Trophic interactions between two medium-sized mammals: the case of the native Dolichotis patagonum and the exotic Lepus europaeus in a hyper-arid ecosystem

As medium-sized herbivores, the exotic Lepus europaeus (European hare) and the native Dolichotis patagonum (mara) have been considered ecological equivalents. These species coexist in Ischigualasto Provincial Park, a hyper-arid ecosystem with scarce food resources. Our objective was to evaluate diet composition, relationship between diets and food availability, and trophic relationships between both herbivores. Collection of feces and vegetation sampling were made in the Mesquite woodland community. Diet composition was analyzed by microhistological analysis of feces. In both seasons, shrub species represented the most abundant cover type in the area, and annual forbs and grasses appeared in the wet season. Herbivores showed similar dietary ecology: shrubs were the main food items along the year, showing a higher plasticity compared to their diets in other ecosystems, where they selected mostly grasses. The mara selected shrubs such as Atriplex sp. and Prosopis torquata, whereas the European hare selected Cyclolepis genistoides, Atriplex sp., and Bulnesia retama. During the wet season, both herbivores supplemented their diets with grasses and annual forbs. In the dry season, there was increased consumption of cacti, such as Tephrocactus sp. The mara and the European hare are likely close ecological equivalents, in terms of dietary similarity, and they showed strong dietary overlap across the dry season (over 60 %). Thus, we can assume the existence of a potential trophic competition between mara and European hare, especially during the season when food resources are scarce. These results can be important for the management of drylands in South America, where populations of threatened herbivorous species, such as the mara, coexist with exotic animals, sharing spatial and trophic resources even in protected areas.     

Genetic diversity of Hemarthria altissima and its related species by EST-SSR and SCoT markers

There is a need for an appropriate evaluation of Hemarthria germplasm resources using genetic analysis. Understanding their genetic background will promote effective development and utilization of its germplasm resources in plant breeding. We examined the genetic diversity and relationships among 46 Hemarthria germplasm resources from four continents. Expressed Sequence Tags-Simple Sequence Repeat (EST-SSR) and Start Codon Targeted (SCoT) markers were used to investigate species Hemarthria altissima (36), Hemarthria compressa (8) and Hemarthria uncinata (2). We selected 19 EST-SSR primers and generated 550 polymorphic (94.7%). Twenty one SCoT primers were selected and amplified to produce 597 bands with 89.4% of polymorphic bands. The Mantel test between EST-SSR and SCoT matrices revealed significant correlations (r = 0.854) and the data from both markers were combined for cluster analysis. The 46 materials were clustered into two main groups by UPGMA clustering with a similarity coefficient ranging from 0.573 to 0.940 and the dendrogram was basically concordant with geographical origins and species. Among the three Hemarthria species, H. altissima was genetically closest to H. compressa while it was not close to H. uncinata. When the utility of the two markers were compared, we found EST-SSR to be more efficient than SCoT in determining the genetic diversity study of Hemarthria species.     

Genetic Variation and Breeding Signature in Mass Selection Lines of the Pacific Oyster (Crassostrea gigas) Assessed by SNP Markers

In breeding industries, a challenging problem is how to keep genetic diversity over generations. To investigate genetic variation and identify breeding signatures in mass selected lines of Pacific oyster (Crassostrea gigas), three sixth-generation selected lines and four wild populations were assessed using 103 single nucleotide polymorphism (SNP) markers. The genetic diversity data indicated that the selected lines exhibited a significant reduction in the observed heterozygosity and observed number of alleles per locus compared with the wild populations (P≤0.05), indicating the selected lines tended to lose genetic diversity contrasted with the wild populations. The unweighted pair-group method with arithmetic mean (UPGMA) analysis showed that the wild populations and selected lines were not separated into two groups. Using four outlier tests, a total of 17 loci were found under selection at two levels. The global outlier detection suggested that 4 common outlier loci were subject to selection using both the hierarchical island model and Bayesian likelihood approaches. At regional level, 3 SNPs were detected as outlier using at least two outlier tests and one outlier SNP (CgSNP309) was overlapped in the two wild-selected population comparisons. The candidate outlier SNPs provide valuable resources for future association studies in C. gigas.     

Afrotropical sand fly-host plant relationships in a leishmaniasis endemic area,Kenya

The bioecology of phlebotomine sand flies is intimately linked to the utilization of environmental resources including plant feeding. However, plant feeding behavior of sand flies remains largely understudied for Afrotropical species. Here, using a combination of biochemical, molecular, and chemical approaches, we decipher specific plant-feeding associations in field-collected sand flies from a dry ecology endemic for leishmaniasis in Kenya. Cold-anthrone test indicative of recent plant feeding showed that fructose positivity rates were similar in both sand fly sexes and between those sampled indoors and outdoors. Analysis of derived sequences of the ribulose-1,5-bisphosphate carboxylase large subunit gene (rbcL) from fructose-positive specimens implicated mainly Acacia plants in the family Fabaceae (73%) as those readily foraged on by both sexes of Phlebotomus and Sergentomyia. Chemical analysis by high performance liquid chromatography detected fructose as the most common sugar in sand flies and leaves of selected plant species in the Fabaceae family. Analysis of similarities (ANOSIM) of the headspace volatile profiles of selected Fabaceae plants identified benzyl alcohol, (Z)-linalool oxide, (E)-β-ocimene, p-cymene, p-cresol, and m-cresol, as discriminating compounds between the plant volatiles. These results indicate selective sand fly plant feeding and suggest that the discriminating volatile organic compounds could be exploited in attractive toxic sugar- and odor- bait technologies control strategies.     

Development of Capsicum EST–SSR markers for species identification and in silico mapping onto the tomato genome sequence

Capsicum spp. are widely cultivated for use as vegetables and spices. The Kihara Institute for Biological Research, Yokohama City University, Japan, has stocks of approximately 800 lines of Capsicum spp. collected from various regions of Central and South America, the regions of origin for Capsicum spp. In this study, 5,751 primer pairs for simple sequence repeat markers, based on 118,060 publicly available sequences of expressed sequence tags of Capsicum annuum, were designed and subjected to a similarity search against the genomic sequence of tomato, a model Solanaceae species. Nucleotide sequences spanning 2,245 C. annuum markers were successfully mapped onto the tomato genome, and 96 of these, which spanned the entire tomato genome, were selected for further analysis. In genotyping analysis, 60 out of the 77 markers that produced specific DNA amplicons showed polymorphism among the Capsicum lines examined. On the basis of the resulting data, the 192 tested lines were grouped into five main clusters. The additional sequencing analysis of the plastid genes, matK and rbcL, divided the resources into three groups. As a result, 19 marker loci exhibited genotypes specific to species and cluster, suggesting that the DNA markers are useful for species identification. Information on the DNA markers will contribute to Capsicum genetics, genomics, and breeding.     

Natural hybridization,introgression breeding,and cultivar improvement in the genus Actinidia

China is the original home of kiwifruit which are derived from the species complex Actinidia chinensis. A short domestication history of a little more than 100 years characterizes kiwifruit as a unique fruit crop whose cultivar improvement is heavily dependent on exploitation and selection of wild resources. Actinidia species are widespread geographically; their distributions often overlap, and hybridization between taxa is common naturally. Actinidia species that vary in ploidy and complex mixtures of cytotypes are prevalent in natural populations. Here, we review the recent emerging knowledge of natural distribution, biogeography, and population genetics in Actinidia with a particular focus on the pattern of overlapping distribution and natural hybridization among Actinidia species. Based on the comparison of the original geographical localities where most kiwifruit commercial cultivars were selected and the whole geographical range of the species complex A. chinensis, we propose that introgression breeding for new selections and cultivars of kiwifruit should utilize targeted exploration in natural hybrid zones as well as the genomic tools and related genetic resources that are becoming available to an unprecedented extent.     

三江源区冬虫夏草资源适宜性空间分布

冬虫夏草(Ophiocordyceps sinensis)是生长在青藏高原高寒地区的一种珍稀物种资源,具有极高的药用和经济价值,然而冬虫夏草资源的数量特征与空间格局尚不明确。以三江源区为例,结合冬虫夏草的生境条件,选取适宜冬虫夏草生长的生态环境指标,利用地理信息系统(GIS)中的空间分析方法对冬虫夏草资源的适宜性空间分布进行了研究,并用野外实地采样和入户调研数据进行验证。结果表明:三江源区冬虫夏草资源主要分布在东南部和中南部,分布面积约为18.45×10~4km~2,占该区总面积的50.74%。达日县、甘德县、玉树县、称多县、玛沁县、班玛县、久治县这7个县冬虫夏草适宜性面积占到了该县50%以上的面积,是三江源区冬虫夏草资源的主产区。基于GIS空间分析的结果与实地调查结果相符,说明利用空间分析方法划分冬虫夏草资源的适宜性分布区域是可行的,可为系统的全面调查冬虫夏草资源的分布及保护与合理开发利用冬虫夏草资源提供科学依据。     

Sexual selection: when to expect trade-offs

Empirical evidence is mixed for interspecific trade-offs in investment among sexually selected traits. One important reason may be the way resources are allocated among species. Consider a set of species that obtains the same fitness pay-off for investment in song or plumage. Simulations where resources were normally distributed among species revealed significant trade-offs between song and plumage ( ± s.d. of r = −0.54 ± 0.06). However, simulations where resources were distributed in a negative binomial fashion usually produced positive correlations (r = 0.11 ± 0.09). Repeating simulations on three published studies that concomitantly quantified elaboration of song and plumage indicated that trade-offs are likely, although these analyses make assumptions that require further evaluation. Moreover, there are currently too few empirical distributions to make generalizations about the likelihood of interspecific trade-offs in sexually selected traits.     

The origins of subsistence agriculture in Oceania and the potentials for future tropical food crops

Subsistence agriculture in the Pacific Islands has a complex prehistory centered on western Melanesia. Based on an analysis of cultigen provenience, a sequential model of a three-tiered crop structure of indigenous agricultural systems has been derived: (1) The independent early domestication of endemic species in the New Guinea region; (2) introduction of species from Southeast Asia; (3) the advent of American crop plants. The temporal sequence has archaeological and linguistic confirmation of 10 000 years ago for the beginnings of agriculture, 6000 years for Southeast Asian introduction, with the sweet potato contributing in Polynesia in prehistory, and in Melanesia only in post-Columbian times. Recent research directed toward issues of domestication in New Guinea and subsistence prehistory in Australia on three genera,Canarium, Colocasia andIpomoea, exemplify under-recognized resources with quite different potentials for economic botany. Unlike past exploitation of indigenous plant resources, future users of plants such as those exemplified, and especially where commercialization is involved, cannot avoid addressing intellectual property rights that pertain to species domesticated, selected or conserved by peoples of the non-industri-alized world.     

Genetic and functional diversity among root-associated psychrotrophic Pseudomonad’s isolated from the Himalayan plants

Out of 534 psychrotrophic bacteria, 12 bacteria were selected on the basis of plant growth promoting activities at 4 °C and identified as Pseudomonas genus. These strains showed high level of genetic polymorphisms based on RAPD and rep-PCR fingerprinting. This genetic variability revealed that isolates belonging to same species were as high as the variability among different species. Further inoculation of these Pseudomonas strains significantly improves root/shoot biomass and nutrients uptake of lentil plant as compared to non-bacterized control after 40 days of seed showing. Agglomerative hierarchical clustering analysis of pot assay results revealed that genetically diverse strains showing the same prototype in functional parameter and representing diverse blueprint of plant growth promoting attributes. Results of present findings explain the huge beneficial microbial resources from root zone of hilly crops of Himalayan region that could be effectively exploited as bio-inoculums for cold climatic condition.     

Ethnobotanical notes about some uses of medicinal plants in Alto Tirreno Cosentino area (Calabria, Southern Italy)

The present zootherapeutic study describes the traditional knowledge related to the use of different animals and animal-derived products as medicines by the Saharia tribe reside in the Shahabad and Kishanganj Panchayat Samiti's of Baran district of Rajasthan, India. A field survey was conducted from April to June 2006 by performing interview through structured questionnaire with 21 selected respondents, who provided information regarding use of animals and their products in folk medicine. A total of 15 animal species were recorded and they are used for different ethnomedical purposes, including cough, asthma, tuberculosis, paralysis, earache, herpes, weakness, muscular pain etc. The zootherapeutic knowledge was mostly based on domestic animals, but some protected species like the peacock (Pavo cristatus,), hard shelled turtle (Kachuga tentoria), sambhar (Cervus unicolor) were also mentioned as medicinal resources. We would suggest that this kind of neglected traditional knowledge should be included into the strategies of conservation and management of faunistic resources. Further studies are required for experimental validation to confirm the presence of bioactive compounds in these traditional remedies and also to emphasize more sustainable use of these resources.     

海南部分荔枝种质资源亲缘关系的SSR分析

利用SSR标记对22份荔枝材料进行了亲缘关系分析,从32对引物中筛选出22对多态性引物用于荔枝SSR扩增,共扩增到52条带,其中多态性条带49条,多态性百分率为94.23%。多态性条带经POPGENE32软件统计分析表明,22个位点的平均有效等位基因频率（Ne）、平均基因杂合度（H）、平均Shannon遗传多样性指数（H_i′）分别为1.364 3、0.296 0、0.417 0。通过NTSYS聚类结果显示,在相似系数为0.51处,供试材料被聚为两大类,第一类包括13份材料,又可分为两个亚类,第二类包括9份材料。     

Generation of ESTs for flowering gene discovery and SSR marker development in upland cotton

Background

Upland cotton, Gossypium hirsutum L., is one of the world''s most important economic crops. In the absence of the entire genomic sequence, a large number of expressed sequence tag (EST) resources of upland cotton have been generated and used in several studies. However, information about the flower development of this species is rare.

Methodology/Principal Findings

To clarify the molecular mechanism of flower development in upland cotton, 22,915 high-quality ESTs were generated and assembled into 14,373 unique sequences consisting of 4,563 contigs and 9,810 singletons from a normalized and full-length cDNA library constructed from pooled RNA isolated from shoot apexes, squares, and flowers. Comparative analysis indicated that 5,352 unique sequences had no high-degree matches to the cotton public database. Functional annotation showed that several upland cotton homologs with flowering-related genes were identified in our library. The majority of these genes were specifically expressed in flowering-related tissues. Three GhSEP (G. hirsutum L. SEPALLATA) genes determining floral organ development were cloned, and quantitative real-time PCR (qRT-PCR) revealed that these genes were expressed preferentially in squares or flowers. Furthermore, 670 new putative microsatellites with flanking sequences sufficient for primer design were identified from the 645 unigenes. Twenty-five EST–simple sequence repeats were randomly selected for validation and transferability testing in 17 Gossypium species. Of these, 23 were identified as true-to-type simple sequence repeat loci and were highly transferable among Gossypium species.

Conclusions/Significance

A high-quality, normalized, full-length cDNA library with a total of 14,373 unique ESTs was generated to provide sequence information for gene discovery and marker development related to upland cotton flower development. These EST resources form a valuable foundation for gene expression profiling analysis, functional analysis of newly discovered genes, genetic linkage, and quantitative trait loci analysis.     

ITS and trnH-psbA as Efficient DNA Barcodes to Identify Threatened Commercial Woody Angiosperms from Southern Brazilian Atlantic Rainforests

The Araucaria Forests in southern Brazil are part of the Atlantic Rainforest, a key hotspot for global biodiversity. This habitat has experienced extensive losses of vegetation cover due to commercial logging and the intense use of wood resources for construction and furniture manufacturing. The absence of precise taxonomic tools for identifying Araucaria Forest tree species motivated us to test the ability of DNA barcoding to distinguish species exploited for wood resources and its suitability for use as an alternative testing technique for the inspection of illegal timber shipments. We tested three cpDNA regions (matK, trnH-psbA, and rbcL) and nrITS according to criteria determined by The Consortium for the Barcode of Life (CBOL). The efficiency of each marker and selected marker combinations were evaluated for 30 commercially valuable woody species in multiple populations, with a special focus on Lauraceae species. Inter- and intraspecific distances, species discrimination rates, and ability to recover species-specific clusters were evaluated. Among the regions and different combinations, ITS was the most efficient for identifying species based on the ‘best close match’ test; similarly, the trnH-psbA + ITS combination also demonstrated satisfactory results. When combining trnH-psbA + ITS, Maximum Likelihood analysis demonstrated a more resolved topology for internal branches, with 91% of species-specific clusters. DNA barcoding was found to be a practical and rapid method for identifying major threatened woody angiosperms from Araucaria Forests such as Lauraceae species, presenting a high confidence for recognizing members of Ocotea. These molecular tools can assist in screening those botanical families that are most targeted by the timber industry in southern Brazil and detecting certain species protected by Brazilian legislation and could be a useful tool for monitoring wood exploitation.     

Genetic diversity in kiwifruit polyploid complexes: insights into cultivar evaluation,conservation, and utilization

Understanding the extent and partitioning of crop genetic diversity is necessary for conserving and utilizing their genetic potentials for breeding. In the present study, fluorescence-labeled amplified fragment length polymorphism markers were used to characterize the genetic diversity and relationships of 79 cultivars and also of 122 F1 hybrids which resulted from six kiwifruit interploid crosses. A high level of mean genetic diversity was detected (Hj > 0.22) for all cultivars investigated, without significant differences among diploids (2x), tetraploids (4x), and hexaploids (6x). This suggested that no significant genetic erosion occurred in these cultivars, which were directly selected from natural resources or created from crosses. The Unweighted Pair Group Method with Arithmetic Mean analysis of the genetic dissimilarity between cultivars showed three main groups mostly based on their three ploidy levels. Among these, the red-fleshed cultivars which were originally derived from ‘Hongyang’ clustered into one subgroup of group I, suggesting their unique genetic background despite they were marked as different cultivars used in the current kiwifruit industry. By analyzing the genetic variation of hybrids with variable ploidy levels, our genetic analyses further revealed that interploid crosses can increase the genetic diversity of F1 offsprings, especially from the parental combinations of 6x–2x and 6x–4x, in which both parents showed significant differences in morphology and genetic backgrounds. Based on these findings, strategies were proposed for the conservation and utilization of the current kiwifruit genetic resources for future breeding programs.     

Comparative genomics analysis of two banana Fusarium wilt biocontrol endophytes Bacillus subtilis R31 and TR21 provides insights into their differences on phytobeneficial trait

Fusarium wilt of banana is considered one of the most destructive plant diseases. Bacillus subtilis R31 and TR21, isolated from Dendrobium sp. leaves, exhibit different phytobeneficial effects on banana Fusarium wilt bio-controlling. Here, we performed genome sequencing and comparative genomics analysis of R31 and TR21 to enhance our understanding of the different phytobeneficial traits. These results revealed that the strain-specific genes of R31 involved in sporulation, quorum sensing, and antibiotic synthesis allow R31 to present a better capacity of sporulation, rhizosphere adaptation, and quorum sensing than TR21. Selective pressure analysis indicated that the glycosylase and endo-alpha-(1- > 5)-L-arabinanase genes were strong positive selected, which may contribute to the TR21 to colonize well in banana's vascular bundles. Altogether, our findings presented here should advance further agricultural application of R31 and TR21 as two promising resources of plant growth promotion and biological control via genetic engineering.     

Homology Modeling and Comparative Profiling of Superoxide Dismutase Among Extremophiles: Exiguobacterium as a Model Organism

Superoxide dismutase (SOD), a well known antioxidant enzyme, is known to exert its presence across bacteria to humans. Apart from their well-known antioxidant defense mechanisms, their association with various extremophiles in response to various stress conditions is poorly understood. Here, we have discussed the conservation and the prevalence of SODs among 21 representative extremophiles. A systematic investigation of aligned amino acid sequences of SOD from all the selected extremophiles revealed a consensus motif D-[VLE]-[FW]-E-H-[AS]-Y-[YM]. To computationally predict the correlation of SOD with the various stress conditions encountered by these extremophiles, Exiguobacterium was selected as a model organism which is known to survive under various adverse extremophilic conditions. Interestingly, our phylogenetic study based on SOD homology revealed that Exiguobacterium sibiricum was one of the closest neighbors of Deinococcus radiodurans and Thermus thermophilus. Next, we sought to predict 3-D model structure of SOD for E. sibiricum (PMDB ID: 0078260), which showed >95 % similarity with D. radiodurans R1 SOD. The reliability of the predicted SOD model was checked by using various validation metrics, including Ramachandran plot, Z-score and normalized qualitative model energy analysis score. Further, various physicochemical properties of E. sibiricum SOD were calculated using different prominent resources.

Electronic supplementary material

The online version of this article (doi:10.1007/s12088-014-0482-8) contains supplementary material, which is available to authorized users.     

Identification and Evaluation of Reference Genes for Accurate Transcription Normalization in Safflower under Different Experimental Conditions

Safflower (Carthamus tinctorius L.) has received a significant amount of attention as a medicinal plant and oilseed crop. Gene expression studies provide a theoretical molecular biology foundation for improving new traits and developing new cultivars. Real-time quantitative PCR (RT-qPCR) has become a crucial approach for gene expression analysis. In addition, appropriate reference genes (RGs) are essential for accurate and rapid relative quantification analysis of gene expression. In this study, fifteen candidate RGs involved in multiple metabolic pathways of plants were finally selected and validated under different experimental treatments, at different seed development stages and in different cultivars and tissues for real-time PCR experiments. These genes were ABCS, 60SRPL10, RANBP1, UBCL, MFC, UBCE2, EIF5A, COA, EF1-β, EF1, GAPDH, ATPS, MBF1, GTPB and GST. The suitability evaluation was executed by the geNorm and NormFinder programs. Overall, EF1, UBCE2, EIF5A, ATPS and 60SRPL10 were the most stable genes, and MBF1, as well as MFC, were the most unstable genes by geNorm and NormFinder software in all experimental samples. To verify the validation of RGs selected by the two programs, the expression analysis of 7 CtFAD2 genes in safflower seeds at different developmental stages under cold stress was executed using different RGs in RT-qPCR experiments for normalization. The results showed similar expression patterns when the most stable RGs selected by geNorm or NormFinder software were used. However, the differences were detected using the most unstable reference genes. The most stable combination of genes selected in this study will help to achieve more accurate and reliable results in a wide variety of samples in safflower.