Genome-Wide Investigation and Expression Analyses of WD40 Protein Family in the Model Plant Foxtail Millet (Setaria italica L.)

WD40 proteins play a crucial role in diverse protein-protein interactions by acting as scaffolding molecules and thus assisting in the proper activity of proteins. Hence, systematic characterization and expression profiling of these WD40 genes in foxtail millet would enable us to understand the networks of WD40 proteins and their biological processes and gene functions. In the present study, a genome-wide survey was conducted and 225 potential WD40 genes were identified. Phylogenetic analysis categorized the WD40 proteins into 5 distinct sub-families (I–V). Gene Ontology annotation revealed the biological roles of the WD40 proteins along with its cellular components and molecular functions. In silico comparative mapping with sorghum, maize and rice demonstrated the orthologous relationships and chromosomal rearrangements including duplication, inversion and deletion of WD40 genes. Estimation of synonymous and non-synonymous substitution rates revealed its evolutionary significance in terms of gene-duplication and divergence. Expression profiling against abiotic stresses provided novel insights into specific and/or overlapping expression patterns of SiWD40 genes. Homology modeling enabled three-dimensional structure prediction was performed to understand the molecular functions of WD40 proteins. Although, recent findings had shown the importance of WD40 domains in acting as hubs for cellular networks during many biological processes, it has invited a lesser research attention unlike other common domains. Being a most promiscuous interactors, WD40 domains are versatile in mediating critical cellular functions and hence this genome-wide study especially in the model crop foxtail millet would serve as a blue-print for functional characterization of WD40s in millets and bioenergy grass species. In addition, the present analyses would also assist the research community in choosing the candidate WD40s for comprehensive studies towards crop improvement of millets and biofuel grasses.     

Characteristics and Expression Patterns of the Aldehyde Dehydrogenase (ALDH) Gene Superfamily of Foxtail Millet (Setaria italica L.)

Recent genomic sequencing of the foxtail millet, an abiotic, stress-tolerant crop, has provided a great opportunity for novel gene discovery and functional analysis of this popularly-grown grass. However, few stress-mediated gene families have been studied. Aldehyde dehydrogenases (ALDHs) comprise a gene superfamily encoding NAD (P) ⁺-dependent enzymes that play the role of “aldehyde scavengers”, which indirectly detoxify cellular ROS and reduce the effect of lipid peroxidation meditated cellular toxicity under various environmental stresses. In the current paper, we identified a total of 20 ALDH genes in the foxtail millet genome using a homology search and a phylogenetic analysis and grouped them into ten distinct families based on their amino acid sequence identity. Furthermore, evolutionary analysis of foxtail millet reveals that both tandem and segmental duplication contributed significantly to the expansion of its ALDH genes. The exon-intron structures of members of the same family in foxtail millet or the orthologous genes in rice display highly diverse distributions of their exonic and intronic regions. Also, synteny analysis shows that the majority of foxtail millet and rice ALDH gene homologs exist in the syntenic blocks between the two, implying that these ALDH genes arose before the divergence of cereals. Semi-quantitative and real-time quantitative PCR data reveals that a few SiALDH genes are expressed in an organ-specific manner and that the expression of a number of foxtail millet ALDH genes, such as, SiALDH7B1, SiALDH12A1 and SiALDH18B2 are up-regulated by osmotic stress, cold, H₂O₂, and phytohormone abscisic acid (ABA). Furthermore, the transformation of SiALDH2B2, SiALDH10A2, SiALDH5F1, SiALDH22A1, and SiALDH3E2 into Escherichia coli (E.coli) was able to improve their salt tolerance. Taken together, our results show that genome-wide identification characteristics and expression analyses provide unique opportunities for assessing the functional roles of foxtail millet ALDH genes in stress responses.     

Grain Yield and Quality of Foxtail Millet (Setaria italica L.) in Response to Tribenuron-Methyl

Foxtail millet (Setaria italica L.) is cultivated around the world for human and animal consumption. There is no suitable herbicide available for weed control in foxtail millet fields during the post-emergence stage. In this study, we investigated the effect and safety of the post-emergence herbicide tribenuron-methyl (TBM) on foxtail millet in terms of grain yield and quality using a split-plot field design. Field experiments were conducted using two varieties in 2013 and 2014, i.e., high-yielding hybrid Zhangzagu 10 and high-quality conventional Jingu 21. TBM treatments at 11.25 to 90 g ai ha⁻¹ reduced root and shoot biomass and grain yield to varying degrees. In each of the two years, grain yield declined by 50.2% in Zhangzagu 10 with a herbicide dosage of 45 g ai ha⁻¹ and by 45.2% in Jingu 21 with a herbicide dosage of 22.5 g ai ha⁻¹ (recommended dosage). Yield reduction was due to lower grains per panicle, 1000-grain weight, panicle length, and panicle diameter. Grain yield was positively correlated with grains per panicle and 1000-grain weight, but not with panicles ha⁻¹. With respect to grain protein content at 22.5 g ai ha⁻¹, Zhangzagu 10 was similar to the control, whereas Jingu 21 was markedly lower. An increase in TBM dosage led to a decrease in grain Mn, Cu, Fe, and Zn concentrations. In conclusion, the recommended dosage of TBM was relatively safe for Zhangzagu 10, but not for Jingu 21. Additionally, the hybrid variety Zhangzagu 10 had a greater tolerance to TBM than the conventional variety Jingu 21.     

谷子籽粒蛋白质、脂肪、千粒重的遗传变异

以来自华北夏谷区、东北春谷区、西北高原早熟春谷区、西北高原中晚熟春谷区等4个主要谷子生态区的270个品种为材料,包括育成品种220份和地方品种50份,测定了籽粒千粒重、蛋白质和脂肪含量。结果表明:270份谷子品种平均蛋白质含量(11.18±1.14)%,脂肪含量(4.00±0.42)%,千粒重(2.87±0.28)g。育成品种的蛋白质含量显著低于地方品种蛋白质含量,而育成品种和地方品种的脂肪含量、千粒重差异不显著;不同生态区品种之间蛋白质含量、千粒重差异显著,但脂肪含量差异不显著。西北早熟春谷区品种蛋白质含量平均最高、千粒重最大,华北夏谷区品种蛋白质含量平均最低、千粒重最小;蛋白质含量和千粒重显著正相关,蛋白质含量、千粒重和生育期显著负相关。本研究报道了近30年来我国谷子主产区谷子品种的蛋白质、脂肪含量和千粒重的差异,对于谷子品质育种具有借鉴意义;研究认为谷子籽粒的蛋白质、脂肪含量和千粒重应作为品质育种的重要指标加以重视。     

影响谷子原生质体看护培养的一些因素

研究了谷子原生质体看护培养中的一些问题。结果表明：不同种植物愈伤组织做看护细胞对谷子原生质体培养植板率有不同的影响。用光头种草愈伤组织对谷子胚性、非胚性或中间型意伤组织的原生质体进行看护培养,以对胚性意伤组织原生质体的效果最好。看护培养主要是作用于原生质体形成完整细胞后的生长发育。试验没有观察到明显的看护细胞数量效应。     

谷子（Setaria italica）分子遗传研究进展

近年来不断发展和完善的生物技术为谷子的研究开辟了新的思路,且提供了新的手段。本文概述了谷子在分子标记、遗传图谱的构建、基因定位、功能蛋白基因的克隆、转基因技术等方面的研究进展,提出了谷子分子遗传研究中存在的问题,并对今后的发展趋势作了初步探讨。     

根癌农杆菌介导转化谷子的影响因素

利用GUS报告基因,建立了农杆菌介导的谷子(Setaria italica)遗传转化体系,并研究了多种影响因素对转化效率的影响,包括受体基因型、外植体类型、菌液浓度、培养基中乙酰丁香酮的浓度、侵染时间和共培养时间.确定了最优的转化条件为:以谷子幼穗诱导的愈伤组织为外植体,用低浓度的农杆菌菌液侵染30～40min,然后在含有0.1mmol/L乙酰丁香酮的LS培养基上共培养2d.     

Establishment of Trisomic Series of Millet (Setaria italica L. Beauv.)

The young-ears of “Yugu No. 1”, a millet (Setaria italica (L.) Beauv. ) variety of good quality, high yielding and stress-resistance, were chosen to induce callus on N6 medium. After 3—5 times of subcultures, the callus was treated with colchicine (0.02%) for 48 hours and then transferred hack to subculture medium to restore growth, after which the callus was transferred to differentiation medium and subsequently, tetraploid plants were obtained. Through crossing, using tetraploid plants as female parent and diploid plant as male parent, 5 triploid plants were found among 2100 offspring plants. The triploid plants were fertilized with pollens from diploid plants. Among the plants developed from the seeds harvested on triploid plants, 9 kinds of trisomics (totally 283 plants) were identified according to chromosomal number and morphologic feature. Each kind of the trisomics has specific marker feature: (Figures in parentheses represent the number of plants obtained) Triplo-1 (52) has rolling leaves, Triplo-2 (18) is dark green, Triplo-3 (43) is bushy and has degenerated spikelets at the tip of panicles: Triplo-4 (58) has long bristle: Triplo-5 (16) has slender stalks: Triplo-6 (36) has twisted panicle neck; Triplo-7 (44) is semi-erect; Triplo-8 (8) has thick panicles; Triplo-9 (8) is pseudonormal (Similar with diploid of “Yugu No. 1”).     

谷子胚性细胞系的超低温冰冻保存

超低温冰冻保存是保存生物材料的一种方法。目前禾本科植物原生质体培养的主要问题之一是胚性细胞系的状态不稳定。试验比较了影响谷子(Setaria italica(L.)Beauv)胚性细胞系超低温冰冻保存的因素如：不同的冰冻保护液组成,不同培养时间的胚性细胞系以及细胞系的恢复生长和原生质体培养。结果表明：本实验采用超低温冰冻保存方法不会影响胚性细胞系原生质体的培养特性,能够保持或提高原生质体培养的植板率。     

Phytoliths Analysis for the Discrimination of Foxtail Millet (Setaria italica) and Common Millet (Panicum miliaceum)

Foxtail millet (Setaria italica) and Common millet (Panicum miliaceum) are the oldest domesticated dry farming crops in Eurasia. Identifying these two millets in the archaeobotanical remains are still problematic, especially because the millet grains preserve only when charred. Phytoliths analysis provides a viable method for identifying this important crop. However, to date, the identification of millet phytoliths has been questionable, because very little study has been done on their morphometry and taxonomy. Particularly, no clear diagnostic feature has been used to distinguish between Foxtail millet and Common millet. Here we examined the anatomy and silicon structure patterns in the glumes, lemmas, and paleas from the inflorescence bracts in 27 modern plants of Foxtail millet, Common millet, and closely related grasses, using light microscopy with phase-contrast and microscopic interferometer. Our research shows that five key diagnostic characteristics in phytolith morphology can be used to distinguish Foxtail millet from Common millet based on the presence of cross-shaped type, regularly arranged papillae, Ω-undulated type, endings structures of epidermal long cell, and surface ridgy line sculpture in the former species. We have established identification criteria that, when used together, give the only reliable way of distinguishing between Foxtail millet and Common millet species based on their phytoliths characteristics, thus making a methodological contribution to phytolith research. Our findings also have important implications in the fields of plant taxonomy, agricultural archaeology, and the culture history of ancient civilizations.     

Silica Distribution in the Caryopsis and Inflorescence Bracts of Foxtail Millet [Setaria italica (L.) Beauv.] and its Possible Significance in Carcinogenesis

Silicon deposits in the caryopsis and inflorescence bracts offoxtail millet [Setaria italica (L.) Beauv.] were investigatedusing light microscopy, scanning electron microscopy and electronprobe microanalysis. The samples were obtained from Lin Xian,Henan province, northern China and CSIRO, Australia. High concentrations of silicon were observed in the papillaeon the external surfaces of the inflorescence bracts, and inthe epidermal cells. In the caryopsis silicon was depositedin the aleurone layer. Silicification was heavier in the LinXian samples. The heavy accumulation of silica in the foxtail millet and thepossibility that fragments of plant silica may be implicatedin the aetiology of oesophageal cancer in the Lin Xian regionare discussed. Setaria italica (L.), Beauv, foxtail millet, caryopsis, silica distribution, scanning electron microscopy     

Nucleotide Sequence Diversity and Linkage Disequilibrium of Four Nuclear Loci in Foxtail Millet (Setaria italica)

Foxtail millet (Setaria italica (L.) Beauv) is one of the earliest domesticated grains, which has been cultivated in northern China by 8,700 years before present (YBP) and across Eurasia by 4,000 YBP. Owing to a small genome and diploid nature, foxtail millet is a tractable model crop for studying functional genomics of millets and bioenergy grasses. In this study, we examined nucleotide sequence diversity, geographic structure, and levels of linkage disequilibrium at four nuclear loci (ADH1, G3PDH, IGS1 and TPI1) in representative samples of 311 landrace accessions across its cultivated range. Higher levels of nucleotide sequence and haplotype diversity were observed in samples from China relative to other sampled regions. Genetic assignment analysis classified the accessions into seven clusters based on nucleotide sequence polymorphisms. Intralocus LD decayed rapidly to half the initial value within ~1.2 kb or less.     

新疆野苹果AP2/ERF转录因子家族鉴定与响应腐烂病的表达分析北大核心CSCD

AP2/ERF转录因子家族参与了植物生长发育、抵抗胁迫以及植物激素响应等诸多生物过程,是植物中最重要的转录因子家族之一。该研究基于腐烂病菌侵染后的新疆野苹果(Malus sieversii)全长转录组,使用AP2保守结构域的隐马可夫模型PF00847,鉴定新疆野苹果的AP2/ERF家族成员。利用MEGA6、NCBI CDD-batch、MEME、EXPASY、BUSCA对MsAP2/ERF家族成员进行鉴定、分类和结构分析、理化性质和亚细胞定位分析。通过RNA-seq数据和qRT-PCR实验对差异表达的MsAP2/ERFs基因的表达水平进行分析和验证,旨在鉴定新疆野苹果中潜在具有腐烂病抗性的AP2/ERF家族基因资源。结果显示:(1)在新疆野苹果中共鉴定获得106个AP2/ERF基因,涵盖全部AP2(17个)、ERF(57个)、DREB(25个)、RAV(5个)和Soloist(2个)5个亚家族。(2)进一步的细化分类发现MsERF亚家族包括B1-B6 6个组,而MsDREB亚家族中只有A2、A4、A5、A6共4个组,缺少A1和A3组的基因成员。(3)RNA-seq表达模式分析结果表明,29个MsAP2/ERF基因在腐烂病感染过程中差异表达,其中MsERF亚家族中差异表达基因数量最多(19个)。(4)12个MsAP2/ERF代表基因的qRT-PCR结果表明:8个ERF亚家族基因均受腐烂病病菌诱导显著上调表达,其中B4类ERF成员基因(MsERF40)在腐烂病病菌侵染后5 d表达量上调表达倍数最高;4个MsDREB基因中,3个受到腐烂病病原菌诱导显著上调,1个下调表达;此外,含有TIR保守结构域的MsERF05在腐烂病病菌侵染1 d后上调表达69倍,表明ERF亚家族的MsERF40和MsERF05在新疆野苹果抗腐烂病过程中发挥重要作用。该研究结果为新疆野苹果AP2/ERF基因响应腐烂病的功能和机理研究奠定了基础。