ALLELE MINING AND ALLELIC DIVERSITY OF GENES GOVERNING GRAIN SIZE RELATED TRAITS IN RICE (Oryza sativa L.)
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Date
2017
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Acharya N.G. Ranga Agricultural University
Abstract
Mining elite alleles for grain size is one of the key aspects for the
improvement of cultivated rice to suit diverse global consumer preferences.
Thus with the goal of identification of novel and superior alleles from the
genes governing the grain size related traits by exploring the natural
variability present in the rice germplasm, the present study was conducted.
In all, 124 rice genotypes were evaluated for different grain traits such
as grain length (GL), grain width (GW), grain length to width ratio (GL/GW),
and 1000-grain weight (TGW). The germplasm of 124 rice genotypes
presented substantial variation for grain size traits. Significant correlations
were detected among the grain size traits. All the four traits exhibited normal
distribution in the germplasm indicating quantitative inheritance of these
traits.
In total, 32 molecular markers comprising of 8 grain size gene-specific
markers and 24 SSR markers covering all 12 chromosomes were used in this
study and all markers showed polymorphism and produced a total of 86
alleles among the 124 rice varieties. Number of alleles ranged from 2 to 4
with an average of 2.68 alleles per locus. The mean polymorphism
information content (PIC) value was 0.34, with values ranging from 0.70
(RM 252) to 0.03 (RM 502).
The screening of the 124 rice genotypes with eight gene-specific
markers viz., GS3 specific marker revealed two alleles, GS5INDEL1 revealed
two alleles, qSW5 specific marker revealed four alleles, qGRL7.1 specific
marker revealed two alleles, GS2 specific marker revealed two alleles, qsgw7
specific marker revealed two alleles, SLG7 specific marker revealed two
alleles and GLW7 specific marker revealed two alleles with substantial
variation in the germplasm.
For finding the allelic diversity a dendrogram consisting of 124 rice
genotypes was drawn using unweighted pair group method using arithmetic
averages (UPGMA) based on genotyping data using NTSY spc -2.02e
software. The dendrogram revealed that 124 genotypes could be made into
two groups, A and B. The group A exclusively includes the extra-long grain
length basmati genotypes. However, the group B could be again divided into
two groups i.e., B1 and B2. The group B1 includes mostly long grain
genotypes. The group B2 comprising of all classes of grain length and size
genotypes.
Based on the population structure Q matrix data the 124 accessions are
divided into four clusters/subpopulations, viz., from POP1 to POP4. POP1
subpopulation was grouped under extra-long grain type, POP2 was grouped
under long grain type, POP3 and POP4 includes all the four grain size classes.
Eight marker-trait associations were identified by screening 124
genotypes with grain size specific primers for GL, GW, L/B and TGW traits.
One GS3 gene-specific marker, GS3RGS1 was found to be associated with
GL, GW, L/B and TGW traits with their PVE as 15.2%, 16.9%, 10.3% and
7.8%, respectively. Earlier results by Fan et al., (2006), Lu et al., (2013) and
Xu et al., (2016) also reported that the GS3 is the major gene governing the
grain length and minor gene for grain width. Similarly, one SSR marker,
RM505 was showed association with GL, GW, L/B and TGW traits with their
PVE as 4.4%, 2.6%, 1.9% and 3.8%, respectively.
The present investigation reinforce the fact that grain size is a complex
trait regulated by many genes located on different chromosomes. However,
the gene specific markers, for GL, GW, TGW and L/B traits, such as
GS3RGS1 and RM505 have potential to be used as foreground markers in
marker-assisted breeding. Mining of complete gene sequences and other
genes governing grain size traits is warranted further investigation adding
some more germplasm. However, harmonious pyramiding of superior and
novel alleles from diverse germplasm facilitates the designing of rice varieties
suitable to diverse consumers in the world
Description
D5526
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