Seeds are essential for flowering plant reproduction because they protect, nourish, and contain the developing embryo that represents the next sporophytic generation. In addition, seeds contain energy resources that sustain the young sporophyte during germination before photosynthesis begins. In legumes, food reserves stored in embryonic cotyledons make seeds important as a food source for both human and animal consumption. For example, soybean (Glycine max) is now one of the most important seed crops in the world (Wilcox, 2004). Research on legume seed development has led to direct applications, such as seeds with more nutrients (Kinney, 1998; Wang et al., 2003; Krishnan, 2005), reduced allergens (Herman et al., 2003), and novel constituents, such as edible vaccines (Moravec et al., 2007). In the current genomic era, it is now possible to begin to understand what genes are required to make a legume seed and how regulatory networks are interconnected in legume genomes to program seed formation. In the future, this information should permit novel approaches to breed and engineer legume seeds with new agronomic traits and, most importantly, help provide a sustainable food supply for a growing human population. This Update outlines how our laboratories have been using legumes and functional genomics to identify genes that program legume seed development. Soybean seed development. A, Cartoon depicting soybean life cycle. B, Schematic representation of soybean seed development. Embryo morphologies and developmental events were adapted and modified from Goldberg et al. (1989). C, Paraffin transverse 10-μm sections of soybean globular, heart, cotyledon, and early maturation seeds. Inset contains a magnified view (40×) of the seed coat. Axis longitudinal section was obtained from an early maturation seed. D, Major unanswered questions in seed development. a, Axis; al, aleurone; c, cotyledon; cu, cuticle; ep, embryo proper; es, endosperm; hg, hourglass cells; ii, inner integument; oi, outer integument; pa, palisade layer; pl, plumule; py, parenchyma; rm, root meristem; s, suspensor; sc, seed coat; sm, shoot meristem; v, vascular tissues; vb, vascular bundle. Many developmental and physiological events occur within each seed compartment during development (Fig. 1B) and are programmed, in part, by the activity of different genes (Goldberg et al., 1989, 1994; Stangeland et al., 2003; Gehring et al., 2004; Haughn and Chaudhury, 2005). Seed development, therefore, is the result of a mosaic of distinct gene expression programs occurring in parallel in different seed compartments (e.g. embryo, endosperm, seed coat) as well as within specific regions and tissues (e.g. embryo proper, suspensor, epidermis). What these programs are and how they are integrated into unique regulatory networks within the plant genome remain major unanswered questions (Fig. 1D). Specifically, it is not yet known what genes in different seed compartments play important roles in cell fate specification, differentiation, and morphogenesis during early seed and embryo development. Molecular identification and characterization of these genes will help identify regulatory networks that program and coordinate the development of each seed compartment. In addition, it is not known what the functions are of many genes that are expressed in different seed compartments. Identifying the function of compartment-specific genes should provide new insight into their roles in seed development. At present, new genomic resources allow seed biologists to use global gene expression profiling and comparative genomics to answer many questions that only a short time ago seemed out of reach. These questions, and others (Fig. 1D), are challenging the field of seed biology, and their answers should provide new insights into the process of seed development and lead to improved seeds for human and animal consumption. Legumes represent one of the largest and most diverse families of flowering plants, with approximately 20,000 species classified (Doyle and Luckow, 2003). There are three subfamilies in legumes and the largest, Papilionoideae, contains most of the model species in which different aspects of plant biology have been studied. The most common legume models are peanut (Arachis hypogaea), Lotus (Lotus japonicus), Medicago (Medicago truncatula), soybean (Glycine max), scarlet runner bean (SRB; Phaseolus coccineus), common bean (Phaseolus vulgaris), pea (Pisum sativum), and broad bean (Vicia faba). The latter five species have been used historically to study seed and embryo development (Goldberg et al., 1989; Johnson et al., 1994; Coste et al., 2001; Weterings et al., 2001; Weber et al., 2005). Several features make legumes an excellent model system to study seed and embryo development. For example, many legumes, such as soybean and peanut, are food crops of major economic importance. The mature seeds of these legumes are rich in proteins, carbohydrates, and oils, and accumulate to high nutritional value. These stored seed food reserves make legumes, such as soybean, the second most important crop for human nutrition and animal feed (Rubel et al., 1972; Duranti and Gius, 1997; Graham and Vance, 2003). One advantage of using crop models to study seed biology is to be able to modify traits of agronomic importance, such as improved seed nutritional composition, reduced allergen levels, or increased seed number and size (Kinney, 1998; Herman et al., 2003; Wang et al., 2003; Gupta et al., 2006). In addition, legume seed biology has been studied for more than 150 years using descriptive, physiological, biochemical, molecular, and genetic approaches (see below). These studies have provided a solid intellectual framework for using legume models to study and dissect seed development in our current genomic era. The recent development of genomic tools, such as genome sequences, ESTs, oligonucleotide and cDNA microarrays, and comprehensive databases, such as the Legume Information System (http://www.comparative-legumes.org), make legumes an excellent model to study seed development at a global scale (VandenBosch and Stacey, 2003; Gepts et al., 2005; Gonzales et al., 2005). These genomic tools allow comparative genomic analyses in closely related species (Zhu et al., 2005) and should facilitate the identification and investigation of genes important for seed development. Diversity of legume seed size and embryo morphology. A, Legume seed shape and size variation. Scale bar = 1 cm. Adapted and modified from Vaughan et al. (1997). B, Variation in embryo-proper (ep) and suspensor (s) morphologies within and between legume tribes. Embryos are not drawn to scale. Images were adapted and modified from Martin (1914), Lersten (1983), and Chamberlin et al. (1994). Pc, P. coccineus; Gm, G. max. A second novel feature of legumes is that their embryos show a wide range of morphological forms (Fig. 2B). For example, two closely related species, soybean and SRB, have morphologically distinct suspensors. The soybean suspensor is small, consisting of a few cells, whereas the SRB suspensor is much larger and contains several hundred cells (Fig. 2B). The variety in size and shape of legume seeds and embryos makes them excellent models for comparative morphological studies using a functional genomics approach. This strategy can lead to a better understanding of the function, evolution, and diversity of legume seeds and their corresponding compartments. Historically, legumes have been used to address important questions of seed and embryo development. In fact, early work with legumes contributed to the development of major ideas in biology. For example, during the early 1800s, Matthias Schleiden used several legumes, including Medicago and Vicia, to investigate the endosperm and describe the process of seed development (Schleiden and Vogel, 1838, 1842). These studies contributed to his role in establishing the cell theory. In the mid-1800s, Gregor Mendel used peas to study the inheritance of phenotypic variation, including seed color and shape, leading to his Laws of Inheritance and the establishment of modern-day genetics (Mendel, 1865). From the late 1800s to the middle of the 1900s, legumes were used to describe the processes of seed and embryo development, including the cellular events that occur before and after fertilization, early embryo cell cleavages, and endosperm differentiation. For example, Guignard's compendium of more than 40 legume species described the rich diversity of legume embryo and suspensor morphologies (Fig. 2B; Guignard, 1882). These studies, and others, contributed to our overall understanding of seed and embryo development at the descriptive level (Martin, 1914; Brown, 1917; Cooper, 1938). Studies on legume seed formation transitioned from descriptive anatomy to experiments at the molecular, biochemical, and physiological levels during the and studies of legume seed development and et al., 1994; et al., in many legumes provided of the of carbohydrates, and levels in seeds (Rubel et al., 1972; et al., and et al., et al., et al., and These studies provided new insights into the processes by which food reserves accumulate and are stored in as well as that genome processes occur in specific seed compartments (e.g. cotyledon, In addition, legumes such as SRB were used to dissect and the embryo and suspensor to study the role of (e.g. in early embryo development et al., et al., et al., this our used experiments to show that approximately to diverse are in soybean embryos at different developmental (Goldberg et al., that most diverse species are seed development, that of including proteins, are at specific developmental (Goldberg et al., Seed genes were as models to investigate gene during legume seed development because they that be and and because of their as a food source for human and animal consumption. Research on genes in legume seed development during the late and it possible to and study and genes and them into using et al., et al., et al., In addition, et al. that the common bean seed gene be to cells and This that gene and be to genes into plant cells and study their Research in several laboratories with legume seed such as and that their are and (Goldberg et al., et al., et al., and by both and processes et al., et al., and et al., work that legume seed genes expression in plants, such as and et al., et al., et al., et al., et al., et al., et al., 1998; et al., 2003). This work provided insights into the gene activity during seed development and that the and legume seed gene expression are in plant At present, the development of new genomic resources makes it possible to study legume gene expression during seed and embryo development at a global and soybean cDNA and oligonucleotide are et al., et al., 2004; et al., 2005). of legume seed and et al., 2003; et al., 2005; et al., 2005; et al., et al., cDNA and et al., et al., et al., 2004; et al., 2005; et al., 2005) have to provide a global view of gene activity at specific seed developmental of the soybean, common and peanut genomes et al., 2003; Gepts et al., 2005; et al., 2005; et al., should provide an for and genes that play roles during seed and embryo development in the strategy for legume seed gene regulatory SRB as a genomics to genes early in A, for the of the embryo and suspensor, adapted and modified from Weterings et al. ep, embryo proper; s, B, SRB plant with a by the C, SRB embryos before and after the embryo and D, of SRB suspensor of In of SRB embryo using a In were from et al. in SRB seed sections before and after the embryo and suspensor by of SRB embryo-proper and suspensor in with an Soybean soybean SRB with a high to soybean on the will the of SRB suspensor and embryo-proper on the is than that for soybean (Fig. of in the suspensor and embryo is in to the number of gene are at and profiling to identify genes required to make a soybean seed. A, soybean seed the number of in the seed using the Soybean and C, soybean seed sections before and after the seed compartments by The number of diverse from seed compartments is in to the number of in the suspensor The number in to suspensor not in seed compartments at the level of the were in the as and can be at D, of soybean suspensor by of the most in seed compartments using and of suspensor of represent the and of the for two with two were to an One represents a in ep, embryo proper; es, endosperm; ii, inner integument; oi, outer integument; s, Identifying important for suspensor A to D, In of SRB embryos using from and and in were from Weterings et al. and activity in and embryos a and analyses in The number to the approximately a to be in the of and et al., were from Weterings et al. The to was by this with a mosaic gene and to et al. Legume including SRB, soybean, and Soybean and from SRB approximately and years et al., 2005). regions legume closely related by or et al., 2005). by and to be in the ep, Embryo proper; Gm, G. years Pc, P. coccineus; s, has SRB as a model system et al., to identify genes and regulatory networks early embryo developmental events using a genomics and have on the of how the embryo-proper and suspensor regions are from the and cells of a embryo, (Fig. Weterings et al., SRB is unique in this because of seed and embryo (Fig. of embryo-proper and suspensor regions at early developmental (Fig. and et al., 1972; et al., Weterings et al., cDNA from embryo-proper and suspensor regions of SRB embryos (Fig. Weterings et al., and were to what genes are in the embryo and SRB early embryo is at both and the of SRB suspensor by functional the diversity of genes that are in a more than suspensor were that are into a variety of gene families and a into the of regulatory genes in one of a legume embryo after What roles these play in suspensor and function remain to be of our out and in experiments (Fig. to and the of SRB during early embryo development. One advantage of using SRB embryos is that can be used to levels in different regions of a For example, in our studies is the SRB embryo (Fig. et al., 2003). is a of the gene that is a of embryo development et al., studies on regions from a SRB embryo at the show in the embryo-proper and suspensor regions (Fig. with a cDNA the of the mosaic gene and on (Fig. a to that obtained with a gene et al., These that is an important of SRB embryo development, the of the SRB system as a gene to regulatory genes that play essential roles in seed development. the SRB embryo is a novel system for the of embryo regions early in development, this legume have for global studies of seed formation. For example, have an for SRB embryo regions few genomic resources are In addition, have not yet been for because SRB is not a major food it is that a genome will be out to the SRB our use of SRB as a gene and these to to the (Goldberg et al., and use soybean to dissect genes important for a seed. At the a number of genomic resources have been for soybean, including microarrays, databases, and genome et al., et al., 2004; et al., 2006). In addition, are well for soybean, it to address questions of gene function et al., et al., 2006). the unique morphological between soybean and SRB embryos (e.g. suspensor size and should permit questions of legume embryo diversity to be studied (Fig. 2B). have been able to advantage of the SRB embryo to dissect by embryo-proper and suspensor regions and this is time and not with legumes that have such as soybean (Fig. 2B). One to the of and to be able to different regions from legume seed and embryo of size (Fig. is to make use of in et al., 2005; et al., 2006). makes it possible to study gene activity in the seed because seed or can be development (Fig. has been used in soybean, and in which a variety of plant tissues and cell have been and including in an early embryo et al., et al., 2003; et al., 2003; et al., 2005; et al., 2005; et al., 2005; et al., 2007). have been using with soybean seeds to identify the genes required to make a seed and In with can investigate the global gene activity in different compartments of the seed. For example, used to the endosperm, suspensor, embryo proper, inner outer and from a soybean seed (Fig. and from each of these seed as well as from seeds (Fig. with soybean and the of diverse in the soybean seed (Fig. to obtained with the seed regions (Fig. and These are at as of our Research 20,000 diverse were to be in the soybean seed (Fig. a to that which obtained more than a of a ago using (Goldberg et al., A number of diverse were to be in soybean seed For example, approximately diverse were in the suspensor, including that (Fig. These are to obtained with each of the seed regions diverse and and Soybean suspensor are into functional (Fig. to what from the of SRB suspensor (Fig. These that is a diversity of functions in the soybean (Fig. and that not to be in the functional of soybean and SRB suspensor in size and (Fig. 2B). that are approximately diverse in a soybean seed (Fig. and by the of each seed by (Fig. in with the result obtained with seeds (Fig. These that at 20,000 to diverse are required to make a soybean the of the diverse in each seed are with and are of seed used to of that are between different soybean seed regions are at a level (Fig. and analyses of that accumulate at a level in a seed (Fig. For example, approximately suspensor accumulate at a or level in the suspensor with seed regions (Fig. of diverse in each of a soybean seed of For example, were in the suspensor that are in seed regions at the level of the (Fig. and experiments the of two of these suspensor and a a of the (Fig. and this that it is possible to and to the of that are in legume seed compartment and development (Fig. The will be to identify which play a role in the of each seed and how their corresponding genes are into regulatory networks in the soybean genome (Fig. Legumes a wide range of diversity in seed size and embryo (Fig. an to use and functional genomics to the in the different legume seeds. For example, it should be possible to and the in legume that in size and (e.g. SRB, and and address the of what in suspensor size in legume embryo development. it is that will be diverse for each legume species, it is possible to advantage of the between legumes at the and levels to use approaches to gene activity within the seed regions of approaches have been in plants, and species have from a common more than years such as and human et al., et al., et al., 2004; et al., 2004; et al., 2004; Wang et al., 2004; et al., 2005; et al., 2005). This is than that SRB, and soybean, which have been to from a common approximately years ago (Fig. et al., 2005). this out using SRB and embryo-proper with soybean (Fig. and that most diverse SRB embryo that are to be by the soybean are by SRB embryo-proper and suspensor regions (Fig. of including are specific to each of the SRB embryo at the level of the (Fig. The from these studies by SRB embryo-proper and suspensor and In addition, they new embryo and including approximately that play roles in embryo during early (Fig. that using from diverse legumes can be in genes during seed development at a global with using legume and (e.g. should provide an for genes that play important roles in the development of model legume such as soybean, and as well as in of legumes few genomic resources are (Fig. 2B). the genomics strategy that to study the early of legume seed and embryo development (Fig. including that are in the embryo and suspensor of SRB and soybean embryos and and and genes that are in compartments of the seed (e.g. endosperm, What and compartment-specific genes within a seed and how compartment-specific genes are into regulatory networks within a plant genome are important questions of seed biology (Fig. 1D). a to regulatory networks that within legume used in to identify from our that accumulate in the SRB suspensor and For example, and accumulate at a high level in the suspensor of SRB embryos (Fig. Weterings et al., 2001; and and with functions et al., and and a related to et al., such as in the (e.g. show a in SRB embryos and that their corresponding genes be into a suspensor regulatory begin suspensor regulatory our in the gene (Fig. Weterings et al., that approximately of the in the suspensor of that expression is at the level (Fig. Weterings et al., In addition, the suspensor in embryos (Fig. and that the is in flowering and analyses regions important for suspensor (Fig. Weterings et al., The five approximately (Fig. is of suspensor that within each are to direct in the suspensor et al., 2001; and a in the regions of the SRB and genes (Fig. Weterings et al., that this play an important role in during early the be in the regions of SRB genes and their in closely related The in legume genome comparative approaches to be used to identify related legume For example, in soybean, and Medicago (Fig. and and Soybean from SRB approximately years ago and from Lotus and Medicago approximately years ago (Fig. et al., 2005). obtained from two different analyses short regions between the of genes in SRB, and Medicago (Fig. The used to identify of between regions (Fig. et al., 2005). In addition, this program that is and one in these three legumes (Fig. that the genes are of in the regions of genes have been to contain et al., The closely related in the legume regions contain important for used for and to identify in the regions (Fig. and regions by in SRB the et al., the is an important suspensor and what in the suspensor remain to be One or more of the that using and analyses and with the and to in the suspensor of SRB and specific to seed compartments (Fig. play an important role in in different of the seed. the by which are interconnected to seed regulatory networks remain the function of is essential for understanding the of these in seed development and for genes to seed gene regulatory networks (Fig. in soybean et al., et al., have it possible to use and to study gene function in soybean (Fig. is used to in et al., 2003), this not be in soybean for several The soybean genome is larger than that of and and contains a of a to at a soybean are not as as the seed used in and it be challenging to of In addition, soybean is a et al., and the of genes the of to gene A more is to to study gene functions that have in a variety of including soybean (Fig. et al., 2005; and et al., 2006). For example, Herman et al. used in soybean to from soybean seeds. The advantage of is that it can be used to specific genes and has the to of closely related genes et al., 2005; et al., 2006). This and an one using to related genes (Fig. et al., 2003), should be for the functions of by and in different compartments of a soybean including that are in the soybean genome (Fig. The of the soybean genome et al., with studies should make it possible to identify genes that are by at the global identification of seed and embryo regulatory networks (Fig. The study of legume seed development has to the of new genomic resources and such as and profiling using have genes that are unique to a seed compartment and that are within the of the soybean seed (Fig. C, and The of the soybean genome et al., should allow to identify the regions of these unique and the identification of compartment-specific that seed genes into regulatory In to the soybean genome legume genome will be et al., 2003; Gepts et al., 2005; et al., 2005). from diverse legume species will provide an for comparative to identify that seed genes into regulatory an that has been in such as the et al., and 2003). between legume genome sequences, with the and obtained from seed and embryo compartments of SRB and soybean and and (e.g. et al., 2005), should facilitate the of genes essential for seed and embryo development, including important for specific legume such as seed size and embryo (Fig. In addition, comparative of legume genomes with such as and will the of genes important for seed development in flowering et al., 2004; et al., 2005). a soybean the of seed and embryo compartments can be the identification of and in genomic resources will allow to answer questions seed and embryo development (Fig. that were not possible only a few years is now in this genomic to understand what genes and regulatory networks are required to make a legume seed. from this can be in the to and are to the of our and present, have to soybean and SRB as to investigate seed development. and Wang for to many of the experiments in this In addition, for out the in to and laboratories to provide a for understanding gene activity during legume seed development.
No takes yet. Share an insight, caveat, or question.
Le et al. (2007) studied this question.
Synapse has enriched 4 closely related papers on similar clinical questions. Consider them for comparative context: