[ChrisK]

When doing these kinds of studies selection of the population is important, you can't have too much minor allele frequency or you have no statistical power to identify association. I found the paper to be quite interesting for what it was and for what their stated objective was.

I found this interesting:

However, the genome-wide genetic basis underlying the divergence between tomatoes for fresh consumption and processing tomatoes was not previously studied.
To search for SNPs underlying this divergence, we computed the population differentiation statistic (FST) of each SNP site for 22 modern processing accessions and the remaining 144 BIG accessions. We observed a non-random distribution of highly divergent sites (the top 1% had FST ≥ 0.4464; the genome average was 0.07). Intriguingly, 90.53% (63,009 of 69,603) of these sites resided on chromosome 5 (Fig. 3a),
spanning the majority of the chromosome (from 3.5 to 62.8 Mb).
We note that a previous study identified three SSC QTLs (ssc5.1, ssc5.2 and ssc5.3) located on the short arm, in the centromeric region and on the long arm of chromosome 5, respectively29. A major fruit firmness QTL, fir5.1, also resides in the centromeric region of chromosome 5 (ref. 30). In addition, the chromosome has a large centromere with a length of ~50 Mb, extending from 10 to 60 Mb on the assembled chromosome14. Therefore, selection of the QTLs for higher SSC and better fruit firmness likely resulted in the hitchhiking of almost the entire chromosome 5, representing a genomic signature of modern processing tomatoes.