had no segregating sites within Z. diploperennis--consistent with a recent and strong selective sweep. Codons identified as having diverged among Poaceae taxa in response to positive selection were significantly overrepresented among targets of selection in Arabis, suggesting common responses to selection in distantly related plant taxa. Divergence of the recent duplicates chiA and chiB is consistent with positive selection but relaxed constraint cannot be rejected. Weak evidence for adaptive divergence of these duplicated downstream components of defense contrasts with strong evidence for adaptive divergence of genes involved in pathogen recognition.

Domestication patterns in common bean (Phaseolus vulgaris L.) and the origin of the Mesoamerican and Andean cultivated races

Chloroplast DNA polymorphisms were studied by PCR sequencing and PCR-restriction fragment length polymorphism in 165 accessions of domesticated landraces of common bean from Latin America and the USA, 23 accessions of weedy beans, and 134 accessions of wild beans covering the entire geographic range of wild Phaseolus vulgaris. Fourteen chloroplast haplotypes were identified in wild beans, only five of which occur also in domesticated beans. The chloroplast data agree with those obtained from analyses based on morphology and isozymes and with other DNA polymorphisms in supporting independent domestications of common bean in Mesoamerica and the Andean region and in demonstrating a founder effect associated with domestication in each region. Andean landraces have been classified into three different racial groups, but all share the same chloroplast haplotype. This suggests that common bean was domesticated once only in South America and that the races diverged post-domestication. The haplotype found in Andean domesticated beans is confined to the southern part of the range of wild beans, so Andean beans were probably domesticated somewhere within this area. Mesoamerican landraces have been classified into four racial groups. Our limited samples of Races Jalisco and Guatemala differ from the more widespread and commercially important Races Mesoamerica and Durango in types and/or frequencies of haplotypes. All four Mesoamerican races share their haplotypes with local wild beans in parts of their ranges. Independent domestications of at least some of the races in Mesoamerica and/or conversion of some locally adapted wild beans to cultigens by hybridization with introduced domesticated beans, followed by introgression of the "domestication syndrome" seem the most plausible explanations of the chloroplast and other molecular data.

An analysis of genetic diversity across the maize genome using microsatellites

How domestication bottlenecks and artificial selection shaped the amount and distribution of genetic variation in the genomes of modern crops is poorly understood. We analyzed diversity at 462 simple sequence repeats (SSRs) or microsatellites spread throughout the maize genome and compared the diversity observed at these SSRs in maize to that observed in its wild progenitor, teosinte. The results reveal a modest genome-wide deficit of diversity in maize relative to teosinte. The relative deficit of diversity is less for SSRs with dinucleotide repeat motifs than for SSRs with repeat motifs of more than two nucleotides, suggesting that the former with their higher mutation rate have partially recovered from the domestication bottleneck. We analyzed the relationship between SSR diversity and proximity to QTL for domestication traits and observed no relationship between these factors. However, we did observe a weak, although significant, spatial correlation for diversity statistics among SSRs within 2 cM of one another, suggesting that SSR diversity is weakly patterned across the genome. Twenty-four of 462 SSRs (5%) show some evidence of positive selection in maize under multiple tests. Overall, the pattern of genetic diversity at maize SSRs can be explained largely by a bottleneck effect with a smaller effect from selection.

Genetic diversity associated with variation in silage corn digestibility for three O-methyltransferase genes involved in lignin biosynthesis

Polymorphisms within three candidate genes for lignin biosynthesis were investigated to identify alleles useful for the improvement of maize digestibility. The allelic diversity of two caffeoyl-CoA 3-O-methyltransferase genes, CCoAOMT2 and CCoAOMT1, as well as that of the aldehyde O-methyltransferase gene, AldOMT, was evaluated for 34 maize lines chosen for their varying degrees of cell wall digestibility. Frequency of nucleotide changes averaged one SNP every 35 bp. Ninety-one indels were identified in non-coding regions and only four in coding regions. Numerous distinct and highly diverse haplotypes were identified at each locus. Numerous sites were in linkage disequilibrium that declined rapidly within a few hundred bases. For F4, an early flint French line with high cell wall digestibility, the CCoAOMT2 first exon presented many non-synonymous polymorphisms. Notably we found an 18-bp indel, which resembled a microsatellite and was associated with cell wall digestibility variation. Additionally, the CCoAOMT2 gene co-localized with a QTL for cell wall digestibility and lignin content. Together, these results suggest that genetic diversity investigated on a broader genetic basis could contribute to the identification of favourable alleles to be used in the molecular breeding of elite maize germplasm.

Molecular Population Genetics and the Search for Adaptive Evolution in Plants

The first papers on plant molecular population genetics were published approximately 10 years ago. Since that time, well over 50 additional studies of plant nucleotide polymorphism have been published, and many of these studies focused on detecting the signature of balancing or positive selection at a locus. In this review, we discuss some of the theoretical and statistical issues surrounding the detection of selection, with focus on plant populations, and we also summarize the empirical plant molecular population genetics literature. At face value, the literature suggests that a history of balancing or positive selection in plant genes is rampant. In two well-studied taxa (maize and Arabidopsis) over 20% of studied genes have been interpreted as containing the signature of selection. We argue that this is probably an overstatement of the prevalence of natural selection in plant genomes, for two reasons. First, demographic effects are difficult to incorporate and have generally not been well integrated into the plant population genetics literature. Second, the genes studied to date are not a random sample, so selected genes may be overrepresented. The next generation of studies in plant molecular population genetics requires additional sampling of local populations, explicit comparisons among loci, and improved theoretical methods to control for demography. Eventually, candidate loci should be confirmed by explicit consideration of phenotypic effects.

Molecular-genetic characterization of CMS-S restorer-of-fertility alleles identified in Mexican maize and teosinte

Restorer-of-fertility (Rf) alleles for S-type cytoplasmic male sterility (CMS-S) are prevalent in Mexican races of maize and teosinte. Forty-five Rf alleles from 26 races of maize and 6 Rf alleles from different accessions of teosinte were found to be homozygous viable, consistent with the hypothesis that they are naturally occurring Rf alleles. Mapping and allelism studies were performed to assess the number of genes represented by these 51 alleles. Forty-two of the Rf alleles mapped to the long arm of chromosome 2 (2L), and 5 of these were further mapped to the whp1-rf3 region. The Rf3 restoring allele, found in some U.S. maize inbred lines, cosegregates with internal processing of CMS-S mitochondrial transcripts. Three of the 5 mapped Rf alleles were associated with a similar RNA processing event. Allelism or tight linkage was confirmed between Rf3 and 2 teosinte alleles (Rf K-69-6 and Rf 9477) and between Rf3 and the Cónico Norteño allele Rf C-N (GTO 22). The rf3 region of 2L potentially encodes a complex of linked rf genes. The prevalence of restoring alleles in this chromosomal region, among normal-cytoplasm accessions of Mexican maize and teosinte, supports the conclusion that these alleles have functions in normal mitochondrial gene expression that by chance allow them to restore male fertility in S cytoplasm.

Molecular-Genetic Characterization of CMS-S Restorer-of-Fertility Alleles Identified in Mexican Maize and Teosinte

Restorer-of-fertility (Rf) alleles for S-type cytoplasmic male sterility (CMS-S) are prevalent in Mexican races of maize and teosinte. Forty-five Rf alleles from 26 races of maize and 6 Rf alleles from different accessions of teosinte were found to be homozygous viable, consistent with the hypothesis that they are naturally occurring Rf alleles. Mapping and allelism studies were performed to assess the number of genes represented by these 51 alleles. Forty-two of the Rf alleles mapped to the long arm of chromosome 2 (2L), and 5 of these were further mapped to the whp1-rf3 region. The Rf3 restoring allele, found in some U.S. maize inbred lines, cosegregates with internal processing of CMS-S mitochondrial transcripts. Three of the 5 mapped Rf alleles were associated with a similar RNA processing event. Allelism or tight linkage was confirmed between Rf3 and 2 teosinte alleles (Rf K-69-6 and Rf 9477) and between Rf3 and the Cónico Norteño allele Rf C-N (GTO 22). The rf3 region of 2L potentially encodes a complex of linked rf genes. The prevalence of restoring alleles in this chromosomal region, among normal-cytoplasm accessions of Mexican maize and teosinte, supports the conclusion that these alleles have functions in normal mitochondrial gene expression that by chance allow them to restore male fertility in S cytoplasm.

Inflorescence development in a new teosinte: Zea nicaraguensis (Poaceae)

Inflorescence development in a newly discovered teosinte, Zea nicaraguensis (Poaceae), from Nicaragua has been investigated using scanning electron microscopy (SEM). The SEM examination revealed that the pattern of both male and female inflorescence development was similar to previously described inflorescence in other Zea taxa. Branch primordia were initiated acropetally in a distichous pattern along the rachis of male and female inflorescences. Spikelet pair primordia bifurcated into pedicellate and sessile spikelet primordia. Predictably, pedicellate spikelet development was arrested and aborted in the female teosinte inflorescence. Organogenesis of functional spikelets and florets was similar to that previously described in maize and teosintes. The results were consistent with our hypothesis that both femininity and masculinity share a common mechanism of inflorescence development in Zea and Tripsacum and are in accord with a putative common mechanism of sex determination in the Andropogoneae. Interestingly, this population of teosinte, unique in its ability to grow in water-logged soils, showed a stable pattern of early inflorescence development. Our results also revealed the uncharacteristic presence of inflorescence polystichy in this population of Zea nicaraguensis. We propose this novel phenotypic variation raises the possibility that a domestic evolution of polystichy in maize was enabled by an occasional polystichous phenotypic in teosinte.

Pattern of diversity in the genomic region near the maize domestication gene tb1

Domesticated maize and its wild ancestor (teosinte) differ strikingly in morphology and afford an opportunity to examine the connection between strong selection and diversity in a major crop species. The tb1 gene largely controls the increase in apical dominance in maize relative to teosinte, and a region of the tb1 locus 5' to the transcript sequence was a target of selection during maize domestication. To better characterize the impact of selection at a major "domestication" locus, we have sequenced the upstream tb1 genomic region and systematically sampled nucleotide diversity for sites located as far as 163 kb upstream to tb1. Our analyses define a selective sweep of approximately 60-90 kb 5' to the tb1 transcribed sequence. The selected region harbors a mixture of unique sequences and large repetitive elements, but it contains no predicted genes. Diversity at the nearest 5' gene to tb1 is typical of that for neutral maize loci, indicating that selection at tb1 has had a minimal impact on the surrounding chromosomal region. Our data also show low intergenic linkage disequilibrium in the region and suggest that selection has had a minor role in shaping the pattern of linkage disequilibrium that is observed. Finally, our data raise the possibility that maize-like tb1 haplotypes are present in extant teosinte populations, and our findings also suggest a model of tb1 gene regulation that differs from traditional views of how plant gene expression is controlled.

Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects

Population-genetic studies have been remarkably productive and successful in the last decade following the invention of PCR technology and the introduction of mitochondrial and microsatellite DNA markers. While mitochondrial DNA has proven powerful for genealogical and evolutionary studies of animal populations, and microsatellite sequences are the most revealing DNA markers available so far for inferring population structure and dynamics, they both have important and unavoidable limitations. To obtain a fuller picture of the history and evolutionary potential of populations, genealogical data from nuclear loci are essential, and the inclusion of other nuclear markers, i.e. single copy nuclear polymorphic (scnp) sequences, is clearly needed. Four major uncertainties for nuclear DNA analyses of populations have been facing us, i.e. the availability of scnp markers for carrying out such analysis, technical laboratory hurdles for resolving haplotypes, difficulty in data analysis because of recombination, low divergence levels and intraspecific multifurcation evolution, and the utility of scnp markers for addressing population-genetic questions. In this review, we discuss the availability of highly polymorphic single copy DNA in the nuclear genome, describe patterns and rate of evolution of nuclear sequences, summarize past empirical and theoretical efforts to recover and analyse data from scnp markers, and examine the difficulties, challenges and opportunities faced in such studies. We show that although challenges still exist, the above-mentioned obstacles are now being removed. Recent advances in technology and increases in statistical power provide the prospect of nuclear DNA analyses becoming routine practice, allowing allele-discriminating characterization of scnp loci and microsatellite loci. This certainly will increase our ability to address more complex questions, and thereby the sophistication of genetic analyses of populations.