acespicoli
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Sire Lines & "Y" They Matter
- Thread starter acespicoli
- Start date
When a gene is lost on the Y chromosome due to degeneration, it is essential for the organism's reproductive success that the corresponding function is still maintained. Therefore, through evolutionary processes, certain genes that were originally on the Y chromosome have been relocated to autosomes or the X chromosome.![The phylogeny is according to the reference of [59]. Idiograms created based on data obtained in [21], [23], [24], [26], [55] and in this study. 5S rDNA: green signals; 45S rDNA: red signals; species-specific subtelomeric repeats (HSR-1for H. lupulus, HJSR for H. japonicus and CS-1 for C. sativa): green signal. The position of pseudoautosomal region on sex chromosomes is indicated by brackets. Time of divergence estimated in [60], [61], [62].](https://www.researchgate.net/profile/Oleg-Aleksandrov/publication/259919693/figure/fig4/AS:202644292411425@1425325572964/The-phylogeny-is-according-to-the-reference-of-59-Idiograms-created-based-on-data.png "The phylogeny is according to the reference of [59]. Idiograms created based on data obtained in [21], [23], [24], [26], [55] and in this study. 5S rDNA: green signals; 45S rDNA: red signals; species-specific subtelomeric repeats (HSR-1for H. lupulus, HJSR for H. japonicus and CS-1 for C. sativa): green signal. The position of pseudoautosomal region on sex chromosomes is indicated by brackets. Time of divergence estimated in [60], [61], [62].")
The phylogeny is according to the reference of [59]. Idiograms created based on data obtained in [21], [23], [24], [26], [55] and in this study. 5S rDNA: green signals; 45S rDNA: red signals; species-specific subtelomeric repeats (HSR-1for H. lupulus, HJSR for H. japonicus and CS-1 for C. sativa): green signal. The position of pseudoautosomal region on sex chromosomes is indicated by brackets. Time of divergence estimated in [60], [61], [62].
An efficient RNA-seq-based segregation analysis identifies the sex chromosomes of Cannabis sativa
Cannabis sativa–derived tetrahydrocannabinol (THC) production is increasing very fast worldwide. C. sativa is a dioecious plant with XY Chromosomes, and only females (XX) are useful for THC production. Identifying the sex chromosome sequence would ...www.ncbi.nlm.nih.gov
Mapping of these sex-linked genes to a C. sativa genome assembly identified the largest chromosome pair being the sex chromosomes. We found that the X-specific region (not recombining between X and Y) is large compared to other plant systems. Further analysis of the sex-linked genes revealed that C. sativa has a strongly degenerated Y Chromosome and may represent the oldest plant sex chromosome system documented so far. Our study revealed that old plant sex chromosomes can have large, highly divergent nonrecombining regions, yet still be roughly homomorphic.
ONE DETAIL ID LIKE TO DISCUSS IF YOUR FOLLOWING IS
strongly degenerated Y Chromosome, AND WHY ?
I assume it can be called rapid degeneration cuz cannabis can lose gene snippets easily...very malleable plant within a few generations, new plant. The heteromorphy they talk about correlates to rapid degeneration in Y chrom cuz the plant wants to live super bad...it doesn't want to evolve into a new shape,form, structure, variant, so it replaces code quick and easy...they will not heteromorphy easily because they can repair chromosome nonrecombining regions. Just cuz it's quickest in the 3 species group ain't no big deal...except if you look at it from the point of view that this plant ain't supposed to dissappear or change dramatically ( wink)
acespicoli
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sativa has a strongly degenerated Y Chromosome and may represent the oldest plant sex chromosome system documented so far. Our study revealed that
old plant sex chromosomes can have large, highly divergent nonrecombining regions, yet still be roughly homomorphic.
Cannabis sativa is an ancient crop (Schultes et al.)
The founder effect is a type of genetic drift, occurring when a small group in a population splinters off from the original population and forms a new one. The new colony may have less genetic variation than the original population, and through the random sampling of alleles during reproduction of subsequent generations, continue rapidly towards fixation.
acespicoli
Well-known member
They made a term "degeneration" and to me I see it as refinement or evolving towards perfection
The non recombining sections are double triple many times stacked in repeat and may be actively or inactively expressed genes... Science likes to use terms like "junk DNA"
and when they say this what are we really talking about ?
Heres what AI tells us
"Junk DNA" is a term used in genetics to describe
non-coding regions of DNA that have no known biological function.
It makes up about 98% of the human genome, and is mostly found in plants and animals, especially higher organisms. Junk DNA is made up of pseudogenes, repetitive DNA, and fragments of viruses and transposons.
More AI...
Pseudogenes are
nonfunctional DNA segments that look similar to functional genes but are unable to code for proteins.
They are often the result of gene duplication or reverse transcription of an mRNA transcript. Over time, pseudogenes can accumulate mutations that cause them to lose their ability to code for proteins, such as stop codons, frameshifts, and deletions.
Nat Rev Genet. 2013 Feb; 14(2): 113–124.
doi: 10.1038/nrg3366
PMCID: PMC4120474
NIHMSID: NIHMS608736
PMID: 23329112
Y chromosome evolution:
emerging insights into processes of Y chromosome degeneration
- Empirical observations in Drosophila neo-sex chromosomes, primate Y chromosomes and theoretical models and computer simulations show that degeneration is not a linear process, and so Y chromosomes in these species will probably not completely degenerate in the future.
TURNS OUT AS TIME GOES ON DEGENERATION SLOWS....
BUT WILL IT EVER STOP "DEGRADING" OR BE LOST?
WHAT DOES IT BRING TO THE EVOLUTIONARY ADVANTAGE TABLE ?
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acespicoli
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Evolutionary history of plants - Wikipedia
MICRO POLLEN
CRYPTOSPORES
Cryptospore - Wikipedia
acespicoli
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Microsporogenesis is the process of forming microspores from microsporocytes in the anther of a plant, which is the first stage of pollen grain development. The word "microsporogenesis" comes from "microspore" and "genesis," which means "creation" or "formation"
From DNA to protein - 3D
Protein synthesis animation
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DNA Mutation 3D Animation
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Plants can count? How they "count" their chromosomes
Repeated turnovers keep sex chromosomes young in willows
- September 2022
- Genome Biology 23(1)
- 23(1)
Background Salicaceae species have diverse sex determination systems and frequent sex chromosome turnovers. However, compared with poplars, the diversity of sex determination in willows is poorly understood, and little is known about the evolutionary forces driving their turnover. Here, we characterized the sex determination in two Salix species, S. chaenomeloides and S. arbutifolia, which have an XY system on chromosome 7 and 15, respectively. Results Based on the assemblies of their sex determination regions, we found that the sex determination mechanism of willows may have underlying similarities with poplars, both involving intact and/or partial homologs of a type A cytokinin response regulator (RR) gene. Comparative analyses suggested that at least two sex turnover events have occurred in Salix, one preserving the ancestral pattern of male heterogamety, and the other changing heterogametic sex from XY to ZW, which could be partly explained by the “deleterious mutation load” and “sexually antagonistic selection” theoretical models. We hypothesize that these repeated turnovers keep sex chromosomes of willow species in a perpetually young state, leading to limited degeneration. Conclusions Our findings further improve the evolutionary trajectory of sex chromosomes in Salicaceae species, explore the evolutionary forces driving the repeated turnovers of their sex chromosomes, and provide a valuable reference for the study of sex chromosomes in other species.DOI:10.1186/s13059-022-02769-w
CURRENTLY IN EDIT...
acespicoli
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Plant genera Cannabis and Humulus share the same pair of well-differentiated sex chromosomes
Djivan Prentout, Natasa Stajner, Andreja Cerenak, Theo Tricou, Celine Brochier-Armanet, Jernej Jakse, Jos Käfer, Gabriel A. B. Marais
First published: 12 May 2021
https://doi.org/10.1111/nph.17456
(Table S3). Upon closer inspection, one H. lupulus male (#3) appeared to have many genotyping errors, as for some XY genes, this male was genotyped as both heterozygous (XY) and homozygous (XX), which increased the error rate p. The identification of Y SNPs with this individual RNA-seq data discarded the hypothesis of a mislabelled female or a XX individual that developed male flowers. A particularly strong Y reads mapping bias in this male may explain these observations. After removal of this male, the error rate p dropped to 0.10
Our results suggest the pseudo-autosomal boundary (PAB) in H. lupulus may be located around 20 Mb, whereas we estimated a PAB around 30 Mb in C. sativa (Prentout et al., 2020); the nonrecombining region thus may be larger in H. lupulus than in C. sativa. With this estimation of the size of the nonrecombining region in H. lupulus, among the 3469 genes present on the X chromosome, 2045 genes would be located in this nonrecombining region (which represents 59.1% of all the genes on the X chromosome).
Humulus lupulus probably is an ancient polyploid that reverted to the ancestral karyotype (Padgitt-Cobb et al., 2019). It is thus possible that the H. lupulus X chromosome comprises two copies of the ancestral X as some cytological data seem to suggest (Divashuk et al., 2011). In this case, SEX-DETector would manage to identify the XY gene pairs, but would fail to identify the X-hemizygous genes as these genes would exhibit unexpected allele transmission patterns (Fig. S8).
Humulus lupulus is a rare case of XY systems in plants in which the Y is smaller than the X (cf. Ming et al., 2011). In C. sativa, both sex chromosomes have similar sizes (Divashuk et al., 2014). If the size difference is caused by deletions of parts of the H. lupulus Y chromosome, which is the hypothesized mechanism in many species (cf. Ming et al., 2011), we expect to observe that many XY gene pairs in C. sativa have missing Y copies in H. lupulus. As explained above, we did not detect any X-hemizygous genes. Furthermore, the XY gene pairs of H. lupulus were distributed uniformly on the C. sativa X chromosome, and no region appeared to be depleted in XY genes, which is not what we would observe if large deletions were present on the H. lupulus Y chromosome. The sex chromosome size differences observed in H. lupulus probably reflect complex dynamics, different from that of old animal systems with tiny Y chromosome resulting from large deletions (e.g. Skaletsky et al., 2003; Ross et al., 2005). The large size of the X chromosome in H. lupulus may be due to a full-chromosome duplication followed by a fusion (see above), whereas the Y chromosome has remained unchanged. Assemblies of the H. lupulus sex chromosomes will be needed to test these hypotheses.
Humulus lupulus sex chromosomes, like those of C. sativa, are well-differentiated, with a large nonrecombining region. Both species show similar patterns of Y degeneration and dosage compensation, despite the fact that a large part of the nonrecombining region evolved independently in both species. These similarities, as well as the age of the chromosomes and the fact that they have been conserved since the most recent common ancestor of the two genera – a unique situation in plants so far – provide an exciting opportunity to test and elaborate hypotheses on sex chromosome evolution in plants.
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acespicoli
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Cannabis DNA Explained for Beginners
Robert Bergman
Jul 15, 2022 — 6 min read
Everyone knows by now that DNA is the molecule that contains all genetic information. All living organisms have DNA.
In nature, the exact content of the DNA is determined by natural selection (with evolution as a result) and in marijuana cultivation by selection of the grower.
Selecting the best plants means that the plants with the desired DNA will create the new generation.
Plants without the desired DNA won’t reproduce, so only the most desired DNA in the group of plants survives.
This will change the characteristics of the plant over time. It’s also possible to grow multiple variants of the same type of plant, for instance weed plants that stay small and flower early, or plants that produce a high level of THC.
They’re all the same type of plant, but the variants differ because they have different DNA.
There are two ways to perform selection; by looking at the plant and by looking at the DNA. In marijuana cultivation, plants are usually selected by looking at the plants.
The best plants regarding THC yield, growth speed, resistance against diseases and overall yield are used to start the next generation of plants with.
Cultivators of other crops do however look at the DNA. They can already see in a laboratory if a certain seed will grow out to become a plant that’s resistant against drought or a certain disease.
Think for instance of Monsanto’s corn and grains.
DNA and chromosomes
GMT (suggested edit to this model)
The Tri Guy
Veteran- 9.19.2024 at 3:44 PM
- #53
Two DNA Molecule
DNA is a very long molecule that consists of different building blocks. The order of the building blocks forms a certain code a cell takes instructions from to produce certain substances and start processes.
Two DNA molecules attach to each other and intertwine like an old-fashioned phone cord. DNA and certain proteins form the chromosomes.
Chromosomes are located in the nucleus of the cell and can be seen through a powerful microscope as little strings during division. They’re often drawn schematically like a spiral like in figure 1.
If you look at the chromosomes of humans, you can see that there are 23 pairs.
There are 46 chromosomes in total, but every chromosome occurs twice. The size and many other characteristics in the pair are the same, but the details are just a bit different.
In humans, one chromosome of the pair comes from the mother and the other one comes from the father.
Some plant types have chromosome pairs, but others have chromosomes that occur 4 or 8 times. Especially many crops have these, such as corn and grains.
A DNA molecule is very long. If you were to roll out the DNA of one human cell, you’d come to a length of almost 7 feet.
This is of course incredibly long for something that thin and narrow. Large parts of the DNA don’t contain any genes, but are remnants of old genes or DNA to give structure to the DNA molecule.
The active parts of the DNA are called genes, and contain specific information about a hereditary trait.
The fact a plant has a certain gene, doesn’t necessarily mean that the trait becomes visible. The other parts of the DNA can eliminate or enhance the effect.
In the end, only the total picture of the DNA and the circumstances under which the plant grows create the final appearance and characteristics of the plant.
Build up of DNA
DNA stands for deoxyribonucleic acid. The name is based on the materials the DNA consists of. It is, in principle, a string various bases hang on.
Bases are molecules that can attach to another base in a certain way. There are only 4 bases present in DNA: guanine (G), cytosine (C), adenine (A) and thymine (T). A G can attach to a C and an A can attach to a T.
A gene can be described with a very long sequence of letters, for instance AAGCTTACC.
The two DNA molecules that attach to each other have the opposite code, so AAGTC is opposite of TTCAG.
It’s like a zipper, where the bases are the teeth of the zipper. It’s a very stable way to store the code sequence.
But obviously it has to be decided which part of the hereditary information has to be used at a certain time and in a certain cell.
Because otherwise it would turn into a big chaos, causing leaves to create flower cells or root cells to produce chlorophyll for photosynthesis.
That’s why most genes are “off” and are not read. Only the necessary genes are switched “on” in a particular cell.
Environmental factors, plant hormones and the neighboring cells in a plant determine which genes in a cell are “on” and “off”.
The “switch” can for instance be flipped by temperature change, day-night rhythm, water shortage, nutrient shortage or the age of the plant.
Reading genes
A gene has to be read to actually make the characteristic visible in the plant. The code in the DNA has to be translated to a substance that can subsequently start operating.
The two opposite DNA molecules that are entwined are partly taken apart, so the bases are no longer coupled. It’s like the zipper is being opened.
The right DNA molecule is then read by specialized proteins. The code in the DNA is converted to a copy in RNA.
RNA is a molecule that looks like DNA and also consists of bases, but it’s much shorter than DNA.
The order of bases in the DNA determines the order of chains of amino acids proteins are made of.
Every three bases of the DNA is translated into one amino acid. For instance, AAG is translated into the amino acid lysine.
The order of the amino acids in the protein makes sure the protein is folded a certain way. And this fold is essential for the operation of the protein.
It is often said that a gene codes for for instance resistance to fungi. This is a simplified way of thinking about genes and it can be quite useful to talk about it this way, but in practice you can’t just code for a characteristic.
You can only code for the production of proteins. Those proteins can start reactions that show the characteristic in the plant.
Genetic modification
Genetic modification is the altering of the DNA of a living creature, not by performing selection on plants to only let the best plants develop, but by artificially changing the genes.
In Europe it’s not allowed to grow genetically modified plants, but this is legal for certain types of plant in other countries, such as the United States.
Corn plants in the US are equipped with a gene that makes them resistant to herbicide.
The corn fields are sprayed with herbicide and all plants are killed, except for the corn. The gene that makes the corn plants resistant originates from a bacterium.
I don’t know about any marijuana plants being modified this way, but technically it is possible. If you know someone or if you have access to this knowledge, feel free to contact me ?
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acespicoli
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Figure 1
Open in figure viewerPowerPoint
The five stages of sex chromosome evolution based on the size of the nonrecombining region, degree of degeneration, and size of Y chromosome. Stage 1: Suppression of recombination at the sex determination locus and its neighboring regions led to mild degeneration of the suppressed region. YY genotype is viable. Stage 2: Suppression of recombination continues to spread, and a small MSY region evolved. YY genotype is not viable. Stage 3: The MSY expands in size and degenerates in gene content by accumulation of transposable element insertions and intrachromosomal rearrangements. The X and Y chromosomes become heteromorphic. Stage 4: Severe degeneration of the Y chromosome causes loss of function for most genes. Deletion of nonfunctional DNA sequences results in shrinking of the Y chromosome in size. Stage 5: Suppression of recombination spreads to the entire Y chromosome. The Y chromosome is lost, and X-to-autosome ratio sex determination system has evolved
Autosome - Wikipedia
het·er·o·mor·phic
/ˌhedərəˈmôrfik/
adjective
BIOLOGY
- occurring in two or more different forms, especially at different stages in the life cycle.
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acespicoli
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Very few dioecious angiosperm species have XY sex determination,[14] such as the Silene latifolia.[15] In these species sex determination is similar to mammals where male is XY and female is XX.[16]
en.wikipedia.org
Dioecy (/daɪˈiːsi/ dy-EE-see;[1] from Ancient Greek διοικία dioikía 'two households'; adj. dioecious, /daɪˈiːʃ(i)əs/ dy-EE-sh(ee-)əs[2][3]) is a characteristic of certain species that have distinct unisexual individuals, each producing either male or female gametes, either directly (in animals) or indirectly (in seed plants). Dioecious reproduction is biparental reproduction. Dioecy has costs, since only the female part of the population directly produces offspring. It is one method for excluding self-fertilization and promoting allogamy (outcrossing), and thus tends to reduce the expression of recessive deleterious mutations present in a population. Plants have several other methods of preventing self-fertilization including, for example, dichogamy, herkogamy, and self-incompatibility.
en.wikipedia.org
en.wikipedia.org
Dioecious Monoecious
www.mdpi.com
en.wikipedia.org
A transposable element (TE, transposon, or jumping gene) is a nucleic acid sequence in DNA that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic identity and genome size.[1]
Dioecy - Wikipedia
Allogamy - Wikipedia
Parthenogenesis - Wikipedia
Dioecious Monoecious
Impact of Repetitive Elements on the Y Chromosome Formation in Plants
In contrast to animals, separate sexes and sex chromosomes in plants are very rare. Although the evolution of sex chromosomes has been the subject of numerous studies, the impact of repetitive sequences on sex chromosome architecture is not fully understood. New genomic approaches shed light on...
www.mdpi.com
6. Conclusions
Although the advent of genomic methods has shed light on many aspects of heteromorphic sex chromosome formation in dioecious plants, there is still limited information about the impact of structural changes on the function of sex-linked genes. Transposable elements can affect sex chromosome evolution directly via insertion into a specific site, and indirectly by affecting the expression of closely linked genes by epigenetic mechanisms. Large-scale genomic response to repetitive DNA accumulation results in changes in chromatin status, which can in some species lead to heterochromatinization. Is an elevated rate of transposon accumulation the cause or consequence of sex chromosome degeneration? How much does cross-talk of transposable elements with genic regions affect dosage compensation evolution? How much are epigenetic processes involved in the degeneration of sex chromosomes? Surprisingly, structurally divergent sex chromosomes in S. latifolia are euchromatic while papaya homomorphic sex chromosomes reveal clear signs of heterochromatization. It is likely that sex chromosome evolution is affected by a number of mechanisms that vary in individual dioecious species such as population size, genome dynamics, regulation of TEs, etc. It remains to be answered which processes are shared among the species and which mechanisms are unique in individual species. Recent studies clearly show that plants possessing sex chromosomes can regulate the activity of TEs and subsequently regulate their spread in non-recombining regions. Whether this phenomenon is specific for dioecious plants or it is a common attribute of angiosperms remains to be elucidated. It is tempting to speculate that not only RNAi (RNA interference) machinery but also specific DNA conformation such as quadruplexes may play a role in the dynamics of the spread of repetitive elements within sex chromosomes.
Transposable element - Wikipedia
A transposable element (TE, transposon, or jumping gene) is a nucleic acid sequence in DNA that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic identity and genome size.[1]
Ten things you should know about transposable elements
Published online 2018 Nov 19. doi: 10.1186/s13059-018-1577-z
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acespicoli
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Diversity and evolution of the repetitive genomic content in Cannabis sativadoi: 10.1186/s12864-018-4494-3
Abstract
Background
The repetitive content of the genome, once considered to be “junk DNA”, is in fact an essential component of genomic architecture and evolution. In this study, we used the genomes of three varieties of Cannabis sativa, three varieties of Humulus lupulus and one genotype of Morus notabilis to explore their repetitive content using a graph-based clustering method, designed to explore and compare repeat content in genomes that have not been fully assembled.Results
The repetitive content in the C. sativa genome is mainly composed of the retrotransposons LTR/Copia and LTR/Gypsy (14% and 14.8%, respectively), ribosomal DNA (2%), and low-complexity sequences (29%). We observed a recent copy number expansion in some transposable element families. Simple repeats and low complexity regions of the genome show higher intra and inter species variation.Conclusions
As with other sequenced genomes, the repetitive content of C. sativa’s genome exhibits a wide range of evolutionary patterns. Some repeat types have patterns of diversity consistent with expansions followed by losses in copy number, while others may have expanded more slowly and reached a steady state. Still, other repetitive sequences, particularly ribosomal DNA (rDNA), show signs of concerted evolution playing a major role in homogenizing sequence variation.
acespicoli
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acespicoli
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acespicoli
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The monoecious individual exhibited a unique flowering structure, with male flowers at lower nodes and female flowers distributed along the upper rachis in an alternate phyllotaxy. Contrary to typical monoecious plants, its inflorescence was a highly branched panicle generally associated with XY males. After isolation and self-pollination, the resulting seeds were germinated and phenotyped, revealing 58 individuals with exclusive female flowers in a compound raceme and 46 monoecious individuals displaying panicle inflorescences, indicating the monoecious trait was fixed through one round of inbreeding, suggesting a simple mode of inheritance
Front Plant Sci. 2024; 15: 1412079.
Published online 2024 Jun 6. doi: 10.3389/fpls.2024.1412079
PMCID: PMC11187236
PMID: 38903434
�
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*indicates individuals from the IPK_CAN_36 accession, +indicates individuals from the stable dioecious IPK_CAN_57 accession.
It is widely accepted that the first vascular plants were outcrossing hermaphrodites.[68]
In flowering plants, hermaphroditism is ancestral to dioecy.[69]
THIS TELLS YOU THAT HERMIES ARE THE MOST ANCIENT OF SEED LINES BASAL ?
Hermaphroditism in plants may promote self fertilization in pioneer populations.[70] However, plants have evolved multiple different mechanisms to avoid self-fertilization in hermaphrodites, including sequential hermaphroditism, molecular recognition systems and mechanical or morphological mechanisms such as heterostyly.[71]: 73, 74
Front Plant Sci. 2024; 15: 1412079.
Published online 2024 Jun 6. doi: 10.3389/fpls.2024.1412079
PMCID: PMC11187236
PMID: 38903434
Why not XY?
Male monoecious sexual phenotypes challenge the female monoecious paradigm in Cannabis sativa L.
Table 1
Crosses that were undertaken to investigate male monoecious (MM) trait and sexual phenotypes of resulting seed (n=100).�
Cross | Flowering type | XX/XY | Flowering type | XX/XY | Germination rate (%) | Pure Male | Pure Female | MM |
|---|---|---|---|---|---|---|---|---|
| Pollen Donor | Ovule producer | Sexual phenotype of progeny (n=100) | |||||
1 | MM* | XY | Dioecious female* | XX | 84 | 0 | 35 | 49 |
2 | MM* | XY | MM* | XY | 42 | 0 | 24 | 18 |
3 | Dioecious female* | XX | Dioecious female* | XX | 78 | 0 | 78 | 0 |
4 | MM* | XY | Dioecious female+ | XX | 68 | 30 | 38 | 0 |
5 | Dioecious male+ | XY | Dioecious female* | XX | 60 | 21 | 36 | 3 |
*indicates individuals from the IPK_CAN_36 accession, +indicates individuals from the stable dioecious IPK_CAN_57 accession.
In plants
See also: Monoecy § Evolution, Andromonoecy § Evolution, and Gynomonoecy § EvolutionIt is widely accepted that the first vascular plants were outcrossing hermaphrodites.[68]
In flowering plants, hermaphroditism is ancestral to dioecy.[69]
THIS TELLS YOU THAT HERMIES ARE THE MOST ANCIENT OF SEED LINES BASAL ?
Hermaphroditism in plants may promote self fertilization in pioneer populations.[70] However, plants have evolved multiple different mechanisms to avoid self-fertilization in hermaphrodites, including sequential hermaphroditism, molecular recognition systems and mechanical or morphological mechanisms such as heterostyly.[71]: 73, 74
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acespicoli
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AI Overview
Island syndrome is a term used to describe the consistent differences between plants that live on islands and their mainland relatives. These differences can include:
Island syndrome is a term used to describe the consistent differences between plants that live on islands and their mainland relatives. These differences can include:
- Size
Island plants may have larger leaves and seeds. The larger seeds are thought to help them survive dispersal at sea. - Flowers
Island plants may have smaller, less colorful flowers that are easy to access. They may also be less specialized and use self-pollination more often to attract pollinators that are scarce on islands. - Woodiness
Island plants may be more woody. - Defensive adaptations
Island plants may lack defensive structures like spines, thorns, and prickles. - Other traits
Island plants may also have different lifespans, overall sizes, and dispersal abilities.
Island syndrome - Wikipedia
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Geranylgeranyl pyrophosphate - Wikipedia
Variants (THCAS, CBDAS, and CBCAS)
| GENE | HGVS.C | HGVS.P | ANNOTATION | ANNOTATION IMPACT | CONTIG | CONTIG POS | REF/ALT | VAR FREQ |
|---|---|---|---|---|---|---|---|---|
| THCAS | c.749C>A | p.Ala250Asp | missense variant | moderate | contig741 | 4417079 IGV: Start, Jump | G/T | NGS: 0.127 C90: 0.632 |
Registered Strain Search | Kannapedia
kannapedia.net
Cannabis Phylotree
Hovering over a strain of interest will highlight the strain along with other strains whose genetic distances to the interested strain are color coded as following:- Red: Very Closely Related
- Yellow: Closely Related
- Green: Moderately Related
- Blue: More Distantly Related
- Purple: Very Distantly Related
Cannabis & Hemp Phylogenic Tree
The cannabis phylogenetic tree or evolutionary tree shown below is a branching diagram or “tree” showing the inferred evolutionary relationships among various cannabis strains—their phylogeny—based upon similarities and differences in their genetic characteristics. Here the genetic characteristics are the identity and frequency of Single Nucleotide Polymorphism (SNP) in the captured regions of each cannabis strain genome (see description in each Tab under the tree for details). Genetic distance is a summary measure of the genetic divergence between cannabis strains, and the genetic distance of any two strains is approximately proportional to the total length of the radial parts in the path connecting each “leaf”, representing the two strains. SNPs of each strain are identified by DNA sequencing (StrainSEEK Panel or Whole Genome) or SNP genotyping (CannSNP90 SNP chip) and bioinformatics analysis from MGC’s Genomics Services.This phylotree is derived using the intersecting high quality SNPs from samples analyzed with StrainSEEK 3Mb (V2) and 10Mb (V3), Whole Genome Sequencing, and CannSNP90 genotyping chip.
StrainSEEK: Over 10 million bases are sequenced to 10x coverage in each plant using a targeted enrichment approach (Agilent SureSelect with Illumina NGS). This targeted approach full coverage of key genes in the cannabinoid and terpene synthase pathway, significant coverage of other important gene categories, including flowering, and pathogen and disease resistance, while also covering hundreds of thousands of randomly distributed SNPs from StrainSEEK V1, StrainSEEK 3Mb (V2), Sawler, Lynch and the Phylos Galaxy. As result, samples sequenced with this method can be cross compared to all data that is public as of 2017. This is over 100x more sequence than other tests on the market and as a result is the most comprehensive sequencing tool for discerning clones from siblings and identifying uniqueness of a given strain. The method delivers 300,000 to 500,000 SNPs across the genome with a concentrated contribution from chemotype related genes. The higher SNP density enables Marker Assisted Selection for breeding. StrainSEEK 3Mb (V2) included approximately 3 million bases sequenced to 10x coverage, using the same targeted enrichment approach, resulting in full coverage for the key cannabinoid synthase genes and 30,000 to 50,000 randomly distributed SNPs.
Whole Genome Sequencing: Using a shotgun approach, the entire 876 Million bases of the Cannabis genome are sequenced using Illumina next generation sequencing, resulting in the widest coverage of genes as well as non-coding regions of the genome. Samples sequencing using WGS have the added benefit of being “future proof”, as new genes or genomic regions of interest are found, existing WGS data can be reanalyzed without needing to be sequenced again.
CannSNP90: A comprehensive SNP chip with over 89K designed markers developed by MGC and Eurofins. The chip includes trait-specific markers for cannabinoid genes, terpene genes, plant sex, disease resistance, chemotypes, as well as randomly distributed SNPs across the genome and approximately 6.5k SNPs that overlap with StrainSEEK.
Cannabis Phylotree | Kannapedia
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Origin and Evolution of the Cannabinoid Oxidocyclase Gene Family - PMC
Cannabis is an ancient crop representing a rapidly increasing legal market, especially for medicinal purposes. Medicinal and psychoactive effects of Cannabis rely on specific terpenophenolic ligands named cannabinoids. Recent whole-genome sequencing ...
www.ncbi.nlm.nih.gov
Published online 2021 Jun 8. doi: 10.1093/gbe/evab130
Cannabinoid Oxidocyclase Gene Evolution
Although environmental factors play a role in determining the amount of cannabinoids present in different parts and stages of the plant (Rustichelli et al. 1998), in most populations the ratio between THCA and CBDA has been found to be under genetic control (Mandolino et al. 2003; Weiblen et al. 2015; Toth et al. 2020; Wenger et al. 2020). Codominant inheritance of CBDA and THCA chemotypes is consistent with a Mendelian single-locus (de Meijer et al. 2003; Onofri et al. 2015; Weiblen et al. 2015). This led to the model in which THCAS and CBDAS are encoded by alternate alleles of the same gene (BT and BD, respectively) (de Meijer et al. 2003). However, later genome sequencing revealed that they are encoded by different genes (rather than alleles) within a large polymorphic genomic region with low levels of recombination (Kojoma et al. 2006; van Bakel et al. 2011; McKernan et al. 2015; Onofri et al. 2015; Weiblen et al. 2015; Laverty et al. 2019; Grassa et al. 2021). Thus, they are treated as separate genes below.
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acespicoli
Well-known member
Registered Strain Search | Kannapedia
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acespicoli
Well-known member
Cannabis Phylotree | Kannapedia
kannapedia.net
Ruderalis Indica
SRR 14708267Grower: Lanzhou University, Guangpeng Ren
Ruderalis Indica | Kannapedia
kannapedia.net
Haze
SRR 14708264Grower: Lanzhou University, Guangpeng Ren
Haze | Kannapedia
kannapedia.net
https://en.wikipedia.org/wiki/Humulus_lupulus
Fig. 1. Population structure of Cannabis accessions.
(A) Geographic distribution (i.e., sampling sites of feral plants or country of origin of landraces and cultivars) of the samples analyzed in this study. Color codes correspond to the four groups obtained in the phylogenetic analysis and shapes indicate domestication types. The two empty red squares symbolize drug-type cultivars obtained from commercial stores located in Europe and the United States. For sample codes, see table S1. (B) Maximum likelihood phylogenetic tree based on single-nucleotide polymorphisms (SNPs) at fourfold degenerate sites, using H. lupulus as outgroup. Bootstrap values for major clades are shown. (C) Bayesian model–based clustering analysis with different number of groups (K = 2 to 4). Each vertical bar represents one Cannabis accession, and the x axis shows the four groups. Each color represents one putative ancestral background, and the y axis quantifies ancestry membership. (D) Nucleotide diversity and population divergence across the four groups. Values in parentheses represent measures of nucleotide diversity (π) for the group, and values between pairs indicate population divergence (FST). (E) Principal component analysis (PCA) with the first two principal components, based on genome-wide SNP data. Colors correspond to the phylogenetic tree grouping.
Discussion:
It has been suggested that the concepts of nld wld sativa indica etc has evolved from Ruderalis
Selection of hemp, drug type...
While females of cannabis accept pollen from perhaps many different pollen donors.
The male cannabis plant remain largely unchanged due to nonrecombinant dna
In mapping studies the offspring that have alleles arranged as in the original parents are non-recombinants. |
Cannabis pollen, specifically, falls between those two ranges. Most reports Hemp Grower has seen places pollens' drift distance around 10 to 30 miles. "Buffer zones around pollen-producing crops should start with at least a 10-mile radius," wrote veteran hemp and cannabis experts Robert C.Feb 14, 2020
Pollen Drift(PDF, 3MB) - El Dorado County
Non-recombinant regions on sex chromosomes in plants can be caused by a number of factors, including:
- Sex-determining genes
When sex-determining genes are acquired, recombination stops around them in the heterogametic sex.
- DNA sequence
The DNA sequence and gene content can differ substantially between the non-recombining regions of the X and Y chromosomes.
- Evolution
The evolution of sex chromosomes is driven by recombination, which ensures that mutations are independent and allows natural selection to work more efficiently.
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