Genomics of Soybean Seed Development

Vodkin, Lila O.; Jones, Sarah I.; Gonzalez, Delkin O.; Thibaud‐Nissen, Françoise; Zabala, Gracia; Tuteja, Jigyasa H.

doi:10.1007/978-0-387-72299-3_11

Cited by 5 publications

(4 citation statements)

References 76 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Barrel medic has been used for study of phenylpropanoid and isoflavonoid pathways and secondary metabolites (Farag et al, 2008), various defense responses (Yang et al, 2008), root architecture (Gonzalez-Rizzo et al, 2006), and aluminum tolerance (Chandran et al, 2008). Soybean has been a model for studies of seed development (for review, see Vodkin et al, 2008), root hair development and early nodulation responses, mineral uptake, and protein and oil biosynthesis. The garden pea is in some senses the founding model for genetics, through Mendel's work in 1866.…”

Section: Many Models In the Legumesmentioning

confidence: 99%

Three Sequenced Legume Genomes and Many Crop Species: Rich Opportunities for Translational Genomics

2009

View full text Add to dashboard Cite

This year marks the essential completion of the genome sequences of soybean (Glycine max), barrel medic (Medicago truncatula), and birdsfoot trefoil (Lotus japonicus). The impact of these assembled, annotated genomes will be enormous. Birdsfoot trefoil and barrel medic, both forage crops, are the preeminent laboratory plants used in legume research. Monetarily, soybean is the most valuable protein and edible oil crop in the world, and serves as a model for seed and other developmental processes. These genome sequences contain the vast majorities of gene and regulatory sequences for these plants, as well as information about evolutionary histories over the approximately 54 million years (Mya) since their common ancestor. These genome sequences are made more useful by virtue of the ability to compare between the genomes, and to transfer information from these biological models to other crop species and vice versa. This review will describe the basic characteristics of the sequenced legume genomes, and will highlight examples, opportunities, and challenges for translational genomics across the legumes.

show abstract

Section: Many Models In the Legumesmentioning

confidence: 99%

Three Sequenced Legume Genomes and Many Crop Species: Rich Opportunities for Translational Genomics

2009

View full text Add to dashboard Cite

show abstract

“…Analyses of transcript profiles by microarrays have provided insight into the genes and processes involved in developing seed of Arabidopsis [ 33 , 34 ], soybean [ 35 - 37 ], Medicago truncatula [ 4 , 38 , 39 ], wheat [ 40 ], barley [ 5 , 41 ], and rice panicles [ 42 ]. Transcript changes, especially when used to contrast NILs, have proven useful for the discovery of genes of interest in soybean and other species [ 5 , 43 - 45 ].…”

Section: Introductionmentioning

confidence: 99%

Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean

et al. 2010

View full text Add to dashboard Cite

BackgroundThe nutritional and economic value of many crops is effectively a function of seed protein and oil content. Insight into the genetic and molecular control mechanisms involved in the deposition of these constituents in the developing seed is needed to guide crop improvement. A quantitative trait locus (QTL) on Linkage Group I (LG I) of soybean (Glycine max (L.) Merrill) has a striking effect on seed protein content.ResultsA soybean near-isogenic line (NIL) pair contrasting in seed protein and differing in an introgressed genomic segment containing the LG I protein QTL was used as a resource to demarcate the QTL region and to study variation in transcript abundance in developing seed. The LG I QTL region was delineated to less than 8.4 Mbp of genomic sequence on chromosome 20. Using Affymetrix® Soy GeneChip and high-throughput Illumina® whole transcriptome sequencing platforms, 13 genes displaying significant seed transcript accumulation differences between NILs were identified that mapped to the 8.4 Mbp LG I protein QTL region.ConclusionsThis study identifies gene candidates at the LG I protein QTL for potential involvement in the regulation of protein content in the soybean seed. The results demonstrate the power of complementary approaches to characterize contrasting NILs and provide genome-wide transcriptome insight towards understanding seed biology and the soybean genome.

show abstract

“…Similarly, The Gene Index Project (The Computational Biology Laboratory, Harvard University) includes a total of 137,174 unigenes, consisting of 73,178 TC (Tentative Consensus) sequences, 63,866 singletons and 130 singletons mature transcripts (ET) [ 10 ]. Additionally, two microarray slide sets are available; each one consisting of 18,432 single-spotted PCR products derived from the low redundancy cDNA sets [ 11 ]. A mixed Soybean GeneChip ( http://www.affymetrix.com ) is commercially available with ~37,500 G. max transcripts, 15,800 Phytophtora root and stem root transcripts, and over 7,500 soybean cyst nematode transcripts [ 3 ].…”

Section: Introductionmentioning

confidence: 99%

Early Transcriptional Response of Soybean Contrasting Accessions to Root Dehydration

et al. 2013

View full text Add to dashboard Cite

Drought is a significant constraint to yield increase in soybean. The early perception of water deprivation is critical for recruitment of genes that promote plant tolerance. DeepSuperSAGE libraries, including one control and a bulk of six stress times imposed (from 25 to 150 min of root dehydration) for drought-tolerant and sensitive soybean accessions, allowed to identify new molecular targets for drought tolerance. The survey uncovered 120,770 unique transcripts expressed by the contrasting accessions. Of these, 57,610 aligned with known cDNA sequences, allowing the annotation of 32,373 unitags. A total of 1,127 unitags were up-regulated only in the tolerant accession, whereas 1,557 were up-regulated in both as compared to their controls. An expression profile concerning the most representative Gene Ontology (GO) categories for the tolerant accession revealed the expression “protein binding” as the most represented for “Molecular Function”, whereas CDPK and CBL were the most up-regulated protein families in this category. Furthermore, particular genes expressed different isoforms according to the accession, showing the potential to operate in the distinction of physiological behaviors. Besides, heat maps comprising GO categories related to abiotic stress response and the unitags regulation observed in the expression contrasts covering tolerant and sensitive accessions, revealed the unitags potential for plant breeding. Candidate genes related to “hormone response” (LOX, ERF1b, XET), “water response” (PUB, BMY), “salt stress response” (WRKY, MYB) and “oxidative stress response” (PER) figured among the most promising molecular targets. Additionally, nine transcripts (HMGR, XET, WRKY20, RAP2-4, EREBP, NAC3, PER, GPX5 and BMY) validated by RT-qPCR (four different time points) confirmed their differential expression and pointed that already after 25 minutes a transcriptional reorganization started in response to the new condition, with important differences between both accessions.

show abstract

Genomics of Soybean Seed Development

Cited by 5 publications

References 76 publications

Three Sequenced Legume Genomes and Many Crop Species: Rich Opportunities for Translational Genomics

Three Sequenced Legume Genomes and Many Crop Species: Rich Opportunities for Translational Genomics

Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean

Early Transcriptional Response of Soybean Contrasting Accessions to Root Dehydration

Contact Info

Product

Resources

About