| Quantitative Trait Locus (QTL) mapping using traditional molecular markers often suffers from low resolution. The advancement and cost reduction of next generation sequencing (NGS) make it possible to obtain fine QTL maps using genome-wide genetic markers for the genetic study of important crops such as soybean.;In this work, a high-density-marker genetic map was constructed using re-sequencing data from a core panel of 96 soybean lines selected from a recombinant inbred (RI) population resulting from a cross between a wild (W05) and a cultivated (C08) soybean accession. More than 1.7M high quality SNP was collected from the re-sequencing data to generate bin markers. This resulting map was 2,991.73 cM in genetic length using Kosombi mapping function and comprised 2,757 bin markers. A total of 18 soybean agronomic traits including stress tolerance, plant morphology, yield, and seed quality and nodule formation rate were analyzed by QTLCartographer. Major QTLs were identified for 11 of the 18 agronomic traits along 11 chromosomes, ranging from 400Kbp to 1.2Mbp in physical length; and the other 7 agronomic traits did not give major QTLs using this population.;To further elucidate the genomic variation between the wild and cultivated soybean parents at the targeted QTL region, our laboratory also de novo sequenced the wild parent. A SSR marker-based genetic map generated from the same RI population was used to assist scaffold ordering and orientation. A set of BAC end clones were selected and sequenced to help with linking adjacent scaffolds into supper scaffolds. |
