What's your must have Black Madeira type?

Figgin' A said:
Lots of interesting and contradictory (to my knowledge) info in this thread. For the sake of fullness of information, here is what Harvey, whom I respect immensely as an expert fig grower and just a humble and very honest person:

"
To the best of my knowledge, all of the Black Madeira trees originated from the same source and are genetically identical.
Slow growth is common for many Black Madeira trees, but not all. KK has a very detailed fertilizer program and gets great growth on all of his trees.
I often graft some Black Madeira scions to improve growth but also root some. If I root one tray of 12 cuttings I will see often seen significantly different rates of growth between the trees with some trees in 3 months being 24 inches tall and others only 10 or 12 inches. Over time, the slower trees usually improve and do better when moved into a larger pot. I have a hypothesis that some of the trees that have smaller/finer hair-like roots do better if given more room for their roots to expand.
The grafted Black Madeira tree I have in my orchard is pruned heavily for cuttings each winter and re-grows about 7' each year. It seems that these cuttings have lots of stored energy in them and grow quite well.
Please do not write me about Black Madeira KK, Black Madeira UCD, or Black Madeira Figaholics LOL. I sell Black Madeira. People have seemed to be quite happy with the quality of cuttings I have provided".

Here is what Harvey says about Preto on his cuttings page:

"We have two trees of this variety and had three Black Madeira and see no difference between them on our farm. Some hobbyists report that Figo Preto is earlier than Black Madeira but I believe that this is very likely just because of individual tree characteristics. On the island of Madeira there is no fig called Black Madeira and a friend of ours from Madeira and from mainland Portugal are certain that Figo Preto and Black Madeira are the same. In addition, our friend from mainland Portugal is sure that both are the same fig as a fig also known in Portugal as Violeta".

Same about Craven's Craving:

"Craven's Craving is a fig discovered in the Point Loma area of San Diego. Our video is a bit dated and our tree has grown well since the recording of the 2020 video. We continue to believe that this fig is likely the same as Black Madeira, Figo Preto, etc. with fruits of medium size, nice berry flavor, and good level of sweetness".

I don't have as much experience growing figs as Harvey, but I also noticed and strongly believe in this statement that Harvey made:
"If I root one tray of 12 cuttings I will see often seen significantly different rates of growth between the trees with some trees in 3 months being 24 inches tall and others only 10 or 12 inches. Over time, the slower trees usually improve and do better when moved into a larger pot. I have a hypothesis that some of the trees that have smaller/finer hair-like roots do better if given more room for their roots to expand."

From my own experience, I've seen good quality cuttings from a really vigorous, productive tree turn into equally excellent trees and sometimes they would grow into stragglers, all being treated equally. I've also seen quality cuttings from the same excellent mother tree grow into champions and sore losers depending on how you treat them - early up-potting, lots soil to grow roots, warm ambient temps, plenty of light, vs. keeping them in small pots for too long, inadequate lighting, etc. What's more interesting, and that contradicts what Harvey says above, is I've noticed that trees that were abused initially struggle later as well, even if you start pampering them. Not all the time, but often enough to be significant.

Which leads me to a strong belief that it's not what you grow, it's how you grow it.
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There was a post a year ago on the other forum that said genetic testing had confirmed figo preto and black madeira are identical.

@TorontoJoe I have had difficulty getting fruit from my bm kk, but this year I underwatered a tree during June. Its loaded with fruit. Will take pics soon.
 
rnexus said:
There was a post a year ago on the other forum that said genetic testing had confirmed figo preto and black madeira are identical.

@TorontoJoe I have had difficulty getting fruit from my bm kk, but this year I underwatered a tree during June. Its loaded with fruit. Will take pics soon.
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I believe Cravens Craven was part of that testing and showed to be genetically the same as well.
 
rnexus said:
There was a post a year ago on the other forum that said genetic testing had confirmed figo preto and black madeira are identical.

@TorontoJoe I have had difficulty getting fruit from my bm kk, but this year I underwatered a tree during June. It’s loaded with fruit. Will take pics soon.
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interesting observation about watering. My CC set a lot of fruit without any issues but later, I noticed that when watering it in the grow tent at the same rate as other varieties, there would be a lot of water sitting In the tray. Eventually I’d water it at about 1/3 the amount of other varieties like WM#1. Still water it less that most other trees. I had some fruit drop initially but it stopped once I stopped overwatering it.
 
Figgin' A said:
interesting observation about watering. My CC set a lot of fruit without any issues but later, I noticed that when watering it in the grow tent at the same rate as other varieties, there would be a lot of water sitting In the tray. Eventually I’d water it at about 1/3 the amount of other varieties like WM#1. Still water it less that most other trees. I had some fruit drop initially but it stopped once I stopped overwatering it.
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I have done quite a bit of bare rooting over the past few years. Its interesting to see the root ball size compared to trunk thickness and top growth. Black Madeira was always very minimal with root growth. Angelito was the other one that stood out with very small root systems and moderate sized tops. All trees were healthy.

@Figgin' A I'm guessing that the reason your CC had extra water in the tray was because of the small root system being unable to absorb it all. Maybe with varieties like this its easier to soak the soil and keep the roots too wet, thus keeping stress levels in the plant too low to set lots of fruit. (Unless the previous year it had enough 'stress /fruit' hormones accumulated. Which are then depleted after high vegetative growth rate is activated).
 
rnexus said:
I have done quite a bit of bare rooting over the past few years. Its interesting to see the root ball size compared to trunk thickness and top growth. Black Madeira was always very minimal with root growth. Angelito was the other one that stood out with very small root systems and moderate sized tops. All trees were healthy.

@Figgin' A I'm guessing that the reason your CC had extra water in the tray was because of the small root system being unable to absorb it all. Maybe with varieties like this it’s easier to soak the soil and keep the roots too wet, thus keeping stress levels in the plant too low to set lots of fruit. (Unless the previous year it had enough 'stress /fruit' hormones accumulated. Which are then depleted after high vegetative growth rate is activated).
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That’s what my observation was too. When uppotting it, it always had a noticeably smaller root system compared to its peers. I can’t soak the soil in my pots as my soil is very water retentive. Lots of compost in it. I also never water until runoff as that depletes nutrients. It’s easier for me to just give it 1/3 the water I supply to most of my other trees of similar age and pot size. It looks very healthy and happy.
 
I would love for someone to do a thorough explanation of the Genetic comparisons in more laymen's terms. Particularly in what parts of the genome and to what degree they analyzing to make the comparison.
My wife works everyday with genomic testing on people in the precision medicine field. Plants and people genomes are very, very different. But the one thing she can attest to is that it all depends on how deep you look to make the comparison. Her analogy was the type of testing that is done with companies such as Ancestry.com. It will tell you who you are related to and to what degree. But on their scale, you are the same as your sibling. For comparison the level of testing her company does is a complete genome to pin point specific genes. things that even full siblings don't share. Like how siblings and very close relatives are not always the same blood type, or organ donor compatible.
 
TorontoJoe said:
Ok…. First here is my BMKK. I’ve had this for maybe 7-8 years and I don’t think I’ve ever ripened more than a handful of figs. This is probably the most it’s ever set for me. If they weren’t so good I’d have tossed it long ago.

View attachment 11288View attachment 11289View attachment 11290

Now this is BM Moonlight. I just got the tree this year. I’m guessing you can tell why I’m so excited.

View attachment 11291View attachment 11292View attachment 11293View attachment 11294View attachment 11295View attachment 11296

Pretty crazy! Can’t wait to share some ripe fig pics! 😃
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Looking good !
 
DCallahan said:
I would love for someone to do a thorough explanation of the Genetic comparisons in more laymen's terms. Particularly in what parts of the genome and to what degree they analyzing to make the comparison.
My wife works everyday with genomic testing on people in the precision medicine field. Plants and people genomes are very, very different. But the one thing she can attest to is that it all depends on how deep you look to make the comparison. Her analogy was the type of testing that is done with companies such as Ancestry.com. It will tell you who you are related to and to what degree. But on their scale, you are the same as your sibling. For comparison the level of testing her company does is a complete genome to pin point specific genes. things that even full siblings don't share. Like how siblings and very close relatives are not always the same blood type, or organ donor compatible.
Click to expand...
This is the original post

Comparing the genetics of Black Maderia KK, Figo Preto and Craven’s Craving
08-30-2024, 05:17 PM
I am nervous to post this because I am afraid of the storm.

But let the storm commence!

Some background:
I have a Masters in Science in Biochemistry and have been involved in genetics for over a decade. I have first hand experience conducting research using PCR and sequencing methods.

I work for a company that provides sequencing services. The sequencing services provided for these fig samples were for training and validation of a new instrument into our fleet. I was lucky to be in the right place and right time to help provide some unique samples. I did not have to pay for these samples to be sequenced. I doubt I will be in a similar position in the future. If you want more sequencing completed, it is $1000+ a sample.

Whole Genome Sequencing (WGS) vs PCR: A few members have posted some results from genetic testing for figs via PCR. PCR is great tool but very different from WGS. PCR does not analyze the whole genome. In PCR, targets are chosen and DNA primers are designed to amplify those selected regions of DNA. During PCR, millions copies of the selected targets are generated, they range from a few hundred base pair to a couple thousand. The PCR results are then ran on a gel and target is visualized with a stain. In theory different fig varieties could produce targets of different sizes and when a few targets are looked at together, one could differentiate different varieties. This is a common technique used in agriculture, some species of plants have well qualified targets and are reliable, ie corn or strawberries. However, from my research there doesn’t seem to be much consensus on targets for figs with researchers around the globe are still exploring better targets. This PCR technique was also developed for commercial breeding of new plant varieties. Breeders will sprout thousands of offspring from a cross and use this technique to cut offspring similar to the parents. The goal of the breeding is to discover unique offspring, not ones similar to the parents. If you can cut similar offspring using this PCR method, then you can save a lot of time, space and money. Using this PCR technique and backing it into the application of determining clones or lineage, in MY OPINION probably isn’t going to be reliable. My opinion on this comes from reading papers of researchers trying to find reliable PCR targets for figs. New targets are explored but sometimes fail in the researchers own tests. Research is ongoing and no consensus has seem to be made. If someone has come across papers that says otherwise, I have happy to read it. I have also yet to read a paper that confirms their PCR results with WGS results.

Another option for genetic testing for figs, would be to find a “finger print” region of DNA that could be targeted for PCR amplification and then conduct sanger sequencing. However, targeted next gen sequencing platforms have become more economical then sanger sequencing in recent years. However, I have yet to come across any literature that provides a “finger print” region for figs. This would be the quickest and most cost effective method for determining clones or lineage.

Wole Genome Sequencing (WGS) is the best method for determining clones or relationships. A PCR method does not sequence the sample DNA. The first step in WGS extraction of the DNA from the plant material. For this experiment, I put on a pair of gloves, a broke off a dime sized piece of leaf and changed gloves between sample collection. The collected samples were placed in a tube with DNA stabilization media to inhibit and DNA degradation. DNA was extracted with a an off the shelf DNA extraction kit for plants. The extracted DNA was check for quantity and quality. The purified DNA then was used to generate a library. The prepared sample was sequenced on an Illumina NovaSeq X. The data was sent to a lab with an High Performance Computer (HPC) Cluster to be demultiplexed, rebuilt and aligned to the published Ficus carica reference genome. Next a data scientist using the HPC compared the whole genomes to each other using a standardized bioinformatic algorithm to determine lineage. As one can imagine this whole process is expensive and time consuming. Since this wasn’t an official study and I had to collect my samples in a short time, I wasn’t able to get a better collection of samples.

My friends comment that worked with molecular biology and biochemistry.

This seems to agree to what I think. WGS is the best method compared to PCR. However it is not perfect, there is also cytoplasmic DNA or mitochondrial DNA that may have a phenotype, not to mention that a single nucleotide mutation can affect the phenotype. In summary relatedness can be assessed very well with WGS, but it is hard to say the two figs are exactly the same, simply because a variant or mutant with a different phenotype may originate with just one single nearly undetectable nucleotide mutation. If the phenotype are identical and the percentage identity is high one can can say with some certainty that originated from the same plant, however if one can detect phenotypic changes it is hard to say that they are the same fig.

It is difficult and plants often have transposable elements. Transposable elements (TEs) are mobile DNA elements that are particularly abundant in the plant genomes. They have long been considered as junk DNA; however, a growing body of evidence suggests that TE insertions promote genetic diversity that is essential for the adaptive evolution of a species.
 
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MattK said:
This is the original post

Comparing the genetics of Black Maderia KK, Figo Preto and Craven’s Craving
08-30-2024, 05:17 PM
I am nervous to post this because I am afraid of the storm.

But let the storm commence!

Some background:
I have a Masters in Science in Biochemistry and have been involved in genetics for over a decade. I have first hand experience conducting research using PCR and sequencing methods.

I work for a company that provides sequencing services. The sequencing services provided for these fig samples were for training and validation of a new instrument into our fleet. I was lucky to be in the right place and right time to help provide some unique samples. I did not have to pay for these samples to be sequenced. I doubt I will be in a similar position in the future. If you want more sequencing completed, it is $1000+ a sample.

Whole Genome Sequencing (WGS) vs PCR: A few members have posted some results from genetic testing for figs via PCR. PCR is great tool but very different from WGS. PCR does not analyze the whole genome. In PCR, targets are chosen and DNA primers are designed to amplify those selected regions of DNA. During PCR, millions copies of the selected targets are generated, they range from a few hundred base pair to a couple thousand. The PCR results are then ran on a gel and target is visualized with a stain. In theory different fig varieties could produce targets of different sizes and when a few targets are looked at together, one could differentiate different varieties. This is a common technique used in agriculture, some species of plants have well qualified targets and are reliable, ie corn or strawberries. However, from my research there doesn’t seem to be much consensus on targets for figs with researchers around the globe are still exploring better targets. This PCR technique was also developed for commercial breeding of new plant varieties. Breeders will sprout thousands of offspring from a cross and use this technique to cut offspring similar to the parents. The goal of the breeding is to discover unique offspring, not ones similar to the parents. If you can cut similar offspring using this PCR method, then you can save a lot of time, space and money. Using this PCR technique and backing it into the application of determining clones or lineage, in MY OPINION probably isn’t going to be reliable. My opinion on this comes from reading papers of researchers trying to find reliable PCR targets for figs. New targets are explored but sometimes fail in the researchers own tests. Research is ongoing and no consensus has seem to be made. If someone has come across papers that says otherwise, I have happy to read it. I have also yet to read a paper that confirms their PCR results with WGS results.

Another option for genetic testing for figs, would be to find a “finger print” region of DNA that could be targeted for PCR amplification and then conduct sanger sequencing. However, targeted next gen sequencing platforms have become more economical then sanger sequencing in recent years. However, I have yet to come across any literature that provides a “finger print” region for figs. This would be the quickest and most cost effective method for determining clones or lineage.

Wole Genome Sequencing (WGS) is the best method for determining clones or relationships. A PCR method does not sequence the sample DNA. The first step in WGS extraction of the DNA from the plant material. For this experiment, I put on a pair of gloves, a broke off a dime sized piece of leaf and changed gloves between sample collection. The collected samples were placed in a tube with DNA stabilization media to inhibit and DNA degradation. DNA was extracted with a an off the shelf DNA extraction kit for plants. The extracted DNA was check for quantity and quality. The purified DNA then was used to generate a library. The prepared sample was sequenced on an Illumina NovaSeq X. The data was sent to a lab with an High Performance Computer (HPC) Cluster to be demultiplexed, rebuilt and aligned to the published Ficus carica reference genome. Next a data scientist using the HPC compared the whole genomes to each other using a standardized bioinformatic algorithm to determine lineage. As one can imagine this whole process is expensive and time consuming. Since this wasn’t an official study and I had to collect my samples in a short time, I wasn’t able to get a better collection of samples.

My friends comment that worked with molecular biology and biochemistry.

This seems to agree to what I think. WGS is the best method compared to PCR. However it is not perfect, there is also cytoplasmic DNA or mitochondrial DNA that may have a phenotype, not to mention that a single nucleotide mutation can affect the phenotype. In summary relatedness can be assessed very well with WGS, but it is hard to say the two figs are exactly the same, simply because a variant or mutant with a different phenotype may originate with just one single nearly undetectable nucleotide mutation. If the phenotype are identical and the percentage identity is high one can can say with some certainty that originated from the same plant, however if one can detect phenotypic changes it is hard to say that they are the same fig.

It is difficult and plants often have transposable elements. Transposable elements (TEs) are mobile DNA elements that are particularly abundant in the plant genomes. They have long been considered as junk DNA; however, a growing body of evidence suggests that TE insertions promote genetic diversity that is essential for the adaptive evolution of a species.
Click to expand...
Thanks for posting this.

At the very least is shows that there are folks out there with the latest technology that have the Fig genome mapping as an interest.

One of the things that bugs me bit, is when I read in posts people say things like "one day DNA testing will be cheap enough". As a fly on the wall, With the discussions I overhear, the type of testing, and the quantity of testing needed may never happen for figs to the degree needed to separate specific named varieties from one another. Because each test is very expensive and you need 1000s of tests to be able to compare with each other.
The current rate for human whole genomic testing of DNA is $5000 to $9000, pricing depends on who is being billed and that is testing using the same instrument as mentioned in the post above. Plant DNA is much more complex.
 
DCallahan said:
Thanks for posting this.

At the very least is shows that there are folks out there with the latest technology that have the Fig genome mapping as an interest.

One of the things that bugs me bit, is when I read in posts people say things like "one day DNA testing will be cheap enough". As a fly on the wall, With the discussions I overhear, the type of testing, and the quantity of testing needed may never happen for figs to the degree needed to separate specific named varieties from one another. Because each test is very expensive and you need 1000s of tests to be able to compare with each other.
The current rate for human whole genomic testing of DNA is $5000 to $9000, pricing depends on who is being billed and that is testing using the same instrument as mentioned in the post above. Plant DNA is much more complex.
Click to expand...
I checked to have some figs compared by a lab in California @Profig recommend. I think it was 320.00 per a sample. Brian has some varieties on file with them I do believe. My friend look over their method and it is a affordable option unless someone wants to spend thousands.
 

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@MattK I guess my chief question for Suhki at the California lab. For the stated fee, will I get anymore information beyond whether the two samples provided are the same or not. He said they have sample analysis from USDA. Will they place your provided samples amongst those in their database?
Are the PI numbers referenced from the USDA or are they numbers assigned by the testing laboratory?
 
DCallahan said:
@MattK I guess my chief question for Suhki at the California lab. For the stated fee, will I get anymore information beyond whether the two samples provided are the same or not. He said they have sample analysis from USDA. Will they place your provided samples amongst those in their database?
Are the PI numbers referenced from the USDA or are they numbers assigned by the testing laboratory?
Click to expand...
I think they are compiling a library of DNA on fig varieties.
I have searched for PI numbers. I found a spreadsheet that had some PI numbers. I will see if I can find it again.
 
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