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In Dune Messiah, Chapter 11, the Reverend Mother Gaius Helen Mohiam is negotiating with Paul. Near the end of the Chapter she looks at Alia and thinks:

And again she looked at the sister. The optimum cross for this female Atreides had been lost, killed by Paul.

Who would this person have been?

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The Bene Gesserit plan was to breed the Kwisatz Haderach and at the time of Dune, they were 2 generations away (until the events of dune).

Lady Jessica was meant to bear a daughter with Leto Atreides but as we well know a son was born. While Paul was a Kwisatz Haderach, he was not the planned Kwisatz Haderach as per the Bene Gesserit breeding program.

When Lady Jessica became pregnant again, with a female, the Bene Gesserit plan could still be salvaged via the breeding of Alia and Feyd-Rautha Harkonnen.

Paul destroyed that when he killed Feyd-Rautha Harkonnen

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    Why would it have been Feyd-Rautha? Was this their original plan for the breeding programme if Jessica would have gotten a daugther? In my edition of "Dune" she thinks on page 522 when Feyd fights against Paul "Two end products of this long and costly programme faced each other in a fight to the death that might easily claim both of them." This would support your theory that Feyd was a part of the breeding scheme.
    – TheFibonacciEffect
    Nov 21, 2021 at 12:55
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    the plan was the Jessica-Leto daughter to breed with Feyd. Why Feyd particularly? who knows, the breeding program spanned 10,000 years. One thing to consider is Jessica's father is Baron Harkonnen so maybe there was something in that cross-breed
    – Naib
    Nov 21, 2021 at 13:20
  • Isn't it also a problem that Alia is an "abomination"? Spice inflicted while in the womb? There could be no salvage from her. With Feyd's and Leto's death, the program was lost. But I think I recall hints at other unnamed programs? Maybe just less successful, or further behind?
    – frеdsbend
    Nov 21, 2021 at 20:54
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    Maybe the BG hoped that with early an intense training their KH would no succumb and also turn into an abomination. Being able to test for has been part of the BG way, hence the test for humanity so at some point they must have run into issues with sisters not being able to control themselves. A small hope is still a hope vs no hope at all
    – Naib
    Nov 21, 2021 at 22:12
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    @Arthur Fenring was an ‘almost Kwisatz Haderach’ but he was incaple of reproduction. He was a dead end of the program..
    – suchiuomizu
    Nov 22, 2021 at 16:57
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She's referring to Feyd-Rautha Harkonnen.

Near the beginning of the first book, Mohiam tells Jessica: "An Atreides daughter could've been wed to a Harkonnen heir and sealed the breach". In your quote she's reflecting that the match could still have been made, if Paul hadn't killed Feyd.

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