Relative Shoot Length Research Articles

Screening and analysis of candidate genes conferring alkalinity tolerance in rice (Oryza sativa L.) at the bud burst stage based on QTL-seq and RNA-seq

BackgroundSoil salinization is one of the key factors restricting the production of cropland. Once rice is subjected to alkali stress at the bud burst stage, the yield will suffer irreparable serious loss. Compared with salt tolerance, studies on QTL mapping and candidate gene analysis of rice alkali tolerance are limited. ResultsIn this study, we used the F2:3 population derived from the alkali-tolerant cultivar LD21 and the alkali-sensitive cultivar WL138 to construct an alkali-tolerant DNA mixing pool, and the BSA (Bulked Segregation Analysis) method was used for re-sequencing. The main QTL qRSLB9 controlling the relative shoot length of rice under alkali stress was mapped by QTL-seq. The candidate interval was narrowed to 346.5 kb by regional linkage mapping, which containing 6 DEGs screened through transcriptome sequencing. The qRT-PCR and candidate gene sequencing showed that LOC_Os09g24260 was most likely to control relative shoot length (RSL) in rice as a major gene who encodes the WD domain, G-beta repeat domain-containing protein. ConclusionsBased on these results, LOC_Os09g24260 was the candidate gene of qRSLB9 conferring alkalinity tolerance to rice at the bud burst stage. Our study provides valuable genetic information and materials for breeding new rice varieties with alkalinity tolerance.How to cite: Wang J, Bian J, Liu L, et al. Screening and analysis of candidate genes conferring alkalinity tolerance in rice (Oryza sativa L.) at the bud burst stage based on QTL-seq and RNA-seq. Electron J Biotechnol 2024;71. https://doi.org/10.1016/j.ejbt.2024.07.002.

Enhancing stress resilience in rice (Oryza sativa L.) through profiling early-stage morpho-physiological and molecular responses to multiple abiotic stress tolerance.

Under changing climatic conditions, crop plants are more adversely affected by a combination of various abiotic stresses than by a single abiotic stress. Therefore, it is essential to identify potential donors to multiple abiotic stresses for developing climate-resilient crop varieties. Hence, the present study was undertaken with 41 germplasm accessions comprising native landraces of Tamil Nadu, Prerelease lines and cultivars were screened independently for drought, salinity, and submergence at the seedling stage during Kharif and Rabi 2022-2023. Stress was imposed separately for these three abiotic stresses on 21-day-old seedlings and was maintained for 10 days. The studied genotypes showed a significant reduction in plant biomass (PB), Relative Growth Index (RGI), relative water content (RWC), leaf photosynthesis, chlorophyll fluorescence, and Chlorophyll Concentration Index (CCI) under drought followed by salinity and submergence. Stress-tolerant indices for drought, salinity, and submergence revealed significant variation for plant biomass. Furthermore, a set of 30 SSR markers linked to drought, salinity, and submergence QTLs has been used to characterize 41 rice germplasm accessions. Our analysis suggests a significantly high polymorphism, with 28 polymorphic markers having a 93.40% in 76 loci. The mean values of polymorphic information content (PIC), heterozygosity index (HI), marker index (MI), and resolving power (RP) were 0.369, 0.433, 1.140, and 2.877, respectively. Jaccard clustering grouped all the genotypes into two major and six subclusters. According to STRUCTURE analysis, all genotypes were grouped into two major clusters, which are concurrent with a very broad genetic base (K = 2). Statistically significant marker-trait associations for biomass were observed for five polymorphic markers, viz., RM211, RM212 (drought), RM10694 (salinity), RM219, and RM21 (submergence). Similarly, significant markers for relative shoot length were observed for RM551 (drought), RM10694 (salinity), and ART5 (submergence). Notably, the genotypes Mattaikar, Varigarudan samba, Arupatham samba, and APD19002 were identified as potential donors for multiple abiotic stress tolerance. Thus, identifying the genetic potential of germplasm could be useful for enhancing stress resilience in rice.

Uncovering Novel QTLs and Candidate Genes for Salt Tolerance at the Bud Burst Stage in Rice through Genome-Wide Association Study.

Salt stress is one of the most important factors limiting rice growth and yield increase. Salt tolerance of rice at the bud burst (STB) stage determines whether germinated seeds can grow normally under salt stress, which is very important for direct seeding. However, reports on quantitative trait loci (QTLs) and candidate genes for STB in rice are very limited. In this study, a natural population of 130 indica and 81 japonica rice accessions was used to identify STB-related QTLs and candidate genes using a genome-wide association study (GWAS). Nine QTLs, including five for relative shoot length (RSL), two for relative root length (RRL), and two for relative root number (RRN), were identified. Five of these STB-related QTLs are located at the same site as the characterized salt tolerance genes, such as OsMDH1, OsSRFP1, and OsCDPK7. However, an important QTL related to RSL, qRSL1-2, has not been previously identified and was detected on chromosome 1. The candidate region for qRSL1-2 was identified by linkage disequilibrium analysis, 18 genes were found to have altered expression levels under salt stress through the RNA-seq database, and 10 of them were found to be highly expressed in the shoot. It was also found that, eight candidate genes (LOC_Os01g62980, LOC_Os01g63190, LOC_Os01g63230, LOC_Os01g63280, LOC_Os01g63400, LOC_Os01g63460, and LOC_Os01g63580) for qRSL1-2 carry different haplotypes between indica and japonica rice, which exactly corresponds to the significant difference in RSL values between indica and japonica rice in this study. Most of the accessions with elite haplotypes were indica rice, which had higher RSL values. These genes with indica-japonica specific haplotypes were identified as candidate genes. Rice accessions with elite haplotypes could be used as important resources for direct seeding. This study also provides new insights into the genetic mechanism of STB.

Joint QTL Mapping and Transcriptome Sequencing Analysis Reveal Candidate Genes for Salinity Tolerance in Oryza sativa L. ssp. Japonica Seedlings.

Salinity stress is one of the major abiotic stresses affecting crop growth and production. Rice is an important food crop in the world, but also a salt-sensitive crop, and the rice seedling stage is the most sensitive to salt stress, which directly affects the final yield formation. In this study, two RIL populations derived from the crosses of CD (salt-sensitive)/WD (salt-tolerant) and KY131 (salt-sensitive)/XBJZ (salt-tolerant) were used as experimental materials, and the score of salinity toxicity (SST), the relative shoot length (RSL), the relative shoot fresh weight (RSFW), and the relative shoot dry weight (RSDW) were used for evaluating the degree of tolerance under salt stress in different lines. The genetic linkage map containing 978 and 527 bin markers were constructed in two RIL populations. A total of 14 QTLs were detected on chromosomes 1, 2, 3, 4, 7, 9, 10, 11, and 12. Among them, qSST12-1, qSST12-2, and qRSL12 were co-localized in a 140-kb overlap interval on chromosome 12, which containing 16 candidate genes. Furthermore, transcriptome sequencing and qRT-PCR were analyzed in CD and WD under normal and 120 mM NaCl stress. LOC_Os12g29330, LOC_Os12g29350, LOC_Os12g29390, and LOC_Os12g29400 were significantly induced by salt stress in both CD and WD. Sequence analysis showed that LOC_Os12g29400 in the salt-sensitive parents CD and KY131 was consistent with the reference sequence (Nipponbare), whereas the salt-tolerant parents WD and XBJZ differed significantly from the reference sequence both in the promoter and exon regions. The salt-tolerant phenotype was identified by using two T3 homozygous mutant plants of LOC_Os12g29400; the results showed that the score of salinity toxicity (SST) of the mutant plants (CR-3 and CR-5) was significantly lower than that of the wild type, and the seedling survival rate (SSR) was significantly higher than that of the wild type, which indicated that LOC_Os12g29400 could negatively regulate the salinity tolerance of rice at the seedling stage. The results lay a foundation for the analysis of the molecular mechanism of rice salinity tolerance and the cultivation of new rice varieties.

Screening of Country Bean (Lablab Purpureus L.) Genotypes for Salinity Tolerance

Thirty-five country bean (Lablab purpureus L.) genotypes collected from coastal belts of Bangladesh were screened for tolerance to a high level of salinity (12 ds m-1 NaCl) in Hogland nutrient solution in a hydroponic system at vegetative growth stage. The experiment was conducted in a complete randomized design with three replications at Genetics and Plant Breeding lab, BSMRAU during January-February, 2016. The genotypes were varied in biochemical properties (proline, carbohydrates, chlorophyll contents etc.), dry root: shoot ratio, relative shoot dry weight and salt susceptibility index (SSI). Wide variation among the genotypes was noticed for root and shoot ratio (p<0.05). Relative shoot length varied from 29.87- 126.04 with an average of 79.29 whereas relative root length showed wide variation with a range of 20.00-300.00. Relative root dry weight (RRDW) varied from 22.06-211.43 with a mean of 79.40 and relative shoot dry weight (RSDW) ranged from 26.57-192.66 with an average of 69.29. Relative root : shoot ratio showed a range of 0.59 to 2.51. On the basis of relative performance of root-shoot dry matter, dry leaves weight, root-shoot ratio, six genotypes were found highly tolerant, seven were moderately tolerant, sixteen were moderately susceptible and six were highly susceptible to salinity stress. Based on visual observation of plants, relative shoot dry weight (RSDW), proline content, total sugar and soil plant analysis development (SPAD) value the genotypes CB031, CB035, CB003, CB023, CB026, CB028, CB013, CB030, CB014, CB024, CB019, CB020 and CB002 were selected as tolerant for further evaluation and use in breeding work. Ann. Bangladesh Agric. (2022) 26 (2) : 19-31

Genome-Wide Association Study Reveals a Genetic Mechanism of Salt Tolerance Germinability in Rice (Oryza sativa L.).

Salt stress is one of the factors that limits rice production, and an important task for researchers is to cultivate rice with strong salt tolerance. In this study, 211 rice accessions were used to determine salt tolerance germinability (STG) indices and conduct a genome-wide association study (GWAS) using 36,727 SNPs. The relative germination energy (RGE), relative germination index (RGI), relative vigor index (RVI), relative mean germination time (RMGT), relative shoot length (RSL), and relative root length (RRL) were used to determine the STG indices in rice. A total of 43 QTLs, including 15 for the RGE, 6 for the RGI, 7 for the RVI, 3 for the RMGT, 1 for the RSL, and 11 for the RRL, were identified on nine chromosome regions under 60 and 100 mM NaCl conditions. For these STG-related QTLs, 18 QTLs were co-localized with previous studies, and some characterized salt-tolerance genes, such as OsCOIN, OsHsp17.0, and OsDREB2A, are located in these QTL candidates. Among the 25 novel QTLs, qRGE60-1-2 co-localized with qRGI60-1-1 on chromosome 1, and qRGE60-3-1 and qRVI60-3-1 co-localized on chromosome 3. According to the RNA-seq database, 16 genes, including nine for qRGE60-1-2 (qRGI60-1-1) and seven for qRGE60-3-1 (qRVI60-3-1), were found to show significant differences in their expression levels between the control and salt treatments. Furthermore, the expression patterns of these differentially expressed genes were analyzed, and nine genes (five for qRGE60-1-2 and four for qRGE60-3-1) were highly expressed in embryos at the germination stage. Haplotype analysis of these nine genes showed that the rice varieties with elite haplotypes in the LOC_Os03g13560, LOC_Os03g13840, and LOC_Os03g14180 genes had high STG. GWAS validated the known genes underlying salt tolerance and identified novel loci that could enrich the current gene pool related to salt tolerance. The resources with high STG and significant loci identified in this study are potentially useful in breeding for salt tolerance.

Genome-Wide Association Study of Salt Tolerance at the Seed Germination Stage in Flax (Linum usitatissimum L.).

Soil salinization seriously affects the growth and distribution of flax. However, there is little information about the salt tolerance of flax. In this study, the salt tolerance of 200 diverse flax accessions during the germination stage was evaluated, and then the Genome-wide Association Study (GWAS) was carried out based on the relative germination rate (RGR), relative shoot length (RSL) and relative root length (RRL), whereby quantitative trait loci (QTLs) related to salt tolerance were identified. The results showed that oil flax had a better salt tolerance than fiber flax. A total of 902 single nucleotide polymorphisms (SNPs) were identified on 15 chromosomes. These SNPs were integrated into 64 QTLs, explaining 14.48 to 29.38% (R2) of the phenotypic variation. In addition, 268 candidate genes were screened by combining previous transcriptome data and homologous gene annotation. Among them, Lus10033213 is a single-point SNP repeat mapping gene, which encodes a Glutathione S-transferase (GST). This study is the first to use GWAS to excavate genes related to salt tolerance during the germination stage of flax. The results of this study provide important information for studying the genetic mechanism of salt tolerance of flax, and also provide the possibility to improve the salt tolerance of flax.

Bio control of water hyacinth with Cercospora piaropi and Myrothecium roridum corn oil formulations for enhanced water resources management and conservation

Water hyacinth hinders extraction and supply of clean water by clogging intake systems. Despite control efforts, it has remained resurgent and difficult to manage under current methods. Efficacious control for the weed is therefore necessary. This study’s goal was determination of effect of corn oil spore formulations of Cercospora piaropi Tharp and Myrothecium roridum Tode Fries on; disease intensity, relative shoot length and relative biomass of water hyacinth. It was conducted in Maseno University and in a greenhouse at Kibos in Kisumu situated at latitude 00 37’ S and longitude 370 20’ E. The conditions were 25 to 300 C and 22 to 270 C temperature averages during the day and night respectively and 60 to 69% relative humidity. Isolations of C. piaropi and M. roridium were made, grown on PDA, harvested and formulated in corn oil at 1x105, 1x106, 1x107, 1x108 and 1x109 spores/ml. Healthy plants were misted with the corn oil formulations and placed in 90 cm diameter and 1.5 cm depth plastic basins filled with 20 liters of water that had been kept in a container for 24 hours for chlorine to be released. The experimental design was completely randomized design with three replications. Disease intensity, relative shoot length and relative biomass were determined biweekly for 6 weeks. Analysis of variance on the means was done using SAS Institute, Inc.1999 computer software and LSD (p?0.05) used for mean separation. Disease intensity, AUDPS, relative shoot length and relative biomass scores for both pathogens showed a significant (p ?. 05) increase as the concentration of spores in the formulations increased. Cercospora piaropi and M. roridum in corn oil formulation at 1x108 and 1x109 spores/ml were found effective for lowering water hyacinth biomass and shoot growth respectively and with potential for use in open waters for water hyacinth control.

Effect of Cercospora piaropi Tharp and Myrothecium roridum Tode Fries Formulated as Corn Oil Emulsion on Water Hyacinth Shoot Growth under Greenhouse Conditions

A study was done to find out the comparative effect of Cercospora piaropi Tharp and Myrothecium roridum Tode Fries formulated as corn oil emulsion on water hyacinth shoot growth and biomass under greenhouse conditions. The study site was located in Kibos at latitude 0037’S and longitude 37020’E with average temperature of 25 to 300C and 22 to 270C during the day and night respectively, and 60 to 69% relative humidity. Healthy water hyacinth plants were inoculated with the pathogens formulated in corn oil at 1x109, 1x108, 1x107, 1x106 and 1x105spores/ml. The control plants were not inoculated. The experiment was set up in completely randomized design (CRD) with each treatment replicated three times. At weeks 2, 4, and 6 after inoculation, the average shoot length and biomass for the treated basins were separately compared to the average shoot length and biomass of the control plants. Increase in spore density for both pathogens significantly increased relative shoot length and relative biomass. Relative shoot length was 55.07 and 51.93 for C. piaropi and M. roridum respectively at 1x109 spores/ml while relative biomass was 73.53 for C. piaropi and 37.60 at 1x109 spores/ml. Inoculation suppressed shoot elongation and biomass with 1x109 spores/ml being most effective. Cercospora piaropi formulated in corn oil lowered shoot length and biomass of water hyacinth more than M. roridum did.

Effects of Some Heavy Metals on Germination and Seedling Growth of Sorghum

Heavy metal contamination in soils can adversely affect seed germination and seedling growth of most plants. This research was conducted to determine the effects of different doses (0, 100, 200, 400 and 800 mg L-1) of Ni (nickel), Cd (cadmium), Pb (lead), Cr (chromium) and Hg (mercury) on seed germination and seedling growth of sorghum. The study was conducted in laboratory conditions at the Agricultural Faculty of Akdeniz University in 2017. Sorghum cv. N48×Early Sumac was used as the plant material. In the research, germination rate (GR), relative germination index (RGI), mean germination time (MGT), relative vigor index (RVI), relative root length (RRL), relative shoot length (RSL), root fresh weight (RFW) and shoot fresh weight (SFW) were measured during germination and seedling growth to determine the effects of heavy metals. The results showed that both germination and seedling growth properties were adversely affected by heavy metals. In addition, while the negative effect of cadmium on germination properties was limited, it had serious negative effects on seedling characteristics of sorghum. Increasing heavy metal doses adversely affected all investigated properties. In conclusion, all heavy metals including Hg and Cd had negative effect on germination and seedling growth of sorghum in the study.

Molecular characterization of QTL-allele system for drought tolerance at seedling stage and optimal genotype design using multi-locus multi-allele genome-wide association analysis in a half-sib population of soybean (Glycine max (L.) Merr.)

AbstractCharacterizing the whole genetic architecture of drought tolerance (DT) is a persistent challenge for the breeders. Here we developed a half-sib population comprising of 404 lines of two recombinant inbred line (RIL) populations with M8206 as the joint parent (M8206 × TongShan and ZhengYang × M8206) and tested for its DT under sand culture. The population was sequenced using restriction-site-associated DNA sequencing filtered with minor allele frequency ≥0.01; 55,936 single nucleotide polymorphisms (SNPs) were obtained and assembled into 6137 SNPLDBs (SNP linkage disequilibrium blocks). The restricted two-stage multi-locus genome-wide association analysis characterized with error and false-positive control identified 40 QTLs with 93 alleles on an average of 34.75% of the phenotypic variance (PV) collectively for relative root length (RRL) and relative shoot length (RSL) that served as potential DT indicators. Among these, eight loci corresponded to previously reported QTLs, whereas 32 loci were therefore novel. The identified QTLs with their corresponding alleles for RRL and RSL were organized into QTL-allele matrices, depicting the comprehensive DT genetic architecture of the three parents/half-sib population. From the matrices, we predicted the possible best/optimal genotype with weighted average value (WAV) 1.553 over two indicators, while for the top 10 single crosses among RILs with 95th percentile WAV was 1.218–1.257, transgressive over the parents (0.693–0.794) yet much less than 1.553. From the detected QTL-allele system, 65 potential candidate genes collectively for both indicators explaining on an average of 24.41% PV were annotated and χ2-tested as a DT candidate gene system involving nine biological processes.

Genome-Wide Association Study and Identification of Candidate Genes for Nitrogen Use Efficiency in Barley (Hordeum vulgare L.).

Nitrogen (N) fertilizer is largely responsible for barley grain yield potential and quality, yet excessive application leads to environmental pollution and high production costs. Therefore, efficient use of N is fundamental for sustainable agriculture. In the present study, we investigated the performance of 282 barley accessions through hydroponic screening using optimal and low NH4NO3 treatments. Low-N treatment led to an average shoot dry weight reduction of 50%, but there were significant genotypic differences among the accessions. Approximately 20% of the genotypes showed high (>75%) relative shoot dry weight under low-N treatment and were classified as low-N tolerant, whereas 20% were low-N sensitive (≤55%). Low-N tolerant accessions exhibited well-developed root systems with an average increase of 60% in relative root dry weight to facilitate more N absorption. A genome-wide association study (GWAS) identified 66 significant marker trait associations (MTAs) conferring high nitrogen use efficiency, four of which were stable across experiments. These four MTAs were located on chromosomes 1H(1), 3H(1), and 7H(2) and were associated with relative shoot length, relative shoot and root dry weight. Genes corresponding to the significant MTAs were retrieved as candidate genes, including members of the asparagine synthetase gene family, several transcription factor families, protein kinases, and nitrate transporters. Most importantly, the high-affinity nitrate transporter 2.7 (HvNRT2.7) was identified as a promising candidate on 7H for root and shoot dry weight. The identified candidate genes provide new insights into our understanding of the molecular mechanisms driving nitrogen use efficiency in barley and represent potential targets for genetic improvement.

Identification of a Major QTL and Candidate Gene Analysis of Salt Tolerance at the Bud Burst Stage in Rice (Oryza sativa L.) Using QTL-Seq and RNA-Seq

BackgroundSalt stress is one of the main abiotic stresses that limits rice production worldwide. Rice salt tolerance at the bud burst stage directly affects the seedling survival rate and the final yield in the direct seeding cultivation model. However, the reports on quantitative trait locus (QTL) mapping and map-based cloning for salt tolerance at the bud burst stage are limited.ResultsHere, an F2:3 population derived from a cross between IR36 (salt-sensitive) and Weiguo (salt-tolerant) was used to identify salt-tolerant QTL interval at the bud burst stage using a whole-genome sequencing-based QTL-seq containing 40 extreme salt-tolerant and 40 extreme salt-sensitive individuals. A major QTL, qRSL7, related to relative shoot length (RSL) was detected on chromosome 7 using ΔSNP index algorithms and Euclidean Distance (ED) algorithms. According to single nucleotide polymorphisms (SNPs) between the parents, 25 Kompetitive allele-specific PCR (KASP) markers were developed near qRSL7, and regional QTL mapping was performed using 199 individuals from the F2:3 population. We then confirmed and narrowed down qRSL7 to a 222 kb genome interval. Additionally, RNA sequencing (RNA-seq) was performed for IR36 and Weiguo at 36 h after salt stress and control condition at the bud burst stage, and 5 differentially expressed genes (DEGs) were detected in the candidate region. The qRT-PCR results showed the same expression patterns as the RNA-seq data. Furthermore, sequence analysis revealed a 1 bp Indel difference in Os07g0569700 (OsSAP16) between IR36 and Weiguo. OsSAP16 encodes a stress-associated protein whose expression is increased under drought stress.ConclusionThese results indicate that OsSAP16 was the candidate gene of qRSL7. The results is useful for gene cloning of qRSL7 and for improving the salt tolerance of rice varieties by marker assisted selection (MAS).

Identification of differentially expressed genes under heat stress conditions in rice (Oryza sativa L.).

Rice production in recent years is highly affected by rapidly increasing temperatures in the tropical and sub-tropical countries, which threatens the sustainable production in near future. Hence, understanding the heat tolerance mechanism and evolving tolerant varieties is an immense need in the staple crop rice. An experiment has been conducted to identify differentially expressed genes in rice under heat stress conditions by employing a diverse set of 32 rice genotypes that includes reported heat tolerant genotypes Nagina 22 (N22) and Dular. Screening of the genotypes at field conditions during Summer-2018 for reproductive stage heat tolerance (wherein the mean minimum (29.8°C) and maximum (38.4°C) temperatures surpassed optimum temperatures (25°C night/30°Cday) required for rice flowering and grain filling stages) and lab conditions employing thermal induction response (TIR) technique to know the genotype's acquired thermal tolerance revealed that the genotype FR13A (indica landrace) showed highest overall performance for multitude of traits viz., 95.29% of spikelet fertility (SF-%) at field level and 100% seedling survival percentage (SSP) at sub-lethal temperatures under laboratory conditions. The relative performance (under TIR) across all the three traits viz., relative shoot length (RSL) (4.91), relative root length (RRL) (equal to the control) and relative seedling dry weight (RSDW) (6.94) over control is high when compared to the other genotypes under study. However, the highly susceptible genotype PUSA1121 performed with 43.59 of SF%, 73.33% SSP, -43.59 of RSL, -36.02 of RRL over control. Hence, these contrasting genotypes were used for molecular analysis for identification of differentially expressed genes by employing 29 heat related gene specific primers. Five genes viz., OsGSK1, TT1, HSP70-OsEnS-45, OsHSP74.8 and OsHSP70 have shown differential expression between the two genotypes. Hence, the genotype FR13A, an 'indica' genotype, can be utilized in heat tolerance breeding programmes as donor parent in addition to the reported 'aus' genotypes, N22 and Dular. To our knowledge this is the first indica genotype identified for heat tolerance. The HSP70s, TT1 and OsGSK1 that proved with differential expression might be used for identification of gene specific InDels and thereby to develop functional markers that help in the marker assisted introgression breeding to develop heat tolerant varieties that can sustain production under dramatically changing climatic conditions.

Effects of deficit irrigation and kaolin application on vegetative growth and fruit traits of two early ripening apple cultivars

BackgroundDrought is one of the main serious problems for agriculture production which its intensity is increasing in many parts of the world, hence, improving water use efficiency is a main goal for sustainable agriculture.ResultsGrowth indices including relative shoot length growth (SL), relative stem diameter increase (SD) and relative trunk cross sectional area growth (TCSA) measured at the start and end of the season decreased by reducing the irrigation level. Chlorophyll index (CI) was decreased at 70% crop evapotranspiration, however water use efficiency (WUE), leaf and fruit total phenolic content (TPC), and fruit anthocyanin content (AC) were among the traits that showed increment by water deficit stress in both cultivars. Shafi-Abadi cultivar showed to be more sensitive to the water stress than ‘Golab’. Kaolin treatment improved SL, SD and CI traits, but this increase was statistically significant only for SD at 5% level. Kaolin had no significant effect on yield and water use efficiency (WUE), however, it had negative effect on yield efficiency (YE). Kaolin treatments also significantly increased fruit and leaf TPC (P < 0.01) but had no effect on leaf and fruit total antioxidant activity (AA), as well as fruit anthocyanin content (AC) and soluble proteins (SP).ConclusionsIrrigation at 85% ETc showed better results than 100% and 70% ETc levels for yield attributes. It seems that the more pronounced effect of kaolin on vegetative traits but not on the fruits, might be attributed to the early ripening and harvest time of the examined cultivars.

Morphological and Molecular Characterization of Novel Salt-tolerant Rice Germplasms from the Philippines and Bangladesh

To screen for new sources of salinity tolerance, 688 traditional rice varieties from the Philippines and Bangladesh were obtained, and their tolerance to hypersaline conditions at the seedling stage was examined. A total of 29 Philippine lines and 15 Bangladeshi lines were scored as salt-tolerant. Morphological assessment (plant height, biomass and Na-K ratio) revealed that among the 44 salt-tolerant accessions, Casibon, Kalagnon and Ikogan had significantly higher relative shoot length difference, relative shoot growth reduction and shoot Na-K ratio than the tolerant check FL478. Additionally, AC and Akundo exhibited significantly higher Na-K ratios than the other genotypes. The genetic diversity of the 44 genotypes was assessed using 34 simple sequence repeat markers. A total of 133 alleles were detected across all loci. Cluster analysis showed that AC, Akundo and Kuplod were clustered along with FL478, indicating a strong genetic relatedness between these genotypes. IR29 (susceptible check) was singly separated. The haplotype analysis revealed that none of the 44 genotypes had a similar allele combination as FL478. These accessions are of interest since each genotype might be different from the classical salinity-tolerant Pokkali.

A combined association mapping and t-test analysis of SNP loci and candidate genes involving in resistance to low nitrogen traits by a wheat mutant population.

Crop productivity is highly dependent on the application of N fertilizers, but ever-increasing N application is causing serious environmental impacts. To facilitate the development of new wheat cultivars that can thrive in low N growth conditions, key loci and genes associated with wheat responses to low N must be identified. In this GWAS and t-test study of 190 M6 mutant wheat lines (Jing 411-derived) based on genotype data from the wheat 660k SNP array, we identified a total of 221 significant SNPs associated four seedling phenotypic traits that have been implicated in resistance to low N: relative root length, relative shoot length, relative root weight, and relative shoot weight. Notably, we detected large numbers of significantly associated SNP in what appear to be genomic ‘hotspots’ for resistance to low N on chromosomes 2A and 6B, strongly suggesting that these regions are functionally related to the resistance phenotypes that we observed in some of the mutant lines. Moreover, the candidate genes, including genes encoding high-affinity nitrate transporter 2.1, gibberellin responsive protein, were identified for resistance to low N. This study raises plausible mechanistic hypotheses that can be evaluated in future applied or basic efforts by breeders or plant biologists seeking to develop new high-NUE wheat cultivars.

Screening of barnyard millet (Echinochloa frumentacea) germplasm for salinity tolerance

Indian Barnyard millet (Echinochloa frumentacea) is a climate resilient crop known for high degree of tolerance to salinity. The present study was undertaken to investigate the nature of genetic variation existing in the barnyard millet germplasm for salt tolerance. Different levels of salt stress (50 mM, 100 mM, 150 mM and 200 mM) were imposed on germination stage. The barnyard millet genotypes are able to tolerate upto 200 mM concentration during germination when compared to the tolerant rice genotype FL478. Among plant characters studied the germination percentage, root length, shoot length, fresh and dry weight, relative root length, relative shoot length, relative germination percentage, vigour index were affected by salinity. The vigour index and germination percentage during 200 mM stress helped to differentiate the salt tolerance genotypes viz., CO (KV) 2, MDU-1, PRJ1, TNEf 301, TNEf 204, TNEf 361, TNEf 364, VL 29 from other germplasm.

Toxicity of copper oxide nanoparticles on spring barley (Hordeum sativum distichum)

The rapid growth of copper oxide nanoparticles (CuO NPs) production and its abundant uses in many industries, and increasing release into an environment from both intentional and unintentional sources, create risks to spring barley (Hordeum sativum distichum), one of the most important staple food crop. Thereby, the aim of this study was to investigate the phytotoxicity of CuO NPs on H. sativum growth in hydroponic system. The CuO NPs inhibited H. sativum growth by affecting the germination rate, root and shoot lengths, maximal quantum yield of photosystem II, and transpiration rate. Structural and ultrastructural examination of H. sativum tissues using light, transmission and scanning electron microscopy showed effects on stomatal aperture and root morphology, metaxylem size and changes in cellular organelles (plastids, mitochondria), as well as in plastoglobules, starch granules, protoplasm, and membranes. The formation of electron-dense materials was noted in the intercellular space of cells of CuO NPs-treated plants. In addition, relative root length was one-third (35%) that of the control, and relative shoot length (10%) was also reduced. Further, the Cu content of roots and leaves of CuO NPs-treated plants was 5.7 and 6.4-folds higher than the control (without CuO NPs), respectively. Presented data were significant at p ≤ 0.05 compared to control. Conclusively, the results provide insights into our understanding of CuO NPs toxicity on H. sativum, and findings could be used for developing strategies for safe disposal of NPs.

Analysis of QTL-allele system conferring drought tolerance at seedling stage in a nested association mapping population of soybean [Glycine max (L.) Merr.] using a novel GWAS procedure.

RTM-GWAS identified 111 DT QTLs, 262 alleles with high proportion of QEI and genetic variation accounting for 88.55-95.92% PV in NAM, from which QTL-allele matrices were established and candidate genes annotated. Drought tolerance (DT) is one of the major challenges for world soybean production. A nested association mapping (NAM) population with 403 lines comprising two recombinant inbred line (RIL) populations: M8206 × TongShan and ZhengYang × M8206 was tested for DT using polyethylene-glycol (PEG) treatment under spring and summer environments. The population was sequenced using restriction-site-associated DNA sequencing (RAD-seq) filtered with minor allele frequency (MAF) ≥ 0.01, 55,936 single nucleotide polymorphisms (SNPs) were obtained and organized into 6137 SNP linkage disequilibrium blocks (SNPLDBs). The restricted two-stage multi-locus genome-wide association studies (RTM-GWAS) identified 73 and 38 QTLs with 174 and 88 alleles contributed main effect 40.43 and 26.11% to phenotypic variance (PV) and QTL-environment interaction (QEI) effect 24.64 and 10.35% to PV for relative root length (RRL) and relative shoot length (RSL), respectively. The DT traits were characterized with high proportion of QEI variation (37.52-41.65%), plus genetic variation (46.90-58.40%) in a total of 88.55-95.92% PV. The identified QTLs-alleles were organized into main-effect and QEI-effect QTL-allele matrices, showing the genetic and QEI architecture of the three parents/NAM population. From the matrices, the possible best genotype was predicted to have a weighted average value over two indicators (WAV) of 1.873, while the top ten optimal crosses among RILs with 95th percentile WAV 1.098-1.132, transgressive over the parents (0.651-0.773) but much less than 1.873, implying further pyramiding potential. From the matrices, 134 candidate genes were annotated involved in nine biological processes. The present results provide a novel way for molecular breeding in QTL-allele-based genomic selection for optimal cross selection.