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Identification of novel allelic combination for salt tolerance through targeted association mapping in rice

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Abstract

The complex and multigenic nature of salt tolerance in rice has made it hard to use Indian rice landraces to breed for salt tolerance and understand genetic diversity. In this study, genetic diversity and targeted association mapping were performed on 124 rice germplasm accessions with 30 (22 unlinked and 8 saltol-linked) SSR markers with varying responses to salt stress. In the 124 accessions, 81 alleles were observed in 22 SSR markers, with an average of 3.68 alleles per locus and a PIC value of 0.4447. Similarly, 35 alleles were found in eight saltol-linked SSR markers, with a PIC value of 0.48 and an average of 4.38 alleles per locus. Using model and distance-based techniques, population structure analysis revealed that the germplasm lines were divided into two separate subgroups (SG1 and SG2), with 46 and 44 accessions in SG1 and SG2, respectively, and 34 accessions as admixture (AD). Based on 22 SSR marker loci, the Analysis of Molecular Variation (AMOVA) found that 93% of genetic variation was due to differences between individuals and only 4% was due to differences between populations. We have observed wide variation for all the physiological traits related to salt tolerance. Targeted association mapping indicated that 12 SSR markers are associated with salt tolerance traits. Six of these markers are located in the Saltol region of chromosome 1, whereas the remaining markers are located on chromosomes 2, 4, 6, 7, 10, and 11. Three of the eight saltol markers, RM 3412, SalT 1, and SKC 1, were associated with six important physiological traits of seedling stage salt tolerance (SSST). Numerous accessions harbored novel alleles in the Saltol region of chromosome 1 for multiple marker loci. Four accessions, including Azgo, CSR-1, CSR-2, and Kuzhivedichan (Vetaikaraniruppu), included unique alleles for SKC1, AP 3206, RM 3412, RM 8094, and SalT 1 in three marker combinations. These germplasm lines might be used in the development of salt-tolerant rice variety/ies through marker-assisted selection (MAS).

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The original contributions (Data and materials) presented in this study are included in the article/Supplementary Materials. Further inquiries can be directed to the corresponding author id required.

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Author notes

  1. Bharathi Raja Ramadoss

    Present address: Plenty Unlimited Inc., 82070, Laramie, Wyoming, United States of America

Authors and Affiliations

  1. Department of Plant Breeding and Genetics, Pandit Jawaharlal Nehru College of Agriculture and Research Institute, Karaikal, Puducherry, 609 603, India

    Vinodha Changappa, Anandhan Tamilselvan, Karthick Jothiganapathy, Paramasivam Krishnaswamy & Thirumeni Saminadane

  2. Department of Soil Science and Agricultural Chemistry, Pandit Jawaharlal Nehru College of Agriculture and Research Institute, Karaikal, Puducherry, 609603, India

    Aruna Lakshminarayanan

  3. Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641 003, India

    Bharathi Raja Ramadoss

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Contributions

VC and KJ performed experiments and written original draft, ST, BRR and AT involved in conceptualization, methodology, validation, review and editing, KP and AB helped in execution of this study and provided facility for the execution of lab and analytical experiments. All authors have read and agreed to the published version of the manuscript.

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Correspondence to Bharathi Raja Ramadoss or Thirumeni Saminadane.

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Changappa, V., Tamilselvan, A., Ramadoss, B.R. et al. Identification of novel allelic combination for salt tolerance through targeted association mapping in rice. Genet Resour Crop Evol 71, 129–143 (2024). https://doi.org/10.1007/s10722-023-01611-x

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