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Tracking the evolution of a cold stress associated gene family in cold tolerant grasses.

ABSTRACT: BACKGROUND: Grasses are adapted to a wide range of climatic conditions. Species of the subfamily Pooideae, which includes wheat, barley and important forage grasses, have evolved extreme frost tolerance. A class of ice binding proteins that inhibit ice re-crystallisation, specific to the Pooideae subfamily lineage, have been identified in perennial ryegrass and wheat, and these proteins are thought to have evolved from a leucine-rich repeat phytosulfokine receptor kinase (LRR-PSR)-like ancestor gene. Even though the ice re-crystallisation inhibition function of these proteins has been studied extensively in vitro, little is known about the evolution of these genes on the molecular level. RESULTS: We identified 15 putative novel ice re-crystallisation inhibition (IRI)-like protein coding genes in perennial ryegrass, barley, and wheat. Using synonymous divergence estimates we reconstructed the evolution of the IRI-like gene family. We also explored the hypothesis that the IRI-domain has evolved through repeated motif expansion and investigated the evolutionary relationship between a LRR-domain containing IRI coding gene in carrot and the Pooideae IRI-like genes. Our analysis showed that the main expansion of the IRI-gene family happened ~36 million years ago (Mya). In addition to IRI-like paralogs, wheat contained several sequences that likely were products of polyploidisation events (homoeologs). Through sequence analysis we identified two short motifs in the rice LRR-PSR gene highly similar to the repeat motifs of the IRI-domain in cold tolerant grasses. Finally we show that the LRR-domain of carrot and grass IRI proteins both share homology to an Arabidopsis thaliana LRR-trans membrane protein kinase (LRR-TPK). CONCLUSION: The diverse IRI-like genes identified in this study tell a tale of a complex evolutionary history including birth of an ice binding domain, a burst of gene duplication events after cold tolerant grasses radiated from rice, protein domain structure differentiation between paralogs, and sub- and/or neofunctionalisation of IRI-like proteins. From our sequence analysis we provide evidence for IRI-domain evolution probably occurring through increased copy number of a repeated motif. Finally, we discuss the possibility of parallel evolution of LRR domain containing IRI proteins in carrot and grasses through two completely different molecular adaptations.

SUBMITTER: Sandve SR

PROVIDER: S-EPMC2542378 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature

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Tracking the evolution of a cold stress associated gene family in cold tolerant grasses.

Sandve Simen R SR Rudi Heidi H Asp Torben T Rognli Odd Arne OA

BMC evolutionary biology 20080905

<h4>Background</h4>Grasses are adapted to a wide range of climatic conditions. Species of the subfamily Pooideae, which includes wheat, barley and important forage grasses, have evolved extreme frost tolerance. A class of ice binding proteins that inhibit ice re-crystallisation, specific to the Pooideae subfamily lineage, have been identified in perennial ryegrass and wheat, and these proteins are thought to have evolved from a leucine-rich repeat phytosulfokine receptor kinase (LRR-PSR)-like an ...[more]

PMID: 18775065

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Project description:Periods of soil water stress have been recurrent in the Cerrado region and have become a growing concern for Brazilian tropical pasture areas. Thus, the search for forage grasses more tolerant to water stress has intensified recently in order to promote more sustainable livestock. In a greenhouse experiment, the degree of water stress tolerance of nine tropical forage grass cultivars was studied under different soil water regimes. The investigation followed a 9 × 3 factorial design in four randomized blocks. Nine cultivars from five species of perennial forage grasses were tested: Urochloa brizantha ('BRS Piatã', 'Marandu', and 'Xaraés'), Panicum maximum ('Aruana', 'Mombaça', and 'Tanzânia'), Pennisetum glaucum ('ADR 300'), Urochloa ruziziensis ('Comum'), and Paspalum atratum ('Pojuca'). These cultivars were grown in pots under three soil water regimes (high soil water regime-HSW (non-stressful condition), middle soil water regime-MSW (moderate water stress), and low soil water regime-LSW (severe water stress)). Plants were exposed to soil water stress for 25 days during the tillering and stalk elongation phases. Twelve tolerance indices, including tolerance index (TOL), mean production (MP), yield stability index (YSI), drought resistance index (DI), stress tolerance index (STI), geometric mean production (GMP), yield index (YI), modified stress tolerance (k1STI and k2STI), stress susceptibility percentage index (SSPI), abiotic tolerance index (ATI), and harmonic mean (HM), were calculated based on shoot biomass production under non-stressful (YP) and stressful (YS) conditions. Soil water stress decreased leaf area, plant height, tillering capacity, root volume, and shoot and root dry matter production in most cultivars, with varying degrees of reduction among tropical forage grasses. Based on shoot biomass production under controlled greenhouse conditions, the most water-stress-tolerant cultivars were P. maximum cv. Mombaça and cv. Tanzânia under the MSW regime and P. maximum cv. Aruana and cv. Mombaça under the LSW regime. P. maximum cv. Mombaça has greater adaptability and stability of shoot biomass production when grown under greenhouse conditions and subjected to soil water stress. Therefore, this forage grass should be tested under field conditions to confirm its forage production potential for cultivation in tropical regions with the occurrence of water stress. The MP, DI, STI, GMP, YI, k2STI, and HM tolerance indices were the most suitable for identifying forage grass cultivars with greater water stress tolerance and a high potential for shoot biomass production under LSW regime.

Project description:BackgroundCold stress at reproductive phase in susceptible chickpea (Cicer arietinum L.) leads to pollen sterility induced flower abortion. The tolerant genotypes, on the other hand, produce viable pollen and set seed under cold stress. Genomic information on pollen development in cold-tolerant chickpea under cold stress is currently unavailable.ResultsDDRT-PCR analysis was carried out to identify anther genes involved in cold tolerance in chickpea genotype ICC16349 (cold-tolerant). A total of 9205 EST bands were analyzed. Cold stress altered expression of 127 ESTs (90 up-regulated, 37 down-regulated) in anthers, more than two third (92) of which were novel with unknown protein identity and function. Remaining about one third (35) belonged to several functional categories such as pollen development, signal transduction, ion transport, transcription, carbohydrate metabolism, translation, energy and cell division. The categories with more number of transcripts were carbohydrate/triacylglycerol metabolism, signal transduction, pollen development and transport. All but two transcripts in these categories were up-regulated under cold stress. To identify time of regulation after stress and organ specificity, expression levels of 25 differentially regulated transcripts were also studied in anthers at six time points and in four organs (anthers, gynoecium, leaves and roots) at four time points.ConclusionsLimited number of genes were involved in regulating cold tolerance in chickpea anthers. Moreover, the cold tolerance was manifested by up-regulation of majority of the differentially expressed transcripts. The anthers appeared to employ dual cold tolerance mechanism based on their protection from cold by enhancing triacylglycerol and carbohydrate metabolism; and maintenance of normal pollen development by regulating pollen development genes. Functional characterization of about two third of the novel genes is needed to have precise understanding of the cold tolerance mechanisms in chickpea anthers.

Project description:Daye No.3 is a novel cultivar of alfalfa (Medicago sativa L.) that is well suited for cultivation in high-altitude regions such as the Qinghai‒Tibet Plateau owing to its high yield and notable cold resistance. However, the limited availability of transcriptomic information has hindered our investigation into the potential mechanisms of cold tolerance in this cultivar. Consequently, we conducted de novo transcriptome assembly to overcome this limitation. Subsequently, we compared the patterns of gene expression in Daye No. 3 during cold acclimatization and exposure to cold stress at various time points. A total of 15 alfalfa samples were included in the transcriptome assembly, resulting in 141.97 Gb of clean bases. A total of 441 DEGs were induced by cold acclimation, while 4525, 5016, and 8056 DEGs were identified at 12 h, 24 h, and 36 h after prolonged cold stress at 4 °C, respectively. The consistency between the RT‒qPCR and transcriptome data confirmed the accuracy and reliability of the transcriptomic data. KEGG enrichment analysis revealed that many genes related to photosynthesis were enriched under cold stress. STEM analysis demonstrated that genes involved in nitrogen metabolism and the TCA cycle were consistently upregulated under cold stress, while genes associated with photosynthesis, particularly antenna protein genes, were downregulated. PPI network analysis revealed that ubiquitination-related ribosomal proteins act as hub genes in response to cold stress. Additionally, the plant hormone signaling pathway was activated under cold stress, suggesting its vital role in the cold stress response of alfalfa. Ubiquitination-related ribosomal proteins induced by cold acclimation play a crucial role in early cold signal transduction. As hub genes, these ubiquitination-related ribosomal proteins regulate a multitude of downstream genes in response to cold stress. The upregulation of genes related to nitrogen metabolism and the TCA cycle and the activation of the plant hormone signaling pathway contribute to the enhanced cold tolerance of alfalfa.

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Tracking the evolution of a cold stress associated gene family in cold tolerant grasses.

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Tracking the evolution of a cold stress associated gene family in cold tolerant grasses.

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