Soybean is one of the most aluminum (Al) sensitive plants. The complex inheritance of Al tolerance trait has so far undermined breeding efforts to develop Al-tolerant soybeans. Discovering the genetic factors underlying the Al tolerance mechanisms would undoubtedly accelerate the pace of such endeavor. As a first step toward this goal, we analyzed the transcriptome profile in roots of Al-tolerant soybean line PI 416937 comparing Al-treated and untreated control plants using DNA microarrays. Many genes involved in transcription activation, stress response, cell metabolism and signaling were differentially expressed. Patterns of gene expression and mechanisms of Al toxicity and tolerance suggest that Cys2His2 and ADR6 transcription activators, cell wall modifying enzymes, and phytosulfokines growth factor play role in soybean Al tolerance. Our data provide insights into the molecular mechanisms of soybean Al tolerance and will have practical value in genetic improvement of Al tolerance trait. 1. Introduction Aluminum (Al) toxicity is a major constraint of crop production on acid soils. In view of the fact that 40% of world’s arable land is acidic [1, 2], Al toxicity remains a major hurdle for increasing world food, fiber, and fuel production particularly via expansion of cultivation into acid soils. Aluminum inflicts a wide range of cellular injuries in plants that ultimately result in reduced root growth, nutrient and water uptake, and productivity [1, 2]. Plants possess some degree of tolerance to Al toxicity that varies among species and genotypes [1, 3–6]. Al tolerance mechanisms include exclusion and internal detoxification. Al exclusion via rhizosphere Al-organic acid anion complex formation is the most widely documented physiological mechanism of Al tolerance in cultivated and wild plants alike [1, 7]. Root-exuded citrate, malate, and oxalate are the key organic acid anions involved in such mechanism. Genes involved in Al-induced root exudation of malate and citrate have been cloned in wheat [8] and sorghum [5], and their variants are being discovered in several plant species. Internal detoxification mechanisms involve the formation of Al complexes with organic acids, acidic polypeptides, and/or proteins and subsequent sequestration of Al in organelles away from sensitive sites in the cell [9, 10]. The genetic components of the internal detoxification pathways are yet to be elucidated. In soybean, Al tolerance is a complex trait perhaps involving several genes and pathways [11, 12]. Quantitative trait loci (QTL) mapping in a population derived from
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