Breeding schemes for cross-pollinated crops
There are many types of breeding programs, some more complex than others. Which breeding method to employ depends entirely on the breeder’s goal. Ideally, potential breeders understand the benefits and drawbacks of each strategy, so a suitable strategy can be chosen to achieve the desired goal. The breeder’s personal preference always comes into play when choosing a breeding program. Previous successes may influence a breeder to use one specific breeding strategy over another. Some breeders rely heavily on science and statistics when analyzing the performance of their hybrids or progeny. Others consider breeding more of an art, and select based on feeling. Over the course of a breeding program, a breeder will often use more than one method to achieve various aspects of the goal.
When breeding cross-pollinators, we discuss hybrid performance in terms of combining ability- the ability of an inbred line to give characteristic performance in hybrid combinations with other lines. The progenies are tested for performance as populations and related back to the parental generation. Some often-used measures of performance are general combining ability (GCA) and specific combining ability (SCA). General combining ability is the average or overall performance of a given line in hybrid combinations open-pollinated with other lines.
Specific combining ability is the performance of a specific line, as compared to other lines, when crossed with the same specific pollen source.
Open Pollination
Open pollination is a very low effort type of seed production and involves minimal, if any, selection. Seeds are planted, grown to maturity, and allowed to interbreed. Off-types, or plants that do not represent the defining characteristics of a variety, are rogued from the breeding population, to ensure the variety remains pure and true to type. Inbred lines, and other populations maintained through open pollination, are often bred by one person, and then produced for commercial production and release by others. Some breeders create true-breeding populations, then license them to other companies who plant them and expand the seed populations by growing out many, many plants and allowing them all to fully seed. This is called a seed-increase.
Inbreeding
Inbreeding is nothing more than crossing a group, family, or variety of plants within themselves with no additions of genetic material from an outside or unrelated population. The most severe form of inbreeding is the self-cross, in which only one individual’s genetic material forms the basis of subsequent generations. 1:1 hybrid populations are only slightly less narrow, derived from the genetic material of 2 individuals. Such tight or narrow breeding populations lead to a condition called “inbreeding depression” upon repeated self-breeding or inbreeding.
Inbreeding depression is a reduction in vigor (or any other characteristic) due to prolonged inbreeding. This can manifest as a reduction in potency or a decrease in yield or rate of growth. Progress of depression is dependent, in part, on the breeding system of the crop. Cross-pollinated crops usually exhibit a higher degree of inbreeding depression when “selfed”, or inbred, than do selfing crops. For example, tomato (an inbreeding or selfing species) can be selfed for 20 generations with no apparent loss in vigor or yield, whereas some experiments have shown that the yield of corn per acre is decreased quite dramatically when inbred for 20 generations.
In cross-pollinated crops, deleterious genes remain hidden within populations, and the negative attributes of these recessive traits can be revealed or unmasked via continual inbreeding. Inbreeding depression can be apparent in S1 populations after a single generation of self-fertilization. When breeding cannabis using small populations, as is often the case with continual 1:1 mating schemes, inbreeding depression typically becomes apparent within three to six generations. To deal with this problem, breeder often separate parallel breeding lines, each of which are selected for similar or identical sets of traits. After generations of inbreeding, when each of the inbred lines, or selfed populations, begin to show inbreeding depression, they are hybridized or outcrossed to each other to restore vigor and eliminate inbreeding depression while preserving the genetic stability of the traits under selection.
The vast majority of texts written to date on the subject of breeding cannabis have espoused 1:1 mating strategies, much to the detriment and health of cannabis germplasm. Sadly, this is the preferred breeding scheme used today by the majority of commercial seed banks. These breeders don’t realize that cannabis is naturally an outcrossing or cross-pollinating species and existed in wild breeding populations of hundreds if not thousands of individuals. Within these many individuals lies a wide range of versions of different genes. When we select only one or two plants from this vast array as our breeding population, we drastically reduce the genetic variability found in the original population (a genetic bottleneck). This variability is lost from the populations, and unavailable to future generations.
Outbreeding
Outbreeding is the process of crossing or hybridizing plants or groups of plants with other plants to which there is no, or only a distant, relation. Any time a breeder is hybridizing using plants that reside outside of the family, group, or variety, hybrid seed is produced. For example, an F1 hybrid seed is the first generation offspring resulting from a cross of two distinct true-breeding plants or populations. Each of the parent populations were hybridized (outcrossed to each other) to produce the new generation, which is now comprised of genetics from both parental populations. Outcrossing results in the introduction of new and different genetic material to each of the respective pools.
Filial Breeding
A type of breeding system where siblings of the same progeny lot and generation are intermated to produce new generations. The first hybrid generation of two distinct true-breeding lines is denoted the F1 generation (F, filial). If two F1 siblings are bred, or the F1 population is allowed to be open pollinated, the resulting generation is labeled F2.
Mating siblings chosen from the F2, results in the F3 population. F4, F5, F6 generations, etc., are obtained in the same manner, by crossing plants of the same generation and progeny lot. Note that as long as any number of siblings of a generation (F(n)) are mated, the resulting generations is denoted (F(n+1)).
Filial inbreeding with selection for specific traits is the most common method for establishing a pure or a true-breeding population, when breeding cross-pollinated species such as cannabis.
Backcross Breeding
A type of breeding that involves repeated crossing of progeny with one of the original parental genotypes; cannabis breeders most often cross progeny to the mother plant. This parent is known as the recurrent parent. The nonrecurrent parent is called the donor parent. More widely, any time a generation is crossed to a previous generation, it is a form of backcross breeding. Backcross breeding has become one of the staple methods clandestine cannabis breeders use, mainly because it is a simple, rapid method when using greenhouses or grow rooms, and requires only small populations. The principle goal of backcross breeding is to create a population of individuals derived mainly from the genetics of one single parent (the recurrent parent).
The donor parent is chosen based on a trait of interest that the recurrent parent lacks; the idea is to introgress this trait into the backcross population, such that the new population is comprised mainly of genetics from the recurrent parent, but also contains the genes responsible for the trait of interest from the donor parent.
The backcross method is a suitable scheme for adding new desirable traits to a mostly ideal, relatively true-breeding genotype. When embarking on a backcross breeding plan, the recurrent parent should be a highly acceptable or nearly ideal genotype (for example, an existing commercial cultivar or inbred line). The ideal traits considered for introgression into the new seed line should be simply inherited and easily scored for phenotype. The best donor parent must possess the desired trait, but should not be seriously deficient in other traits. Backcross line production is repeatable, if the same parents are used.
Backcross breeding is best used when adding simply inherited dominant traits that can easily be identified in the progeny of each generation (Example 1). Recessive traits are more difficult to select for in backcross breeding, since their expression is masked by dominance in each backcross to the recurrent parent. An additional round of open pollination or sib-mating is needed after each backcross generation, to expose homozygous-recessive plants. Individuals showing the recessive condition are selected from F2 segregating generations and backcrossed to the recurrent parent (see example 2).
Example 1- Backcrossing: Incorporating A Dominant Trait
Step 1-
Recurrent Parent x Donor Parent
F1 Hybrid generation
Step 2-
Selecting desirable plants showing dominant trait, and hybridize selected plants to recurrent parent. The generation produced is denoted BC1 (some cannabis breeders break from botanical convention and denote this generation Bx1. (BC1=Bx1)).
Step 3-
Select plants from BC1 and hybridize with the recurrent parent; the resulting generation is denoted BC3.
Step 4-
Select plants from BC2 and hybridize with the recurrent parent; the resulting generation is denoted BC3.
Example 2- Backcrossing: Incorporating a Recessive Trait
Step 1-
Recurrent Parent x Donor Parent
F1 Hybrid generation
Step 2-
Select desirable plants, and create an F2 population via full sib-mating.
Step 3-
Select plants showing the desired recessive trait in the F2 generation, then hybridize selected F2-recessive plants to the recurrent parent. The generation produced is denoted BC1.
Step 4-
Select plants from BC1, and create a generation of F2 plants via sib-mating; the resulting generation can be denoted BC2.
Step 5-
Select desirable BC1F2 plants showing the recessive condition, and hybridize with the recurrent parent; the resulting generation is denoted BC2.
Step 6-
Select plants from BC2, and create an F2 population via sib-mating; denote the resulting generation BC2F2.
Step 7-
Select plants showing the recessive condition from the BC2F2 generation, and hybridize to the recurrent parent; the resulting generation is denoted BC3.
Step 8-
Grow out BC3, select and sib-mate the most ideal candidates to create an F2 population, where plants showing the recessive condition are then selected and used as a basis for a new inbred, or open-pollinated, seed line.
This new generation created from the F2 is a population that consists of, on average, about 93.7% of genes from the recurrent parent, and only about 6.3% of genes leftover from the donor parent. Most importantly, one should note that since only homozygous-recessive were chosen for mating in the BC3F2 generation, the entire resulting BCF3 generation is homozygous for the recessive trait, and breeds true for this recessive trait. Our new population meets our breeding objective. It is a population derived mainly from the genetics of the recurrent parent, yet breeds true for our introgressed recessive trait.
Backcross-derived lines are expected to be well-adapted to the environment in which they will be grown, which is another reason backcrossing is often used by cannabis breeders who operate indoors. Indoor grow rooms are easily replicated all over the world, so the grower is able to grow the plants in a similar environment in which they were bred. Progeny therefore need less extensive field-testing by the breeder across a wide range of environments.
If two or more characters are to be introgressed into a new seed line, these would usually be tracked in separate backcross programs, and the individual products would be combined in a final set of crosses after the new populations have been created by backcrossing.
The backcross scheme has specific drawbacks, however. When the recurrent parent is not very true-breeding, the resulting backcross generations segregate, and many of the traits deemed desirable to the line fail to be reproduced reliably. Another limitation of the backcross is that the “improved” variety differs only slightly from recurrent parent (e.g., one trait). If multiple traits are to be introgressed into the new population, other techniques such as inbreeding or recurrent selection, may be more rewarding.
Selfing
Selfing is the process of creating seed by fertilizing a plant with pollen obtained from itself. The result of a self-cross is a population of plants that derive from a single individual. The first generation population derived from selfing an individual is called the S1 population. If an individual is chosen from the S1, and again selfed, the resulting population is denoted the S2 generation. Subsequent generations derived in the same manner are denoted S3, S4, etc.
Traits for which the plant is homozygous remain homozygous upon selfing, whereas heterozygous loci segregate, and may demonstrate novel expressions of these characters.
We know homozygous loci remain homozygous in future generations upon selfing, but what about the heterozygous loci? Each selfed generation leads to an increase in homozygosity by 50% for each heterozygous locus, and each subsequent generation, derived from selfing an S1 individual, is 50% more homozygous than the parent from which it was derived. Repeated selfing, or single-seed descent, is the fastest way to achieve homozygosity within a group or family. Again, the more plants grown from a selfed population, the better probability a breeder has of finding selfed progeny that show all of the desired traits.
Single-Seed Descent
Single-seed descent- A plant is self-fertilized and the resulting seed collected. One of these seeds is selected and grown, again self-fertilized, and seed produced. All progeny and future generation have descended from a single ancestor, as long as no pollen from an external family is introduced. Each generation is the result of selfing one individual from the previous generation.
After six generations of selfing without selection, 98.44% of the genes of an individual are homozygous- this refers to genes, not the number of plants that are homozygous.
Recurrent Selection
Recurrent Selection- An breeding program designed to concentrate favorable genes scattered among a number of individuals by repeated cycles of selection for favorable traits.
- Step 1- Identify superior genotypes for the trait under selection.
- Step 2- Intermate the superior genotypes and select improved progeny.
- Step 3- Repeat steps 1 & 2 over a series of generations.
Pedigree Selection
Pedigree Selection- A system of breeding in which individual plants are selected in the segregating generations from a cross on the basis of their desirability, judged individually, and on the basis of a pedigree record.
Ploidy
Ploidy- Cannabis plants are, by nature, diploids with twenty chromosomes. At meiosis, each parent’s gamete contributes ten chromosomes to the zygote they have formed. Cannabis cells may be haploid (have 1 copy of each chromosome set) as in gametes, or diploid (2 chromosome sets per cell).
Some researchers have wondered whether triploid, or tetraploid cannabis (cells with either 3 or 4 chromosomes sets respectively) are agronomically important. In some species, polyploid plants grow bigger, yield more, or outperform typical diploid members of the same species. Some early reports touted polyploid cannabis as being more potent. This research was flimsy and unscientific at best, and ever since this report many cannabis growers have attempted inducing polyploidy in many varieties, none leading to agronomic success.
Diploid plants are considered normal and have one set of chromosomes, which occur in pairs within each plant cell. Polyploid plants have more than one set of chromosomes per cell. Polyploid plant chromosomes occur in groups of 3-4 instead of in pairs. Tetraploid plant groups occur with four chromosomes in each cell.
At one time, breeders believed that polyploid and tetraploid plants would produce a superior resin-packed plant.
The polyploid characteristic can be induced with an application of colchicine. Just remember, colchicine is a poison, and polyploid plants do not contain more THC-potent resin.
Mutagenesis-Inducing Variation
If variation does not exist for the trait or traits of interest, or cannot be found in other populations, it is theoretically possible to induce variation by exposing seeds or other tissues to radiation, alkylating agents, or other mutagens such as colchicine or EMS (ethylmethylsulfonate). These treatments cause changes at the DNA level that have the remote potential to result in desirable, novel phenotypes.
There is much rumor and speculation about this technique amongst breeders and growers. It’s a common myth that treating cannabis seeds with colchicine and growing the plants results in more potent cannabis plants. This myth is completely untrue. While the possibility does exist on a theoretical level, no valid experiments have ever shown this to be true. Potential breeders would be better off using their time and space for selecting better plants than trying this technique as a method for improving plant stock.
That being said, let’s take a look at the theory behind the concept.
Imagine you have a population of plants which, when grown from seed and inbred within the population, consistently produces high-THC plants. It is theoretically possible to treat many of these seeds with a mutagen, grow and inbreed the seeds, and find plants in subsequent generations that produce no THC. These mutagens can destroy genes along a chromosome, and when copies of this chromosome are inherited by future generations, a new or “novel” phenotype can appear. In our example the no THC condition is the novel phenotype.
These mutations, however, occur at random and are extremely unreliable. The probability of finding plants which have a desired mutation in the gene of interest is very low. A breeder may trat many thousands of seeds, grow 100,000 plants, and still not see the desired altered phenotypes. This technique is costly in both time and space. It is often used in the breeding of “legal plants” when growing out thousands of individuals and searching for these novel phenotypes is not problematic. Performing such population screens in cannabis is not practical, especially for clandestine breeders. The potentially hazardous nature of these mutagenic agents is another very good reason to choose other breeding options. Inducing variability is likely not the best option, at least for the hobby breeder.
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