Alternative Transcription Initiation Sites in Soybean Genes

 The discovery of DNA's double helix structure occurred more than 70 years ago. Scientists have found a new way to read this structure within genes. Many species of plants and animals have reference genomes which are used by researchers for their own genetic analysis. The soybean genome is used widely in agricultural research for commercial and industrial purposes. While the soybean reference genome may be very advanced, it was missing locations for transcription initiation sites for individual genes within it-- until now.

Transcription initiation sites are locations in DNA that act as the start of transcription, where an mRNA copy of DNA is synthesized to then be translated into a protein. By finding where these sites are within a genome, it allows for a better understanding of how genes are expressed. Normally, transcription initiation sites are located around a TATA box (a thymine and adenine rich DNA sequence), but researcher and major contributor to the soybean reference genome Jianxin Ma disagrees. He and his researchers found that the predicted transcription initiation sites on the reference gene had only about 3% accuracy based on their new study. They identified transcription initiation sites in roughly 40,000 genes. These sites had sequences that varied from what was normally expected. By further completing the database, it improves its effectiveness as a research tool for many geneticists.

https://www.sciencedaily.com/releases/2024/11/241119181836.htm
https://academic.oup.com/plcell/advance-article/doi/10.1093/plcell/koae288/7900478#493737809

Soybean agriculture and genetic transcription

Findings published in The Plant Cell showed recent advancements in genomic research led by researchers from Purdue University. There was a conventional understanding that each gene had a single transcription initiation site. The research led by Jianxin Ma, discovered that over 97% of previously predicted transcription initiation sites are incorrect, and that soybean genes exhibit different transcription initiation sites. These alternative sites allow the transcription factors to bind in different locations, causing different proteins to be produced from the same gene.

The researchers used STRIPE-seq technology which allowed for clear mapping of the initiation sites across the genome. This data will be incorporated into SoyBase, a database that stores genomic information of soybean by many different researchers. Many other researchers share crucial information for the breeding and cultivation of soybeans. A post-doc researcher from Chilvers lab at Michigan State U created a large, free, publicly available database to show plant breeders trends in resistance and gene efficacy in different regions. Austin went as far as using google translate from old surveys from China and South America that were not in English (which is not a monumental task, as the article might lead you to believe), to produce a better and more complete database of phenotypic data and responses to different stressors.

Soybean seams to be a very collaborative field of science that I would have never expected to have such completeness and level of study. I suppose most agricultural companies nowadays benefit from scientific research for the development of crops and soil as farming becomes more and more pressurized for rises and demands in efficiency. Having 97% of pieces of genomic data corrected is, however, an extremely interesting turnover of the previous literature understanding of this variable.

https://m.farms.com/news/new-resource-for-breeding-better-soybeans-219997.aspx

https://phys.org/news/2024-11-advancements-genomic-reveal-alternative-transcription.html

Potential Economical Ramifications from Genetically Modified Agriculture

 

        Since Mendel's theory of inheritance was adapted by the agriculture industry and the FDA approved consumption of the first genetically modified food in 1982, the price of popular seeds has gradually increased. The biggest growth has occurred in the last 25 years, as noted in the graph and in an article by farmaid, "USDA data show that the per-acre cost of soybean and corn seed spiked dramatically between 1995 and 2014, by 351% and 321%, respectively." The price of soybean and corn in groceries stores will not increase tremendously. These products will continue to undergo typical societal inflation along with other produce. The purpose of this article is to shine light on the growing difficulties smaller farmers will face to obtain enough seed to fill their acres of land. Corporate agriculture companies like Monsanto, DuPont, Syngenta, and Dow can afford these spiking prices in seeds because they are the ones raising the prices. The "Big Four" companies own 70% of the soybean market and 80% of the corn market. This dominance unequivocally makes it harder for the small-market farmer to obtain and grow corn and seed in their fields. 

https://www.farmaid.org/issues/gmos/gmos-top-5-concerns-for-family-farmers/

https://www.nature.com/scitable/topicpage/genetically-modified-organisms-gmos-transgenic-crops-and-732/