HAL (Le Centre pour la Communication Scientifique Directe), Apr 23, 2017
Book of abstracts p. 61ISBN: 978-3-900932-48-0Stb16q-mediated resistance against Zymoseptoria tri... more Book of abstracts p. 61ISBN: 978-3-900932-48-0Stb16q-mediated resistance against Zymoseptoria tritici is conferred by a new class of R gene. 13. International Wheat Genetics Symposiu
HAL (Le Centre pour la Communication Scientifique Directe), Apr 8, 2015
Fine mapping of Stb16q, a major resistance gene effective against Zymoseptoria tritici in wheat. ... more Fine mapping of Stb16q, a major resistance gene effective against Zymoseptoria tritici in wheat. 4. Workshop on Pathogen-informed crop improvemen
Central to the diversity of wheat products was the origin of hexaploid bread wheat, which added t... more Central to the diversity of wheat products was the origin of hexaploid bread wheat, which added the D-genome ofAegilops tauschiito tetraploid wheat giving rise to superior dough properties in leavened breads. The polyploidization, however, imposed a genetic bottleneck, with only limited diversity introduced in the wheat D-subgenome. To understand genetic variants for quality, we sequenced 273 accessions spanning the known diversity ofAe. tauschii. We discovered 45 haplotypes inGlu-D1, a major determinant of quality, relative to the two predominant haplotypes in wheat. The wheat allele2 + 12was found inAe. tauschiiLineage 2, the donor of the wheat D-subgenome. Conversely, the superior quality wheat allele5 + 10allele originated in Lineage 3, a recently characterized lineage ofAe. tauschii, showing a unique origin of this important allele. These two wheat alleles were also quite similar relative to the total observed molecular diversity inAe. tauschiiatGlu-D1.Ae. tauschiiis thus a res...
Aegilops tauschii, the diploid wild progenitor of the D subgenome of bread wheat, is a reservoir ... more Aegilops tauschii, the diploid wild progenitor of the D subgenome of bread wheat, is a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. Here we sequenced 242 Ae. tauschii accessions and compared them to the wheat D subgenome to characterize genomic diversity. We found that a rare lineage of Ae. tauschii geographically restricted to present-day Georgia contributed to the wheat D subgenome in the independent hybridizations that gave rise to modern bread wheat. Through k-mer-based association mapping, we identified discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of hexaploids incorporating diverse Ae. tauschii genomes. Exploiting the genomic diversity of the Ae. tauschii ancestral diploid genome permits rapid trait discovery and functional genetic validation in a hexaploid backgroun...
University of Sydney Plant Breeding Institute-Cobbitty, PMB4011, Narellan, NSW2567, Australia, De... more University of Sydney Plant Breeding Institute-Cobbitty, PMB4011, Narellan, NSW2567, Australia, Department of Environment and Primary Industries, Australia (3) USDA-ARS Cereal Disease Laboratory, St Paul, MN, USA; CIMMYT, Kenya; Ethiopian Institute for Agricultural Research, Debre Zeit, Ethiopia; Institute of Experimental Botany, Olomouc, Czech Republic; USDA-Agricultural Research Service, Cereal Crops Research Unit, Fargo, ND USA; CSIRO Agriculture Flagship, ACT, Australia, John Innes Centre, Norwich, UK
Aegilops tauschii, the diploid wild progenitor of the D-subgenome of bread wheat, constitutes a r... more Aegilops tauschii, the diploid wild progenitor of the D-subgenome of bread wheat, constitutes a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. To better define and understand this diversity, we sequenced 242 Ae. tauschii accessions and compared them to the wheat D-subgenome. We characterized a rare, geographically-restricted lineage of Ae. tauschii and discovered that it contributed to the wheat D-subgenome, thereby elucidating the origin of bread wheat from at least two independent hybridizations. We then used k-mer-based association mapping to identify discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of ‘synthetic’ hexaploids incorporating diverse Ae. tauschii genomes. This pipeline permits rapid trait discovery in the diploid ancestor through to functional genetic validation ...
Background and aimsRoot system architecture is a vital part of the plant that has been shown to v... more Background and aimsRoot system architecture is a vital part of the plant that has been shown to vary between species and within species based on response to genotypic and/or environmental influences. The root traits of wheat seedlings is critical for the establishment and evidently linked to plant height and seed yield. However, plant breeders have not efficiently developed the role of RSA in wheat selection due to the difficulty of studying root traits.MethodsWe set up a root phenotyping platform to characterize RSA in 34 wheat accessions. The phenotyping pipeline consists of the germination paper-based moisture replacement system, image capture units, and root-image processing software. The 34 accessions from two different wheat ploidy levels (hexaploids and tetraploids), were characterized in ten replicates. A total of 19 root traits were quantified from the root architecture generated.ResultsThis pipeline allowed for rapid screening of 340 wheat seedlings within 10days. Also, at...
Wheat is an important contributor to global food security, and further improvements are required ... more Wheat is an important contributor to global food security, and further improvements are required to feed a growing human population. New functional genetics and genomics tools can help us to understand the function of different genes and to engineer beneficial changes. In this study, we used a promoter capture assay to sequence 2-kb regions upstream of all high-confidence annotated genes from 1,513 mutagenized plants from the tetraploid wheat variety Kronos. We identified 4.3 million induced mutations with an accuracy of 99.8%, resulting in a mutation density of 41.9 mutations per kb. We also remapped Kronos exome capture reads to Chinese Spring RefSeq v1.1, identified 4.7 million mutations, and predicted their effects on annotated genes. Using these predictions, we identified 59% more non-synonymous substitutions and 49% more truncation mutations than in the original study. To show the biological value of the new promoter dataset, we selected two mutations within the promoter of th...
Wheat plants are infected by diverse pathogens of economic significance. They include biotrophic ... more Wheat plants are infected by diverse pathogens of economic significance. They include biotrophic pathogens like mildews and rusts that require living plant cells to proliferate. By contrast necrotrophic pathogens that cause diseases such as tan spot, Septoria nodurum blotch and spot blotch require dead or dying cells to acquire nutrients. Pioneering studies in the flax plant-flax rust pathosystem led to the 'gene-for-gene' hypothesis which posits that a resistance gene product in the host plant recognizes a corresponding pathogen gene product, resulting in disease resistance. In contrast, necrotrophic wheat pathosystems have an 'inverse gene-forgene' system whereby recognition of a necrotrophic fungal product by a dominant host gene product causes disease susceptibility, and the lack of recognition of this pathogen molecule leads to resistance. More than 300 resistance/susceptibility genes have been identified genetically in wheat and of those cloned the majority encode nucleotide binding, leucine rich repeat immune receptors. Other resistance gene types are also present in wheat, in particular adult plant resistance genes. Advances in mutational genomics and the wheat pan-genome are accelerating causative disease resistance/susceptibility gene discovery. This has enabled multiple disease resistance genes to be engineered as a transgenic gene stack for developing more durable disease resistance in wheat.
HAL (Le Centre pour la Communication Scientifique Directe), Apr 23, 2017
Book of abstracts p. 61ISBN: 978-3-900932-48-0Stb16q-mediated resistance against Zymoseptoria tri... more Book of abstracts p. 61ISBN: 978-3-900932-48-0Stb16q-mediated resistance against Zymoseptoria tritici is conferred by a new class of R gene. 13. International Wheat Genetics Symposiu
HAL (Le Centre pour la Communication Scientifique Directe), Apr 8, 2015
Fine mapping of Stb16q, a major resistance gene effective against Zymoseptoria tritici in wheat. ... more Fine mapping of Stb16q, a major resistance gene effective against Zymoseptoria tritici in wheat. 4. Workshop on Pathogen-informed crop improvemen
Central to the diversity of wheat products was the origin of hexaploid bread wheat, which added t... more Central to the diversity of wheat products was the origin of hexaploid bread wheat, which added the D-genome ofAegilops tauschiito tetraploid wheat giving rise to superior dough properties in leavened breads. The polyploidization, however, imposed a genetic bottleneck, with only limited diversity introduced in the wheat D-subgenome. To understand genetic variants for quality, we sequenced 273 accessions spanning the known diversity ofAe. tauschii. We discovered 45 haplotypes inGlu-D1, a major determinant of quality, relative to the two predominant haplotypes in wheat. The wheat allele2 + 12was found inAe. tauschiiLineage 2, the donor of the wheat D-subgenome. Conversely, the superior quality wheat allele5 + 10allele originated in Lineage 3, a recently characterized lineage ofAe. tauschii, showing a unique origin of this important allele. These two wheat alleles were also quite similar relative to the total observed molecular diversity inAe. tauschiiatGlu-D1.Ae. tauschiiis thus a res...
Aegilops tauschii, the diploid wild progenitor of the D subgenome of bread wheat, is a reservoir ... more Aegilops tauschii, the diploid wild progenitor of the D subgenome of bread wheat, is a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. Here we sequenced 242 Ae. tauschii accessions and compared them to the wheat D subgenome to characterize genomic diversity. We found that a rare lineage of Ae. tauschii geographically restricted to present-day Georgia contributed to the wheat D subgenome in the independent hybridizations that gave rise to modern bread wheat. Through k-mer-based association mapping, we identified discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of hexaploids incorporating diverse Ae. tauschii genomes. Exploiting the genomic diversity of the Ae. tauschii ancestral diploid genome permits rapid trait discovery and functional genetic validation in a hexaploid backgroun...
University of Sydney Plant Breeding Institute-Cobbitty, PMB4011, Narellan, NSW2567, Australia, De... more University of Sydney Plant Breeding Institute-Cobbitty, PMB4011, Narellan, NSW2567, Australia, Department of Environment and Primary Industries, Australia (3) USDA-ARS Cereal Disease Laboratory, St Paul, MN, USA; CIMMYT, Kenya; Ethiopian Institute for Agricultural Research, Debre Zeit, Ethiopia; Institute of Experimental Botany, Olomouc, Czech Republic; USDA-Agricultural Research Service, Cereal Crops Research Unit, Fargo, ND USA; CSIRO Agriculture Flagship, ACT, Australia, John Innes Centre, Norwich, UK
Aegilops tauschii, the diploid wild progenitor of the D-subgenome of bread wheat, constitutes a r... more Aegilops tauschii, the diploid wild progenitor of the D-subgenome of bread wheat, constitutes a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. To better define and understand this diversity, we sequenced 242 Ae. tauschii accessions and compared them to the wheat D-subgenome. We characterized a rare, geographically-restricted lineage of Ae. tauschii and discovered that it contributed to the wheat D-subgenome, thereby elucidating the origin of bread wheat from at least two independent hybridizations. We then used k-mer-based association mapping to identify discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of ‘synthetic’ hexaploids incorporating diverse Ae. tauschii genomes. This pipeline permits rapid trait discovery in the diploid ancestor through to functional genetic validation ...
Background and aimsRoot system architecture is a vital part of the plant that has been shown to v... more Background and aimsRoot system architecture is a vital part of the plant that has been shown to vary between species and within species based on response to genotypic and/or environmental influences. The root traits of wheat seedlings is critical for the establishment and evidently linked to plant height and seed yield. However, plant breeders have not efficiently developed the role of RSA in wheat selection due to the difficulty of studying root traits.MethodsWe set up a root phenotyping platform to characterize RSA in 34 wheat accessions. The phenotyping pipeline consists of the germination paper-based moisture replacement system, image capture units, and root-image processing software. The 34 accessions from two different wheat ploidy levels (hexaploids and tetraploids), were characterized in ten replicates. A total of 19 root traits were quantified from the root architecture generated.ResultsThis pipeline allowed for rapid screening of 340 wheat seedlings within 10days. Also, at...
Wheat is an important contributor to global food security, and further improvements are required ... more Wheat is an important contributor to global food security, and further improvements are required to feed a growing human population. New functional genetics and genomics tools can help us to understand the function of different genes and to engineer beneficial changes. In this study, we used a promoter capture assay to sequence 2-kb regions upstream of all high-confidence annotated genes from 1,513 mutagenized plants from the tetraploid wheat variety Kronos. We identified 4.3 million induced mutations with an accuracy of 99.8%, resulting in a mutation density of 41.9 mutations per kb. We also remapped Kronos exome capture reads to Chinese Spring RefSeq v1.1, identified 4.7 million mutations, and predicted their effects on annotated genes. Using these predictions, we identified 59% more non-synonymous substitutions and 49% more truncation mutations than in the original study. To show the biological value of the new promoter dataset, we selected two mutations within the promoter of th...
Wheat plants are infected by diverse pathogens of economic significance. They include biotrophic ... more Wheat plants are infected by diverse pathogens of economic significance. They include biotrophic pathogens like mildews and rusts that require living plant cells to proliferate. By contrast necrotrophic pathogens that cause diseases such as tan spot, Septoria nodurum blotch and spot blotch require dead or dying cells to acquire nutrients. Pioneering studies in the flax plant-flax rust pathosystem led to the 'gene-for-gene' hypothesis which posits that a resistance gene product in the host plant recognizes a corresponding pathogen gene product, resulting in disease resistance. In contrast, necrotrophic wheat pathosystems have an 'inverse gene-forgene' system whereby recognition of a necrotrophic fungal product by a dominant host gene product causes disease susceptibility, and the lack of recognition of this pathogen molecule leads to resistance. More than 300 resistance/susceptibility genes have been identified genetically in wheat and of those cloned the majority encode nucleotide binding, leucine rich repeat immune receptors. Other resistance gene types are also present in wheat, in particular adult plant resistance genes. Advances in mutational genomics and the wheat pan-genome are accelerating causative disease resistance/susceptibility gene discovery. This has enabled multiple disease resistance genes to be engineered as a transgenic gene stack for developing more durable disease resistance in wheat.
Uploads
Papers by Justin Faris