Rotational Line Breeding Program

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Line Breeding Program
by Shannon Hiatt, Gecko Gallery, Texas


I’ve seen great posts in the forum that explain what line breeding is, along with its merits and shortcomings. However, few posts advocate any particular line breeding approach that might help someone unfamiliar with the notion. Not that a “recipe” will help a breeder produce distinctive, exciting geckos, but . . . understanding how one system works will allow the forward thinking breeder to tweak his approach when, and if, the need arises. This line breeding program is aimed at helping breeders enhance a polygenic trait in their collection. Let's say they want to enhance the tangerine color of their colony, or extend or maintain the orange of their carrot-tails, or even change the predominant pattern in their collection—Halloween Masks, for example, or boldly marked geckos. This simple but elegant line breeding system can help them accomplish this goal.

Any breeder embarking on this line breeding system must start with the best young males available, whether they bred them or bought them. These males must have the best of the trait they want to enhance, either color or pattern. Before outlining this line breeding program, it is necessary to offer a couple of quick definitions to clarify some major points.


Inbreeding is a system of breeding in which closely related geckos are mated. This includes a male bred back to a daughter, a female back to a son, and full brother-sister pairings. This is the mating of geckos more closely related than the average relationship within the colony concerned. The primary genetic consequence of inbreeding is to increase the frequency of pairing of similar genes. This makes the colony in question more homozygous. This will increase the good traits expressed in a colony, like clean ground color or bright ground color.

Inbreeding is essential to the development of prepotent geckos — geckos that uniformly "stamp" their characteristics on their progeny. The well known “Moose” is a good example here. Inbreeding may also be used to uncover genes that produce abnormalities or death — genes that, in outbred colonies, are generally present in low frequencies. Inbreeding is suggested for only highly qualified breeders who are making an effort to stabilize important traits in a given set of geckos. Don’t inbreed because it’s possible or you can; inbreed for a specific reason.

Inbreeding can result in an overall lowering in vigor, disease resistance, reproductive efficiency, and survivability. It also increases the frequency of abnormalities. And several forum posts have emphasized this quite adequately. There is no rational reason to fear inbreeding, however. It has its place in a well thought out breeding program

Line Breeding

Line breeding is systematic inbreeding in which an effort is made to avoid breeding too closely. Line breeding, as its name implies, is the restricting of matings to a certain line of descent from one or two top quality geckos, to geckos bred from a certain family, or to a limited number or breeders representing similar polygenic traits.

There are two ways to select males for a line breeding program: related males, say all three from Breeder A, or males of the same quality (all carry the polygenic trait in good measure) but from unrelated lines. A good example is the selection of SHTCT males--one from Breeder A, one from Breeder B, and one from Breeder C, comes to mind. A line breeding system will ensure that the degree of relationship among the gecko colony is less intense than with an inbreeding program. Line breeding attempts to limit the degree of heterosis (as opposed to homozygosity) while maximizing the polygenic traits. Heterosis simply means the amount of “relatedness” is minimized in a group of geckos. An outcross of unrelated geckos gives maximum heterosis to a colony; an excellent example is when a breeder crosses a gecko from wild caught lines into his line to improve vigor. This is the source of the term hybrid vigor.

The Program

OK, back to the line breeding program. A breeder should obtain quality young females carrying the same polygenic trait to breed to the selected males. They’ll need at least two females for each young male. Don't skimp on quality here. It’s not necessary to have ten females per male IF the females don’t have the trait in sufficient quantity; example: someone working on spreading that carrot-tail orange down the tail needs males with 75% to 85% orange tails. The females should be close to that. Don’t use just ANY female thinking that numbers will enhance the chance to improve the colony. If you can only find or afford a few males, this program will work. However, I suggest that a breeder start with at least three males, heavy in the polygenic trait for which they are line breeding. Select the corresponding number of females noted above (two top quality females per male). Develop an interest in top quality, NOT quantity. Ensure the females are from the same source as their corresponding male. With polygenic traits this is important. So to start the program obtain:

Male line 1 and two females from Line 1
Male Line 2 and two females from Line 2
Male Line 3 and two females from Line 3

A quick digression: yes, when introducing a new gene to a colony, like Caramel Albino, THEN breeding a male with several females is wise. This produces several hets carrying the Caramel Albino gene. More is better. That’s not the case with a line breeding program.

Why a minimum of three males? This is a rotational line breeding program that can:

1) Balance inbreeding and out breeding by providing a breeder with relatively unrelated pairings, depending, of course, on the males used as the basis for the program.
2) Alternate between line crosses within a bloodline (more inbreeding) and out crosses between bloodlines (less inbreeding). Every other year, females from one line are out crossed to males of a slightly different bloodline. During the alternate year they are bred to a male of their own basic bloodline.
3) Keep the overall level of inbreeding at a manageable level, while maintaining a degree of genetic separation between the groups.

Line Breeding Adds Nothing to a Gene Pool

One important consideration--a line breeding program is not additive. It will NOT "add" something to the gene pool that isn't already there. This is a point many breeders fail to understand at the beginning of a program. If the selected males don't already have fairly good color orange carrot-tail coverage, and that is the trait targeted for enhancement, then don’t expect rapid, breakthrough progress. Males with 50% carrot-tails mated to females with 50% carrot-tails will breed, mostly, more 50% carrot-tails or even 25% carrot-tails. How long does the average breeder have to work on a project like this?

If the goal is a good pattern, like superb Halloween Masks or bold spotting, use males that have those patterns at the onset. The bottom line is, again: begin with the BEST breeding stock that visually shows the trait or traits desired. Don't rely on guesswork. Know the stock and don't select geckos that "might" carry the trait. They must manifest the trait; the trait must be visual.

Some SHTCTs carry the bright orange body coloration into adulthood. They are certainly rare but they DO exist. A few Blood Hypos carry this trait. Make sure the males show this trait as adults; make sure the females also carry the bright orange coloration, and don't muddy up or lose color, into adulthood. To produce those bright orange or bright orange-red geckos everyone wants, then begin with males with good ground color and get females that complement them.

The Program Outlined

Label the males for the program: male #1, male #2, male #3, if there are only three males. Select two top quality females related to each male and begin the breeding program. Carefully monitor each clutch produced--place clutches from females mated to male #1 in the same container in the incubator, same for eggs from females mated to each male in turn--#2 and #3. Maintain the integrity of each line. We'll call this generation the R1 generation, for Rotational 1.

First Breeding Year*

Male Line 1 X two females from Line 1 = 1R1
Male Line 2 X two females from Line 2 = 2R1
Male Line 3 X two females from Line 3 = 3R1

*The implication here is that this is NOT a chronological year; depends upon the maturity and size of the females used.

When the young females produced the first breeding year are ready to breed, select the two best females from 1R1 strong in the target trait, two from line 2R1, etc. Females from line #1 are bred back to their sire; same for females from Line #2 and #3. This is the R2 generation. Will there be progress at this stage in the program? Could be; might not be. If Ole Murphy doesn’t rear his ugly head that is. Who is Ole Murphy? He’s the fictional “guy” from Murphy’s Law. Google it.

Second Breeding Year

Original Male Line 1 X best two females Line 1R1 = 1R2
Original Male Line 2 X best two females Line 2R1 = 2R2
Original Male Line 3 X two females from Line 3R1 = 3R2

For the R3 generation, select the two best females from each line; select the best male (he will replace his sire) from each line but ROTATE the males. Once the system is up and running, males are used twice, then retired in preference to a son. Males rotate one line over every other year. This gives you a year of outcross and a year of line breeding with each male.

Third Breeding Year

Male Line 1R2 X two best females Line 2R2 = Line 1R3
Male Line 2R2 X two best females Line 3R2 = Line 2R3
Male Line 3R2 X two best females Line 1R2 = Line 3R3

The breeder needs to keep rotating the males every other year for the R4 and R5 generations if progress is adequate. Or they can bring in an outcross at R4 but from a line that is as good as the one produced at R3. Some breeders who have the space, time, and money begin a program similar to this but with TWO rotational line breeding programs seeking to produce the SAME trait or traits. These are the source of the outcross for BOTH programs at R4. Otherwise, buy a male better than the one produced in R4 to serve as that outcross.

The reality at this juncture is that most breeders don’t have the patience and fortitude to see this program though to fruition. Yup, most breeders don't, and that's why geckos of any species from line breeding programs into the 3rd and 4th breeding year or generation deserve higher prices, in my estimation. Of course, the quality of the ensuing progeny is of prime importance. Simply following a line breeding program without stringent SELECTION is sheer folly and is not a guarantee of success or progress. Select, select, select, but visualize three basic lines crossed in a systematic approach where a breeder could maintain a breeding program for 10 to 15 years without the introduction of outside lines. This is also a recipe, of sorts, for a closed breeding system, but that’s fodder for another article.

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