Mu1-Related Transposable Elements of Maize Preferentially Insert into Low Copy Number DNA

The Mutator transposable element system of maize was originally identified through its induction of mutations at an exceptionally high frequency and at a wide variety of loci. The Mu1 subfamily of transposable elements within this system are responsible for the majority of Mutator-induced mutations. Mu 1-related elements were isolated from active Mutator plants and their flanking DNA was characterized. Sequence analyses revealed perfect nine base target duplications directly flanking the insert for 13 of the 14 elements studied. Hybridizational studies indicated that Mu1-like elements insert primarily into regions of the maize genome that are of low copy number. This preferential selection of low copy number DNA as targets for Mu element insertion was not directed by any specific secondary structure(s) that could be detected in this study, but the 9-bp target duplications exhibited a discernibly higher than random match with the consensus sequence 5'-G-T-T-G-G/C-A-G-G/A-G-3'.     

SEMAPHORE1 functions during the regulation of ancestrally duplicated knox genes and polar auxin transport in maize

The expression of class 1 knotted1-like homeobox (knox) genes affects numerous plant developmental processes, including cell-fate acquisition, lateral organ initiation, and maintenance of shoot apical meristems. The SEMAPHORE1 gene product is required for the negative regulation of a subset of maize knox genes, the duplicated loci rough sheath 1 and gnarley1 (knox4). Recessive mutations in semaphore1 result in the ectopic expression of knox genes in leaf and endosperm tissue. Genetic analyses suggest that SEMAPHORE1 may regulate knox gene expression in a different developmental pathway than ROUGH SHEATH2, the first-identified regulator of knox gene expression in maize. Mutations at semaphore1 are pleiotropic, disrupting specific domains of the shoot. However, unlike previously described mutations that cause ectopic knox gene expression, semaphore1 mutations affect development of the embryo, endosperm, lateral roots, and pollen. Moreover, polar transport of the phytohormone auxin is significantly reduced in semaphore1 mutant shoots. The data suggest that many of the pleiotropic semaphore1 phenotypes result from defective polar auxin transport (PAT) in sem1 mutant shoots, and support models correlating down-regulated knox gene expression and PAT in maize shoots.     

Mapping of quantitative trait loci for kernel row number in maize across seven environments

Genetic factors controlling quantitative inheritance of grain yield and its components have been intensively investigated during recent decades using diverse populations in maize (Zea mays L.). Notwithstanding this, quantitative trait loci (QTL) for kernel row number (KRN) with large and consistent effect have not been identified. In this study, a linkage map of 150 simple sequence repeat (SSR) loci was constructed by using a population of 500 F2 individuals derived from a cross between elite inbreds Ye478 and Dan340. The linkage map spanned a total of 1478 cM with an average interval of 10.0 cM. A total of 397 F2:3 lines were evaluated across seven diverse environments for mapping QTL for KRN. Some QTL for grain yield and its components had previously been confirmed with this population across environments. A total of 13 QTL for KRN were identified, with each QTL explaining from 3.0 to 17.9% of phenotypic variance. The gene action for KRN was mainly additive to partial dominance. A large-effect QTL (qkrn7) with partial dominance effect accounting for 17.9% of the phenotypic variation for KRN was identified on chromosome 7 near marker umc1865 with consistent gene effect across seven diverse environments. This study has laid a foundation for map-based cloning of this major QTL and for developing molecular markers for marker-assisted selection of high KRN.     

The thick aleurone1 mutant defines a negative regulation of maize aleurone cell fate that functions downstream of defective kernel1

The maize (Zea mays) aleurone layer occupies the single outermost layer of the endosperm. The defective kernel1 (dek1) gene is a central regulator required for aleurone cell fate specification. dek1 mutants have pleiotropic phenotypes including lack of aleurone cells, aborted embryos, carotenoid deficiency, and a soft, floury endosperm deficient in zeins. Here we describe the thick aleurone1 (thk1) mutant that defines a novel negative function in the regulation of aleurone differentiation. Mutants possess multiple layers of aleurone cells as well as aborted embryos. Clonal sectors of thk1 mutant tissue in otherwise normal endosperm showed localized expression of the phenotype with sharp boundaries, indicating a localized cellular function for the gene. Sectors in leaves showed expanded epidermal cell morphology but the mutant epidermis generally remained in a single cell layer. Double mutant analysis indicated that the thk1 mutant is epistatic to dek1 for several aspects of the pleiotropic dek1 phenotype. dek1 mutant endosperm that was mosaic for thk1 mutant sectors showed localized patches of multilayered aleurone. Localized sectors were surrounded by halos of carotenoid pigments and double mutant kernels had restored zein profiles. In sum, loss of thk1 function restored the ability of dek1 mutant endosperm to accumulate carotenoids and zeins and to differentiate aleurone. Therefore the thk1 mutation defines a negative regulator that functions downstream of dek1 in the signaling system that controls aleurone specification and other aspects of endosperm development. The thk1 mutation was found to be caused by a deletion of approximately 2 megabases.     

Linkage mapping of maize and barley myo-inositol 1-phosphate synthase DNA sequences: correspondence with a low phytic acid mutation

 We sequenced and genetically mapped the myo-inositol 1-phosphate synthase (MIPS) genes of maize (Zea mays L.) and barley (Hordeum vulgare L). Our objective was to determine whether the genetic map positions of these MIPS loci correspond with the location of the low phtyic acid 1 (lpa1) mutations that were previously identified in maize and barley. Seven MIPS-homologous sequences were mapped to positions on maize chromosomes 1S, 4L, 5S, 6S, 8L, 9S and 9L, and a similar number of divergent MIPS sequences were amplified from maize. To the extent that we can compare across different genetic mapping populations, the position of the MIPS gene on maize chromosome 1S is identical to the location of the maize lpa1 mutation. However, only one MIPS sequence was identified in barley and this gene was mapped to a locus on chromosome 4H that is separate from the barley lpa1 mutation on chromosome 2H. Although several RFLP markers linked to the barley MIPS gene on chromosome 4H also detect loci near barley lpa1 on chromosome 2H, our experiments failed to reveal a second MIPS gene that could be associated with the barley lpa1 mutation. Therefore, genetic mapping results from this study support the MIPS candidate-gene hypothesis for maize lpa1, but do not support the MIPS candidate-gene-hypothesis for barley lpa1. These opposing results contradict the hypothesis that maize lpa1 and barley lpa1 are mutations of orthologous genes, which is suggested by the similar biochemical phenotypes of these mutants. Yet, comparisons of RFLP mapping studies show loci that are homologous between maize chromosome 1S, barley chromosome 4H and barley chromosome 2H, including regions flanking the respective MIPS and/or lpa1 loci. This putative relationship, between the regions flanking the lpa1 mutations on maize 1S and barley 2H, also supports the assertion that these mutations are orthologous despite contradictory results between our maize and barley candidate-gene experiments. Received: 24 August 1998 / Accepted: 19 December 1998     

The Auxin-Deficient <Emphasis Type="Italic">Defective Kernel18 (dek18)</Emphasis> Mutation Alters the Expression of Seed-Specific Biosynthetic Genes in Maize

The dek18 mutant of maize was previously classified as a collapsed kernel mutant named cp*-931A, which has a decreased auxin content in kernels. Molecular and functional characterization of this mutant line offers the possibility to better understand auxin biology during maize seed development. Seeds of the dek18 mutants are smaller compared to wild-type seeds and the vegetative development of dek18 is delayed. Here we analyzed the expression of several auxin-related genes in dek18 homozygous seeds and normal-sized seeds (Dek18/-) segregating on the same ear. Three genes related to auxin biosynthesis ZmAlliinase/Tar3, ZmTar1, and ZmYuc1 were highly downregulated in the mutant compared to the wild type. Sequence analysis of these genes revealed that no nucleotide difference is present in dek18 homozygous seeds compared to Dek18/-, except for ZmYuc1. Two different ZmYuc1 cDNAs sequences are produced: a normal-sized sequence of 1197 bp and a shorter coding sequence lacking the third exon. Ectopic expression of ZmYuc1 cDNAs in Arabidopsis indicates that (i) the ZmYuc1 gene is functional in Arabidopsis and (ii) the third exon is required for the enzymatic activity of the YUCCA1 protein. Because ZmYuc1, ZmTar1, and ZmAlliinase are barely expressed in dek18 homozygous seeds, it is proposed that the mutation responsible for the dek18 phenotype alters the upstream regulation of the auxin biosynthetic pathway.     

Genetics of methyl-accepting chemotaxis proteins in Escherichia coli: organization of the tar region.

The tar locus of Escherichia coli specifies one of the major species of methyl-accepting proteins involved in the chemotactic behavior of this organism. The physical and genetic organization of the tar region was investigated with a series of specialized lambda transducing phages and plasmid clones. The tar gene was mapped at the promoter-proximal end of an operon containing five other chemotaxis-related loci. Four of those genes (cheR, cheB, cheY and cheZ) are required for all chemotactic responses; consequently, polar mutations in the tar gene resulted in a generally nonchemotactic phenotype. The fifth gene, tap, was mapped between the tar and cheR loci and specified the production of a 65-kilodalton methyl-accepting protein. Unlike the tar locus, which is required for chemotaxis to aspartate and maltose, mutants lacking only the tap function had no obvious defects in chemotactic ability. Genetic and physical maps of the tar-tap region were constructed with Mu d1 (Apr lac) insertion mutations, whose polar properties conferred a phenotype suitable for deletion mapping studies. Restriction endonuclease analyses of phage and plasmid clones indicated that all of the genetic coding capacity in the tar region is now accounted for.     

Phosphate starvation regulon of Salmonella typhimurium.

Several phosphate-starvation-inducible (psi) genetic loci in Salmonella typhimurium were identified by fusing the lacZ gene to psi promoters by using the Mu d1 and Mu d1-8 bacteriophages. Although several different starvation conditions were examined, the psi loci responded solely to phosphate deprivation. A regulatory locus, psiR, was identified as controlling the psiC locus. The psiR locus did not affect the expression of the Escherichia coli phoA locus or any of the other psi loci described.     

Combined linkage mapping and association analysis reveals genetic control of maize kernel moisture content

The free moisture in crop kernels after being naturally dried is referred to as kernel moisture content (KMC). Maize KMC reflects grain quality and influences transportation and storage of seeds. We used an IBM Syn10 DH maize population consisting of 249 lines and an association panel comprising 310 maize inbred lines to identify the genetic loci affecting maize KMC in three environments. Using the IBM population detected 13 QTL on seven chromosomes, which were clustered into nine common QTL. Genome-wide association analysis (GWAS) identified 16 significant SNPs across the 3 environments, which were linked to 158 genes across the three environments. Combined QTL mapping and GWAS found two SNPs that were located in two of the mapped QTL, respectively. Twenty-three genes were linked with the loci co-localized in both populations. Of these 181 genes, five have previously been reported to be associated with KMC or to regulate seed development. These associations were verified by candidate gene association analysis. Two superior alleles and one favorable haplotype for Zm00001d007774 and Zm00001d047868 were found to influence KMC. These findings provide insights into molecular mechanisms underlying maize KMC and contribute to the use of marker-assisted selection for breeding low-KMC maize.     

The Knotted-1 mutants of maize: investigating the circuitry of leaf development

The maize homeobox gene, Knotted-1 (KN1), was first identified by dominant mutations conditioning aberrant leaf development. Thirteen mutant Kn1 alleles have facilitated a molecular and genetic dissection of the gene and some of its regulatory components. These studies illuminate areas of plant developmental biology that include a demonstration of how transposable elements can control the expression of genes specifying meristematic activity. Genetic approaches have been used to identify collaborating loci, while the Kn1 homeobox has permitted the identification and cloning of related plant homeobox genes. The functions of these genes are being addressed in the context of pattern formation and acquisition of cell fate. This review will focus upon the array of Kn1 mutations and how they have been utilized in genetics and molecular biology.     

Evolution of Anthocyanin Biosynthesis in Maize Kernels: The Role of Regulatory and Enzymatic Loci

Understanding which genes contribute to evolutionary change and the nature of the alterations in them are fundamental challenges in evolution. We analyzed regulatory and enzymatic genes in the maize anthocyanin pathway as related to the evolution of anthocyanin-pigmented kernels in maize from colorless kernels of its progenitor, teosinte. Genetic tests indicate that teosinte possesses functional alleles at all enzymatic loci. At two regulatory loci, most teosintes possess alleles that encode functional proteins, but ones that are not expressed during kernel development and not capable of activating anthocyanin biosynthesis there. We investigated nucleotide polymorphism at one of the regulatory loci, c1. Several observations suggest that c1 has not evolved in a strictly neutral manner, including an exceptionally low level of polymorphism and a biased representation of haplotypes in maize. Curiously, sequence data show that most of our teosinte samples possess a promoter element necessary for the activation of the anthocyanin pathway during kernel development, although genetic tests indicate that teosinte c1 alleles are not active during kernel development. Our analyses suggest that the evolution of the purple kernels resulted from changes in cis regulatory elements at regulatory loci and not changes in either regulatory protein function nor the enzymatic loci.     

玉米抗甘蔗花叶病毒基因的比较定位

收集了玉米抗甘蔗花叶病毒基因/QTL定位信息, 借助玉米遗传图谱IBM2 2005 Neighbors进行了整合。在国内外研究中, 累计报道81个抗病毒基因位点, 分布在玉米7条染色体上, 比较定位发现这些位点集中分布于第3和6染色体。采用元分析技术, 确定3个“一致性”抗病毒QTL, 其中1个位于第3染色体, 在遗传图谱IBM2 2005 Neighbors上覆盖的范围为6.44 cM; 2个位于第6染色体, 覆盖范围分别为6.16 cM和27.48 cM。借助比较基因组学策略, 在第3染色体“一致性”QTL区间内筛选出4个抗病位置候选基因。该研究结果为确定和克隆抗病主效基因提供了基础。     

玉米籽粒淀粉含量遗传基础与调控机制*

玉米是世界上种植面积最大、总产量最高的粮食作物,其籽粒重量的70%来自于淀粉。淀粉不仅是人类及其他动物的主要能量来源,同时也是化工等行业的重要原料。利用拟南芥、水稻等模式植物,淀粉合成相关基因克隆与功能研究已取得较多进展。近年来,随着玉米淀粉含量相关遗传学研究的深入开展,通过数量性状位点(quantitative trait locus mapping,QTL)定位、全基因组关联分析(genome-wide association study, GWAS)及各种组学分析方法,发现了较多新的与淀粉含量相关的遗传位点及候选基因,但是尚缺乏归纳总结。综述了玉米籽粒淀粉合成与调控研究进展,对玉米籽粒淀粉含量相关的QTL和基因进行汇总和分析,通过构建一致性物理图谱,提炼玉米籽粒淀粉含量遗传定位热点区间,这为进一步解析玉米籽粒淀粉合成与代谢相关基因的功能提供参考,并为分子标记辅助育种提供遗传资源。     

QTLs and candidate genes for desiccation and abscisic acid content in maize kernels

Background

Kernel moisture at harvest is an important trait since a low value is required to prevent unexpected early germination and ensure seed preservation. It is also well known that early germination occurs in viviparous mutants, which are impaired in abscisic acid (ABA) biosynthesis. To provide some insight into the genetic determinism of kernel desiccation in maize, quantitative trait loci (QTLs) were detected for traits related to kernel moisture and ABA content in both embryo and endosperm during kernel desiccation. In parallel, the expression and mapping of genes involved in kernel desiccation and ABA biosynthesis, were examined to detect candidate genes.

Results

The use of an intermated recombinant inbred line population allowed for precise QTL mapping. For 29 traits examined in an unreplicated time course trial of days after pollination, a total of 78 QTLs were detected, 43 being related to kernel desiccation, 15 to kernel weight and 20 to ABA content. Multi QTL models explained 35 to 50% of the phenotypic variation for traits related to water status, indicating a large genetic control amenable to breeding. Ten of the 20 loci controlling ABA content colocated with previously detected QTLs controlling water status and ABA content in water stressed leaves. Mapping of candidate genes associated with kernel desiccation and ABA biosynthesis revealed several colocations between genes with putative functions and QTLs. Parallel investigation via RT-PCR experiments showed that the expression patterns of the ABA-responsive Rab17 and Rab28 genes as well as the late embryogenesis abundant Emb5 and aquaporin genes were related to desiccation rate and parental allele effect. Database searches led to the identification and mapping of two zeaxanthin epoxidase (ZEP) and five novel 9-cis-epoxycarotenoid dioxygenase (NCED) related genes, both gene families being involved in ABA biosynthesis. The expression of these genes appeared independent in the embryo and endosperm and not correlated with ABA content in either tissue.

Conclusions

A high resolution QTL map for kernel desiccation and ABA content in embryo and endosperm showed several precise colocations between desiccation and ABA traits. Five new members of the maize NCED gene family and another maize ZEP gene were identified and mapped. Among all the identified candidates, aquaporins and members of the Responsive to ABA gene family appeared better candidates than NCEDs and ZEPs.     

Molecular cloning of the t complex responder genetic locus

Although mouse t haplotypes carry recessive mutations causing male sterility and embryonic lethality, they persist in wild mouse populations via male transmission ratio distortion (TRD). Genetic evidence suggests that at least five t-haplotype-encoded loci combine to cause TRD. One of these loci, called the t complex responder (Tcr), is absolutely required for any deviation from Mendelian segregation to occur. A candidate for the Tcr gene has previously been identified. Evidence that this gene represents Tcr is its localization to the appropriate genomic subregion and testis-specific expression pattern. Here, we report the molecular cloning of the region between recombinant chromosome breakpoints defining the Tcr locus. These results circumscribe Tcr to a 150- to 220-kb region of DNA, including the 22-kb candidate responder gene. This gene and two other homologs were created by large genomic duplications, each involving segments of DNA 10-fold larger than the individual genes.     

Gene coexpression network alignment and conservation of gene modules between two grass species: maize and rice

One major objective for plant biology is the discovery of molecular subsystems underlying complex traits. The use of genetic and genomic resources combined in a systems genetics approach offers a means for approaching this goal. This study describes a maize (Zea mays) gene coexpression network built from publicly available expression arrays. The maize network consisted of 2,071 loci that were divided into 34 distinct modules that contained 1,928 enriched functional annotation terms and 35 cofunctional gene clusters. Of note, 391 maize genes of unknown function were found to be coexpressed within modules along with genes of known function. A global network alignment was made between this maize network and a previously described rice (Oryza sativa) coexpression network. The IsoRankN tool was used, which incorporates both gene homology and network topology for the alignment. A total of 1,173 aligned loci were detected between the two grass networks, which condensed into 154 conserved subgraphs that preserved 4,758 coexpression edges in rice and 6,105 coexpression edges in maize. This study provides an early view into maize coexpression space and provides an initial network-based framework for the translation of functional genomic and genetic information between these two vital agricultural species.