甘薯近缘种Ipomoea cordatotriloba基因组大小测定及高通量调查测序

利用流式细胞术,以大豆Williams 82为内参,对甘薯近缘野生种Ipomoea cordatotriloba进行基因组大小测定,结合染色体压片技术进行倍性鉴定,并利用二代高通量测序技术对测定结果进行验证。结果表明:利用流式细胞术测得I. cordatotriloba基因组大小为(539.69±13.76)Mb;染色体压片结果显示其染色体数目为30条,由于其基数x=15,从而获知I. cordatotriloba为二倍体;经K-mer计算并修正后得出的C值为560.70 Mb,与流式细胞分析结果相近;同时,测序结果显示其基因组杂合率为0.40%;重复序列比率为57.93%;GC含量为38.10%。以上结果为此物种全基因组精细图谱绘制打下基础,同时为甘薯近缘野生种的利用提供参考。     

基于SLAF-seq技术的甘薯种质资源群体遗传进化分析

基于简化基因组测序技术对122份甘薯种质资源进行分析,开发SNP位点并将其应用于种质资源群体结构和遗传进化分析。结果表明, 从122份甘薯种质资源中共获得563.18 Mb读长,不同材料的读长数量在1 419 809~8 392 785范围之间。测序质量值Q30在90.61%~96.82%之间,平均Q30为92.78%。测序获得的GC含量在36.46%~40.33%之间,平均GC含量为38.17%,对照GC含量为40.72%。根据测序结果共开发出高质量的SLAF标签2 388 759个,平均测序深度为17.45×。其中,多态性的SLAF标签77 761个,占SLAF标签总数的3.26%。根据所获得多态性SLAF标签统计SNP位点信息,共计获得129 063个群体SNP位点。遗传进化分析表明122份种质资源可以分为3个大类,分类结果与它们的地理来源无直接关系,聚类结果可为甘薯育种亲本组配和杂种优势利用提供科学依据。     

生防菌株Bacillus velezensis Z全基因组测序分析

生防菌株Bacillus velezensis Z对胡椒瘟病等多种植物病害具有良好的生防效果;全基因组测序能够为其分子机理研究和开发应用提供信息基础。本研究开展该菌株全基因组测序,并进行比较基因组学和抑菌次生代谢产物合成基因簇预测研究。结果表明：B. velezensis Z菌株的基因组中含有1条4 054 780 bp大小的环形染色体DNA和1个17 122 bp大小的环形质粒,总基因组的GC含量为46.24%,共编码基因4173个;包含27个rRNA,86个tRNA基因,34个sRNA;含有串联重复序列179个,其中13个微卫星DNA,138个小卫星DNA;通过比较基因组学分析,结果发现该菌株与贝莱斯芽孢杆菌模式菌株FZB42同源性极高,与枯草芽孢杆菌模式菌株168之间具有一定的遗传距离;同时发现B. velezensis Z基因组中共编码次生代谢产物合成基因簇13个,其中8个与表面活性素（surfactin）、泛革素（fengycin）、溶杆菌素（bacilysin）、macrolactin H、bacillaene、difficidin、plantazolicin、amylocyclicin等已知基因簇完全相似或高度相似,其他5个基因簇皆功能未知。总之,本研究揭示了B. velezensis Z的全基因组遗传信息,明确其与贝莱斯芽孢杆菌和枯草芽孢杆菌的比较基因组学关系,预测了抑菌产物合成编码基因簇,为该生防菌株及其抑菌产物的机理研究和开发应用奠定基础。     

扁核木属植物叶绿体基因组特征分析

扁核木属（Prinsepia）植物在中国分布有4个种,均具有极高的食用和药用价值。为解析扁核木属植物的叶绿体基因组特征,基于现已发表的扁核木属植物叶绿体基因组,利用相关生物信息学手段进行其叶绿体基因结构、SSR、密码子偏好性和序列变异情况分析,并构建系统发育树。结果表明,2种扁核木属植物叶绿体基因组大小介于159 179~ 168 206 bp之间,平均GC含量为37.3%,从编码基因数目来看,仅相差2个tRNA,而蛋白编码基因和rRNA数目均一致,种间具有较高的保守性;在扁核木和蕤核叶绿体全基因组序列中各检测出分散重复49个,其中以正向重复和回文重复为主,占比达73%~82%,而串联重复数目分别为49个和58个,经简单重复序列SSR分析,分别在2种植物叶绿体基因组序列中分别筛选出100个和84个SSR位点,且多是以A/T碱基为主的单核苷酸重复类型;扁核木属植物叶绿体基因组密码子偏好性分析发现GC3的碱基含量显著低于GC1和GC2,说明密码子偏好以A、U结尾,ENC取值均大于48%,表明其密码子偏性较弱,中性绘图和PR2-plot分析发现自然选择是影响扁核木属植物密码子使用偏好性的主要原因,通过建立高、低基因表达库,以RSCU值为参考,确定了6个扁核木属最优密码子。经叶绿体基因组序列变异分析,根据核苷酸多态性指数Pi>0.015筛选出trnH-GUG-psbA,psbZ-trnG-UCC-trnfM-CAU-rps14和psaJ-rpl33-rps18等3个高变区,以蕤核叶绿体基因组为参考,在扁核木叶绿体基因组编码区发现存在大量的插入、缺失和SNP突变位点,并在蕤核叶绿体基因组中发现了多个该物种的特有基因。基于叶绿体基因组的trnS-trnG间隔区构建的系统发育树显示,4种扁核木属植物可分为南系（扁核木、台湾扁核木）和北系（蕤核、东北扁核木）两类。研究结果可为扁核木属植物的系统发育、分类鉴定及其资源的开发利用等相关研究提供理论基础。     

“热带植物基因组学与基因编辑”专题序言

<正>动植物全基因组测序在过去20年快速发展。1990年人类基因组计划开启了基因组DNA测序的大门,2000年基本完成人类基因组草图绘制,标志着大规模DNA测序成为一种切实可行的研究手段。植物基因组通常是多倍体,基因组大,杂合度高,具有高度重复序列和全部(或部分)的基因组重复     

甘蓝型油菜抗草甘膦基因遗传转化及抗性鉴定

为自主研发抗除草剂的甘蓝型油菜,从细菌（Isotericola variabilis）中克隆I.variabilis-EPSPS*基因,使油菜产生草甘膦抗性。通过农杆菌介导法将I.variabilis-EPSPS*转入甘蓝型油菜自交系育127,获得转I.variabilis-EPSPS*基因单株E₁。草甘膦耐受性结果表明,转I.variabilis-EPSPS*基因T₁代在不同浓度草甘膦的培养基中能够正常生长,而非转基因对照生长严重受阻。I.variabilis-EPSPS*成功整合于油菜基因组并可稳定遗传,草甘膦处理后表达量增加,而且在草甘膦浓度改变时仍保持稳定表达。在温室用41%草甘膦异丙胺盐商品制剂（农达）600倍稀释液（1/3田间生产推荐中剂量）处理转I.variabilis-EPSPS*基因E₁的T₁植株,体内莽草酸累计量远低于非转基因对照。通过对角果长、每角果粒数和千粒重等农艺性状考察发现,转基因植株和对照相比无显著性差异。田间喷施农达400倍液（1/2田间生产推荐中剂量）,发现转基因E₁T₁植株正常生长而对照全部死亡。鉴于I.variabilis-EPSPS*基因在转基因油菜中能够稳定遗传并赋予了油菜草甘膦除草剂抗性,认为该抗草甘膦转基因油菜是一份新种质。     

黑喉石斛叶绿体基因组特征及比较分析

本研究结合Illumina高通量测序和Nanopore测序技术,对黑喉石斛（Dendrobium ochreatum）的叶绿体基因组（cpDNA）进行测序,组装得到其cpDNA全长序列并绘制结构图谱。黑喉石斛cpDNA全长154 935 bp,注释共得到125个基因,其中有unigenes 103种,包含73种蛋白编码基因,26种tRNA基因和4种rRNA基因。特征分析结果表明：黑喉石斛cpDNA中共存在58个SSR （simple sequence repeat）位点,大部分为单核苷酸重复和二核苷酸重复类型,碱基组成以A/T碱基类型为主;其偏好的密码子共32个,其中有30个以A/U碱基结尾。以黑喉石斛与其他13种石斛的cpDNA构建系统发育进化树,结果显示,鼓槌石斛（D. chrysotoxum）和梳唇石斛（D. strongylanthum）与黑喉石斛具有较近的亲缘关系,IR/SC边界分析结果也映证了此结论。以黑喉石斛为参照,与3种近缘石斛的cpDNA进行全序列长对比,结果显示,4种石斛的序列变异主要发生在单拷贝区,基因间隔区的变异明显高于基因编码区。     

三七基因组SSR位点分析和多态性引物开发

本研究通过分析三七(Panax notoginseng)基因组中简单重复序列(simple sequence repeats,SSRs)位点信息,对基因组中SSR位点的分布特征进行描述,并开发多态性引物,为评价三七遗传多样性和群体结构提供理论依据。利用MISA软件对重新组装的三七基因组进行SSR位点搜索,primer3设计引物。用随机合成的200对引物,在16个三七单株中进行PCR扩增,来筛选具有多态性的引物。在去除冗余序列后组装得到2.39 Gb大小的三七基因组中总共识别到314 060个SSR位点,SSR分布频率为0.13/kb,其中占主导地位的是二核苷酸重复基序,占所有重复基序类型的68.55%,其次是三核苷酸56 250(17.91%)和单核苷酸22 475(7.16%)。在二核苷酸为主的重复类型中,出现频率最高的是AT/AT重复基序占所有二核苷酸重复的63.66%,最低的是CG/CG重复基序占0.15%。同时,在单核苷酸重复中出现频率最高的也是A/T重复类型(79.01%)。经过多态性筛选最终得到41对多态性较好的引物,PIC值范围为0.11~0.78,平均值为0.46。本研究获得的大量SSR位点信息为三七全基因组SSR标记的开发,三七分子标记辅助育种以及遗传多样性分析提供方便。     

黄桃叶绿体基因组的组装与序列分析

以‘锦绣'黄桃为试材,利用Illumina NovaSeq 6000测定‘锦绣'黄桃的DNA序列,用SPAdes v3.10.1组装叶绿体基因组,以桃树叶绿体基因组为参考,对其进行叶绿体基因组特征和进化树分析,为进一步开展‘锦绣'黄桃遗传与鉴定学研究奠定良好基础。结果表明：‘锦绣'黄桃叶绿体基因组全长为157 786 bp,具有典型的四分体环状结构,GC含量为36.77%,AT含量为63.23%,包括1个大单拷贝区（LSC）、1对反向重复区（IR）和1个小单拷贝区（SSC）,序列长度分别为85 924、26 381、19 100 bp,LSC、IR和SSC区域中的GC含量分别为34.61%、42.58%、30.41%。‘锦绣'黄桃的叶绿体基因组共注释得到130个基因,包括85个蛋白编码基因、37个tRNA基因和8个rRNA基因;按照功能分类将其分为光合作用相关基因、自我复制相关基因、其他基因和未知功能基因4大类,在这些基因中包括18个双拷贝基因,分别是1个NADH脱氢酶亚基基因（ndhB）、4个自我复制基因（rpl2、rpl23、rps12、rps7）、4个rRNA基因（rrn16、rrn23、rrn4.5、rrn5）、7个tRNA基因（trnA-UGC、trnI-CAU、trnI-GAU、trnL-CAA、trnN-GUU、trnR-ACG、trnV-GAC）、2个未知功能蛋白基因（ycf1、ycf2）。在‘锦绣'黄桃叶绿体基因组中查找248个SSR位点,分布在LSC、SSC、IR区域的SSR数量分别为165、44、39个,占比分别为66.53%、17.74%、15.73%,以单核苷酸重复占绝对优势,主要是A/T,其次是三核苷酸类型,其优势重复单元类型是ATA、TAT和TTA。进化树分析表明,‘锦绣'黄桃与桃树（Prunus persica,MH169125.1）亲缘关系最近。本研究建立了适于‘锦绣'黄桃完整叶绿体基因组组装及其特征分析的方法,为‘锦绣'黄桃的鉴定和系统发育研究奠定基础。     

一步法RT-PCR扩增PRSV海南分离物全长基因组cDNA

以植物总RNA提取试剂盒提取的高纯度的总RNA为模板,使用Oligo dT-Adaptor和Random9引物合成了番木瓜环斑病病毒海南分离物(PRSV HN-2)的cDNA第一链,基于已报道的PRSV全长基因组序列,设计合成了一对引物,一步法RT-PCR扩增出PRSV海南分离物全长基因组cDNA。为了验证获得的全长基因组cDNA的正确性,并以扩增出的全长cDNA为模板,将PRSV全长基因组分成A、B 2个大片段进行扩增,应用T载体进行克隆和测序以验证所获得的全长基因组cDNA序列的正确性。测序结果显示,该cDNA序列与国内外报道的PRSV各分离物全长核苷酸序列的相似性很高,表明本文建立的一步法RT-PCR扩增PRSV全长基因组cDNA的方法正确、可行。     

104个甘薯品种的cpSSR指纹图谱构建及遗传多样性分析

基于甘薯叶绿体基因组,利用cpSSR分子标记,对104份甘薯栽培品种和地方品种进行遗传多样性分析并构建指纹图谱,为甘薯资源的保护鉴定和遗传改良提供参考。使用了11对cpSSR引物,在104个甘薯材料中总共扩增得到58条条带,多态性条带为47条,单条引物平均扩增的条带数为5.27,平均多态性百分率为81.03%。根据引物在甘薯材料中的扩增结果,构建104个甘薯品种的指纹图谱。对104个甘薯品种的扩增结果进行聚类分析,每个品种间的遗传距离为0.0386~5.2723,平均遗传距离为0.2201,在遗传系数为0.74时将104个甘薯品种分为5组。     

侵染湖南甘薯种质资源的曲叶病毒和杆状病毒的检测及其亲缘关系分析

采用PCR技术对2015—2016年从湖南省多个市县采集的180份甘薯种质资源进行两种DNA病毒（sweet potato leaf curl virus,SPLCV和sweet potato badnavirus,SPBV）检测,并以PCR扩增产物序列为基础,对这两种病毒的亲缘关系进行分析。结果表明：（1）180份甘薯种质资源中,22份检测出SPLCV,占总数的12.2%;32份检测出SPBV,占总数的17.8%;8份同时检出SPLCV和SPBV这两种病毒,占总数的3.9%。（2）检出SPLCV的市县有长沙、永州、怀化、邵阳、郴州、常德、娄底、益阳、岳阳和株洲;检出SPBV的市县有长沙、永州、怀化、衡阳和邵阳;检出两病毒复合侵染的市县有怀化、长沙、永州和邵阳。（3）基于病毒全基因组序列分析显示,全球已报道的36个SPLCV分离物可分为3组,本研究获得的12个湖南分离物可分别归于3个组中,其中6个归于组Ⅰ,1个归于组Ⅱ,5个归于组Ⅲ,表明湖南SPLCV具有高度多样性。（4）基于病毒运动蛋白和外壳蛋白编码基因部分序列分析显示,全球已报道的36个SPBV分离物可分为4组,绝大部分分离物属于组Ⅰ,我国1个安徽分离物单独成组（组Ⅱ）,我国2个山东分离物和1个海南分离物构成1个组（组Ⅲ）,本研究获得的2个湖南分离物其中1个归于组Ⅰ,而另1个与已报道各分离物的核苷酸序列均存在显著差异,相似性仅为74.92%,单独成组（组Ⅳ）,表明我国SPBV具有高度的变异性,存在多个变异类型。本研究结果可为湖南地区这两种病毒病防控提供依据。     

采后脱落酸处理促进甘薯块根愈伤木栓组织的形成

本研究以‘北京1号’甘薯为试验材料,人工模拟机械损伤后采用不同浓度（25、50、100、200 mg/L）脱落酸（ABA）进行愈伤处理,研究采后ABA处理对甘薯块根的愈伤作用。结果表明:采后ABA处理能有效促进甘薯伤口处愈伤木栓组织的形成,其中以100 mg/L ABA愈伤3 d效果最佳。采后ABA处理能有效提高甘薯愈伤组织苯丙氨酸解氨酶（PAL）、过氧化物酶（POD）和多酚氧化酶（PPO）活性,提升总酚、类黄酮含量,减少甘薯重量损失。相关性分析表明,ABA处理甘薯木质素含量与总酚、类黄酮含量之间呈极显著相关（P<0.01）,PAL酶活力与POD和PPO酶活力呈极显著相关（P<0.01）。综上所述,采后ABA处理可通过激发甘薯损伤部位组织的苯丙烷代谢、提高愈伤防御酶活性及次生代谢产物的合成,达到促进甘薯块根愈伤形成的目的。     

利用流式细胞术鉴定茉莉花基因组大小和染色体倍性

以收集的16份茉莉花资源及50份实生种质为材料,以玉米B73为内参,采用流式细胞术估测茉莉花基因组大小,并以二倍体品种为对照,计算茉莉花染色体倍性。结果表明：内参与待测样品峰值能完全分开,无重叠峰,峰型清晰集中,可对茉莉花基因组大小进行有效估测;供试材料中有56份二倍体,基因组大小为0.54~0.63 Gb,有7份三倍体,基因组大小为0.79~0.96 Gb,有3份四倍体,基因组大小为1.04~1.12 Gb;从收集的资源中鉴定出二倍体和三倍体,未见四倍体,而从实生种质中鉴定出3个四倍体、2个三倍体,表明实生选种是茉莉花种质创新的一条有效途径;在已明确花冠类型的材料中,三倍体及四倍体均为单瓣型茉莉。该研究结果为茉莉花倍性育种及实生选种提供科学依据。     

Proximate composition and selected functional properties of African Breadfruit and sweet potato flour blends

Full-fat African breadfruit flour was used to replace 30, 40, 50, 60 and 70% of sweet potato flour. The chemical composition and functional properties of composite flours showed that they contains more protein, fat, and ash and less carbohydrate than sweet potato flour. With increasing level of supplementation of breadfruit, ash, protein and fat contents increased while carbohydrate decreased. The composite flours possessed higher water absorption than sweet potato flour. The water absorption capacity increased from 20% for sweet potato flour to the range of 85–120% for composite flours. The oil absorption capacities for some composite flours were higher than that for sweet potato but less than that of breadfruit. Composite flours had good foaming capacity but lacked foaming stability. The bulk density of the composite flours was found to be low which will be an advantage in the preparation of weaning food formulations.     

Suppression of the invasive plant mile-a-minute (Mikania micrantha) by local crop sweet potato (Ipomoea batatas) by means of higher growth rate and competition for soil nutrients

Background

There are a variety of ways of increasing crop diversity to increase agricultural sustainability and in turn having a positive influence on nearby natural ecosystems. Competitive crops may provide potent management tools against invasive plants. To elucidate the competitive mechanisms between a sweet potato crop (Ipomoea batatas) and an invasive plant, mile-a-minute (Mikania micrantha), field experiments were carried out in Longchuan County of Yunnan Province, Southwest China, utilizing a de Wit replacement series. The trial incorporated seven ratios of sweet potato and mile-a-minute plants in 25 m² plots.

Results

In monoculture, the total biomass, biomass of adventitious root, leafstalk length, and leaf area of sweet potato were all higher than those of mile-a-minute, and in mixed culture the plant height, branch, leaf, stem node, adventitious root, flowering and biomass of mile-a-minute were suppressed significantly (P < 0.05). The relative yield (RY) of mile-a-minute and sweet potato was less than 1.0 in mixed culture, indicating that intraspecific competition was less than interspecific competition. The competitive balance index of sweet potato demonstrated a higher competitive ability than mile-a-minute. Except pH, other soil nutrient contents of initial soil (CK) were significantly higher than those of seven treatments. The concentrations of soil organic matter, total N, total K, available N, available P, available K, exchange Ca, exchange Mg, available Mn, and available B were significantly greater (P < 0.05) in mile-a-minute monoculture soil than in sweet potato monoculture soil, and were reduced by the competition of sweet potato in the mixture.

Conclusions

Evidently sweet potato has a competitive advantage in terms of plant growth characteristics and greater absorption of soil nutrients. Thus, planting sweet potato is a promising technique for reducing infestations of mile-a-minute, providing weed management benefits and economic returns from harvest of sweet potatoes. This study also shows the potential value of replacement control methods which may apply to other crop-weed systems or invaded natural ecosystems.     

Resistance levels and fitness of glufosinate-resistant transgenic sweet potato in field experiments

Transgenic herbicide-resistant sweet potato plants [Ipomoea batatas (L.) Lam.] produced through a biolistic transformation were used in this study. The objectives of this research were to (a) quantify resistance levels of transgenic sweet potato expressing the bar gene to glutamine synthetase (GS)-inhibitors, glufosinate and methionine sulfoximine, protoporphyrinogen oxidase (PPO)-inhibiting herbicide, oxyfluorfen and photosynthesis-inhibiting herbicide, paraquat; (b) compare the relative chlorophyll content, quantum yield, growth, and tuberous root yield between transgenic and wild-type sweet potato; (c) compare the response of transgenic and wild-type sweet potato plants to chilling and high temperature, and (d) compare amino acids, minerals and sugar contents of transgenic and wild-type sweet potato tubers. The transgenic sweet potato lines were 20-82-fold more resistant to glufosinate than the wild-type. The representative transgenic line 7171 also showed resistance to methionine sulfoximine, but was not resistant to oxyfluorfen and paraquat, which have different target sites. The stem length, number of leaves, petiole length, shoot fresh weight, and storage roots of transgenic lines were lower than those of the wild-type in field experiments. Reduced growth and root yield were not due to reduced quantum yield and relative chlorophyll contents. Glufosinate increased the ammonium accumulation in leaves of wild-type plants, but had minimal or no effect on leaves of transgenic line 7171. There were differences in mineral contents, free sugars, total amino acids, and free amino acids in the petiole and storage roots between wild-type and line 7171. There was no difference in drought tolerance between wild-type and line 7171, but the transgenic line was more tolerant to chilling temperature than wild-type plants. Follow-up research is required to elucidate the mechanisms underlying the growth and yield differences, different nutritional values, and differential response to low temperature between wild-type and transgenic sweet potato.     

Sweet Potato Weevil Damage,Production Constraints,and Variety Preferences in Western Tanzania: Farmers’ Perception

Sweet potato weevils (Cylas spp.) are among the most important constraints to sweet potato (Ipomoea batatas [L.] Lam.) production in most agro-ecological zones of Tanzania. Integration of farmers’ perception on sweet potato weevil damage, production constraints, and variety preferences is crucial in developing sweet potato varieties with farmer-preferred traits and weevil resistance. The aim of this study was to identify farmers’ perceptions on sweet potato weevil damage, production constraints, postharvest storage options, and criteria used to select and grow the best sweet potato varieties in western Tanzania. Surveys were conducted in four selected districts of western Tanzania (Nzega, Sikonge, Kigoma rural, and Kasulu) known for sweet potato production. Data were collected using a structured questionnaire, focus group discussions (FGDs), and transect walk involving 122 sweet potato farmers. Weevil damage was reported by 84% of the respondents to be the overriding constraint to sweet potato production. Sweet potato diseases and drought were the next production constraints, reported by 57% and 54% of the respondents, respectively. Farmers’ preferred agronomic traits of sweet potato included high yield (25% of respondents), drought tolerance (24%), and disease and pest resistance (21%). Farmers’ preferred sweet potato culinary traits in the study areas were high dry matter content (reported by 21% of the respondents), followed by reduced cooking time, taste and fiber content (each reported by 19% of the respondents). The above-mentioned production constraints and farmers’ preferred traits are useful selection criteria for improving sweet potato with respect to weevil resistance and enhanced storage-root yield and quality.