The genome diversity of major crops tells the story of their evolution

https://phys.org/news/2024-07-genome-diversity-major-crops-story.html

by PaulHoule • 2 years ago

57 49 2 years ago

phys.org

sharpshadow2• 2 years ago

Anbody heard of the Urzeit Code?

https://archive.org/details/der_urzei_code

PaulHoule4• 2 years ago

How do they apply the field?

There actually are electric fields in nature that can get pretty strong sometimes. My undergrad school was New Mexico Tech which has a strong atmospheric physics program so one of our senior lab projects was

https://en.wikipedia.org/wiki/Field_mill

which demonstrates the principle of turning a DC signal into an AC signal which can be more readily measured and introduces the powerful

https://en.wikipedia.org/wiki/Lock-in_amplifier

So I have a pretty good picture of how you measure environmental fields but not how you apply them. Do you put a net over the crop and charge that up?

NotGMan• 2 years ago

I don't remember the source but in one experiment (some other researches) put plant seeds between two strong magnets.

sharpshadow2• 2 years ago

They applied a static electric field. [1]

1. https://patentimages.storage.googleapis.com/d9/34/04/3395571... 2. https://patentimages.storage.googleapis.com/1c/60/8d/4ddfe08...

PaulHoule4• 2 years ago

I'd add that the "omics" train has really left the station. It seems almost every week I hear about some new species that has been sequenced, including crazy polyploid species with huge genomes. For that matter it seems that after 20-30 years they finally are figuring out the regulatory function of "Junk DNA" is. It seems like molecular biology is in a golden age now.

mjburgess6• 2 years ago

Sure, but much of what has been discovered is that there arent "genes for X". The human genome is only 20k genes, 90%+ we share with a mouse.

This really sours the whole edifice of 20th C. 'genetic statistics' (, heritability, etc.) -- and puts well into light the eugenicist origins of frequentist statistics itself, and the vast amount of pseudoscience it's given rise to.

Yet, popsci, and many research areas have yet to catch up.

Children are still taught there are such things as dominant traits, and genes for eye colour, etc. Yet we've no idea of the full genetics of eye colour.

I would say this "golden age" is more a discovery of how everything we have previously believed is BS.

PaulHoule4• 2 years ago

Yeah, I have this 1970 book that I like to copy pictures out of

https://mastodon.social/@UP8/112780705488252948

which I think is usually ahead of it's time but the genetics unit seems backwards in that it doesn't say a word about molbio and has the same experiments were you observe the same few phenotypes that are sorta-kinda described by Mendelian inheritance, not telling you that those are the only ones, that we can't trust Mendel's lab notebook with the peas, etc.

"Personal Genomics" in the sense of 23 and me has been a wash. For one thing the SNP approach is limited in what it can do, but even if you had a real sequence teasing out the personal variation in terms of Genes x Environment can only go so far. What's interesting to me about genomics is the things that are the same and can be understood to a great deal mechanistically such as all of us Eukaryotes sharing a common "operating system" in terms of the machinery of protein synthesis, cell division and such. Hundreds of genes are known that affect diseases such as asthma, diabetes and schizophrenia and even if a polygenic risk score is possible a doctor is going to give a person with a high risk score the same advice as a person with a low risk score and give the same tests (fasting glucose, A1C) except maybe he ought to be a little more emphatic to the high risk person and the high risk person should take it more seriously.

(For that matter my experience with animals leads me to think animals are much more the same as us than different even when it comes to things like intelligence and communication. My belief was confirmed when my stray cat, "Bob B" seemed to understand that his path to a better life went through me when after 2 1/2 months of stonewalling me he got quite articulate in terms of using his "voice" and gestures such as pointing at the window and door to indicate he wants to go out, pointing at the TV and having an expression that seemed like disapproval, etc. I think these behaviors are basically intrinsic to mammals and birds if not some reptiles. You can certainly learn to communicate with animals better but a lot of it is instinctual)

pfdietz4• 2 years ago

So, if the difference between humans and mice isn't because of genetics, what is it due to?

"Genetics" isn't just "protein coding genes". Nor do genomes being X% similar mean the organisms must be X% similar.

concordDance• 2 years ago

The human genome is only 20k genes, 90%+ we share with a mouse.

Non-protein-coding genes are still genes.

Children are still taught there are such things as dominant traits, and genes for eye colour

I'm 90% sure you've got some motte-and-bailey definitions going on here. Dominant traits as commonly defined are plentiful, e.g. various skin issues.

dekhn2• 2 years ago

There are definitely things like dominant and recessive traits- it's just that only a limited number of genes actually demonstrate this behavior in a non-ambiguous way.

Eye color and hair color have been studies pretty intensively and they definitely have models which are more complex than "if you have value Y at position 37 of gene X, you have blue eyes". The way it's normally stated is that we can explain 50% of the heritance of eye color using a limited set of SNPs.

What we don't have is a comprehensive model of how complex phenotypes arise from genotypes. This is only because of historical oversimplification, and partly because the underlying causality of phenotypes is remarkably sophisticated due to a combination of many factors, overlapped with enormous amounts of noise and confounding factors.

jjtheblunt• 2 years ago

I would say this "golden age" is more a discovery of how everything we have previously believed is BS.

Whoa. I think your wording works more accurately observing previous beliefs are only a subset of a bigger picture, and are at times context dependent in such bigger pictures.

bpodgursky• 2 years ago

Children are still taught there are such things as dominant traits, and genes for eye colour, etc. Yet we've no idea of the full genetics of eye colour.

Adding FUD doesn't help. There are perfectly knowable things to teach kids —

- Blue-eyed parents have blue-eyed kids.

- Brown eyed parents have brown-eyed kids, if they are homozygous.

- Sometimes, two brown-eyed parents have recessive alleles! But it's rare!

- A blue-eyed parent and a brown eyed parent will have ~50% blue-eyed children

You don't have to 100% characterize all hazel and green shades to capture most of the state of knowledge. These are 99.9% true. You're just trying to cast doubt on an increasingly well-understood field, akin to people trying to pick apart climate change research.

robwwilliams5• 2 years ago

I don’t understand your arguments at all. Why does the homology of genes between apes and rodents bother you? They are part of a single “super-primate” clade—the euarchontoglires: https://en.wikipedia.org/wiki/Euarchontoglires

This degree of overlap is entirely expected and accepted and has been for many decades before fully genome sequence gave us hard numbers.

Can you clarify your second paragraph? Heritability is not a controversial topic but if you are saying the estimates are often abused, then I definitely will agree.

There are clearly dominant traits (and recessive traits). Huntington’s disease is the canonical example. If a student does not understand Mendelian genetics first they will not be able to understand complex quantitative genetics.

Your last statement is extreme. Do you also think that all of Newtonian physics is BS and should not be taught to kids.

Cupertino950144• 2 years ago

I don't think you've ever studied molbio.

Whether and when a gene gets expressed is everything. The non-coding part of the DNA quite often plays a role in that, as do many other factors.

Myrmornis5• 2 years ago

Painting yourself as the sort of person who thinks frequentist statistics is flawed because of unsavory associations with its founders in the early 20th century is not a way to make anything else you write be taken seriously.

photochemsyn• 2 years ago

The sheer amount of data being generated seems overwhelming. For example these researchers created a new family tree of just the grass species (very import agriculturally and industrially of course):

"The research team generated transcriptomes — DNA sequences of all of the genes expressed by an organism — for 342 grass species and whole-genome sequences for seven additional species."

https://www.psu.edu/news/eberly-college-science/story/new-mo...

This does allow analysis of very complex but desirable traits like drought tolerance, which involve a great many genes, but sorting through these huge volumes of data to ascertain which gene variants are the most important is challenging at best.

Sabinus• 2 years ago

sorting through these huge volumes of data to ascertain which gene variants are the most important is challenging at best

Seems like a promising task for LLMs.

robwwilliams5• 2 years ago

True. and the quality of the genome assemblies is getting far better thanks to sequencing technologies that can easily generate data for 200,000 consecutive basepairs.

But just to circle back on junk DNA—-most of it is non-functional baggage—-the result of our constant battles with viruses and replication errors.

NFVLCP• 2 years ago

Perhaps at least some of that "non-functional" DNA is so only after the completion of our nanotechnological self-assembly process, which is surely somewhat complex.

Qem• 2 years ago

But just to circle back on junk DNA—-most of it is non-functional baggage—-the result of our constant battles with viruses and replication errors.

So, like the middle managers for the genome.

tetris11• 2 years ago

but their preservation/conservation lends credence to their (as of yet still unknown) utility

amy-petrik-214• 2 years ago

meh a lot of the mega size genome have been well known. i can think of ameoba at 200x more genome than human and a gorillion polyploid plants. Some have this has been known the last 20-30 years. Some further back. Anyone can look at some chromosomes in a microscope, no sequencing, can say if something is polyploid or not. It's a whole field, called cytobanding.

Now as far as assemblies what is interesting there, we never sequencing the human genome . What we did was sequence a lot of the human genome "except for the hard parts, seems impossible". Well in the past few years the T2T projects has successfully sequenced the whole dang thing. Just because something is "hard" or "more repetitive" don't mean ain't nothing interdasting in dere.

Cupertino950144• 2 years ago

Honest, no-agenda question: if you go to East Africa where homo sapiens originated, there is (reportedly) much more genetic diversity than in the rest of the world. I haven't been there, myself.

So forgetting scientific studies for the moment: if you just walk around in a city, is that apparent to you? Do you think, "Wow, there sure are a lot of different types of people here?"

robwwilliams5• 2 years ago

No you would not. The underlying level of genetic diversity is often not reflected in the diversity of classical phenotypes and traits.

Cupertino950144• 2 years ago

I can't argue, not having been there. Still, I wonder if anyone here has?

CSMastermind• 2 years ago

I grew up in the US but have traveled through East Africa as well as most of the rest of the world, I don't think there's any major human population center I haven't been to.

My answer to your question would be a qualified no.

You'll see more phenotypical diversity walking around New York than Nairobi thanks to globalization.

With that said, the qualification I'd put on that is that if I consciously think about what region of the world I've seen the most variation in body plan/portions and facial geometry, I'd probably pick East Africa. You do do encounter pretty much the full spectrum of shapes human beings come in.

I will also say that I remember being surprised by how much variation in body shape I saw in China. Maybe this is pure western ignorance but I had an idea in my mind about what the average Chinese person looked like and I found myself having to adjust my expectations in ways I have no had to do anywhere else.

The last thought I'd leave you with is that you absolutely should make it a priority to visit East Africa. Kenya in particular is where I always tell people to go but Uganda, Rwanda, Ethiopia are all good options. It far exceeded my expectations.

Stay out of Nigeria though lol

Cupertino950144• 2 years ago

Thanks. I've been to Sweden and Italy, and they definitely do not follow stereotypes. Swedes, especially, are not all or even mostly blond & blue-eyed.

The genome diversity of major crops tells the story of their evolution

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