Morphophysiological Diversity and Haplotype Analysis of Saltol QTL Region in Diverse Rice Landraces for Salinity Tolerance

Rice is sensitive to salinity stress at both the seedling and reproductive stages.The present study used 145 rice genotypes comprising of 100 landraces and 45 advanced breeding lines collected from different regions of India.These genotypes were evaluated in hydroponics under control[electrical conductivity(ECe)~1.2 dS/m]and saline(ECe~10.0 dS/m)environments along with susceptible(IR29)and tolerant(FL478)checks.The stress susceptibility index for eight morphophysiological traits was estimated.Analysis of variance showed significant differences among the genotypes for all the parameters studied in control,stress and relative stress conditions.We identified 3 landraces(Kuttimanja,Tulasimog and IET-13713I)as tolerant and 14 lines as moderately tolerant to salt stress.Strong correlations in the morphological(root and shoot lengths)and physiological traits(shoot Na^(+),Ca^(2+)and Mg^(2+)contents,and Na^(+)/K^(+)ratio)were observed under all the conditions.The hierarchical cluster analysis grouped the genotypes into five clusters,among which cluster Ⅱ comprised salt-tolerant lines.Haplotyping of Saltol region using 11 simple sequence repeat markers on 17 saline tolerant and moderately tolerant lines was conducted.Markers AP3206F,RM10793 and RM3412b,located close to SKC1 gene(11.23‒12.55 Mb),displayed diverse allelic variations and they were not related to the FL478 type.In this region,tolerant lines like Kuttimanja,IET-13713I and Tulasimog have new alleles.As a result,these lines may be suitable candidates for novel genomic regions governing rice salinity tolerance.Salt-tolerance ability of Kuttimanja,Tulasimog and IET-13713I was validated in two years in three salinity stress environments.These promising lines can be used in breeding programs to broaden the genetic base of salinity tolerance in rice,and it may help to dissect key genomic regions responsible for salinity tolerance.

Introgression the Salinity Tolerance QTLs <i>Saltol</i>into AS996, the Elite Rice Variety of Vietnam

This study focus on developing new salinity tolerance and high yielding rice lines, using markers assisted backrossing (MABC). Total of 500 SSR markers on 12 rice chromosomes were screened for parental polymorphic markers. Of which, 52 primers in the Saltol region were checked with the two parents varieties to identify polymorphic primers for screening the Saltol region of the breeding populations. For each backcross generation of ASS996/FL478, approx. 500 plants were screened with 63 polymorphic markers distributed on 12 chromosomes. The two BC1F1 plants P284 and P307 which had the highest recipient alleles up to 89.06% and 86.36%, were chosen for the next backcrossing. Three BC2F1 plants with the recipient alleles up to 94.03% and 93.18% were used to develop BC3F1 generation. The best BC3F1 plant was P284-112-209 with all the recipient alleles and Saltol region. The four plants P307-305-21, P284-112-195, P284-112-198, P284-112-213 were the second ranking with only one loci heterozygous (applied 63 markers covered on 12 chromosomes). These five plants were chosen as the breeding lines for result of Saltol-AS996 introgression. The breeding line BC4F1 having 100% genetic background of donor variety is ready for develop new salinity tolerant variety ASS996-Saltol to cope with climate change.

Haplotyping of Rice Genotypes Using Simple Sequence Repeat Markers Associated with Salt Tolerance

Salt stress is a major problem in most of the rice growing areas in the world. A major QTLSaltol associated with salt tolerance at the seedling stage has been mapped on chromosome 1 in rice.This study aimed to characterize the haplotype diversity at Saltol and additional QTLs associated withsalt tolerance. Salt tolerance at the seedling stage was assessed in 54 rice genotypes in the scale of 1to 9 score at EC = 10 dSm^-1 under controlled environmental conditions. Seven new breeding linesincluding three KMR3/O. rufipogon introgression lines showed similar salt tolerant ability as FL478 andcan be good sources of new genes/alleles for salt tolerance. Simple sequence repeat （SSR） markerRM289 showed only two alleles and RM8094 showed seven alleles. Polymorphic information contentvalue varied from 0.55 for RM289 to 0.99 for RM8094 and RM493. Based on 14 SSR markers, the 54lines were clearly separated into two major clusters. Fourteen haplotypes were identified based onSaltol linked markers with FL478 as the reference. Alleles of RM8094 and RM3412 can discriminatebetween the salt tolerant and susceptible genotypes clearly and hence can be useful in marker-assistedselection at the seedling stage. Other markers RM10720 on chromosome 1 and RM149 and RM264 onchromosome 8 can also distinguish tolerant and susceptible lines but with lesser stringency.

A comprehensive study of the proteins involved in salinity stress response in roots and shoots of the FL478 genotype of rice(Oryza sativa L. ssp. indica)

Rice,a major staple,is the most salt-sensitive cereal.High salinity triggers several adaptive responses in rice to cope with osmotic and ionic stress at the physiological,cellular,and molecular levels.A major QTL for salinity tolerance,named Saltol,is present on chromosome 1 of Indian landraces such as Pokkali and Nona Bokra.The early proteomic and physiological responses to salinity in roots and shoots of FL478,an inbred rice line harboring the Saltol QTL,were characterized.Plantlets were cultured in hydroponic cultures with 100 mmol L^(-1) Na Cl and evaluated at 6,24,and 48 h.At the physiological level,root length significantly increased at 48 h,whereas shoot length was reduced.The Na^(+)/K^(+) ratio was maintained at lower levels in shoots than in roots,suggesting that roots play a protective role.More than 2000 proteins were detected in both tissues.Roots showed a faster and more coordinated proteomic response than shoots,evident after only 6 h of treatment.These responses showed clear correspondence with those of proteins involved in transcription and translation.Maintenance of mitochondrial activity and amino acid metabolism in roots,and activation of stress-responsive proteins such as dehydrins and PLAT in shoots,may play a key role during the response of the plant to salinity stress.Proteomic and physiological responses showed that roots respond in a more highly adaptive manner than shoots to salinity stress,suggesting that this tissue is critical to the tolerance observed in cultivars harboring Saltol.

Root-Specific Transcript Profiling of Contrasting Rice Genotypes in Response to Salinity Stress

Elevated salinity imposes osmotic and ion toxicity stresses on living cells and requires a multitude of responses in order to enable plant survival. Building on earlier work profiling transcript levels in rice （Oryza sativa） shoots of FL478, a salt-tolerant indica recombinant inbred line, and IR29, a salt-sensitive cultivar, transcript levels were compared in roots of these two accessions as well as in the roots of two additional salt-tolerant indica genotypes, the landrace Pokkali and the recombinant inbred line IR63731. The aim of this study was to compare transcripts in the sensitive and the tolerant lines in order to identify genes likely to be involved in plant salinity tolerance, rather than in responses to salinity perse. Transcript profiles of several gene families with known links to salinity tolerance are described （e.g. HKTs, NHXs）. The putative function of a set of genes identified through their salt responsiveness, transcript levels, and/or chro- mosomal location （i.e. underneath QTLs for salinity tolerance） is also discussed. Finally, the parental origin of the Saltol region in FL478 is further investigated. Overall, the dataset presented appears to be robust and it seems likely that this system could provide a reliable strategy for the discovery of novel genes involved in salinity tolerance.