Authors :
Bhagyarabi Pani; G.M. Lal; Parameswaran C; Selvaraj Sabarinathan; Tejasmita Prusty; Asit Prasad Dash
Volume/Issue :
Volume 9 - 2024, Issue 10 - October
Google Scholar :
https://tinyurl.com/bdezspmw
Scribd :
https://tinyurl.com/yubt8pf4
DOI :
https://doi.org/10.38124/ijisrt/IJISRT24OCT1263
Note : A published paper may take 4-5 working days from the publication date to appear in PlumX Metrics, Semantic Scholar, and ResearchGate.
Abstract :
Early seedling vigour (ESV) is a complex trait
in rice. Detection of QTLs/genes controlling these traits
can help us in enhancing the yield potential in rice
varieties. Association mapping is a technique based on the
principle of linkage disequilibrium that is used to find
genes or quantitative trait loci (QTL) underlying the
complex traits. In this study of haplotype breeding 281
rice genotypes were taken. ANOVA analysis showed P-
value for traits and genotypes was found significant.
Similarly, P-value for interaction between the traits and
genotypes was also found to be highly significant
(1.8663*10-208). Further, mean germination data
positively correlated with mean shoot length, mean leaf
number, mean culm diameter, mean shoot dry weight,
and mean shoot area of 21st day among the 281 genotypes.
Among the 281 number of genotypes, 111 genotypes are
found to be in PCA1 and 170 genotypes are found to be in
PCA2 based on the phenotypic analysis. PCA1 component
constituted 29.93% and PCA2 constituted the 13.68% of
total variation in the analysis. Besides, whole genome
phylogenetic analysis showed three major groups of
which Group 1 consists of 215 genotypes, group 2 consists
of 38 genotypes and group 3 consists of 28 genotypes
respectively. Especially, both the subgroups II and III
comprised of the unique genotypes from the indica and
aus subpopulations of rice. In this analysis, 16 significant
associations (LOD Score >7) for different traits were
identified using the three different models (MLM,
farmCPU, and blink) for GWAS studies Especially, one
major QTL was identified for the mean coleoptiles’
emergence for 10 DAS on 11th chromosome (18983591)
which explained 49% of the phenotypic variance.
Additionally, another major QTL contributing to the
shoot length variation of 29.75% was identified in the
Chr02 (32954393) for shoot length trait on 28 DAS. A
candidate gene namely Os02g0778400 UMP/CMP kinase
A/adenylate kinase (LOC_Os02g53790) was located in the
significant SNP region of the GWAS analysis. Further
characterization of this gene would assist in elucidation of
the mechanism regulating the early seedling length in rice
under direct seeded rice.
Keywords :
ESV, GWAS, PCA, ANOVA, QTLs.
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Early seedling vigour (ESV) is a complex trait
in rice. Detection of QTLs/genes controlling these traits
can help us in enhancing the yield potential in rice
varieties. Association mapping is a technique based on the
principle of linkage disequilibrium that is used to find
genes or quantitative trait loci (QTL) underlying the
complex traits. In this study of haplotype breeding 281
rice genotypes were taken. ANOVA analysis showed P-
value for traits and genotypes was found significant.
Similarly, P-value for interaction between the traits and
genotypes was also found to be highly significant
(1.8663*10-208). Further, mean germination data
positively correlated with mean shoot length, mean leaf
number, mean culm diameter, mean shoot dry weight,
and mean shoot area of 21st day among the 281 genotypes.
Among the 281 number of genotypes, 111 genotypes are
found to be in PCA1 and 170 genotypes are found to be in
PCA2 based on the phenotypic analysis. PCA1 component
constituted 29.93% and PCA2 constituted the 13.68% of
total variation in the analysis. Besides, whole genome
phylogenetic analysis showed three major groups of
which Group 1 consists of 215 genotypes, group 2 consists
of 38 genotypes and group 3 consists of 28 genotypes
respectively. Especially, both the subgroups II and III
comprised of the unique genotypes from the indica and
aus subpopulations of rice. In this analysis, 16 significant
associations (LOD Score >7) for different traits were
identified using the three different models (MLM,
farmCPU, and blink) for GWAS studies Especially, one
major QTL was identified for the mean coleoptiles’
emergence for 10 DAS on 11th chromosome (18983591)
which explained 49% of the phenotypic variance.
Additionally, another major QTL contributing to the
shoot length variation of 29.75% was identified in the
Chr02 (32954393) for shoot length trait on 28 DAS. A
candidate gene namely Os02g0778400 UMP/CMP kinase
A/adenylate kinase (LOC_Os02g53790) was located in the
significant SNP region of the GWAS analysis. Further
characterization of this gene would assist in elucidation of
the mechanism regulating the early seedling length in rice
under direct seeded rice.
Keywords :
ESV, GWAS, PCA, ANOVA, QTLs.