School of Agriculture, Food and Ecosystem Sciences - Research Publications
Permanent URI for this collection
Search Results
1 - 10 of 23
-
ItemNo Preview AvailableMapping of the eibi1 gene responsible for the drought hypersensitive cuticle in wild barley (Hordeum spontaneum)(JAPANESE SOC BREEDING, 2009-03)Segregation analysis showed that eibi1, a drought hypersensitive cuticle wild barley mutant, was monogenic and recessive, and mapped in two F2 populations, one made from a cross between the mutant and a cultivated barley (cv. Morex), and the other between the mutant and another wild barley. A microsatellite marker screen showed that the gene was located on barley chromosome 3H, and a set of markers already assigned to this chromosome, including both microsatellites and ESTs, was used to construct a genetic map. eibi1 co-segregated with barley EST AV918546, and was located to bin 6. The synteny between barley and rice in this region is incomplete, with a large discrepancy in map distances, and the presence of multiple inversions.
-
ItemAnalysis of Intraspecies Diversity in Wheat and Barley Genomes Identifies Breakpoints of Ancient Haplotypes and Provides Insight into the Structure of Diploid and Hexaploid Triticeae Gene Pools(AMER SOC PLANT BIOLOGISTS, 2009-01)A large number of wheat (Triticum aestivum) and barley (Hordeum vulgare) varieties have evolved in agricultural ecosystems since domestication. Because of the large, repetitive genomes of these Triticeae crops, sequence information is limited and molecular differences between modern varieties are poorly understood. To study intraspecies genomic diversity, we compared large genomic sequences at the Lr34 locus of the wheat varieties Chinese Spring, Renan, and Glenlea, and diploid wheat Aegilops tauschii. Additionally, we compared the barley loci Vrs1 and Rym4 of the varieties Morex, Cebada Capa, and Haruna Nijo. Molecular dating showed that the wheat D genome haplotypes diverged only a few thousand years ago, while some barley and Ae. tauschii haplotypes diverged more than 500,000 years ago. This suggests gene flow from wild barley relatives after domestication, whereas this was rare or absent in the D genome of hexaploid wheat. In some segments, the compared haplotypes were very similar to each other, but for two varieties each at the Rym4 and Lr34 loci, sequence conservation showed a breakpoint that separates a highly conserved from a less conserved segment. We interpret this as recombination breakpoints of two ancient haplotypes, indicating that the Triticeae genomes are a heterogeneous and variable mosaic of haplotype fragments. Analysis of insertions and deletions showed that large events caused by transposable element insertions, illegitimate recombination, or unequal crossing over were relatively rare. Most insertions and deletions were small and caused by template slippage in short homopolymers of only a few base pairs in size. Such frequent polymorphisms could be exploited for future molecular marker development.
-
ItemNo Preview AvailableMolecular evolution and phylogeny of the RPB2 gene in the genus Hordeum(OXFORD UNIV PRESS, 2009-04)BACKGROUND AND AIMS: It is known that the miniature inverted-repeat terminal element (MITE) preferentially inserts into low-copy-number sequences or genic regions. Characterization of the second largest subunit of low-copy nuclear RNA polymerase II (RPB2) has indicated that MITE and indels have shaped the homoeologous RPB2 loci in the St and H genome of Eymus species in Triticeae. The aims of this study was to determine if there is MITE in the RPB2 gene in Hordeum genomes, and to compare the gene evolution of RPB2 with other diploid Triticeae species. The sequences were used to reconstruct the phylogeny of the genus Hordeum. METHODS: RPB2 regions from all diploid species of Hordeum, one tetraploid species (H. brevisubulatum) and ten accessions of diploid Triticeae species were amplified and sequenced. Parsimony analysis of the DNA dataset was performed in order to reveal the phylogeny of Hordeum species. KEY RESULTS: MITE was detected in the Xu genome. A 27-36 bp indel sequence was found in the I and Xu genome, but deleted in the Xa and some H genome species. Interestingly, the indel length in H genomes corresponds well to their geographical distribution. Phylogenetic analysis of the RPB2 sequences positioned the H and Xa genome in one monophyletic group. The I and Xu genomes are distinctly separated from the H and Xa ones. The RPB2 data also separated all New World H genome species except H. patagonicum ssp. patagonicum from the Old World H genome species. CONCLUSIONS: MITE and large indels have shaped the RPB2 loci between the Xu and H, I and Xa genomes. The phylogenetic analysis of the RPB2 sequences confirmed the monophyly of Hordeum. The maximum-parsimony analysis demonstrated the four genomes to be subdivided into two groups.
-
ItemNo Preview AvailableMapping of QTL for intermedium spike on barley chromosome 4H using EST-based markers(JAPANESE SOC BREEDING, 2009-12)The lateral spikelets of two-rowed barley are reduced in size and sterile, but in six-rowed barley all three spikelets are fully fertile. The trait is largely controlled by alleles at the vrs1 locus on chromosome arm 2HL, as modified by the allele present at the I locus on chromosome arm 4HS. Molecular markers were developed to saturate the 4HS region by exploiting expressed sequence-tags, either previously mapped in barley to this region, or present in the syntenic region of rice chromosome 3. Collinearity between rice and barley was strong in the 4.8 cM interval BJ468164-AV933435 and the 10 cM interval AV942364-BJ455560. A major QTL for lateral spikelet fertility (the I locus) explained 44% of phenotypic variance, and was located in the interval CB873567-BJ473916. The genotyping of near-isogenic lines for I placed the locus in a region between CB873567 and EBmac635, and therefore the most likely position of the I locus was proximal to CB873567 in a 5.3 cM interval between CB873567-BJ473916.
-
ItemNo Preview AvailableGenetic targeting of candidate genes for drought sensitive gene eibi1 of wild barley (Hordeum spontaneum)(JAPANESE SOC BREEDING, 2009-12)Drought stress is one of the most severe abiotic stresses that cause the loss of crop yield. The cuticle protects the leaf from dehydration in the face of drought stress. The barley cuticle mutant eibi1 is highly drought sensitive. Here, we describe the fine-scale genetic mapping of the eibi1 locus, based on a cv. Morex × eibi1 F population of 1,682 individuals. Barley-rice synteny was exploited to identify markers for mapping and to identify candidate genes for Eibi1. The target segment of chromosome 3H is perfectly collinear with the equivalent region on rice chromosome 1. Marker enrichment delimited eibi1 to a 0.11 cM barley region defined by the interval BI958842-Os01g0176800*, which in rice consists of a 112.8 kbp segment. Gene prediction revealed that this rice segment harbours 16 genes. Of them, five (Os01g0177100, Os01g0177200, Os01g0177900, Os01g0178200 and Os01g0178400) were proposed as candidate genes of Eibi1. 2
-
ItemNo Preview AvailableAllelic variation of row type gene Vrs1 in barley and implication of the functional divergence(JAPANESE SOC BREEDING, 2009-12)Domesticated barleys produce either two- or six- rowed spikes, whereas their immediate wild ancestor, wild barley, is monomorphic for the two-rowed type. The six-rowed spike is a recessive character, conditioned by a major gene at the vrs1 locus. The wild-type (two-rowed) gene includes a homeodomain-leucine zipper I (HD-Zip I) sequence (HvHox1). The correspondence between peptide sequence and some spike variants was studied by re-sequencing the HvHox1 sequence across a large sample of both wild and domesticated accessions.
-
ItemMolecular characterisation and genetic mapping of candidate genes for qualitative disease resistance in perennial ryegrass (Lolium perenne L.)(BMC, 2009-05-19)BACKGROUND: Qualitative pathogen resistance in both dicotyledenous and monocotyledonous plants has been attributed to the action of resistance (R) genes, including those encoding nucleotide binding site--leucine rich repeat (NBS-LRR) proteins and receptor-like kinase enzymes. This study describes the large-scale isolation and characterisation of candidate R genes from perennial ryegrass. The analysis was based on the availability of an expressed sequence tag (EST) resource and a functionally-integrated bioinformatics database. RESULTS: Amplification of R gene sequences was performed using template EST data and information from orthologous candidate using a degenerate consensus PCR approach. A total of 102 unique partial R genes were cloned, sequenced and functionally annotated. Analysis of motif structure and R gene phylogeny demonstrated that Lolium R genes cluster with putative ortholoci, and evolved from common ancestral origins. Single nucleotide polymorphisms (SNPs) predicted through resequencing of amplicons from the parental genotypes of a genetic mapping family were validated, and 26 distinct R gene loci were assigned to multiple genetic maps. Clusters of largely non-related NBS-LRR genes were located at multiple distinct genomic locations and were commonly found in close proximity to previously mapped defence response (DR) genes. A comparative genomics analysis revealed the co-location of several candidate R genes with disease resistance quantitative trait loci (QTLs). CONCLUSION: This study is the most comprehensive analysis to date of qualitative disease resistance candidate genes in perennial ryegrass. SNPs identified within candidate genes provide a valuable resource for mapping in various ryegrass pair cross-derived populations and further germplasm analysis using association genetics. In parallel with the use of specific pathogen virulence races, such resources provide the means to identify gene-for-gene mechanisms for multiple host pathogen-interactions and ultimately to obtain durable field-based resistance.
-
ItemWood density and its radial variation in six canopy tree species differing in shade-tolerance in western Thailand(OXFORD UNIV PRESS, 2009-08)BACKGROUND AND AIMS: Wood density is a key variable for understanding life history strategies in tropical trees. Differences in wood density and its radial variation were related to the shade-tolerance of six canopy tree species in seasonally dry tropical forest in Thailand. In addition, using tree ring measurements, the influence of tree size, age and annual increment on radial density gradients was analysed. METHODS: Wood density was determined from tree cores using X-ray densitometry. X-ray films were digitized and images were measured, resulting in a continuous density profile for each sample. Mixed models were then developed to analyse differences in average wood density and in radial gradients in density among the six tree species, as well as the effects of tree age, size and annual increment on radial increases in Melia azedarach. KEY RESULTS: Average wood density generally reflected differences in shade-tolerance, varying by nearly a factor of two. Radial gradients occurred in all species, ranging from an increase of (approx. 70%) in the shade-intolerant Melia azedarach to a decrease of approx. 13% in the shade-tolerant Neolitsea obtusifolia, but the slopes of radial gradients were generally unrelated to shade-tolerance. For Melia azedarach, radial increases were most-parsimoniously explained by log-transformed tree age and annual increment rather than by tree size. CONCLUSIONS: The results indicate that average wood density generally reflects differences in shade-tolerance in seasonally dry tropical forests; however, inferences based on wood density alone are potentially misleading for species with complex life histories. In addition, the findings suggest that a 'whole-tree' view of life history and biomechanics is important for understanding patterns of radial variation in wood density. Finally, accounting for wood density gradients is likely to improve the accuracy of estimates of stem biomass and carbon in tropical trees.
-
ItemMapping of IgE-binding regions on recombinant Cyn d 1, a major allergen from Bermuda Grass Pollen (BGP)(Biomed Central, 2009-02-02)
-
ItemA Validated Genome Wide Association Study to Breed Cattle Adapted to an Environment Altered by Climate Change(PUBLIC LIBRARY SCIENCE, 2009-08-18)Continued production of food in areas predicted to be most affected by climate change, such as dairy farming regions of Australia, will be a major challenge in coming decades. Along with rising temperatures and water shortages, scarcity of inputs such as high energy feeds is predicted. With the motivation of selecting cattle adapted to these changing environments, we conducted a genome wide association study to detect DNA markers (single nucleotide polymorphisms) associated with the sensitivity of milk production to environmental conditions. To do this we combined historical milk production and weather records with dense marker genotypes on dairy sires with many daughters milking across a wide range of production environments in Australia. Markers associated with sensitivity of milk production to feeding level and sensitivity of milk production to temperature humidity index on chromosome nine and twenty nine respectively were validated in two independent populations, one a different breed of cattle. As the extent of linkage disequilibrium across cattle breeds is limited, the underlying causative mutations have been mapped to a small genomic interval containing two promising candidate genes. The validated marker panels we have reported here will aid selection for high milk production under anticipated climate change scenarios, for example selection of sires whose daughters will be most productive at low levels of feeding.