The big question behind this project is: What shapes genetic variation for phenotype within populations, in particular, this population of Capsella grandiflora (2/10)
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We'd previously found loci associated with the expression of nearby genes and showed that negative selection keeps these loci rare, especially if they have large effects (https://doi.org/10.1073/pnas.1503027112 …) (3/10)
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We wanted to look for loci that affected the expression of lots of genes and presumably have larger phenotypic effects. Were the same selective pressures acting on these large-effect trans eQTL as on cis-eQTL? (4/10)
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But, testing all SNPs against all genes would require doing 39 billion tests, which seemed like a bad idea (although we ended up doing it anway!). (5/10)
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So, we used coexpression networks to clump genes into modules and then looked for loci associated with expression of modules of genes. And we found stuff! (6/10)
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Like, a locus that affects expression of a nearby gene in cis, and is also associated with a 3-day difference in flowering time. (7/10)
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However, despite finding these relatively common, large effect trans-eQTLs segregating in this population, we didn't see any evidence of balancing selection in the sequence surrounding these loci. (8/10)
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We're left with a conundrum: what forces actually shape large-effect trans-eQTLs? Undetected balancing selection? Migration? Drift? How will we tell? I don't know but I'm excited to tackle these kinds of questions in my own lab. (9/10)
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Also, on a personal note, I started this project as a first-year phd student (9 years ago!), so I am both relieved to be wrapping it up and a bit sad because I've had such a great time working with my co-authors. (10/10)
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I forgot! It would be great to hear people's thoughts and feedback!!! (11/10, oops)
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