Development of microsatellite markers from loquat, Eriobotrya japonica (Thunb.) Lindl

Loquat (Eriobotrya japonica) is a minor fruit which has become an interesting alternative into the European fruit industry. This interest resulted in a loquat germplasm collection established at the Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain. Currently, it is the main reservoir of this species outside Asia. We developed and characterized the first 21 polymorphic microsatellite loci from a CT/AG-enriched loquat genomic library. The observed heterozygosity ranged between 0.20 and 1.00, expected heterozygosity ranged between 0.17 and 0.81, three markers were multilocus and eight loci departed significantly from Hardy-Weinberg equilibrium. These markers will facilitate diversity and genetic studies into the species.     

Phenological growth stages of loquat tree (Eriobotrya japonica (Thunb.) Lindl.)

Conservation, characterisation and utilisation of minor fruit tree species is an important objective for diversification of agro-food production. One such fruit tree is the loquat, a tree that originated in China but is well adapted to the Mediterranean area. The conservation and utilisation of suitable germplasm requires an accurate characterisation and evaluation of the material. A first step in characterisation is to use phenotypic traits. This paper describes the phenological growth stages of loquat tree using the extended BBCH scale. Seven principal growth stages (PGS) for bud, leaf and shoot development, inflorescence emergence, flowering, fruit development and fruit maturity and 31 secondary growth stages are described and compared with a previous scale based on Fleckinger classical methodology. An example of application of the extended BBCH scale for characterisation of loquat cultivars from IVIA germplasm collection is reported.     

Development of two loquat [Eriobotrya japonica (Thunb.) Lindl.] linkage maps based on AFLPs and SSR markers from different Rosaceae species

Loquat [Eriobotrya japonica (Thunb.) Lindl.] is a Rosaceae fruit species of growing interest as an alternative to the main fruit crops. However, only a few genetic studies have been carried out on this species. This paper reports the construction of the first genetic maps of two loquat cultivars based on AFLP and microsatellite markers from Malus, Eriobotrya, Pyrus and Prunus genera. An F₁ population consisting of 81 individuals, derived from the cross between ‘Algerie’ and ‘Zaozhong-6’ cultivars, was used to construct both maps. A total of 111 scorable simple sequence repeat (SSR) loci resulted from the testing of 440 SSR primer pairs in the analyzed progeny and the SSR transferability to Eriobotrya was found to be 74% from apple, 58% from pear and 49% from Prunus spp. In addition, 183 AFLP polymorphic bands were produced using 42 primer combinations. The ‘Algerie’ map was organized in 17 linkage groups covering a distance of 900 cM and comprising 177 loci (83 SSRs and 94 AFLPs) with an average marker distance of 5.1 cM. Self-incompatibility trait was mapped at the distal part of the LG17 linkage group, as previously reported in Malus and Pyrus. The ‘Zaozhong-6’ map covered 870 cM comprising 146 loci (64 SSRs and 82 AFLPs) with an average marker distance of 5.9 cM. The 44 SSRs and the 48 AFLPs share in common by both maps were essentially collinear and, moreover, the order of the 75% of apple and pear SSRs mapped in Eriobotrya was shown to be consistent across the Maloideae subfamily. As a whole, these maps represent a useful tool to facilitate loquat breeding and an interesting framework for map comparison in the Rosaceae.     

Hypoglycemic effects of a sesquiterpene glycoside isolated from leaves of loquat (Eriobotrya japonica (Thunb.) Lindl.).

Sesquiterpene glycoside, nerolidol-3-O-alpha-l-rhamnopyranosyl(1-->4)-alpha-l-rhamnopyranosyl(1-->2)-[alpha-l-rhamnopyranosyl(1-->6)]-beta-d-glucopyranoside was isolated from dried leaves of loquat [Eriobotrya japonica (Thunb.) Lindl., Rosaceae]. Hypoglycemic effects of this natural product were assessed in normal and alloxan-diabetic mice model. Animals received orally administration of the sesquiterpene glycoside in dose of 25 and 75 mg/kg. The anti-hyperglycemic effect was compared with gliclazide's. The dose of 25 and 75 mg/kg both exerted a significant (p<0.05) hypoglycemic effect in alloxan-diabetic mice throughout the test and a slight effect in normal mice.     

Genomic characterization of self-incompatibility ribonucleases (S-RNases) in loquat (Eriobotrya japonica Lindl.) (Rosaceae, Pyrinae)

Loquat (Eriobotrya japonica Lindl.) is a fruit tree species of the Pyrinae subtribe of the Rosaceae that behaves as self incompatible. Since self-incompatibility in the Rosaceae is of the gametophytic type where a stylar ribonuclease (S-RNase) controls the female function of pollen–pistil recognition, consensus primers derived from the alignment of S-RNase sequences from other Pyrinae species were used to search for S-RNases in loquat. As a result, the first four S-RNases were sequenced for this species. The genomic sequences obtained showed the structural features of Pyrinae S-RNases. Moreover, microscopic observations of pollen tube growth in the style confirmed the inter-(in)compatibility relationships predicted from the molecular analyses. Phylogenetic analysis of the deduced amino acid sequences with other Pyrinae S-RNases confirmed that divergence of S-alleles in loquat and the Pyrinae predated speciation. This study reports for the first time the genomic characterization of S-RNases in loquat, providing a sound basis for an appropriate selection of pollinator cultivars and an adequate design of breeding programs.     

Genetic diversity of elite sweet sorghum genotypes assessed by SSR markers

To determine genetic diversity among 47 elite sweet sorghum (Sorghum bicolor ssp. bicolor L.) genotypes, 46 simple sequence repeat (SSR) markers evenly distributed on all 10 chromosomes were selected. All SSR markers used were polymorphic among the genotypes studied. A total of 228 alleles were identified with an average of 4.96 alleles per marker. Furthermore, the genotypes studied showed medium genetic diversity. Clustering analysis grouped the 47 genotypes into 5 distinct clusters.     

Genetic diversity of cultivated flax (Linum usitatissimum L.) germplasm assessed by retrotransposon-based markers

Retrotransposon segments were characterized and inter-retrotransposon amplified polymorphism (IRAP) markers developed for cultivated flax (Linum usitatissimum L.) and the Linum genus. Over 75 distinct long terminal repeat retrotransposon segments were cloned, the first set for Linum, and specific primers designed for them. IRAP was then used to evaluate genetic diversity among 708 accessions of cultivated flax comprising 143 landraces, 387 varieties, and 178 breeding lines. These included both traditional and modern, oil (86), fiber (351), and combined-use (271) accessions, originating from 36 countries, and 10 wild Linum species. The set of 10 most polymorphic primers yielded 141 reproducible informative data points per accession, with 52% polymorphism and a 0.34 Shannon diversity index. The maximal genetic diversity was detected among wild Linum species (100% IRAP polymorphism and 0.57 Jaccard similarity), while diversity within cultivated germplasm decreased from landraces (58%, 0.63) to breeding lines (48%, 0.85) and cultivars (50%, 0.81). Application of Bayesian methods for clustering resulted in the robust identification of 20 clusters of accessions, which were unstratified according to origin or user type. This indicates an overlap in genetic diversity despite disruptive selection for fiber versus oil types. Nevertheless, eight clusters contained high proportions (70?C100%) of commercial cultivars, whereas two clusters were rich (60%) in landraces. These findings provide a basis for better flax germplasm management, core collection establishment, and exploration of diversity in breeding, as well as for exploration of the role of retrotransposons in flax genome dynamics.     

Genetic diversity of Crotalaria germplasm assessed through phylogenetic analysis of EST-SSR markers.

The genetic diversity of the genus Crotalaria is unknown even though many species in this genus are economically valuable. We report the first study in which polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers derived from Medicago and soybean were used to assess the genetic diversity of the Crotalaria germplasm collection. This collection consisted of 26 accessions representing 4 morphologically characterized species. Phylogenetic analysis partitioned accessions into 4 main groups generally along species lines and revealed that 2 accessions were incorrectly identified as Crotalaria juncea and Crotalaria spectabilis instead of Crotalaria retusa. Morphological re-examination confirmed that these 2 accessions were misclassified during curation or conservation and were indeed C. retusa. Some amplicons from Crotalaria were sequenced and their sequences showed a high similarity (89% sequence identity) to Medicago truncatula from which the EST-SSR primers were designed; however, the SSRs were completely deleted in Crotalaria. Highly distinguishing markers or more sequences are required to further classify accessions within C. juncea.     

Genetic diversity in basmati rice (Oryza sativa L.) germplasm as revealed by microsatellite (SSR) markers

Genetic diversity among rice genotypes, including 15 indica basmati advance lines and 5 basmati improved varieties were investigated by 28 SSR markets including one indel marker. The SSRs covered all the 12 chromosomes that distributed across the rice genomes. The mean number of alleles per locus was 3.60, showing average number of polymorphism information content was 0.48. A total of 101 alleles were also identified from the microsatellite marker loci. A number of SSR markers were also identified that could be utilized to differentiate between rice genotypes. Pair wise Nei,s genetic distance between rice genotypes ranged from 0.07 to 0.95. The dendrogram based on cluster analysis by using SSR polymorphism that grouped the 20 genotypes of rice in to five clusters based on their genetic similarity. The result could be useful for the identification and selection of the diverse genotypes for the future cross breeding program and development of new rice varieties.     

Anti-oxidative effect of triterpene acids of Eriobotrya japonica (Thunb.) Lindl. leaf in chronic bronchitis rats

The study was to evaluate the effect of triterpene acids of Eriobotrya japonica (Thunb.) Lindl. leaf (TAL) on expression of antioxidative mediators by alveolar macrophages (AM) in rats with chronic bronchitis (CB), CB was induced by endotracheal instillation of lipopolysaccharedes (LPS) followed by Bacillus Calmette-Guérin (BCG) injection through caudal vein 1 week later. Treatment groups received TAL at there different doses (50, 150, or 450 mg/kg daily, intragastrically (i.g.)) or dexamethasone (1.2 mg/kg daily i.g.) for 2 weeks, 7 days after LPS injection. AM were then isolated and incubated. Superoxide dismutase (SOD) and methylene dianiline (MDA) levels in AM were measured by commercial kits; meanwhile, heme oxygenase-1 (HO-1) expression and its mRNA expression in AM were detected by immunocytochemistry and RT-PCR, respectively. HO-1 activity of the lung was also detected by a specific biochemistry reaction. The levels of MDA and HO-1 expressed by cultured AM and the HO-1 activity in the lung of the TAL groups were significantly lower than those from the CB group without treatment (p < 0.01 and p < 0.05, respectively), while the SOD levels were increased in a dose-dependent manner by TAL treatment. These results suggest that TAL inhibits HO-1 expression and MDA production and up-regulates SOD expression in AM from CB rats, which might be one of molecular mechanisms of its anti-inflammatory effects in CB rats.     

利用SSR分析红菜苔的遗传多样性

红菜苔是我国独有的蔬菜资源,深受消费者喜爱。利用63对SSR引物检测来自全国的45份红菜苔种质资源的遗传多样性,63对引物扩增出124条带,平均每条引物扩增出近2条带,扩增产物片段大小都在150～300bp之间,相似系数在0.56～0.89之间。结果表明,红菜苔具有丰富的遗传多样性,本研究为菜苔资源的利用和育种提供了分子生物学依据。     

枇杷叶片胚性愈伤组织诱导与内源激素含量的关系

为揭示胚性愈伤组织发生过程中内源激素的变化规律,本研究以枇杷叶片为实验材料,通过诱导胚性愈伤组织获得体细胞胚,采用高效液相色谱法测定枇杷叶片及愈伤组织的赤霉素（GA₃）、生长素（IAA）、脱落酸（ABA）和玉米素（ZT）4种内源激素的含量,探讨胚性愈伤组织发育过程中4种内源激素的动态变化。结果显示,不同成熟度叶片内IAA/ZT比值对胚性愈伤组织的发生有正效应,而GA₃/IAA的比值具有负效应。胚性愈伤组织的发生需要较低含量的GA₃及高含量的IAA和ABA,IAA/ZT比值高有利于胚性愈伤组织形成,培养后期及时添加一定量的外源激素有利于胚性保持。本研究可为离体培养时选择外植体、添加外源激素及控制继代时间提供理论指导,并为快速获得枇杷胚性材料、开展基因转化研究奠定基础。     

Genetic diversity analysis in sorghum germplasm as estimated by AFLP, SSR and morpho-agronomical markers

A comparison of the different methods of the estimation of genetic diversity is important to evaluate their utility as a tool in germplasm conservation and plant breeding. Amplified fragment length polymorphism (AFLP), microsatellites or SSR and morphological traits markers were used to evaluate 45 sorghum germplasm for genetic diversity assessment and discrimination power. The mean polymorphism information content (PIC) values were 0.65 (AFLPs) and 0.46 (SSRs). The average pairwise genetic distance estimates were 0.57 (morphological traits), 0.62 (AFLPs) and 0.60 (SSRs) markers data sets. The Shannon diversity index was higher for morphological traits (0.678) than AFLP (0.487) and SSR (0.539). The correlation coefficients obtained by the Mantel matrix correspondence test, which was used to compare the cophenetic matrices for the different markers, showed that estimated values of genetic relationship given for AFLP and SSR markers, as well as for morphological and SSR markers were significantly related (p <0.001). However, morphological and AFLP data showed non-significant correlation (p >0.05). Both data sets from AFLP and SSR allowed all accessions to be uniquely identified; two accessions could not be distinguished by the morphological data. In summary, AFLP and SSR markers proved to be efficient tools in assessing the genetic variability among sorghum genotypes. The patterns of variation appeared to be consistent for the three marker systems, and they can be used for designing breeding programmes, conservation of germplasm and management of sorghum genetic resources.     

Genetic mapping of the loquat canker resistance locus in bronze loquat (Eriobotrya deflexa)

Loquat canker disease, caused by Pseudomonas syringae pv. eriobotryae, is one of the most harmful diseases of commercial cultivars of loquat (Eriobotrya japonica). To introgress resistance to loquat canker, we identified the linkage group and position of the resistance locus derived from the related wild species bronze loquat (Eriobotrya deflexa). The segregation of resistance and susceptibility fit the expected ratio of 1:1 in 96 individuals from a three-way cross involving bronze loquat (heterozygous for resistance) and two cultivars of loquat (susceptible). The genomic region containing Pse-a was identified by using a genome scanning approach, and the loquat canker resistance locus was mapped at the top of linkage group 10 by applying novel simple sequence repeat (SSR) markers designed on the basis of the ‘Golden Delicious’ apple genome sequence. The constructed linkage group spans 69.4 cM and has an average marker density of 2.6 cM per marker. The developed molecular markers tightly linked to the loquat canker resistance locus will be useful for marker-assisted selection and for introgression of resistance into loquat in breeding programs.     

Genetic diversity of the Bambara groundnut (Vigna subterranea (L.) Verdc.) as assessed by SSR markers

Bambara groundnut ( Vigna subterranea (L.) Verdc.) is an important African legume crop. In this study, a collection consisting of 240 accessions was analyzed using 22 simple sequence repeat (SSR) markers. In total, 166 alleles were detected, with a mean of 7.59 alleles per locus. Allelic and gene diversities were higher in the west African and Cameroon/Nigeria regions with 6.68 and 6.18 alleles per locus, and 0.601 and 0.571, respectively. The genetic distance showed high similarity between west African and Cameroon/Nigeria accessions. Principal coordinate analyses and neighbor-joining analysis consistently revealed that the majority of west African accessions were grouped with Cameroon/Nigeria accessions, but they were differentiated from east African, central African, and southeast Asian accessions. Population structure analysis showed that two subpopulations existed, and most of the east African accessions were restricted to one subpopulation with some Cameroon/Nigeria accessions, whereas most of the west African accessions were associated with most of the Cameroon/Nigeria accessions in the other subpopulation. Comparison with SSR analysis of other Vigna cultigens, i.e., cultivated azuki bean ( Vigna angularis ) and mungbean ( Vigna radiata ), reveals that the mean gene diversity of Bambara groundnut was lower than azuki bean but higher than mungbean.     

用ISSR标记技术分析山药品种遗传多样性

利用ISSR标记技术对28个山药品种的遗传多样性进行分析。结果表明,从44条ISSR引物中可筛选出7条能够扩增出清晰、稳定条带的引物;这7条ISSR引物对28个山药品种扩增条带间存在较大差异,多态性条带比率为83．01％,Shannon多样性指数为0．3191;构建的分子树状图将28个山药品种划分为4组：第一组含有日本白、花山药和日本园3个品种;第二组为小叶山药;第三组为嵩野1号;其余23个品种归入第四组。而且主成分分析结果支持上述的聚类分析结果。这为利用ISSR标记技术鉴定山药品种,为有效地利用山药种质资源提供了依据。