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.

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SummaryCotton (Gossypium spp.) is an important economic crop and the largest source of textile fiber in the world. However, to date, only a few genes have been identified that exhibit critical roles in fiber development, and few has shown positive effects on fiber yield and quality in transgenic cotton. Here, we report the characterization of a novel sucrose synthase (SusA1) gene from a superior quality fiber germplasm line 7235 in Gossypium hirsutum. By association analysis, GhSusA1 was highly correlated with fiber qualities in (7235· TM-1) recombinant inbred lines based on polymorphism of GhSusA1 between 7235 and TM-1. Subsequently, based on an interspecific population of 141 BC 1 individuals generated from the cross between TM-1 and Gossypium barbadense line, Hai7124, we further mapped GhSusA1 genes on homeologous chromosomes A8 (chro.8) and D8 (chro.24). Suppression of GhSusA1 in transgenic cotton reduced fiber quality and decreased the boll size and seed weight. Importantly, overexpression of this gene increased fiber length and strength, with the latter indicated by the enhanced thickening of cell wall during secondary wall formation stage. Moreover, increasing GhSusA1 transcript abundance in vegetative tissues led to elevated seedling biomass. Together, these findings identified GhSusA1 as a key regulator of sink strength in cotton, which is tightly associated with productivity, and hence a promising candidate gene that can be developed to increase cotton fiber yield and quality.