Analysis of genetic diversity and population structure using SSR markers and validation of a Cleavage Amplified Polymorphic Sequences (CAPS) marker involving the sodium transporter OsHKT1;5 in saline tolerant rice (Oryza sativa L.) landraces

Sakthivel, Natarajan; Pulipati, Shalini; Ramasamy, Karthikeyan; Jaganathan, Deepa; Venkatesan, Sowmiya Devi; Vijay, Gopikaa; Kumari, Kumkum; Raju, Kalaimani; Hariharan, G.; Venkataraman, Gayatri

doi:10.1016/j.gene.2019.143976

Cited by 15 publications

(7 citation statements)

References 45 publications

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“…In this study, we have not observed any post stress induction of OsHKT1;5 in the sensitive genotype PB 1509, indicating that the OsHKT1;5 expression is associated with salt stress tolerance via regulating Na + /K + homeostasis as found in other studies also 60 . Further, SNP variation in OsHKT1;5 has been identified between salt tolerant and susceptible rice genotypes, evidencing that OsHKT1;5 is the major gene governing salt tolerance imparted by Saltol QTL 61 . Notwithstanding, Saltol region is quite long, and harbours loci that modify the expression of salt tolerance, that has puzzled the breeders who tried to introgress this QTL into different genetic backgrounds.…”

Section: Discussionmentioning

confidence: 95%

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: 95%

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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“…The SNP variation (A/G; rs10234287911) identified in the Oryza spp. above was validated in additional 43 landraces from coastal regions of India 24 . PCR primers were designed to amplify a 141 bp fragment of pre- miR396c (Supplementary Fig.…”

Section: Resultsmentioning

confidence: 99%

A conserved SNP variation in the pre-miR396c flanking region in Oryza sativa indica landraces correlates with mature miRNA abundance

Jaganathan

Rajakani

Doddamani

et al. 2023

Sci Rep

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Plant precursor miRNAs (pre-miRNA) have conserved evolutionary footprints that correlate with mode of miRNA biogenesis. In plants, base to loop and loop to base modes of biogenesis have been reported. Conserved structural element(s) in pre-miRNA play a major role in turn over and abundance of mature miRNA. Pre-miR396c sequences and secondary structural characteristics across Oryza species are presented. Based on secondary structure, twelve Oryza pre-miR396c sequences are divided into three groups, with the precursor from halophytic Oryza coarctata forming a distinct group. The miRNA-miRNA* duplex region is completely conserved across eleven Oryza species as are other structural elements in the pre-miRNA, suggestive of an evolutionarily conserved base-to-loop mode of miRNA biogenesis. SNPs within O. coarctata mature miR396c sequence and miRNA* region have the potential to alter target specificity and association with the RNA-induced silencing complex. A conserved SNP variation, rs10234287911 (G/A), identified in O. sativa pre-miR396c sequences alters base pairing above the miRNA-miRNA* duplex. The more stable structure conferred by the ‘A10234287911’ allele may promote better processing vis-à-vis the structure conferred by ‘G10234287911’ allele. We also examine pri- and pre-miR396c expression in cultivated rice under heat and salinity and their correlation with miR396c expression.

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“…W. Li et al, 2011;Nuñez-Muñoz et al, 2021;Paul et al, 2018). Other individual genes can confer osmoprotection, such as the Na+ transporter SKC1 (Os01g0307500) with a V395L that provides salt tolerance (Jayabalan et al, 2019).…”

Section: Stress Tolerancementioning

confidence: 99%

Rice breeding in the new era: comparison of useful agronomic traits

Hernández-Soto

Echeverría-Beirute

Abdelnour-Esquivel

et al. 2021

Preprint

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Understanding agronomic traits at a genetic level enables the leveraging of this knowledge to produce crops that are more productive and resilient, have better quality and are adjusted for consumer preferences. In the last decade, rice has become a model to validate the function of specific genes, resulting in valuable but scattered information. Here, we aimed to identify particular genes in rice related to traits that can be targeted by different mutation techniques in the breeding of crops. We selected gain of function, misfunction, and specific mutations associated with phenotypes of agronomic interest. The review includes specific trait-related genes involved in domestication, stress, herbicide tolerance, pathogen resistance, grain number/quality/weight, plant structure, nitrogen use, and others. The information presented can be used for rice, other cereals, and orphan crops to achieve a superior and sustainable production in challenging farming conditions.

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Analysis of genetic diversity and population structure using SSR markers and validation of a Cleavage Amplified Polymorphic Sequences (CAPS) marker involving the sodium transporter OsHKT1;5 in saline tolerant rice (Oryza sativa L.) landraces

Cited by 15 publications

References 45 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’

A conserved SNP variation in the pre-miR396c flanking region in Oryza sativa indica landraces correlates with mature miRNA abundance

Rice breeding in the new era: comparison of useful agronomic traits

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