A comparative gene analysis with rice identified orthologous group II HKT genes and their association with Na+ concentration in bread wheat

Background Although the HKT transporter genes ascertain some of the key determinants of crop salt tolerance mechanisms, the diversity and functional role of group II HKT genes are not clearly understood in bread wheat. The advanced knowledge on rice HKT and whole genome sequence was, therefore, used in comparative gene analysis to identify orthologous wheat group II HKT genes and their role in trait variation under different saline environments. Results The four group II HKTs in rice identified two orthologous gene families from bread wheat, including the known TaHKT2;1 gene family and a new distinctly different gene family designated as TaHKT2;2. A single copy of TaHKT2;2 was found on each homeologous chromosome arm 7AL, 7BL and 7DL and each gene was expressed in leaf blade, sheath and root tissues under non-stressed and at 200 mM salt stressed conditions. The proteins encoded by genes of the TaHKT2;2 family revealed more than 93 % amino acid sequence identity but ≤52 % amino acid identity compared to the proteins encoded by TaHKT2;1 family. Specifically, variations in known critical domains predicted functional differences between the two protein families. Similar to orthologous rice genes on chromosome 6L, TaHKT2;1 and TaHKT2;2 genes were located approximately 3 kb apart on wheat chromosomes 7AL, 7BL and 7DL, forming a static syntenic block in the two species. The chromosomal region on 7AL containing TaHKT2;1 7AL-1 co-located with QTL for shoot Na+ concentration and yield in some saline environments. Conclusion The differences in copy number, genes sequences and encoded proteins between TaHKT2;2 homeologous genes and other group II HKT gene families within and across species likely reflect functional diversity for ion selectivity and transport in plants. Evidence indicated that neither TaHKT2;2 nor TaHKT2;1 were associated with primary root Na+ uptake but TaHKT2;1 may be associated with trait variation for Na+ exclusion and yield in some but not all saline environments

A comparative gene analysis with rice identified orthologous group II HKT genes and their association with Na+ concentration in bread wheat

Background Although the HKT transporter genes ascertain some of the key determinants of crop salt tolerance mechanisms, the diversity and functional role of group II HKT genes are not clearly understood in bread wheat. The advanced knowledge on rice HKT and whole genome sequence was, therefore, used in comparative gene analysis to identify orthologous wheat group II HKT genes and their role in trait variation under different saline environments. Results The four group II HKTs in rice identified two orthologous gene families from bread wheat, including the known TaHKT2;1 gene family and a new distinctly different gene family designated as TaHKT2;2. A single copy of TaHKT2;2 was found on each homeologous chromosome arm 7AL, 7BL and 7DL and each gene was expressed in leaf blade, sheath and root tissues under non-stressed and at 200 mM salt stressed conditions. The proteins encoded by genes of the TaHKT2;2 family revealed more than 93 % amino acid sequence identity but ≤52 % amino acid identity compared to the proteins encoded by TaHKT2;1 family. Specifically, variations in known critical domains predicted functional differences between the two protein families. Similar to orthologous rice genes on chromosome 6L, TaHKT2;1 and TaHKT2;2 genes were located approximately 3 kb apart on wheat chromosomes 7AL, 7BL and 7DL, forming a static syntenic block in the two species. The chromosomal region on 7AL containing TaHKT2;1 7AL-1 co-located with QTL for shoot Na+ concentration and yield in some saline environments. Conclusion The differences in copy number, genes sequences and encoded proteins between TaHKT2;2 homeologous genes and other group II HKT gene families within and across species likely reflect functional diversity for ion selectivity and transport in plants. Evidence indicated that neither TaHKT2;2 nor TaHKT2;1 were associated with primary root Na+ uptake but TaHKT2;1 may be associated with trait variation for Na+ exclusion and yield in some but not all saline environments

Phenotypic evaluation and genetic analysis of seedling emergence in a global collection of wheat genotypes (Triticum aestivum L.) under limited water availability

The challenge in establishing an early-sown wheat crop in southern Australia is the need for consistently high seedling emergence when sowing deep in subsoil moisture (>10 cm) or into dry top-soil (4 cm). However, the latter is strongly reliant on a minimum soil water availability to ensure successful seedling emergence. This study aimed to: (1) evaluate 233 Australian and selected international wheat genotypes for consistently high seedling emergence under limited soil water availability when sown in 4 cm of top-soil in field and glasshouse (GH) studies; (2) ascertain genetic loci associated with phenotypic variation using a genome-wide association study (GWAS); and (3) compare across loci for traits controlling coleoptile characteristics, germination, dormancy, and pre-harvest sprouting. Despite significant (P 85%) across nine environments. Moreover, 21 environment-specific quantitative trait loci (QTL) were detected in GWAS analysis on chromosomes 1B, 1D, 2B, 3A, 3B, 4A, 4B, 5B, 5D, and 7D, indicating complex genetic inheritance controlling seedling emergence. We aligned QTL for known traits and individual genes onto the reference genome of wheat and identified 16 QTL for seedling emergence in linkage disequilibrium with coleoptile length, width, and cross-sectional area, pre-harvest sprouting and dormancy, germination, seed longevity, and anthocyanin development. Therefore, it appears that seedling emergence is controlled by multifaceted networks of interrelated genes and traits regulated by different environmental cues

Phenotypic Evaluation and Genetic Analysis of Seedling Emergence in a Global Collection of Wheat Genotypes (Triticum aestivum L.) Under Limited Water Availability

The challenge in establishing an early-sown wheat crop in southern Australia is the need for consistently high seedling emergence when sowing deep in subsoil moisture (>10 cm) or into dry top-soil (4 cm). However, the latter is strongly reliant on a minimum soil water availability to ensure successful seedling emergence. This study aimed to: (1) evaluate 233 Australian and selected international wheat genotypes for consistently high seedling emergence under limited soil water availability when sown in 4 cm of top-soil in field and glasshouse (GH) studies; (2) ascertain genetic loci associated with phenotypic variation using a genome-wide association study (GWAS); and (3) compare across loci for traits controlling coleoptile characteristics, germination, dormancy, and pre-harvest sprouting. Despite significant (P 85%) across nine environments. Moreover, 21 environment-specific quantitative trait loci (QTL) were detected in GWAS analysis on chromosomes 1B, 1D, 2B, 3A, 3B, 4A, 4B, 5B, 5D, and 7D, indicating complex genetic inheritance controlling seedling emergence. We aligned QTL for known traits and individual genes onto the reference genome of wheat and identified 16 QTL for seedling emergence in linkage disequilibrium with coleoptile length, width, and cross-sectional area, pre-harvest sprouting and dormancy, germination, seed longevity, and anthocyanin development. Therefore, it appears that seedling emergence is controlled by multifaceted networks of interrelated genes and traits regulated by different environmental cues

Improving Stagonospora nodorum resistance in wheat: A review

Stagonospora nodorum blotch (SNB) is a significant fungal disease of bread wheat (Triticum aestivum L.) caused by Stagonospora nodorum, in which reduced grain yield is caused when the pathogen infects flag leaves and glumes at the critical time of grain filling. Wheat breeding programs have made limited progress in improving resistance to SNB due to the underlying complexity of the pathogen, host resistance, and their interactions. There has been an increase in knowledge of components of host-pathogen interactions in the past five decades, including pathogen diversity, biological factors contributing toward pathogen infection, environmental conditions favoring disease progression, and the genetics of host resistance. This review captures major outcomes and assesses different approaches and methodologies for improving resistance to SNB. The review concludes by proposing strategies for deploying, selecting, and combining gene and trait combinations in genetic backgrounds and improving methods for evaluation and selection of SNB resistance in wheat breeding

Genomics for wheat improvement

The ability to meet the demands of global food production will require efficient means to develop modern cultivars adaptable to a range of adverse environmental conditions in marginal wheat production zones. Breeding programs will be relying on the tools used to track allelic combinations contributing to trait variation through DNA marker-assisted selection and efficient selection of genotypes expressing desirable phenotypes in target environments. The recent developments in wheat genomics have provided resources to develop new molecular markers and strategies for genetic analysis and identification of marker-trait associations. Included are new DNA marker technologies capable of developing high resolution genetic maps and QTL mapping allowing detection of trait variation at specific loci. The ability to locate the chromosomal region associated with phenotypic variation provides a leading edge towards developing functionally-associated markers (FAM) to track alleles in a breeding program. Map-based cloning, comparative genomics and sequencing the wheat genome provides current and future opportunities for discovering genes responsible for trait variation. Determining the function of newly discovered genes will allow their effective use in wheat improvement as FAM markers for marker-assisted breeding. Therefore, transgenic plants overexpressing or silencing genes by RNA interference (RNAi) and non-transgenic approaches such as virus-induced gene silencing (VIGS) and Targeting Induced Local Lesions IN Genomes (TILLING) provide strategies to determine gene function and their effects on phenotypic variation. Transgenic wheat plants and TILLING approaches also has the advantage in developing potential new varieties but the latter would be the only option in countries where the release of genetically modified wheat is constrained

Identification of Bilby, a diverged centromeric Ty1-copia retrotransposon family from cereal rye (Secale cereale L.)

A diminutive rye chromosome (midget) in wheat was used as a model system to isolate a highly reiterated centromeric sequence from a rye chromosome. Fluorescence in situ hybridization (FISH) shows this sequence localized within all rye centromeres and no signal was detected on wheat chromosomes. DNA sequencing of the repetitive element has revealed the presence of some catalytic domains and signature motifs typical of retrotransposon genes and has been called the Bilby family, representing a diverged family of retrotransposon-like elements. Extensive DNA database searching revealed some sequence similarity to centromeric retrotransposons from wheat, barley, and centromeric repetitive sequences from rice. Very low levels of signal were observed when Bilby was used as a probe against barley, and no signal was detected with rice DNA during Southern hybridization. The abundance of Bilby in rye indicates that this family may have diverged from other distantly related centromeric retrotransposons or incorporated in the centromere but rapidly evolved in rye during speciation. The isolation of a rye retrotransposon also allowed the analysis of centromeric breakpoints in wheat-rye translocation lines. A quantitative analysis shows that the breakpoint in 1DS.1RL and 1DL.1RS and recombinant lines containing proximal rye chromatin have a portion of the rye centromere that may contribute to the normal function of the centromeric region.Key words: centromere, retrotransposon, rye, midget chromosome, cereals

Detection of DsRNA viruses in isolates of Australian smut fungi and their serological relationship to viruses found in Ustilago maydis from the U.S.A.

DsRNA was detected in two killer strains of smut fungi collected in Australia. This was determined by digestion of dsRNA preparations with RNase in the presence of high and low salt concentrations and detection of the nucleic acid using agarose gel electrophoresis. Isometric particles approximately 40 nm in diameter were detected using electron microscopy in the same isolates. These particles were shown to be serologically related but not identical to the P1 Ustilago maydis. virus-like particle (VLP) as determined by immunodiffusion using an antiserum to the P1 VLP. This shows that VLPs similar to those in North America also occur in Australia. Neither isometric particles nor dsRNA were detected in three other killer strains of smut fungi or in 11 sensitive strains. This indicates that there is a lack of correlation between killer activity and the presence of a dsRNA VLP in some Australian isolates of smut fungi

Lycopene-ε-cyclase (e-LCY3A) is functionally associated with quantitative trait loci for flour b* colour on chromosome 3A in wheat (Triticum aestivum L.)

Flour b* colour is an important grain quality parameter for specific wheat end-products. The genetic control of b* colour in Australian wheat accessions is controlled by quantitative trait loci (QTL) on chromosomes 3A, 3B, 7A and 7B accumulating lutein, a compound of the carotenoid biosynthetic pathway. The relationship between lutein accumulation and flour b* colour provides an opportunity to identify sequence variants of genes encoding enzymes from the biosynthetic pathway that may control trait variation. This study identified a single nucleotide polymorphism (SNP) in the gene encoding lycopene-ε-cylcase on chromosome 3A (e-LYC3A) between two wheat accessions Ajana and WAWHT2074, identifying two alleles, e-LYC3Aa and e-LYC3Ab, respectively. e-LCY3Ab was present in 62. 5 % of the wheat accessions analysed. A highly significant (P < 0. 01) association with QTL on chromosome 3A in two mapping populations indicated that e-LYC3A is functionally associated with b* colour variation in some Australian wheat accessions. The SNP induced a serine/glycine substitution at amino acid residue 123 and a subtle change in protein folding at amino acid residue 119. The e-LYC3A SNP may be considered along with other alleles and genes on homoeologous group 3 and 7 chromosomes for selecting desirable flour b* colour variation in marker-assisted breeding