School of Agriculture, Food and Ecosystem Sciences - Research Publications
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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.
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ItemNo Preview AvailableSix-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene(NATL ACAD SCIENCES, 2007-01-23)Increased seed production has been a common goal during the domestication of cereal crops, and early cultivators of barley (Hordeum vulgare ssp. vulgare) selected a phenotype with a six-rowed spike that stably produced three times the usual grain number. This improved yield established barley as a founder crop for the Near Eastern Neolithic civilization. The barley spike has one central and two lateral spikelets at each rachis node. The wild-type progenitor (H. vulgare ssp. spontaneum) has a two-rowed phenotype, with additional, strictly rudimentary, lateral rows; this natural adaptation is advantageous for seed dispersal after shattering. Until recently, the origin of the six-rowed phenotype remained unknown. In the present study, we isolated vrs1 (six-rowed spike 1), the gene responsible for the six-rowed spike in barley, by means of positional cloning. The wild-type Vrs1 allele (for two-rowed barley) encodes a transcription factor that includes a homeodomain with a closely linked leucine zipper motif. Expression of Vrs1 was strictly localized in the lateral-spikelet primordia of immature spikes, suggesting that the VRS1 protein suppresses development of the lateral rows. Loss of function of Vrs1 resulted in complete conversion of the rudimentary lateral spikelets in two-rowed barley into fully developed fertile spikelets in the six-rowed phenotype. Phylogenetic analysis demonstrated that the six-rowed phenotype originated repeatedly, at different times and in different regions, through independent mutations of Vrs1.
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ItemNo Preview AvailableAnalysis of the barley chromosome 2 region containing the six-rowed spike gene vrs1 reveals a breakdown of rice-barley micro collinearity by a transposition(SPRINGER, 2007-05)In cultivated barley (Hordeum vulgare ssp. vulgare), six-rowed spikes produce three times as many seeds per spike as do two-rowed spikes. The determinant of this trait is the Mendelian gene vrs1, located on chromosome 2H, which is syntenous with rice (Oryza sativa) chromosomes 4 and 7. We exploited barley-rice micro-synteny to increase marker density in the vrs1 region as a prelude to its map-based cloning. The rice genomic sequence, covering a 980 kb contig, identified barley ESTs linked to vrs1. A high level of conservation of gene sequence was obtained between barley chromosome 2H and rice chromosome 4. A total of 22 EST-based STS markers were placed within the target region, and the linear order of these markers in barley and rice was identical. The genetic window containing vrs1 was narrowed from 0.5 to 0.06 cM, which facilitated covering the vrs1 region by a 518 kb barley BAC contig. An analysis of the contig sequence revealed that a rice Vrs1 orthologue is present on chromosome 7, suggesting a transposition of the chromosomal segment containing Vrs1 within barley chromosome 2H. The breakdown of micro-collinearity illustrates the limitations of synteny cloning, and stresses the importance of implementing genomic studies directly in the target species.
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ItemNo Preview AvailableGenetic characterization of Iranian native Bombyx mori strains using amplified fragment length polymorphism markers(OXFORD UNIV PRESS INC, 2007-06)Genetic relationships within and among seven Iranian native silkworm strains was determined by DNA fingerprinting by using amplified fragment length polymorphism (AFLP) markers. In total, 189 informative AFLP markers were generated and analyzed. Estimates of Nei's gene diversity for all loci in individual strains showed a higher degree of genetic similarity within each studied strain. The highest and the least degrees of gene diversity were related to Khorasan Pink (h = 0.1804) and Baghdadi (h = 0.1412) strains, respectively. The unweighted pair-group method with arithmetic average dendrogram revealed seven strains of silkworm, Bombyx mori (L.), resolving into two major clusters. The highest degree of genetic similarity was related to Baghdadi and Harati White, and the least degree was related to Guilan Orange and Harati Yellow. The genetic similarity estimated within and among silkworms could be explained by the pedigrees, historical and geographical distribution of the strains, effective population size, inbreeding rate, selection intensity, and gene flow. This study revealed that the variability of DNA fingerprints within and among silkworm strains could provide an essential basis for breeders in planning crossbreeding strategies to produce potentially hetrotic hybrids in addition to contributing in conservation programs.
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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.
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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.
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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.
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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
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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.
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ItemNo Preview AvailableUsing local knowledge to identify drivers of historic native vegetation change(Modelling and Simulation Society of Australia and New Zealand Inc, 2009-07-17)Research underway with three Catchment Management Authorities in Victoria (Goulburn Broken, North Central and North East) is examining the impacts these bodies have had, and could potentially have, on native vegetation extent and quality (condition) on private land. This paper outlines how local knowledge together with spatial data and ecological information is being used to develop Bayesian Networks (BNs) that show historic changes in native vegetation quality and extent in three regions of northern Victoria since the 1880's. The research is being focused on three case study areas, one located in each partner CMA (Figure 1). Comparison of aerial photography from 1946/7 with contemporary modelled tree canopy cover identified that native vegetation extent has increased or decreased to varying degrees over time and space in each case study areas. Local knowledge elicited from the regional workshops has identified the catalysts of change over time as including episodic events, the viability of the farming industry, demand for 'lifestyle' properties, rabbit control, NRM and Landcare initiatives and policy instruments. Changes in extent and quality of native vegetation varied spatially and temporally across the landscape depending on the presence of remnant native vegetation, land tenure, agronomic potential of the land, historic events (e.g. bushfires), characteristics of the local population and targeted policy instruments. Expansion and intensification of farming between the mid-1950s and the late 1970s was matched by a general decline in the extent of woody native vegetation on private land. A decline in farm profitability from the 1980s to 2006 was associated with declines in farm employment, the number of farmers, population, and businesses and services in small rural towns dependent on agriculture and increases in 'lifestyle' farming around rural towns and regional centres. A general increase in the extent of woody native vegetation on private land was noted over this period by workshop participants. BNs are being used to integrate local knowledge on historic land cover and vegetation change, and its drivers, with analysis of spatial data to capture changes in condition over time (60+ years). The regional workshops have been crucial in developing conceptual understanding of the relationships between external drivers (e.g. climate, market forces), actions (e.g. land clearing, de-stocking, revegetation) and outcomes (e.g. vegetation change). The knowledge and understanding of changes in land use and management and their drivers that was gained from the workshops have been used to refine the influence diagram for the historic vegetation extent and quality BNs, define the details of each variable (e.g. states, key assumptions) and identify key decades to represent in the models.