- Controlling the world's marriages/relationships/pregnancies to create a new generation, closer to fulfilling its Prophecy or Plan.
- Where the members of the cult are itself the result of the Breeding Program, secretly choosing their partners in line with the aims and desires of the Cult.
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Anime and Manga
- This turns out to be the secret behind the Washuu clan in Tokyo Ghoul. They've been engaging in slavery and incest to produce both breeding slaves and child soldiers to serve them. Clan patriarch Tsuneyoshi has numerous bastard children, including not only Big Bad Nimura Furuta, but Kishou Arima and Rize Kamishiro; Rize herself was raised for the purpose of bearing children to Tsuneyoshi and his legitimate heirs.
- In Planetary Axel Brass is the last child from a breeding program started by a eclectic group of intellectuals in post-Revolutionary France, gathered together with the goal of creating a perfect human.
- Cable once fought a cult of psychic women whose leader claimed to have been arranging events to lead to the birth of Jean Grey. However, she was in the middle of a Villainous Breakdown at the time and Cable expressed skepticism of it.
- The fanatical Judda from Judge Dredd, a cult centered around a former High Judge named Morton Judd, who wanted to use genetic engineering and cloning to pacify the population of Mega-City One. After his coup failed, he and his followers escaped into the Australian outback along with a batch of genetic material from the Judge clone banks. They eventually resurfaced during the "Oz" storyarc, having spent the past 30 years breeding an army of Judda to conquer Mega-City One. Nearly all of them are wiped out when Dredd teleports a nucelar device into their hideout in Ayers Rock, except for three survivors: Judge Kraken from the "Necropolis" arc and Jonah and Pandora from the "Jihad" audio drama.
- In Dune, the Bene Gesserit have worked for 90 generations to create the Chosen One, the 'Kwisatz Haderach'. They got within two generations of succeeding - Jessica, who married Leto Atreides, was supposed to bear a daughter, who would have married Feyd-Rautha Harkonnen, producing the Kwisatz Haderach. However, she instead bore a son, Paul, who was the Kwisatz Haderach himself.
- Leto II takes over their program when he ascends to the throne. By the time of God-Emperor of Dune, he has made some success: he's bred an individual who cannot be seen with prescience. He plans for her to kill him and pass on her genes as humanity spreads out of its forced confinement so humanity will never be subject to a tyrant like him again.
- The Howard Families are a fictional group created by Robert A. Heinlein, featuring heavily in books such as Methuselah's Children and Time Enough for Love. The Howard Foundation was started in the 19th century by Ira Howard, a millionaire dying of old age in his forties, for the purpose of extending human lifespans.
- In the Vorkosigan Saga, especially Cetaganda and Diplomatic Immunity, version I is the raison d'etre for the Star Creche, and drives the main plots.
- Creepy immortal bodysnatcher Doro of Octavia Butler's Wild Seed establishes one, with "seed villages" all over the world. Someone who's six thousand years old and automatically possesses the body of the nearest person whenever he dies really doesn't view the rest of humanity as much more than his toy.
- In Charles Stross's The Apocalypse Codex, a vicious cult camouflaged as a televangelist church uses a breeding program to create the next generation of true believers. The way they do it deserves notice: they kidnap young women, inflict spinal cord injuries to permanently paralyze them, and use artificial insemination to repeatedly use their bodies as unwilling host mothers.
- In Flight of the Godkin Griffin the Godkindred Kingdom's state religion is that by mingling species their descendants can become gods, and they conquer neighboring countries in pursuit of new bloodlines. In contrast, the Mountain Pards believe that by inbreeding they can achieve purity by inbreeding themselves into a bestial state, which involves having their psychotic male young rape their females repeatedly. They're both wrong. Ascension is a matter of belief, all the Godkindred were doing was breeding towards the phenotype their ancestors had immediately after descending from godhood.
- In The Blood Ladders the founder of the Church in the human lands was the first human mage and while her gift was given by angels it is also carried by blood. The early Church was known for Bacchanalian orgies to spread her bloodline as widely as possible before they realized they could protect more people from demons by slipping a drop of magic-carrying blood into the communion wine.
- In Ringworld, it turns out that the Puppeteers are utilizing a "birth lottery" to breed genetically lucky humans. Teela is a result of this scheme.
- The Hatchery program in The Lives Of Tao is used by the Genjix to breed the next generation of hosts, specifically by breeding for both intelligence and beauty, with an intense regiment of Training from Hell.
Live Action TV
- In Dark Angel's second season, the enemies of the X-series are breeding cult members of "pure-blood" that have comparable abilities to the impure, gene-hacked super soldiers. The transgenics are obstacles to the realisation of the cult's planned extinction of the rest of humanity.
- On Orphan Black, Hank, the leader of the Prolethian cult intends on impregnating several women with his and Helena's children.
- Genestealer Cults in Warhammer 40,000 infiltrate a planet, interbreed with its population to pass on their genes, and then cause strife to weaken them in preparation for Tyranid invasion.
- The Illuminati are a secret society composed mostly of radical Inquisitors who plan to create a reincarnation of the God-Emperor, though selective breeding is just one of the proposed methods. Most want to gather together all of the Emperor's descendants and sacrifice them all at once to return their power to him.
- Tales of Symphonia: The Chosen of Regeneration is specifically bred to serve as a perfect vessel for the Big Bad's dead/comatose sister, among other functions related to the setting's Corrupt Church.
- Fire Emblem
- In Fire Emblem: Genealogy of the Holy War, the Loptyrians are worshippers of Loptyr, an evil dragon, who needs a human vessel to return. After a long period of being Reformed, but Rejected, the Lotpyrians under Manfroy decide to produce another vessel via interbreeding the descendants of the original vessel.
- In Fire Emblem Awakening, the Grimleal are worshippers of the Fell Dragon Grima trying to create him a vessel, much like Loptyr and the Loptyrians. Unlike the Loptyrians, the Grimleal have been attempting to create a child to serve as a vessel for the dragon's spirit for a straight one thousand years. Grimleal leadership is done by failed vessels of Grima. It turns out that the player's tactician character is the end result.
- Xenoblade has the High Entia royal line, which has a planned interbreeding program with humans in order to rid themselves of the genes that cause them to mutate into Telethia, macroscopic digestive organisms for Xanza's true body, the Bionis.
- Baldur's Gate The god of murder Bhaal learned of his impending death and started a few of these along with 'independent efforts'. The rescue of one of them sets off the plot. (The children were to be sacrificed at birth.)
- In Last Res0rt the Celeste pseudo-religiously breed with as many species as possible. Arikos of Nile took it a step further by conning a couple hundred Talmi women into believing he could turn them into humans if they bore him Celeste children. He killed the ones who grew too old to bear children and the kids who "failed", until a bunch of his kids had enough and turned him in.