Pea Breeding Resources

Pea Breeding is actually really awesome. Especially when you can get really neat colors to recombine into new combinations. Punnet Squares to predict the genetics of pea breeding is also very helpful and fun too. This page contains a multitude of information on pea genetics.

(This page was originally hosted on my test website Biolumo.com, but since i am hosting it myself on my own computer it is not exactly a reliable place, and hence i have copied all of the relevant information here to my blog as a permanent place to find it.)

Details of Mendel’s Pea Breeding

Here is a copy of Mendel’s original paper, for those who are interested.

biologyThe Results of Mendel's crosses for seven characters in pea plants

The following pea breeding illustrations were obtained from the Eighth Edition of Biology by Neil A. Campbell. I’ve scanned the relevant illustrations about pea breeding. If you would like to view the genetics section in PDF form instead, then here you go: You can read the whole genetics chapter in a virtual pdf online.

crossing pea plantsF1 Hybrid Pea Plants

Pea Alleles, Locuspeas F2 generation

random combination of the gametes results in the 3:1 ration that Mendel observed in the F2 generationMendel Pea TestcrossMendel Independent Assortment

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Rebsie Fairholm's Red-Podded Pea
Rebsie Fairholm’s Red-Podded Pea

If your still interested in pea breeding, then you might be interested in Rebsie Fairholm’s breeding projects involving peas. Not only is she breeding a very neat yellow sugar snap pea called Luna Trick, but she is also breeding an awesome red-podded pea as well! She not only shares photos and info about her crosses on her blog, but she has also provided 2 excellent tutorials for crossing peas with photos! Many of us amateur plant breeders are attempting and making progress on recreating Rebsie’s red-podded pea success here.

Trying to figure out the gentics for this rare red-podded pea is facinationg! Here are my attemopts to figure it all out with punnett squares below.

Parent Generation (P)
F1 generation if purple-pod parent is homozygous for the purple gene

F1 yp yp
GP GyPp
purple pea
GyPp
purple pea
GP GyPp
purple pea
GyPp
purple pea
OR
F1 generation if purple-pod parent is heterozygous for the purple gene
F1 yp yp
GP GyPp
purple pea
GyPp
purple pea
Gp Gypp
green pea
Gypp
green pea

But as it turns out, Rebsie’s results actually had mostly green pods. And upon doing some research about the genes responsible for the purple-podded trait, we actually find that there may instead be 3 genes needed for the anthocyanins to be present. One gene commonly called “A” is a master swich gene and is epistatic to the other genes coding for anthocyanins. The other two genes are also both required for the pod to have purple-pod’s. If this is correct than that means the punnit squares i completed above are no where close to being accurate. Here is the F1 hypothesis again, and this one as far as i know is correct this time. I have used the letter “A” to represent the on/off gene, along with “P” and “U” to represent the two purple-pod genes. I have left out the yellow podded gene because all offspring will be hetozygous for a base pod color of yellow/green.

Here is the corrected F1 generation hypothesis using the three genes for purple anthocyanin colors. We are ignoring the gene for green/yellow pods for the moment since all offspring in the F1 generation are heterozygous for dominant green and recessive yellow.

:+

That gives us a ratio of 28 Purple : 36 Green.

So I guess Rebsie was right; in the F1 generation mostly green pods appear.

Here is the F2 Generation Hypothesis using the rule of independent assortment. Now this table is not entirely correct, but represents the “average” offspring collected from the purple-podded plants in the F1 generation. I say the average because in the best case scenario you can get purple-podded plants that be homozygous for ALL of the purple genes. On the other hand, the worst case scenario is that the purple-podded plants in the F1 will be heterozygous for ALL of the purple genes. In most cases though i think that the average purple-podded plant in the F1 will have two homozygous genes and the third gene will be heterozygous. In that case you would only need to worry about two sets of genes in the F2, nameley 1 set for anthocyanin and 1 set for yellow pods underneath.
Which in this “average” scenario results in the typical 9:3:3:1 Phenotypic Ratio.
And in this case the red-podded peas are the recombinant offspring that we are loking for.
If we take that a little furthur, that means that if you plant 50 F2 generation seeds, you should get a ratio of about 43 non-red pods : 7 red-pods.

Inheritance Of The Colors Of Pea Flowers

Mendelian Inheritance Of The Colour OF The Flower In The Culinary Pea

Pea flowers (the edible kind) come in three major colors. They can come in the “wild” form which is a Bicolour Purple, White, or Salmon Pink (pink-and-white). I first encountered this information on Rebsie’s blog, and after doing some research of my own, i found one refrence to the same imformation in a very old book from 1912 (Breeding and the Mendelian discovery by A.D. Darbishire). The purple form is dominant and is a trait mostly common in field peas. The pink form is recessive to the the purple, but is dominant to the white. The white form is recessive to all color, and is commonly associated with modern peas that have been selected for high sugar content. It’s a bit amusing the way the book talks about the purple form in relation to the other two. Apparently if you breed the pink with the white you will get purple in the F1 generation because the pink has the gene that expresses color, but the white is actually hiding the gene for purple flowers. In the book this is talked about as an ancestral trait, a throwback, and the theory of reversion.

In Darwins book, The Origin of Species, Darwin himself encounters something similar with his breeding of pigeons. Darwin bred a pure white pigeon with another white pigeon (with black tail feathers), and was very surprised because in the next generation he got a blue pigeon (which has the same coloring as the wild rock pigeon). But Darwin didn’t know about genetics, so he could only conclude that it was a ancestral throwback phenomenon. We now know that the white one with black stripes had the gene for color (black) and the pure white pidgeon was actually a blue pidgeon but did not have any active color genes. To my knowlwdge the only variety of pea known to have pink flowers is the one called ‘Salmon-flowered’.

Salmon-flowered, pink, pink-and-white pea flower Bicolour Purple pea flower white pea flower

DIY Modified Bread Machine Incubator

I hereby present: “The Breadman Incubator”… TaDa!

I will admit that i never truly got into the DIYbio movement, but to say it didn’t leave an impact on me also wouldn’t be truthful. So what is this machine? And what is it for? Well, I’m glad you asked…

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In short this is a modified bread machine. Only modified to the extent that the native electronics have been replaced with an arduino (in this case an old low-cost diavolino), an arduino screw-shield, the native thermistor replaced with my own 10k ntc thermistor, and a 7 segment display from sparkfun electronics. Oh, and my own custom orange plexiglass cover! I’m quite proud of that cover! It’s main design is to regulate specific temperatures. In the case of DIYbio, in theory it can be used to regulate a temperature to be an incubator. Mainly bacteria, but it could also be used as an egg incubator, or a “hyper germination chamber” for squash seeds!. This last one is the only one i have actually tested, and i was able to see a squash seedling emerge in only one day! All of these potential uses still fall within the category of do-it-yourself biology.

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Currently the programming is limited to a pre-set temperature at 37 degrees Celsius. This is often the optimal temperature to cultivate bacteria. Or so i’m told by Wikipedia. It is also the max temperature listed as being able to germinate squash seeds. huh, who knew?

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Now, a lot of people out there might say: “why on earth would would you want to cultivate bacteria!” and one step further: “why on earth would you make a machine to grow bacteria!; Isn’t that dangerous?!” Well, umm.. I never said i actually would grow bacteria in this thing, more i created it just because i like the “i could” factor. In reality this is more of a proof-of-concept design built only to impress myself. But to answer the second question/statement.. Yes, growing bacteria is potentially dangerous.. unless you know what you are doing, what kind of bacteria is safe to work with, and proper safety protocols. Those who are familiar with the DIYbio movement will know that such safety concerns have been discussed before and that the general consensus is basically “use common sense” and “know what you are doing”. If these two principles are followed everything will be fine.

Besides, the great thing about this is that in theory this could be programmed to be it’s own sterilizer too! That’s a great plus for safety. Wikipedia say’s this:

Eventually, the entire item reaches the proper temperature needed to achieve sterilization. The proper time and temperature for Dry-Heat sterilization is 160 °C (320 °F) for 2 hours. Instruments should be dry before sterilization since water will interfere with the process. Dry-heat destroys microorganisms by causing coagulation of proteins.

I did a basic programming test to see if this machine could reach 160 degrees Celsius. It seemed like it could. The only thing needed would be a way to accurately keep track of time (like the unused chronodot i have lying around) and a button or something to initiate a programmed sterilization routine.

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In this design i have not implemented use of the motor. One because i really couldn’t think of a good use for it. But two because in my initial testing phase i accidentally destroyed both an arduino mega and my computer (i assume by not properly protecting them from the kickback electricity from the motor). Yeah, it was “my bad”! Quite literally. Yeah, so a caution to anyone who decided to build a similar project, i recommend not programming your arduino while it is plugged into the electronics of your bread machine. Program it first, and then hook it up to test it. It was only when the usb cable of my arduino were plugged into my computer (with the motor running (i think)) that bad things happened. :(

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I found this old piece of scrap aluminum that handily fits at the bottom to cover the motor thingy. It gives it a nice flat surface. Petri dishes or anything that needs a flat surface will need something like this.

So.. Does it work?.. Yup. At least in a basic sense. It definitely could use some improvement. The programming is very basic in terms of turning the relay on if it is under a preset temperature (in this case 37°C) and turning it off it is above. While this works, it is not efficient nor really all that accurate. A PID loop would probably improve it much. Also adding a chronodot would help to have a temperature compensated accurate time clock in case i wanted to incubate something for a specific amount of time. I probably will add the chronodot at some point.

bread_machine_pinout

The arduino code for this project can be found here.

Breadman Incubator Arduino Code

The following arduino code is for my Modified Bread Machine Incubator project. The display code was not written by me, but was the only example code i was able to cobble together with my working thermistor and relay code that actually worked. I understand a little of it, but not all of it. If someone knows a better way to transmit the temperature from the thermistor to the 7 segment display, then i welcome improvements. Otherwise enjoy. :)

//* Working Code for modified bread machine incubator w/ safety code
//By Andrew Barney
//Loveland, Colorado, USA
//#DIYBIO
//Test code for Display and thermistor
//seems to work...

#include <math.h>
double Temp;
int RelayHOT = 9; //Caution: Heater on Pin 9!
int led = 13; //Led on pin 13

//display code starts here
#define TXDATA  8       // Pin used to transmit data.
#define POT     0       // pin used to read the analog value.
//int potVal=0;
int potVal=Temp;
#define BITTIME 93      // adjusted to obtain 104 milliseconds delay (9600bauds).
//display code ends here

double Thermistor(int RawADC) {
Temp = log(((10240000/RawADC) - 10000));
Temp = 1 / (0.001129148 + (0.000234125 + (0.0000000876741 * Temp * Temp ))* Temp );
Temp = Temp - 273.15;            // Convert Kelvin to Celsius
return Temp;
}

void setup() {
Serial.begin(9600); // begin the serial monitor
pinMode(RelayHOT, OUTPUT); //set pin 9 (known as relayHOT - to an output)
pinMode(led, OUTPUT); //Led on pin 13 to correlate when relayHOT is ON!

//display code continued here
 pinMode(TXDATA, OUTPUT);   // initialize the TXDATA pin as an output.
 digitalWrite(TXDATA,HIGH); // TXDATA = 5V when is resting.
 //delay(10);                 //Wait for Serial Display startup.
 sendChar('v');             //Reset the display 0x76.
//display code ends here 
 
 delay(500);  // Delay a bit… (both for display and safe start-up)
}

//display code
void sendChar(char c){
  delayMicroseconds(BITTIME*2);          // wait 2 Stop bits before sending the char
  digitalWrite(TXDATA,LOW);              // low the line
  delayMicroseconds(BITTIME);            // wait Start bit
  for (int i=0; i<8;i++){
    digitalWrite(TXDATA,bitRead(c, i));  // bit out.
    delayMicroseconds(BITTIME);          // wait bit
  }
   digitalWrite(TXDATA,HIGH);            //Return TXDATA pin to "1".
}

//-------------------------------------------------------------------------
void show(String s){
  for(int i=0;i<4;i++){
    sendChar(s[i]);
  }
}
//display code ends

void loop() {
//delay(500); // Delay a bit…
int(Thermistor(analogRead(0)));
//Serial.println(analogRead(A0)); // print the raw analog values (diagnostic purposes only)
//Serial.println(int(Thermistor(analogRead(0))));  // print Celsius temp reading in serial monitor
Serial.println(Temp);
delay(1000);  // wait 1 seconds before sampling temperature again

if (Temp < 37)
{//digitalWrite(RelayHOT, HIGH);  //if the temperature is less than 37C, turn on the relay
digitalWrite(led, HIGH);}       //LED indicator

else if (Temp > 37)
{digitalWrite(RelayHOT, LOW);  //if the temperature is greater than 37C, turn the Heater off because it is too hot!
digitalWrite(led, LOW);}

//else if (Temp == 0)
//{digitalWrite(RelayHOT, LOW);  //turn the Heater off!
//digitalWrite(led, LOW);}

//else if (Temp == NAN)
//{digitalWrite(RelayHOT, LOW);  //turn the Heater off!
//digitalWrite(led, LOW);}

else if (analogRead(0) == LOW)  //check if thermistor is plugged in
{digitalWrite(RelayHOT, LOW);  //if it isn't turn the Heater off!
digitalWrite(led, LOW);}

//display code
//potVal= analogRead(0);
//potVal = Thermistor(analogRead(0));
potVal = Temp;
  String strPot = String (potVal);
  while(strPot.length()<4)strPot= " " + strPot;   //format to 4 characters.
  show(strPot);
  //delay(100);  
//display code ends

}

Pea Breeding 2015: The Quest for the Red Podded (snap) Pea

A rough example of how the genetics work in peas to create a red-podded pea.
A rough example of how the genetics work in peas to create a red-podded pea.

Gardening this year has been sparse. Mainly Peas, Watermelon, a few purple-stalked indian corn plants, 2 sunflowers, and some pepper seedlings. However progress is being made on the pea breeding front. Thanks to Joseph Lofthouse i was able to receive a small sample of his F4 cross between an unremarkable and unnamed, but yellow snow pea and Sugar Magnolia a good purple snap pea. This has expedited my own quest for a good red podded pea.

Joseph’s F4 Red Podded (snap) Pea
Contrast between a red podded snap pea and a yellow snow pea
partially red-podded peas
yellow snap pea with red spots
Partially red partially yellow snow peas

For those who are interested roughly in how the genetics works i will give my best simple explanations here. The modified google logo above is a horrible, but extremely basic diagram of how the red podded peas are bred. It requires the combination of yellow podded peas (which are recessive) and purple podded peas which are dominant (however there are three genes involved, which means that if only some are present they are only partially dominant). Purple pods have a green pod underneath, but if you can get a yellow pod as the base color, then you get red pods. The real trick after crossing such peas is to get the recombinant offspring that you desire. You need to get two recessive genes for yellow pods in addition to at least 1 of each of the purple genes. But if you only get some of the purple genes and not two copies for each then you get splotchy pods. You get partially yellow partially red pods. Sometimes this can be fixed by just growing several generations and letting them segregate themselves. This is possible because peas are naturally self pollinating. The problem is sometimes one of the purple genes will segregate out and you will forever have only a partially red pea pod which will never stabilize unless you use it to do another cross.

Here is the predicted results of the F1 generation between a purple podded parent and a yellow podded parent, with the assumption that the purple podded parent is heterozygous for all 3 purple genes. This chart was done after reading about rebsie’s F1 generation having mostly green pods.

:+

Here is an “average” prediction of the F2 generation. This is excluding one of the purple genes, because by this point you should be selecting from only purple pods. green pods will never give you purple pods, which in turn will never give you red pods.

Even Joseph’s F4 generation is still segregating between Snap pods and Snow pods, and red and yellow pea pods. So, I have some of my first red podded peas thanks to Joseph Lofthouse in Utah. And i’ve been doing as many pea crosses as i can myself. Not only for red-podded peas, but umbellatum types, pink pea flowers, large pods, snap pods, dwarf plants, etc. Should be fun. :)

Proklamo Pri La Familio

—————————————–

LA FAMILIO

—————————————–

PROKLAMO AL LA MONDO

(aŭ PROKLAMO POR LA MONDO)

—————————————–

LA UNUA PREZIDANTARO KAJ KONSILANTARO DE LA DEKDU APOSTOLOJ DE LA
EKLEZIO DE JESUO KRISTO DE LA SANKTULOJ DE LA LASTAJ TAGOJ

—————————————–

NI, LA UNUA PREZIDANTARO kaj la Konsilantaro de la
Dekdu Apostoloj de la Eklezio de Jesuo Kristo de la
Sanktuloj de la Lastaj Tagoj, solene proklamas ke
geedzeco inter viro kaj virino estas ordonita de Dio kaj ke
la familio estas centra en la plano de la Kreinto por la
eterna destino de Liaj gefiloj.

ĈIUJ HOMAJ ESTAĴOJ – viraj kaj virinaj – estas kreitaj
laŭ la bildo de Dio. Ĉiu estas amata spirita filo aŭ filino
de ĉielaj gepatroj, kaj tiel, ĉiu havas dian naturon kaj
destinon. Sekso estas esenca trajto de individua
antaŭmorta, morta, kaj eterna identeco kaj celo.

EN LA ANTAŬ-MORTEMA REGNO, spirit-filoj kaj
filinoj konis kaj adoris Dion kiel ilian Eternan Patron kaj
akceptis Lian planon, per kiu Liaj infanoj povis akiri
fizikan korpon kaj gajni surteran sperton por progresi al
perfekteco kaj finfine realigi ilian dian destinon kiel
heredantoj de eterna vivo. La dia plano de feliĉo ebligas
eternigi familiajn rilatojn trans la tombon. Sanktaj
ordonoj kaj interligoj disponeblaj en sanktaj temploj
ebligas por individuoj revenon al la ĉeesto de Dio kaj por
familioj kuniĝi eterne.

LA UNUA ORDONO kiun Dio donis al Adamo kaj Eva
apartenas al ilia potencialo por gepatreco kiel edzo kaj
edzino. Ni deklaras ke la ordono de Dio por Liaj gefiloj
por multiĝi kaj por plenigi la teron restas valida. Ni cetere
deklaras ke Dio ordonis, ke la sanktaj potencoj de
generado estu uzataj nur inter viro kaj virino, laŭleĝe
edziĝintaj kiel edzo kaj edzino.

NI DEKLARAS ke la rimedoj per kiuj la mortema vivo
estas kreita, estas elektitaj de Dio. Ni asertas la sanktecon
de vivo kaj ĝian gravecon en la eterna plano de Dio.

EDZO KAJ EDZINO havas solenan respondecon ami kaj
prizorgi unu la alian kaj siajn infanojn. “Infanoj estas
heredaĵo de la Eternulo” (Psalmo 127:3). Gepatroj havas
sanktan devon kreskigi iliajn infanojn en amo kaj justeco,
provizi liajn fizikajn kaj spiritajn bezonojn, kaj instrui ilin
ami kaj servi unu la alian, observi la ordonojn de Dio, kaj
esti leĝ-obeantaj civitanoj kie ajn ili loĝas. Edzoj kaj
edzinoj – patrinoj kaj patroj – respondecos antaŭ Dio pro
la malplenumo de tiuj devoj.

LA FAMILIO estas ordonita de Dio. Geedzeco inter viro
kaj virino estas esenca al Lia eterna plano. Infanoj rajtas
naskiĝon en la ligoj de geedzeco, kaj esti edukitaj de
patro kaj patrino kiuj honoras geedzajn promesojn kun
kompleta fideleco. Feliĉo en familia vivo plej verŝajne
estos atingita kiam fondita sur la instruoj de la Sinjoro
Jesuo Kristo. Sukcesaj geedzecoj kaj familioj estas
fondiĝintaj kaj teniĝintaj sur la principoj de fido, preĝo,
pento, pardono, respekto, amo, kompato, laboro, kaj sanaj
distraj aktivecoj. Laŭ dia plano, patroj devas prezidi en
siaj familioj kun amo kaj justeco kaj respondecas por
havigi la necesaĵojn de la vivo kaj por doni protekton por
iliaj familioj. Patrinoj unuavice respondecas pri la
nutrado de iliaj infanoj. En tiuj sanktaj respondecoj,
patroj kaj patrinoj devas helpi unu la alian kiel egalaj
partneroj. Malkapablo, morto, aŭ aliaj cirkonstancoj
povas necesigi individuan adapton. La pligranda familia
rondo devus subteni kiam bezonata.

NI AVERTAS ke individuoj kiuj malobservas interligojn
de ĉasteco, kiuj misuzas edz(in)on aŭ idaron, aŭ kiuj ne
plenumas familiajn respondecojn, iun tagon respondecos
antaŭ Dio. Plue ni avertas ke la malintegriĝo de la familio
kaŭzos malfeliĉojn al individuoj, komunumoj kaj nacioj
kiel antaŭdirite per antikvaj kaj nuntempaj profetoj.

Ni ALVOKAS ĉiujn respondecajn civitanojn kaj
funkciulojn de ĉiuj registaroj ĉie por apogi tiujn paŝojn
celantajn la subtenon kaj fortigon de la familio kiel la
fundamentan unuon de la socio.

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Tiu proklamo estis laŭtlegita de Prezidanto Gordon B. Hinckley kiel parton de lia mesaĝo ĉe la Ĝenerala Kunveno de la Help-Societo kiu okazis je la 23a de septembro, 1995, en Salt Lake City, Utaho.

proklamo_pri_la_familio.pdf

http://poresperantamormonaro.weebly.com/

HP/Agilent 03458-66509 7V DC Reference Clone

This past week I’ve been helping my dad design some replacement boards for the HP/Agilent 3458A multimeter.  I don’t know much about what these actually do, but he says that this board is the heart of the 3458A. Apparently it is some sort of DC reference board which uses the LTZ1000.  Anyway the protoypes seem to have tuned out great. He thinks he might try to sell his boards on ebay soon since in his design he has improved upon HP’s version. He mentioned that he has been able to make his version more stable with less drift. The cool thing is that we tried hard to keep everything pin compatible so they should work fine in an actual 3458A or standalone in a project like this one.

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DSCF1512