Identification and heritability of fumonisin insensitivity in Zea mays

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.     

Morphological traits defining species differences in wild relatives of maize are controlled by multiple quantitative trait loci

We analyzed the genetic basis of morphological differences between two wild species of teosinte (Zea diploperennis and Z. mays ssp. parviglumis), which are relatives of maize. These two species differ in a number of taxonomically important traits including the structure of the tassel (male inflorescence), which is the focus of this report. To investigate the genetic inheritance of six tassel traits, quantitative trait locus (QTL) mapping with 95 RFLP markers was employed on a population of 425 F2 plants. Each trait was analyzed by interval mapping (IM) and composite interval mapping (CIM) to identify and characterize the QTL controlling the differences in tassel morphology. We detected two to eight QTL for each trait. In total, 30 QTL with IM and 33 QTL with CIM were found for tassel morphology. QTL for several of the traits mapped near each other, suggesting pleiotropy and/or linkage of QTL. The QTL showed small to moderate magnitudes of effect. No QTL of exceptionally large effect were found as seen under domestication and in the case of some other natural species. Thus, the model involving major QTL of large effect seems not to apply to the traits and species analyzed. A mixture of QTL with positive and negative allelic effects was found for most tassel traits and may suggest a history of periodic changes in the direction of selection during the divergence of Z. diploperennis and Z. mays ssp. parviglumis or fixation of QTL alleles by random genetic drift rather than selection.     

Inheritance of the Morphological Differences between Maize and Teosinte: Comparison of Results for Two F(2) Populations

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.     

Spontaneous hybridization between maize and teosinte

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%).     

Evidence for a natural allelic series at the Maize domestication Locus teosinte branched1

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.     

GISHGenomic in situ hybridization reveals cryptic genetic differences between maize and its putative wild progenitor Zea mays subsp. parviglumis.

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.     

Chromosome C-banding of the teosinte Zea nicaraguensis and comparison to other Zea species

The Nicaraguan teosinte Zea nicaraguensis was studied cytologically to determine its chromosome number and C-banding pattern. The C-banding pattern was compared with that of the close relative Zea luxurians as well as with Zea diploperennis and cultivated maize, Zea mays ssp. mays. Karyograms were constructed for the four Zea species. It is shown that Z. nicaraguensis, like most other Zea species, is a diploid with 2n=20 chromosomes. The C-banding pattern shows that Z. nicaraguensis is very similar to Z. luxurians and more similar to Z. luxurians than to Z. diploperennis and cultivated maize. Whether or not Z. nicaraguensis and Z. luxurians should be regarded as subspecies instead of individual species is, however, not possible to conclude from this study.     

A linkage map of maize × teosinte <Emphasis Type="Italic">Zea luxurians</Emphasis> and identification of QTLs controlling root aerenchyma formation

The objectives of this study were to construct a linkage map and identify quantitative trait loci (QTLs) controlling root aerenchyma formation in drained soil conditions using 195 F₂ individuals derived from a cross between maize inbred line B73 × teosinte Zea luxurians. A 107 SSR marker based map covering 1,331 cM across all ten chromosomes was developed. One significant difference between the parents utilized in the study was that under non-flooding conditions, B73 exhibits a minor capacity to develop root aerenchyma, whereas Z. luxurians exhibits a high tendency to form aerenchyma. Linkage analysis indicated segregation distortion regions on chromosomes 2, 4 and 8, and severe recombination suppression on the long arm of chromosome 4. Multiple interval mapping analysis suggests that five QTLs for aerenchyma formation in non-flooding conditions are located on chromosomes 2, 3, 5, 9 and 10, and these explained 36.3% of the total phenotyphic variance. The Z. luxurians alleles in all five QTLs increased the capacity to form aerenchyma and the locations of these QTLs did not overlap those previously identified in the teosinte Z. nicaraguensis. By transferring aerenchyma-forming QTLs from both Z. luxurians and Z. nicaraguensis, it may be possible to pyramid these genes and develop a maize line with exceptional aerenchyma formation and a high level of tolerance to flooding conditions.     

QTL mapping ofFusarium moniliforme ear rot resistance in maize. 1. Map construction with microsatellite and AFLP markers

To map the QTLsof Fusarium moniliforme ear rot resistance inZea mays L., a total of 230 F₂ individuals, derived from a single cross between inbred maize lines R15 (resistant) and Ye478 (susceptible), were genotyped for genetic map construction using simple sequence repeat (SSR) markers and amplified fragment length polymorphism (AFLP) markers. We used 778 pairs of SSR primers and 63 combinations of AFLP primers to detect the polymorphisms between parents, R15 and Ye478. From the polymorphic 30 AFLP primer combinations and 159 SSR primers, we scored 260 loci in the F₂ population, among which 8 SSR and 13 AFLP loci could not be assigned to any of the linkage groups. An integrated molecular genetic linkage map was constructed by the remaining 151 SSR and 88 AFLP markers, which distributed throughout the 10 linkage groups of maize and spanned the genome of about 3463.5 cM with an average of 14.5 cM between two markers. On 4 chromosomes, we detected 5 putative segregation distortion regions (SDR_s), including 2 new ones (SDR₂ and SDR₇). The other 3 SDR_s were located near the regions where gametophyte genes were mapped, indicating that segregation distortion could be partially caused by gametophytic factors.     

Genetic diversity and population structure of teosinte

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.     

玉米近缘种中玉米着丝粒序列的FISH检测

为分析玉米着丝粒卫星DNA(CentC)和着丝粒反转录转座子(CRM)在玉米种的亚种及近缘种中的保守性,采用双色荧光原位杂交检测了这两种重复序列在墨西哥玉米、二倍体多年生类玉米、多年生类玉米、摩擦禾、薏苡、高粱中的存在和分布。CentC、CRM探针在墨西哥玉米、二倍体多年生类玉米和多年生类玉米的所有染色体的着丝粒区产生了强或较强的杂交信号, 而且不同染色体的杂交信号的强度存在差异, 表明两种玉米着丝粒重复序列在不同着丝粒中的数量不同; 此外, 部分着丝粒中的CentC和CRM信号的强度存在差异, 不完全重叠。CentC、CRM探针仅在摩擦禾的多数染色体的着丝粒区产生了弱的杂交信号。在薏苡和高粱中仅测检到主要分布在着丝粒区的较强或强的CRM信号。这些结果表明, CentC在玉米种的亚种间及玉蜀黍属的物种间高度保守, 在与玉蜀黍属亲缘关系最近的摩擦禾属物种中也具有较高的保守性; CRM在与玉蜀黍属亲缘关系较近和较远的禾本科种属中都具有保守性。     

Physical mapping of the 5S and 45S rDNA in teosintes

The physical locations of the 5S and 45S rDNA sequences were examined in three types of teosinte, Zea mays ssp. mexicana (2n = 20), Zea diploperennis (2n = 20) and Zea perennis (2n = 40) by biotinylated fluorescence in situ hybridization (FISH). The tested materials only showed one hybridization site of 5S rDNA on their genomes, but they were different in the position of the signals. The hybridization site of Zea mays ssp. mexicana was located on the long arm of chromosome 2, indicating that it is the same as the cultivated maize in the position of 5S rDNA, while the sites of Zea diploperennis and Zea perennis were on the short arms of other chromosomes. For 45S rDNA, one hybridization site was detected at secondary constriction region of the satellite chromosomes in Zea mays ssp. mexicana and Zea diploperennis, while in Zea perennis, besides the site located at the secondary constriction region, a second site on the short arm of another chromosome pair was observed. Our results provide additional evidence for Zea mays ssp. mexicana being a subspecies of Zea mays.     

Transmission genetics of chromatin from a synthetic amphidiploid to cultivated peanut (Arachis hypogaea L.). broadening the gene pool of a monophyletic polyploid species

Polyploidy creates severe genetic bottlenecks, contributing to the genetic vulnerability of leading crops. Cultivated peanut is thought to be of monophyletic origin, harboring relatively little genetic diversity. To introduce variability from diploid wild species into tetraploid cultivated Arachis hypogaea, a synthetic amphidiploid [[A. batizocoi K9484 x (A. cardenasii GKP10017 x A. diogoi GKP10602)](4x)] was used as donor parent to generate a backcross population of 78 progeny. Three hundred seventy RFLP loci were mapped onto 23 linkage groups, spanning 2210 cM. Chromatin derived from the two A-genome diploid ancestors (A. cardenasii and A. diogoi) comprised mosaic chromosomes, reflecting crossing over in the diploid A-genome interspecific F(1) hybrid. Recombination between chromosomes in the tetraploid progeny was similar to chromosome pairing reported for A. hypogaea, with recombination generally between chromosomes of the same subgenomic affinity. Segregation distortion was observed for 25% of the markers, distributed over 20 linkage groups. Unexpectedly, 68% of the markers deviating from expected segregation showed an excess of the synthetic parent allele. Genetic consequences, relationship to species origins, and significance for comparative genetics are discussed.     

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

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.     

Zea systematics: ribosomal ITS evidence

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.      

Effect of teosinte cytoplasmic genomes on maize phenotype

Determining the contribution of organelle genes to plant phenotype is hampered by several factors, including the paucity of variation in the plastid and mitochondrial genomes. To circumvent this problem, evolutionary divergence between maize (Zea mays ssp. mays) and the teosintes, its closest relatives, was utilized as a source of cytoplasmic genetic variation. Maize lines in which the maize organelle genomes were replaced through serial backcrossing by those representing the entire genus, yielding alloplasmic sublines, or cytolines were created. To avoid the confounding effects of segregating nuclear alleles, an inbred maize line was utilized. Cytolines with Z. mays teosinte cytoplasms were generally indistinguishable from maize. However, cytolines with cytoplasm from the more distantly related Z. luxurians, Z. diploperennis, or Z. perennis exhibited a plethora of differences in growth, development, morphology, and function. Significant differences were observed for 56 of the 58 characters studied. Each cytoline was significantly different from the inbred line for most characters. For a given character, variation was often greater among cytolines having cytoplasms from the same species than among those from different species. The characters differed largely independently of each other. These results suggest that the cytoplasm contributes significantly to a large proportion of plant traits and that many of the organelle genes are phenotypically important.     

Patterns of isozyme variation between maize and Mexican annual teosinte

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.     

Linkage mapping of domestication loci in a large maize teosinte backcross resource

An ultimate objective of QTL mapping is cloning genes responsible for quantitative traits. However, projects seldom go beyond segments <5 cM without subsequent breeding and genotyping lines to identify additional crossovers in a genomic region of interest. We report on a QTL analysis performed as a preliminary step in the development of a resource for map-based cloning of domestication and improvement genes in corn. A large backcross (BC)1 population derived from a cross between maize (Zea mays ssp. mays) and teosinte (ssp. parviglumis) was grown for the analysis. A total of 1749 progenies were genotyped for 304 markers and measured for 22 morphological traits. The results are in agreement with earlier studies showing a small number of genomic regions having greater impact on the morphological traits distinguishing maize and teosinte. Despite considerable power to detect epistasis, few QTL interactions were identified. To create a permanent resource, seed of BC1 plants was archived and 1000 BC2S6 BC1-derived lines are in development for fine mapping and cloning. The identification of four BC1 progeny with crossovers in a single gene, tb1, indicated that enough derived lines already exist to clone many QTL without the need to generate and identify additional crossovers.     

Exploring the Genetic Characteristics of Two Recombinant Inbred Line Populations via High-Density SNP Markers in Maize

Understanding genetic characteristics can reveal the genetic diversity in maize and be used to explore evolutionary mechanisms and gene cloning. A high-density linkage map was constructed to determine recombination rates (RRs), segregation distortion regions (SDRs), and recombinant blocks (RBs) in two recombinant inbred line populations (RILs) (B73/By804 and Zong3/87-1) generated by the single seed descent method. Population B73/By804 containing 174 lines were genotyped with 198 simple sequence repeats (SSRs) markers while population Zong3/87-1 comprised of 175 lines, were genotyped with 210 SSR markers along with 1536 single nucleotide polymorphism (SNP) markers for each population, spanning 1526.7 cM and 1996.2 cM in the B73/By804 and Zong3/87-1 populations, respectively. The total variance of the RR in the whole genome was nearly 100 fold, and the maximum average was 10.43–11.50 cM/Mb while the minimum was 0.08–0.10 cM/Mb in the two populations. The average number of RB was 44 and 37 in the Zong3/87-1 and B73/By804 populations, respectively, whereas 28 SDRs were observed in both populations. We investigated 11 traits in Zong3/87-1 and 10 traits in B73/By804. Quantitative trait locus (QTLs) mapping of SNP+SSR with SNP and SSR marker sets were compared to showed the impact of different density markers on QTL mapping and resolution. The confidence interval of QTL Pa19 (FatB gene controlling palmitic acid content) was reduced from 3.5 Mb to 1.72 Mb, and the QTL Oil6 (DGAT1-2 gene controlling oil concentration) was significantly reduced from 10.8 Mb to 1.62 Mb. Thus, the use of high-density markers considerably improved QTL mapping resolution. The genetic information resulting from this study will support forthcoming efforts to understand recombination events, SDRs, and variations among different germplasm. Furthermore, this study will facilitate gene cloning and understanding of the fundamental sources of total variation and RR in maize, which is the most widely cultivated cereal crop.     

Microsatellite marker analysis of an anther-derived potato family: skewed segregation and gene-centromere mapping.

Segregation patterns of polymorphic simple sequence repeat (SSR) primer pairs were investigated in monoploid potato families derived from anther culture. A total of 14 primers developed from the sequences in the database, as well as from a genomic library of potato, was used. Distorted segregation was observed for seven (50%) polymorphic loci among monoploids derived from an interspecific hybrid. Similar distortion was observed for only one of five loci that could be contrasted between the two monoploid families. Segregation distortion was less common in the sexually derived backcross population between the interspecific hybrid and either of its parents. One locus could be putatively linked to a lethal allele because it showed distorted segregation in both monoploid families, a group of 70 heterozygous diploids derived from unreduced gametes through anther culture, and a backcross population. These diploids were used to map the polymorphic SSR markers with respect to the centromeres using half-tetrad analysis. The majority of the SSR loci mapped more than 33 cM from the centromere, suggesting the occurrence of a single crossover per chromosome arm.