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Title:   Author  item
                                            BROWN, ANNE - Purdue Universityitem
                                            Hudson, Karen
  Submitted to: BMC Plant Biology
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 6/15/2015
                                    Publication  Date: 7/3/2015
                                    Citation: Brown, A.V., Hudson, K.A. 2015. Developmental profiling of gene expression in soybean trifoliate leaves and cotyledons. Biomed Central (BMC) Plant Biology. 15:169.Interpretive Summary: After  seed germination, a soybean seedling uses nutrients (proteins, fats, and minerals) stored in the seedling leaves (called cotyledons) to establish the plant body until the young plant is able to acquire sufficient energy from photosynthesis and establish a root system to take up minerals. As the cotyledons develop, these nutrients are broken down and transported to other plant organs, and when fully exhausted the cotyledons undergo cell death, turning yellow and falling off the plant. To better understand this process and how it is controlled in soybean, this experiment examined the genes expressed in the soybean cotyledons during multiple stages of development. We identified 61,000 genes that are expressed in developing cotyledons or leaves, and identified a set of 6000 genes that increase in expression as these organs age, including over 1000 regulatory genes. The results of this work establish a catalog of genes and promoters that are expressed at different times during cotyledon or leaf development. These genes can either be targeted by biotechnological approaches or used in genetic selection to create the best genetic combinations to maintain leaf or cotyledon function and maximize plant productivity.
                                Technical Abstract: Immediately following germination, the developing soybean seedling relies on the nutrient reserves stored in the cotyledons to sustain heterotrophic growth. During the seed filling period on a mature plant, developing seeds rely on the transport of nutrients from the trifoliate leaves. In soybean, both cotyledons and leaves develop the capacity for photosynthesis, and subsequently senesce and abscise once their function has ended. Before this happens, the nutrients they contain are mobilized and transported to other parts of the plant. These processes are carefully orchestrated by genetic regulation throughout the development of the leaf or cotyledon. To identify genes involved in the processes of leaf or cotyledon development and senescence in soybean, we used RNA-seq to profile multiple stages of cotyledon and leaf tissues. Differentially expressed genes between stages of leaf or cotyledon development were determined, major patterns of gene expression were defined, and shared genes were identified. Over 38,000 transcripts were found to be expressed during the course of  leaf and cotyledon development. Of those transcripts, 5,000 were expressed in a tissue specific pattern. Of the genes that were differentially expressed between both later stage tissues, 90% had the same directionally of change, suggesting that the mechanisms of senescence are conserved between tissues.  Analysis of the enrichment of functions within genes sharing common expression profiles highlights the main biological processes occurring within these defined temporal windows of leaf and cotyledon development. Finally, over 1,000 regulatory genes were identified with predicted regulatory functions that may have a role in control of leaf or cotyledon senescence. The process of leaf and cotyledon development can be divided into distinct stages characterized by the expression of specific gene sets. The importance of the WRKY and GRAS family transcription factors as major regulators of plant senescence is confirmed for both soybean leaf and cotyledon tissues. These results help validate functional annotation for soybean genes and promoters.


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