An eight-parent multiparent advanced generation inter-cross population for winter-sown wheat: creation, properties, and validation

MAGIC populations represent one of a new generation of crop genetic mapping resources combining high genetic recombination and diversity. We describe the creation and validation of an eight-parent MAGIC population consisting of 1091 F7 lines of winter-sown wheat (Triticum aestivum L.). Analyses based on genotypes from a 90,000-single nucleotide polymorphism (SNP) array find the population to be well-suited as a platform for fine-mapping quantitative trait loci (QTL) and gene isolation. Patterns of linkage disequilibrium (LD) show the population to be highly recombined; genetic marker diversity among the founders was 74% of that captured in a larger set of 64 wheat varieties, and 54% of SNPs segregating among the 64 lines also segregated among the eight founder lines. In contrast, a commonly used reference bi-parental population had only 54% of the diversity of the 64 varieties with 27% of SNPs segregating. We demonstrate the potential of this MAGIC resource by identifying a highly diagnostic marker for the morphological character "awn presence/absence" and independently validate it in an association-mapping panel. These analyses show this large, diverse, and highly recombined MAGIC population to be a powerful resource for the genetic dissection of target traits in wheat, and it is well-placed to efficiently exploit ongoing advances in phenomics and genomics. Genetic marker and trait data, together with instructions for access to seed, are available at http://www.niab.com/MAGIC/

A PSTOL-like gene, TaPSTOL, controls a number of agronomically important traits in wheat

Background Phosphorus (P) is an essential macronutrient for plant growth, and is required in large quantities by elite varieties of crops to maintain yields. Approximately 70% of global cultivated land suffers from P deficiency, and it has recently been estimated that worldwide P resources will be exhausted by the end of this century, increasing the demand for crops more efficient in their P usage. A greater understanding of how plants are able to maintain yield with lower P inputs is, therefore, highly desirable to both breeders and farmers. Here, we clone the wheat (Triticum aestivum L.) homologue of the rice PSTOL gene (OsPSTOL), and characterize its role in phosphate nutrition plus other agronomically important traits. Results TaPSTOL is a single copy gene located on the short arm of chromosome 5A, encoding a putative kinase protein, and shares a high level of sequence similarity to OsPSTOL. We re-sequenced TaPSTOL from 24 different wheat accessions and (3) three T. durum varieties. No sequence differences were detected in 26 of the accessions, whereas two indels were identified in the promoter region of one of the durum wheats. We characterised the expression of TaPSTOL under different P concentrations and demonstrated that the promoter was induced in root tips and hairs under P limiting conditions. Overexpression and RNAi silencing of TaPSTOL in transgenic wheat lines showed that there was a significant effect upon root biomass, flowering time independent of P treatment, tiller number and seed yield, correlating with the expression of TaPSTOL. However this did not increase PUE as elevated P concentration in the grain did not correspond to increased yields. Conclusions Manipulation of TaPSTOL expression in wheat shows it is responsible for many of the previously described phenotypic advantages as OsPSTOL except yield. Furthermore, we show TaPSTOL contributes to additional agronomically important traits including flowering time and grain size. Analysis of TaPSTOL sequences from a broad selection of wheat varieties, encompassing 91% of the genetic diversity in UK bread wheat, showed that there is very little genetic variation in this gene, which would suggest that this locus may have been under high selection pressure

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Segmental chromosomal duplications harbouring group IV CONSTANS-like genes in cereals

Comparative mapping is an important component of map-based cloning in large-genome cereal species. We describe evidence of a segmental chromosomal duplication harbouring CONSTANS-like genes in barley that predates the divergence of the Oryzoideae (rice) and Pooideae (brachypodium, barley, wheat) clades, and discuss the implications of such events for comparative mapping and QTL cloning in temperate cereal crops

Additional file 3: of A PSTOL-like gene, TaPSTOL, controls a number of agronomically important traits in wheat

Figure S2. T-DNA structure for the three TaPSTOL constructs used in this study. (DOCX 30 kb) (DOCX 80 kb

Additional file 4: of A PSTOL-like gene, TaPSTOL, controls a number of agronomically important traits in wheat

Figure S3. ClustalW alignment of the rice and wheat PSTOL predicted proteins. Conserved amino acids are coloured in red. (DOCX 162 kb

Additional file 2: of A PSTOL-like gene, TaPSTOL, controls a number of agronomically important traits in wheat

Figure S1. Location of gene-specific primers and PCR amplification of TaPSTOL genomic regions on DNA extracted from nullisomic (N) / tetrasomic (T) wheat lines. The PCR amplicons correspond to a promoter region (PCR1, 1458 bp), a promoter and coding region (PCR2, 553 bp), and a coding region (PCR3, 870 bp), to demonstrate that TaPSTOL is only present on chromosome 5A. (DOCX 63 kb

Snapshots of gene expression in rice: limitations for allelic expression imbalance determination

In an initial investigation of differential expression of genes caused by cis-acting regulatory elements in rice, the lack of reproducibility led us to question the basic premise of allelic expression imbalance determination: namely that departures of cDNA expression ratios from those observed in genomic DNA provide unequivocal evidence of cis-acting polymorphisms. This paper describes experiments designed to demonstrate that stochastic variation in low copy number of targets in PCR reactions give variable allelic ratios even when starting with the same copy numbers of the two alleles. These significant departures from an expected 1:1 ratio provide an explanation to the lack of reproducibility observed for our cDNA measurements. </jats:p

Periglacial disruption and subsequent glacitectonic deformation of bedrock : an example from Anglesey, North Wales, UK

The deformed metasedimentary bedrock and overlying diamictons in western Anglesey, NW Wales, record evidence of glacier-permafrost interactions during the Late Devensian (Weichselian). The locally highly brecciated New Harbour Group bedrock is directly overlain by a bedrock-rich diamicton which preserves evidence of having undergone both periglacial (brecciation, hydrofracturing) and glacitectonic deformation (thrusting, folding), and is therefore interpreted as periglacial head deposit. The diamicton locally posses a well-developed clast macrofabric which preserves the orientation of the pre-existing tectonic structures within underlying metasedimentary rocks. Both the diamicton and New Harbour Group were variably reworked during the deposition of the later Irish Sea diamicton, resulting in the detachment of bedrock rafts and formation of a pervasively deformed glacitectonite. These structural and stratigraphic relationships are used to demonstrate that a potentially extensive layer of permafrost developed across the island before it was overridden by the Irish Sea Ice Stream. These findings have important implications for the glacial history of Anglesey, indicating that the island remained relatively ice-free prior to its inundation by ice flowing southwards down the Irish Sea Basin. Palynological data obtained from the diamictons across Anglesey clearly demonstrates that they have an Irish Sea provenance. Importantly no Lower Palaeozoic palynomorphs were identified, indicating that it is unlikely that Anglesey was overridden by ice emanating from the Snowdon ice cap developed on the adjacent Welsh mainland. Permafrost was once again re-established across Anglesey after the Irish Sea Ice Stream had retreated, resulting in the formation of involutions which deform both the lower bedrock-rich and overlying Irish Sea diamictons. � 2012 Natural Environment Research Council. Published by Elsevier Ltd on behalf of The Geologists’ Association. All rights reserved