Maize Chromosomes Research Articles

Strong epigenetic similarity between maize centromeric and pericentromeric regions at the level of small RNAs, DNA methylation and H3 chromatin modifications

Both kinetochore function and sister chromatid cohesion can depend upon pericentromere chromatin structure, and factors associated with heterochromatin have been proposed to have general, conserved roles in distinguishing centromeres and pericentromeres and in conferring pericentromere-intrinsic functions. We applied genome-wide sequencing approaches to quantify RNA expression, DNA methylation and histone modification distributions in maize (Zea mays), focusing on two maize chromosomes with nearly fully sequenced centromeres and pericentromeres. Aside from the presence of the Histone H3 variant common to all centromeres, Centromeric Histone H3 (CENH3), we found no RNA expression or chromatin modifications that clearly differentiate pericentromeres from either centromeres or from chromosome arms, nor did we identify an epigenetic signature that accurately predicts CENH3 location. RNA expression and chromatin modification frequencies were broadly associated with distance from centromeres, gradually peaking or dipping toward arms. When interpreted in the context of experimental data from other systems, our results suggest that centromeres may confer essential functions (such as cohesion retention) to flanking sequence regardless of the local heterochromatin profile.

QTL mapping and epistasis analysis of brace root traits in maize

Root architecture is a major factor influencing root lodging, which limits greater yield stability at high planting density. Total brace root tier number (TBRTN) and effective brace root tier number (EBRTN) are the two most important root architecture traits influencing root lodging. However, the genetic mechanisms that underlie these traits remain poorly understood. In this study, quantitative trait loci (QTL) for TBRTN and EBRTN were mapped using a set of 201 recombinant inbred lines (RILs) and 278 immortalized F2 (IF2) populations derived from these RILs, which were evaluated in three environments. Ten QTL in the RILs and 15 QTL in the IF2 population were detected. In the two populations, we identified two coincident major QTL for TBRTN and a single identical major QTL for EBRTN. The QTL for TBRTN showed the largest additive effect, accounting for 16.36 and 17.88% of the phenotypic variance in the RILs and IF2 population, respectively. Additional epistatic effects were identified for all the maize chromosomes, except for chromosome 4. Most epistatic effects involved pairs of loci that were on different chromosomes. At the same time, we found loci that interacted simultaneously with several other loci to affect expression of the traits, which was particularly evident in the IF2 population. For example, qTAR1-2 interacted simultaneously with qTAR2-1, qTAR3-1, qTAR5-1, and qITAR8-2 to affect the expression of TBRTN. Therefore, a complex network controlling the traits was found in maize. These results provide useful information for understanding the molecular mechanisms controlling root architecture.

T-DNA integration patterns in transgenic maize lines mediated by Agrobacterium tumefaciens

To explore transfer deoxyribonucleic acid (T-DNA) integration patterns in the maize genome, we improved the protocol of thermal asymmetric interlaced polymerase chain reaction (TAIL-PCR), and amplified the flanking sequences around T-DNA integration sites from 70 independent transgenic maize lines mediated by Agrobacterium tumefaciens . Out of 64 specific amplified fragments, 32 and 9 are homologous to the sequences of the maize genome and the expression plasmid, respectively. For 26 of them, a filler sequence was found flanking the cleavage sites. These results demonstrate that cleavage occurs not only during the T-DNA borders but also inside or outside the borders. The border sequences and some inside sequences can be deleted, and filler sequences can be inserted. Illegitimate recombination is a major pattern of T-DNA integration, while some hot spots and preference are present on maize chromosomes. Key words : Agrobacterium tumefaciens, maize, thermal asymmetric interlaced PCR, transfer DNA,transgenics.

Variable transposition of eight maize activator (ac) elements located on the short arm of chromosome 1.

Eight Activator (Ac) transposable elements mapped to the maize chromosome arm 1S were assessed for Ac transposition rates. For each of the Ac stocks, plants homozygous for the single Ac element and the Ds reporter r1-sc:m3 on chromosome 10 were crossed as females by a homozygous r1-sc:m3 tester color-converted W22 line. The resulting ears produced mostly coarsely spotted kernels and a low frequency of either near-colorless fine-spotted kernels or nonspotted kernels. The relative frequency of these two types of near-colorless kernels differed among the eight Ac stocks. The extent to which increased Ac dosage results in nonspotted kernels may be Ac-specific. Although all of the Ac elements are in near-isogenic inbred W22 lines, they varied to a large extent in their transposition frequency. These differences might possibly result from structural differences among the Ac elements. Because one pair of Ac elements derived from Ac33 on chromosome arm 5S differed about 13-fold in transposition frequency and a second pair of Ac elements derived from Ac12 on chromosome arm 1S differed about 3-fold in transposition frequency, this is not a likely explanation for all eight Ac elements. The data presented here support the notion that the differences in transposition frequency of the eight Ac elements may be a reflection of variability in Ac transcription or accessibility of the transposase to the Ac element, resulting from differences in the chromatin environments wherein the Ac elements are located. This is the first report of variability in transposition rates among different Ac donor lines.

Molecular characterization of a genomic interval with highly uneven recombination distribution on maize chromosome 10 L

Homologous recombination in meiosis provides the evolutionary driving force in eukaryotic organisms by generating genetic variability. Meiotic recombination does not always occur evenly across the chromosome, and therefore genetic and physical distances are not consistently in proportion. We discovered a 278 kb interval on the long arm of chromosome 10 (10 L) through analyzed 13,933 descendants of backcross population. The recombinant events distributed unevenly in the interval. The ratio of genetic to physical distance in the interval fluctuated about 47-fold. With the assistance of molecular markers, the interval was divided into several subintervals for further characterization. In agreement with previous observations, high gene-density regions such as subinterval A and B were also genetic recombination hot subintervals, and repetitive sequence-riched region such as subinterval C was also found to be recombination inert at the detection level of the study. However, we found an unusual subinterval D, in which the 72-kb region contained 6 genes. The gene-density of subinterval D was 5.8 times that of the genome-wide average. The ratio of genetic to physical distance in subinterval D was 0.58 cM/Mb, only about 3/4 of the genome average. We carried out an analysis of sequence polymorphisms and methylation status in subinterval D, and the potential causes of recombination suppression were discussed. This study was another case of a detailed genetic analysis of an unusual recombination region in the maize genome.

Diversification, phylogeny and evolution of auxin response factor (ARF) family: insights gained from analyzing maize ARF genes

Auxin response factors (ARFs), member of the plant-specific B3 DNA binding superfamily, target specifically to auxin response elements (AuxREs) in promoters of primary auxin-responsive genes and heterodimerize with Aux/IAA proteins in auxin signaling transduction cascade. In previous research, we have isolated and characterized maize Aux/IAA genes in whole-genome scale. Here, we report the comprehensive analysis of ARF genes in maize. A total of 36 ARF genes were identified and validated from the B73 maize genome through an iterative strategy. Thirty-six maize ARF genes are distributed in all maize chromosomes except chromosome 7. Maize ARF genes expansion is mainly due to recent segmental duplications. Maize ARF proteins share one B3 DNA binding domain which consists of seven-stranded β sheets and two short α helixes. Twelve maize ARFs with glutamine-rich middle regions could be as activators in modulating expression of auxin-responsive genes. Eleven maize ARF proteins are lack of homo- and heterodimerization domains. Putative cis-elements involved in phytohormones and light signaling responses, biotic and abiotic stress adaption locate in promoters of maize ARF genes. Expression patterns vary greatly between clades and sister pairs of maize ARF genes. The B3 DNA binding and auxin response factor domains of maize ARF proteins are primarily subjected to negative selection during selective sweep. The mixed selective forces drive the diversification and evolution of genomic regions outside of B3 and ARF domains. Additionally, the dicot-specific proliferation of ARF genes was detected. Comparative genomics analysis indicated that maize, sorghum and rice duplicate chromosomal blocks containing ARF homologs are highly syntenic. This study provides insights into the distribution, phylogeny and evolution of ARF gene family.

One-to-one quantum dot-labeled single long DNA probes

Quantum dots (QDs) have been received most attention due to their unique properties. Constructing QDs conjugated with certain number of biomolecules is considered as one of the most important research goals in nanobiotechnology. In this study, we report polymerase chain reaction (PCR) amplification of primer oligonucleotides bound to QDs, termed as QD-based PCR. Characterization of QD-based PCR products by gel electrophoresis and atomic force microscopy showed that QD-labeled long DNA strands were synthesized and only a single long DNA strand was conjugated with a QD. The QD-based PCR products still kept fluorescence properties. Moreover, the one-to-one QD-labeled long DNA conjugates as probes could detect a single-copy gene on maize chromosomes by fluorescence in situ hybridization. Labeling a single QD to a single long DNA will make detection of small single-copy DNA fragments, quantitative detection and single molecule imaging come true by nanotechnology, and it will promote medical diagnosis and basic biological research as well as nano-material fabrication.

Distinct DNA methylation patterns associated with active and inactive centromeres of the maize B chromosome

Centromeres are determined by poorly understood epigenetic mechanisms. Centromeres can be activated or inactivated without changing the underlying DNA sequences. However, virtually nothing is known about the epigenetic transition of a centromere from an active to an inactive state because of the lack of examples of the same centromere exhibiting alternative forms and being distinguishable from other centromeres. The centromere of the supernumerary B chromosome of maize provides such an opportunity because its functional core can be cytologically tracked, and an inactive version of the centromere is available. We developed a DNA fiber-based technique that can be used to assess the levels of cytosine methylation associated with repetitive DNA sequences. We report that DNA sequences in the normal B centromere exhibit hypomethylation. This methylation pattern is not affected by the genetic background or structural rearrangement of the B chromosome, but is slightly changed when the B chromosome is transferred to oat as an addition chromosome. In contrast, an inactive version of this same centromere exhibits hypermethylation, indicating that the inactive centromere was modified into a different epigenetic state at the DNA level.

Modified protocol for obtaining isolated and high-resolution pachytene chromosomes

The expansion of molecular cytogenetics has called for the evaluation of pachytene chromosomes as targets for in situ hybridization (ISH) and micro-dissection. These techniques represent powerful tools for chromosome identification, karyotype comparison, physical mapping and phylogenetic analyses. Because cytogenetic preparations showing well-individualized and cytoplasm-free chromosomes are pre-requisites for ISH and micro-dissection, this work was performed with the aim of developing an improved methodology to obtain individualized pachytene chromosomes of maize (Zea mays L.). The used protocol, based on two steps of enzymatic treatment for establishment of cell suspension, released the pollen mother cells (PMCs) from maize anthers. All slides, prepared from maize PMC suspensions, showed pachytene cells with at least one individualized bivalent. This result was considered a major methodological advance, since it facilitated the scattering of all bivalents. These chromosomes were digitally straightened and four morphological parameters were established to characterize all ten maize bivalents. Considering the conditions of an excellent pachytene cytogenetic preparation for ISH and micro-dissection, the results showed that the applied methodology provided adequate pachytene chromosomes for distinct purposes and can be adapted for other plant species.

The Selection and Use of Sorghum (Sorghum propinquum) Bacterial Artificial Chromosomes as Cytogenetic FISH Probes for Maize (Zea mays L.)

The integration of genetic and physical maps of maize is progressing rapidly, but the cytogenetic maps lag behind, with the exception of the pachytene fluorescence in situ hybridization (FISH) maps of maize chromosome 9. We sought to produce integrated FISH maps of other maize chromosomes using Core Bin Marker loci. Because these 1 Kb restriction fragment length polymorphism (RFLP) probes are below the FISH detection limit, we used BACs from sorghum, a small-genome relative of maize, as surrogate clones for FISH mapping. We sequenced 151 maize RFLP probes and compared in silico BAC selection methods to that of library filter hybridization and found the latter to be the best. BAC library screening, clone verification, and single-clone selection criteria are presented along with an example of transgenomic BAC FISH mapping. This strategy has been used to facilitate the integration of RFLP and FISH maps in other large-genome species.

An Ac transposon system based on maize chromosome 4S for isolating long-distance-transposed Ac tags in the maize genome

Transposon tagging is an important tool for gene isolation and functional studies. In maize, several transposon-tagging systems have been developed, mostly using Activator/Dissociation (Ac/Ds) and Mutator systems. Here, we establish another Ac-based transposon system with the donor Ac tightly linked with sugary1 (su1) on maize chromosome 4S. Newly transposed Ac (tr-Acs) were detected based on a negative dosage effect, and long-distance-transposed Ac events were identified and isolated from the donor Ac by a simple backcross scheme. In this study, we identified 208 independent long-distance-transposed Ac lines. Thirty-one flanking sequences of these tr-Acs were isolated and localized in the maize genome. As found in previous studies, the tr-Acs preferentially inserted into genic sequences. The distribution of tr-Acs is not random. In our study, the tr-Acs preferentially transposed into chromosomes 1, 2, 9 and 10. We discuss the preferential distribution of tr-Acs from Ac systems. Our system is complementary to two other Ac-based regional-mutagenesis systems in maize, and the combined use of these systems will achieve an even and high-density distribution of Ac elements throughout the maize genome for functional-genomics studies.

The wheat (T. aestivum) sucrose synthase 2 gene (TaSus2) active in endosperm development is associated with yield traits

Sucrose synthase catalyzes the reaction sucrose + UDP → UDP-glucose + fructose, the first step in the conversion of sucrose to starch in endosperm. Previous studies identified two tissue-specific, yet functionally redundant, sucrose synthase (SUS) genes, Sus1 and Sus2. In the present study, the wheat Sus2 orthologous gene (TaSus2) series was isolated and mapped on chromosomes 2A, 2B, and 2D. Based on sequencing in 61 wheat accessions, three single-nucleotide polymorphisms (SNPs) were detected in TaSus2-2B. These formed two haplotypes (Hap-H and Hap-L), but no diversity was found in either TaSus2-2A or TaSus2-2D. Based on the sequences of the two haplotypes, we developed a co-dominant marker, TaSus2-2B ( tgw ), which amplified 423 or 381-bp fragments in different wheat accessions. TaSus2-2B ( tgw ) was located between markers Xbarc102.2 and Xbarc91 on chromosome 2BS in a RIL population from Xiaoyan 54 × Jing 411. Association analysis suggested that the two haplotypes were significantly associated with 1,000 grain weight (TGW) in 89 modern wheat varieties in the Chinese mini-core collection. Mean TGW difference between the two haplotypes over three cropping seasons was 4.26 g (varying from 3.71 to 4.94 g). Comparative genomics analysis detected major kernel weight QTLs not only in the chromosome region containing TaSus2-2B (tgw), but also in the collinear regions of TaSus2 on rice chromosome 7 and maize chromosome 9. The preferred Hap-H haplotype for high TGW underwent very strong positive selection in Chinese wheat breeding, but not in Europe. The geographic distribution of Hap-H was perhaps determined by both latitude and the intensity of selection in wheat breeding.

MASiVE: Mapping and Analysis of SireVirus Elements in plant genome sequences

We present MASiVE, an expertly built tool for the large-scale, yet sensitive and highly accurate, discovery, preliminary analysis and insertion age estimation of intact Sirevirus LTR-retrotransposons in plant genomic sequences. Validation was based on the recently available and annotated large maize chromosome one. Results show a considerable improvement in the annotation of Sireviruses, and support our approach as an important addition to the bioinformatics toolbox of plant biologists. PERL source code and essential files are available online at http://bat.ina.certh.gr/tools/masive/. The freely available Vmatch, LTRharvest, Wise2, and MAFFT algorithms are required.

DISTURBED SEGREGATION RATIOS IN GALEOPSIS CAUSED BY INTRASPECIFIC STERILITY

HereditasVolume 16, Issue 1-2 p. 73-104 Open Access DISTURBED SEGREGATION RATIOS IN GALEOPSIS CAUSED BY INTRASPECIFIC STERILITY ARNE MÜNTZING, ARNE MÜNTZING SVALÖF, SWEDENSearch for more papers by this author ARNE MÜNTZING, ARNE MÜNTZING SVALÖF, SWEDENSearch for more papers by this author First published: January 1932 https://doi.org/10.1111/j.1601-5223.1932.tb02563.xCitations: 2AboutPDF ToolsExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat Literature Cited 1 Brieger, F. G. and Mangelsdorf, A. J. 1926. Linkage between a flower colour factor and self-sterility factors. Proceed. Nat. Acad. Sciences Vol. 12, No. 4, pp. 248– 255. 2 Brieger, F. G. and Mangelsdorf, A. J. 1927. Linkage between morphological characters and factors for self-sterility. Mem. of the Horticult. Soc. of New York, Vol. 3, pp. 369– 371. 3 Brink, R. A. 1929. The linkage groups in maize affected by semisterility. The Anatomical Record Vol. 44, p. 280. 4 Burnham, C. R. 1930. Genetical and cytological studies of semisterility and related phenomena in maize. Proceed. Nat. Acad. Sciences Vol. 16, No. 4, pp. 269– 277. 5 Clausen, J. 1931. Cyto-genetic and taxonomic investigations on Melanium violets. Hereditas XV, pp. 219– 308. 6 Cooper, D. C. and Brink, R. A. 1931. Cytological evidence for segmental interchange between non-homologous chromosomes in maize. Proceed. Nat. Acad. Sciences Vol. 17, No. 6, pp. 334– 338. 7 Hammarlund, C. 1929. Dritte Mitteilung über einen Fall von Koppelung und freier Kombination bei Erbsen. Hereditas XII, pp. 210– 216. 8 Hammarlund, C. and Håkansson, A. 1930. Parallelism of chromosome ring formation, sterility and linkage in Pisum. Hereditas XIV, pp. 97– 98. 9 Håkansson, A. 1931. Über Chromosomenverkettung in Pisum. Hereditas XV, pp. 17– 61. 10 Jones, D. F. 1928. Selective fertilization. — The University of Chicago Science Series. 11 McClintock, B. 1930. A cytological demonstration of the location of an interchange between two non-homologous chromosomes of Zea mays. Proceed. Nat. Acad. Sciences Vol. 16, No. 12, pp. 791– 796. 12 Müntzing, A. 1929. Cases of partial sterility in crosses within a Linnean species. Hereditas XII, pp. 297– 319. 13 Müntzing, A. 1930. Outlines to a genetic monograph of the genus Galeopsis. With special reference to the nature and inheritance of partial sterility. Hereditas XIII, pp. 185– 341. 14 Philp, J. and Huskins, C. L. 1931. The cytology of Matthiola incana R. Br., especially in relation to the inheritance of double flowers. Journ. of Genetics, Vol. XXIV, No. 3, pp. 359– 404. 15 Sirks, M. J. 1929. Mendelian factors in Datura. III. Genetica XI, 3– 4. 16 Waddington, C. H. 1929. Pollen germination in Stocks and the possibility of applying a lethal factor hypothesis to the interpretation of their breeding. Journ. of Genetics Vol. 21, No. 2. 17 Winkler, H. 1930. Die Konversion der Gene. — Jena. Citing Literature Volume16, Issue1-2January 1932Pages 73-104 ReferencesRelatedInformation

PACHYTENE ANALYSIS OF A DEFICIENT ACCESSORY CHROMOSOME IN RYE

HereditasVolume 38, Issue 1 p. 1-10 Open Access PACHYTENE ANALYSIS OF A DEFICIENT ACCESSORY CHROMOSOME IN RYE A. MÜNTZING, A. MÜNTZING Institute of Genetics, University of Lund, SwedenSearch for more papers by this authorA. LIMA-DE-FARIA, A. LIMA-DE-FARIA Institute of Genetics, University of Lund, SwedenSearch for more papers by this author A. MÜNTZING, A. MÜNTZING Institute of Genetics, University of Lund, SwedenSearch for more papers by this authorA. LIMA-DE-FARIA, A. LIMA-DE-FARIA Institute of Genetics, University of Lund, SwedenSearch for more papers by this author First published: January 1952 https://doi.org/10.1111/j.1601-5223.1952.tb02911.xCitations: 5AboutPDF ToolsExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat Literature Cited 1 Håkansson, A. 1948. Behaviour of accessory rye chromosomes in the embryosac. Hereditas XXXIV, pp. 35– 59. 2 Lima-de-Faria, A. 1948. B chromosomes of rye at pachytene. Portug. Acta Biol. (A) 2 (3), pp. 167– 174. 3 Lima-de-Faria, A. 1952. Chromomere analysis of the chromosome complement of rye. (In the press.). 4 McClintock, B. 1941. The stability of broken ends of chromosomes in Zea mays. Genetics 26, pp. 234– 282. 5 Müntzing, A. 1943. Genetical effects of duplicated fragment chromosomes in rye. Hereditas XXIX, pp. 91– 112. 6 Müntzing, A. 1944. Cytological studies of extra fragment chromosomes in rye. I. Isofragments produced by misdivision. Hereditas XXX, pp. 231– 248. 7 Müntzing, A. 1946. Cytological studies of extra fragment chromosomes in rye. III. The mechanism of non-disjunction at the pollen mitosis. Hereditas XXXII, pp. 97– 119. 8 Müntzing, A. 1948. Cytological studies of extra fragment chromosomes in rye. V. A new fragment type arisen by deletion. Hereditas XXXIV, pp. 435– 442. 9 Müntzing, A. 1949. Accessory chromosomes in Secale and Poa. — Proc. of the Eighth Int. Congr. of Genetics (Hereditas, Suppl. Vol.), pp. 402– 411. 10 Müntzing, A. and Lima-de-Faria, A. 1949. Pachytene analysis of standard fragments and large iso-fragments in rye. Hereditas XXXV, pp. 253– 208. 11 Randolph, L. F. 1941. Genetic characteristics of the B chromosomes in maize. Genetics 26, pp. 608– 831. 12 Rhoades, M. and Kerr, W. E. 1949. A note on centromere organization. Proc. Nat. Acad. Sci. Vol. 35, pp. 129– 132. Citing Literature Volume38, Issue1January 1952Pages 1-10 ReferencesRelatedInformation

Recent and Frequent Insertions of Chloroplast DNA into Maize Nuclear Chromosomes

Organellar DNA transfer into the nucleus and incorporation into chromosomes are continuing processes. We have examined chloroplast DNA insertions in maize chromosomes using fluorescence in situ hybridization (FISH). Probes to detect the nuclear-plastid sequences (NUPTs) were generated using 14 overlapping fragments of the chloroplast genome. Using current FISH methods, detection of NUPTs on mitotic metaphase chromosomes requires relatively large insertions (>3 kb) with strong sequence similarity to chloroplast DNA. In the B73 inbred line, hybridization of each fragment separately resolved a total of 49 NUPT sites; fewer sites (30) were detectable when all the probes were combined. The combined set of probes was hybridized to 10 genetically useful maize inbred lines and identified 19–30 NUPTs in each line. In all but two of the lines, a prominent NUPT was present on the long arm of chromosome 5. Collectively, the number of NUPTs exceeds the number of nuclear-mitochondrial (NUMT) sites identified within the same set of inbred lines. A majority of the NUPTs are found at sites that are different from the NUMTs. Like NUMTs, the positions of the NUPTs vary greatly among the lines, suggesting that the transfers are recent as well as frequent. Thus, insertions of large segments of chloroplast and mitochondrial DNA are components of the dynamic fraction of maize nuclear genomes.

Engineered Minichromosomes in Plants

Engineered minichromosomes provide the ability to target transgenes to a defined insertion position for predictable expression on an independent chromosome. This technology promises to provide a means to add many genes to a synthetic chromosome in sequential manner. An additional advantage is that the multiple transgenes will not be inserted into the normal chromosomes and thus will not exhibit linkage drag when converging the transgenes to different germplasm nor will they be mutagenic. Telomere truncation coupled with the introduction of site-specific recombination cassettes has proven to be an easy method to produce minichromosomes. Telomere truncation results from the transformation of plasmids carrying a block of telomere repeats at one end. Minichromosomes consisting of little more than a centromere have been produced for B chromosomes of maize. Such small chromosomes have been studied for their meiotic behavior, which differs from normal sized chromosomes in that homologue pairing is rare or nonexistent and sister chromatid cohesion fails at meiosis I. Potential modifications of the minichromosomes that can address these issues are discussed. Minichromosomes can be recovered from transformed plants that are polyploid or that carry an additional chromosome as the preferred target for truncation. Site-specific recombination has been demonstrated to operate on these terminally located sites. By introducing normal B chromosomes into lines with engineered mini-B chromosomes, the latter can be increased in copy number, which provides the potential to augment the expression of the introduced genes. Because the vast majority of plant species have the same telomere sequence, the truncating transgenes should be effective in most plants to generate engineered minichromosomes. Such chromosomes establish the means to add or subtract multiple transgenes, multigene complexes, or whole biochemical pathways to plants to change their properties for agronomic applications or to use plants as factories for the production of foreign proteins or metabolites.

Identification of differentially expressed genes at two key endosperm development stages using two maize inbreds with large and small grain and integration with detected QTL for grain weight

Maize endosperm accounts for more than 80% of the grain weight. Cell division and grain filling are the two key stages for endosperm development. Previous studies showed that gene expression during differential stages in endosperm development is greatly different. However, information on systematic identification and characterization of the differentially expressed genes between the two stages are limited. In this study, suppression subtractive hybridization (SSH) was used to generate four subtracted cDNA libraries for the two stages using two maize inbreds with large and small grain. Totally, 4,784 differentially expressed sequence tags (ESTs) were sequenced and 902 were non-redundant, which consisted of 344 unique ESTs. Among them 192 had high sequence similarity to the GenBank entries and represent diverse of functional categories, such as metabolism, cell growth/division, transcription, signal transduction, protein destination/storage, protein synthesis and others. The expression patterns of 75.7% SSH-derived cDNAs were confirmed by reverse Northern blot and semi-quantitative reverse transcription polymerase chain reaction, and exhibited the similar results (75.0%). Genes differentially expressed between two key stages for the two inbreds were involved in diverse physiological process pathway, which might be responsible for the formation of grain weight. 43.8% (70 of the 160 unique ESTs) of the identified ESTs were assigned to 39 chromosome bins distributed over all ten maize chromosomes. Eleven ESTs were found to co-localize with previous detected QTLs for grain weight, which might be considered as the candidate genes of grain weight for further study.

Genome-wide analysis of primary auxin-responsive Aux/IAA gene family in maize (Zea mays. L.)

The phytohormone auxin is important in various aspects of organism growth and development. Aux/IAA genes encoding short-lived nuclear proteins are responsive primarily to auxin induction. Despite their physiological importance, systematic analysis of Aux/IAA genes in maize have not yet been reported. In this paper, we presented the isolation and characterization of maize Aux/IAA genes in whole-genome scale. A total of 31 maize Aux/IAA genes (ZmIAA1 to ZmIAA31) were identified. ZmIAA genes are distributed in all the maize chromosomes except chromosome 2. Aux/IAA genes expand in the maize genome partly due to tandem and segmental duplication events. Multiple alignment and motif display results revealed major maize Aux/IAA proteins share all the four conserved domains. Phylogenetic analysis indicated Aux/IAA family can be divided into seven subfamilies. Putative cis-acting regulatory DNA elements involved in auxin response, light signaling transduction and abiotic stress adaption were observed in the promoters of ZmIAA genes. Expression data mining suggested maize Aux/IAA genes have temporal and spatial expression pattern. Collectively, these results will provide molecular insights into the auxin metabolism, transport and signaling research.

Genome-wide analysis of cyclins in maize (Zea mays)

Cyclins are primary regulators of the activity of cyclin-dependent kinases and play crucial roles in cell cycle progression in eukaryotes. Although extensive studies have revealed the roles of some cyclins and underlying mechanisms in plants, relatively few cyclins have been functionally analyzed in maize. We identified 59 cyclins in the maize genome, distributed on 10 chromosomes; these were grouped into six types by phylogenetic analysis. The cyclin genes in the maize genome went through numerous tandem gene duplications on five chromosomes. However, no segmental duplications, which occur in rice, were found on maize chromosomes. This information allows us to assess the position of plant cyclin genes in terms of evolution and classification, which will be useful for functional studies of maize cyclins.