Plant Biochemistry
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RESEARCH ARTICLE Nanocarrier-mediated foliar zinc fertilization influences expression of metal homeostasis related genes in flag leaves and enhances gluten content in durum wheat

Abstract 
Background Wheat is the staple food for most of the world’s population; however, it is a poor source of zinc. Foliar fertilization of zinc via zinc loaded chitosan nanocarriers (Zn-CNP) post-anthesis has proved to be a promising approach for grain zinc enhancement in durum wheat as evidenced in our earlier study. However, the molecular mechanism of uptake of zinc via ZnCNP remains unclear.
Methods/Principle findings Foliar application of Zn-CNP was performed at post anthesis stages in two durum wheat cultivars (MACS 3125 and UC1114, containing the Gpc-B1 gene), and expression levels of several metal-related genes were analyzed during early senescence. Zn-CNP application indeed caused changes in gene expression as revealed by qPCR data on representative genes involved in metal homeostasis, phloem transporters, and leaf senescence. Furthermore, zinc-regulated transporters and iron (Fe)-regulated transporter-like protein (ZIP) family [ZIP1, ZIP7, ZIP15], CA (carbonic anhydrase), and DMAS (2’-deoxymugineic acid synthase) in flag leaves exhibited significant correlation with zinc content in the seeds. The analysis of grain endosperm proteins showed enhancement of gamma gliadins while other gluten subunits decreased. Gene expression within ZIP family members varied with the type of cultivar mostly attributed to the Gpc-B1, concentration of external zinc ions as well as the type of tissue analyzed. Correlation analysis revealed the involvement of the selected genes in zinc enhancement. 
Conclusion At the molecular level, uptake of zinc via Zn-CNP nanocarrier was comparable to the uptake of zinc via common zinc fertilizers i.e. ZnSO4
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BIODIVERSITY - Harnessing Agrobiodiversity To Reduce Food Insecurity

BIODIVERSITY - Harnessing Agrobiodiversity To Reduce Food Insecurity | Plant Biochemistry | Scoop.it
A new report on the state of Tucson’s food system reveals that Tucson is one of the top U.S. cities in providing food diversity and access.

Rather than witnessing a decline in access to food diversity that has resulted in more homogeneous, nutrient-poor diets in most cities and countries in the world over the last 50 years, Tucsonans can take pride in the fact that their innovations are helping reverse such trends.

Via Jonathan Lapleau
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CRISPR/Cpf1-mediated DNA-free plant genome editing

CRISPR/Cpf1-mediated DNA-free plant genome editing | Plant Biochemistry | Scoop.it

Cpf1, a type V CRISPR effector, recognizes a thymidine-rich protospacer-adjacent motif and induces cohesive double-stranded breaks at the target site guided by a single CRISPR RNA (crRNA). Here we show that Cpf1 can be used as a tool for DNA-free editing of plant genomes. We describe the delivery of recombinant Cpf1 proteins with in vitro transcribed or chemically synthesized target-specific crRNAs into protoplasts isolated from soybean and wild tobacco. Designed crRNAs are unique and do not have similar sequences (≤3 mismatches) in the entire soybean reference genome. Targeted deep sequencing analyses show that mutations are successfully induced in FAD2 paralogues in soybean and AOC in wild tobacco. Unlike SpCas9, Cpf1 mainly induces various nucleotide deletions at target sites. No significant mutations are detected at potential off-target sites in the soybean genome. These results demonstrate that Cpf1–crRNA complex is an effective DNA-free genome-editing tool for plant genome editing.


Via Jorge Lozano-Juste
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Long and attenuated: comparative trends in the domestication of tree fruits

Long and attenuated: comparative trends in the domestication of tree fruits | Plant Biochemistry | Scoop.it
This paper asks whether we can identify a recurrent domestication syndrome for tree crops (fruits, nuts) and track archaeologically the evolution of domestication of fruits from woody perennials. While archaeobotany has made major contributions to documenting the domestication process in cereals and other annual grains, long-lived perennials have received less comparative attention. Drawing on examples from across Eurasia, comparisons suggest a tendency for the larger domesticated fruits to contain seeds that are proportionally longer, thinner and with more pointed (acute to attenuated) apices. Therefore, although changes in flavour, such as increased sweetness, are not recoverable, seed metrics and shape provide an archaeological basis for tracking domestication episodes in fruits from woody perennials. Where available, metrical data suggest length increases, as well as size diversification over time, with examples drawn from the Jomon of Japan (Castanea crenata), Neolithic China (Prunus persica) and the later Neolithic of the Near East (Olea europaea, Phoenix dactylifera) to estimate rates of change. More limited data allow us to also compare Mesoamerica avocado (Persea americana) and western Pacific Canarium sp. nuts and Spondias sp. fruits. Data from modern Indian jujube (Ziziphus mauritiana) are also considered in relation to seed length:width trends in relation to fruit contents (flesh proportion, sugar content). Despite the long generation time in tree fruits, rates of change in their seeds are generally comparable to rates of phenotypic evolution in annual grain crops, suggesting that gradual evolution via unconscious selection played a key role in initial processes of tree domestication, and that this had begun in the later Neolithic once annual crops had been domesticated, in both west and east Asia.

Via Dorian Q Fuller
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Low number of fixed somatic mutations in a long-lived oak tree

Low number of fixed somatic mutations in a long-lived oak tree | Plant Biochemistry | Scoop.it

Because plants do not possess a defined germline, deleterious somatic mutations can be passed to gametes, and a large number of cell divisions separating zygote from gamete formation may lead to many mutations in long-lived plants. We sequenced the genome of two terminal branches of a 234-year-old oak tree and found several fixed somatic single-nucleotide variants whose sequential appearance in the tree could be traced along nested sectors of younger branches. Our data suggest that stem cells of shoot meristems in trees are robustly protected from the accumulation of mutations.


Via Jean-Pierre Zryd
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New Phytol.: Sustaining global agriculture through rapid detection and deployment of genetic resistance to deadly crop diseases

New Phytol.: Sustaining global agriculture through rapid detection and deployment of genetic resistance to deadly crop diseases | Plant Biochemistry | Scoop.it
Genetically encoded resistance is a major component of crop disease management. Historically, gene loci conferring resistance to pathogens have been identified through classical genetic methods. In recent years, accelerated gene cloning strategies have become available through advances in sequencing, gene capture and strategies for reducing genome complexity. Here, I describe these approaches with key emphasis on the isolation of resistance genes to the cereal crop diseases that are an ongoing threat to global food security. Rapid gene isolation enables their efficient deployment through marker-assisted selection and transgenic technology. Together with innovations in genome editing and progress in pathogen virulence studies, this creates further opportunities to engineer long-lasting resistance. These approaches will speed progress towards a future of farming using fewer pesticides.

Via Nicolas Denancé, Jennifer Mach
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New Phytol.: A functional imaging study of germinating oilseed rape seed (2017)

New Phytol.: A functional imaging study of germinating oilseed rape seed (2017) | Plant Biochemistry | Scoop.it
Germination, the process whereby a dry, quiescent seed springs to life, has been a focus of plant biologist for many years, yet the early events following water uptake, during which metabolism of the embryo is restarted, remain enigmatic. Here, the nature of the cues required for this restarting in oilseed rape (Brassica napus) seed has been investigated. A holistic in vivo approach was designed to display the link between the entry and allocation of water, metabolic events and structural changes occurring during germination. For this, we combined functional magnetic resonance imaging with Fourier transform infrared microscopy, fluorescence-based respiration mapping, computer-aided seed modeling and biochemical tools. We uncovered an endospermal lipid gap, which channels water to the radicle tip, from whence it is distributed via embryonic vasculature toward cotyledon tissues. The resumption of respiration is initiated first in the endosperm, only later spreading to the embryo. Sugar metabolism and lipid utilization are linked to the spatiotemporal sequence of tissue rehydration. Together, this imaging study provides insights into the spatial aspects of key events in oilseed rape seeds leading to germination. It demonstrates how seed architecture predetermines the pattern of water intake, which sets the stage for the orchestrated restart of life.

Via Nicolas Denancé
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VRS3 is a histone demethylase

VRS3 is a histone demethylase | Plant Biochemistry | Scoop.it

Image from van Esse et al., 2017


Two recent papers (van Esse and Walla et al.,2017; Bull et al., 2017) have identified VRS3 as a histone demethylase that controls lateral spikelet development in barley.


Six-rowed spike 3 (VRS3) is a histone demethylase that controls lateral spikelet development in barley


van Esse and Walla et al.,2017

http://www.plantphysiol.org/content/early/2017/06/27/pp.17.00108


"The complex nature of crop genomes has long prohibited the efficient isolation of agronomically relevant genes. However, recent advances in next-generation sequencing (NGS) technologies provide new ways to accelerate fine-mapping and gene isolation in crops. We used RNA-sequencing of allelic six-rowed spike 3 (vrs3) mutants with altered spikelet development for gene identification and functional analysis in barley (Hordeum vulgare). Variant calling in two allelic vrs3 mutants revealed that VRS3 encodes a putative histone lysine demethylase with a conserved zinc finger, Jumonji C and N domain. Sanger sequencing of this candidate gene in independent allelic vrs3 mutants revealed a series of mutations in conserved domains, thus confirming our candidate as the VRS3 gene and suggesting that the row type in barley is determined epigenetically. Global transcriptional profiling in developing shoot apical meristems of vrs3 suggested that VRS3 acts as a transcriptional activator of the row-type genes VRS1 (Hv.Hox 1) and INTERMEDIUM-C (INT-C; Hv.TEOSINTE BRANCHED 1). Comparative transcriptome analysis of the row-type mutants vrs3, vrs4 (Hv.RAMOSA2) and int-c confirmed that all three genes act as transcriptional activators of VRS1 and quantitative variation in the expression levels of VRS1 in these mutants correlated with differences in the number of fertile lateral spikelets. The identification of genes and pathways affecting seed number in small grain cereals will enable to further unravel the transcriptional networks controlling this important yield component."




Barley SIX-ROWED SPIKE3 encodes a putative Jumonji C-type H3K9me2/me3 demethylase that represses lateral spikelet fertility


Bull et al.,2017

https://www.nature.com/articles/s41467-017-00940-7.pdf


"The barley inflorescence (spike) comprises a multi-noded central stalk (rachis) with tripartite clusters of uni-floretted spikelets attached alternately along its length. Relative fertility of lateral spikelets within each cluster leads to spikes with two or six rows of grain, or an intermediate morphology. Understanding the mechanisms controlling this key developmental step could provide novel solutions to enhanced grain yield. Classical genetic studies identified five major SIX-ROWED SPIKE (VRS) genes, with four now known to encode transcription factors. Here we identify and characterise the remaining major VRS gene, VRS3, as encoding a putative Jumonji C-type H3K9me2/me3 demethylase, a regulator of chromatin state. Exploring the expression network modulated by VRS3 reveals specific interactions, both with other VRS genes and genes involved in stress, hormone and sugar metabolism. We show that combining a vrs3 mutant allele with natural six-rowed alleles of VRS1 and VRS5 leads to increased lateral grain size and greater grain uniformity."




Via Wilma van Esse
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Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments : Nature Biotechnology : Nature Research

Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments : Nature Biotechnology : Nature Research | Plant Biochemistry | Scoop.it
Draft genome, 994 re-sequenced lines and GWAS for yield-traits provide a resource of genetics and genomics tools for pearl millet researchers and breeders.
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The conserved and unique genetic architecture of kernel size and weight in maize and rice

The conserved and unique genetic architecture of kernel size and weight in maize and rice | Plant Biochemistry | Scoop.it
Maize is a major staple crop. Maize kernel size and weight are important contributors to its yield. Here, we measured kernel length, kernel width, kernel thickness, hundred kernel weight and kernel test weight in 10 recombinant inbred line populations and dissected their genetic architecture using three statistical models. In total, 729 quantitative trait loci (QTLs) were identified, many of which were identified in all three models, including 22 major QTLs that each can explain more than 10% of phenotypic variation. To provide candidate genes for these QTLs, we identified 30 maize genes that are orthologs of 18 rice genes reported to affect rice seed size or weight. Interestingly, 24 of these 30 genes are located in the identified QTLs or within 1 Mb region of the significant single nucleotide polymorphisms (SNPs). We further confirmed the effect of five genes on maize kernel size/weight in an independent association mapping panel with 540 lines by candidate gene association analysis. Lastly, the function of ZmINCW1, a homolog of rice GRAIN INCOMPLETE FILLING 1 (GIF1) that affects seed size and weight, was characterized in detail. ZmINCW1 is close to QTL peaks for kernel size/weight (< 1 Mb) and contains significant SNPs affecting kernel size/weight in the association panel. Over-expression of this gene can rescue the reduced weight of the Arabidopsis homozygous mutant line in the AtcwINV2 gene (Arabidopsis ortholog of ZmINCW1). These results indicate that the molecular mechanisms affecting kernel/seed development are conserved in maize, rice, and possibly in Arabidopsis.

Via Loïc Lepiniec
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Molecular characterization of the acquisition of longevity during seed maturation in soybean

Molecular characterization of the acquisition of longevity during seed maturation in soybean | Plant Biochemistry | Scoop.it
Seed longevity, defined as the ability to remain alive during storage, is an important agronomic factor. Poor longevity negatively impacts seedling establishment and consequently crop yield. This is particularly problematic for soybean as seeds have a short lifespan. While the economic importance of soybean has fueled a large number of transcriptome studies during embryogenesis and seed filling, the mechanisms regulating seed longevity during late maturation remain poorly understood. Here, a detailed physiological and molecular characterization of late seed maturation was performed in soybean to obtain a comprehensive overview of the regulatory genes that are potentially involved in longevity. Longevity appeared at physiological maturity at the end of seed filling before maturation drying and progressively doubled until the seeds reached the dry state. The increase in longevity was associated with the expression of genes encoding protective chaperones such as heat shock proteins and the repression of nuclear and chloroplast genes involved in a range of chloroplast activities, including photosynthesis. An increase in the raffinose family oligosaccharides (RFO)/sucrose ratio together with changes in RFO metabolism genes was also associated with longevity. A gene co-expression network analysis revealed 27 transcription factors whose expression profiles were highly correlated with longevity. Eight of them were previously identified in the longevity network of Medicago truncatula, including homologues of ERF110, HSF6AB, NFXL1 and members of the DREB2 family. The network also contained several transcription factors associated with auxin and developmental cell fate during flowering, organ growth and differentiation. A transcriptional transition occurred concomitant with seed chlorophyll loss and detachment from the mother plant, suggesting the activation of a post-abscission program. This transition was enriched with AP2/EREBP and WRKY transcription factors and genes associated with growth, germination and post-transcriptional processes, suggesting that this program prepares the seed for the dry quiescent state and germination.

Via Loïc Lepiniec
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84% Of Delhi's Bread, Pizzas And Burgers Contain Cancer Causing Chemicals!

84% Of Delhi's Bread, Pizzas And Burgers Contain Cancer Causing Chemicals! | Plant Biochemistry | Scoop.it
This article is about a study by CSE which says 84% of the bread in Delhi has cancer causing chemicals | indiatimes.com

Via InfoBlaze
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The conserved and unique genetic architecture of kernel size and weight in maize and rice

The conserved and unique genetic architecture of kernel size and weight in maize and rice | Plant Biochemistry | Scoop.it
Maize is a major staple crop. Maize kernel size and weight are important contributors to its yield. Here, we measured kernel length, kernel width, kernel thickness, hundred kernel weight and kernel test weight in 10 recombinant inbred line populations and dissected their genetic architecture using three statistical models. In total, 729 quantitative trait loci (QTLs) were identified, many of which were identified in all three models, including 22 major QTLs that each can explain more than 10% of phenotypic variation. To provide candidate genes for these QTLs, we identified 30 maize genes that are orthologs of 18 rice genes reported to affect rice seed size or weight. Interestingly, 24 of these 30 genes are located in the identified QTLs or within 1 Mb region of the significant single nucleotide polymorphisms (SNPs). We further confirmed the effect of five genes on maize kernel size/weight in an independent association mapping panel with 540 lines by candidate gene association analysis. Lastly, the function of ZmINCW1, a homolog of rice GRAIN INCOMPLETE FILLING 1 (GIF1) that affects seed size and weight, was characterized in detail. ZmINCW1 is close to QTL peaks for kernel size/weight (< 1 Mb) and contains significant SNPs affecting kernel size/weight in the association panel. Over-expression of this gene can rescue the reduced weight of the Arabidopsis homozygous mutant line in the AtcwINV2 gene (Arabidopsis ortholog of ZmINCW1). These results indicate that the molecular mechanisms affecting kernel/seed development are conserved in maize, rice, and possibly in Arabidopsis.

Via Loïc Lepiniec
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An investigation into the nutritional composition and cost of gluten‐free versus regular food products in the UK - J Hum Nutr Diet (2018) 

An investigation into the nutritional composition and cost of gluten‐free versus regular food products in the UK - J Hum Nutr Diet (2018)  | Plant Biochemistry | Scoop.it

The gluten-free (GF) food market has expanded considerably, although there is limited comparative evidence for the nutritional quality and cost of GF food products. The present study aims to compare the nutrient composition and cost of GF and gluten-containing (regular) foods across 10 food categories in the UK.

Nutritional information and the cost of GF foods available in the UK (n = 679) and comparable regular foods (n = 1045) were systematically collected from manufacturer and supermarket websites. Foods were classified using UK front-of-pack labelling for content of fat, saturated fat, sugar and salt and nutrient content, and cost per 100 g were identified and compared... 


More GF foods were classified as containing high and medium fat, saturated fat, sugar and salt than regular foods, although this was not universally consistent. More GF bread and flour products contained high fat and sugar... High salt content was found more frequently in GF than regular products... GF products were 159% more expensive... GF items were also more likely to be lower in fibre and protein content... 


Differences exist in the nutritional composition of GF and regular food. GF food is unlikely to offer healthier alternatives to regular foods, except for those who require a GF diet for medically diagnosed conditions, and it is associated with higher costs.


http://doi.org/10.1111/jhn.12502

 


Via Alexander J. Stein
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Alexander J. Stein's curator insight, January 18, 1:20 PM
"except for those who require a GF diet for medically diagnosed conditions"
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GREEN BIOTECH - Preparing Rubisco For A Tune Up

GREEN BIOTECH - Preparing Rubisco For A Tune Up | Plant Biochemistry | Scoop.it

New capabilities for assembling plant Rubisco in bacteria offer a revolution for enhancing photosynthesis. The technology provides a breakthrough to identify and test solutions for improving CO2 fixation by crop Rubisco.


Via Jonathan Lapleau
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Abscisic Acid-Induced Reactive Oxygen Species Are Modulated by Flavonols to Control Stomata Aperture

Abscisic Acid-Induced Reactive Oxygen Species Are Modulated by Flavonols to Control Stomata Aperture | Plant Biochemistry | Scoop.it
Abscisic acid (ABA) increases reactive oxygen species (ROS) in guard cells to close Arabidopsis (Arabidopsis thaliana) stomata. In tomato (Solanum lycopersicum), we find that ABA-increased ROS is followed by stomatal closure and that both responses are blocked by inhibitors of ROS-producing respiratory burst oxidase enzymes. ABA-induced ROS sensor fluorescence accumulates in the nucleus, chloroplasts, and endomembranes. The accumulation of flavonol antioxidants in guard cells, but not surrounding pavement cells, was visualized by confocal microscopy using a flavonol-specific fluorescent dye. Decreased flavonols in guard cells in the anthocyanin reduced (are) mutant and elevated levels in the anthocyanin without (aw) mutant were quantified by confocal microscopy and in leaf extracts by mass spectrometry. Consistent with flavonols acting as antioxidants, higher levels of ROS were detected in guard cells of the tomato are mutant and lower levels were detected in aw both at homeostasis and after treatment with ABA. These results demonstrate the inverse relationship between flavonols and ROS. Guard cells of are show greater ABA-induced closure than the wild type, reduced light-dependent guard cell opening, and reduced water loss, with aw having opposite responses. Ethylene treatment of wild-type tomato plants increased flavonol accumulation in guard cells; however, no flavonol increases were observed in Neverripe (Nr), an ethylene receptor mutant. Consistent with lower levels of ROS due to elevated flavonols, ethylene treatments decreased ABA-induced stomatal closure in the wild type, but not Nr, with ethylene responses attenuated in the are mutant. Together, these results are consistent with flavonols dampening the ABA-dependent ROS burst that drives stomatal closure and facilitating stomatal opening to modulate leaf gas exchange.

Via Loïc Lepiniec
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An Integrated “Multi-Omics” Comparison of Embryo and Endosperm Tissue-Specific Features and Their Impact on Rice Seed Quality

An Integrated “Multi-Omics” Comparison of Embryo and Endosperm Tissue-Specific Features and Their Impact on Rice Seed Quality | Plant Biochemistry | Scoop.it
Although rice is a key crop species, few studies have addressed both rice seed physiological and nutritional quality, especially at the tissue level. In this study, an exhaustive “multi-omics” dataset on the mature rice seed was obtained by combining transcriptomics, label-free shotgun proteomics and metabolomics from embryo and endosperm, independently. These high-throughput analyses provide a new insight on the tissue-specificity related to rice seed quality. Foremost, we pinpointed that extensive post-transcriptional regulations occur at the end of rice seed development such that the embryo proteome becomes much more diversified than the endosperm proteome. Secondly, we observed that survival in the dry state in each seed compartment depends on contrasted metabolic and enzymatic apparatus in the embryo and the endosperm, respectively. Thirdly, it was remarkable to identify two different sets of starch biosynthesis enzymes as well as seed storage proteins (glutelins) in both embryo and endosperm consistently with the supernumerary embryo hypothesis origin of the endosperm. The presence of a putative new glutelin with a possible embryonic favoured abundance is described here for the first time. Finally, we quantified the rate of mRNA translation into proteins. Consistently, the embryonic panel of protein translation initiation factors is much more diverse than that of the endosperm. This work emphasizes the value of tissue-specificity-centered “multi-omics” study in the seed to highlight new features even from well-characterized pathways. It paves the way for future studies of critical genetic determinants of rice seed physiological and nutritional quality.

Via Saclay Plant Sciences, Loïc Lepiniec
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Membrane Dynamics and Multiple Functions of Oil Bodies in Seeds and Leaves

Membrane Dynamics and Multiple Functions of Oil Bodies in Seeds and Leaves | Plant Biochemistry | Scoop.it
Membrane Dynamics and Multiple Functions of Oil Bodies in Seeds and Leaves

Via Loïc Lepiniec
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Genome sequence of the progenitor of the wheat D genome Aegilops tauschii

Genome sequence of the progenitor of the wheat D genome Aegilops tauschii | Plant Biochemistry | Scoop.it

Aegilops tauschii is the diploid progenitor of the D genome of hexaploid wheat1 (Triticum aestivum, genomes AABBDD) and an important genetic resource for wheat2,3,4. The large size and highly repetitive nature of the Ae. tauschii genome has until now precluded the development of a reference-quality genome sequence5. Here we use an array of advanced technologies, including ordered-clone genome sequencing, whole-genome shotgun sequencing, and BioNano optical genome mapping, to generate a reference-quality genome sequence for Ae. tauschii ssp. strangulata accession AL8/78, which is closely related to the wheat D genome. We show that compared to other sequenced plant genomes, including a much larger conifer genome, the Ae. tauschii genome contains unprecedented amounts of very similar repeated sequences. Our genome comparisons reveal that the Ae. tauschii genome has a greater number of dispersed duplicated genes than other sequenced genomes and its chromosomes have been structurally evolving an order of magnitude faster than those of other grass genomes. The decay of colinearity with other grass genomes correlates with recombination rates along chromosomes. We propose that the vast amounts of very similar repeated sequences cause frequent errors in recombination and lead to gene duplications and structural chromosome changes that drive fast genome evolution.


Via Jean-Pierre Zryd
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Small group scoops international effort to sequence huge wheat genome

Small group scoops international effort to sequence huge wheat genome | Plant Biochemistry | Scoop.it
Just six scientists conquer one of the most complicated genomes ever read.
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BMC Biology: Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination (2017)

BMC Biology: Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination (2017) | Plant Biochemistry | Scoop.it

Background. Root and tuber crops are a major food source in tropical Africa. Among these crops are several species in the monocotyledonous genus Dioscorea collectively known as yam, a staple tuber crop that contributes enormously to the subsistence and socio-cultural lives of millions of people, principally in West and Central Africa. Yam cultivation is constrained by several factors, and yam can be considered a neglected “orphan” crop that would benefit from crop improvement efforts. However, the lack of genetic and genomic tools has impeded the improvement of this staple crop.

 

Results. To accelerate marker-assisted breeding of yam, we performed genome analysis of white Guinea yam (Dioscorea rotundata) and assembled a 594-Mb genome, 76.4% of which was distributed among 21 linkage groups. In total, we predicted 26,198 genes. Phylogenetic analyses with 2381 conserved genes revealed that Dioscorea is a unique lineage of monocotyledons distinct from the Poales (rice), Arecales (palm), and Zingiberales (banana). The entire Dioscorea genus is characterized by the occurrence of separate male and female plants (dioecy), a feature that has limited efficient yam breeding. To infer the genetics of sex determination, we performed whole-genome resequencing of bulked segregants (quantitative trait locus sequencing [QTL-seq]) in F1 progeny segregating for male and female plants and identified a genomic region associated with female heterogametic (male = ZZ, female = ZW) sex determination. We further delineated the W locus and used it to develop a molecular marker for sex identification of Guinea yam plants at the seedling stage.

 

Conclusions. Guinea yam belongs to a unique and highly differentiated clade of monocotyledons. The genome analyses and sex-linked marker development performed in this study should greatly accelerate marker-assisted breeding of Guinea yam. In addition, our QTL-seq approach can be utilized in genetic studies of other outcrossing crops and organisms with highly heterozygous genomes. Genomic analysis of orphan crops such as yam promotes efforts to improve food security and the sustainability of tropical agriculture.


Via Kamoun Lab @ TSL
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The conserved and unique genetic architecture of kernel size and weight in maize and rice

The conserved and unique genetic architecture of kernel size and weight in maize and rice | Plant Biochemistry | Scoop.it
Maize is a major staple crop. Maize kernel size and weight are important contributors to its yield. Here, we measured kernel length, kernel width, kernel thickness, hundred kernel weight and kernel test weight in 10 recombinant inbred line populations and dissected their genetic architecture using three statistical models. In total, 729 quantitative trait loci (QTLs) were identified, many of which were identified in all three models, including 22 major QTLs that each can explain more than 10% of phenotypic variation. To provide candidate genes for these QTLs, we identified 30 maize genes that are orthologs of 18 rice genes reported to affect rice seed size or weight. Interestingly, 24 of these 30 genes are located in the identified QTLs or within 1 Mb region of the significant single nucleotide polymorphisms (SNPs). We further confirmed the effect of five genes on maize kernel size/weight in an independent association mapping panel with 540 lines by candidate gene association analysis. Lastly, the function of ZmINCW1, a homolog of rice GRAIN INCOMPLETE FILLING 1 (GIF1) that affects seed size and weight, was characterized in detail. ZmINCW1 is close to QTL peaks for kernel size/weight (< 1 Mb) and contains significant SNPs affecting kernel size/weight in the association panel. Over-expression of this gene can rescue the reduced weight of the Arabidopsis homozygous mutant line in the AtcwINV2 gene (Arabidopsis ortholog of ZmINCW1). These results indicate that the molecular mechanisms affecting kernel/seed development are conserved in maize, rice, and possibly in Arabidopsis.

Via Loïc Lepiniec
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Molecular Plant: PacBio Sequencing Reveals Transposable Element as a Key Contributor to Genomic Plasticity and Virulence Variation in Magnaporthe oryzae (2017)

Molecular Plant: PacBio Sequencing Reveals Transposable Element as a Key Contributor to Genomic Plasticity and Virulence Variation in Magnaporthe oryzae (2017) | Plant Biochemistry | Scoop.it
We deployed single molecule real-time (SMRT) sequencing developed by Pacific BioSciences (PacBio), to generate near complete genome assembly for M. oryzae field isolates FJ81278 and Guy11, and evaluated the possible contribution of TEs to genomic variation events such as chromosomal translocation, gene presence/absence in LS regions and virulence-associated secreted proteins (SPs) polymorphism.

Via Philip Carella, Elsa Ballini, Yogesh Gupta, Kamoun Lab @ TSL
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Tomato development: MADS-box engineering

Tomato development: MADS-box engineering | Plant Biochemistry | Scoop.it


Tomato development: MADS-box engineering


Wild-type tomato plants bear unbranched inflorescences with jointed pedicels. Branched inflorescences produce more flowers and, presumably, more fruits. However, excessively branched variants exhibit sterility and are avoided by breeders. Compared to jointed pedicels, jointless pedicels enhance fruit retention and facilitate machine harvesting. A desirable tomato inflorescence is thus weakly branched with jointless pedicels. Although a range of inflorescence variants exist in tomato germplasm, our understanding of the genetic programme controlling inflorescence architecture has remained limited, hindering effective breeding. By exploring branched tomato variants, Sebastian Soyk, from the Cold Spring Harbor Laboratory, and colleagues uncovered two artificially selected MADS-box genes that control meristem maturation and inflorescence development....


Via Christophe Jacquet
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