ARS | Publication request: Evolutionary and comparative analyses of the soybean genome

Submitted to: Journal of Breeding Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 19, 2011
Publication Date: February 4, 2012
Citation: Cannon, S.B., Shoemaker, R.C. 2012. Evolutionary and comparative analyses of the soybean genome. Journal of Breeding Science. 61(5):437-444.

Interpretive Summary: Major challenges for soybean breeders have included the relatively limited amount of genetic diversity in this crop species, the difficulty of separating desired from undesirable traits (such as for yield or growth characteristics), and the difficulty of introducing valuable traits from related species. The soybean genome sequence (the set of all DNA letters that determine the characteristics of a plant) was determined by the end of 2008. An understanding of how the soybean genome is organized can help plant breeders and researchers address those challenges. With access to the genome sequence, breeders can rapidly design tests to find useful genetic variants that might be present in the many soybean varieties that are maintained in U.S. and international gene banks. The genome sequence also allows researchers to identify when desirable and undesirable traits may be strongly associated. And new, targeted gene transformation methods may enable soybean researchers to precisely modify genes and make use of valuable traits from related species. Altogether, the soybean genome sequence should enable many improvements for soybean breeders -- and eventually, for farmers and consumers.

Technical Abstract: The soybean genome assembly has been available since the end of 2008. Significant features of the genome include large, gene-poor, repeat-dense pericentromeric regions, spanning roughly 57% of the genome sequence; a relatively large genome size of ~1.15 billion bases; remnants of a genome duplication that occurred ~13 million years ago (Mya); and fainter remnants of older polyploidies that occurred ~58 Mya and > 130 Mya. The genome sequence has been used to identify the genetic basis for numerous traits, including disease resistance, nutritional characteristics, and developmental features. The genome sequence has provided a scaffold for placement of many genomic feature elements, both from within soybean and from related species. These may be accessed at several websites, including http://www.phytozome.net, http://soybase.org, http://comparative-legumes.org, and http://www.legumebase.brc.miyazaki-u.ac.jp. The taxonomic position of soybean in the Phaseoleae tribe of the legumes means that there are approximately two dozen other beans and relatives that have undergone independent domestication, and which may have traits that will be useful for transfer to soybean. Methods of translating information between species in the Phaseoleae range from design of markers for marker assisted selection, to transformation with Agrobacterium or with other experimental transformation methods.