番茄(Solanum lycopersicum)SlGLR基因家族的生物信息学分析

本研究通过对番茄高质量全基因组序列同源搜索分析,找到番茄中共有13个SlGLRs家族成员。并利用生物信息学方法详细分析了该家族所有成员的基因结构、蛋白结构域、进化关系。结果显示:番茄SlGLR家族的13个成员均含有5～7个外显子,各个成员都包含IPR001828、IPR001320和IPR001638这三个结构域,整个家族可分为三个亚家族,且Sl GLRⅡ亚家族各成员,除了SlGLR2.6以外均成簇分布在6号染色体上。不同激素处理下的表达分析显示该家族不同成员对不同激素处理的响应不同;组织表达分析表明SlGLR3.2在番茄的果实中特异高表达,暗示其在果实发育中可能起着重要作用。为了进一步分析其功能,我们对SlGLR3.2的理化性质、亲水性/疏水性、跨膜区、亚细胞定位、蛋白二级结构进行了详细分析。结果表明SlGLR3.2为亲水性膜蛋白,含有三个跨膜区,二级结构主要由α-螺旋、延伸链、β-转角、无规则卷曲组成。本研究将为进一步研究番茄SlGLRs基因家族的功能提供参考依据。     

小麦NIP蛋白的生物信息学分析

为了探讨小麦NIP蛋白的结构特征和性质差异,本研究通过生物信息学手段,鉴定了两条新的小麦NIP蛋白,并和两条已知的小麦NIP蛋白一起,进行了蛋白质氨基酸序列比对、基序、二级结构、跨膜结构以及亚细胞定位等相关分析。发现两条新的小麦NIP蛋白TaNIP1-2、TaNIP4-1,与已知的TaNIP2-1-LIKE、TaNIP2-2一样,均为脂溶性蛋白,且都具有6个跨膜结构域、N-末端和C-末端位于膜内等MIP蛋白结构共性。亚细胞定位分析结果表明,除TaNIP4-1定位于质膜外,其他3个小麦NIP蛋白均定位于内质网。Motif分析结果显示,除都含有MIP基序外,TaNIP1-2还含有BCHF基序和DUF 2 157基序。磷酸化位点预测分析结果显示,4个小麦NIP蛋白都未预测到磷酸化位点。本研究可为小麦NIP蛋白亚家族的研究和利用提供理论参考及分析依据。     

甜橙PHT1基因的克隆与表达分析

磷是柑橘生长发育过程中必需的元素。在拟南芥中PHT1家族成员至少介导了植株根部95%以上的磷吸收过程,至今已在水稻、油茶和杨树等多种植物中发现了具有相似功能的PHT1基因,说明PHT1基因在植物的磷吸收过程具有重要作用及在植物进化过程中具有保守性。本研究从柑橘基因组序列信息中分析出7个柑橘PHT1基因,其中在根部表达较强的基因Cs3g27660编码产物与At PHT1;8(或At PHT1;9)的蛋白序列相似性最高;而Cs9g10540、Cs5g29860、Cs9g10530与At PHT1;1(或At PHT1;4)的蛋白序列相似性最高,并且三者均能在根部表达及表达受低磷胁迫诱导,亚细胞定位结果亦显示三者均能定位在细胞的质膜上,推测Cs9g10540、Cs9g10530、Cs5g29860可能为柑橘中类At PHT1;1(或At PHT1;4)基因。     

砂藓RcPIP2基因的克隆及生物信息学分析

水通道蛋白是一类较小的跨膜蛋白质,在植物抵御非生物胁迫过程中具有非常重要的作用。为了研究砂藓水通道蛋白基因的生物学功能,利用干旱处理转录组测序获得的序列信息,克隆获得1个水通道蛋白家族中质膜内在蛋白基因序列,命名为RcPIP2。生物信息学结果显示,RcPIP2基因全长序列为1 267 bp,包含807 bp的开放阅读框,编码含有268个氨基酸残基的蛋白质。该蛋白质分子质量预测为28.3 ku,理论等电点为6.64,为疏水性较强的稳定性蛋白;无信号肽,为非分泌型蛋白;含有6个跨膜结构域。保守结构域分析发现,RcPIP2具有膜内在蛋白(MIP)家族信号序列、高等植物高度保守序列HINPAVTFG和2个天门冬酰胺-脯氨酸-丙氨酸(NPA)基序。二级结构包括α螺旋(37.31%)、β折叠(20.9%)、无规则卷曲(38.43%)。三级结构预测发现,RcPIP2蛋白质的立体结构为典型的四聚体形式,由4个圆筒状亚基和中间的孔道构成。系统进化树分析表明,RcPIP2与小立碗藓中的PIP2蛋白质亲缘关系较近,聚为一类。由此推测,RcPIP2基因为水通道蛋白家族成员。     

藜麦DAPB基因丰度及生物信息学分析

二氢砒啶二羧酸还原酶(DAPB)是赖氨酸合成途径中的一个重要酶,在蛋白质和细胞壁的合成中起着重要作用。本研究基于KEGG总数据库分析表明,藜麦中DAPB的基因拷贝数远高于水稻、玉米及大豆等作物。对藜麦基因组数据筛选得到4个DAPB基因成员,均属于碱性蛋白质,氨基酸序列长度约330 bp,分子量为36.623~36.880 k D,等电点(p I)为5.79~6.01,最大疏水系数为0.028~0.123,为疏水性蛋白,亚细胞定位于细胞质中,不存在跨膜区。4个DAPB基因之间的Ka/Ks值均小于0.5,表明该基因在进化过程中比较保守。系统进化分析发现,藜麦DAPB家族成员位于同一个亚家族,且与菠菜的亲缘关系较近。启动子顺式作用元件分析结果显示,DAPB家族除含有TATA-box和CAAT-box以外,还含有多个参与激素响应、光照、低温及其它应激反应相关的顺式作用元件和转录因子结合位点,暗示藜麦DAPB家族成员可能参与以上多种响应。本研究分析了藜麦DAPB基因的拷贝数并对DAPB进行了生物信息学分析,可为进一步了解DAPB基因家族的生物学功能提供参考。     

植物酰基载体蛋白基因家族序列分析

以拟南芥酰基载体蛋白为查询序列,检索18个植物物种的基因组数据库,获得138个酰基载体蛋白基因和12个基因片段。植物酰基载体蛋白由1个基因家族编码,成员2～16个。植物酰基载体蛋白磷酸泛酰巯基乙胺结合位点(Ser)周围的氨基酸序列高度保守,该位点包含在保守的DSL基序中。植物酰基载体蛋白基因结构类型分为5种,其中类型III酰基载体蛋白基因所占比例最大。绝大多数植物酰基载体蛋白基因家族成员单独或2～4个成员分布在一条染色体上。在138个植物酰基载体蛋白基因中,19个具有不同剪接体。植物酰基载体蛋白基因家族成员可能起源于一个共同的祖先基因。     

油棕GDSL酯酶/脂肪酶基因的全基因组鉴定及表达分析

全基因组范围内挖掘并鉴定油棕脂肪酶基因(GDSL)家族成员,并对其进行生物信息学及表达分析,为今后油棕GDSL的功能研究奠定基础。以拟南芥GDSL蛋白序列为标签,在油棕全基因组数据库中BLAST同源GDSL蛋白序列,并通过CDD和PFAM数据库完成GDSL蛋白序列的分析,剔除无保守结构的序列,最后利用生物信息学对油棕GDSL家族成员进行可视化分析。共获得109个油棕GDSL基因,其中有90个基因分布在油棕的15条染色体上,1号染色体上含有的基因数最多,为14个;基因结构较为稳定,大多数基因具有5个外显子,少数基因的外显子数目变化较大;油棕GDSL基因家族motif保守性较高;通过预测蛋白的二级结构,发现EgGDSL蛋白均存在α-螺旋、β-转角、无规则卷曲及延伸链这4种结构,其中75个EgGDSL以无规则卷曲为主要结构,α-螺旋为次要结构,34个蛋白以α-螺旋为主要结构,无规则卷曲为次要结构;通过热图分析发现EgGDSL基因在油棕不同组织中(中果皮,果仁,根,叶,茎和花)均有一定的表达,且具有显著的组织和时空表达特异性。本研究首次提供了油棕GDSL基因家族的染色体定位、基因结构、保守mo...     

葡萄AMT基因家族生物信息学分析

运用隐马尔柯夫模型,对葡萄的蛋白质数据库进行搜索,共找到12个AMT蛋白同源序列。利用生物信息学方法对葡萄12个AMT基因进行染色体定位,进而预测它们的氨基酸组成成分、理化性质以及二级结构,并分析葡萄与拟南芥、水稻和杨树AMT基因家族之间的联系。基因组定位结果发现12个AMT基因分布在6条染色体上,较拟南芥AMT基因在染色体上的分布更为集中。12个葡萄AMT蛋白序列可分成2个亚族,AMT1亚族有3个成员,其余为AMT2亚族成员。本研究发现不同成员间氨基酸数目、氨基酸序列间的疏水性存在一定的差异;二级结构预测结果显示,12个AMT氨基酸序列以α-螺旋和无规则卷曲为主要组成部分。基因结构分析表明,仅有2个葡萄AMT基因家族成员不含内含子,其余10个AMT基因含有1~4个内含子。对葡萄AMT蛋白的亚细胞定位分析表明：12个VvAMT均定位于膜结构上。对获得的12个葡萄AMT基因进行EST分析,只有5个有对应的EST序列,而仅有2个有相应的电子表达谱。     

甘蓝型油菜GPDH基因克隆及其生物信息学分析

为了进一步研究甘蓝型油菜GPDH基因,通过从拟南芥GPDH基因与甘蓝型油菜的共线性分析发现:拟南芥GPDH基因(At2g41540)在甘蓝型油菜A基因组和C基因组中有4个拷贝,分别为:GSBRNA2T00132785001、GSBRNA2T00024258001、GSBRNA2T00058395001、GSBRNA2T00019118001。从Gen Bank分别下载了它们的DNA序列和c DNA序列,c DNA序列依次命名为GPDH1、GPDH2、GPDH3、GPDH4。根据序列信息设计了4对不同的引物,从甘蓝型油菜湘油15号c DNA全长序列中扩增出了4条片段,分别命名为Bn GPDH1、Bn GPDH2、Bn GPDH3、Bn GPDH4。利用生物信息学软件和在线系统进行核苷酸序列分析和蛋白进化分析。结果显示:4条片段大小依次为1 395,1 395,1 389,1 536 bp。其中,Bn GPDH4翻译成氨基酸时序列中间出现终止密码子,不能合成有效蛋白。3个Bn GPDH蛋白的氨基酸数目为464,464和462个,理论分子量为51.584 4~51.829 7 k Da,二级结构α螺旋和无规则卷曲所占比例在42%左右,其次是延伸链所占比例约为15%。三者的跨膜结构总体来说是相同的。3个蛋白都由保守结构Gps A、NADB_Rossmann superfamily和NAD_Gly3P_dh_C superfamily组成,属于GPDH超基因家族。同源建模分析表明3个蛋白均能适用甘油3磷酸脱氢酶(Glycerol-3-phosphate dehydrogenase,GPDH)模型。对其进行亚细胞定位预测在细胞质膜的概率为79.0%。从序列分析、核苷酸聚类、理化性质预测、二级、三级结构预测、亚细胞定位预测、氨基酸聚类分析得出结论,它们具有GPDH基因家族的特征,为甘蓝型油菜GPDH基因家族中的成员。     

椰子DNMT家族基因的鉴定和生物信息学分析

DNA甲基化(DNA methylation)能引起染色质结构、DNA结构和稳定性等的改变,影响基因的时空表达。DNA甲基转移酶(DNA methyltrans ferase, DNMT)负责催化完成DNA的甲基化。本研究通过比对已有的椰子基因组数据,找到CnDNMT家族基因,删除不含DNA＿methylase结构域的蛋白,共鉴定4个具有DNA甲基转移酶保守结构域的DNMT基因,分别命名为CnDNMT1～CnDNMT4。采用生物信息学的方法,对基因结构、表达量、蛋白保守结构域、启动子序列等进行了分析。结果表明：这4个基因为DNA甲基转移酶家族中的2个亚家族：CMT和DRM。氨基酸序列分析表明,椰子CnDNMT家族蛋白均为酸性蛋白,且亚细胞定位预测定位在细胞核中。motif搜索结果表明CnDNMT蛋白家族含有5个椰子CnDNMT基因家族含有5个保守元件,5个保守元件的结构域所含有的氨基酸位点数量基本一致,CnDNMT2基因在胚乳中表达量很高,这说明CnDNMT2可能在椰子胚乳发育过程中起重要作用。     

QTL mapping of bio-energy related traits in Sorghum

Plant height (PHT), stem and leaf fresh weight (SLFW), juice weight (JW) and sugar content of stem (Brix) are important traits for biofuel production in sweet Sorghum. QTL analysis of PHT, SLFW, JW and Brix was conducted with composite interval mapping using F₂ and F_2:3 populations derived from the cross between grain Sorghum (Shihong137) × sweet Sorghum (L-Tian). Three QTLs controlling PHT were mapped on SBI-01, SBI-07 and SBI-09 under four different environments. These QTLs could explain 10.16 to 45.29% of the phenotypic variance. Two major effect QTLs on SBI-07 and SBI-09 were consistently detected under four environments. Eight QTLs controlling SLFW were mapped across three environments and accounted for 5.49–25.36% of the phenotypic variance. One major QTL on SBI-09 located between marker Sb5-206 and SbAGE03 was observed under three environments. Four QTLs controlling Brix were identified under two environments and accounted for 11.03–17.65% of the phenotypic variance. Six QTLs controlling JW were detected under two environments, and explained 6.63–23.56% of the phenotypic variance. QTLs for JW on SBI-07 and SBI-09 were consistent in two environments showing higher environmental stability. In addition, two chromosome regions on SBI-07 and SBI-09 were identified in our study having major effect on PHT, SFLW and JW. The results would be useful for the genetic improvement of sweet Sorghum to be used for biofuel production.     

相同碳氮比有机物料矿化1年对植烟土壤养分的影响

为探索不同有机物料相同碳氮比矿化1年对植烟土壤肥效作用,通过盆栽试验,将猪粪、玉米秸秆和生物炭调节碳氮比为25:1,经过1年自然矿化后在添加基础肥料的基础上分析不同有机物料对植烟土壤酶活性及氮磷钾含量的影响。结果表明,猪粪和玉米秸秆分别显著提高了土壤脲酶(最大值2.91 mg/(g·d))和蔗糖酶活性(最大值17.02 mg/(g·d))。与对照(不施有机物料)相比,施用有机物料在自然矿化1年后对土壤氮素仍有显著提升作用,其中猪粪处理表现出明显优势。同时,猪粪与生物炭显著提高了土壤速效钾和有机质含量,最大值分别达到1101 mg/kg和54.56 g/kg;猪粪也明显提升了土壤速效磷含量(727.95 mg/kg)。综上所述,相同碳氮比下豫中烟区土壤施用猪粪和生物炭在自然矿化1年后对植烟土壤养分含量的提升作用显著。     

The combined effect of plant stature and maturity on the response of wheat and triticale accessions to Septoria tritici

Summary The relationships between percent pycnidia coverage on the four uppermost leaves (PCD), plant height (PHT) and days to heading (HED) were evaluated for 21,000 wheat and triticale accessions tested in artificially inoculated (with fixed combination of S. tritici isolates) field nurseries over 8 trial years. A general Linear Model procedure (GLM) estimated Septoria severity using two correlative models: model 133-1 Year and model II–PCD=b₁PHT+b₂HED+C. The regression coefficients for PHT and HED in the two models were –0.54 and –0.40, respectively, with a R²=0.80^** and R²=0.29^** for model I and model II, respectively. The predicted cultivar best fitted to the model would be characterized as a semidwarf (PHT=115 cm) with an early-moderate maturity (HED=95 days to heading). The estimated mean percent pycnidial coverage for the two models over the 8 trial years was 40.8%. The performance of a group of 38 cultivars replicated yearly during the 8 trial years was assessed relative to model I. The deviation of each cultivar from the model was calculated using two functions: a) Sum Relative Serial Deviation (SRSD) and b) Total Relative deviation (TRD), in addition to Standard errors (SE). The proposed analytical protocol enabled identification of cultivars which expressed consistent yearly deviation (from the model) in host response combined with low-moderate mean pycnidial coverage (±30%). Such cultivars may possess a more stable type of genetic protection against the adverse effects of septoria tritici blotch.     

Identification of QTL for stalk sugar-related traits in a population of recombinant inbred lines of maize

Increasing sugar content in silage maize stalk improves its forage quality and palatability. The genetic mapping and characterization of quantitative trait loci (QTLs) is considered a valuable tool for trait enhancement, yet little information on QTL for stalk sugar content in maize has been reported. To this end, we investigated QTLs associated with stalk sugar traits including Brix, plant height (PHT), three ear leaves area (TELA), and days to silking (DTS) in two environments using a population of 202 recombinant inbred lines from a cross between YXD053, which has a high stalk sugar content, and Y6-1, which has a low stalk sugar content. A genetic map with 180 SSR and 10 AFLP markers was constructed, which spanned 1,648.6 cM of the maize genome with an average marker distance of 8.68 cM, and QTLs were detected using composite interval mapping. Seven QTLs controlling Brix were mapped on chromosomes 1, 2, 6 and 9 in the combined environments. These QTLs could explain 2.69–13.08 % of the phenotypic variance. One major QTL for Brix on chromosome 2 located between the markers bnlg1909 and umc1635 explained 13.08 % of the phenotypic variance. Y6-1 also contributed QTL allele for increased Brix on chromosome 6. One major QTLs controlling PHT on chromosome 1 and TELA on chromosome 4 were also identified and accounted for 13.68 and 12.49 % of the phenotypic variance, respectively. QTL alleles for increased DTS were located on chromosomes 1 and 5 of YXD053. Significant epistatic effects were identified in four traits, but no significant QTL × environment interactions were observed. The information presented here may be valuable for stalk sugar content improvement via marker-assisted selection in silage maize breeding programs.     

Genetic architecture of plant height in maize phenotype‐selected introgression families

This study aimed at developing, characterizing and evaluating two maize phenotypic‐selected introgression libraries for a collection of dominant plant height (PHT)‐increasing alleles by introgressing donor chromosome segments (DCS) from Germplasm Enhancement of Maize (GEM) accessions into elite inbred lines: PHB47 and PHZ51. Different backcross generations (BC₁‐BC₄) were developed and the tallest 23 phenotype‐selected introgression families (PIFs) from each introgression library (PHB47 or PHZ51) were selected for single nucleotide polymorphism genotyping to localize DCS underlying PHT. The result shows that most PIFs carrying DCS were significantly (α = 0.01) taller than the respective recurrent parent. In addition, they contained larger donor genome proportions than expected in the absence of selection or random mating across all BC generations. The DCS were distributed over the whole genome, indicating a complex genetic nature underlying PHT. We conclude that our PIFs are enriched for favourable PHT‐increasing alleles. These two libraries offer opportunities for future PHT gene isolation and allele characterization and for breeding purposes, such as novel cultivars for biofuel production.     

Development of SNP assays associated with oleic acid QTLs in N00-3350 soybean

Increasing the amount of oleic acid in soybean oil would reduce the need for hydrogenation, a process that creates unhealthy trans fatty acids. A previous study mapped six oleic acid quantitative trait loci (QTLs) from N00-3350 (~550 g kg⁻¹ oleic acid) on soybean chromosomes (Gm) 5, 17, 18, and 19, which corresponds to linkage groups (LG) A1, D2, G, and L, respectively. The objectives of this study were to develop high throughput assays to detect single nucleotide polymorphism (SNP) markers associated with these oleic acid QTLs. Several candidate genes that are putatively responsible for the oleic acid phenotype in N00-3350 were identified by BLAST searches against the soybean genomic assembly using the sequences of fatty acid synthesis genes from soybean and Arabidopsis. Putative accC-2 and KAS I genes were located in the region of the cqOle-001 on Gm05 (LG-A1). A putative KAS I gene was located in the region of the cqOle-003 on Gm18 (LG-G) and a putative accB-1 gene was located in the region of the cqOle-004 on Gm18 (LG-G). These fatty acid candidate genes and sequence-tagged sites were used to identify SNPs between N00-3350 and ‘Boggs’. Based on these SNPs, seven SimpleProbe probes for melting curve analysis were developed to rapidly identify the alleles from the mid-oleic acid soybean line N00-3350 at the desired loci. These assays provide a high-throughput and rapid SNP genotyping method which can be used to accelerate the development of mid-oleic acid content soybean cultivars.     

10种药用植物萜类合酶(DXS)生物信息学分析

为研究药用植物DXS酶的性质及其结构功能,利用生物信息学方法对GenBank中青蒿、砂仁、铁皮石斛等10种药用植物DXS编码氨基酸序列的理化特性、系统发育进化、亲/疏水性、亚细胞定位、磷酸化位点、二级结构、信号肽、跨膜结构、功能域等进行分析和预测。结果表明：不同植物DXS酶氨基酸序列的理化性质基本一致;在进化关系上可划分为2类;DXS酶蛋白主要表现为亲水性蛋白;大多数定位于叶绿体,少数定位于线粒体;丝氨酸磷酸化位点占据主导地位;α-螺旋是DXS多肽链中大量的结构元件,散布于整个肽链中;除了铁皮石斛具有1个信号肽,其余DXS氨基酸序列不具有信号肽,可推测出DXS可能不是分泌性蛋白;没有跨膜结构域;具有3个功能域分别为TPP_superfamily、Transket_pyr_ superfamily和Transketolase_C superfamily。研究结果将为DXS的酶学特性及萜类生物合成的分子机理研究提供理论参考。     

Freezing tolerance of selected perennial ryegrass (<Emphasis Type="Italic">Lolium perenne</Emphasis> L.) accessions and its association with field winterhardiness and turf traits

Reproductive output and fertility variation in teak were evaluated in five study sites in Western Ghats region of southern India. In four seed production areas (SPA1-4)) and a natural population (NAT) plots with 100 trees were investigated. The 40-year-old seed production areas are located in high rainfall (>2,500 mm) sites in Kerala state and the natural stand is at a drier location in Tamil Nadu. Fruit production per tree was rather high in the natural stand (1500) and quite variable in the seed production areas. SPA 4, located far south from the other sites, had the highest fruit production (almost twice that in the other study sites), high relative population size (N _r = 0.5) and predicted low genetic drift in two consecutive years. Fecundity was very low in SPAs 2 & 3 (200 fruits per tree). Reproductive output was similar in successive years except SPA 1, where the fruit production in the first year was almost five times that in the second year. Fertility variation (computed as sibling coefficient, Ψ) was in general higher in NAT and hence the relative population size was lower than in SPAs. The variation in female fertility in the natural stand was, somewhat surprisingly, similar to that in the seed production areas, while the male fertility variation was higher. In the seed production areas the male fertility variation was lower or similar to the female fertility variation. The fertility variation, Ψ was on average around 3 and correspondingly the relative effective population size, N _r = 0.36 and the variance effective number around 60. Selection for tree diameter would improve predicted diversity of the seed crop as it was positively correlated with reproductive output and negatively correlated with fertility variation among trees.     

甘蓝型油菜遗传图谱构建与无花瓣性状QTL定位

以无花瓣油菜APL01与正常有花瓣品种M083杂交的BC₁F₁为基础群体,利用RAPD、SSR和SRAP技术获得251个分子标记,包括219个SRAP、25个SSR和7个RAPD标记,构建了由19个连锁群组成的分子标记遗传图谱,根据共同的分子标记,建立该图谱与甘蓝型油菜高密度图谱的对应关系。利用WinQTLCart 2.0软件对无花瓣性状进行QTL扫描,获得4个与无花瓣性状相关的QTL,QAP5位于N5连锁群的A0226Bb152~m31e40b区间,解释花瓣度表型变异的3.71%;QAP6位于N6连锁群的m25e7~OPY9区间,解释花瓣度表型变异的3.02%;QAP8位于N8连锁群的A0226Gb468~m29e20区间,解释花瓣度表型变异的30.94%;QAP15位于N15连锁群的m21e4b~A0225Bb201区间,解释花瓣度表型变异的21.96%。QAP8和QAP15为2个主效QTL,可用于无花瓣性状的标记辅助选择,QAP5和QAP6为修饰基因位点。