There are several reports on cloning genes in plant using QTL or GWAS methods.

In the following paper by Prof. Han, NGS was used to genotype the RILs(recombinant inbred lines).

Then QTL method was applied  to map the key loci. As the sequences only cover a part of genome,

some statistcs was involved. The pipelines were provided with the paper.

High-throughput genotyping by whole-genome resequencing
Xuehui Huang1,6, Qi Feng1,2,6, Qian Qian3,6, Qiang Zhao1,2,6, Lu Wang1,6, Ahong Wang1,6, Jianping Guan1, Danlin Fan1, Qijun Weng1, Tao Huang1, Guojun Dong3, Tao Sang1,4 and Bin Han1,5,7

http://171.66.122.45/content/19/6/1068.abstract