Genome sequence of the palaeopolyploid soybean
By J. Schmutz, Steven B. Cannon, J. Schlueter, Jianxin Ma, T. Mitros, W. Nelson, David L. Hyten, Qijian Song, J. Thelen, Jianlin Cheng and 35 more. Nature, 2010
4,121 citations recorded by the source corpus.
Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.
Subfields: Plant Science
View Paper: https://www.semanticscholar.org/paper/f8b224e7119a55974f62a25727de7d2bde9443db
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Citations in the corpus
- Genome‐Wide Association Analysis Identifies Candidate Genes Associated with Iron Deficiency Chlorosis in Soybean (2011, methodology): “We located these QTL on the 1.01 build of soybean (Schmutz et al., 2010) using the location of the reference SSR and restriction fragment length polymorphism (RFLP) sequences that were associated with the QTL.”
- RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome (2010, methodology): “Of the 66,210 predicted gene models in G. max (consisting of 46,430 high-confidence models and 19,780 lower-confidence models), 49,151 (74.2%) genes were transcriptionally active by the following definition: having a sum of at least two counts in one or more tissues in this study (Additional file 2)”
- The plant heat stress transcription factor (Hsf) family: structure, function and evolution. (2012, background): “In contrast, in the soybean lineage also two rounds of WGD have occurred, however, these events were more recent (~59 and ~13 Myr ago, respectively [61]).”
- Cowpea–Soybean Synteny Clarified through an Improved Genetic Map (2011, methodology): “For soybean the JGI Glyma1 database (Schmutz et al., 2010) was used while for M.”
- Evolution of Gene Duplication in Plants1[OPEN] (2016, background): “Similarly, in soybean, nodulation and oil production gene duplicates tend to be retained post WGD (Schmutz et al., 2010) and may contribute to soybean domestication traits.”
- Response and interaction of Bradyrhizobium japonicum and arbuscular mycorrhizal fungi in the soybean rhizosphere (2018, background): “Based on genomic sequences, the case study of soybean is interesting for it is believed to have undergone a recent (13 million years ago) genome duplication event which may have contributed to the recruitment of nodulation and seed oil biosynthetic genes in important biochemical pathways (Schmutz et”
- Phytozome: a comparative platform for green plant genomics (2011, neutral): “0 annotation (17) Manihot esculenta Cassava JGI/Roche/U.”
- Improving Flooding Tolerance of Crop Plants (2018, background): “Glycine max yes yes (Table 4) [51] available Brassica napus yes yes [52] available Helianthus annuus unknown no [53] not available Beta vulgaris unknown no [54] not available Solanum tuberosum unknown no [55] not available”