Analysis of Viability Affecting on Genetic Integrity in Soybean Germ-plasm Zhonghuang 18 by AFLP Markers

Shallot (Allium cepa var. aggregatum), a small bulb onion, is widely grown in the world. We previously reported a droplet-vitrification for cryopreservation of in vitro-grown shoot tips of shallot genotype ‘10603’. The present study further evaluated rooting, vegetative growth, bulb production and contents of biochemical compounds, as well as genetic stability in cryo-derived plants. The results showed no significant differences in rooting, vegetative growth, bulb production and contents of soluble sugars and flavonols between the cryo- and in vitro-derived plants. Analyses of ISSR and AFLP markers did not detect any polymorphic bands in the cryo-derived plants. These results indicate rooting and vegetative growth ability, biochemical compounds and genetic stability were maintained in cryo-derived plants. The present study provides experimental evidences that support the use of cryopreservation method for long-term preservation of genetic resources of shallots and other Allium species. Rooting, vegetative growth, bulb production, genetic stability and biochemical compounds were maintained in cryopreserved plants of shallot. Our results support use of cryopreservation for long-term preservation of shallot germplasm.

Interspecific gene flow from crop species into wild relatives may compromise the genetic integrity of native species and in the case of transgenic crops lead to the escape of transgenes into natural populations. Approximately 72% of the upland cotton (Gossypium hirsutum L.) acreage grown in the United States in 2000 utilized transgenic cultivars. The closest relative of G. hirsutum is G. tomentosum Nuttall ex Seeman, endemic to the Hawaiian archipelago. Because these two species are fully interfertile, cultivation of transgenic G. hirsutum in the Hawaiian Islands is restricted. We investigated the possibility of identifying AFLP genetic markers that are diagnostic for each species and thus could be used in future studies to detect introgression between them. In addition, we were interested in comparing levels and geographic patterns of AFLP diversity in G. tomentosum to previous estimates using allozyme data. AFLP analysis led to the detection of 11 and 16 species-specific markers for G. tomentosum and G. hirsutum, respectively. These species-specific AFLP markers will be useful for detecting gene flow between G. hirsutum and G. tomentosum that has occurred in the past and thus might occur in the future if the restrictions on cultivation of transgenic G. hirsutum are relaxed in the Hawaiian Islands. Little genetic diversity and limited geographic patterning were discovered using AFLP markers, consistent with data from previous allozyme studies.

In the present study, the genetic variations of leaf calli regenerants of Musa paradisiaca cv Karibale-Monthan has been analyzed using AFLP markers. The highest (86.66%) frequency of compact callus formation was obtained when leaf explants were cultured on MS media, containing 3mg/L 2,4-D and 0.5 mg/L BAP. The optimum shoot formation and multiplication (5.70±1.49) was achieved from the leaf derived callus on MS medium fortified with 3mg/L BAP+0.5mg/L TDZ. The 3-4 cm small shoots produced distinct roots on MS media containing 0.5mg/l NAA with 0.2% activated charcoal. The AFLP analyses produced 1012 monomorphic bands from total 1094 bands with 7.5% polymorphism between mother plant and callus derived regenerants. The percentage of monomorphism for individual primer combinations was very high and varied from 90.3% (EcoRI-AG×MseI-CCG) to 97.6% (EcoRI-AT×MseI-CGA). The result showed lack of polymorphism is due to genetic integrity of the plants that was not altered indifferent to the hormonal treatment.

Natural introgression can cause negative effects where rare species experience genetic assimilation and invade by their abundant congeners. Quercus austrocochinchinensis and Q. kerrii (subgenus Cyclobalanopsis) are a pair of closely related species in the Indo-China area. Morphological intermediates of the two species have been reported in this region. In this study, we used AFLP, SSR and two key leaf morphological diagnostic traits to study the two Q. austrocochinchinensis populations, two pure Q. kerrii and two putative hybrid populations in China. Rates of individual admixture were examined using the Bayesian clustering programs STRUCTURE and NewHybrids, with no a priori species assignment. In total, we obtained 151 SSR alleles and 781 polymorphic loci of AFLP markers. Population differentiation inferred by SSR and AFLP was incoherent with recognized species boundaries. Bayesian admixture analyses and principal coordinate analysis identified more hybrids and backcrossed individuals than morphological intermediates in the populations. SSR inferred a wide genetic assimilation in Q. austrocochinchinensis, except for subpopulation D2 in the core area of Xi-Shuang-Ban-Na Nature Reserve (XSBN). However, AFLP recognized more Q. austrocochinchinensis purebreds than SSR. Analysis using NewHybrids on AFLP data indicated that these hybridized individuals were few F2 and predominantly backcrosses with both parental species. All these evidences indicate the formation of a hybrid swarm at XSBN where the two species co-exist. Both AFLP and SSR recognized that the core protected area of XSBN (D2) has a high percentage of Q. austrocochinchinensis purebreds and a unique germplasm. The Hainan population and the other subpopulations of XSBN of the species might have lost their genetic integrity. Our results revealed a clear genetic differentiation in the populations and subpopulations of Q. austrocochinchinensis and ongoing introgression between Q. austrocochinchinensis and Q. kerrii at the disturbed contact areas. Combining the results from genetic and morphological analyses, the conservation of subpopulation D2 should be prioritized. Conservation and restoration of the integrity of tropical ravine rainforest is an important long-term goal for the successful conservation of Q. austrocochinchinensis. The fine-scale landscape might play an essential role in shaping the spatial patterns of hybridization. Further studies are needed to evaluate these patterns and dynamics.

Population viability analyses in plants: challenges and opportunities

Population viability analyses (PVA) are important tools for decision-making and planning of adaptive wildlife management actions. While earlier approaches on individual based PVAs have often been age-based, analyses of species with strong social structure might benefit from a stage-based model approach. In this study, we designed an individual-based and stage-based PVA within the software Vortex. As a case study, we applied our model to the German part of the European wolf population, making use of comprehensive data sets originating from the German monitoring regime including individual genotypes. Genetic diversity and inbreeding were important considerations in our analysis, as they could greatly impact population dynamics. We aimed to assess the population's trajectory, extinction risk, and genetic integrity under different scenarios while analyzing factors that could affect its survival. We found that mortality rates at different life cycle stages had varying effects on population growth. Higher mortality rates among pups and dispersers led to negative growth and increased the risk of extinction. In comparison, higher mortality rates among yearlings and subdominant wolves still resulted in positive growth but at a slower rate. Mortality among the breeding individuals within the pack (territorials) had the highest impact on population trajectory. Although the German wolves represent a rather recently founded population, our simulations predicted generally good genetic diversity as long as the population was not held at artificially low numbers.Ultimately, we present a generic, easy-to-use-and-adapt model built within the Vortex environment, that after appropriate modification, calibration and testing could be used within conservation practice and management in collaboration with scientific research. Our study highlights the importance of stage-based modeling for understanding the demographic traits of social species like wolves.

9012AB, a recessive genic male sterility (RGMS) line derived from spontaneous mutation in Brassica napus, has been playing an important role in rapeseed hybrid production in China. The male sterility of 9012AB is controlled by two recessive genes (ms3 and ms4) interacting with one recessive epistatic suppressor gene (esp). The objective of this study was to develop PCR-based markers tightly linked to the esp gene and construct a high-resolution map surrounding the esp gene. From the survey of 512 AFLP primer combinations, 3 tightly linked AFLP markers were obtained and successfully converted to codominant or dominant SCAR markers. Furthermore, a codominant SSR marker (Ra2G08) associated with the esp gene was identified through genetic map integration. For fine mapping of the esp gene, these PCR-based markers were analyzed in a large BC1 population of 2545 plants. The esp gene was then genetically restricted to a region of 1.03 cM, 0.35 cM from SSR marker Ra2G08 and 0.68 cM from SCAR marker WSC6. The SCAR marker WSC5 co-segregated with the target gene. These results lay a solid foundation for map-based cloning of esp and will facilitate the selection of RGMS lines and their temporary maintainers.

Maintaining pure cultures using preservation methods is of high importance for biotechnological purposes. However, preservation does not necessarily guarantee the genetic stability of these cultures. Therefore, preservation methods are currently needed to assure viability as well as genetic, physiological, and morphological integrity across storage periods. In this study, preservation of five isolates from the microalgae and cyanobacteria collection of the Plant Biology Department, Federal University of Vicosa, Minas Gerais, Brazil was investigated via monthly analyses of cell viability, biomass recovery, and contaminant concentrations over a period of 120 days. Lyophilization was adequate for both heterocystous cyanobacteria and other strains that were able to differentiate hormogones or to synthesize thick layers of exopolysaccharides. Lyophilization was also able to maintain cultures with low levels of contaminants. Dimethyl sulfoxide was relatively efficient, though some of the strains were susceptible to its cytotoxic effects. Our results demonstrated that cryopreservation with glycerol was the most efficient method. The ability to routinely preserve cyanobacterial strains reduces costs associated with maintaining large culture collections and reduces the risks of losing particular strains or species through contamination and genetic drift. The results obtained in this study are therefore discussed in the context of the efficiency of the methods and the current need to develop suitable methods for maintenance of cyanobacterial collections.

By definition, restoration projects involve small populations, which are subject to demographic, genetic, and environmental stochasticities. Besides its fundamental interest for ecology, the integration of these stochastic factors in population viability models is required to make such models more realistic. In this paper, we report previous attempts to integrate population dynamics and population genetics, two disciplines that are generally treated as separate fields. We then evaluate their potential interactions in the context of population restoration. In the first part, we investigate the interactions among stochastic factors of extinction and various species characteristics, such as growth rate, generation length, and mating system. In the second part, we discuss how demographic and genetic models can be used to compare the relative efficiencies of different reintroduction and reinforcement strategies in different environments. For that purpose, we examine spatial and temporal aspects of release, as well as the number and type of individuals to release. In many cases, these comparisons uncover opposite effects among the genetic and demographic factors that antagonistically influence short- and long-term viabilities. Choosing an appropriate restoration strategy should therefore involve the integration of different disciplines in population viability analyses.

Forty-four soybean genotypes with different photoperiod response were selected after screening of 1000 soybean accessions under artificial condition and were profiled using 40 SSR and 5 AFLP primer pairs. The average polymorphism information content (PIC) for SSR and AFLP marker systems was 0.507 and 0.120, respectively. Clustering of genotypes was done using UPGMA method for SSR and AFLP and correlation was 0.337 and 0.504, respectively. Mantel's correlation coefficients between Jaccard's similarity coefficient and the cophenetic values were fairly high in both the marker systems (SSR = 0.924; AFLP = 0.958) indicating very good fit for the clustering pattern. UPGMA based cluster analysis classified soybean genotypes into four major groups with fairly moderate bootstrap support. These major clusters corresponded with the photoperiod response and place of origin. The results indicate that the photoperiod insensitive genotypes, 11/2/1939 (EC 325097) and MACS 330 would be better choice for broadening the genetic base of soybean for this trait.

Population dynamics and viability are driven by interactions among habitat and species biology. The Florida scrub-jay (Aphelocoma coerulescens) is a declining and Federally Threatened bird species that requires mid-succession habitat of partly open soil surface with mid-height vegetation. This habitat is created and sustained in a dynamic state of vegetation growth and periodic natural (e.g., fire) or managed (e.g., mechanical clearing) disturbances. Florida scrub-jays once occupied open oak scrub habitats across much of peninsular Florida but have been reduced to a few regional metapopulations and scattered isolated remnant populations. Many of these populations are undergoing continuing decline as open scrub is either converted to residential development or transitions into closed pine and oak forests due to fire suppression. Long-term field studies have shown that breeding and survival rates are determined by the quality of the scrub habitat, with the demography influenced by and in turn mediating the social structure. Prior Population Viability Analyses (PVA) that included dependencies of demographic rates on habitat and social structure indicated that the east coast Florida metapopulations were fragmented into remnant protected patches that were too small and isolated to support long-term persistence, even if the remaining habitat area and quality was sustained. Moreover, recent modeling of habitat transitions under various proposed management schemes, in conjunction with implementation of Adaptive Resource Management (ARM), projected that the proportion of optimal habitat will continue to decline. In this study, we integrated these habitat projections within the PVA and found that the Brevard County mainland metapopulation is projected to decline toward extinction unless habitat quality, extent, and connectivity can be improved. Land managers have recently implemented new innovative methods for restoring optimal scrub habitat, identifying potential improvements in habitat connectivity of nearby populations, and translocation methods to increase and reinforce the demographic and genetic integrity of local populations. Our linked habitat-population models project that the combination of such habitat and population management actions can stabilize the metapopulation and achieve long-term viability.