Characterization of new microsatellite markers in mung bean,Vigna radiata (L.)

The present work reports the isolation and characterization of new polymorphic microsatellites in mung bean (Vigna radiata L.). Of 93 designed primer pairs, seven were found to amplify polymorphic microsatellite loci, which were then characterized using 34 mung bean accessions. The number of alleles ranged from two to five alleles per locus with an average of three alleles. Observed and expected heterozygosity values ranged from 0 to 0.088 and from 0.275 to 0.683, respectively. All seven loci showed significant deviations from Hardy–Weinberg equilibrium, whereas only one pairwise combination (GBssr‐MB77 and GBssr‐MB91) exhibited significant departure from linkage disequilibrium. These newly developed markers are currently being utilized for diversity assessment within the mung bean germplasm collection of the Korean Gene Bank.     

Developing and characterising Ricinus communis SSR markers by data mining of whole-genome sequences

Ricinus communis is a versatile industrial oil crop that is cultivated worldwide. Genetic improvement and marker-assisted breeding of castor bean have been slowed owing to the lack of abundant and efficient molecular markers. As co-dominant markers, simple sequence repeats (SSRs) are useful for genetic evaluation and molecular breeding. The recently released whole-genome sequence of castor bean provides useful genomic resources for developing markers on a genome-wide scale. In the present study, the distribution and frequency of microsatellites in the castor bean genome were characterised and numerous SSR markers were developed using genomic data mining. In total, 18,647 SSR loci at a density of one SSR per 18.89 Kb in the castor bean genome sequence (representing approximately 352.27 Mb) were identified. Dinucleotide repeats were the most frequently observed microsatellites, although the AAT repeat motif was also prevalent. Using six cultivars as screening samples, 670 polymorphic SSR markers from 1,435 primer pairs (46.7 %) were developed. Trinucleotide motif loci contained a higher proportion of polymorphisms (48.5 %) than dinucleotide motif loci (39.2 %). The polymorphism level in the SSR loci was positively correlated with the increasing number of repeat units in the microsatellites. The phylogenetic relationship among 32 varieties was evaluated using the developed SSR markers. Cultivars developed at the same institute clustered together, suggesting that these cultivars have a narrow genetic background. The large number of SSR markers developed in this study will be useful for genetic mapping and for breeding improved castor-oil plants. These markers will also facilitate genetic and genomic studies of Euphorbiaceae.     

世界特种油料种质资源保存概况

为加强特种油料种质资源的收集保存,更好地为育种研究利用提供服务,本文阐述了特种油料种质资源在我国及世界上重点国家的保存情况.美国、印度、欧盟、中国等13个国家共保存向日葵、红花、亚麻(含纤用)、蓖麻及苏子等特种油料种质资源约9万份,其中亚麻30000多份,向日葵21800多份,红花15000多份,蓖麻约5000多份,苏子近900份.欧盟、美国、俄罗斯和加拿大是亚麻资源的主要保存国家(地区);向日葵资源主要集中在美国、欧盟和中国;红花种质主要分布在印度、美国、中国和俄罗斯;蓖麻种质以中国、美国和印度居多.比较这些国家所拥有的特种油料种质资源数量,美国位居第一,保存数量最多,超过22000份;印度其次;欧盟、中国和俄罗斯居中.中国保存特油作物种质资源(蓖麻、向日葵、红花、苏子)8400余份,其中21%为国外种质,国内种质主要来源于湖北省、华北、东北、西北和西南地区.本文为我国特种油料种质资源的引进、收集保存提出了建议.     

我国优势油脂类生物柴油植物蓖麻的种质资源发掘和生物柴油利用

发展可再生生物质能源是解决人类能源危机和环境污染的重要途径。利用边际土地发展油脂类生物质能是生物质能的重要组成部分。蓖麻因为适应性强和油脂成份独特被誉为"理想的生物柴油植物"。蓖麻是我国优势油脂类能源植物,利用边际土地,发展蓖麻产业为我国生物柴油产业化提供原料,是我国现阶段生物柴油产业化发展的相对理想而又现实的选择,而且具有重要的发展前景和巨大的发掘潜力。立足我国现阶段生物柴油产业化的瓶颈问题,着重阐述了蓖麻种质资源发掘的现状、优良品种培育的途径和发展前景,以及利用蓖麻种子油生产商业化生物柴油的现状,以期推动我国利用边际土地发展蓖麻产业以及生物柴油商业化生产。     

Genetic diversity,seed size associations and population structure of a core collection of common beans (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.)

Cultivated common bean germplasm is especially diverse due to the parallel domestication of two genepools in the Mesoamerican and Andean centers of diversity and introgression between these gene pools. Classification into morphological races has helped to provide a framework for utilization of this cultivated germplasm. Meanwhile, core collections along with molecular markers are useful tools for organizing and analyzing representative sets of these genotypes. In this study, we evaluated 604 accessions from the CIAT core germplasm collection representing wide genetic variability from both primary and secondary centers of diversity with a newly developed, fluorescent microsatellite marker set of 36 genomic and gene-based SSRs to determine molecular diversity and with seed protein analysis to determine phaseolin alleles. The entire collection could be divided into two genepools and five predominant races with the division between the Mesoamerica race and the Durango–Jalisco group showing strong support within the Mesoamerican genepool and the Nueva Granada and Peru races showing less diversity overall and some between-group admixture within the Andean genepool. The Chile race could not be distinguished within the Andean genepool but there was support for the Guatemala race within the Mesoamerican genepool and this race was unique in its high level of diversity and distance from other Mesoamerican races. Based on this population structure, significant associations were found between SSR loci and seed size characteristics, some on the same linkage group as the phaseolin locus, which previously had been associated with seed size, or in other regions of the genome. In conclusion, this study has shown that common bean has very significant population structure that can help guide the construction of genetic crosses that maximize diversity as well as serving as a basis for additional association studies.     

Single nucleotide polymorphisms for assessing genetic diversity in castor bean (<Emphasis Type="Italic">Ricinus communis</Emphasis>)

Background  

Castor bean (Ricinus communis) is an agricultural crop and garden ornamental that is widely cultivated and has been introduced worldwide. Understanding population structure and the distribution of castor bean cultivars has been challenging because of limited genetic variability. We analyzed the population genetics of R. communis in a worldwide collection of plants from germplasm and from naturalized populations in Florida, U.S. To assess genetic diversity we conducted survey sequencing of the genomes of seven diverse cultivars and compared the data to a reference genome assembly of a widespread cultivar (Hale). We determined the population genetic structure of 676 samples using single nucleotide polymorphisms (SNPs) at 48 loci.     

Isolation and characterization of a first set of polymorphic microsatellite markers in saffron, Crocus sativus (Iridaceae)

? Premise of the study: Twelve novel polymorphic microsatellite loci were developed and characterized from a repeat-enriched genomic library of Crocus sativus to study population and conservation genetics of this economically and medically important species. ? Methods and Results: The microsatellite loci were isolated using a modified Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) method. The average number of alleles per locus was 2.6. The observed and expected heterozygosities varied from 0.07 to 0.92 and 0.1 to 0.58, respectively. Polymorphic information content value ranged from 0.09 to 0.55 with an average of 0.34. Four out of twelve loci showed significant departures from Hardy-Weinberg equilibrium. ? Conclusions: The microsatellite markers reported here will be useful for evaluating genetic diversity and will likely serve as an ideal resource for use in marker-assisted breeding programs, germplasm analysis, and varietal identification.     

Marigold,Castor Bean,and Chrysanthemum as Controls of Meloidogyne incognita and Pratylenchus alleni

Root and soil populations of Meloidogyne incognita were significantly fewer from marigold, castor bean, and chrysanthemum than from tomato roots and soil, but not from fallow soil. Root populations of Pratvlenchus alleni were significantly fewer from marigold, castor bean, and chrysanthemum than from tomato: marigold had the fewest. Root populations of M. incognita and P. alleni from tomato simultaneously cultivated with marigold, castor bean, and chrysanthemum were significantly fewer than from tomato cultivated alone. Aborted giant cells and dead M. incognita (larvae and females) were observed in roots of marigold and castor bean, but not in chrysanthemum or tomato. Significantly more males than females occurred in castor bean roots. lnfcction sites of P. alleni appeared normal in all hosts. Thin-layer and column chromatography of alcoholic extracts from castor bean revealed no nematicidal thiophenc derivatives.     

Microsatellite primers in the Chinese dove tree, Davidia involucrata (Cornaceae), a relic species of the Tertiary

? Premise of the study: The first microsatellite primers were developed for Davidia involucrata, an endangered relic species of the Tertiary in China, to further describe its genetic variability and population structure. ? Methods and Results: Using the Fast Isolation by AFLP of Sequences Containing Repeats (FIASCO) protocol, 15 polymorphic microsatellite loci were isolated and characterized in 20 individuals from the germplasm collections of D. involucrata at the Hunan Forest Botanical Garden. High levels of polymorphism were revealed, with the total number of alleles per locus and the number of alleles per locus per individual ranging from two to 13 and from one to six, respectively. ? Conclusions: The multibanded patterns of microsatellite loci obtained in the current study confirmed that D. involucrata might be a polyploid species. The primers will be useful for studies of genetic diversity and for guiding conservation strategies for D. involucrata.     

Structure and level of genetic diversity in various bean types evidenced with microsatellite markers isolated from a genomic enriched library

We have constructed a common bean genomic library enriched for microsatellite motifs (ATA), (CA), (CAC) and (GA). After screening, 60% of the clones selected from the library enriched for the (ATA) repeat contained microsatellites versus 21% of the clones from the library enriched for (GA) (CA) and (CAC) repeats. Fifteen primer pairs have been developed allowing for the amplification of SSR loci. We have evaluated the genetic diversity of these loci between 45 different bean lines belonging to nine various quality types. A total of 81 alleles were detected at the 15 microsatellite loci with an average of 5.3 alleles per locus. We have investigated the origin of allelic size polymorphism at the locus PvATA20 in which the number of repeats ranges from 24 to 85. We have related these large differences in repeat number to unequal crossing-over between repeated DNA regions. The diversity analysis revealed contrasted levels of variability according to the bean type. The lower level was evidenced for the very fine French bean, showing the effect of breeders intensive selection.     

Genetic diversity analysis in the section Caulorrhizae (genus Arachis) using microsatellite markers

Diversity in 26 microsatellite loci from section Caulorrhizae germplasm was evaluated by using 33 accessions of A. pintoi Krapov. & W.C. Gregory and ten accessions of Arachis repens Handro. Twenty loci proved to be polymorphic and a total of 196 alleles were detected with an average of 9.8 alleles per locus. The variability found in those loci was greater than the variability found using morphological characters, seed storage proteins and RAPD markers previously used in this germplasm. The high potential of these markers to detect species-specific alleles and discriminate among accessions was demonstrated. The set of microsatellite primer pairs developed by our group for A. pintoi are useful molecular tools for evaluating Section Caulorrhizae germplasm, as well as that of species belonging to other Arachis sections.     

Genetic diversity of Tunisian date palms (Phoenixdactylifera L.) revealed by nuclear microsatellite polymprohism

Fourteen microsatellite loci of Phoenix dactylifera were targeted to examine the genetic diversity in Tunisian date-palms germplasm. They showed a high level of polymorphism in 49 accessions from three main oases with little geographic structure within Tunisia. The microsatellite data agrees with previous analyses of Tunisian germplasm using other molecular markers. 100% of local date-palms accessions were successfully fingerprinted and easily distinguished by the help of only three loci. The possibility of using microsatellites for large scale molecular labelling of offshoots and in vitro plantlets and their implication in the plant material certification is discussed.     

Isolation and characterization of polymorphic microsatellites in Cocos nucifera L.

Microsatellites or simple sequence repeats (SSRs) were isolated from coconut (Cocos nucifera) and tested for polymorphism on restricted germplasm. Sequencing of 197 clones from a cv. Tagnanan Tall-enriched genomic library showed that 75% contained a microsatellite, of which 64% were dinucleotide (GA/CT, CA/GT and GC/CG), 6% were trinucleotide, and 30% were compound repeats. Of 41 primer pairs tested on Tagnanan Tall genomic DNA, 38 gave the expected size product, two amplified two loci, and another gave a multilocus pattern. On 20 coconut samples, the 38 SSRs detected 198 alleles (average: 5.2 alleles per microsatellite). Genetic diversity (D = 1 - sigma pi2) values ranged from 0.141 to 0.809. Heterozygotes were present at high frequencies among some dwarf samples. Analysis of similarity matrices based either on shared alleles at each locus (simple matching coefficient) or on allele bands across all loci (Jaccard coefficient) showed similar results. Dwarfs grouped separately from talls and showed less genetic diversity. In a wider test on 40 samples, 8 SSRs detected 64 alleles (average: eight alleles per microsatellite). These results indicate the high potential of microsatellites to detect genetic diversity in coconut germplasm.     

Development and characterization of polymorphic microsatellite markers in Linum usitatissimum

Thirty-five microsatellite loci were isolated and characterized in Linum usitatissimum using enriched genomic libraries. These loci were screened in eight cultivars from different countries and regions and were found to be polymorphic, with the number of alleles per locus ranging from two to six, and observed and expected heterozygosities ranging from 0.125 to 0.375 (mean 0.013) and from 0.233 to 0.842 (mean 0.601), respectively. These polymorphic new microsatellite loci will be useful for genetic linkage map construction, germplasm classification and identification, gene identification and quantitative trait loci mapping, and marker-assisted selection in breeding in L. usitatissimum.     

Polymorphic microsatellite and cryptic simple repeat sequence markers in pineapples (Ananas comosus var. comosus)

A rapid method for isolating microsatellite loci in pineapples, based on the 5′‐anchored polymerase chain reaction technique, revealed 137 microsatellite loci (consisting of 62 dinucleotide, 24 trinucleotide, 49 tetranucleotide and 2 hexanucleotide repeats) and 16 cryptically simple repeat sequences. We report on the characterization of 19 polymorphic microsatellite loci and one cryptic simple repeat loci in pineapples. The number of alleles per locus ranged from two to four while the observed heterozygosity ranged from 0.1705 to 1. These markers are useful as tools for detecting levels of genetic variation in pineapple varieties for germplasm management and crossbreeding purposes.     

蓖麻杂交种的SSR鉴定及遗传变异分析

采用SSR标记对蓖麻CSR24×CSR181杂交所得的F1种子进行分析,为蓖麻早期杂种鉴定和遗传变异分析奠定技术与理论基础。结果表明:(1)各位点鉴定所得结果基本一致,除RCM207和RC129位点鉴定的杂种率未超过10%外,其它位点的杂种率都十分接近,在13.46%～17.27%之间。(2)少数个体在相关位点发生了变异,在引物RC242的扩增图谱中有4个单株出现了双亲特异条带的缺失,产生了双亲都没有的新条带;在引物Rco23、Rco26、Rco29、RC129、RCM613和RCM999的扩增结果中出现了父本特异条带的缺失,同时产生了一条新条带。(3)多样性及UPGMA聚类分析表明杂交后代遗传变异显著,子代个体与亲本间的遗传相似系数在0.45～1.0之间,个体间差异明显。     

Characterization and development of SSR markers of schizothoracine fish (Cypriniformes: Cyprinidae) based on SLAF-seq Technique

Highly specialized grade of Schizothoracine fishe is primarily distributed in the drainage of Qinghai-Tibet Plateau and its surrounding region, which has precious biological resources. However, overfishing and habitat destruction have seriously affected the germplasm resources and population genetic structure of HSG, so it is a significance to search for reliable genetic markers to protect its wild resources. In this work, 27 novel polymorphic microsatellite were firstly generated for the entire HSG based on the SLAF data of the grade and assess their polymorphism in HSG from 4 genera of 8 species. Among which W24, W41, W50 were existed only in 3–4 populations with low amplification efficiency, and loci of W3, W6, W12, W25, W28, and W32 were absent in 1–3 species, the rest of that 18 loci were successfully amplified in all specimens. The average of the number of alleles (NA) per locus was 46.04, ranging from 12 to 79, and the average observed and expected heterozygosities were estimated from 0.539 to 0.785 and 0.471 to 0.669 in 8 species, respectively. The average polymorphic information content (PIC) of each species was from 0.669 to 0.433. The range of average Shannon-Weiner diversity index (H') were calculated from 0.914 to 1.717 in 8 species. To sum up, we developed 27 microsatellite loci with higher quality and stability, which could provide effective technical support for the study of germplasm resources of highly specialized grade of schizothoracine fishe.     

Isolation of microsatellite markers in mungbean,Vigna radiata

A simple and rapid method for isolating microsatellite loci in mungbean, Vigna radiata, based on the 5′‐anchored polymerase chain reaction technique revealed 23 microsatellite loci and six cryptically simple sequence repeats. We report on the characterization of seven polymorphic microsatellite loci in V. radiata. The number of alleles per locus ranged from 2 to 5 while the observed heterozygosity ranged from 0 to 0.9048. These markers should prove useful as tools for detecting genetic variation in mungbean varieties for germplasm management and crossbreeding purposes.     

Development and Leaf Consumption by Spodoptera cosmioides (Walker) (Lepidoptera: Noctuidae) Reared on Leaves of Agroenergy Crops

Spodoptera cosmioides (Walker) (Lepidoptera: Noctuidae) is a polyphagous pest that threatens more than 24 species of crop plants including those used for biodiesel production such as Ricinus communis (castor bean), Jatropha curcas (Barbados nut), and Aleurites fordii (tung oil tree). The development and leaf consumption by S. cosmioides reared on leaves of these three species were studied under controlled laboratory conditions. The egg-to-adult development time of S. cosmioides was shortest when reared on castor bean leaves and longest when reared on tung oil tree leaves. Larvae reared on castor bean and Barbados nut leaves had seven instars, whereas those reared on tung oil tree leaves had eight. Females originating from larvae reared on castor bean and Barbados nut leaves showed greater fecundity than did females originating from larvae reared on tung oil tree leaves. Insects fed on castor bean leaves had shorter life spans than those fed on tung oil tree and Barbados nut leaves although the oviposition period did not differ significantly. The intrinsic and finite rates of increase were highest for females reared on castor bean leaves. Total leaf consumption was highest for larvae reared on tung oil tree leaves and lowest for those reared on Barbados nut leaves. We conclude that castor bean is a more appropriate host plant for the development of S. cosmioides than are Barbados nut and tung oil tree.     

Development and evaluation of microsatellite markers in Phoenix dactylifera L. and their transferability to other Phoenix species

Forty one simple sequence repeats were isolated from two microsatellite enriched libraries of date palm (Phoenix dactylifera L.). After screening, 17 selected microsatellite loci were characterized and evaluated on a set of 31 cultivars and clones from Algerian and Californian germplasm. All primer pairs produced an amplification product of the expected size and detected high polymorphism among the analysed samples. These nuclear simple sequence repeat (SSR) markers are expected to be a very effective tool for evaluating genetic diversity in date palm germplasm. Acrosstaxa amplification showed the usefulness of most SSR markers in 14 other species across the genus Phoenix.