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Title: Complementary Genetic and Genomic Approaches Help Characterize the Linkage Group I Seed Protein QTL in Soybean

Author
item Bolon, Yung Tsi
item JOSEPH, BINDU - Iowa State University
item Cannon, Steven
item Graham, Michelle
item DIERS, BRIAN - University Of Illinois
item FARMER, ANDREW - National Center For Genome Resources
item MAY, GREGORY - National Center For Genome Resources
item MUEHLBAUER, GARY - University Of Minnesota
item SPECHT, JAMES - University Of Nebraska
item TU, ZHENG JIN - University Of Minnesota
item Weeks, Nathan
item XU, WAYNE - University Of Minnesota
item Shoemaker, Randy
item Vance, Carroll

Submitted to: BMC Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/3/2010
Publication Date: 3/15/2010
Citation: Bolon, Y.E., Joseph, B., Cannon, S.B., Graham, M.A., Diers, B.W., Farmer, A.D., May, G.D., Muehlbauer, G.J., Specht, J.E., Tu, Z., Weeks, N.T., Xu, W.W., Shoemaker, R.C., Vance, C.P. 2010. Complementary Genetic and Genomic Approaches Help Characterize the Linkage Group I Seed Protein QTL in Soybean. Biomed Central (BMC) Plant Biology. 10:41. Available: http://www.biomedcentral.com/1471-2229/10/41.

Interpretive Summary: Soybeans are a highly valued crop due to seed protein and oil content. However, soybeans grown in the Upper Midwest suffer a loss in market price because of reduced protein content. A region of the soybean genome designated Linkage Group I has been shown to be closely linked to increased soybean protein. In this collaborative study we identified where Linkage Group I resides in the soybean genome. Using two complementary approaches we identified genes that are found in Linkage Group I. One of the methods we used for characterizing Linkage Group I was high-throughput sequencing of gene transcripts. We sequenced 2.76 x 10**9 nucleotides. This is the first report of using high-throughput sequencing to characterize a specific part of the soybean genome associated with protein production. The genes identified in Linkage Group I are good candidates for use in improving soybean protein through plant breeding and biotechnology.

Technical Abstract: The nutritional and economic value of soybean [Glycine max (L.) Merrill] is effectively a function of its 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 future soybean improvement. A major quantitative trait locus (QTL) located on soybean Linkage Group I (LG I) has the largest effect on seed protein of any QTL detected to date. Identification of candidate genes controlling this QTL would enable a better understanding of how this locus regulates protein accumulation in the developing seed. A near-isogenic line (NIL) pair contrasting in seed protein content and differing in an introgressed genomic segment containing the LG I protein QTL region was used as a resource to demarcate the QTL region and to study transcript profiles in the developing seed. We delineated the marker-flanked QTL region to less than 8.4 Mbp of genomic sequence on chromosome 20 (LG I). In parallel, transcript profiles were obtained from multiple stages of seed fill in each NIL, and transcript accumulation changes were characterized. Using Affymetrix (R) Soy GeneChip microarray and high-throughput Illumina (R) transcriptome sequencing platforms, 13 genes displaying significant transcript accumulation differences between the NILs were found and mapped to the 8.4 Mbp LG I protein QTL region. This study demonstrates the power of complementary approaches to characterize contrasting NILs and provides genome-wide transcriptome data towards the improvement of gene annotation in the soybean genome.