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Title of http://prr.hec.gov.pk/Thesis
Molecular Mapping of Na+ Accumulation Quantitative Trait Loci (QTLs) in Rice (Qryza Sativa L) Under Salt Stress

Tanveer Ul Haq
Institute/University/Department Details
Institute of Soil & Environmental Sciences, University of Agriculture, Fasialabad Pakistan
Soil Science
Number of Pages
Keywords (Extracted from title, table of contents and abstract of http://prr.hec.gov.pk/Thesis)
Moroberekan, morphological, chromosome-1.

A mapping population of recombinant inbred lines (RILs) derived from the cross between Co39 (lowland, Indica rice cultivar) and Moroberekan (upland, Japonica) was used, in two experiments to map QTLs associated with salt tolerance, particularly, ion accumulation under salinity stress by composite interval mapping (CIM). In QTL mapping study-I, plants were transplanted in compost filled pots and exposed to non saline and saline treatments (100 mol m-3 NaCl + 5 mol m 3 CaCl2) in a flood bench system and data were recorded for various physiological and morphological parameters at different exposure times to salt stress. There were three replications in mapping study-I. The plants were grown only at 100 mol m-3 NaCl + 5 mol m-3 CaCl2 salt stress in mapping study-II, with three replications. QTL mapping study-I used 32 RILs, whereas, in study-II a total of 120 RILs were evaluated for phenotypic response. The integrated genetic map of rice chromosome-1, consisting of 45 molecular markers had a distance of 201.2 cM with an average interval of 4.57 cM between markers, saturating a region that has previously been identified as a hot-spot for ion accumulation QTLs. In mapping study-II, Na+, K+ concentration and K+/Na+ ratio in the sap of different parts of the plant were recorded at 7 and 21 days of salt stress. A total of 38 QTLs for ion accumulation were detected in the 80 to 101 cM region of the genetic map of chromosome-1. We identified three separate regions that were active in controlling ion concentration at 21 days of salt stress, suggesting that a minimum of three different genes were acting to regulate leaf sap ion concentrations. QTLs for various physiological and morphological traits associated with salt tolerance were also detected on other chromosomes of rice. In mapping study-I, 6QTLs for Na+ in expanded leaf were detected on chrom.1 (2QTLs), 2 (1QTL), 3 (1QTL) and 9 (2QTLs), whereas, 4QTLs were found on chrom.1 at 21 days salt stress in mapping study-II. Similarly, 6QTLs for K+ in expanded leaf were detected on chrom.1 (1QTL), 2 (1QTL), 6 (1QTL), 7 (1QTL) and 9 (2QTLs), whereas, no QTL was identified in mapping study-II at 21 days salt stress. Regarding, K+/Na+ ratio of expanded leaf 5QTLs were detected on chrom.1 (4QTLs) and 12 (1QTLs) in mapping study-I, whereas, 4QTLs were identified on chrom.1 at 21 days salt stress in mapping study-II. QTLs for these traits were also detected in other tissue types in mapping study-II. The QTLs for Na+ accumulation were detected at different regions under salt stress and non stress conditions suggesting that same genes are not involved in the control of ions under salt stress and non stress conditions. Moroberekan alleles at most of the loci increase Na+ and decrease K+ conc. in the leaf sap under salt stress. The markers RM10710, RM8094, K061, RM3412 and RM493 are important for salt tolerance on chromosome-1 because of the presence of consistent QTLs for K+ and Na+ accumulation in this region. The relationship is also discussed between these QTLs and others such as Saltol, SalT, SKC-1 etc. reported by different authors. QTL for days to heading were also found under non saline conditions.

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S. No. Chapter Title of the http://prr.hec.gov.pk/Chapters Page Size (KB)
1 1 Introduction 1

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2 2 Review of Literature 8

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  2.1 Origin of salt-affected soils 8
  2.2 Extent and distribution of soil salinity 9
  2.3 Possible strategies to tackle the problem of soil salinity 10
  2.4 The approach of saline agriculture 10
  2.5 Influx of Na+ in plants under salt stress 10
  2.6 Effects of high Na+ ions on plant growth under salt stress 12
  2.7 Mechanisms to tolerate high Na+ under salt stress in plants 13
  2.8 Important indicators of salinity tolerance in plants 19
  2.9 Genetics of plant salt tolerance 20
  2.10 Scope of molecular techniques in enhancement of salt tolerance 21
  2.11 Response of rice to salt stress 21
  2.12 Rice, a model system for molecular studies 22
  2.13 Sequencing of rice genome 23
  2.14 Uses of genetic markers to improve plant salt tolerance 23
  2.15 Quantitative traits 30
  2.16 Quantitative trait loci (QTLs) 30
  2.17 Molecular Genetic mapping in rice 31
  2.18 QTL mapping in relation to plant salinity tolerance 37
  2.19 QTL mapping in rice for salinity tolerance 38
  2.20 Gene expression studies in the region of Saltol 47
  2.21 QTL mapping for days to Anhttp://prr.hec.gov.pk/Thesis in rice 48
  2.22 QTL mapping for plant height in rice 50
  2.23 Marker assisted selection 51
  2.24 Gene cloning and transformation 53
  2.25 Genes involved in the regulation of Na+ in plants under salinity stress 54
  2.26 Scope of transgenics for salt tolerance 54
  2.27 Validation of QTLs 57
3 3 Materials and Methods 59  


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  3.1 Preliminary Study –I (a) 59
  3.2 Preliminary Study –I (b) 59
  3.3 QTL Mapping Study –I 59
  3.4 QTL Mapping Study –II 77
  3.5 QTL Mapping Study –III 86
  3.6 Statistical analysis 86
4 4 Results 87

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  4.1 Morpho-Physiological response of Co39/Moroberekan 87
  4.2 Preliminary Study-I (a) 87
  4.3 Preliminary Study-I (b) 89
  4.4 QTL Mapping Study-I 93
  4.5 Description of molecular work 127
  4.6 Number of QTLs, controlling various traits at saline conditions on chromosome-1, of rice (Oryza sativa L.) 133
  4.7 Number of QTLs, for various traits on chromosomes-2 to 12 of rice (Oryza sativa L.) at saline and non-saline conditions 143
  4.8 Comparison of QTLs for salt tolerance associated traits at saline and
non-saline conditions
  4.9 QTL Mapping Study-II 157
  4.10 Description of molecular work 168
  4.11 Number of QTLs associated with ion accumulation on chromosome -1, at 7 days salt stress 168
  4.12 Number of QTLs associated with ion accumulation traits on chromosome-1, at 21 days salt stress 179
  4.13 QTLs for shoot growth traits at 42 days salt stress 186
  4.14 Number of QTLs, controlling traits associated with salt tolerance on chromosomes 2 to12 of rice (Oryza sativa L.) 206
  4.15 QTL Mapping Study-III 218
5 5 Discussion 225
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  5.1 Response of rice varieties at germination to salt stress 225
  5.2 QTL mapping of traits associated with salt tolerance in RILs population from the cross between Co39×Moroberekan 226
6 6 Summary 247
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