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Association analysis, genetic diversity and haplotyping of rice plants under salt stress using SSR markers linked to SalTol and morpho-physiological characteristics

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Abstract

Knowledge of genetic diversity could aid in providing useful information in the selection of material for breeding such as hybridization programs and quantitative trait loci mapping. The present study was conducted to evaluate salinity tolerance of Iranian rice varieties. This research was carried out in three separate experiments (control, 6 and 12 dS m−1 NaCl) each based on completely randomized design with 44 rice varieties and three replications. Fourteen days after salt treatments, root and shoot fresh and dry weight, Na+ and K+ concentration, Na+/K+ ratio, root and shoot length, biomass gain, total fresh weight, root/shoot length ratio and shoot/root weight ratio were measured. The varieties were also genotyped for 12 closely linked microsatellite markers to SalTol. Haplotype and association analysis was conducted using these SSR markers for identification of loci related to salt tolerance. The tolerance scores under salinity stress showed that the varieties FL478, Hassani, Gharib, Shahpasand, Nemat, Domzard, Ghasroddashti, Ahlamitarom, Hassansaraee and Binam with more biomass, root and shoot lengths, and low Na+/K+ ratio were tolerant to salinity stress. Association analysis was indicated that there are some informative markers on chromosome 1 in the local and improved Iranian rice varieties genetic background including RM8094, RM1287, AP3206 and RM3412 explaining considerable percentage of the salt tolerance-related traits. These informative markers can be used in future breeding programs such as marker-assisted selection.

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Authors and Affiliations

  1. Department of Plant Biotechnology, Faculty of Agricultural Science, University of Guilan, P.O. Box: 41635-1314, Rasht, Iran

    Mojtaba Kordrostami & Hassan Hassani Kumleh

  2. Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, P.O. Box: 41635-1314, Rasht, Iran

    Babak Rabiei

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  1. Mojtaba Kordrostami
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Correspondence to Babak Rabiei.

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Handling editor: Eric Schranz.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 Online Resource 1. The origin/pedigree of rice varieties used in this experiment. (PDF 100 kb)

606_2016_1304_MOESM2_ESM.pdf

Supplementary material 2 Online Resource 2. Standard evaluation system of the visual salt injury at rice seedling stage (Gregorio et al. 1) (PDF 85 kb)

Supplementary material 3 Online Resource 3. The closely linked markers to Saltol and SKC1 on chromosome 1. (PDF 124 kb)

606_2016_1304_MOESM4_ESM.pdf

Supplementary material 4 Online Resource 4. Mean comparison of genotype × environment interaction for some morphological and physiological traits of rice seedlings under three salinity conditions. (PDF 243 kb)

606_2016_1304_MOESM5_ESM.pdf

Supplementary material 5 Online Resource 5. Mean comparison of genotype × environment interaction for some morphological and physiological traits of rice seedlings under three salinity conditions. (PDF 215 kb)

606_2016_1304_MOESM6_ESM.pdf

Supplementary material 6 Online Resource 6. Mean comparison of genotype × environment interaction for some morphological and physiological traits of rice seedlings under three salinity conditions. (PDF 264 kb)

606_2016_1304_MOESM7_ESM.pdf

Supplementary material 7 Online Resource 7. Mean comparison of genotype × environment interaction for some morphological and physiological traits of rice seedlings under three salinity conditions. (PDF 253 kb)

606_2016_1304_MOESM8_ESM.pdf

Supplementary material 8 Online Resource 8. Mean comparison of genotype × environment interaction for some morphological and physiological traits of rice seedlings under three salinity conditions. (PDF 246 kb)

606_2016_1304_MOESM9_ESM.pdf

Supplementary material 9 Online Resource 9. Mean comparison of genotype × environment interaction for some morphological and physiological traits of rice seedlings under three salinity conditions. (PDF 249 kb)

606_2016_1304_MOESM10_ESM.pdf

Supplementary material 10 Online Resource 10. Correlation coefficients among morphological and physiological traits and salinity tolerance indices of rice seedlings at 6 dS.m−1 NaCl. (PDF 139 kb)

606_2016_1304_MOESM11_ESM.pdf

Supplementary material 11 Online Resource 11a and b. Correlation coefficients among morphological and physiological traits (non-stress) and salinity tolerance indices of rice seedlings at 6 and 12 dS.m−1 NaCl respectively. (PDF 188 kb)

606_2016_1304_MOESM12_ESM.pdf

Supplementary material 12 Online Resource 12. Correlation coefficients among morphological and physiological traits and salinity tolerance indices of rice seedlings at 12 dS.m−1 NaCl. (PDF 139 kb)

606_2016_1304_MOESM13_ESM.pdf

Supplementary material 13 Online Resource 13. Dendrogram of the cluster analysis based on the measured morphological and physiological traits and tolerance indices in 44 studied rice varieties under 12 dS.m−1. (PDF 217 kb)

606_2016_1304_MOESM14_ESM.pdf

Supplementary material 14 Online Resource 14. Clustering of the studied genotypes using microsatellite markers linked to the QTL controlling salinity tolerance on chromosome 1 using UPGMA algorithm. (PDF 215 kb)

606_2016_1304_MOESM15_ESM.pdf

Supplementary material 15 Online Resource 16. Association of SSR markers with phenotypic traits and tolerance indices under salinity of 6 dS.m−1. (PDF 106 kb)

606_2016_1304_MOESM16_ESM.pdf

Supplementary material 16 Online Resource 16. Association of SSR markers with phenotypic traits and tolerance indices under salinity of 6 dS.m−1. (PDF 118 kb)

606_2016_1304_MOESM17_ESM.pdf

Supplementary material 17 Online Resource 17. Dendrogram of the cluster analysis of the measured morphological and physiological traits and tolerance indices based on the haplotypes: 6, 7, 8 under 6 dS.m−1 NaCl condition. (PDF 104 kb)

606_2016_1304_MOESM18_ESM.pdf

Supplementary material 18 Online Resource 18. Dendrogram of the cluster analysis of the measured morphological and physiological traits and tolerance indices based on the haplotypes: 3 and 4 under 6 dS.m−1 NaCl condition. (PDF 104 kb)

606_2016_1304_MOESM19_ESM.pdf

Supplementary material 19 Online Resource 19. Dendrogram of the cluster analysis of the measured morphological and physiological traits and tolerance indices based on the haplotypes: 9, 10, 11 and 12 under 6 dS.m−1 NaCl condition. (PDF 104 kb)

606_2016_1304_MOESM20_ESM.pdf

Supplementary material 20 Online Resource 20. Dendrogram of the cluster analysis of the measured morphological and physiological traits and tolerance indices based on the haplotypes: 6, 7, 8 under 12 dS.m−1 NaCl condition. (PDF 101 kb)

606_2016_1304_MOESM21_ESM.pdf

Supplementary material 21 Online Resource 21. Dendrogram of the cluster analysis of the measured morphological and physiological traits and tolerance indices based on the haplotypes: 3 and 4 under 12 dS.m−1 NaCl condition. (PDF 104 kb)

606_2016_1304_MOESM22_ESM.pdf

Supplementary material 22 Online Resource 22. Dendrogram of the cluster analysis of the measured morphological and physiological traits and tolerance indices based on the haplotypes: 9, 10, 11 and 12 under 12 dS.m−1 NaCl condition. (PDF 104 kb)

606_2016_1304_MOESM23_ESM.pdf

Supplementary material 23 Online Resource 23. Dendrogram of the cluster analysis of the measured morphological and physiological traits and tolerance indices based on the haplotypes: 6, 7, 8 under normal conditions. (PDF 100 kb)

Information on Electronic Supplementary Material

Information on Electronic Supplementary Material

Online Resource 1. The origin/pedigree of rice varieties used in this experiment.

Online Resource 2. Standard evaluation system of the visual salt injury at rice seedling stage (Gregorio et al. 1).

Online Resource 3. The closely linked markers to Saltol and SKC1 on chromosome 1.

Online Resource 4-9. Mean comparison of genotype × environment interaction for some morphological and physiological traits of rice seedlings under three salinity conditions.

Online Resource 10. Correlation coefficients among morphological and physiological traits and salinity tolerance indices of rice seedlings at 6 dS.m−1 NaCl.

Online Resource 11a and b. Correlation coefficients among morphological and physiological traits (non-stress) and salinity tolerance indices of rice seedlings at 6 and 12 dS.m−1 NaCl respectively.

Online Resource 12. Correlation coefficients among morphological and physiological traits and salinity tolerance indices of rice seedlings at 12 dS.m−1 NaCl.

Online Resource 13. Dendrogram of the cluster analysis based on the measured morphological and physiological traits and tolerance indices in 44 studied rice varieties under 12 dS.m−1.

Online Resource 14. Clustering of the studied genotypes using microsatellite markers linked to the QTL controlling salinity tolerance on chromosome 1 using UPGMA algorithm.

Online Resource 15. Association of SSR markers with phenotypic traits and tolerance indices under normal conditions.

Online Resource 16. Association of SSR markers with phenotypic traits and tolerance indices under salinity of 6 dS.m−1.

Online Resource 17. Dendrogram of the cluster analysis of the measured morphological and physiological traits and tolerance indices based on the haplotypes: 6, 7, 8 under 6 dS.m−1 NaCl condition.

Online Resource 18. Dendrogram of the cluster analysis of the measured morphological and physiological traits and tolerance indices based on the haplotypes: 3 and 4 under 6 dS.m−1 NaCl condition.

Online Resource 19. Dendrogram of the cluster analysis of the measured morphological and physiological traits and tolerance indices based on the haplotypes: 9, 10, 11 and 12 under 6 dS.m−1 NaCl condition.

Online Resource 20. Dendrogram of the cluster analysis of the measured morphological and physiological traits and tolerance indices based on the haplotypes: 6, 7, 8 under 12 dS.m−1 NaCl condition.

Online Resource 21. Dendrogram of the cluster analysis of the measured morphological and physiological traits and tolerance indices based on the haplotypes: 3 and 4 under 12 dS.m−1 NaCl condition.

Online Resource 22. Dendrogram of the cluster analysis of the measured morphological and physiological traits and tolerance indices based on the haplotypes: 9, 10, 11 and 12 under 12 dS.m−1 NaCl condition.

Online Resource 23. Dendrogram of the cluster analysis of the measured morphological and physiological traits and tolerance indices based on the haplotypes: 6, 7, 8 under normal conditions.

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Kordrostami, M., Rabiei, B. & Hassani Kumleh, H. Association analysis, genetic diversity and haplotyping of rice plants under salt stress using SSR markers linked to SalTol and morpho-physiological characteristics. Plant Syst Evol 302, 871–890 (2016). https://doi.org/10.1007/s00606-016-1304-8

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