Selecting Phenotypes: From Seed to Mother Plant

Cannabis seedlings in black plastic pots

For growers interested in breeding, it is important to understand the variations in phenotype. Knowing which phenotype to choose will ensure that you arrive at a mother plant rich with the characteristics you love. This mother plant will hopefully go on to spawn many future generations in your loving care.

When purchasing seeds, it’s likely that the resulting plants will possess a high degree of phenotypic variation. If you wish to keep mothers to provide cuttings for future crops, you may wish to select plants based upon specific characteristics. This is the process of selecting a phenotype to serve as the parental source of future generations of strains in your garden.

Scattered cannabis seeds against the white background

How to set up your equipment

You will need seeds, pots, soil (or whatever your chosen substrate is), lights (cool CFL or LED lights are preferable for young, tender seedlings), distilled or RO (reverse osmosis)-filtered water, and airflow. You may also wish to use a light vegetative growth solution. However, this will not be appropriate until the first true leaves have appeared. Before this, seedlings should be fed nothing but distilled/RO water. You may also choose a root stimulator to give your young radicles (primary tap-roots) the best start in life.

Some growers germinate their seeds in distilled water, while others simply sow seeds directly into well-watered substrate. However, many growers prefer to use the saucer method, which entails placing seeds on moistened tissue and containing them within two saucers. This technique is highly effective, simple to master and presents little risk of harming your seeds. A full guide to the saucer method can be found here.

How to care for your seedlings

Seeds should be sown into small pots at first, and transplanted (roughly every 7-10 days) as they begin to outgrow their pots. Soil/substrate should be lightly packed, but not so compacted that drainage (and growth of young roots!) is restricted. Lights should be set low over your pots and raised as necessary.

Cannabis seedlings in black pots

A good rule of thumb at this stage is to keep temperatures around 25°C/75°F to accelerate germination and initial growth. If germinating your seeds in water, warm it to this temperature first and try to maintain it. Many growers and breeders argue over the correct relative humidity for germination, and it often depends on the strain, but generally, sticking to the 50-70% range is advisable.

How to take cuttings from your young plants

After the first two weeks or so of vegetative growth, your young mother plants should have developed sufficiently that they can be pruned. You can begin around halfway down the central stalk, immediately above a set of side branches, which will then become the primary branches.

The sections that you have removed should each yield at least two or three usable cuttings. They can then be rooted and flowered so that you can determine their characteristics and make your ultimate selection. Make sure to label all of your clones so that you do not lose track of which mother plant they came from!

Close-up of a cannabis flower

Root your cuttings in the usual way, and allow them a week or two of vegetative growth before switching your lighting regime to 12/12 to induce flowering. Some growers would argue that there is no reason not to switch your lighting regime as soon as the clones have rooted and begun to put out visible new growth. However, in order to allow flowers to develop to their full potential, it helps to develop a strong central stem and primary branches first.

Throughout the process, ensure that you maintain your mother plants with the utmost care and attention. For more information and tips on maintaining healthy mothers, check out our handy tutorial.

How to choose your desired traits

As your cuttings flower, you can begin to analyse them for desirable traits. Initially, look for traits such as internodal length, speed at which flowering begins, and general health and vigour. Ideally, for indoor growing you generally want short internodes and plants that start flowering quickly, which is why indica genetics are present in practically all indoor strains. However, many sativa strains have long internodes and flower relatively slowly, yet are desirable for their own specific reasons such as flavour and cannabinoid content.

As flowers develop, take notes on the quality of the aroma, the structure of the buds, and the overall condition of the plants. If high humidity is an issue, you may wish to focus on plants with loose, light bud structures, rather than the dense buds that can allow mould spores to penetrate with ease. Look out for plants that show signs of stretching, deformation or infection, and discard those.

For the most part, you should be keeping your flowering cuttings in typical growing conditions. However, for selection of specific traits, you may wish to “test” the plants by causing some environmental stress. You can test many traits, such as resistance to mould, humidity or extreme heat. If conducting your selections outdoors, this is as simple as growing the seeds in the environment that they are intended for and seeing which ones come out best. Indoors, you can tweak your growing conditions as necessary to mimic various outdoor habitats.

Cannabis plants hang upside-down to dry

The ultimate test of your selection comes once it has been harvested, dried and cured, and is ready to sample. At this stage, you can make a final judgement on flavour, aroma, trichome coverage, and effect. Then it’s as simple as discarding the losers from your mother plants, and taking as many cuttings from the winners as is needed for your next crop!

  • Disclaimer:
    Laws and regulations regarding cannabis cultivation differ from country to country. Sensi Seeds therefore strongly advises you to check your local laws and regulations. Do not act in conflict with the law.


11 thoughts on “Selecting Phenotypes: From Seed to Mother Plant”

  1. Hi there..quick question..

    Myth or true.. If you are planning to grow mother plants only – its better to use regular seeds rather than feminized seeds?

    Any thoughts from Sensi Seeds?


    1. Mark Smith - Sensi Seeds

      Good morning Leini,

      Thanks for your question; I hope you’re having a great day,
      Feminized seeds are ideal if you are looking to eliminate the process of sexing.
      However, in general, if growers are looking to grow a healthy mother plant, regular seeds would be preferred.
      Regular plants give the grower a chance to select “the one” from the different phenotypes.

      I hope you continue to enjoy the blog,


  2. would it be fast to let the mother flower first then do cutting with the clones?…..iknow theres always a method to the madness was just really confused on this subject along with breeding need help asap

    1. Scarlet Palmer - Sensi Seeds

      Hi Paul,

      Thank you for your comment ? Unfortunately, for legal reasons we cannot respond to grow questions on the blog, but we do have the Sensi Seeds Forum where you can ask a thriving community of gardening fans for advice, share your experiences, and see if your question has already been covered. I hope this helps.

      With best wishes


      PS I really recommend checking the forum before deciding to flower your mother plant.

    2. Taking clones form a plant that is already flowering just requires the clones to take more time to root, generally.

  3. Evelyn Paoletti

    Thank you for this helpful information. I will start growing Cannabis in the Spring of 2017, as it’s becoming legal here in Manitoba. I don’t want to grow a huge Op, I just want to grow 2 or 3 different kinds of Cannabis.

    I have Fibromyalgia, and that is one creepy annoying PAIN, that’s been keeping me awake at night. Thanks for Cannabis to the rescue – The pain was driving me to the side of the bridge – not good. I found some relief and now I want to grow it.

    It’s a really Beautiful Herb that holds out a lot of good and Healing toward mankind. Blessed be this Herb. Thank You.

  4. It has been my experience that a lot of the small details in seed germination are not necessary and can be detrimental to the seedlings. I have chucked the paper towel method. When transplanting the root tip can be knocked off. I have on more than once forgotten the seeds in the paper towel and they dried up.
    So I start them in peat pots 4 to a 4in plant tray with a small amt of dirt to help with moisture. I cover the tray with a small piece of plastic wrap. the new seedlings can stay in the pot for a week or so. ( I had been using 18oz cups ) I now transplant right into 4l pots and let them veg till they go outside.
    I guess that since I wanted to grow more I found easier ways to do things.
    To identify Pheno types veg indicas at ~ 15 hr light the seedlings will show their differences.

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    The Sensi Seeds Editorial team has been built throughout our more than 30 years of existence. Our writers and editors include botanists, medical and legal experts as well as renown activists the world over including Lester Grinspoon, Micha Knodt, Robert Connell Clarke, Maurice Veldman, Sebastian Maríncolo, James Burton and Seshata.
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