来自用户 哪有情可长 的文献。
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21.
哪有情可长
(2022-12-31 16:21):
#paper MicroTom Metabolic Network: Rewiring Tomato Metabolic Regulatory Network throughout the Growth Cycle,Molecular Plant , August 2020 ,https://doi.org/10.1016/j.molp.2020.06.005. 作者对整个番茄生命周期的根、茎、叶、花、果实进行取样进行转录组和代谢中测序,构建了番茄生长时期的代谢图谱和番茄发育过程的时间天空网络。除了验证前人已经发表过的重要代谢物的调控网络,也鉴定到一个一个转录因子可以调节重要的次级代谢物的合成,黄酮类的代谢物。该文章的模式跟该课题组发水稻的代谢调控网络类似,包括处理方法都是类似(Rice metabolic regulatory network spanning the entire life cycle)。作为植物中进行代谢组和转录组数据联合分析的入门可以精读下。但是内在的代谢物的作用,还是需要一篇篇文献积累。
MicroTom Metabolic Network: Rewiring Tomato Metabolic Regulatory Network throughout the Growth Cycle
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Abstract:
Tomato (Solanum lycopersicum) is a major horticultural crop worldwide and has emerged as a preeminent model for metabolic research. Although many research efforts have focused on the analysis of metabolite …
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Tomato (Solanum lycopersicum) is a major horticultural crop worldwide and has emerged as a preeminent model for metabolic research. Although many research efforts have focused on the analysis of metabolite differences between varieties and species, the dynamics of metabolic changes during the tomato growth cycle and the regulatory networks that underlie these changes are poorly understood. In this study, we integrated high-resolution spatio-temporal metabolome and transcriptome data to systematically explore the metabolic landscape across 20 major tomato tissues and growth stages. In the resulting MicroTom Metabolic Network, the 540 detected metabolites and their co-expressed genes could be divided into 10 distinct clusters based on their biological functions. Using this dataset, we constructed a global map of the major metabolic changes that occur throughout the tomato growth cycle and dissected the underlying regulatory network. In addition to verifying previously well-established regulatory networks for important metabolites, we identified novel transcription factors that regulate the biosynthesis of important secondary metabolites such as steroidal glycoalkaloids and flavonoids. Our findings provide insights into spatio-temporal changes in tomato metabolism and generate a valuable resource for the study of metabolic regulatory processes in model plants.
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22.
哪有情可长
(2022-11-30 19:24):
#paper THP9 enhances seed protein content and nitrogen-use efficiency in maize, Nature 2022 October, https://doi.org/10.1038/s41586-022-05441-2. 鉴定未驯化的野生型玉米大刍草的蛋白发现其要比现代玉米籽粒蛋白含量高,由于玉米大刍草的基因型复杂,其参考基因组一直没有被组装,作者通过构建已知参考基因组B73和大刍草杂交后代,测定后代基因型去掉已知的参考基因组B73进行组装大刍草的参考基因组,将两套参考基因组进行共线性分析发现存在大量的结构变异,推测蛋白含量的高低可能是由于结构变异引起。作者们继续构建群体,通过BSA鉴定到了控制籽粒蛋白含量的基因THP9,该基因在现代品种中存在48bp的缺失,导致剪切位点发生变化后导致基因翻译提前终止,最终导致现代玉米籽粒蛋白含量降低。作者又利用525份自然群体进行GWAS分析,也鉴定到该基因所处的区间。对525份材料按照基因型可以分成三种单倍型,Hap1跟野生型基因型一致,作者又通过转基因验证该基因的确能够提高蛋白含量,又通过构建NIL群体,继续验证该基因的功能,发现当籽粒蛋白含量高时,根部的氮吸收效率高,该基因也是首次在玉米中鉴定的第一个高蛋白基因。
Abstract:
Teosinte, the wild ancestor of maize (Zea mays subsp. mays), has three times the seed protein content of most modern inbreds and hybrids, but the mechanisms that are responsible for …
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Teosinte, the wild ancestor of maize (Zea mays subsp. mays), has three times the seed protein content of most modern inbreds and hybrids, but the mechanisms that are responsible for this trait are unknown. Here we use trio binning to create a contiguous haplotype DNA sequence of a teosinte (Zea mays subsp. parviglumis) and, through map-based cloning, identify a major high-protein quantitative trait locus, TEOSINTE HIGH PROTEIN 9 (THP9), on chromosome 9. THP9 encodes an asparagine synthetase 4 enzyme that is highly expressed in teosinte, but not in the B73 inbred, in which a deletion in the tenth intron of THP9-B73 causes incorrect splicing of THP9-B73 transcripts. Transgenic expression of THP9-teosinte in B73 significantly increased the seed protein content. Introgression of THP9-teosinte into modern maize inbreds and hybrids greatly enhanced the accumulation of free amino acids, especially asparagine, throughout the plant, and increased seed protein content without affecting yield. THP9-teosinte seems to increase nitrogen-use efficiency, which is important for promoting a high yield under low-nitrogen conditions.
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23.
哪有情可长
(2022-10-26 20:33):
#paper doi:#paper doi:doi:10.1038/ng.592, OsSPL14 promotes panicle branching and higher grainproductivity in rice.作物产量三要素主要是亩穗数、穗粒数和千粒重。提高产量主要是提高三要素之间的协同作用。水稻的第二次“绿色革命”是通过降低株高来增加了水稻的产量。而现在有人认为在水稻中IPA这个基因是新型的"绿色革命"基因。该基因能够能够在水稻的生殖期通过在水稻幼穗内高表达促进水稻穗分枝和籽粒产量。小麦中关于SBP蛋白的研究有很多,通过同源blast,在小麦中也鉴定到了IPA的同源基因。文章在2017年发表在《Plant Physiology》“Functional conservation and divergence among homoeologs of TaSPL20 and TaSPL21, two SBP-box genes governing yield-related traits in hexaploid wheat”,作者发现普通小麦部分同源基因TaSPL20和TaSPL21在小麦长期的驯化和遗传改良过程中产生功能分化,其优异的自然变异在我国小麦育种进程中受到了定向选择并被广泛应用,但是这个文中中验证基因由于当初小麦转基因比较难,文中中验证是在水稻中进行的,证明该基因增加了籽粒大小,从而增加了产量。如果是在小麦中验证会更好。
Abstract:
Identification of alleles that improve crop production and lead to higher-yielding varieties are needed for food security. Here we show that the quantitative trait locus WFP (WEALTHY FARMER'S PANICLE) encodes …
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Identification of alleles that improve crop production and lead to higher-yielding varieties are needed for food security. Here we show that the quantitative trait locus WFP (WEALTHY FARMER'S PANICLE) encodes OsSPL14 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 14, also known as IPA1). Higher expression of OsSPL14 in the reproductive stage promotes panicle branching and higher grain yield in rice. OsSPL14 controls shoot branching in the vegetative stage and is affected by microRNA excision. We also demonstrate the feasibility of using the OsSLP14(WFP) allele to increase rice crop yield. Introduction of the high-yielding OsSPL14(WFP) allele into the standard rice variety Nipponbare resulted in increased rice production.
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24.
哪有情可长
(2022-09-18 20:36):
#paper 'Green revolution' genes encode mutant gibberellin response modulators, Nature 1999 Jul 15;400(6741):256-61. doi: 10.1038/22307.
绿色革命是将在拟南芥中发现的矮杆的基因引用到作物中,降低了水稻、小麦等作物的株高,然后加上水肥等配套设施开始完善,从而使得作物产量增加,也降低了作物成熟后期大风和降雨导致的倒伏减产。进而使得矮杆基因在’绿色革命‘中得以应用。作物中的矮杆突变主要是由于该类基因突变后,导致对GA(赤霉素)不敏感,反应异常导致的。该文主要从拟南芥、水稻、玉米、小麦中的矮杆基因的基因结构,蛋白功能以及突变位点的差异导致的表型的差异变化。分析物种之间矮杆基因的共线性、矮杆基因中发现的SH2 domain结构。且赤霉素信号转导在单子叶和双子叶植物中非常相似,可能涉及SH2 domian与磷酸化酪氨酸残基的相互作用。
该作者首先在1993年在拟南芥中发现了一个GAI的基因,该基因是负调控赤霉素(GA)信号通路的一个基因。获取拟南芥中该基因突变体,后再1997年又发了一篇关于拟南芥GAI基因的文章,后续他又在小麦中进行研究,发现无论是双子叶植物还是单子叶植物,该类基因的功能是同源性较好的基因。
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World wheat grain yields increased substantially in the 1960s and 1970s because farmers rapidly adopted the new varieties and cultivation methods of the so-called ‘green revolution’1,2,3,4. The new varieties are …
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World wheat grain yields increased substantially in the 1960s and 1970s because farmers rapidly adopted the new varieties and cultivation methods of the so-called ‘green revolution’1,2,3,4. The new varieties are shorter, increase grain yield at the expense of straw biomass, and are more resistant to damage by wind and rain3,4. These wheats are short because they respond abnormally to the plant growth hormone gibberellin. This reduced response to gibberellin is conferred by mutant dwarfing alleles at one of two Reduced height-1 (Rht-B1 and Rht-D1) loci4,5. Here we show that Rht-B1/Rht-D1 and maize dwarf-8 (d8)6,7 are orthologues of the Arabidopsis Gibberellin Insensitive (GAI) gene8,9. These genes encode proteins that resemble nuclear transcription factors and contain an SH2-like10 domain, indicating that phosphotyrosine may participate in gibberellin signalling. Six different orthologous dwarfing mutant alleles encode proteins that are altered in a conserved amino-terminal gibberellin signalling domain. Transgenic rice plants containing a mutant GAI allele give reduced responses to gibberellin and are dwarfed, indicating that mutant GAI orthologues could be used to increase yield in a wide range of crop species.
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25.
哪有情可长
(2022-08-31 21:57):
#paper The integrated genomics of crop domestication and breeding , Cell. 2022 Sep 20;9(10):944. doi:10.1016/j.cell.2022.04.036.
这是一篇关于作物驯化和育种中整合基因组学的综述,野生植物驯化成农作物是一个长期且伴随着人类文明发展的一个重要事件。驯化的成功有一大部分原因是人工选择的结果。例如小麦的驯化的现在研究的方向主要为脆轴性、落粒性等。在2006年cell发表了一篇”The Molecular Genetics of Crop Domestication“综述,该片主要重点讲述了驯化的分子遗传机制。随着测序技术的发展,以及测序在作物群体中的应用,使得作物驯化的研究从单个基因的点扩展到整个作物基因组的面,故2022年这篇对于驯化的文章主要是从基因组学、群体遗传学、遗传学图谱和功能基因组学等方面在作物驯化领域应用及取得的进展,期望能够利用复杂的遗传信息的方法来高效的从头设计物种或者对野生种进行重新驯化。
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As a major event in human civilization, wild plants were successfully domesticated to be crops, largely owing to continuing artificial selection. Here, we summarize new discoveries made during the past …
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As a major event in human civilization, wild plants were successfully domesticated to be crops, largely owing to continuing artificial selection. Here, we summarize new discoveries made during the past decade in crop domestication and breeding. The construction of crop genome maps and the functional characterization of numerous trait genes provide foundational information. Approaches to read, interpret, and write complex genetic information are being leveraged in many plants for highly efficient de novo or re-domestication. Understanding the underlying mechanisms of crop microevolution and applying the knowledge to agricultural productions will give possible solutions for future challenges in food security.
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26.
哪有情可长
(2022-07-30 21:34):
#paper doi: 10.1126/science.abl7392 Gametophyte genome activation occurs at pollen mitosis I in maize. 孢子体经过减数分裂成单倍体的孢子,然后经细胞增殖和分化,形成配子体。配子体世代的主要功能是形成单倍体配子,而精、卵细胞的融合又产生了新的孢子体,从而完成了一个生活周期。母体基因控制着植物受精后大多数早期事件,随后是母体到合子的转变,这个过程中母体产物的降解与合子基因组的激活相协调。本研究对玉米减数分裂开始到花粉脱落的26天内单个玉米花粉前体细胞和籽粒RNA含量进行测序,发现,花粉发育到一半的过程中,花粉粒的单倍体基因组从亲本的二倍体基因组中夺取控制权,随着孢子体到配子体的转变,为下一代的生长发育奠定了基础。
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Flowering plants alternate between multicellular haploid (gametophyte) and diploid (sporophyte) generations. Pollen actively transcribes its haploid genome, providing phenotypic diversity even among pollen grains from a single plant. In this …
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Flowering plants alternate between multicellular haploid (gametophyte) and diploid (sporophyte) generations. Pollen actively transcribes its haploid genome, providing phenotypic diversity even among pollen grains from a single plant. In this study, we used allele-specific RNA sequencing of single pollen precursors to follow the shift to haploid expression in maize pollen. We observed widespread biallelic expression for 11 days after meiosis, indicating that transcripts synthesized by the diploid sporophyte persist long into the haploid phase. Subsequently, there was a rapid and global conversion to monoallelic expression at pollen mitosis I, driven by active new transcription from the haploid genome. Genes showed evidence of increased purifying selection if they were expressed after (but not before) pollen mitosis I. This work establishes the timing during which haploid selection may act in pollen.
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27.
哪有情可长
(2022-06-30 22:52):
#paper 10.1038/s41586-020-03091-w. Nature. Genomic basis of geographical adaptation to soil nitrogen in rice. 推荐理由:这篇文章是水稻里面发现了一个关于适应当地土壤环境相关氮利用效率的基因。本研究课题的试验方式是先通过GWAS在不同区域环境下氮素利用的密切相关的性状进行定位,鉴定发现OsTCP19。后续发现该基因缺失了29bp的插入导致不同水稻品种之间不同的基因表达量和对氮素反应分蘖能力的变化。在野生稻和栽培稻中鉴定该基因29bp位点的变化,且发现现代栽培品种中该位点丢失,丢失的位点导致氮的利用率低。后续又进行全国各个区域试验,证明这个基因能够提高氮利用率,可以减少氮肥的施用,也能改善土壤中过量的氮素对环境的污染。很漂亮的正向遗传研究,从基因定位,得到转基因,转基因验证,大田产量验证,每一步逻辑都很严谨且证明的过程流畅。
Abstract:
The intensive application of inorganic nitrogen underlies marked increases in crop production, but imposes detrimental effects on ecosystems: it is therefore crucial for future sustainable agriculture to improve the nitrogen-use …
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The intensive application of inorganic nitrogen underlies marked increases in crop production, but imposes detrimental effects on ecosystems: it is therefore crucial for future sustainable agriculture to improve the nitrogen-use efficiency of crop plants. Here we report the genetic basis of nitrogen-use efficiency associated with adaptation to local soils in rice (Oryza sativa L.). Using a panel of diverse rice germplasm collected from different ecogeographical regions, we performed a genome-wide association study on the tillering response to nitrogen-the trait that is most closely correlated with nitrogen-use efficiency in rice-and identified OsTCP19 as a modulator of this tillering response through its transcriptional response to nitrogen and its targeting to the tiller-promoting gene DWARF AND LOW-TILLERING (DLT). A 29-bp insertion and/or deletion in the OsTCP19 promoter confers a differential transcriptional response and variation in the tillering response to nitrogen among rice varieties. The allele of OsTCP19 associated with a high tillering response to nitrogen is prevalent in wild rice populations, but has largely been lost in modern cultivars: this loss correlates with increased local soil nitrogen content, which suggests that it might have contributed to geographical adaptation in rice. Introgression of the allele associated with a high tillering response into modern rice cultivars boosts grain yield and nitrogen-use efficiency under low or moderate levels of nitrogen, which demonstrates substantial potential for rice breeding and the amelioration of negative environment effects by reducing the application of nitrogen to crops.
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