QTLs for resistance to the false brome rust Puccinia brachypodii in the model grass Brachypodium distachyon L.

Genome ◽  
2012 ◽  
Vol 55 (2) ◽  
pp. 152-163 ◽  
Author(s):  
Mirko Barbieri ◽  
Thierry C. Marcel ◽  
Rients E. Niks ◽  
Enrico Francia ◽  
Marianna Pasquariello ◽  
...  
Keyword(s):  
Quantitative Resistance ◽  
Rust Fungus ◽  
Brachypodium Distachyon ◽  
Transgressive Segregation ◽  
Snp Markers ◽  
Growth Stages ◽  
Resistance Qtls ◽  
Ssr And Snp Markers ◽  
Model Grass ◽  
Genomic Regions

The potential of the model grass Brachypodium distachyon L. (Brachypodium) for studying grass–pathogen interactions is still underexploited. We aimed to identify genomic regions in Brachypodium associated with quantitative resistance to the false brome rust fungus Puccinia brachypodii . The inbred lines Bd3-1 and Bd1-1, differing in their level of resistance to P. brachypodii, were crossed to develop an F2 population. This was evaluated for reaction to a virulent isolate of P. brachypodii at both the seedling and advanced growth stages. To validate the results obtained on the F2, resistance was quantified in F2-derived F3 families in two experiments. Disease evaluations showed quantitative and transgressive segregation for resistance. A new AFLP-based Brachypodium linkage map consisting of 203 loci and spanning 812 cM was developed and anchored to the genome sequence with SSR and SNP markers. Three false brome rust resistance QTLs were identified on chromosomes 2, 3, and 4, and they were detected across experiments. This study is the first quantitative trait analysis in Brachypodium. Resistance to P. brachypodii was governed by a few QTLs: two acting at the seedling stage and one acting at both seedling and advanced growth stages. The results obtained offer perspectives to elucidate the molecular basis of quantitative resistance to rust fungi.

scholarly journals Brachypodium distachyon–Cochliobolus sativus Pathosystem is a New Model for Studying Plant–Fungal Interactions in Cereal Crops

2015 ◽  
Vol 105 (4) ◽  
pp. 482-489 ◽  
Author(s):  
Shaobin Zhong ◽  
Shaukat Ali ◽  
Yueqiang Leng ◽  
Rui Wang ◽  
David F. Garvin
Keyword(s):  
Molecular Mechanisms ◽  
Brachypodium Distachyon ◽  
Bipolaris Sorokiniana ◽  
Transgressive Segregation ◽  
Cochliobolus Sativus ◽  
Cereal Crops ◽  
New Model ◽  
Model Grass ◽  
Fungal Interactions ◽  
Important Disease

Cochliobolus sativus (anamorph: Bipolaris sorokiniana) causes spot blotch, common root rot, and kernel blight or black point in barley and wheat. However, little is known about the molecular mechanisms underlying the pathogenicity of C. sativus or the molecular basis of resistance and susceptibility in the hosts. This study aims to establish the model grass Brachypodium distachyon as a new model for studying plant–fungus interactions in cereal crops. Six B. distachyon lines were inoculated with five C. sativus isolates. The results indicated that all six B. distachyon lines were infected by the C. sativus isolates, with their levels of resistance varying depending on the fungal isolates used. Responses ranging from hypersensitive response-mediated resistance to complete susceptibility were observed in a large collection of B. distachyon (2n = 2x = 10) and B. hybridum (2n = 4x = 30) accessions inoculated with four of the C. sativus isolates. Evaluation of an F2 population derived from the cross between two of the B. distachyon lines, Bd1-1 and Bd3-1, with isolate Cs07-47-1 showed quantitative and transgressive segregation for resistance to C. sativus, suggesting that the resistance may be governed by quantitative trait loci from both parents. The availability of whole-genome sequences of both the host (B. distachyon) and the pathogen (C. sativus) makes this pathosystem an attractive model for studying this important disease of cereal crops.

scholarly journals Mapping Quantitative Trait Loci onto Chromosome-scale Pseudomolecules in Flax

2019 ◽  
Author(s):  
Frank M. You ◽  
Sylvie Cloutier
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Quantitative Traits ◽  
Snp Markers ◽  
Genetic Maps ◽  
Genome Wide ◽  
Trait Loci ◽  
Ssr And Snp Markers ◽  
Gene Scanning ◽  
Genomic Regions

Quantitative trait loci (QTL) are genomic regions associated with phenotype variation of quantitative traits in a population. To date, a total of 267 QTL for 29 quantitative traits have been reported in 13 studies on flax. Of these, 200 QTL from 12 studies were identified based on genetic maps, scaffold sequences, or pre-released chromosome-scale pseudomolecules. Molecular markers for QTL identification differed across studies but were mainly based on simple sequence repeat (SSR) or single nucleotide polymorphism (SNP) markers. This article provides methods with software tools and database files to uniquely map SSR and SNP markers from different references onto the recently released chromosome-scale pseudomolecules. Using these methods, 195 QTL were successfully sorted onto the 15 flax chromosomes and grouped into 133 co-located QTL clusters. Mapping of QTL from different studies to the same reference enables comparisons and facilitates genome-wide QTL analysis, candidate gene scanning, and breeding applications.

scholarly journals Determination of growth stages and metabolic profiles in Brachypodium distachyon for comparison of developmental context with Triticeae crops

2015 ◽  
Vol 282 (1811) ◽  
pp. 20150964 ◽  
Author(s):  
Yoshihiko Onda ◽  
Kei Hashimoto ◽  
Takuhiro Yoshida ◽  
Tetsuya Sakurai ◽  
Yuji Sawada ◽  
...  
Keyword(s):  
Life Cycle ◽  
Knowledge Integration ◽  
Brachypodium Distachyon ◽  
Chemical Properties ◽  
Stress Conditions ◽  
Growth Stages ◽  
Metabolome Analysis ◽  
Developmental Context ◽  
Chinese Spring Wheat ◽  
Model Grass

Brachypodium distachyon is an emerging model plant for studying biological phenomena in temperate grasses. Study of the growth scale is essential to analyse spatio-temporal changes in molecular factors throughout the life cycle. For sensitive and robust staging based on morphology in B. distachyon , we demonstrated the utility of the BBCH (Biologische Bundesanstalt, Bundessortenamt and CHemical industry) scale, which is comparable to the Zadoks scale conventionally used for Triticeae crops. We compared the chronological progression of B. distachyon accessions Bd21 and Bd3-1, in addition to the progression of Chinese Spring wheat. The comparison of growth stages illustrates the morphological similarities and differences in the timing of life cycle events. Furthermore, we compared metabolite accumulation patterns across different growth stages and across different stress conditions using a widely targeted metabolome analysis. Metabolic profiling determined commonalities and specificities in chemical properties that were dependent on organisms, growth stages and/or stress conditions. Most metabolites accumulated equivalently in B. distachyon and wheat. This qualitative similarity indicated the superiority of B. distachyon as a model for Triticeae crops. The growth scale of B. distachyon should provide a conceptual framework for comparative analysis and for knowledge integration between this model grass and crops in the Pooideae subfamily.

scholarly journals Genomic regions associated with chocolate spot (Botrytis fabae Sard.) resistance in faba bean (Vicia faba L.)

2021 ◽  
Author(s):  
Tadesse S. Gela ◽  
Margaret Bruce ◽  
Wei Chang ◽  
Frederick L. Stoddard ◽  
Alan H. Schulman ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Faba Bean ◽  
Snp Markers ◽  
Chromosome 1 ◽  
Phenotypic Variance ◽  
Resistance Qtls ◽  
Climate Conditions ◽  
Botrytis Fabae ◽  
Chocolate Spot ◽  
Genomic Regions

Chocolate spot (CS), caused by Botrytis fabae Sard., is an important threat to global faba bean production. Growing resistant faba bean cultivars is, therefore, paramount to preventing yield loss. To date, there have been no reported quantitative trait loci (QTLs) associated with CS resistance in faba bean. The objective of this study was to identify genomic regions associated with CS resistance using a recombinant inbred line (RIL) population derived from resistant accession ILB 938. A total of 165 RILs from the cross between Melodie/2 and ILB 938/2 were genotyped and evaluated for CS reactions under replicated, controlled climate conditions. QTL analysis identified five loci contributing to CS resistance on faba bean chromosomes 1 and 6, accounting for 5.0-23.4% of the total phenotypic variance. The sequences of SNP markers linked to resistance QTLs on chromosome 1 that have the largest effects encode multiple classes of putative disease and/or defense-related genes. The results of this study not only provide insight into disease-resistance QTLs, but can also be used as potential targets for marker-assisted breeding in faba bean genetic improvement for CS resistance. Keywords: Botrytis fabae; chocolate spot; faba bean; disease resistance; QTL mapping; candidate gene

scholarly journals Candidate Genes for the High-Altitude Adaptations of Two Mountain Pine Taxa

2021 ◽  
Vol 22 (7) ◽  
pp. 3477
Author(s):  
Julia Zaborowska ◽  
Bartosz Łabiszak ◽  
Annika Perry ◽  
Stephen Cavers ◽  
Witold Wachowiak
Keyword(s):  
Population Structure ◽  
Candidate Genes ◽  
Genetic Basis ◽  
Redox Homeostasis ◽  
Snp Markers ◽  
Regulation Of Transcription ◽  
Single Nucleotide ◽  
Homeostasis Regulation ◽  
Genomic Regions ◽  
Mountain Plants

Mountain plants, challenged by vegetation time contractions and dynamic changes in environmental conditions, developed adaptations that help them to balance their growth, reproduction, survival, and regeneration. However, knowledge regarding the genetic basis of species adaptation to higher altitudes remain scarce for most plant species. Here, we attempted to identify such corresponding genomic regions of high evolutionary importance in two closely related European pines, Pinus mugo and P. uncinata, contrasting them with a reference lowland relative—P. sylvestris. We genotyped 438 samples at thousands of single nucleotide polymorphism (SNP) markers, tested their genetic differentiation and population structure followed by outlier detection and gene ontology annotations. Markers clearly differentiated the species and uncovered patterns of population structure in two of them. In P. uncinata three Pyrenean sites were grouped together, while two outlying populations constituted a separate cluster. In P. sylvestris, Spanish population appeared distinct from the remaining four European sites. Between mountain pines and the reference species, 35 candidate genes for altitude-dependent selection were identified, including such encoding proteins responsible for photosynthesis, photorespiration and cell redox homeostasis, regulation of transcription, and mRNA processing. In comparison between two mountain pines, 75 outlier SNPs were found in proteins involved mainly in the gene expression and metabolism.

scholarly journals Grain dormancy and light quality effects on germination in the model grass Brachypodium distachyon

2011 ◽  
Vol 193 (2) ◽  
pp. 376-386 ◽  
Author(s):  
José M. Barrero ◽  
John V. Jacobsen ◽  
Mark J. Talbot ◽  
Rosemary G. White ◽  
Stephen M. Swain ◽  
...  
Keyword(s):  
Light Quality ◽  
Brachypodium Distachyon ◽  
Grain Dormancy ◽  
Model Grass

Phenological growth stages of Brachypodium distachyon: codification and description

Weed Research ◽  
2011 ◽  
Vol 51 (6) ◽  
pp. 612-620 ◽  
Author(s):  
S-Y HONG ◽  
J-H PARK ◽  
S-H CHO ◽  
M-S YANG ◽  
C-M PARK
Keyword(s):  
Brachypodium Distachyon ◽  
Growth Stages

scholarly journals Development of EST-Molecular Markers from RNA Sequencing for Genetic Management and Identification of Growth Traits in Potato Grouper (Epinephelus tukula)

Biology ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 36
Author(s):  
Te-Hua Hsu ◽  
Yu-Ting Chiu ◽  
Hung-Tai Lee ◽  
Hong-Yi Gong ◽  
Chang-Wen Huang
Keyword(s):  
Molecular Markers ◽  
Expressed Sequence Tag ◽  
De Novo ◽  
Growth Traits ◽  
Gene Diversity ◽  
Snp Markers ◽  
Cdna Libraries ◽  
Functional Markers ◽  
Genetic Management ◽  
Ssr And Snp Markers

The accuracy and efficiency of marker-assisted selection (MAS) has been proven for economically critical aquaculture species. The potato grouper (Epinephelus tukula), a novel cultured grouper species in Taiwan, shows large potential in aquaculture because of its fast growth rate among other groupers. Because of the lack of genetic information for the potato grouper, the first transcriptome and expressed sequence tag (EST)-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were developed. Initially, the transcriptome was obtained from seven cDNA libraries by using the Illumina platform. De novo transcriptome of the potato grouper yielded 51.34 Gb and 111,490 unigenes. The EST-derived SSR and SNP markers were applied in genetic management, in parentage analysis, and to discover the functional markers of economic traits. The F1 juveniles were identified as siblings from one pair of parents (80 broodstocks). Fast- and slow-growth individuals were analyzed using functional molecular markers and through their association with growth performance. The results revealed that two SNPs were correlated with growth traits. The transcriptome database obtained in this study and its derived SSR and SNP markers may be applied not only for MAS but also to maintain functional gene diversity in the novel cultured grouper.

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