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Key message: Our manuscript is the first to find a link between activity of SAL1/OLD101 against IP3 and plant leaf senescence regulation and ROS levels assigning a potential biological role for IP3. Leaf senescence is a genetically programmed process that limits the longevity of a leaf. We identified and analyzed the recessive Arabidopsis stay-green mutation onset of leaf death 101 (old101). Developmental leaf longevity is extended in old101 plants, which coincided with higher peroxidase activity and decreased H2O2 levels in young 10-day-old, but not 25-day-old plants. The old101 phenotype is caused by a point mutation in SAL1, which encodes a bifunctional enzyme with inositol polyphosphate-1-phosphatase and 3′ (2′), 5′-bisphosphate nucleotidase activity. SAL1 activity is highly specific for its substrates 3-polyadenosine 5-phosphate (PAP) and inositol 1, 4, 5-trisphosphate (IP3), where it removes the 1-phosphate group from the IP3 second messenger. The in vitro activity of recombinant old101 protein against its substrate IP3 was 2.5-fold lower than that of wild type SAL1 protein. However, the in vitro activity of recombinant old101 mutant protein against PAP remained the same as that of the wild type SAL1 protein. The results open the possibility that the activity of SAL1 against IP3 may affect the redox balance of young seedlings and that this delays the onset of leaf senescence. [ABSTRACT FROM AUTHOR]

Domestication and diversification have had profound effects on crop genomes. Originating in Africa and subsequently spreading to different continents, sorghum (Sorghum bicolor) has experienced multiple onsets of domestication and intensive breeding selection for various end uses. However, how these processes have shaped sorghum genomes is not fully understood. In the present study, population genomics analyses were performed on a worldwide collection of 445 sorghum accessions, covering wild sorghum and four end-use subpopulations with diverse agronomic traits. Frequent genetic exchanges were found among various subpopulations, and strong selective sweeps affected 14.68% (∼107.5 Mb) of the sorghum genome, including 3649, 4287, and 3888 genes during sorghum domestication, improvement of grain sorghum, and improvement of sweet sorghum, respectively. Eight different models of haplotype changes in domestication genes from wild sorghum to landraces and improved sorghum were observed, and Sh1 - and SbTB1 -type genes were representative of two prominent models, one of soft selection or multiple origins and one of hard selection or an early single domestication event. We also demonstrated that the Dry gene, which regulates stem juiciness, was unconsciously selected during the improvement of grain sorghum. Taken together, these findings provide new genomic insights into sorghum domestication and breeding selection, and will facilitate further dissection of the domestication and molecular breeding of sorghum. Population genomics analyses revealed the profound effects of domestication and genetic improvement on sorghum genomes. Eight different models of haplotype changes in domestication genes were observed, and Sh1 - and SbTB1 -type genes were representative of two prominent models of soft selection and hard selection, respectively. The genomic footprints identified here will facilitate further dissection of the domestication and molecular breeding of sorghum. [ABSTRACT FROM AUTHOR]

Key message: The importance and potential of the multi-purpose crop sorghum in global food security have not yet been fully exploited, and the integration of the state-of-art genomics and high-throughput technologies into breeding practice is required. Sorghum, a historically vital staple food source and currently the fifth most important major cereal, is emerging as a crop with diverse end-uses as food, feed, fuel and forage and a model for functional genetics and genomics of tropical grasses. Rapid development in high-throughput experimental and data processing technologies has significantly speeded up sorghum genomic researches in the past few years. The genomes of three sorghum lines are available, thousands of genetic stocks accessible and various genetic populations, including NAM, MAGIC, and mutagenised populations released. Functional and comparative genomics have elucidated key genetic loci and genes controlling agronomical and adaptive traits. However, the knowledge gained has far away from being translated into real breeding practices. We argue that the way forward is to take a genome-based approach for tailored designing of sorghum as a multi-functional crop combining excellent agricultural traits for various end uses. In this review, we update the new concepts and innovation systems in crop breeding and summarise recent advances in sorghum genomic researches, especially the genome-wide dissection of variations in genes and alleles for agronomically important traits. Future directions and opportunities for sorghum breeding are highlighted to stimulate discussion amongst sorghum academic and industrial communities. [ABSTRACT FROM AUTHOR]

Leaf senescence is important for crop yield as delaying it can increase the average yield. In this study, population genetics and transcriptomic profiling were combined to dissect its genetic basis in maize. To do this, the progenies of an elite maize hybrid Jidan27 and its parental lines Si-287 (early senescence) and Si-144 (stay-green), as well as 173 maize inbred lines were used. We identified two novel loci and their candidate genes, Stg3 (ZmATG18b) and Stg7 (ZmGH3.8), which are predicted to be members of autophagy and auxin pathways, respectively. Genomic variations in the promoter regions of these two genes were detected, and four allelic combinations existed in the examined maize inbred lines. The Stg3 Si-144/ Stg7 Si-144 allelic combination with lower ZmATG18b expression and higher ZmGH3.8 expression could distinctively delay leaf senescence, increase ear weight and the improved hybrid of NIL- Stg3Si-144 / Stg7Si-144 × Si-144 significantly reduced ear weight loss under drought stress, while opposite effects were observed in the Stg3 Si-287/ Stg7 Si-287 combination with a higher ZmATG18b expression and lower ZmGH3.8 expression. Thus, we identify a potential interaction between autophagy and auxin which could modulate the timing of maize leaf senescence. [ABSTRACT FROM AUTHOR]

Abstract Background Cysteine is a component in organic compounds including glutathione that have been implicated in the adaptation of plants to stresses. O-acetylserine (thiol) lyase (OAS-TL) catalyses the final step of cysteine biosynthesis. OAS-TL enzyme isoforms are localised in the cytoplasm, the plastids and mitochondria but the contribution of individual OAS-TL isoforms to plant sulphur metabolism has not yet been fully clarified. Results The seedling lethal phenotype of the Arabidopsis onset of leaf death3-1 (old3-1) mutant is due to a point mutation in the OAS-A1 gene, encoding the cytosolic OAS-TL. The mutation causes a single amino acid substitution from Gly162 to Glu162, abolishing old3-1 OAS-TL activity in vitro. The old3-1 mutation segregates as a monogenic semi-dominant trait when backcrossed to its wild type accession Landsberg erecta (Ler-0) and the Di-2 accession. Consistent with its semi-dominant behaviour, wild type Ler-0 plants transformed with the mutated old3-1 gene, displayed the early leaf death phenotype. However, the old3-1 mutation segregates in an 11:4:1 (wild type: semi-dominant: mutant) ratio when backcrossed to the Colombia-0 and Wassilewskija accessions. Thus, the early leaf death phenotype depends on two semi-dominant loci. The second locus that determines the old3-1 early leaf death phenotype is referred to as odd-ler (for old3 determinant in the Ler accession) and is located on chromosome 3. The early leaf death phenotype is temperature dependent and is associated with increased expression of defence-response and oxidative-stress marker genes. Independent of the presence of the odd-ler gene, OAS-A1 is involved in maintaining sulphur and thiol levels and is required for resistance against cadmium stress. Conclusions The cytosolic OAS-TL is involved in maintaining organic sulphur levels. The old3-1 mutation causes genome-dependent and independent phenotypes and uncovers a novel function for the mutated OAS-TL in cell death regulation.

Abstract Background Triticum monococcum (2n = 2x = 14) is an ancient diploid wheat with many useful traits and is used as a model for wheat gene discovery. DArT (Diversity Arrays Technology) employs a hybridisation-based approach to type thousands of genomic loci in parallel. DArT markers were developed for T. monococcum to assess genetic diversity, compare relationships with hexaploid genomes, and construct a genetic linkage map integrating DArT and microsatellite markers. Results A DArT array, consisting of 2304 hexaploid wheat, 1536 tetraploid wheat, 1536 T. monococcum as well as 1536 T. boeoticum representative genomic clones, was used to fingerprint 16 T. monococcum accessions of diverse geographical origins. In total, 846 polymorphic DArT markers were identified, of which 317 were of T. monococcum origin, 246 of hexaploid, 157 of tetraploid, and 126 of T. boeoticum genomes. The fingerprinting data indicated that the geographic origin of T. monococcum accessions was partially correlated with their genetic variation. DArT markers could also well distinguish the genetic differences amongst a panel of 23 hexaploid wheat and nine T. monococcum genomes. For the first time, 274 DArT markers were integrated with 82 simple sequence repeat (SSR) and two morphological trait loci in a genetic map spanning 1062.72 cM in T. monococcum. Six chromosomes were represented by single linkage groups, and chromosome 4Am was formed by three linkage groups. The DArT and SSR genetic loci tended to form independent clusters along the chromosomes. Segregation distortion was observed for one third of the DArT loci. The Ba (black awn) locus was refined to a 23.2 cM region between the DArT marker locus wPt-2584 and the microsatellite locus Xgwmd33 on 1Am; and the Hl (hairy leaf) locus to a 4.0 cM region between DArT loci 376589 and 469591 on 5Am. Conclusion DArT is a rapid and efficient approach to develop many new molecular markers for genetic studies in T. monococcum. The constructed genetic linkage map will facilitate localisation and map-based cloning of genes of interest, comparative mapping as well as genome organisation and evolution studies between this ancient diploid species and other crops.

Compared to other potential feedstocks such as sugarcane, sugar beet, maize, and watermelon, sweet sorghum possesses higher levels of directly fermentable reducing sugars within the culm and the ability to accumulate high biomass under low-input production systems. In addition, it is tolerant to drought and has more efficient utilization of solar radiation and nitrogen-based fertilizers than maize and sugar cane on marginal lands that are not optimal for food production. These collectively make sweet sorghum to be considered with huge potential as a biofuel crop. Novel phenotypes generated during plant domestication and continued crop improvements via artificial selection constitute the domestication syndrome ( Am. J. Bot., 101, 2014, 1711). Here, we draw an analogy and introduce the term the biofuel syndrome to refer to a suite of sweet sorghum traits, such as plant architecture (root, leave, and stem), flowering time and maturity as well as biomass bioconversion efficiency, that are associated with biofuel production and distinguish it from grain and forage sorghum traits. We discuss the biofuel syndrome amenable for targeted genetic modulation and what is currently known about the genetics and genomics of these traits as a potential route to optimize sweet sorghum for biofuel production. Continuous availability of sweet sorghum, transport and storing much mass and minimizing the postharvest loss of fermentable sugars are fundamental to exploiting sweet sorghum as a bioenergy crop. Due to the relatively short history of sweet sorghum breeding, we consider the development of ideotypes adapting to various phenological requirements to maximize the rapid deployment of sweet sorghum for biofuel production. [ABSTRACT FROM AUTHOR]

Stress tolerance is a prerequisite for the success of biofuel production, which normally requires the use of marginal lands and nonfood biofuel feedstocks. Sorghum is known for its ability to withstand stress conditions, however, terminal stresses threaten its growth and development negatively impacting yield and sugar accumulation. It is crucial, therefore, that research aimed at developing sorghum resistance to stress factors should be pursued to expand the range of its growth to marginal and barren soils to meet the needs of a growing population, changing diets, and biofuel production. In this context, the leaf architectural trait of stay-green drought tolerance, in addition to salinity, cold, and aluminium toxicity and biotic stress tolerance and their genetic basis discussed in this review are expected to be available in future sweet sorghum ideotypes. Also highlighted is the key role of efficient management of farming systems, in particular the use of herbicides to control weeds, to ensure the sustainability of the sweet sorghum biomass productions. [ABSTRACT FROM AUTHOR]

In halophytic plants, the high-affinity potassium transporter HKT gene family can selectively uptake K+ in the presence of toxic concentrations of Na+. This has so far not been well examined in glycophytic crops. Here, we report the characterization of SbHKT1;4, a member of the HKT gene family from Sorghum bicolor. Upon Na+ stress, SbHKT1;4 expression was more strongly upregulated in salt-tolerant sorghum accession, correlating with a better balanced Na+/K+ ratio and enhanced plant growth. Heterogeneous expression analyses in mutants of Saccharomyces cerevisiae and Arabidopsis thaliana indicated that overexpressing SbHKT1;4 resulted in hypersensitivity to Na+ stress, and such hypersensitivity could be alleviated with the supply of elevated levels of K+, implicating that SbHKT1;4 may mediate K+ uptake in the presence of excessive Na+. Further electrophysiological evidence demonstrated that SbHKT1;4 could transport Na+ and K+ when expressed in Xenopus laevis oocytes. The relevance of the finding that SbHKT1;4 functions to maintain optimal Na+/K+ balance under Na+ stress to the breeding of salt-tolerant glycophytic crops is discussed. [ABSTRACT FROM AUTHOR]

The presence/absence variants (PAVs) are a major source of genome structural variation and have profound effects on phenotypic and genomic variation in animals and humans. However, little is understood about PAVs in plant genomes. Our previous resequencing effort on three sorghum ( Sorghum bicolour L.) genomes, each 12× coverage, uncovered 5 364 PAVs. Here, we report a detailed characterization of 51 large-size (>30 kb) PAVs. These PAVs spanned a total size of 2.92 Mb of the sorghum genome containing 202 known and predicted genes, including 38 genes annotated to encode cell death and stress response genes. The PAVs varied considerably for repeat sequences and mobile elements with DNA transposons as the major components. The frequency and distribution of these PAVs differed substantially across 96 sorghum inbred lines, and the low- and high frequency PAVs differed in their gene categories. This report shed new light on the occurrence and diversity of PAVs in sorghum genomes. Our research exemplifies a new perspective to explore genome structural variation for genetic improvement in plant breeding. [ABSTRACT FROM AUTHOR]

Sodium carbonate (Na2CO3) presents a huge challenge to plants by the combined damaging effects of Na+, high pH, and CO32-. Little is known about the cellular responses to Na2CO3 stress. In this study, the transcriptome of maize ( Zea mays L. cv. B73) roots exposed to Na2CO3 stress for 5 h was compared with those of NaCl and NaOH stresses. The expression of 8,319 genes, representing over a quarter of the total number of genes in the maize genome, was altered by Na2CO3 stress, and the downregulated genes (5,232) outnumbered the upregulated genes (3,087). The effects of Na2CO3 differed from those of NaCl and NaOH, primarily by downregulating different categories of genes. Pathways commonly altered by Na2CO3, NaCl, and NaOH were enriched in phenylpropanoid biosynthesis, oxidation of unsaturated fatty acids, ATP-binding cassette (ABC) transporters, as well as the metabolism of secondary metabolites. Genes for brassinosteroid biosynthesis were specifically upregulated by Na2CO3, while genes involved in ascorbate and aldarate metabolism, protein processing in the endoplasmic reticulum and by N-glycosylation, fatty acid biosynthesis, and the circadian rhythm were downregulated. This work provides the first holistic picture of early transcriptomic adaptation to Na2CO3 stress, and highlights potential molecular pathways that could be manipulated to improve tolerance in maize. [ABSTRACT FROM AUTHOR]

Summary: O‐acetylserine (thiol) lyases (OASTLs) are evolutionarily conserved proteins among many prokaryotes and eukaryotes that perform sulfur acquisition and synthesis of cysteine. A mutation in the cytosolic OASTL‐A1 protein ONSET OF LEAF DEATH3 (OLD3) was previously shown to reduce the OASTL activity of the old3‐1 protein in vitro and cause auto‐necrosis in specific Arabidopsis accessions. Here we investigated why a mutation in this protein causes auto‐necrosis in some but not other accessions. The auto‐necrosis was found to depend on Recognition of Peronospora Parasitica 1 (RPP1)‐like disease resistance R gene(s) from an evolutionarily divergent R gene cluster that is present in Ler‐0 but not the reference accession Col‐0. RPP1‐like gene(s) show a negative epistatic interaction with the old3‐1 mutation that is not linked to reduced cysteine biosynthesis. Metabolic profiling and transcriptional analysis further indicate that an effector triggered‐like immune response and metabolic disorder are associated with auto‐necrosis in old3‐1 mutants, probably activated by an RPP1‐like gene. However, the old3‐1 protein in itself results in largely neutral changes in primary plant metabolism, stress defence and immune responses. Finally, we showed that lack of a functional OASTL‐A1 results in enhanced disease susceptibility against infection with virulent and non‐virulent Pseudomonas syringae pv. tomato DC3000 strains. These results reveal an interaction between the cytosolic OASTL and components of plant immunity. [ABSTRACT FROM AUTHOR]

Leaf senescence can impact crop production by either changing photosynthesis duration, or by modifying the nutrient remobilization efficiency and harvest index. The doubling of the grain yield in major cereals in the last 50 years was primarily achieved through the extension of photosynthesis duration and the increase in crop biomass partitioning, two things that are intrinsically coupled with leaf senescence. In this review, we consider the functionality of a leaf as a function of leaf age, and divide a leaf's life into three phases: the functionality increasing phase at the early growth stage, the full functionality phase, and the senescence and functionality decreasing phase. A genetic framework is proposed to describe gene actions at various checkpoints to regulate leaf development and senescence. Four categories of genes contribute to crop production: those which regulate (I) the speed and transition of early leaf growth, (II) photosynthesis rate, (III) the onset and (IV) the progression of leaf senescence. Current advances in isolating and characterizing senescence regulatory genes are discussed in the leaf aging and crop production context. We argue that the breeding of crops with leaf senescence ideotypes should be an essential part of further crop genetic improvement. [ABSTRACT FROM AUTHOR]

High‐resolution melting (HRM) analysis relies on the use of fluorescent dyes, such as LCGreen, ResoLight, and SYTO9, which bind in a saturated manner to the double‐stranded DNAs. These dyes are expensive in use and may not be affordable when dealing with a large quantity of samples. EvaGreen is a much cheaper DNA helix intercalating dye and has been used in quantitative real‐time polymerase chain reaction (PCR) and post‐PCR DNA melt curve analysis. Here we report on the development of an EvaGreen‐based HRM analysis and its performance, in comparison with the popular LCGreen‐based HRM analysis, in detection of DNA polymorphism in plants. We found that various polymorphisms ranged from single nucleotide polymorphisms (SNPs) to Indels were equally detected by using EvaGreen‐ or LCGreen‐based HRM. EvaGreen dye was sensitive enough in discovery of SNPs in fivefold pooled samples. Using this economical dye we successfully identified multiple novel mutant alleles of Gln1‐3 gene, which produces a cytosolic glutamine synthetase isoenzyme (GS1), in a maize ethyl methanesulfonate (EMS)‐mutagenized library, and genotyped rice mapping populations with SNP markers. The current results suggest that EvaGreen is a promising dye for HRM analysis for its ease to use and cost effectiveness. [ABSTRACT FROM AUTHOR]

In view of the effects of global climate changes on plant growth conditions in Europe, specific traits of sorghum make it a promising candidate for a future bioenergy crop in this region. The main limiting factor seems to be low tolerance of sorghum seedlings to chilling temperature and possible damage caused by cold spells in April and May. Seedlings of six sorghum genotypes (M71/SS79/Etian/Keller/Ji2731/Btx623) at third-leaf stage were exposed to five-day chilling (13/10 °C, day/night) in a growth chamber and then recovered for five days at control temperature (25/20 °C). Before and during cold treatment as well as during recovery, photosynthetic efficiency (PE), stomata status, and osmotic potential (OP) were measured for the first three leaves. As early as after 4 h of chilling there was a significant drop in PE measured as chlorophyll a fluorescence parameters, which decreased further in the course of chilling with significant genotypic differences. These were particularly pronounced after five- day recovery – M71 and Ji2731 recovered almost fully while SS79, Keller, and Btx623 – to a very limited degree. In these susceptible lines a significantly bigger drop in PE was observed for the first (oldest) leaf compared to the third (youngest) one, whereas in the tolerant lines these differences were not significant. All genotypes exhibited stomata closure as late as the fifth chilling or first recovery day and a drop in leaf OP after 52 h of chilling. The results show that the fast and significant drop in PE of sorghum seedlings under chilling conditions is caused by metabolic (non-stomatal) limitations during exposure to low temperature and by stomatal limitations after its cessation. The most pronounced genotypic differences in the reaction of sorghum seedlings to chilling stress were in the extent of osmotic adjustment and the capability for PE recovery after chilling treatment. Research supported by NCBR, Poland, ERA-NET-BIOENERGY-3/2013. [ABSTRACT FROM AUTHOR]

Abstract: Xylans are the major hemicelluloses in grasses, but their effects on biomass saccharification remain unclear. In this study, we examined the 79 representative Miscanthus accessions that displayed a diverse cell wall composition and varied biomass digestibility. Correlation analysis showed that hemicelluloses level has a strong positive effect on lignocellulose enzymatic digestion after NaOH or H2SO4 pretreatment. Characterization of the monosaccharide compositions in the KOH-extractable and non-KOH-extractable hemicelluloses indicated that arabinose substitution degree of xylan is the key factor that positively affects biomass saccharification. The xylose/arabinose ratio after individual enzyme digestion revealed that the arabinose in xylan is partially associated with cellulose in the amorphous regions, which negatively affects cellulose crystallinity for high biomass digestibility. The results provide insights into the mechanism of lignocellulose enzymatic digestion upon pretreatment, and also suggest a goal for the genetic modification of hemicelluloses towards the bioenergy crop breeding of Miscanthus and grasses. [Copyright &y& Elsevier]