Genome-wide gene expression analysis supports a developmental model of low temperature tolerance gene regulation in wheat (Triticum aestivum L.)

<p>Abstract</p> <p>Background</p> <p>To identify the genes involved in the development of low temperature (LT) tolerance in hexaploid wheat, we examined the global changes in expression in response to cold of the 55,052 potentially unique genes represented in the Affymetrix Wheat Genome microarray. We compared the expression of genes in winter-habit (winter Norstar and winter Manitou) and spring-habit (spring Manitou and spring Norstar)) cultivars, wherein the locus for the vernalization gene <it>Vrn-A1 </it>was swapped between the parental winter Norstar and spring Manitou in the derived near-isogenic lines winter Manitou and spring Norstar. Global expression of genes in the crowns of 3-leaf stage plants cold-acclimated at 6°C for 0, 2, 14, 21, 38, 42, 56 and 70 days was examined.</p> <p>Results</p> <p>Analysis of variance of gene expression separated the samples by genetic background and by the developmental stage before or after vernalization saturation was reached. Using gene-specific ANOVA we identified 12,901 genes (at <it>p </it>< 0.001) that change in expression with respect to both genotype and the duration of cold-treatment. We examined in more detail a subset of these genes (2,771) where expression was highly influenced by the interaction between these two main factors. Functional assignments using GO annotations showed that genes involved in transport, oxidation-reduction, and stress response were highly represented. Clustering based on the pattern of transcript accumulation identified genes that were up or down-regulated by cold-treatment. Our data indicate that the cold-sensitive lines can up-regulate known cold-responsive genes comparable to that of cold-hardy lines. The levels of expression of these genes were highly influenced by the initial rate and the duration of the gene's response to cold. We show that the <it>Vrn-A1 </it>locus controls the duration of gene expression but not its initial rate of response to cold treatment. Furthermore, we provide evidence that <it>Ta.Vrn-A1 </it>and <it>Ta.Vrt1 </it>originally hypothesized to encode for the same gene showed different patterns of expression and therefore are distinct.</p> <p>Conclusion</p> <p>This study provides novel insight into the underlying mechanisms that regulate the expression of cold-responsive genes in wheat. The results support the developmental model of LT tolerance gene regulation and demonstrate the complex genotype by environment interactions that determine LT adaptation in winter annual cereals.</p

Polyploidization as a Retraction Force in Plant Genome Evolution: Sequence Rearrangements in Triticale

BACKGROUND: Polyploidization is a major evolutionary process in plants where hybridization and chromosome doubling induce enormous genomic stress and can generate genetic and epigenetic modifications. However, proper evaluation of DNA sequence restructuring events and the precise characterization of sequences involved are still sparse. METHODOLOGY/PRINCIPAL FINDINGS: Inter Retrotransposons Amplified Polymorphism (IRAP), Retrotransposons Microsatellite Amplified Polymorphism (REMAP) and Inter Simple Sequence Repeat (ISSR) largely confirmed the absence of any intraspecific variation in wheat, rye and triticale. The comparative analysis of banding profiles between wheat and rye inbred lines revealed 34% of monomorphic (common to both parental species) bands for the ten different primer combinations used. The analysis of triticale plants uncovered nearly 51% of rearranged bands in the polyploid, being the majority of these modifications, due to the loss of rye bands (83%). Sequence analysis of rye fragments absent in triticale revealed for instance homology with hydroxyproline-rich glycoproteins (HRGP), a protein that belongs to a major family of inducible defence response proteins. Conversely, a wheat-specific band absent in triticale comprises a nested structure of copia-like retrotransposons elements, namely Claudia and Barbara. Sequencing of a polyploid-specific band (absent in both parents) revealed a microsatellite related sequence. Cytological studies using Fluorescent In Situ Hybridization (FISH) with REMAP products revealed a widespread distribution of retrotransposon and/or microsatellite flanking sequences on rye chromosomes, with a preferential accumulation in heterochromatic sub-telomeric domains. CONCLUSIONS/SIGNIFICANCE: Here, we used PCR-based molecular marker techniques involving retrotransposons and microsatellites to uncover polyploidization induced genetic restructuring in triticale. Sequence analysis of rearranged genomic fragments either from rye or wheat origin showed these to be retrotransposon-related as well as coding sequences. Further FISH analysis revealed possible chromosome hotspots for sequence rearrangements. The role of chromatin condensation on the origin of genomic rearrangements mediated by polyploidization in triticale is also discussed

Wild pea Pisum fulvum and Pisum elatius chromosome segment substitution lines in cultivated P. sativum genetic background

BAPGEAPSIPlant evolution under domestication has altered numerous traits, introducing domestication bottleneck resulting in high degree of relatedness, leading to narrower genetic base of cultivated germplasm, prone to pests and diseases. The study of genetic diversity showed that although wide diversity is captured among cultivated pea, wild material provides yet broader diversity (Smýkal et al. 2013, 2015). The chromosome segment substitution lines (CSSL) containing genomic segments of wild pea (Pisum fulvum WL2140 or Pisum elatius L100) in the cultivated pea (P. sativum subsp. sativum cv. Terno or cv. Cameor) genetic background were developed. These lines have been molecularly analyzed using microsatellite and gene-specific markers at 2 to 82 cM spacing at early generations (BC2-3F2-4). There were 5 to 14 segments per line, with mean of 9.6. Higher density genotyping of 50 selected BC3F6 P. fulvum/Terno CSSL lines using pea 13.2k Pea SNP (Tayeh et al. 2015) and further 100 lines using DARTseq approach is in progress. Establishment of such permanent introgression library will allow phenotypic characterization of unlimited number of target traits, which, coupled together with higher density markers, will provide means for QTL and gene identification and subsequent incorporation in desired genotypes. Field testing of agronomical performance of 50 lines of P. fulvum/Terno CSSL lines is under way. This work received funding from the European Community's Seventh Framework Programme (FP)

Flow cytometry measurements contribute to<em> Pisum taxonomy</em>

International audiencePea (Pisum sativum L.) has been widely used in early hybridization studies, as model for experimental morphology and physiology, and was Mendel’s model species to untangle the laws of inheritance, which puts it at the foundation of modern genetics. Its large genome size (4775 Mbp as assessed by Feulgen method in 1976) slowed down progress in pea genomics compared with other plant species, but the recent availability of genome sequences of various legume species now permits genome wide comparison and allows to identify genes underlying agronomically important traits by combining candidate gene and synteny approaches. The efficient use of existing genomic resources is a key to success in these goals and several types of molecular marker sets as well as both transcriptome and proteome datasets exist. Despite this impressive background, and the fact that P. sativum is one of the most frequently used internal standards for flow cytometry studies with other species, there is still a need to further clarify the taxonomy within species of the genus Pisum. Thus, we have analysed by flow cytometry 42 accessions from a range of geographic origins and belonging to two wild species: P. sativum subsp. elatius (e.g. including former P. elatius and P. humile/syriacum), P. fulvum and cultivated: P. abyssinicum, P. sativum as well as some primitive P. sativum cultigens (such as subsp. transcaucassicum, asiaticum), where some of them had been identified differently or tentatively in the past based on botanical characteristics. In these studies, all materials were analysed simultaneously with Medicago truncatula as the internal standard, and with various fluorochromes (DAPI, Propidium Iodide, Chromomycine A3) to assess the relative nuclear DNA content, genome size and AT/GC ratio. For some of the species studied this is the first report on these traits

Flow cytometry measurements contribute to Pisum taxonomy

Pea (Pisum sativum L.) has been widely used in early hybridization studies, as model for experimental morphology and physiology, and was Mendel’s model species to untangle the laws of inheritance, which puts it at the foundation of modern genetics. Its large genome size (4775 Mbp as assessed by Feulgen method in 1976) slowed down progress in pea genomics compared with other plant species, but the recent availability of genome sequences of various legume species now permits genome wide comparison and allows to identify genes underlying agronomically important traits by combining candidate gene and synteny approaches. The efficient use of existing genomic resources is a key to success in these goals and several types of molecular marker sets as well as both transcriptome and proteome datasets exist. Despite this impressive background, and the fact that P. sativum is one of the most frequently used internal standards for flow cytometry studies with other species, there is still a need to further clarify the taxonomy within species of the genus Pisum. Thus, we have analysed by flow cytometry 42 accessions from a range of geographic origins and belonging to two wild species: P. sativum subsp. elatius (e.g. including former P. elatius and P. humile/syriacum), P. fulvum and cultivated: P. abyssinicum, P. sativum as well as some primitive P. sativum cultigens (such as subsp. transcaucassicum, asiaticum), where some of them had been identified differently or tentatively in the past based on botanical characteristics. In these studies, all materials were analysed simultaneously with Medicago truncatula as the internal standard, and with various fluorochromes (DAPI, Propidium Iodide, Chromomycine A3) to assess the relative nuclear DNA content, genome size and AT/GC ratio. For some of the species studied this is the first report on these traits

Management of legume genetic ressources to enhance food and nutritional security

International audienc