Transcriptomic Difference between Two Eutrema salsugineum Accessions and Quantitative Trait Loci Identified Using Bulk Segregant Analysis from F2 Population

Eutrema salsugineum (formerly Thellungiella halophila), a close relative of Arabidopsis, has become an important model extremophile species primarily to facilitate the identification of novel stress tolerance determinant alleles. Two Eutrema accessions Shandong (SH) and Yukon (YK) with contrasting traits including water use efficiency (WUE) were used for transcriptome profiling. However, only 31 genes were identified differentially expressed in SH and YK, and no known ones that would obviously contribute to the differences between the two accessions in WUE. On the other hand, more than 14,000 single nucleotide polymorphisms (SNPs) were also identified. Among those, about 3,000 high quality SNPs were used in a YK x SH F₂ bulked segregant analysis in order to identify genetic determinants of WUE and biomass accumulation. Quantitative trait loci (QTL) correlated to WUE and biomass accumulation were identified. To further narrow down the identified QTL regions, a recombinant inbred lines population (F₈) will be phenotyped for traits of interests, e.g. WUE and genotyped using a genotyping-by-sequencing method.