Candidate Gene Prediction in Qtl Regions and Expression Analysis in Field Evaluated Near Isogenic Lines (NILs) Carrying Stay-Green and Water use Efficiency Qty Combination in Three Recurrent Background of Rabi Sorghum
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Date
2013
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UAS, Dharwad
Abstract
Stay-green (stg) and water use efficiency (wue) are important target traits considered
for improving drought tolerance in sorghum. The zygosity of introgressed quantitative trait
loci (QTLs) of stg and wue was determined in three recurrent backgrounds of NILs derived
from SPV86, SPV570 and M35-1. The NILs were field evaluated to assess impact stg and
wue QTLs. Significant positive correlations were observed between yield and stay-greeness
of different stages in SPV 570 background indicating NILs possessing stg trait have
significant yield advantage under post-anthesis drought stress condition. Three different ab
initio gene prediction algorithms viz., FGENESH, GENSCAN, GENMARK indicated
number of predicted genes anchored within targeted QTLs. Five genes (NSP, NAD, PHD,
MADS, MLO) for stay-green QTL qSTG1A (1.82 Mbp), ten (IAA, SORBIDRAFT, CYP450,
GAG/POL, PK, GENE X, UGTS, MTC, AGP16, VP25) for qSTG2 (2.54 Mbp) and one (SF
CC1) for qSTG3 (2.18 Mbp) were predicted on sorghum chromosome No. 3 and 1, qCID2
(2.33 Mb) on chromosome 10. Based on the predicted features and functions of candidate
genes, total of 24 predicted genes from different transcription factor families like MADS,
PHD, NAD, EIF-4A and SPLICING FACTOR, CYP450, IAA were tested for their
expressional analysis through quantitative real-time PCR in 15, 30 and 45DAF leaf tissue
samples from introgressed line with M35-1 genomic background. Among all tested samples
most of the candidate genes were found to be up regulation with fold change of 3 to 6 and 6
to 10 folds. Senescence related gene DIN1 was down regulated in M-35-1 introgressed lines.
Result indicated the potential use of stg and wue QTL pyramided lines for improving
sorghum performance under drought stress.