Frances M Shapter

Mining rice domestication related genes in in Microlaena stipoides

S Malory et al. — Thu, 30 Aug 2012 16:56:46 PDT

Genomics and metabolomics for new plant products

Daniel LE Waters et al. — Thu, 30 Aug 2012 16:56:39 PDT

A new niche cereal may offer on-farm diversification that mitigates risks associated with climate variability

Frances M. Shapter et al. — Thu, 30 Aug 2012 16:56:33 PDT

An Australian native grass, Microlaena stipoides, has been targeted for accelerated domestication utilising a combination of mutation breeding and high throughput genomics. In its natural environment, ecotypes of M .stipoides have shown tolerances to a suite of Australia's environmental challenges including drought, frost, shade, salinity and acid soil. M .stipoides is a perennial species with high water use efficiency and once established becomes a zero-till crop.

Towards the domestication of a wild rice relative, Microlaena stipoides using large scale gene sequencing

Sylvia Malory et al. — Thu, 30 Aug 2012 16:56:32 PDT

Microlaena stipoides, commonly known as weeping grass, is a distant relative of rice. It is a drought, frost and shade tolerant perennial evergreen plant and produces seeds similar to rice. M. stipoides can be used for grain production and additionally it can be grazed as a pasture. This species responds well to nitrogen application and also regular irrigation, making commercial production possible and making it a target for domestication. Extensive sequencing and comparative mapping has established a high degree of conservation between rice and other grasses, allowing the isolation of the corresponding homologues of important rice genes in other grasses. In this study the rice genome sequence is being used for comparison with corresponding genes in M. stipoides. A high range of variability occurs within the natural populations for domestication traits and this can be harnessed for selective breeding programs. An induced mutation population has also been established to capture desired traits for crop improvement. High-throughput next generation sequencing using the Illumina Genome Analyser IIx is being used to discover single nucleotide polymorphisms (SNPs) in M. stipoides which can be used in establishing domesticated lines of M. stipoides. Once domesticated, M. stipoides will become a new cereal crop for commercial food production. This technique can also be utilised for other wild grasses to screen for desirable domestication traits and possibly to create new crops for food consumption.

Characterising homologues of crop domestication genes in poorly described wild crop relatives by high throughput sequencing of whole genomes

Sylvia Malory et al. — Thu, 30 Aug 2012 16:56:19 PDT

Wild crop relatives represent a source of novel alleles for crop genetic improvement. Screening biodiversity for useful or diverse gene homologues has often been based upon the amplification of targeted genes using available sequence information to design primers that amplify the target gene region across species. The crucial requirement of this approach is the presence of sequences with sufficient conservation across species to allow for the design of universal primers. This approach is often not successful with diverse organisms or highly variable genes. Massively parallel sequencing (MPS) can quickly produce large amounts of sequence data and provides a viable option for characterizing homologues of known genes in poorly described genomes. MPS of genomic DNA was used to obtain species-specific sequence information for 18 rice genes related to domestication characteristics in a wild relative of rice, Microlaena stipoides. Species-specific primers were available for 16 genes compared with 12 genes using the universal primer method. The use of species-specific primers had the potential to cover 92% of the sequence of these genes, while traditional universal primers could only be designed to cover 80%. A total of 24 species-specific primer pairs were used to amplify gene homologues, and 11 primer pairs were successful in capturing six gene homologues. The 23 million, 36-base pair (bp) paired end reads, equated to an average of 2X genome coverage, facilitated the successful amplification and sequencing of six target gene homologues, illustrating an important approach to the discovery of useful genes in wild crop relatives.

Analysis of adaptive ribosomal gene diversity in wild plant populations from contrasting climatic environments

Frances M. Shapter et al. — Thu, 30 Aug 2012 15:31:20 PDT

Plant populations may contain variation that reflects adaptation to local environmental conditions. Clues to adaptive evolution of plants may be found in the genomes of species growing in diverse environments or across steep environmental gradients, and under stress. We have examined populations of wild relatives of barley and rice across diverse environmental gradients. Greater diversity, in a nuclear biotic stress defense gene and in chloroplast genes, was found in the more stressed, hotter and dryer environments. This may reflect the greater heterogeneity of these environments. Adaptation of plants to different abiotic stresses (temperatures and levels of water availability) may also require significant adaptation to the different biotic (pest and disease) pressures in these environments. Plants growing across environmental gradients revealed greater diversity in a defense gene (Isa) in more stressed, hotter and dryer environments.2 Chloroplast genome diversity also exhibited a similar variation with environment.3 We now report analysis of nuclear ribosomal genes from the same wild population. Two contrasting environments did not show significant differences in the level of diversity. However the pattern of SNP distribution within the rDNA did vary with greater SNP density in the RNA coding sequences compared with the internal transcribed spacers.

The endosperm morphology of rice and its wild relatives as observed by scanning electron microscopy

Shabana Kasem et al. — Thu, 19 Jul 2012 22:36:27 PDT

While cultivated rice, Oryza sativa, is arguably the world’s most important cereal crop, there is little comparative morphological information available for the grain of rice wild relatives. In this study, the endosperm of 16 rice wild relatives were compared to O. sativa subspecies indica and O. sativa subspeciesjaponica using scanning electron microscopy. Although the aleurone, starch granules, protein bodies and endosperm cell shapes of the cultivated and non-cultivated species were similar, several differences were observed. The starch granules of some wild species had internal channels that have not been reported in cultivated rice. Oryza longiglumis, Microlaena stipoides and Potamophila parviflora, had an aleurone that was only one-cell thick in contrast to the multiple cell layers observed in the aleurone of the remainingOryza species. The similarity of the endosperm morphology of undomesticated species with cultivated rice suggests that some wild species may have similar functional properties. Obtaining a better understanding of the wild rice species grain ultrastructure will assist in identifying potential opportunities for development of these wild species as new cultivated crops or for their inclusion in plant improvement programmes.

Genome diversity in wild grasses under environmental stress

Timothy L. Fitzgerald et al. — Thu, 19 Jul 2012 22:36:26 PDT

Patterns of diversity distribution in the Isa defense locus in wild-barley populations suggest adaptive selection at this locus. The extent to which environmental selection may act at additional nuclear-encoded defense loci and within the whole chloroplast genome has now been examined by analyses in two grass species. Analysis of genetic diversity in wild barley (Hordeum spontaneum) defense genes revealed much greater variation in biotic stress-related genes than abiotic stress-related genes. Genetic diversity at the Isa defense locus in wild populations of weeping ricegrass [Microlaena stipoides (Labill.) R. Br.], a very distant wild-rice relative, was more diverse in samples from relatively hotter and drier environments, a phenomenon that reflects observations in wild barley populations. Whole-chloroplast genome sequences of bulked weeping ricegrass individuals sourced from contrasting environments showed higher levels of diversity in the drier environment in both coding and noncoding portions of the genome. Increased genetic diversity may be important in allowing plant populations to adapt to greater environmental variation in warmer and drier climatic conditions.

Mining homologues of rice domestication genes in an Australian wild grass species

Sylvia Malory et al. — Thu, 19 Jul 2012 22:36:25 PDT

Extensive sequencing and comparative mapping has established a high degree of conservation between rice and other grasses, allowing the isolation of the corresponding homologues of important rice genes in other grasses. In this study, a number of known rice domestication genes are being used as references to characterize homologues in a wild rice relative, Microlaena stipoides, also known as weeping grass. Whole genome sequence data for M. stipoides was generated by Illumina GAII and assembled by reference to the genome sequence of domesticated rice to generate species specific PCR primers for putative BADH2, GW2 and Hd6 homologues in M. stipoides. Pooled PCR amplicons for these homologues generated from both chemically induced mutant and naturally occurring populations were then screened using the Illumina GAII platform to discover single nucleotide polymorphisms (SNPs). We present a new method of SNPs discovery using the Illumina GAII as a quick and efficient method comparable to Sanger sequencing. We will report the SNPs frequency of putative homologues of BADH2, GW2 and Hd6 in M. stipoides. Potentially useful SNP can be used in establishing new breeding lines of M. stipoides suitable for domestication. Once domesticated, M. stipoides will become a new crop for commercial food production.

Utility of mutagenesis and next generation sequencing for accelerating the domestication of a new niche cereal

Frances M. Shapter et al. — Thu, 19 Jul 2012 22:36:24 PDT

A native Australian perennial grass has been targeted for accelerated domestication utilising a combination of mutation breeding and high throughput genomics. Ecovars of Microlaena stipoides exhibit high water use efficiency and have demonstrated adaptability to a suite of abiotic stresses including drought, frost, shade, salt and acid soils. Once established, M. stipoides would be maintained as a zero-till crop which produces reasonable yields of grain of similar size, taste, texture and cooking properties as rice. Accelerated domestication primarily targeted the development of a non-shattering phenotype. Ethyl methanesulfonate was used to induce point mutations in a selected breeding line of M. stipoides with the aim of inducing a loss of function at the homologues of the qSH1 and SHA1 shattering loci identified in Oryza sativa. Amplicons of both of these loci were pooled from 109 control samples and compared with a pool of 109 potential mutant samples and a further pool of 754 potential mutants, and screened for single nucleotide polymorphisms (SNP) using next generation sequencing on the Illumina GA II platform. Putatively functional SNP were identified at both homologous loci. Forty-six elite breeding lines, of which 24 were non-shattering at the M2 generation, have been developed and are currently under cultivation for M3 phenotypic screening. It is envisaged that this methodology could be employed to accelerate the domestication of other wild grasses, which have intrinsic abiotic adaptability, as new food, fibre and fuel crops.

Sorghum

Anjanabha Bhattacharya et al. — Thu, 19 Jul 2012 22:36:19 PDT

Sorghum is an important cereal and fodder crop, which is adaptable to extreme climatic conditions and soil types. The diverse wild Sorghum species represent valuable germplasm and are an important repository of genes, which can be exploited for crop improvement. They are resistant to a variety of diseases and pests. The 25 species include some that are able to be readily crossed with cultivated sorghum. They will also help us to understand the evolution and adaptations of the Sorghum genus. Wild Sorghum species also allow comparative genomic approaches for understanding the genetic basis of important phenotypes such as plant architecture, flowering, and grain yield. Sorghum species have a diverse array of useful traits that are available for use in sorghum improvement as a food, feed fodder, or industrial crop.

Accelerated domestication of an Australian native grain utilising advances in molecular technology

Frances M. Shapter et al. — Tue, 23 Feb 2010 21:58:45 PST

Aleurone and subaleurone morphology in native Australian wild cereal relatives

Frances M. Shapter et al. — Tue, 23 Feb 2010 21:58:45 PST

The pericarp and aleurone layer of cereal grains are associated with the accumulation of anti-nutritional factors, vitamins, high-value proteins and trace elements. Variations in these tissues may be associated with important differences in the nutritional and functional value of cereals as human or animal feeds. Wild crop relatives (WCR) have been successfully utilised in breeding programs to improve agronomic traits such as dwarfism and pest and disease resistance. Australia’s undomesticated grass species (Poaceae) provide a unique and genetically diverse array of WCRs and therefore the grains of 17 Australian WCRs were examined by scanning electron microscopy (SEM). Aleurone of each WCR was compared with that of its nearest domesticated cereal relative, with little significant morphological variation observed to this structure. A novel subaleurone morphology was observed in the Sorghum WCRs which had the appearance of being a very dense protein matrix only sparsely embedded with small starch granules or completely lacking starch granules. Histochemical analysis of a subsample of the specimens confirmed that the described morphology was lacking starch granules and had a proteinaceous matrix. Such morphological variations within Australian wild crop relatives of commercial cereals may provide novel sources of genetic diversity for future grain improvement programs.

Whole grain morphology of Australian rice species

Shabana Kasem et al. — Tue, 23 Feb 2010 21:58:44 PST

The grain morphology of 17 wild rice relatives were studied by light and scanning electron microscopy and compared to two cultivated rice varieties (Oryza sativa cv. Nipponbare and O. sativa cv. Teqing). Observations were made of the grain colour, size and shape. Grains from wild rice species exhibited a variety of colours that have potential aesthetic and nutritional value. The grains of these species exhibited a wide array of sizes and shapes, but still fell within the standard classification scale that rice breeders use for routine breeding evaluation. These results highlight the potential of these species as whole grain foods or as sources of novel alleles in conventional rice breeding programmes.

Domestication of a wild relative of rice, Microlaena stipoides

Sylvia Malory et al. — Tue, 23 Feb 2010 21:58:43 PST

A scanning electron microscope study of endosperm morphology in native grains

Frances M. Shapter et al. — Tue, 13 Oct 2009 19:51:42 PDT

A scanning electron microscope study of endosperm morphology in native sorghums

Frances M. Shapter et al. — Tue, 13 Oct 2009 19:51:41 PDT

Accelerated domestication of Australian grasses as new sustainable food and fodder crops

Frances M. Shapter et al. — Wed, 30 Sep 2009 21:25:46 PDT

Global cereal production is sourced from approximately only 0.2% of the world’s grass (Poaceae) species. None of the currently domesticated species are native to Australia and are therefore not well adapted to our environment. Australia’s short agricultural history and geographic isolation provide a unique opportunity to mine the 1000 grass species naturalised to this continent for new fodder and cereal crop alternatives which are intrinsically adapted to Australia’s variable and changing climate. Advances in molecular genetics over recent decades have provided new insights into the process of domestication and the key genes which have been selected for, both actively and passively, to produce cultivated species. Microlaena stipoides, a distant relative of rice, is being used as a model species for accelerated domestication by harnessing its genetic variation from both natural and induced mutations. The abundance of cereal genomic data is a key resource and is utlilsed in conjunction with endonucleolytic mutation analysis by internal labelling (EMAIL) and large scale SNP analyses for breeding selection. Accelerated domestication of native species may help to ensure food security in a future of declining water availability and changing climate.

SNP discovery in microsatellites and ESTs in hexaploid wheat using pryosequencing

Gary A. Ablett et al. — Tue, 11 Aug 2009 23:33:51 PDT

Mining genomes for improved product quality and human nutrition

Robert J. Henry et al. — Mon, 03 Aug 2009 14:43:35 PDT

Analysis of polymorphisms at the SNP level has been facilitated by the development and application of a range of new tools. New approaches to polymorphism detection such as robust allele specific PCR, RT-PCR with novel chemistries, pyrosequencing and primer extension assay by mass analysis, allow high throughput screening of large numbers of genes. These tools have accelerated the rate of discovery of the DNA sequence variations linked to important genetic traits. Examples of recent associations made in our work, include the discovery of the basis of fragrance and gelatinization temperature in rice. We have established a Plant DNA bank to collect and store genomic DNA from native and mutated genotypes for use in allele mining and genomic diversity studies. The bank is now being mined for alleles contributing to improved cereal grain quality and human nutrition in barley, rice, sorghum and wheat. SAGE and microarray analysis are being used to extend the range of candidate genes subjected to polymorphism analysis.