Genomic and transcriptomic analysis reveal molecular basis of salinity tolerance in a novel strong salt-tolerant rice landrace Changmaogu
Bing-Rui
Sun1†, Chong-Yun Fu1†, Zhi-Lan Fan1,2, Yu
Chen1,2, Wen-Feng Chen1,2, Jing Zhang1,2,
Li-Qun Jiang1,2, Shuwei Lv1,2, Da-Jian Pan1,2*and Chen Li1,2*
Rice
Abstract
Background:Salt
stress is an important factor that limits rice yield. We identified a novel,
strongly salt tolerant rice landrace called Changmaogu (CMG) collected from a
coastal beach of Zhanjiang, Guangdong Province, China. The salt tolerance of
CMG was much better than that of the international recognized salt tolerant
rice cultivar Pokkali in the germination and seedling stages.
Results:To
understand the molecular basis of salt tolerance in CMG, we performed BSA-seq
for two extreme bulks derived from the cross between CMG and a cultivar
sensitive to salt, Zhefu802. Transcriptomic sequencing was conducted for CMG at
the germination and young seedling stages. Six candidate regions for salt
tolerance weremapped
on Chromosome 1 by BSA-seq using the extreme populations. Based on the
polymorphisms identified between both parents, we detected 32 genes containing
nonsynonymous coding single nucleotide polymorphisms (SNPs) and frameshift
mutations in the open reading frame (ORF) regions. With transcriptomic
sequencing, we detected a large number of differentially expressed genes (DEGs)
at the germination and seedling stages under salt stress. KEGG analysis
indicated two of 69 DEGs shared at the germination and seedling stages were
significantly enriched in the pathway of carotenoid biosynthesis. Of the 169
overlapping DEGs among three sample points atthe
seedling stage, 13 and six DEGs were clustered into the pathways of ABA signal
transduction and carotenoid biosynthesis, respectively. Of the 32 genes
carrying sequence variation, only OsPP2C8 (Os01g0656200) was differentially
expressed in the young seedling stage under salt stress and also showed
sequence polymorphism inthe
ORFs between CMG and Zhefu802.
Conclusion:OsPP2C8was identified as
the target candidate gene for salinity tolerance in the seedling stage. This provides
an important genetic resource for the breeding of novel salt tolerant rice
cultivars.
Keywords:Rice
landrace, Salt tolerance, BSA-seq, Transcriptome sequencing
