Small RNAs, DNA methylation and transposable elements in wheat

<p>Abstract</p> <p>Background</p> <p>More than 80% of the wheat genome is composed of transposable elements (TEs). Since active TEs can move to different locations and potentially impose a significant mutational load, their expression is suppressed in the genome via small non-coding RNAs (sRNAs). sRNAs guide silencing of TEs at the transcriptional (mainly 24-nt sRNAs) and post-transcriptional (mainly 21-nt sRNAs) levels. In this study, we report the distribution of these two types of sRNAs among the different classes of wheat TEs, the regions targeted within the TEs, and their impact on the methylation patterns of the targeted regions.</p> <p>Results</p> <p>We constructed an sRNA library from hexaploid wheat and developed a database that included our library and three other publicly available sRNA libraries from wheat. For five completely-sequenced wheat BAC contigs, most perfectly matching sRNAs represented TE sequences, suggesting that a large fraction of the wheat sRNAs originated from TEs. An analysis of all wheat TEs present in the <it>Triticeae </it>Repeat Sequence database showed that sRNA abundance was correlated with the estimated number of TEs within each class. Most of the sRNAs perfectly matching miniature inverted repeat transposable elements (<it>MITEs</it>) belonged to the 21-nt class and were mainly targeted to the terminal inverted repeats (TIRs). In contrast, most of the sRNAs matching class I and class II TEs belonged to the 24-nt class and were mainly targeted to the long terminal repeats (LTRs) in the class I TEs and to the terminal repeats in <it>CACTA </it>transposons. An analysis of the mutation frequency in potentially methylated sites revealed a three-fold increase in TE mutation frequency relative to intron and untranslated genic regions. This increase is consistent with wheat TEs being preferentially methylated, likely by sRNA targeting.</p> <p>Conclusions</p> <p>Our study examines the wheat epigenome in relation to known TEs. sRNA-directed transcriptional and post-transcriptional silencing plays important roles in the short-term suppression of TEs in the wheat genome, whereas DNA methylation and increased mutation rates may provide a long-term mechanism to inactivate TEs.</p

Regulation of Zn and Fe transporters by the GPC1 gene during early wheat monocarpic senescence

BACKGROUND: During wheat senescence, leaf components are degraded in a coordinated manner, releasing amino acids and micronutrients which are subsequently transported to the developing grain. We have previously shown that the simultaneous downregulation of Grain Protein Content (GPC) transcription factors, GPC1 and GPC2, greatly delays senescence and disrupts nutrient remobilization, and therefore provide a valuable entry point to identify genes involved in micronutrient transport to the wheat grain. RESULTS: We generated loss-of-function mutations for GPC1 and GPC2 in tetraploid wheat and showed in field trials that gpc1 mutants exhibit significant delays in senescence and reductions in grain Zn and Fe content, but that mutations in GPC2 had no significant effect on these traits. An RNA-seq study of these mutants at different time points showed a larger proportion of senescence-regulated genes among the GPC1 (64%) than among the GPC2 (37%) regulated genes. Combined, the two GPC genes regulate a subset (21.2%) of the senescence-regulated genes, 76.1% of which are upregulated at 12 days after anthesis, before the appearance of any visible signs of senescence. Taken together, these results demonstrate that GPC1 is a key regulator of nutrient remobilization which acts predominantly during the early stages of senescence. Genes upregulated at this stage include transporters from the ZIP and YSL gene families, which facilitate Zn and Fe export from the cytoplasm to the phloem, and genes involved in the biosynthesis of chelators that facilitate the phloem-based transport of these nutrients to the grains. CONCLUSIONS: This study provides an overview of the transport mechanisms activated in the wheat flag leaf during monocarpic senescence. It also identifies promising targets to improve nutrient remobilization to the wheat grain, which can help mitigate Zn and Fe deficiencies that afflict many regions of the developing world.Fil: Pearce, Stephen. University of California; Estados UnidosFil: Tabbita, Facundo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación de Recursos Naturales. Instituto de Recursos Biológicos; ArgentinaFil: Cantu, Dario. University of California; Estados UnidosFil: Buffalo, Vince. University of California; Estados UnidosFil: Avni, Raz. Tel Aviv University; IsraelFil: Vazquez Gross, Hans. University of California; Estados UnidosFil: Zhao, Rongrong. China Agricultural University; ChinaFil: Conley, Christopher J.. University of California; Estados UnidosFil: Distelfeld, Assaf. Faculty Of Life Sciences, Department Of Molecular Biolo;Fil: Dubcovsky, Jorge. University of California; Estados Unidos. Howard Hughes Medical Institute ; Estados Unidos. Gordon & Betty Moore Foundation Investigator; Estados Unido

Three previously characterized resistances to yellow rust are encoded by a single locus Wtk1.

The wild emmer wheat (Triticum turgidum ssp. dicoccoides; WEW) yellow (stripe) rust resistance genes Yr15, YrG303, and YrH52 were discovered in natural populations from different geographic locations. They all localize to chromosome 1B but were thought to be non-allelic based on differences in resistance response. We recently cloned Yr15 as a Wheat Tandem Kinase 1 (WTK1) and show here that these three resistance loci co-segregate in fine-mapping populations and share an identical full-length genomic sequence of functional Wtk1. Independent ethyl methanesulfonate (EMS)-mutagenized susceptible yrG303 and yrH52 lines carried single nucleotide mutations in Wtk1 that disrupted function. A comparison of the mutations for yr15, yrG303, and yrH52 mutants showed that while key conserved residues were intact, other conserved regions in critical kinase subdomains were frequently affected. Thus, we concluded that Yr15-, YrG303-, and YrH52-mediated resistances to yellow rust are encoded by a single locus, Wtk1. Introgression of Wtk1 into multiple genetic backgrounds resulted in variable phenotypic responses, confirming that Wtk1-mediated resistance is part of a complex immune response network. WEW natural populations subjected to natural selection and adaptation have potential to serve as a good source for evolutionary studies of different traits and multifaceted gene networks

Agressividade e especialização fisiológica em isolados de Septoria tritici Rob.

Pathogenicity tests verifying the behavior of Septoria tritici isolates should be considered as a priority in the selection of resistant wheat materials to this pathogen, since the aggressiveness of each isolate can vary significantly, causing problems in the evaluation and selection of resistant genotypes. The objective of this work was to determine whether physiologic specialization exists among Argentinean and American Septoria tritici isolates, through the analysis of their pathogenicity on cultivars and lines of bread wheat (Triticum aestivum L.). The experiments were carried out in Castelar-Argentina and in Davis-USA. In Castelar, a split plot design (n = 4) was used. The cultivars or lines were randomized in the plots and the isolates in the subplots. Each subplot consisted of three plants belonging to a cultivar or line. In Davis, a strip split plot design (n = 6) was used. A pot containing three plants of each cultivar or line constituted the experimental plots. In both sites, the inoculation was made at the flag leaf phenological stage through foliar aspersion of a conidial suspension adjusted to 10(6)-10(8) conidia mL-1. Evaluations were made by recording the leaf area covered with pycnidia (LACP) at the flag leaf stage with the use of rating scales. Differences (P < 0.0001) in LACP were detected among cultivars or lines. Isolate effects and the interaction cultivar &times; isolate were significant (P < 0.0001). Variations in aggressiveness and virulence were found among the isolates, indicating the presence of horizontal and vertical resistance in the host cultivars.Testes de patogenicidade destinados a verificar o comportamento de isolados de Septoria tritici frente a genótipos de trigo (Triticum aestivum L.) devem ser considerados como uma prioridade na seleção de materiais resistentes, já que a agressividade de cada isolado pode variar significativamente em função do hospedeiro. O objetivo do presente trabalho foi determinar se existe variação da agressividade ou especialização fisiológica em isolados de Septoria tritici Rob. originários de Argentina e EUA em cultivares e linhagens de trigo. Os experimentos foram estabelecidos em Castelar-Argentina e em Davis-EUA. Na primeira localidade utilizou-se um delineamento experimental em parcelas divididas com quatro repetições, onde as cultivares foram aleatorizadas nas parcelas e os isolados nas subparcelas. Cada subparcela foi composta por três plantas pertencentes a um determinado cultivar. Na segunda localidade, foi adotado um delineamento em blocos casualizados e arranjo em faixas, com seis repetições, onde as parcelas experimentais foram constituídas por um vaso contendo três plantas de cada cultivar. A inoculação foi feita no estádio fenológico de folha bandeira em ambas localidades com uma suspensão de conídios ajustada a uma concentração de 10(6)-10(8) esporos mL-1, empregando a técnica de inoculação por aspersão foliar. As avaliações foram feitas registrando-se a área foliar coberta por picnídios (AFCP) no estádio de folha bandeira com auxílio de escalas de notas. Em ambas localidades foram detectadas diferenças significativas (P < 0,0001) em AFCP entre cultivares. Foram também detectados efeitos significativos de isolados e da interação cultivares x isolados (P < 0,0001). Foram detectadas variações na agressividade e virulência dos isolados sugerindo a presença de resistência horizontal e vertical no material vegetal testado. Testes de patogenicidade destinados a verificar o comportamento de isolados de Septoria tritici devem ser considerados como uma prioridade na seleção de materiais de trigo resistentes a este patógeno

Interação entre resistência a Septoria tritici e estádios fenológicos em trigo

Estudos destinados a entender o comportamento de patógenos em relação a seus hospedeiros são o ponto de partida para qualquer programa de melhoramento cujo objetivo é obter cultivares resistentes. O objetivo do presente trabalho foi analisar a resistência a Septoria tritici Rob em 77 progênies F11 de trigo derivadas do cruzamento Tadinia ;&acute;; (Yecora rojo ;&acute;; UC554) nos estádios fenológicos de plântula, perfilhamento e folha bandeira. Para tal, foram conduzidos três experimentos de campo, onde as plantas foram inoculadas em um dos estádios fenológicos acima mencionados através da pulverização com uma suspensão de conídios, em um delineamento em blocos casualizados, com quatro repetições, onde as parcelas experimentais foram constituídas por uma fileira de um metro de comprimento contendo oito plantas, com um espaçamento de 0,17 m entre linhas e 0,13 m entre plantas. As avaliações da severidade da doença foram feitas registrando-se a área foliar coberta por lesões necróticas e cloróticas, nos estádios de plântula e perfilhamento e área foliar coberta por picnídios no estádio de folha bandeira-floração com auxílio de escalas de notas. Foram detectadas diferenças (P < 0,0001) entre progênies para área foliar lesionada (AFL) nos estádios fenológicos estudados. Análises de variância conjuntas para AFL indicaram uma interação entre progênies e estádios fenológicos (P < 0,0001) para todas as combinações binárias analisadas (plântula-perfilhamento, plântula-folha bandeira e perfilhamento-folha bandeira) assim como para a combinação tripla envolvendo os três estádios fenológicos. É necessário avaliar resistência em mais de um estádio fenológico para garantir a correta seleção de genótipos resistentes.Studies dedicated to understanding the behavior of pathogens in relation to their hosts are the starting point for any breeding program aimed to develop resistant cultivars. The objective of this study was to analyze the resistance to Septoria tritici Rob in 77 F11 progenies of wheat derived from the three-way cross Tadinia ;&acute;; (Yecora rojo ;&acute;; UC554) in the phenological stages of seedling, tillering, and flag leaf/flowering. Three field experiments were conducted where plants were artificially inoculated at one of the above mentioned phenological stages by spraying with a suspension of conidia. A randomized block design with four replications was used in each experiment. Disease evaluations were made by measuring the foliar area covered with chlorotic and necrotic lesions in the seedling and tillering stages and the leaf area covered with pycnidia in the flag leaf/flowering stage, using disease rating scales. Differences (P < 0.0001) were detected among progenies for Damaged Leaf Area (DLA) in all phenological stages. Joint analysis of variance for DLA indicated interaction between progeny and phenological stage (P < 0.0001) for all binary combinations analyzed (seedling-tillering, seedling-flag leaf and tillering-flag leaf) as it also did for the triple combination involving the three phenological stages. It is necessary to evaluate resistance in more than one phenological stage to guarantee the correct selection of resistant genotypes

Effect of the Hope FT-B1 Allele on wheat heading time and yield components

Precise regulation of flowering time is critical for plant reproductive success and, in cereals, to maximize grain yields. Seasonal cues including temperature and day length are integrated to regulate the timing of flowering. In temperate cereals, extended periods of cold (vernalization) release the repression of FLOWERING LOCUS T1 (FT1), which is upregulated in the leaves in response to inductive long-day photoperiods. FT1 is a homolog of rice HD3a, which encodes a protein transported from leaves to the shoot apical meristem to induce flowering. A rare FT-B1 allele from the wheat variety “Hope” has been previously shown to be associated with an early flowering phenotype under long-day photoperiods. Here, we demonstrate that the Hope FT-B1 allele accelerates flowering even under short days, and that it is epistatic to the VERNALIZATION 1 (VRN1) gene. On average, the introgression of Hope FT-B1 into 6 genetic backgrounds resulted in 2.6 days acceleration of flowering (P < 0.0001) and 4.1% increase in spike weight (P = 0.0093), although in one variety, it was associated with a decrease in spike weight. These results suggest that the Hope FT-B1 allele could be useful in wheat breeding programs to subtly accelerate floral development and increase adaptation to changing environments.Fil: Nitcher, Rebecca. University of California. Department of Plant Sciences; Estados UnidosFil: Pearce, Stephen. University of California. Department of Plant Sciences; Estados UnidosFil: Tranquilli, Gabriela. University of California. Department of Plant Sciences; Estados Unidos. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; ArgentinaFil: Xiaoqin, Zhang. University of California. Department of Plant Sciences; Estados UnidosFil: Dubcovsky, Jorge. University of California. Department of Plant Sciences; Estados Unidos. Howard Hughes Medical Institute; Estados Unido