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So in Game Of Thrones Grand Maester Pycelle says to Eddard that Jon Arryn was rambling a lot before he died but he kept repeating "The seed is strong." Now I have seen all four seasons all the way through and I still don't know what it means. Lysa Arryn says that he was talking about Robin but she is pretty crazy so I'm just wondering if I have missed something or if it is explained in the books.

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In the the first series Eddard Stark discovers that

Cersei's children are not king Robert's, but Jamie's.

He does this by using the same book that Jon Arryn uses to research the genealogy of the Baratheons through the ages.

Eddard discovers that every Baratheon child for centuries has black hair. This is proven when he searches out all of King Robert's bastards and finds that they too have black hair.

The reason he finds this out is because he's following Jon Arryn's footsteps before he died, so we can conclude that Jon Arryn discovered the same secret and was murdered for it.

Genealogically, people tend to have certain traits because certain characteristics of a human are more likely to occur because of dominant genes.

However before scientific breakthroughs people would have assumed it's because of the person, rather than the genes themselves, why this occurred.

So when Jon Arryn was repeating "The seed is strong", he was trying to reveal the secret he had discovered before he died.

In the throes of death when he was poisoned he wouldn't have been able to give a full description about his findings, so he hoped that someone would understand from these words what he had found. Which Eddard eventually did.

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    +1 Just to be specific: we could conclude that Jon Arryn was murdered for his secret until in season 4 we found out what was the real reason of his death. – Chanandler Bong Mar 30 '15 at 11:24
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    I still don't get why he was saying "the seed is strong" how was that supposed to indicate that Joffrey wasn't a Baratheon? Is it because all Baratheons are strong? – Matthew Stevenson Jun 27 '15 at 8:09
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    In modern times, Jon Arryn might say "the trait is dominant" :) – IMil Jul 8 '15 at 6:44
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    @MatthewStevenson Although this is the most plausible explanation, there's an alternate one. Princess Rhaenyra married Laenor Velaryon. She however had an extra-marital affair with Ser Harwin Strong. Her first three "Velaryon" Children were rumored to be sired by Ser Harwin as they lacked the Valyrian silver hair, aquiline nose, Blue-ish eyes despite the supposed parents both being Valyrian. So "Seed is Strong" could be pointing to that, Strong a reference to the Strong family. Just like Laenor was cuckolded, so was Robert. – Aegon Jul 17 '17 at 15:14
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    @IMil - Or "the dominant alleles show a high degree of penetrance." :D – PoloHoleSet Aug 22 '17 at 14:49
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He's talking about the Baratheon seed. It's strong so all Baratheons have black hair, regardless of who they breed with. All of Robert's bastards have black hair. All Baratheons going back years have black hair. Since the seed is strong, Robert's "children" by Cersei couldn't possibly be his, because they have blonde hair.

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