GENE EXPRESSION AND SEQUENCE ANALYSIS OF KNOWN YIELD GENES IN HIGH YIELDING VARIETIES OF RICE (Oryza sativa L.)
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Date
2017
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Acharya N.G. Ranga Agricultural University
Abstract
Rice (Oryza sative. L) is one of the major food crops in the world. Half of the
world's population depends on rice as their staple food. Rice yield is governed by
mainly three major traits i.e., number of tillers per plant, grain number per panicle,
grain size and are directly associated with rice grain productivity. Rice yield is a
complexly inherited trait governed by many genes/QTLs. As of now more than 34
genes have been molecularly cloned and characterized, however, using donors
from China and Japan only. However, their gene expression and sequence
variation needs to be validated before directly using them in the rice breeding
programmes. In the present investigation, an attempt has been made to validate the
gene expression and sequence variation of the important cloned genes governing
yield traits in known India donor varieties.
In all, 21indica rice genotypes have been selected including 15 high
yielding and 6 low yielding. The phenotypic data of the important yield and its
component traits such as, plant height, culm height, number of tillers per plant,
panicle length, number of grains per panicle, days to 50% flowering, filled grains,
chaffy grains, spikelet fertility, grain weight, grain length, grain width, biological
yield, harvest index, and economic yield have been recorded. The analysis of
variance (ANOVA) for the 21 rice genotypes for all the agronomic traits revealed
highly significant differences among the entries for all the characters except for
panicle length, grain length, and grain width.
The expression analysis was carried out with gene specific primers
designed from key yield genes from the flag leaf and young panicles. The semi
qRT PCR gene expression analysis in the selected rice genotypes revealed
differential expression of all yield genes. The Gn1a gene expression analysis
revealed that the known Indian high grain number donor varieties with low or nil
gene expression such as, NLR33892, Ranjit, BPT2601, BPT5204 and Rasi can be
used as donors for. The gene expression analysis of OsSPL14 revealed that the
high grain number varieties with high gene expression can be used as donor
varieties viz., MTU1064, Dee-geo-woo-gen, Rasi, BPT5204, and MTU1010 from
Indian rice germplasm. The DEP1 gene expression revealed that the high
expression varieties with high grain number could be value for marker assisted
introgression of this trait into highly adaptable low grain number varieties. The
GIF1 gene expression analysis revealed that the high gene expression varieties with
high grain weight such as, BPT 2678 and Basmati370 are the potential donors for
grain weight/grain filling trait. The GW8 gene expression analysis in all 21 rice
genotypes revealed that the high grain weight varieties with high GW8 expression
such as, MTU3626, IR-8, Dee-geo-woo-gen, MTU1010, MTU1001, and
INRC10192 can be used as donors from Indian rice germplasm. The Ghd7
expression analysis revealed that the high grain number, tall plant, and late
flowering varieties with high Ghd7 expression such as, NLR33892, BPT 2678,
Ranjit are can be used a donors from Indian rice germplasm.
Besides gene expression analysis, the DNA sequence variation of most
differentially expressed yield genes such as Ghd7, DEP1 and Gn1a also analyzed
in all high yielding and low yielding varieties. The whole genome DNA sequence
of Ghd7 gene (3918 bp) was resequenced in all 21 rice genotypes. In all, 104
SNPs and 141 indels were detected. It was found that certain nucleotide variations
are unique to high grain number varieties such as, MTU1121, MTU1010, and
Dee-Geo-Woo-Gen. It was found that certain nucleotide variations are unique to
tall (>95cm) varieties such as, INRC10192, Tetep, and MTU1001. It was found
certain nucleotide variations are unique to late flowering (>105 days) varieties
such as, MTU7029 (G/A) at 1426, MTU1001 (T/C) at 1425 bp positions of the
gene. However, there is no nucleotide variations were found for their specific traits
in all the varieties. The whole genome DNA sequence of DEP1 gene (4363 bp)
was resequenced in all high yielding and low yielding rice genotypes. In all, 99
SNPs and 338 indels were detected in the 5732 base pair alignment and of these,
three SNPs (IR-8) and 61 indels were detected in the promoter region of the gene.
However, there are no nucleotide variations found specific to either low or high
grain number varieties. The whole genomic DNA sequence of Gn1a gene (6476
base pair) was resequenced in all genotypes. In total, 97 SNPs and 121 indels were
detected in the 4837 base pair alignment. Of these, one SNP (MTU1064) and 28
indels were detected in the promoter region. It was found certain nucleotide
variations are unique to high grain number varieties such as, NLR33892,
MTU1064, MTU1010 (G/G) and Dee-geo-woo-gen (A/T) having SNPs at 1426
base pair position of the gene. However, there are no nucleotide variations in
specific to either low or high grain number varieties were observed.
In short, an attempt was made to identify the Indian donor varieties
comparison of important yield genes based on consistent gene expression and
sequence analysis with reported donors. The shortlisted donors for the yield traits can
be right away used in the rice breeding programmes.
Description
D5524
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