Philip Cunningham hat tipped us earlier on the article at Quartz that raised the possibility that all genes affect every complex trait. He also writes to say, “The paper makes the genotype-phenotype mapping problem that much worse for neo-Darwinists. Here are few notes to that throw a little light on how bad the problem is:”
These news items from recent years give some sense of the issues, he says:
The next evolutionary synthesis: from Lamarck and Darwin to genomic variation and systems biology (Bard, 2011) Excerpt: If more than about three genes (nature unspecified) underpin a phenotype, the mathematics of population genetics, while qualitatively analyzable, requires too many unknown parameters to make quantitatively testable predictions . The inadequacy of this approach is demonstrated by illustrations of the molecular pathways that generates traits : the network underpinning something as simple as growth may have forty or fifty participating proteins whose production involves perhaps twice as many DNA sequences, if one includes enhancers, splice variants etc. Theoretical genetics simply cannot handle this level of complexity, let alone analyse the effects of mutation. (BioSignaling)
Not Junk After All—Conclusion (August 29, 2013) Excerpt: Many scientists have pointed out that the relationship between the genome and the organism — the genotype-phenotype mapping — cannot be reduced to a genetic program encoded in DNA sequences. Atlan and Koppel wrote in 1990 that advances in artificial intelligence showed that cellular operations are not controlled by a linear sequence of instructions in DNA but by a “distributed multilayer network” . According to Denton and his co-workers, protein folding appears to involve formal causes that transcend material mechanisms , and according to Sternberg this is even more evident at higher levels of the genotype-phenotype mapping 
Gene previously linked to obesity is unrelated (June 29, 2015)
Excerpt: … in the real world of careful analysis, scientists are just not finding the “genes” that the headline writers need. British geneticist Steve Jones points out that most human traits are influenced by so many genes that there is no likely systematic cause and effect:
“We know of more than 50 different genes associated with height … That has not percolated into the public mind, as the Google search for “scientists find the gene for” shows. The three letter word for — the gene FOR something — is the most dangerous word in gen etics.”And the craze is not harmless, he warns. …
What If (Almost) Every Gene Affects (Almost) Everything? (Atlantic, 2017)
Excerpt: If you told a modern geneticist that a complex trait—whether a physical characteristic like height or weight, or the risk of a disease like cancer or schizophrenia—was the work of just 15 genes, they’d probably laugh. It’s now thought that such traits are the work of thousands of genetic variants, working in concert. The vast majority of them have only tiny effects, but together, they can dramatically shape our bodies and our health. They’re weak individually, but powerful en masse.
Genetic fundamentalism is probably not due for a revival any time soon.
The Fairyland of Evolutionary Modeling (ENST, May 7, 2013)
Excerpt: Salazar-Ciudad and Marín-Riera have shown that not only are suboptimal dead ends an evolutionary possibility, but they are also exceedingly likely to occur in real, developmentally complex structures when fitness is determined by the exact form of the phenotype.
See also: Do all genes affect every complex trait? Veronique Greenwood: The roots of many traits, from how tall you are to your susceptibility to schizophrenia, are far more tangled. In fact, they may be so complex that almost the entire genome may be involved in some way
New book from Michael Behe on how today’s DNA findings “devolve” Darwin. Devolution… at last, something Darwinism really explains!