Soil biodiversity and DNA barcodes: opportunities and challenges

Soils encompass a huge diversity of organisms which mostly remains to be characterized due to a number of methodological and logistical issues. Nonetheless, remarkable progress has been made in recent years toward developing strategies to characterize and describe soil biodiversity, especially thanks to the development of molecular approaches relying on direct DNA extraction from the soil matrix.Metabarcoding can be applied to DNA from any environment or organism, and is gaining increasing prominence in biodiversity studies. This approach is already commonly used to characterize soil microbial communities and its application is now being extended to other soil organisms, i.e. meso- and macro-fauna.These developments offer unprecedented scientific and operational opportunities in order to better understand soil biodiversity distribution and dynamics, and to propose tools and strategies for biodiversity diagnosis. However, these opportunities also come with challenges that the scientific community must face. Such challenges are related to i) clarification of terminology, (ii) standardisation of methods and further methodological development for additional taxonomic groups, (iii) development of a common database, and (iv) ways to avoid waste of information and data derived from metabarcoding. In order to facilitate common application of metabarcoding in soil biodiversity assessment, we discuss these opportunities and challenges and propose solutions towards a more homogeneous framework.     

植物生长调节剂对忍冬科植物生根的影响

【目的】为提高忍冬科(Lonicera)植物在兰州地区的扦插成活率,缩短其生根时间和育苗周期.【方法】以3种忍冬科植物为材料,研究不同质量浓度(50、100 mg/L)下3种植物生长调节剂吲哚乙酸(IAA)、吲哚丁酸(IBA)和萘乙酸(NAA)在不同处理时间(30、60min)对其扦插生根的影响.【结果】IAA和IBA对天目琼花生根率的影响最大,对金叶接骨木生根数量的促进作用最大,对天目琼花和蓝叶忍冬根的伸长具有抑制作用.NAA对金叶接骨木、天目琼花、蓝叶忍冬的生根率的促进作用不显著(P0.05),对金叶接骨木和蓝叶忍冬根伸长的促进作用不显著(P0.05),但对天目琼花根的伸长具有显著的促进作用(P0.05).在进行苗木扦插繁殖时,为获得较理想的扦插效果,要根据所采集母条的生长特性在特定的时间采集半木质化的嫩枝,同时选用适当的植物生长调节剂和质量浓度,以提高扦插的成活率.【结论】3种植物生长调节剂对3种忍冬科植物的生根率、生根数量及根长的影响存在差异.     

m6A甲基化在鸡肌肉生长发育中的表达研究

试验旨在研究RNA m6A修饰相关基因去甲基化酶Alk B同源蛋白5（Alk B homologue 5，ALKBH5）、去甲基化酶肥胖相关蛋白（fat mass and obesity-associated protein，FTO）、甲基转移酶样蛋白3（methyltransferase like 3，METTL3）、甲基转移酶样蛋白14（methyltransferase like 14，METTL14）和成肾细胞瘤1-结合蛋白（Wilms’tumor 1-associating protein，WTAP）在鸡骨骼肌发育过程中的表达，分析其与骨骼肌m6A甲基化水平的相关性。首先，利用实时荧光定量PCR技术检测m6A甲基化相关基因在金茅花鸡12（E12）、14（E14）、16（E16）、18（E18）胚龄和1日龄腿肌和胸肌组织中mRNA表达水平，以及其在鸡成肌细胞50%、100%增殖期和1、2、3、4、5 d分化期的mRNA表达水平；随后，利用m6A甲基化试剂盒检测金茅花鸡E12和1日龄腿肌和胸肌组织中m6A甲基化修饰水平，与m6A甲基化相关基因表达水平进行相关性分析。结果显示，m6A去甲基化基因ALKBH5和FTO mRNA表达水平在骨骼肌发育过程中显著上调（P<0.05），即在E12、E14低表达，E16、E18逐渐上调，1日龄达到最高。m6A甲基化写入基因METTL14、METTL3和WTAP mRNA表达水平在E12、E14、E16逐渐上升，E18下降，随后至1日龄表达量回升。在细胞增殖过程中，ALKBH5、FTO、METTL14、METTL3和WTAP基因表达均上调；在细胞分化过程中ALKBH5和FTO基因表达水平显著上调（P<0.05），在分化第5天达到最高。METTL14、METTL3和WTAP基因mRNA表达水平在细胞诱导分化的1、2、3、4 d表达量呈下降趋势，而在诱导分化的第5天有所回升。甲基化水平检测结果显示，腿肌和胸肌m6A甲基化水平变化趋势一致，均在胚胎发育过程中显著下降（P<0.05），至1日龄达到最低。相关性分析结果显示，鸡骨骼肌RNA m6A甲基化水平与m6A去甲基化修饰基因ALKBH5、FTO mRNA表达水平呈显著负相关（P<0.05）。综合以上试验结果，推测m6A甲基化修饰与鸡骨骼肌发育相关，而去甲基化基因ALKBH5、FTO可能通过调控RNA m6A甲基化水平，影响鸡骨骼肌发育。本研究结果为进一步研究m6A甲基化修饰调控鸡骨骼肌生长发育的功能和分子机制提供理论依据。     

大豆植株分杈数自动提取算法研究

根据大豆植株分杈个数可以预估大豆的产量。为了满足现代农业预测农产品产量的需要,本文提出一种大豆植株分杈数自动提取算法,即首先将采集到的大豆植株图片进行灰度变换、滤波、阈值分割得到二值图像,再进行形态学中的闭运算操作得到大豆植株的轮廓,然后基于Zhang并行快速细化算法提取骨架,最后借助改进的角点检测算法对大豆植株的所有分杈点进行标记并自动统计分杈数,仿真结果与大豆植株实际分杈点一致。     

极小种群野生植物八蕊单室茱萸的种群状况研究

八蕊单室茱萸为云南省特有的极小种群野生植物和濒危物种。通过查阅相关文献并结合访问调查,确定八蕊单室茱萸可能分布的区域,开展种群资源调查。结果显示:八蕊单室茱萸目前仅在普洱市和西双版纳州有10个天然种群,其种群规模已低于最小可存活种群,属极小种群野生植物和濒危物种,亟需开展保护工作。生境破坏和生境片段化是导致八蕊单室茱单室茱萸濒危的人为因素。提出收集种质资源、营建和管护近地保护种群、建立迁地和回归种群等保育建议。     

The priority of management factors for reducing the yield gap of summer maize in the north of Huang-Huai-Hai region,China

Understanding yield potential, yield gap and the priority of management factors for reducing the yield gap in current intensive maize production is essential for meeting future food demand with the limited resources. In this study, we conducted field experiments using different planting modes, which were basic productivity(CK), farmer practice(FP), high yield and high efficiency(HH), and super high yield(SH), to estimate the yield gap. Different factorial experiments(fertilizer, planting density, hybrids, and irrigation) were also conducted to evaluate the priority of individual management factors for reducing the yield gap between the different planting modes. We found significant differences between the maize yields of different planting modes. The treatments of CK, FP, HH, and SH achieved 54.26, 58.76, 65.77, and 71.99% of the yield potential, respectively. The yield gaps between three pairs: CK and FP, FP and HH, and HH and SH, were 0.76, 1.23 and 0.85 t ha~(–1), respectively. By further analyzing the priority of management factors for reducing the yield gap between FP and HH, as well as HH and SH, we found that the priorities of the management factors(contribution rates) were plant density(13.29%)fertilizer(11.95%)hybrids(8.19%)irrigation(4%) for FP to HH, and hybrids(8.94%)plant density(4.84%)fertilizer(1.91%) for HH to SH. Therefore, increasing the planting density of FP was the key factor for decreasing the yield gap between FP and HH, while choosing hybrids with density and lodging tolerance was the key factor for decreasing the yield gap between HH and SH.     

草果AtNCED基因克隆、表达和植物表达载体构建

9-顺式环氧类胡萝卜素双加氧酶(9-cis-epoxycarotenoid dioxygenase, NCED)是ABA生物合成的限速酶。诸多研究表明NCED基因表达量的变化与ABA含量显著相关,在种子休眠过程中发挥重要作用。为探究草果AtNCED基因的序列特征和功能,本研究以草果(Amomum tsaoko Crevost et Lemarie)种子转录组为基础,采用RT-PCR技术克隆了一个AtNCED基因。该基因全长2 372 bp,包含一个1 830 bp的开放阅读框(open reading frame, ORF),编码610个氨基酸。生物信息学分析显示,AtNCED基因编码的蛋白在N-末端包含典型的叶绿体转运肽序列,在催化结构域含有4个高度保守的组氨酸残基。AtNCED蛋白与芭蕉科马来西亚蕉同源性较高,与其他单子叶植物处在同一进化分支。实时荧光定量PCR分析结果表明,AtNCED基因表达量随着层积时间的增加逐渐下降,该基因可能正向调控种子休眠,在草果种子休眠诱导与维持中发挥重要作用。进一步地,利用同源重组方法,成功构建了pBI121-AtNCED过表达载体,并转化至农杆菌EHA105。该研究结果为弄清ABA激素信号在种子休眠中的调控作用提供了帮助。     

Characterization of Genomic Integration and Transgene Organization in Six Transgenic Rapeseed Events

To characterize the DNA rearrangement of both the T-DNA region and the genomic insertion site during T-DNA insertion, the Genomewalker strategy was used to isolate the junctions between the inserted DNA and the plant genomic DNA in six rapeseed events as well as the genomic DNA at the sites before integration. During transformation in each of the six events, portions of both the right border（RB） and left border（LB） regions of the T-DNA were deleted, ranging from a 7 nucleotide deletion of the LB repeats in event RF1 to a 207 bp deletion of the LB region in event RF2. For the six events, T-DNA integration resulted in a deletion at the target site spanning less than 100 bp. Sequence analysis indicated that the T-DNA was integrated into the coding region of various native rapeseed genes in events RF1 and RF2. Duplications of the genomic DNA target site were observed in events RF2, RF3 and Topas 19/2. And multimerization of transgenes was found in event Topas 19/2, in which, the T-DNA was integrated as a head-to-head（RB-to-RB） concatemer into the recipient genome. In event MS1, chromosomal translocation or a large target-site deletion may have occurred during T-DNA integration, which was identified due to a failure to amplify the presumptive insertion site based on the flanking rapeseed DNA sequences. Our results provide comprehensive data concerning transgene organization and the genomic context of the T-DNA in six rapeseed events, which can aid in the developing of insert fingerprinting and the monitoring of long-term genetic stability and potential unintended effects of transgenic events.     

Controlling sprouting in potato tubers using ultraviolet-C irradiance

Legislation limiting the use of chlorpropham (CIPC), the major potato sprout suppressant, has led to a need for new technologies to extend storage life of tubers. Ultra violet C (UV-C) has been used postharvest to reduce disease incidence on many crops, yet its use and efficacy as a sprout suppressant has not been investigated. The aim of this project was to identify the optimum dose and treatment timing of UV-C treatment on potato tubers as an alternative method of sprout suppression to reduce the dependence on chemical sprout suppressants. Up to six potato cultivars over two seasons were treated with varying doses of UV-C ranging from 0 to 30 kJ m⁻² either at harvest or at first indication of dormancy break. The tubers were stored at 9 °C and sprout growth and incidence assessed. Treatment with moderate UV-C doses (5–20 kJ m⁻²) suppressed sprout length and sprout incidence in a range of cultivars. Periderm DNA damage and programmed cell death were not detected in response to any of the UV-C doses. The inactive ABA metabolite, ABA-GE, increased in response to 10 or 20 kJ m⁻² within 72 h of treatment. Multivariate analysis showed a negative relationship between ABA metabolites and sprout growth/incidence during storage. This study found that UV-C reduced sprout growth in potato with no deleterious effects on tuber quality. This suggests potential for further development as an alternative or supplement to conventional sprout suppressant technologies.