TITLE:
Genome-Wide SNPs Identification and Determination of Proteins Associated with Stress Response in Sorghum (Sorghum bicolor L. Monech) Accessions
AUTHORS:
Hind Emad Fadoul, Marmar A. El Siddig, Abdel Wahab H. Abdalla, Adil A. El Hussein
KEYWORDS:
SNPs, Sorghum, Stress Response, GBS
JOURNAL NAME:
American Journal of Plant Sciences,
Vol.8 No.7,
June
23,
2017
ABSTRACT: Current
efforts in sorghum breeding programs are exploiting genotyping-by-sequencing
(GBS) data to provide full-genome scans for desired traits. The aim of this
study was to utilize GBS approach for the identification of genomic regions
associated with stress response in sorghum (Sorghum
bicolor L. Monech)
accessions. DNA samples of twenty sorghum accessions, having different response
to drought, were used to prepare GBS libraries for sequencing. SNPs were called
using the TASSELGBS pipeline and the tags that present at least 10 times in the
dataset were considered and aligned to the reference genome of Sorghum bicolor. The
identified SNPs were all compared with the published sorghum transcript related
to stress response gene activity. Overall; 94.40% tags were aligned and 69,736 putative SNPs positions
were identified. Blast search revealed homology to annotated heat and
drought–tolerance associated genes which code for ATPases, Peroxidase,
Hydrophobic protein LTI6A, Aquaporin SIP2-1, Aconitate hydratase and
phosphatidylinositol-4-phosphate-5-kinase. The phylogeny of the 20 accessions
was constructed using the generated SNPs data. Phylogenetic analysis data
showed that the phenotypically tolerant line (El9)makes a separate cluster and the same for
the accessions HSD8653 and HSD5612 near to the cluster that includes most accessions with known post-flowering drought
tolerance (HSD7410, HDS10033, HSD8552, GESHEISH and HSD8849).
Post-flowering drought sensitive accessions (Tabat, Wadahmed, HSD6468 and
HSD6478) formed a separate cluster while the sensitive accession HSD9959 and
the tolerant accessions HSD8511 and HSD9566 were distributed between the two
clusters. Thus, cluster analysis confirmed the variation among accessions in
post-flowering drought tolerance. With further validation, these markers may be
used for marker assisted selection for breeding new sorghum genotypes with
stress adaptation.