The application of next-generation sequencing (NGS) technologies for the development of simple sequence repeat (SSR) or microsatellite loci for genetic research in the botanical sciences is described. Microsatellite markers are one of the most informative and versatile DNA-based markers used in plant genetic research, but their development has traditionally been a difficult and costly process. NGS technologies allow the efficient identification of large numbers of microsatellites at a fraction of the cost and effort of traditional approaches. The major advantage of NGS methods is their ability to produce large amounts of sequence data from which to isolate and develop numerous genome-wide and gene-based microsatellite loci. The two major NGS technologies with emergent application in SSR isolation are 454 and Illumina. A review is provided of several recent studies demonstrating the efficient use of 454 and Illumina technologies for the discovery of microsatellites in plants. Additionally, important aspects during NGS isolation and development of microsatellites are discussed, including the use of computational tools and high-throughput genotyping methods. A data set of microsatellite loci in the plastome and mitochondriome of cranberry (Vaccinium macrocarpon Ait.) is provided to illustrate a successful application of 454 sequencing for SSR discovery. In the future, NGS technologies will massively increase the number of SSRs and other genetic markers available to conduct genetic research in understudied but economically important crops such as cranberry.

The light screen hypothesis states that foliar anthocyanins shade the photosynthetic apparatus from excess light. In this paper we extend the light screen hypothesis, postulating that plant species at risk of photoinhibitory conditions during autumnal leaf senescence often utilize anthocyanins to protect the photosynthetic apparatus during the period of nutrient resorption. When senescence-related photosynthetic instabilities are compounded by other environmental stresses, particularly low temperature, severe photoinhibition may result in reduced resorption of critical foliar nutrients, which can significantly affect plant fitness. There is evidence that environments where low and often freezing temperatures are common in autumn selectively favor the production of anthocyanins in senescing foliage. The stimuli for, and the timing and location of, autumnal anthocyanin production are all consistent with a photoprotective role for these pigments in senescing leaves. Furthermore, differences in nitrogen allocation strategies between early and late successional species appear to affect photosynthetic stability during leaf senescence, resulting in a reduced need for foliar autumnal anthocyanins in many early successional plants. The ecological and physiological evidence presented in this paper suggest that, for many deciduous species, the production of anthocyanins provides effective photoprotection during the critical period of foliar nutrient resorption.

A U.S. farm policy shift to joint production of commodities and ecological services will advance sustainable agriculture.

The resorption protection hypothesis, which states that anthocyanins protect foliar nutrient resorption during senescence by shielding photosynthetic tissues from excess light, was tested using wild-type (WT) and anthocyanin-deficient mutants of three deciduous woody species, Cornus sericea, Vaccinium elliottii (Chapmn.), and Viburnum sargentii (Koehne). WT Betula papyrifera (Marsh) was included to compare the senescence performance of a species that does not produce anthocyanins in autumn. Plants were subjected to three environmental regimes during senescence: an outdoor treatment; a 5-d high-stress (high light and low temperature) treatment followed by transfer to a low-stress environment and a low-stress treatment that served as control. In the outdoor treatment, the appearance of anthocyanins in senescing leaves of WT plants was concomitant with the development of photo-inhibition in mutant plants of all three anthocyanin-producing species. In the high-stress environment, WT plants maintained higher photochemical efficiencies than mutants and were able to recover when transferred to the low-stress environment, whereas mutant leaves dropped while still green and displayed signs of irreversible photooxidative damage. Nitrogen resorption efficiencies and proficiencies of all mutants in both stressful treatments were significantly lower than the WT counterparts. B. papyrifera displayed photochemical efficiencies and nitrogen resorption performance comparable with the highest of the anthocyanin-producing species in all three senescing environments, indicating a photoprotective strategy divergent from the other species studied. These results strongly support the resorption protection hypothesis of anthocyanins in senescing leaves.The role of anthocyanins in plant foliage has long been the subject of study and speculation (for review, see Chalker-Scott, 1999;Steyn et al., 2002). Foliar anthocyanins arise in a great diversity of plant species across a broad range of environments, often occurring in response to environmental stresses such as nutrient deficiency, drought, and low temperature (Steyn et al., 2002). In many species, anthocyanins are produced at specific physiological stages, appearing in expanding, mature, or senescing leaves exposed to high light. Observations over a century ago led to the light screen hypothesis, which states that foliar anthocyanins shade the photosynthetic apparatus from excess light (for review, see Wheldale, 1916).The resorption protection hypothesis (Hoch et al., 2001) proposed that the shading of photosynthetic tissues by anthocyanins produced during senescence helps protect the plant's ability to resorb foliar nutrients by shielding leaves from potentially harmful light levels. This hypothesis is based on the ideas that senescence-related processes lead to increased vulnerability to damage from visible light, resulting in reduced photosynthetic capacity (photo-inhibition) and that severe photo-inhibition during senescence can significantly affect a plant's ability to resorb foli...

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As a general group, long-lived perennial plants probably present the most challenging obstacles to the researcher, breeder or propagator utilizing microculture as a tool. These challenges appear during all stages of the microculture process, but are probably most resplendent during the stabilization phase. What may be particularly frustrating is that much of this 'recalcitrance' is genetically driven and is thus difficult to control by environmental and nutritional manipulations in microculture. Perennials have complex seasonal cycles and life cycles, which complicate control of their growth in microculture. As shoot cultures have provided useful tools for overcoming these limitations, the inability to establish stabilized shoot cultures is a major form of recalcitrance. Plants having seasonal growth dynamics dominated by strong episodic or determinant shoot growth are some of the most recalcitrant species because stabilized shoot cultures cannot be readily generated. In some cases, episodic growth may be tied closely to phase state and can thus be controlled by manipulating phase; nevertheless, adequate controls have not been identified for many problematic plants. Another trait contributing to recalcitrance of perennials is the relatively slow growth rate in microculture. Slow growth complicates such procedures as selection of transformed tissues. The high phenolic content of many perennial tissues can interfere with the efficacy of transgenic traits such as b-glucuronidase. Developmentally determined growth characteristics such as plagiotropism may persist through all stages of microculture and complicate the recovery of commercially useful micropropagules. Although some technical approaches can occasionally circumvent immediate microculture limitations, general solutions await the development of a deeper understanding of physiological bases of such genetically predetermined phenomena.