Profiling of selected indigenous rice (Oryza sativa L.) landraces of Rarh Bengal in relation to osmotic stress tolerance

A total of ten rare indigenous rice landraces of West Bengal were screened for germination potential and seedling growth under varying concentrations of sodium chloride (NaCl) and polyethylene glycol (PEG) solutions as osmotic stress inducing agents. Among the studied rice landraces Kelas and Bhut Moori showed highest degree of tolerance to induced osmotic stresses. Proline content of the studied lines was also determined. Genetic relationship among the studied rice landraces was assessed with 22 previously reported osmotic stress tolerance linked Simple Sequence Repeat (SSR) markers. The identified allelic variants in form of amplified products size (molecular weight) for each SSR marker were documented to find out allele mining set for the linked markers of the studied genotypes in relation to osmotic stress tolerance. A Microsatellite Panel was constructed for the different allelic forms (size of amplified products) of each used marker. Among 22 SSR markers, ten showed unique alleles in form of single specific amplified product for the studied four genotypes which can be used for varietal identification. Genetic relationship among the studied rice lines was determined and a dendrogram was constructed to reveal their genetic inter-relationship. Polymorphism Information Content (PIC) for each used marker was also calculated for the studied rice lines.     

Development of AFLP and STS markers linked to a waterlogging tolerance in Korean soybean landraces

Among the 400 soybean (Glycine max) landraces, we selected 3 tolerant (KAS150-9, KAS160-15, and KAS170-9) and 3 susceptible lines (KAS160-14, KAS160-20, and KAS201-6-1) by the survival percentage and injury scores. Susceptible lines showed decrease in chlorophyll content and increase in glucose and malondialdehyde (MDA) contents under waterlogging stress, while tolerant lines did not change significantly. For AFLP analysis, 8 EcoRI (+3) and 8 MseI (+3) primers used in 32 primer combinations generated a total of 2 566 bands with a mean of 80 bands per primer combination, of which 1 117 (43.5 %) were clearly polymorphic between the tolerant and susceptible lines. A genetic similarity coefficient, based on cluster analysis using an unweighted pair grouping method of average (UPGMA), was 0.79 for the tolerant group, while the susceptible landraces were genetically less related, with a genetic similarity coefficient of 0.17. The 10 reproducible polymorphic PCR products present in the 3 tolerant or susceptible lines were sequenced and converted into sequence tagged site (STS) markers. These STS primer sets were designated GmWT01-GmWT06 and GmWS01-GmWS04. Two STS primer sets, GmWT06 and GmWS02, generated a single monomorphic PCR product identical in size to the original AFLP fragments. For the broad application of these STS markers in marker-assisted selection (MAS) for soybean genotypes tolerant to waterlogging stress, two developed STS markers are being evaluated with putative waterlogging tolerant mutant lines induced by γ-radiation in soybean mutation breeding programs.     

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.     

Screening of selected West Bengal plants for antifungal activity

A systematic screening of 170 different West Bengal plants was carried out to find antifungal antibiotics, usingAspergillus niger andTrichophyton rubrum as test organisms. From them, four plant species, viz.Curcuma zedoaria, C. aromatica, C. amada, and aBrassica sp. have been found to contain active antibiotic principles with strong inhibitory effects against both test organisms.     

QTL: their place in engineering tolerance of rice to salinity

Secondary salinization and its relationship to irrigation are strong incentives to improve the tolerance of crops to salinity and to drought. Achieving this through the pyramiding of physiological traits (phenotypic selection without knowledge of genotype) is feasible. However, wide application of this approach is limited by the practicalities of assessing not only the parents, but also large numbers of individuals and families in segregating generations. Genotypic information is required in the form of markers for any quantitative trait loci involved (marker-assisted selection) or of direct knowledge of the genes. In the absence of adequate candidate genes for salt tolerance, a quantitative trait locus/marker-assisted selection approach has been used here. Putative markers for ion transport and selectivity, identified from analysis of amplified fragment length polymorphism, had been discovered within a custom-made mapping population of rice. Here it is reported that none of these markers showed any association with similar traits in a closely related population of recombinant inbred lines or in selections of a cultivar. Whilst markers will be of value in using élite lines from the mapping population in backcrossing, this has to be considered alongside the effort required to develop and map any given population. This result cautions against any expectation of a general applicability of markers for physiological traits. It is concluded that direct knowledge of the genes involved is needed. This cannot be achieved at present by positional cloning. The elucidation of candidate genes is required. Here the problem lies not in the analysis of gene expression but in devising protocols in which only those genes of interest are differentially affected by the experimental treatments.     

Evaluation of wheat landrace genotypes for salinity tolerance at vegetative stage by using morphological and molecular markers

Identification of new sources of salt tolerance is particularly important to develop crop varieties suitable for saline soils. We evaluated 129 Pakistani and 58 exotic wheat landraces/cultivars grown in Hoagland's hydroponic nutrient solution, under control (tap water equivalent to 10 mM salt) and salt stress (200 mM NaCl) conditions. Forty-four genotypes were also tested under 250 mM NaCl stress. High heritability and positive correlations suggested that number of tillers per plant, root length, root fresh and dry weights, and shoot fresh and dry weights are associated with salt tolerance and could be used as selection criteria. SSR markers revealed high genetic variation in the wheat genotypes. Twelve SSR markers (cfd 1, cfd 9, cfd 18, cfd 46, cfd 49, cfd 183, wmc 11, wmc 17, wmc 18, wmc 154, wmc 432, and wmc 503) were found to be associated with salt tolerance because they were amplified in tolerant genotypes only. Five markers, cfd 9, cfd 18, cfd 183, wmc 96, and wmc 405, were identified as most suitable to evaluate salt tolerance because they were associated with four or more salt tolerance traits studied. Cultivars Pasban 90, accessions 10790, 10828, 10823, and 4098805 from Pakistan and Sakha-92 from Egypt performed best at both stress levels.     

Field level evaluation of rice introgression lines for heat tolerance and validation of markers linked to spikelet fertility

Rice lines derived from wild species and mutants can serve as a good resource for favorable alleles for heat tolerance. In all, 48 stable lines including 17 KMR3/O. rufipogon introgression lines (KMR3 ILs), 15 Swarna/O. nivara ILs (Swarna ILs) along with their parents, Nagina 22 (N22) and its 4 EMS induced mutants and 7 varieties were evaluated for heat tolerance under irrigated conditions under field in two seasons, wet season 2012 using poly cover house method and dry season 2013 using late sown method. Spikelet fertility (SF), yield per plant (YP) and heat susceptibility index (HSI) for these two traits were considered as criteria to assess heat tolerance compared to control. Four KMR3 ILs and eight Swarna ILs were identified as heat tolerant based on SF and YP and their HSIs in both wet and dry seasons. S-65 and S-70 showed low SF and high YP consistently in response to heat in both seasons. We provide evidence that SF alone may not be the best criterion to assess heat tolerance and including YP is important as lines with low SF but high YP and vice versa were identified under heat stress. Out of 49 SSR markers linked to spikelet fertility, 18 were validated for five traits. RM229 in wet season and RM430 and RM210 in dry season were significantly associated with both SF and its HSI under heat stress. RM430 was also significantly associated with both YP and its HSI in dry season. Thirty two candidate genes were identified close to nine markers associated with traits under heat stress.     

Genetic analysis of salinity tolerance in rice (Oryza sativa L.)

Summary The genetics of salinity tolerance in rice was investigated by a nine-parent complete diallel including reciprocals. Test materials involved susceptible (IR28, IR29, and MI-48), moderately tolerant (IR4595-4-1-13, IR9884-54-3-1E-P1, and IR10206-29-2-1), and tolerant (Nona Bokra, Pokkali, and SR26B) parents. Twoweek-old seedlings were grown in a salinized (EC = 12 dS/m) culture solution for 19 days under controlled conditions in the IRRI phytotron. Typical characteristics of salinity tolerance in rice were found to be Na⁺ exclusion and an increased absorption of K⁺ to maintain a good Na-K balance in the shoot. Genetic component analysis (GCA) revealed that a low Na-K ratio is governed by both additive and dominance gene effects. The trait exhibited overdominance, and two groups of genes were detected. Environmental effects were large, and the heritability of the trait was low. Our findings suggest that when breeding for salt tolerance, selection must be done in a later generation and under controlled conditions in order to minimize environmental effects. Modified bulk and single-seed descent would be the suitable breeding methods. Combining ability analysis revealed that both GCA and specific combining ability (SCA) effects were important in the genetics of salt tolerance. Moderately tolerant parents — e.g., IR4595-4-1-13 and IR9884-54-3-1E-P1 — were the best general combiners. Most of the best combinations had susceptible parents crossed either to moderate or tolerant parents. The presence of reciprocal effects among crosses necessitates the use of susceptible parents as males in hybridization programs. Large heterotic effects suggest the potential of hybrid rice for salt-affected lands.     

Physiological and molecular analysis of aluminum tolerance in selected Kenyan maize lines

Aims

Aluminum (Al) toxicity is an important limitation to maize production in many tropical and sub-tropical acid soil areas. The aim of this study was to survey the variation in Al tolerance in a panel of maize lines adapted for Kenya and look for novel sources of Al tolerance.

Methods

112 Kenyan maize accessions were phenotyped for Al tolerance in solution culture. Several Al tolerance-related parameters including relative net root growth (RNRG), root apex Al accumulation, Al-activated root organic acid exudation, and expression of the maize Al tolerance gene, ZmMATE1, were used to classify Kenyan maize accessions.

Results

Based on RNRG, 42 %, 28 %, and 30 % of the lines were classified as highly tolerant, moderately tolerant and sensitive, respectively. Tolerant accessions accumulated less Al in their root apices compared to sensitive lines. The Kenyan maize line, CON 5, and the Brazilian standard for tolerance, Cateto, exhibited the greatest Al tolerance based on RNRG, but CON 5 had only about 50 % of ZmMATE1 gene expression relative to Cateto. CON 5 also had low root apex Al content and high citrate exudation, suggesting that it may employ a citrate transporter other than ZmMATE1.

Conclusions

We identified a very Al tolerant Kenyan maize line whose Al tolerance may be based in part on a novel tolerance gene. The maize lines identified in this study are useful germplasm for the development of varieties suitable for agriculture on acid soils in Kenya.

     

Characterization of tissue tolerance to iron by molecular markers in different lines of rice

Ferrous iron (Fe2+) toxicity is a major disorder in rice prod uction on acid, flooded soils. Rice ( Oryza sativa L.) genotypes differ widely in tolerance to Fe2+ toxicity, which makes it possible to bre ed more tolerant rice varieties. Tissue tolerance to higher iron concentrations in plants has been considered to be important to Fe2+ tolerance in ri ce. Segregation for leaf bronzing and growth reduction due to Fe2+ to xicity was observed in a doubled haploid (DH) population with 135 lines derived from a Fe2+ tolerant japonica variety, Azucena, and a sensitive indic a variety, IR64 in a solution culture with Fe2+ stress condition at a Fe2+concentration of 250 mg L-1 at pH 4.5. To better understand the mechanism of tissue tolerance, Leaf Bronzing Index (LBI), total iron concentration in shoot tissue and the enzymes of ascorbate peroxidase (AP), dehydroascorbate reductase (DR) and glutathione reductase (GR), and concentrations of ascorbate (AS) and dehydroascorbate (DHA), which are involved in the ascorbate-specific H2O2-scavenging system, were determined for the population under Fe2+ stress. A non-normal distribution of LBI was found. About 38 lines showed no bronzing, while the lines with non-zero LBI values ranged from 0.05 to 0.85 and showed a normal distribution. The other parameters measured showed normal distribution. The total iron concentrations in the 38 tolerant lines ranged from 1.76 mg Fe g-1 to 4.12 mg Fe g-1 and was in a similar range as in the non-tolerant genotype (2.04 – 4.55 mg Fe g-1). No significant differences in the activities of the enzymes were found between the parents under normal culture, but remarkably higher Fe2+ induced enzyme activities were observed in the tolerant parent. AS was similar between the parents under both normal and Fe2+ stress, but its concentration was sharply decreased under Fe2+ stress. DHA was much lower in the tolerant parent than in the sensitive parent under Fe2+ stress. Single locus analysis and interval mapping analysis based on 175 molecular markers revealed that the interval flanked by RG345 and RZ19 on chromosome one was an important location of gene(s) for Fe2+ tolerance. The ascorbate-specific system for scavenging Fe2+-mediated oxygen free radicals may be an important mechanism for tissue Fe2+ tolerance. A gene locus with relative small effect on root ability to exclude Fe2+ was also detected.     

Screening tolerance to phosphorus starvation and haplotype analysis using phosphorus uptake 1 (Pup1) QTL linked markers in rice genotypes

Phosphorus (P) deficiency tolerance is a pivotal trait for plant growth and development. Most of the commercial modern cultivars lack this trait and reported it as a very serious problem limiting crop productivity. This trait is advantageous if present in modern high yielding varieties as it increases the yield under the phosphorus-deficient soil conditions. With the importance of phosphorus deficiency tolerance, the present investigation was carried out with an objective to screen for tolerance to phosphorus deficiency using solution culture and phosphorus uptake 1 (Pup1) locus linked markers in 30 diverse rice genotypes. A wide range of varied responses to P deficiency in rice genotypes for all the traits were observed. Root length and enzyme activity showed increased mean performance under the − P condition when compared to + P condition. Medium to high heritability estimates were obtained for most of the traits. Correlation analysis showed that the traits: root P content, fresh shoot weight, dry shoot weight, and shoot length showed highly significant correlations with each other under − P conditions. Based on the hydroponics and molecular screening, three genotypes viz., ADT (R) 48, Improved Pusa Basmati 1 and UPLRI 5 were classified as tolerant for its response to P deficiency as they possessed significant increase in desirable root and shoot traits, increased acid phosphatase enzyme and these genotypes also possessed the Pup1 allele for all the five markers. The selected genotypes may be useful for the exploration of novel genes conferring phosphorus deficiency tolerance and used as donor parents in the breeding programs. Absence of this allele in the rice genotypes viz., drought tolerant (Anna (R) 4) and submergence tolerant (CR 1009 Sub 1) may warrant the development of multiple abiotic stress tolerance cultivars for upland and submergence cropping systems in future rice breeding program.Electronic supplementary materialThe online version of this article (10.1007/s12298-020-00903-1) contains supplementary material, which is available to authorized users.     

Identification of genetic factors for alachlor tolerance in maize by molecular markers analysis

Genetic factors controlling tolerance to the herbicide Alachlor in maize were localised by means of two different strategies. In the first approach, backcross (BC) plants, derived from pollen which had been subjected to selective pressure for resistance to the herbicide, were analysed for segregation distortion at 47 RFLP loci and compared to BC plants obtained from non-selected pollen. Preferential transmission of five chromosomal regions where putative QTLs (Quantitative Trait Loci) are localised was revealed in the BC plants from selected pollen. A second approach was based on a classical linkage analysis for segregation of the same set of RFLPs and factors controlling the trait, in a BC population of 210 individuals, by means of regression analysis. This study detected seven significant loci in four genomic regions. Overall, two loci revealed both segregation distortion and association with the expression of the trait, indicating linkage to genes expressed in both gametophytic and sporophytic phase. Three chromosomal regions appeared to carry factors involved in plant tolerance to Alachlor which are not expressed in pollen. Conversely, three loci were linked to factors selectable in pollen, but did not reveal significant association with tolerance in the plant in the segregating populations.     

Diversity analysis of antagonists from rice-associated bacteria and their application in biocontrol of rice diseases

Aims:  To understand the diversity, taxonomy and antagonistic potential of rice-associated bacteria, and to discover new bacteria for biocontrol of rice foliar pathogens.
Methods and Results:  Amplified ribosomal DNA restriction analysis (ARDRA), BOX-PCR and 16S rRNA gene sequence analysis were used to identify the diversity of 203 rice-associated antagonistic bacteria. Eleven potential biocontrol bacteria were used to test their biological control of rice blast in a natural field experiment. Eleven different genera were encountered in five divisions, including Bacilli , Alphaproteobacteria , Betaproteobacteria , Gammaproteobacteria and Deinococci . The most prominent genus in all microenvironments was Bacillus (68·5%). The efficacy of rice leaf blast biocontrol was 64·35% for strain 1Pe2, 57·86% for strain 2R37 and 56·44% for strain 1Re14.
Conclusions:  Biocontrol data from the field experiments demonstrated no positive correlation between antagonism, physiological characteristics and biocontrol efficacy. There was significant diversity among the rice-associated bacteria isolated from different microenvironments. The most prominent genus of all microenvironments was Bacillus . Brevibacillus brevis strain 1Pe2 and Deinococcus aquaticus strain 1Re14 have good potential for field application and commercial use.
Significance and Impact of the Study:  This is the first attempt to study the diversity and identification of rice-associated antagonistic bacteria from different microenvironments, and endophytic bacteria Deinococcus aquaticus strain 1Re14, Acidovorax sp. isolate 3Re21 and Brevibacillus brevis strain 1Pe2 are first reported as rice-associated bacteria.     

Relative salinity tolerance of rice cultivars native to North East India: a physiological,biochemical and molecular perspective

Salinity is the second most prevalent abiotic stress faced by plants, and rice is not an exception. Through this study, it has been tried upon, to study the relative salinity tolerance of eight local varieties of North East India. Preliminary screening was based on their dose- and time-dependent physiological responses to salinity stress. Among the cultivars, Tampha was found to be relatively more tolerant, whereas MSE9 the most sensitive. To further ascertain their tolerance capacity, MDA and H₂O₂ content was determined, which also confirmed the tolerance level of the two cultivars. Histochemical assays for root plasma membrane integrity and leaf and root H₂O₂ and O₂ ^? content also showed more damage in Tampha in comparison to MSE9. Finally, gene expression analysis for Na⁺/K⁺ co-transporters, OsHKT2;1, OsHKT2;3 and OsHKT2;4, was performed to observe how the expression level of these transporters varies with the tolerance capacity of these two cultivars in leaves and roots under different time frames. The study reveals Tampha to be the most tolerant and MSE9 the most sensitive when compared to the other six screened cultivars for salinity stress.     

Identification of molecular markers for aluminium tolerance in diploid oat through comparative mapping and QTL analysis

The degree of aluminium tolerance varies widely across cereal species, with oats (Avena spp.) being among the most tolerant. The objective of this study was to identify molecular markers linked to aluminium tolerance in the diploid oat A. strigosa. Restriction fragment length polymorphism markers were tested in regions where comparative mapping indicated the potential for orthologous quantitative trait loci (QTL) for aluminium tolerance in other grass species. Amplified fragment length polymorphism (AFLP) and sequence-characterized amplified region (SCAR) markers were used to provide additional coverage of the genome. Four QTL were identified. The largest QTL explained 39% of the variation and is possibly orthologous to the major gene found in the Triticeae as well as Alm1 in maize and a minor gene in rice. A second QTL may be orthologous to the Alm2 gene in maize. Two other QTL were associated with anonymous markers. Together, these QTL accounted for 55% of the variation. A SCAR marker linked to the major QTL identified in this study could be used to introgress the aluminium tolerance trait from A. strigosa into cultivated oat germplasm. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users. S. Kibite: In Memoriam     

Diversity of propanil-degrading bacteria isolated from rice rhizosphere and their potential for plant growth promotion

The herbicide propanil has long been used in rice production in southern Brazil. Bacteria isolated from contaminated soils in Massaranduba, Santa Catarina, Brazil, were found to be able to grow in the presence of propanil, using this compound as a carbon source. Thirty strains were identified as Pseudomonas (86.7%), Serratia (10.0%), and Acinetobacter (3.3%), based on phylogenetic analysis of 16S rDNA. Little genetic diversity was found within species, more than 95% homology, suggesting that there is selective pressure to metabolize propanil in the microbial community. Two strains of Pseudomonas (AF7 and AF1) were selected in bioreactor containing chemotactic growth medium, with the highest degradation activity of propanil exhibited by strain AF7, followed by AF1 (60 and 40%, respectively). These strains when encapsulated in alginate exhibited a high survival rate and were able to colonize the rice root surfaces. Inoculation with Pseudomonas strains AF7 and AF1 significantly improved the plant height of rice. Most of the Pseudomonas strains produced indoleacetic acid, soluble mineral phosphate, and fixed nitrogen. These bacterial strains could potentially be used for the bioremediation of propanil-contaminated soils and the promotion of plant growth.     

Comparative analysis of microsatellite DNA polymorphism in landraces and cultivars of rice

Genetic polymorphisms of ten microsatellite DNA loci were examined among 238 accessions of landraces and cultivars that represent a significant portion of the distribution range for both indica and japonica groups of cultivated rice. In all, 93 alleles were identified with these ten markers. The number of alleles varied from a low of 3 or 4 at each of four loci, to an intermediate value of 9–14 at five loci, and to an extra-ordinarily high 25 at one locus. The numbers of alleles per locus are much larger than those detected using other types of markers. The number of alleles detected at a locus is significantly correlated with the number of simple sequence repeats in the targeted microsatellite DNA. Indica rice has about 14% more alleles than japonica rice, and such allele number differences are more pronounced in landraces than in cultivars. The indica-japonica differentiation component accounted for about 10% of the diversity in the total sample, and twice as much differentiation was detected in cultivars as in landraces. About two-thirds as many alleles were observed in cultivars as in landraces; another two-thirds of the alleles in the cultivar group were found in modern elite cultivars or parents of hybrid rice. The majority of the simple sequence repeat (SSR) alleles that were present in high or intermediate frequencies in landraces ultimately survived into modern elite cultivars and hybrids. The greater resolving power and the efficient production of massive amounts of SSR data may be particularly useful for germplasm assessment and evolutionary studies of crop plants.