Microsatellite based linkage disequilibrium analyses reveal Saltol haplotype fragmentation and identify novel QTLs for seedling stage salinity tolerance in rice (Oryza sativa L.)

Babu, N. Naresh; Vinod, K. K.; Krishnamurthy, S. L.; Krishnan, S. Gopala; Yadav, Ashutosh Kumar; Bhowmick, Prolay Kumar; Nagarajan, M.; Singh, Nagendra; Prabhu, K. V.; Singh, Ashok Kumar

doi:10.1007/s13562-016-0393-3

Cited by 13 publications

(11 citation statements)

References 38 publications

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“…However, such NILs could not be recovered as they were rejected during the selection process based on marker genotype without exposing them to salinity stress. Since the Saltol region spans over ~ 1.5Mbp, the possibility of intra-QTL recombination does exist, which was evident from the haplotype variation in the Saltol region in the rice germplasm 54 . Salt tolerance of rice is an indicative of several components related to Na + and K + homeostasis.…”

Section: Discussionmentioning

confidence: 99%

Marker aided introgression of ‘Saltol’, a major QTL for seedling stage salinity tolerance into an elite Basmati rice variety ‘Pusa Basmati 1509’

Yadav

Kumar

Grover

et al. 2020

Sci Rep

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Marker assisted backcross breeding was used to transfer Saltol, a major QtL for seedling stage salinity tolerance from the donor FL478 to Pusa Basmati 1509 (PB 1509), a high yielding and early maturing Basmati rice variety. Foreground selection was carried out using three markers namely, AP3206f, RM3412b and RM10793, linked to Saltol. In addition, 105 genome-wide SSR markers polymorphic between FL478 and PB 1509 were used in background selection. Among the BC 3 f 4 near isogenic lines (NILs) developed, recurrent parent genome recovery ranged from 96.67 to 98.57%. Multi-season evaluation identified some of the NILs showing significantly higher yield with grain and cooking quality comparable to PB 1509. All the NILs exhibited tolerance to salinity with significantly higher relative water content, membrane stability index and proline content as compared to PB 1509. the root and shoot concentration of na + , K + and na + /K + in NILs was at par with FL478 under stress conditions. the gene OsHKT1;5 located in the Saltol region showed higher expression levels under stress indicating its role in conferring salinity tolerance. Salt tolerant NILs of PB 1509 will be useful in stabilizing production in salt affected areas. Rice is highly sensitive to salinity stress at seedling and reproductive stages. The symptoms of salt injury in rice are stunted growth, rolling of leaves, white tips, drying of older leaves and grain sterility. The most common injuries are attributed to the destabilization of the membrane, osmotic imbalance and disruption of photosynthetic mechanism 1,2. Water uptake by rice plant is also hindered due to salt stress which causes leaf damage 3,4. Soil salinity limits the rice plant's growth and development, resulting in yield losses of more than 50% 5. Though salinity affects all stages of the growth and development of the rice plant, its effect on young seedlings is highly detrimental as it directly influences plant establishment, thus affecting yield. With every dS/m increase of electrical conductivity (EC) beyond the threshold salt level of 3.0 dS/m, the rice yield is decreased by 12% which implies a yield reduction up to 50% at EC 7.2 dS/m 6. Therefore, development of varieties with seedling stage salinity tolerance can sustain the production of the crop in salt affected areas by promoting the good initial establishment of plants, leading to healthy vegetative growth that can increase crop yield 7. In India, rice is grown on 44 million ha with an annual production of 110 million tons of milled rice. Basmati is premium quality rice which is grown in ~ 2 million ha across seven states of India which has been earmarked as the Geographical Indication (GI) area for the cultivation 8. Basmati rice is well-known worldwide for its exquisite quality traits, superfine grains, fluffy cooked rice with superior eating quality and pleasant aroma 9. It is a valuable agricultural export commodity, which earned foreign exchange worth US$ 4.72 billion during 2018-2019 10 .

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Section: Discussionmentioning

confidence: 99%

Marker aided introgression of ‘Saltol’, a major QTL for seedling stage salinity tolerance into an elite Basmati rice variety ‘Pusa Basmati 1509’

Yadav

Kumar

Grover

et al. 2020

Sci Rep

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“…Another possibility is cryptic intra- Saltol QTL recombination that could not be detected by the three markers used for the foreground selection. It is emphasised that Saltol region is fairly large (having a size of ~1.5Mbp) enough to accede intra-QTL recombination, as evident from its highly fragmented existence in the rice genome [ 40 ]. Further, introgression of additional hitherto unidentified QTLs from donor into the salt tolerant NILs cannot be ruled out.…”

Section: Discussionmentioning

confidence: 99%

Marker-Assisted Introgression of Saltol QTL Enhances Seedling Stage Salt Tolerance in the Rice Variety “Pusa Basmati 1”

Singh

Kumar

et al. 2018

International Journal of Genomics

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Marker-assisted selection is an unequivocal translational research tool for crop improvement in the genomics era. Pusa Basmati 1 (PB1) is an elite Indian Basmati rice cultivar sensitive to salinity. Here, we report enhanced seedling stage salt tolerance in improved PB1 genotypes developed through marker-assisted transfer of a major QTL, Saltol. A highly salt tolerant line, FL478, was used as the Saltol donor. Parental polymorphism survey using 456 microsatellite (SSR)/QTL-linked markers revealed 14.3% polymorphism between PB1 and FL478. Foreground selection was carried out using three Saltol-linked polymorphic SSR markers RM8094, RM493, and RM10793 and background selection by 62 genome-wide polymorphic SSR markers. In every backcross generation, foreground selection was restricted to the triple heterozygotes of foreground markers, which was followed by phenotypic and background selections. Twenty-four near isogenic lines (NILs), with recurrent parent genome recovery of 96.0–98.4%, were selected after two backcrosses followed by three selfing generations. NILs exhibited agronomic traits similar to those of PB1 and additional improvement in the seedling stage salt tolerance. They are being tested for per se performance under salt-affected locations for release as commercial varieties. These NILs appear promising for enhancing rice production in salinity-affected pockets of Basmati Geographical Indication (GI) areas of India.

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“…However, the problem with conventional method of breeding is that the developed progenies acquired unwanted traits due to linkage drag and possible negative effects on yield and grain quality traits of rice (Gregorio et al, 2002;Ismail et al, 2007;Thomson et al, 2010). Many researchers has introgressed the Saltol QTL in to different rice varieties Huyen et al (2012) in AS996, Babu et al (2017b) in PB1121, Geetha et al (2017) in ADT43. Therefore the present effort was made to improve these cultivars using MABB method.…”

Section: Discussionmentioning

confidence: 99%

“…To counter the damaging effects of salinity on rice production new improved salt tolerant varieties are being developed through conventional breeding method (Krishnamurthy et al, 2019a;Krishnamurthy et al, 2019b;Krishnamurthy et al, 2019c) and also through marker assisted breeding (Singh et al, 2016;Babu et al, 2017b;Geetha et al, 2017;Singh et al, 2018;Bhandari et al, 2019). The conventional method of breeding however is time consuming and more labour intensive (Salvi and Tuberosa, 2005).…”

Section: Introductionmentioning

confidence: 99%

“…Marker assisted breeding in rice was successful in developing new improved salt tolerance line in rice (Linh et al, 2012;Luu et al, 2012;Usatov et al, 2015;Singh et al, 2016;Babu et al, 2017b;Singh et al, 2018;Bhandari et al, 2019). Molecular markers based technologies helped in mapping of salt tolerant genes on rice chromosomes and few Saltol linked marker like RM3412, AP3206, RM8094, RM493, RM10793 have been identified for marker assisted breeding and screening (Ismail et al, 2007;Thomson et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

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Introgressed Saltol QTL Lines Improves the Salinity Tolerance in Rice at Seedling Stage

Krishnamurthy¹,

Pundir²,

Warraich³

et al. 2020

Front. Plant Sci.

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Rice is a staple food crop in Asia and plays a crucial role in the economy of this region. However, production of rice and its cultivating areas are under constant threat of soil salinity. A major QTL, Saltol, responsible for salinity tolerance at seedling stage has been mapped on chromosome 1 using Pokkali/IR29 Recombinant Inbred Lines (RIL) population. The present study was aimed to incorporate Saltol Quantitative Trait Loci (QTL) in two high yielding mega rice varieties i.e. Pusa44 and Sarjoo52 through Marker Assisted Backcross Breeding (MABB). To improve the seedling stage salinity tolerance in these cultivars, we introgressed the Saltol QTL from donor parent FL478 a derivative of Pokkali. A total of three backcrosses (BC 3) followed by selfing have led to successful introgression of Saltol QTL. Foreground selection at each breeding cycle was done using micro-satellite markers RM3412 and AP3206 to confirm Saltol QTL. The precise transfer of Saltol region was established using recombinant selection through flanking markers RM493 and G11a. Finally, 10 Saltol near isogenic lines (NILs) of Pusa44 and eight NILs of Sarjoo52 were successfully developed. These NILs (BC 3 F 4) were evaluated for seedling stage salinity under hydroponic system. The NILs PU99,

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Microsatellite based linkage disequilibrium analyses reveal Saltol haplotype fragmentation and identify novel QTLs for seedling stage salinity tolerance in rice (Oryza sativa L.)

Cited by 13 publications

References 38 publications

Marker aided introgression of ‘Saltol’, a major QTL for seedling stage salinity tolerance into an elite Basmati rice variety ‘Pusa Basmati 1509’

Marker aided introgression of ‘Saltol’, a major QTL for seedling stage salinity tolerance into an elite Basmati rice variety ‘Pusa Basmati 1509’

Marker-Assisted Introgression of Saltol QTL Enhances Seedling Stage Salt Tolerance in the Rice Variety “Pusa Basmati 1”

Introgressed Saltol QTL Lines Improves the Salinity Tolerance in Rice at Seedling Stage

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