Superior haplotypes of key drought-responsive genes reveal opportunities for the development of climate-resilient rice varieties

Abstract

Haplotype-based breeding is an emerging and innovative concept that enables the development of designer crop varieties by exploiting and exploring superior alleles/haplotypes among target genes to create new traits in breeding programs. In this regard, whole-genome re-sequencing of 399 genotypes (landraces and breeding lines) from the 3000 rice genomes panel (3K-RG) is mined to identify the superior haplotypes for 95 drought-responsive candidate genes. Candidate gene-based association analysis reveals 69 marker-trait associations (MTAs) in 16 genes for single plant yield (SPY) under drought stress. Haplo-pheno analysis of these 16 genes identifies superior haplotypes for seven genes associated with the higher SPY under drought stress. Our study reveals that the performance of lines possessing superior haplotypes is significantly higher (p ≤ 0.05) as measured by single plant yield (SPY), for the OsGSK1-H4, OsDSR2-H3, OsDIL1-H22, OsDREB1C-H3, ASR3-H88, DSM3-H4 and ZFP182-H4 genes as compared to lines without the superior haplotypes. The validation results indicate that a superior haplotype for the DREB transcription factor (OsDREB1C) is present in all the drought-tolerant rice varieties, while it was notably absent in all susceptible varieties. These lines carrying the superior haplotypes can be used as potential donors in haplotype-based breeding to develop high-yielding drought-tolerant rice varieties.

Fig. 1. Haplotype diversity in the drought-responsive genes.

The frequency and relative distribution of drought-responsive genes carrying >2 haplotypes in subset panel of 3K rice genomes are represented in the Circos diagram. The outermost circle represents 12 rice chromosomes (Chr 01–Chr 12) in different colors, and the inner two circles represent the number of haplotypes and their frequency distribution. The histogram displays the number of haplotypes obtained for each gene. The bubbles represent the frequencies of each haplotype particular to the gene. The range of haplotype frequencies is represented by different colors as indicated.

Fig. 2. Haplotype analysis of the OsDIL1 gene associated with the trait across the subset panel.

A Haplotypic variation in the OsDIL1 gene associated with single plant yield trait (SPY) in the subset panel. B Phenotypic evaluation of the subset panel (n = 399) in field conditions under non-stress and drought stress conditions. C Violin plot showing variation in SPY trait in rice accessions significant at p-value < 0.05. Different alphabets denote significant differences between haplotypes. The median is depicted by the horizontal line in the box. Note: Haplotype variation reflects only those haplotypes that are used in haplo-pheno analyses. The violin plot uses an orange color to depict the distribution of the superior haplotype, while the green color is employed to represent the distribution of the remaining haplotypes associated with the OsDIL1 gene.

Fig. 3. Tailor-made rice with superior haplotypes for developing high-yielding drought-tolerant varieties.

A Representative rice plant carrying inferior haplotype combination (OsDREB1C-H1, ASR3-H89, OsDIL1-H1, DSM3-H2, and ZFP182-H20). B Superior haplotype combination (OsDREB1C-H3, ASR3-H88, OsDIL1-H22, DSM3-H4, and ZFP182-H4) for SPY trait under reproductive stage drought stress. New breeding lines can be developed by introgressing superior haplotype combinations through haplotype-based breeding. SPY single plant yield.

Fig. 4. Validation of the superior haplotypes in drought-tolerant rice varieties for the OsDREB1C gene.

A Haplotypic variation of OsDREB1C gene in 3K-subset. B Subpopulation- wise distribution of haplotypes in the subset and violin plot showing variation in SPY trait in rice accessions significant at p-value < 0.05. The violin plot uses an orange color to depict the distribution of the superior haplotype, while the green color is employed to represent the distribution of the remaining haplotypes associated with the OsDREB1C gene. C Gene structure and haplotype sequence variation of the OsDREB1C gene. Four drought-susceptible (DS) and seven drought-tolerant (DT) varieties of rice were examined for haplotypic variation between the superior/favorable (H3) and the unfavorable (H1) haplotypes. DT drought tolerant lines, DS drought susceptible lines. Figure created using Biorender (https://biorender.com/ accessed on 16 August 2023).