Predicting genomic breeding values by using methods that rely on the
estimation of the effects of haplotype blocks (i.e., a set of at least
two neighboring SNPs), that are presumably transmitted together across
generations, may result in more accurate evaluations compared to doing
genomic predictions by using methods that rely on the estimation of
the effects of single SNPs.
How about this? I turned the that are presumably transmitted together across generations part into an appositive, providing some clarity.
As for the part about "effects of single SNPs or the single SNPs effects, this depends on the message you are trying to convey. Are you talking about one specific single SNP? In that case you would use the single SNPs effects. If you are talking about ALL single SNPs, you would use the effects of single SNPs.
Note that this may be better edited by someone who understands the subject of the sentence.