Barnyard millet global core collection evaluation in the submontane Himalayan region of India using multivariate analysis

Barnyard millet(Echinochloa spp.) is one of the most underresearched crops with respect to characterization of genetic resources and genetic enhancement. A total of 95 germplasm lines representing global collection were evaluated in two rainy seasons at Almora,Uttarakhand, India for qualitative and quantitative traits and the data were subjected to multivariate analysis. High variation was observed for days to maturity, five-ear grain weight, and yield components. The first three principal component axes explained 73% of the total multivariate variation. Three major groups were detected by projection of the accessions on the first two principal components. The separation of accessions was based mainly on trait morphology. Almost all Indian and origin-unknown accessions grouped together to form an Echinochloa frumentacea group. Japanese accessions grouped together except for a few outliers to form an Echinochloa esculenta group. The third group contained accessions from Russia, Japan, Cameroon, and Egypt. They formed a separate group on the scatterplot and represented accessions with lower values for all traits except basal tiller number. The interrelationships between the traits indicated that accessions with tall plants, long and broad leaves, longer inflorescences, and greater numbers of racemes should be given priority as donors or parents in varietal development initiatives. Cluster analysis identified two main clusters based on agro-morphological characters.     

Genetic Diversity and Core Collection for Potato (<Emphasis Type="BoldItalic">Solanum tuberosum</Emphasis> L.) Cultivars from Cameroon as Revealed by SSR Markers

Twelve pairs of SSR markers were used to evaluate the genetic diversity of 138 accessions of potato cultivars from the Western Highlands region of Cameroon. The average Polymorphism information content (PIC) value (0.74) and number of alleles (7.08) indicated a high genetic diversity of the potato cultivars tested. Analysis of molecular variance revealed that most of the genetic variations are found within geographic region (≥ 91%), resulting in high gene flow (Nm > 4 individuals). Local varieties had significantly more alleles than exotic varieties. Genetic diversity estimates for accessions from low elevations were significantly lower than those from medium and high elevations. Cluster analysis showed three clusters; the model-based approach inferred two gene pools. Genotypes revealed a high level of admixture between gene pools within locations and elevations. A core collection identified in this study composed of 27 individuals representing 19.57% of the whole collection and captured 99.15% of the total alleles found.     

19个亚洲国家大麦种质材料的遗传多样性分析

为了解大麦种质材料的遗传多样性,并为合理选择育种亲本及保护与利用大麦种质资源材料提供依据,采用21对SSR荧光标记引物对来自19个亚洲国家的175份大麦种质材料进行遗传多样性分析,筛选出的19对SSR引物共检测到134个等位变异,平均每对引物检测到7.05个等位变异,其中SSR17位点对亚洲大麦基因组DNA变异检测最有效,其多态性信息含量指数(PIC)和标记指数MI均最高,分别为0.9和10.77;基于SSR数据,对19个亚洲国家175份大麦材料进行UPGMA聚类分析,结果聚为三组:组群Ⅰ共包含19个国家的161个品种;组群Ⅱ共包含4个国家的12个品种;组群Ⅲ只包括来自土库曼斯坦的2个品种。根据按国家划分的19个群体的遗传一致度数据,聚类分析可以分为3组群(其中组群1可分为4个亚组),主坐标分析可分为3个组群和7个亚组。本研究表明,聚类法和主坐标分析法结果基本吻合,均表明亚洲大麦种质资源存在丰富的变异,但主坐标分析法更精细。     

基于ISSR标记的火龙果种质资源遗传多样性分析

为明确火龙果种质资源的遗传多样性水平和亲缘关系,以69份火龙果核心种质为研究对象,采用ISSR分子标记进行火龙果遗传分析.结果表明:13条ISSR引物共检测到247个位点,其中多态性位点数为232个,多态性条带百分比(PPB)为93.93％,平均多态性信息含量(PIC)为0.9189;平均观测等位基因数(Na)为1.9...     

部分美国及我国小麦品种的遗传多样性分析

为了比较美国及我国小麦品种的遗传多样性,选用55对SSR引物对引自美国的67份小麦品种及我国黄淮麦区推广面积较大的17个品种进行了遗传多样性分析。结果表明,67份美国小麦品种共检测到443个等位变异,单个引物位点的等位变异为2～24个,平均每个位点8.10个,各位点多态性信息含量(PIC)变幅为0.11～0.92,平均为0.59;黄淮麦区小麦品种共检测到266个等位变异,单个引物位点的等位变异为2～9个,平均每个位点4.82个,PIC变幅为0.10～0.84,平均为0.55。67个美国小麦品种A、B、D三个基因组的平均等位变异与平均PIC值大小分别为:B(8.60)>D(7.88)>A(7.63)和B(0.62)>A(0.58)>D(0.56);黄淮麦区17个小麦品种三个基因组的平均等位变异与平均PIC值大小分别为:B(5.30)>A(5.10)>D(3.94)和B(0.58)>A(0.57)>D(0.48)。聚类分析结果表明,55对SSR引物能将84份材料区分开来,并分为六大类,15个国内小麦品种被聚为一类,中国春自成一类,其余材料被聚为四类。由此可知,美国小麦品种的遗传多样性较高,与黄淮麦区小麦品种的遗传差异较大。     

转甘蔗抗虫基因CpTI的RT-PCR检测

利用已修饰的CpTI基因进行转基因检测,根据修饰后的目的基因片段序列对两个甘蔗品种(P44和福农94-0403)的转基因甘蔗进行RT-PCK检测研究,结果在被检测的10 株甘蔗中验证了3株已转入植株中,RT-PCR检测到的20、25、26号植株均呈阳性,证明被修饰的sck基因已成功转入甘蔗.     

Genetic Diversity and Allelic Frequency of Selected Thai and Exotic Rice Germplasm Using SSR Markers

A collection of 167 Thai and exotic rice accessions was subjected for evaluation of genetic diversity and assessment of relationship by simple sequence repeat(SSR) markers. Among a total of 49 SSR markers, 13 markers distributing over 12 rice chromosomes showed clear polymorphic band patterns, and they were selected for genetic assessment. A total of 110 alleles were detected with an average of 8.46 alleles per locus. The averages of gene diversity, heterozygosity and polymorphic information content were 0.59, 0.02 and 0.56, respectively. The unweighted-pair group method with arithmetic averages(UPGMA) clustering analysis was performed for genetic distance, and phylogenetic tree was constructed. The result showed that this rice collection was divided into two major groups, classified as japonica and indica subspecies. Within the japonica group, temperate japonica and tropical japonica subgroups can be clearly separated. Three-dimensional principal component analysis projection and model-based population structure analysis showed consistent clustering results with two major groups of UPGMA analysis, supporting the classification of japonica and indica subspecies. The indica allelic frequency was also investigated to provide an indicative guide for breeders to overcome the practical problems on sterility of inter-subspecies hybrid offspring. This rice collection and information obtained in this study will be useful for rice breeding programs.     

中国节节麦基于ISSR标记的遗传多样性分析

为揭示中国节节麦的遗传多样性并发掘可能具有独特变异的节节麦种质资源,采用ISSR标记对75份中国节节麦的遗传多样性进行分析。结果表明,筛选出的9条ISSR引物共检测得到155个位点,多态性位点(138个)百分率为89.31%。Nei’s多样性指数(He)、Shannon’s信息指数(I)、基因分化系数(Gst)和基因流(Nm)分别为0.273 4、0.415 2、0.138 5和3.11,表明中国节节麦有较高的遗传多样性,群体间有中等程度的遗传分化。基于简单相似系数的UPGMA聚类分析表明,除5份河南和陕西节节麦聚类形成独立的分支Group 2(T078、T102和SC1)和Group 3(SX38和T006)外,绝大多数节节麦均聚类形成较大的分支Group 1,且在Group 1中,除4份节节麦(T002、T023、XJ6和XJ49)外,绝大多数节节麦均依据地理分布分别形成了黄河流域节节麦亚组和新疆节节麦亚组,在遗传距离约0.77处,又可依次分为河南、陕西和新疆节节麦小分支。二维主成分分析、群体的遗传一致度和分子变异分析也表明了类似的结果,同属于黄河流域节节麦亚组的河南、陕西节节麦遗传一致度(S=0.971 8)较高,群体内个体差异是中国节节麦变异的主要原因,但两大亚组和三居群的遗传差异分别占总变异的18.57%和10.38%。可见,不同节节麦的地理分布和生境差异,是导致中国节节麦居群遗传分化的主要原因,而聚类分析中单独形成独立分支Group 2和Group 3的5份黄河流域节节麦,可能是具有独特遗传变异的种质资源。     

Genetic Diversity and Redundancy Among Potato Accessions in the Montenegrin Collection as Revealed by Microsatellite Markers

Potato was introduced in Montenegro in the middle of the eighteenth century. Since then it has become the most important crop in plant production. During the period between 2008 and 2010 a total of 52 potato accessions was collected across Montenegro and stored in a national gene bank. In the study reported here 23 accessions from the collection were examined using microsatellite (also known as simple sequence repeats or SSRs) molecular markers with the aim to explore genetic diversity and redundancy within the germplasm. The accessions were selected on the basis of preliminary characterization of all 52 accessions for 11 lightsprout traits. Molecular characterization of 23 accessions by 12 SSR markers was carried out at SASA (Science and Advice for Scottish Agriculture) that manages a database of more than 3000 genetic profiles of potato from Europe and abroad. Comparison of SSR genetic profiles of Montenegrin collection against the existing SASA database allowed us to test the authenticity of the Montenegrin accessions. Out of the 23 accessions examined, 13 showed distinct genetic profiles of which seven showed perfect matching with known cultivars, two profiles showed strong similarity to another two cultivars, and four profiles were found unique with regards to the SASA database. Application of microsatellite markers in this study provided valuable information on the extent of genetic diversity residing within Montenegrin potato germplasm; it gave clear indications of the scale of redundancy within the collection; and helped clarify the identity of the accessions. Four accessions within the collection might incorporate unique variation and will be subjected to further agronomical examinations to assess their potential for breeding purposes.     

基于nSSR和cpDNA序列的城步峒茶群体遗传多样性和结构研究

采用简单重复序列标记(nSSR)与叶绿体DNA序列(cpDNA)分析技术,对城步峒茶群体进行了遗传多样性、遗传结构和遗传分化等研究。结果表明,15对nSSR引物在参试81份资源中共获得142个等位位点,平均每对引物9.47个,城步峒茶群体的观测杂合度(Ho)、期望杂合度(He)和Nei期望杂合度(Nei)分别为0.49、0.62和0.62,具有较高的遗传多样性。Structure分析将79份峒茶资源分成3个类群,但各类群的遗传背景较为复杂,没有明显的群体结构。F检验表明,城步峒茶群体的近交系数F_IS为正值(F_IS=0.177 5),群体间的遗传分化系数F_ST较小(F_ST=0.034 5),分化程度较低,基因流Nm较高(Nm=7.01)。3对cpDNA引物分别获得了473 bp(rbcL)、704 bp(matK)和320 bp(psbH-trnA)的片段序列,变异位点占总位点的比例分别为0.42%、0.71%和1.25%。将3个序列依次拼接,共产生了9个单倍型,单倍型数由多到少的居群依次为TXZ(6)、DZC(4)、DPS(4)、TYS(3)、HJZ(2),群体的单倍型多样性(Hd)和核苷酸多样性(π)分别为0.732和0.001 39。9个单倍型中,单倍型H1和H5处于进化网络图的中心节点上,并且包含资源数量最多,属于比较原始的单倍型。同时,nSSR和cpDNA的AMOVA分析结果基本一致,居群内的变异百分比分别达到96.69%和80.54%,城步峒茶的遗传变异主要存在于居群内。     

稻属AA染色体组8个种间SSR多样性与亲缘关系

选用平均分布于水稻基因组的30对SSR 引物,对AA染色体组8个野生稻种共42份材料的遗传多样性及遗传关系进行了研究。结果显示,本试验选取的30个SSR标记均具有多态性,多态性位点百分率为100%。30个多态性位点共扩增出的等位基因数为224, 每个位点可扩增出3～10个等位基因,平均7.47个;等位基因有效数(Ae)变幅为1.25～891,平均5.45。多样性指数中,Shannon多样性指数(I)为0.454～2.386,平均1.826;而Nei基因多样性指数变幅为0.199～0.888,平均0.774。系统聚类和带型分析结果表明,亚洲栽培稻(Oryza sativa) 与普通野生稻(O. rufipogon) 的亲缘关系最近,非洲栽培稻(O. glaberrima) 则与巴蒂野生稻(O. barthii) 关系最为密切,杂草稻(O. spontanea) 与普通野生稻 (O. rufipogon)、亚洲栽培稻(O. sativa) 之间有较近的亲缘关系,而展颖野生稻(O. glumaepatula)、长雄蕊野生稻(O. longistaminata)与AA组其他稻种之间的亲缘关系较远。     

Genetic diversity and association mapping for salinity tolerance in Bangladeshi rice landraces

Breeding for salinity tolerance using Bangladeshi rice landraces and understand genetic diversity has been limited by the complex and polygenic nature of salt tolerance in rice genotypes. A genetic diversity and association mapping analysis was conducted using 96 germplasm accessions with variable response to salt stress at the seedling stage. These included86 landraces and 10 indica varieties and lines including Nona Bokra, from southern Bangladesh. A total of 220 alleles were detected at 58 Simple Sequence Repeat(SSR) marker loci randomly distributed on all 12 rice chromosomes and 8 Sequence Tagged Site(STS) markers developed for genes SKC1, DST, and SalT. The average gene diversity was 0.5075 and polymorphism information content value was 0.4426, respectively. Cluster analysis revealed that 68 and 21 accessions were clustered into 2 distinct groups, possibly corresponding to indica and japonica groups, respectively and the remaining 7 landraces were classified as an admixed group. In addition to Wn11463, the STS marker for SKC1, RM22418 on Chr. 8 was significantly associated with salinity tolerance, at the location of a QTL detected in previous studies. Our findings of favorable alleles associated with salinity tolerance in Bangladeshi rice landraces, as well as the development of STS markers for salt tolerance genes, will be helpful in future efforts to breed salinity tolerance in rice.     

甜菜种质资源数量性状遗传距离差异及其应用的研究

对60份参试材料的5个性状主成分分析结果表明,确定甜菜主成分因子有根产量、含糖量和抗褐斑病性;聚类分析结果,按类群间遗传距离大于类群内遗传距离的原则分为6类.类群间的平均遗传距离(?)~2=16.781,大于该平均遗传距离的类群组合有Ⅰ和Ⅳ,Ⅰ和Ⅴ,Ⅰ和Ⅵ,Ⅱ和Ⅵ,Ⅲ和Ⅴ,Ⅲ和Ⅵ,在上述类群间选择亲本有效.     

78份杧果种质资源AFLP分析

利用AFLP标记技术对78份杧果种质进行遗传多样性分析,结果显示,9对AFLP引物共产生908个等位位点,平均每对引物产生100.89个等位位点,多态性带为794条,共产生42个特异性位点,能区分21份种质,单态带25条,缺失带17条,特异性条带比例为4.63％,多态性比例为87.44％。不同种质间的相似系数范围是0.603~0.913,平均相似系数为0.735。聚类分析结果显示,以遗传相似性系数0.726为阈值,供试的78份种质可分成5个类群。主成分分析结果将供试的78份种质可分成4个类群,通过空间距离更能直观地表现种质间关系远近。     

Chemical characterization of the essential oil from patchouli accessions harvested over four seasons

The genus Pogostemon of the Lamiaceae family includes several species known for their medicinal and aromatic properties. The species P. cablin is especially notable because the essential oil extracted from its leaves is internationally important and valuable, principally for the perfume and cosmetic industries. Because multiple factors can affect the chemical composition of the essential oil, the aim of this work was to evaluate the chemical variations in the essential oils of nine Pogostemon accessions harvested over four seasons. Two Pogostemon accessions (P. heyneanus, but received as P. cablin) and seven P. cablin accessions from different sources were evaluated. The transplants were planted in January 2008, and the harvests were conducted in May, August, and November 2008 and February 2009. The chemical composition of the essential oils was evaluated quantitatively and qualitatively. Patchoulol was the major compound from the four harvests of all of the P. cablin accessions. The principal compound from the accessions POG-001 and POG-006 was β-pinene. Two clusters were detected by multivariate analyses of the four harvests. Cluster I was formed by the accessions POG-001 and POG-006 (P. heyneanus), and Cluster II was formed by the accessions of P. cablin (POG-002, POG-014, POG-015, POG-016, POG-019, POG-021, and POG-022).     

应用ISSR标记分析12份臂形草种质的遗传差异

选用17条ISSR引物分析12份臂形草种质遗传差异,结果表明:臂形草种质问的多态性高,17条引物产生了286条DNA片段,其中280条具有多态性,多态性比率高达97.90%;每个引物可扩增出6～23条DNA片段,平均16.8条,种质问遗传相似系数变化范围为0.486～0.968,平均值为0.681;通过聚类分析可将12份臂形草种质分为两类:一类为巴拉草和湿生臂形草,其余品种则聚为另一类.     

基于ISSR标记的咖啡资源遗传多样性分析

采用ISSR分子标记对87份咖啡资源进行遗传多样性和亲缘关系分析。结果表明,19条ISSR引物扩增出140条带,其中多态性带107条,多态性位点为76.4%。运用UPGMA方法构建了聚类图,在遗传相似系数0.625水平下,87份资源被分为3大类。第Ⅰ类群包括了3份大粒种（Coffea liberica Bull ex Hiern）;第Ⅱ类群为中粒种咖啡（C. canephora Pierre）;第Ⅲ类群包括了全部小粒种资源（C. arabica Linne）,共83份。咖啡种质的遗传关系种间容易划分,在种的分类水平上存在遗传关系多样性,而小粒种咖啡种内遗传多样性较窄。该研究结果将为咖啡种质鉴定、分类及分子育种提供重要科学依据。表明用ISSR分子标记进行咖啡资源遗传多样性的分析是可行的。     

Rice root morphological traits are related to isozyme group and adaptation

Rice accessions from the International Rice Research Institute (IRRI) germplasm bank were evaluated for root traits of 40-day-old plants grown in soil in the greenhouse. The 136 accessions represented six groups defined on the basis of isozyme classification, with isozyme group six further subdivided on the basis of origin and morphology. An additional 28 rice cultivars were evaluated for seminal root xylem vessel diameter when grown in pots in a growth chamber. Rice groups differed in root thickness, root xylem vessel diameter, root:shoot ratio, and patterns of root distribution. Isozyme group 1, which corresponds generally to the indica subspecies, had thin, superficial roots with narrow vessels and a low root:shoot ratio. The other major isozyme group, group 6, comprising japonica types, was characterized by thick roots with wider vessels, a greater proportion of the root weight below 15 cm, and a larger root:shoot ratio. On an average, the bulu and temperate group 6 accessions were similar to the non-bulu types except that their root:shoot ratios and proportion of root weight above 15 cm were more similar to group 1. Group 2, with aus types from South Asia, was characterized by intermediate root thickness, but vertical root distribution and root:shoot ratio were more similar to group 6. The minor isozyme groups 3–5 were represented by few accessions, and in general, they had root thickness and root distribution profiles more similar to group 1 than to group 6. While significant differences were observed among isozyme groups for all the traits under study, there was significant variation within groups and groups overlapped for all traits measured. This study highlights the wide range of variability for constitutive root traits in rice. For example, root thickness ranged from 0.68 to 1.04 mm, seminal root xylem vessel diameters from 30 to 58 μm, root:shoot ratios from 0.05 to 0.21, and accessions had from 44 to 73% of the total root weight concentrated in the surface 15 cm of soil. For the 28 cultivars evaluated, root xylem vessel diameter was highly correlated with reported values of leaf epicuticular wax content (r=0.89). These values indicate the range of genetic variation within the rice genome for root morphological traits.     

柱花草种质的RAPD多态性和对炭疽病的抗性分析

利用RAPD技术分析了45个柱花草品种的遗传多样性和抗病性,从200条随机引物中筛选出20条引物进行扩增,其多态性水平为71.5%。根据RAPD扩增结果,采用非加权成对平均数法（UPGMA）对45个柱花草品种进行了聚类分析并建立了树系图,其遗传相似系数为0.5-0.94,在0.665水平上分为14类（A~N）。通过盆栽植株接种我国2种典型的柱花草胶孢炭疽菌试验进行了抗病性筛选,结果表明∶抗病品种对2种病原菌的抗性相关系数为0.904。应用多重对应分析（MCA）方法对RAPD扩增结果和柱花草品种抗性鉴定结果进行了分析∶分为6类并计算了每一类的平均距离;除第1类外,柱花草对试验采用的2个炭疽菌生理小种的抗病性或感病性在其RAPD所检测到的遗传多样性分类中呈随机分布,表现出高度的多样性。