Screening of rice landraces (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) for seedling stage salinity tolerance using morpho-physiological and molecular markers

Traditional rice landraces of coastal area in Bangladesh are distinct regarding their phenotype, response to salt stress and yield attributes. With characterization of these landraces, suitable candidate genes for salinity tolerance could be identified to introgress into modern rice varieties. Therefore, the aim of this experiment was to uncover prospective rice landraces tolerant to salinity. Relying on morphological, biochemical and molecular parameters 25 rice genotypes were tested for salt tolerance at germination and seedling stage. At germination stage 0 and 12 dSm^?1 salinity were imposed on rice genotypes. Ward’s cluster analysis divided rice genotypes into three clusters (susceptible, moderately tolerant and tolerant) based on the physiological indices. The tolerant rice landraces to salinity were Sona Toly, Nakraji and Komol Bhog. At seedling stage screening was performed following IRRI standard protocol at 12 dSm^?1 salinity level. Based on all morphological and biochemical parameters Komol Bhog was identified as the highly salinity tolerant landrace while Bolonga, Sona Toly, Dud Sail, Tal Mugur and Nakraji were found as tolerant to salinity. Molecular characterization using two simple sequence repeats (SSR) markers, viz. RM121 and RM337 displayed Bolonga, Til Kapor, Panbra, Sona Toly, Bina Sail, Komol Bhog, Nakraji, Tilkapur, Gajor Goria and Gota were tolerant landraces through genetic similarity in dendrogram. These identified salt-resistant landraces can be used as promising germplasm resources for breeding salt-tolerant high-yielding rice varieties in future.     

<Emphasis Type="Italic">Wsi18</Emphasis> promoter from wild rice genotype, <Emphasis Type="Italic">Oryza nivara</Emphasis>, shows enhanced expression under soil water stress in contrast to elite cultivar, <Emphasis Type="Italic">IR20</Emphasis>

Identification and characterization of plant promoters from wild rice genotypes showing inducible expression under soil water stress (SWS) is desirable for transgene expression to generate stress tolerant rice cultivars. A comparative expression profiling of Wsi18, a group 3 LEA gene, revealed differential response under SWS conditions between modern cultivated rice (IR20) and its wild progenitor (Oryza nivara). Wsi18 promoter from O. nivara showed enhanced inducible expression of the reporter gusA gene, encoding β-glucuronidase, in transgenic rice plants in comparison to similar promoter from IR20. Deletion analysis unravelled the cis-acting regulatory elements minimally required for optimal expression of Wsi18 promoter from O. nivara under SWS condition. This is the first report of characterization of an inducible promoter from a wild rice genotype to drive the gene expression under water stress conditions. The Wsi18 promoter element from the wild rice genotype can be used in future genetic manipulation strategies for the generation of SWS tolerant rice cultivars with improved yield characteristics.     

Salt oversensitivity derived from mutation breeding improves salinity tolerance in barley <Emphasis Type="Italic">via</Emphasis> ion homeostasis

Salt stress imposes a major environmental threat to agriculture, therefore, understanding the basic physiology and genetics of cell under salt stress is crucial for developing any breeding strategy. In the present study, the expression profile of genes involved in ion homeostasis including salt overly sensitive (HvSOS1, HvSOS2, HvSOS3), vacuolar Na⁺/H⁺ antiporter (HvNHX1), and H⁺-ATPase (HVA) along with ion content measurement were investigated in two genotypes of Hordeum vulgare under 300 mM NaCl. The gene expressions were measured in the roots and shoots of a salt-tolerant mutant genotype M4-73-30 and in its wild-type cv. Zarjou by real-time qPCR technique. The critical differences between the salt-tolerant mutant and its wild-type were observed in the expressions of HvSOS1 (105-fold), HvSOS2 (24-fold), HvSOS3 (31-fold), and HVA (202-fold) genes in roots after 6-h exposure to NaCl. The parallel early up-regulation of these genes in root samples of the salt-tolerant mutant genotype indicated induction of Na⁺/H⁺ antiporters activity and Na+ exclusion into apoplast and vacuole. The earlier up-regulation of HvSOS1, HVA, and HvNHX1 genes in shoot of the wild-type genotype corresponded to the relative accumulation of Na⁺ which was not observed in salt-tolerant mutant genotype because of efficient inhibitory role of the root in Na+ transport to the shoot. In conclusion, the lack of similarity in gene expression patterns between the two genotypes with similar genetic background may confirm the hypothesis that mutation breeding could change the ability of salt-tolerant mutant genotype for efficient ion homeostasis via salinity oversensitivity response.     

Analysis of genomic region spanning <Emphasis Type="Italic">Saltol</Emphasis> using SSR markers in rice genotypes showing differential seedlings stage salt tolerance

Micro satellite markers located in the Saltol QTL of 5 Mb region (10.4–15.6 Mb) in chromosome 1 confering seedling stage salt tolerance were used to evaluate 94 rice genotypes. Out of 21, eight SSR markers at Saltol region of Chromosome were found polymorphic. Based on the phenotypic screening, 94 genotypes were grouped as highly tolerant (20), tolerant (18) moderately tolerant (32), sensitive (19) and highly sensitive (5). The marker RM3412 appears to be diagnostic of salinity tolerance and associate to salinity tolerance at seedling stage as it is closely linked to SKC gene. Based on Saltol markers study, CSR 31, CSR 38, CSR 41, CSR 32, Wild 11, CSR 18, Azgo, Pant Dhan 4, Trichi 1, CSR 10 and IR64426-4B-11-1 could not be identified as tolerant genotypes though had expressed tolerant to highly tolerant phenotype to salinity stress at seedling stage, suggesting that QTLs other than Saltol might be controlling their salinity tolerance. It is suggested that these genotypes could serve as potentially novel germplasm and could be exploited for the development of new breeding lines with high level of salinity tolerance by pyramiding of the Saltol and other QTLs.     

Assessment of genetic diversity of <Emphasis Type="Italic">Saltol</Emphasis> QTL among the rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) genotypes

Eight Saltol quantitative trait locus (QTL) linked simple sequence repeat (SSR) markers of rice (Oryza sativa L.) were used to study the polymorphism of this QTL in 142 diverse rice genotypes that comprised salt tolerant as well as sensitive genotypes. The SSR profiles of the eight markers generated 99 alleles including 20rare alleles and 16 null alleles. RM8094 showed the highest number (13) of alleles followed by RM3412 (12), RM562 (11), RM493 (9) and RM1287 (8) while as, RM10764 and RM10745 showed the lowest number (6) of alleles. Based on the highest number of alleles and PIC value (0.991), we identified RM8094 as suitable marker for discerning salt tolerant genotypes from the sensitive ones. Based upon the haplotype analysis using FL478 as a reference (salt tolerant genotypes containing Saltol QTL), we short listed 68 rice genotypes that may have at least one allele of FL478 haplotype. Further study may confirm that some of these genotypes might have Saltol QTL and can be used as alternative donors in salt tolerant rice breeding programmes.     

The use of molecular genetic methods for prognosis of aerobic and anaerobic performance in athletes

The distribution of genotypes and alleles of ACE (I/D polymorphism), ACTN3 (R577X), NOS3 (5/4), UCP2 (Ala55Val), and UCP3 (-55C/T) genes, as well as the correlation between the genotype and physiological parameters, was studied in rowers (n = 230) and in a control group (n = 855). The genotypes were determined by analyzing restriction fragment length polymorphism. Physiological parameters were determined with a PM 3 rowing ergometer and a MetaMax 3B gas analyzer. The frequency of the ACE II genotype was significantly higher in elite rowers (n = 107) than in the control subjects. The frequency of the ACTN3 XX genotype, unfavorable for development of speed and strength qualities, was twofold lower in all rowers than in the control subjects. The frequencies of the ACE I, ACTN3 R, UCP2 Val, and UCP3 T alleles increased in the athletes along with an increase in skill, which suggested natural sports selection. In addition, ACE I, NOS3 5, UCP2 Val, and UCP3 T alleles correlated with a high aerobic performance. Thus, the ACE I, NOS3 5, UCP2 Val, and UCP3 T alleles may be regarded as genetic markers associated with enhanced aerobic performance and may be included in a diagnostic system for prognosis of human physical performance.     

<Emphasis Type="Italic">In Planta</Emphasis> transformation for conferring salt tolerance to a tissue-culture unresponsive indica rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) cultivar

Many farmer-popular indica rice (Oryza sativa L.) cultivars are recalcitrant to Agrobacterium-mediated transformation through tissue culture and regeneration. In planta transformation using Agrobacterium could therefore be a useful alternative for indica rice. A simple and reproducible in planta protocol with higher transformation efficiencies than earlier reports was established for a recalcitrant indica rice genotype. Agrobacterium tumefaciens containing the salt tolerance-enhancing Pea DNA Helicase45 (PDH45) gene, with the reporter and selectable marker genes, gus-INT (β-glucuronidase with intron) and hygromycin phosphotransferase (hpt), respectively, were used. Overnight-soaked mature embryos were infected and allowed to germinate, flower, and set T₁ seeds. T₀ plants were considered positive for the transgene if the spikelets of one or more of their panicles were positive for gus. Thereafter, selection at T₁ was done by germination in hygromycin and transgenic status re-confirmation by subjecting plantlet DNA/RNA to gene-specific PCR, Southern and semi-quantitative RT-PCR. Additionally, physiological screening under saline stress was done at the T₂ generation. Transformation efficiency was found to be 30–32% at the T₀ generation. Two lines of the in planta transformed seedlings of the recalcitrant rice genotype were shown to be saline tolerant having lower electrolyte leakage, lower Na⁺/K⁺, minimal leaf damage, and higher chlorophyll content under stress, compared to the WT at the T₂ generation.     

Changes in physiological,biochemical and antioxidant enzyme activities of green gram (<Emphasis Type="Italic">Vigna radiata</Emphasis> L.) genotypes under drought

Water deficit is one of the major factors affecting the growth and productivity field crops. This study was conducted to characterize four popularly genotypes, viz. SGC 16, TMB 37, SG 21-5, and Pratap, of green gram (Vigna radiata L.) on physiological, biochemical and morphological basis under water deficit at vegetative, flowering and pod filling stages. A substantial decrease in the mid-day leaf water potential (Ψ_L), net photosynthesis (P _N), total soluble protein (TSP) and membrane stability index (MSI) were recorded under water deficit. However, the membrane lipid peroxidation (MDA), total free amino acid, and the activities of super oxide dismutase and catalase increased significantly (p ≤ 0.05). Percentage reduction of grain yield, under water deficit, was the maximum in the genotype TMB 37 (50.05–63.80 %) indicating its sensitivity towards water deficit. In contrast, the genotype Pratap was the most tolerant to water deficit as it had the minimum reduction (20.76–34.87 %) in grain yield. Flowering was the most critical crop growth stage to water deficit. Among the studied parameters, Ψ_L, P _N, TSP, MSI and MDA were identified as the marker parameters for explaining the response mechanism of green gram genotypes to water deficit.     

Genetic analyses for deciphering the status and role of photoperiodic and maturity genes in major Indian soybean cultivars

Allelic combinations of major photoperiodic (E1, E3, E4) and maturity (E2) genes have extended the adaptation of quantitative photoperiod sensitive soybean crop from its origin (China ～35 ^°N latitude) to both north (up to ～50 ^°N) and south (up to 40 ^°S) latitudes, but their allelic status and role in India (6–35 ^°N) are unknown. Loss of function and hypoactive alleles of these genes are known to confer photoinsensitivity to long days and early maturity. Early maturity has helped to adapt soybean to short growing season of India. We had earlier found that all the Indian cultivars are sensitive to incandescent long day (ILD) and could identify six insensitive accessions through screening 2071 accessions under ILD. Available models for ILD insensitivity suggested that identified insensitive genotypes should be either e3 /e4 or e1 (e1-nl or e1-fs) with either e3 or e4. We found that one of the insensitive accessions (EC 390977) was of e3 /e4 genotype and hybridized it with four ILD sensitive cultivars JS 335, JS 95-60, JS 93-05, NRC 37 and an accession EC 538828. Inheritance studies and marker-based cosegregation analyses confirmed the segregation of E3 and E4 genes and identified JS 93-05 and NRC 37 as E3E3E4E4 and EC 538828 as e3e3E4E4. Further, genotyping through sequencing, derived cleaved amplified polymorphic sequences (dCAPS) and cleaved amplified polymorphic sequences (CAPS) markers identified JS 95-60 with hypoactive e1-as and JS 335 with loss of function e3-fs alleles. Presence of photoperiodic recessive alleles in these two most popular Indian cultivars suggested for their role in conferring early flowering and maturity. This observation could be confirmed in F ₂ population derived from the cross JS 95-60 × EC 390977, where individuals with e1-as e1-as and e4e4 genotypes could flower 7 and 2.4 days earlier, respectively. Possibility of identification of new alleles or mechanism for ILD insensitivity and use of photoinsensitivity in Indian conditions have been discussed.     

A major QTL (<Emphasis Type="Italic">qFT12.1</Emphasis>) allele from wild soybean delays flowering time

Soybean is highly sensitive to photoperiod. To improve the adaptability and productivity of soybean, it is essential to understand the molecular mechanisms regulating flowering time. To identify new flowering time QTLs, we evaluated a BC₃F₅ population consisting of 120 chromosome segment substitution lines (CSSLs) over 2 years under field conditions. CSSLs were derived from a cross between the cultivated soybean cultivar Jackson and the wild soybean accession JWS156-1, followed by continuous backcrossing using Jackson as the recurrent parent. Four QTLs (qFT07.1, qFT12.1, qFT12.2, and qFT19.1) were detected on three chromosomes. Of these, qFT12.1 showed the highest effect, accounting for 36.37–38.27% of the total phenotypic variation over 2 years. This QTL was further confirmed in the F₇ recombinant inbred line population (n?=?94) derived from the same cross (Jackson × JWS156-1). Analysis of the qFT12.1 BC₃F₅ residual heterozygous line RHL509 validated the allele effect of qFT12.1 and revealed that the recessive allele of qFT12.1 resulted in delayed flowering. Evaluating the qFT12.1 near-isogenic lines (NILs) under different growth conditions showed that NILs with the wild soybean genotype always showed later flowering than those with the cultivated soybean genotype. qFT12.1 was delimited to a 2703-kb interval between the markers BARCSOYSSR_12_0220 and BARCSOYSSR_12_0368 on chromosome 12. qFT12.1 may be a new flowering time gene locus in soybean.     

Growth,ionic response,and gene expression of shoots and roots of perennial ryegrass under salinity stress

Growth, ionic responses, and expression of candidate genes to salinity stress were examined in two perennial ryegrass accessions differing in salinity tolerance. The salinity tolerant (PI265349) and sensitive accessions (PI231595) were subjected to 75-mM NaCl for 14 days in a growth chamber. Across two accessions, salinity stress increased shoot dry weight and concentrations of malondialdehyde (MDA) and Na⁺ in the shoots and roots, but decreased shoot Ca²⁺ and root K⁺ concentrations. Salinity stress also increased root expressions of SOS1, PIP1, and TIP1. Plant height and chlorophyll content were unaffected by salinity stress in the tolerant accession but significantly decreased in the sensitive accession. Shoot MDA content did not change in the tolerant accession but increased in the sensitive accession. A more dramatic increase in Na⁺ was found in the roots of the sensitive accession. Relative to the control, salinity stress reduced expression of SOS1, NHX1, PIP1, and TIP1 in the shoots but increased expression of these genes in the roots of the tolerant accession. Expression levels of SOS1 increased in the roots and expression of NHX1 increased in the shoots but decreased in the roots of the sensitive accession under salinity stress. A decline in PIP1 expression in the shoots and dramatic increases in TIP expression in both shoots and roots were found in the sensitive accession under salinity stress. The results suggested maintenance of plant growth and leaf chlorophyll content, lesser Na⁺ accumulation in the roots, and lower lipid peroxidation in the shoots which could be associated with salinity tolerance. The decreased expressions of SOS1, NHX1, and TIP1 in the shoots, and increased expressions of NHX1 and PIP1 in the roots might also be related to salinity tolerance in perennial ryegrass.     

Genetic mapping of a novel recessive allele for non-glaucousness in wild diploid wheat <Emphasis Type="Italic">Aegilops tauschii</Emphasis>: implications for the evolution of common wheat

Cuticular wax on the aerial surface of plants has a protective function against many environmental stresses. The bluish–whitish appearance of wheat leaves and stems is called glaucousness. Most modern cultivars of polyploid wheat species exhibit the glaucous phenotype, while in a wild wheat progenitor, Ae. tauschii, both glaucous and non-glaucous accessions exist. Iw2, a wax inhibitor locus on the short arm of chromosome 2D, is the main contributor to this phenotypic variation in Ae. tauschii, and the glaucous/non-glaucous phenotype of Ae. tauschii is usually inherited by synthetic hexaploid wheat. However, a few synthetic lines show the glaucous phenotype although the parental Ae. tauschii accessions are non-glaucous. Molecular marker genotypes indicate that the exceptional non-glaucous Ae. tauschii accessions share the same genotype in the Iw2 chromosomal region as glaucous accessions, suggesting that these accessions have a different causal locus for their phenotype. This locus was assigned to the long arm of chromosome 3D using an F₂ mapping population and designated W4, a novel glaucous locus in Ae. tauschii. The dominant W4 allele confers glaucousness, consistent with phenotypic observation of Ae. tauschii accessions and the derived synthetic lines. These results implied that glaucous accessions of Ae. tauschii with the W2W2iw2iw2W4W4 genotype could have been the D-genome donor of common wheat.     

Dependence of endurance performance on <Emphasis Type="Italic">ACE</Emphasis> gene polymorphism in athletes

A group of elite 400-m distance runners carrying different alleles of the polymorphic angiotensinconverting enzyme (ACE) gene participated in an experiment that included aerobic exercise accompanied by measurement of the heart rate (HR) before, during, and after the exercise. Upon determination of the genotype for the ACE gene, the athletes were divided into three subgroups, carrying the II, ID, and DD alleles of the ACE gene. All athletes performed the same exercise: 25 min of running at an HR of 165–170 beats/min. The runners with the II genotype ran a significantly (p < 0.01) longer distance than the runners with the ID and DD genotypes. After the exercise, the HR recovery was the fastest in the runners with the II genotype.     

Choice of a spin singlet or triplet: electronic properties of Bis-Co(II), Bis-Ni(II), Bis-Cu(II) and Bis-Zn(II) oxygen doubly N-confused hexaphyrin (1.1.1.1.1.1)

Fused hexaphyrins have many physical and chemical properties and can coordinate transition metal ions. In this study, we investigated the geometric structure, charge decomposition analysis (CDA), spin density, frontier molecular orbital (FMO) compositions and absorption spectra of four oxygen doubly N-confused hexaphyrin (1.1.1.1.1.1) (ONCP) complexes with the metal ions Co(II), Ni(II), Cu(II) and Zn(II) (designated ONCP-d-Co, ONCP-d-Ni, ONCP-d-Cu and ONCP-d-Zn). Based on their energies, geometric structures, FMO characteristics and comparison to experiments, ONCP-d-Co and ONCP-d-Cu have the mix-states of the triplet state and broken-symmetry state (antiferromagnetic state) rather than the spin singlet of a closed shell as previously reported. Moreover, based on analyses of the spin density and spin population of the spin triplet ONCP-d-Co and ONCP-d-Cu complexes, the charge transfer in ONCP-d-Cu is greater than that in ONCP-d-Co because the spin density in ONCP-d-Cu is concentrated not only on the Cu ion but also on the ONCP ligand. Thus, the CDA value for ONCP-d-Cu is larger. Finally, through comparative analysis of the FMO compositions and absorption spectra, the complexes and ligand are shown to have very similar absorption spectra with characteristics that arise mainly from π?→?π* transitions both in the B-band and the Q-band, which is due to the FMO compositions being dominated by the highly delocalized conjugated system, rather than by the metal ions. The absorption maxima of the Q-band are ONCP-d-Co (1020 nm)?>?ONCP-d-Zn (1012 nm)?>?ONCP-d-Ni (997 nm)?>?ONCP-d-Cu (988 nm), which is inversely proportional to the energy gap in their FMOs.

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Graphical Abstract The present work investigates the geometric structure, charge decomposition analysis (CDA), spin density, frontier molecular orbital (FMO) compositions and absorption spectra of four oxygen doubly N-confused hexaphyrin (1.1.1.1.1.1) (ONCP) complexes with the metal ions Co(II), Ni(II), Cu(II) and Zn(II) (designated ONCP-d-Co, ONCP-d-Ni, ONCP-d-Cu and ONCP-d-Zn). Based on their energies, geometric structures, FMO characteristics and comparison to experiments, ONCP-d-Co and ONCP-d-Cu have the mix-state of the triplet state and broken-symmetry state (antiferromagnetic state) rather than the spin singlet of a close shell as were previously reported. Meanwhile, ONCP-d-Ni and ONCP-d-Zn show spin singlet structure. The calculated CDA shows the following order: ONCP-d-Cu (1.487)?>?ONCP-d-Ni (1.255)?>?ONCP-d-Co (1.211)?>?ONCP-d-Zn (1.201). Through comparisons of spin density and spin populations of ONCP-d-Co and ONCP-d-Cu, charge transfer between Cu and ligand ONCP is greater than that of Co and ONCP, which makes the CDA value of ONCP-d-Cu obviously larger than that of the other complexes