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Identification of genomic regions governing moisture and heat stress tolerance employing association mapping in rice (Oryza sativa L.)

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Abstract

Background

Rice crop is damaged extremely by abiotic stress world-wide. The best approach to enhance drought tolerance in rice varieties is to identify and introgress yield QTLs with major effects. The Association mapping approach helps in the identification of genomic regions governing physiological, yield and yield attributes under moisture and heat stress conditions in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome.

Methods and Results

The association mapping panel of 110 rice germplasm lines exhibited significant variation for all the traits in both irrigated and moisture stress conditions. The extent of yield reduction ranged to 83% during rabi, 2018–19, 53% in rabi, 2019–20 and 68% in pooled analysis. The genotypes Badami, Badshabhog, Pankaj, Varalu, Vasundhara, Vivekdhan, Krishna and Minghui63 exhibited drought tolerance with least yield penalty under moisture stress conditions. The genotypes Konark, MTU3626, NLR33671, PR118 and Triguna exhibited minimal reduction in heat stress tolerance traits. Association mapping of germplasm using 37808 SNP markers detected a total of 10 major MTA (Marker-trait association) clusters distributed on chromosomes 1, 3, 4 and 11 through mixed linear model (MLM) governing multiple traits from individual data analysis which are consistent across the years and situations. The pooled data generated a total of five MTA clusters located on chromosome 6. In addition, several novel unique MTAs were also identified. Heat stress analysis generated a total of 23 MTAs distributed on chromosomes 1, 5, 6 and 11. Candidate gene analysis detected a total of 53 and 38 genes under individual and pooled data analysis for various yield and yield attributes under control and moisture stress conditions, respectively and a total of 11 candidate genes in heat stress Conditions.

Conclusion

The major and novel MTAs identified in the present investigation for various drought and heat tolerant traits can be utilized for breeding climate-resilient rice varieties. The candidate genes predicted for key MTAs are of great value to deploy into the rice breeding after functional characterization.

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Data availability

All the supporting data of the article has been provided in the supplementary files.

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Funding

Madhavilatha Kommana gratefully acknowledge to Bayer for providing fellowship.

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Authors and Affiliations

  1. Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India

    Madhavilatha Kommana, D. Mohan Reddy, K. Amarnath, M. Vinod Kumar Naik, D. M. Withanawasam, Reddyyamini Bommisetty, K. Maneesha, M. Bhargavi & Lakshminarayana R. Vemireddy

  2. Department of Molecular Biology and Biotechnology, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India

    Aparna Eragam & Lakshminarayana R. Vemireddy

  3. Regional Agricultural Research Station, ANGRAU, Tirupati, 517502, Andhra Pradesh, India

    B. V. Bhaskara Reddy & P. Sudhakar

  4. AgriGenome Labs Pvt Ltd, Hyderabad, 500 078, India

    Lalam Krishna, Sivarama P. Lekkala, Navajeet Chakravartty & V. B. Reddy Lachagari

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  1. Madhavilatha Kommana
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Contributions

LRV, DMR and MLK conceived the experiment and prepared the manuscript. MLK, LRV, DMR, BVBR and PS conducted the experiment. KA, MVKN, DMW, BRY, KM, MB, EA assisted in field work and LK, SL, NC, VBRL has carried out data analysis.

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Correspondence to Lakshminarayana R. Vemireddy.

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This is an observational study. The Research Ethics Committee of the University has confirmed that no ethical approval is required.

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Kommana, M., Reddy, D.M., Amarnath, K. et al. Identification of genomic regions governing moisture and heat stress tolerance employing association mapping in rice (Oryza sativa L.). Mol Biol Rep 50, 1499–1515 (2023). https://doi.org/10.1007/s11033-022-08153-y

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