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I've recently been working on further developing a bioinformatics pipeline called YMAP [1] that I wrote during grad school. YMAP was originally designed for genomes on the scale of the 16 Mbase genome of Candida albicans , and primarily handled short-read Illumina sequence type data (as well as a custom microarry I designed that basically nobody ever used). Eventually, I'll release an updated…
My ongoing project to produce distinctly blue dry beans occasionally throws a surprise at me. This spring, two plants with bright red flowers appeared in one of my gardens. The blue lines had until now showed a mix of white and pale pink flowers, so this change was rather dramatic. I immediately began thinking about how these plants came to be. They clearly grew from blue seeds I'd planted, but…
Plant breeding involves a great deal of luck and you can have some really good success with that. Luther Burbank produced numerous amazing plant varieties, but at the same time, he never believed in genetics. The key aspects of his method were to just try things, to grow large numbers at every stage, and to pay close attention to every plant (to find the differences). He tried crossing a…
After several years of looking for a truly blue dry bean, I started actively working to produce my own variety in 2018 when I was gifted a few bluish-black hybrid seeds from a bean collector. At the end of 2022, I was essentially done. Five years of selecting the best blue seeds each season and my new variety finally produced a consistently blue crop. There's probably still going to be a few more…
In my last post ( https://the-biologist-is-in.blogspot.com/2023/01/the-color-of-beans-3.html ), I shared a couple figures illustrating the flavonoid/anthocyanin pigment pathway in plants and in common beans ( Phaseolus vulgaris ) specifically. A couple days later, I found some additional evidence which led me to feel the need to update my figures somewhat. Certain combinations of published genes…
Years ago I heard a story. The story teller's cousin has been growing potatoes and tomatoes each of the last several years. Some years, her cousin reported finding hybrid plants that produce edible potatoes and green tomatoes. From the story, second-hand as it was, I imagined ripe-red tomatoes on a plant that when pulled up had mature potatoes hanging from the roots. There is usually some truth…
A great deal of research has gone into our understanding of how colors are made in plants. I've previously written about the carotenoid pigment pathways in tomatoes [1] and peppers [2] , condensing a great deal of published literature in the process. Until recently, I didn't have a solid grasp of the pathway plants use to make a second major category of pigments, the flavonoid pigments. These…
The pineapple we all grew up with is a bright yellow color. The pineapples of today isn't necessarily the same shade. Del Monte is now selling a variety with a distinctly pink flesh, called PinkGlow TM or Rosé pineapple. This is a bio-engineered variety, first conceptualized way back in 2005. A patent for the variety was issued in 2012 and the US FDA deregulated the variety in 2016 , deciding the…
A few years back I wrote a short post to introduced a project I had started to breed up a nicely blue colored dry bean. https://the-biologist-is-in.blogspot.com/2018/10/the-color-of-beans-1.html The project as been moving forward nicely since then. This year's crop was very consistently blue in color, the first time I didn't harvest a large fraction of tan/blue seeds as well. The picture at left…
The last year has been a mess. I'm fine. My family is fine. Most of my friends are fine. The increased anxiety and stress basically shut off any motivation or ability I had to write posts here. I was still active over on twitter or instagram, as those require less focused thought, but I just couldn't will myself to sit down at a computer and type up anything I felt was worthwhile to post. I'm now…
