Tissue-specific expression and drought responsiveness of cell-wall invertase genes of rice at flowering.

Drought stress near heading reduces grain yield in rice cultivars by inhibiting processes such as anther dehiscence and panicle exsertion. Because cell-wall invertases play an important role in carbon allocation to developing organs, we examined the tissue-specific expression and drought sensitivity of the corresponding genes (OsCIN1-9) at heading in the widely grown cultivar IR64. OsCIN1-5,8 were expressed to varying degrees in flag leaf, panicle, anthers and peduncle at 1 day before heading (1 DBH). When water was withheld for 2 days starting 3 DBH, anthesis and peduncle elongation were halted. At the same time, transcript levels for OsCIN1-5,8 genes were all markedly down-regulated in anthers and/or peduncles but were not affected in flag leaves. Re-watering allowed anthesis and peduncle elongation to proceed and restored expression of OsCIN1-5,8. We conclude that cell-wall invertase genes, as a class, respond rapidly to water deficit in anthers and peduncles and through a reduction in sink strength help to coordinate a delay in anthesis and heading. By contrast, vacuolar invertase OsVIN2 was up-regulated by drought stress in flag leaves, panicles, anthers and peduncles. Although OsCIN1-3,5,8 were active in the peduncle, only OsCIN2 was expressed strongly and preferentially at the base, where cell division and cell elongation occur. OsCIN2 was expressed principally in the primary and secondary vascular systems, consistent with a role in diverting sucrose from the phloem to the dividing and expanding cells of the peduncle, whereas the less abundant OsCIN1,3,5,8 transcripts were found principally in parenchyma cells. The OsCIN2 transcript levels in the base were highest at 1 DBH, when rapid peduncle elongation began. Drought stress halted peduncle elongation and reduced OsCIN2 transcript level to 8% of the control level. On re-watering, peduncle elongation was restored and OsCIN2 transcript level recovered to 24% of the control. The abscisic acid (ABA) level of peduncles increased 7-fold on drought stress and returned to the control level on re-watering. Detached peduncles floated on water elongated little and lost all OsCIN2 transcripts, but on 50-100 microM GA3 they elongated rapidly and maintained high OsCIN2 transcript levels. ABA antagonized both peduncle elongation and maintenance of OsCIN2 transcript levels. We conclude that this antagonism is a potential intervention point for breeding strategies directed at enhancing panicle exsertion during or after drought stress at heading.

A SNP resource for human chromosome 22: extracting dense clusters of SNPs from the genomic sequence.

The recent publication of the complete sequence of human chromosome 22 provides a platform from which to investigate genomic sequence variation. We report the identification and characterization of 12,267 potential variants (SNPs and other small insertions/deletions) of human chromosome 22, discovered in the overlaps of 460 clones used for the chromosome sequencing. We found, on average, 1 potential variant every 1.07 kb and approximately 18% of the potential variants involve insertions/deletions. The SNPs have been positioned both relative to each other, and to genes, predicted genes, repeat sequences, other genetic markers, and the 2730 SNPs previously identified on the chromosome. A subset of the SNPs were verified experimentally using either PCR-RFLP or genomic Invader assays. These experiments confirmed 92% of the potential variants in a panel of 92 individuals. [Details of the SNPs and RFLP assays can be found at http://www.sanger.ac.uk and in dbSNP.]

An SNP map of human chromosome 22.

The human genome sequence will provide a reference for measuring DNA sequence variation in human populations. Sequence variants are responsible for the genetic component of individuality, including complex characteristics such as disease susceptibility and drug response. Most sequence variants are single nucleotide polymorphisms (SNPs), where two alternate bases occur at one position. Comparison of any two genomes reveals around 1 SNP per kilobase. A sufficiently dense map of SNPs would allow the detection of sequence variants responsible for particular characteristics on the basis that they are associated with a specific SNP allele. Here we have evaluated large-scale sequencing approaches to obtaining SNPs, and have constructed a map of 2,730 SNPs on human chromosome 22. Most of the SNPs are within 25 kilobases of a transcribed exon, and are valuable for association studies. We have scaled up the process, detecting over 65,000 SNPs in the genome as part of The SNP Consortium programme, which is on target to build a map of 1 SNP every 5 kilobases that is integrated with the human genome sequence and that is freely available in the public domain.

The DNA sequence of human chromosome 22.

Knowledge of the complete genomic DNA sequence of an organism allows a systematic approach to defining its genetic components. The genomic sequence provides access to the complete structures of all genes, including those without known function, their control elements, and, by inference, the proteins they encode, as well as all other biologically important sequences. Furthermore, the sequence is a rich and permanent source of information for the design of further biological studies of the organism and for the study of evolution through cross-species sequence comparison. The power of this approach has been amply demonstrated by the determination of the sequences of a number of microbial and model organisms. The next step is to obtain the complete sequence of the entire human genome. Here we report the sequence of the euchromatic part of human chromosome 22. The sequence obtained consists of 12 contiguous segments spanning 33.4 megabases, contains at least 545 genes and 134 pseudogenes, and provides the first view of the complex chromosomal landscapes that will be found in the rest of the genome.

A 2.8 megabase YAC contig spanning D8S339, which is tightly linked to the Werner syndrome locus.

A number of gene loci, including the locus for Werner syndrome (WRN), map to proximal human chromosome 8p near the genetic marker D8S339. In this report, we present a long range physical map of an approximately 2.8 megabase yeast artificial chromosome contig centred on D8S339. In this map, we localize the WRN-linked polymorphic sequence-tagged sites (STS) D8S339 and D8S1055, as well as a novel polymorphic STS, D8S2297. We also refine the positions of three known gene loci, GTF2E2, GSR, and PPP2CB, relative to the location of WRN within the map.

Analysis of CA repeat polymorphisms places three human gene loci on the 8p linkage map.

The gene loci for luteinizing hormone-releasing hormone (LHRH), the beta-3 adrenergic receptor (ADRB3), and heregulin (HGL) have been assigned to the short arm of human chromosome 8, but the positions of these loci on the human genetic linkage map have not been previously reported. We have isolated simple tandem repeat polymorphisms (STRPs) for these loci. These STRPs enabled us to determine the genetic map locations for these genes.