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. 2022 May 10:13:876522.
doi: 10.3389/fgene.2022.876522. eCollection 2022.

Genome-Wide Association Mapping Reveals Novel Putative Gene Candidates Governing Reproductive Stage Heat Stress Tolerance in Rice

K T Ravikiran  1 , S Gopala Krishnan  1 , K P Abhijith  1 , H Bollinedi  1 , M Nagarajan  2 , K K Vinod  1 , P K Bhowmick  1 , Madan Pal  3 , R K Ellur  1 , A K Singh  1
Affiliations

Genome-Wide Association Mapping Reveals Novel Putative Gene Candidates Governing Reproductive Stage Heat Stress Tolerance in Rice

K T Ravikiran et al. Front Genet. .

Abstract

Temperature rise predicted for the future will severely affect rice productivity because the crop is highly sensitive to heat stress at the reproductive stage. Breeding tolerant varieties is an economically viable option to combat heat stress, for which the knowledge of target genomic regions associated with the reproductive stage heat stress tolerance (RSHT) is essential. A set of 192 rice genotypes of diverse origins were evaluated under natural field conditions through staggered sowings for RSHT using two surrogate traits, spikelet fertility and grain yield, which showed significant reduction under heat stress. These genotypes were genotyped using a 50 k SNP array, and the association analysis identified 10 quantitative trait nucleotides (QTNs) for grain yield, of which one QTN (qHTGY8.1) was consistent across the different models used. Only two out of 10 MTAs coincided with the previously reported QTLs, making the remaing eight novel. A total of 22 QTNs were observed for spikelet fertility, among which qHTSF5.1 was consistently found across three models. Of the QTNs identified, seven coincided with previous reports, while the remaining QTNs were new. The genes near the QTNs were found associated with the protein-protein interaction, protein ubiquitination, stress signal transduction, and so forth, qualifying them to be putative for RSHT. An in silico expression analysis revealed the predominant expression of genes identified for spikelet fertility in reproductive organs. Further validation of the biological relevance of QTNs in conferring heat stress tolerance will enable their utilization in improving the reproductive stage heat stress tolerance in rice.

Keywords: GWAS; marker-trait association; quantitative trait nucleotides; reproductive stage heat stress tolerance; rice.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Boxplots depicting the distribution of (A) grain yield plant−1 (g) and (B) spikelet fertility (%) under control and heat stress conditions.
FIGURE 2
FIGURE 2
Density of SNP across the genome. The highest coverage can be observed on chromosomes 1 and 6, while the lowest is on chromosome 12.
FIGURE 3
FIGURE 3
(A) Scree plot depicting the proportion (%) of total variance captured by various principal components. (B) PCA 3D plot illustrating the distribution of genotypes across three principal components. (C) Pair-wise kinship heat map between the genotypes. The figure in the inset describes the color code of the heat map and the frequency curve of kinship values among the genotypes.
FIGURE 4
FIGURE 4
Circular Manhattan plots depicting significant MTAs using MLM (A), FarmCPU (B), and BLINK (C) for various traits. From outside to inside: grain yield per plant (GYPP) under stress, spikelet fertility (SF) under stress, STI calculated for GYPP, and STI calculated for SF.
FIGURE 5
FIGURE 5
Physical positions (Mb) of various MTAs identified across the rice genome through various models employed in GAPIT.
FIGURE 6
FIGURE 6
MTAs identified through MLM, FarmCPU, and BLINK models for (A) GYPP and (B) SF. Novel MTAs are highlighted in red.
FIGURE 7
FIGURE 7
Comparison of allelic effects of major QTNs identified in the present study for grain yield per plant under reproductive stage heat stress.
FIGURE 8
FIGURE 8
Comparison of allelic effects of major QTNs identified in the present study for spikelet fertility under reproductive stage heat stress.
See this image and copyright information in PMC

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