Genome-Wide Association Mapping for Yield and Yield-Related Traits in Rice (Oryza Sativa L.) Using SNPs Markers.

Rice (Oryza sativa L.) is a staple food for more than 50% of the world's population. Rice cultivar improvement is critical in order to feed the world's growing population. Improving yield is one of the main aims of rice breeders. However, yield is a complex quantitative trait controlled by many genes. The presence of genetic diversity is the key factor to improve the yield hence, the presence of diversity in any germplasm is important for yield improvement. In the current study, the rice germplasm was collected from Pakistan and the United States of America and a panel of 100 diverse genotypes was utilized to identify important yield and yield-related traits. For this, a genome-wide association study (GWAS) was performed to identify the genetic loci related to yield. The GWAS on the diverse germplasm will lead to the identification of new genes which can be utilized in the breeding program for improvement of yield. For this reason, firstly, the germplasm was phenotypically evaluated in two growing seasons for yield and yield-related traits. The analysis of variance results showed significant differences among traits which showed the presence of diversity in the current germplasm. Secondly, the germplasm was also genotypically evaluated using 10K SNP. Genetic structure analysis showed the presence of four groups which showed that enough genetic diversity was present in the rice germplasm to be used for association mapping analysis. The results of GWAS identified 201 significant marker trait associations (MTAs. 16 MTAs were identified for plant height, 49 for days to flowering, three for days to maturity, four for tillers per plant, four for panicle length, eight for grains per panicle, 20 unfilled grains per panicle, 81 for seed setting %, four for thousand-grain weight, five for yield per plot and seven for yield per hectare. Apart from this, some pleiotropic loci were also identified. The results showed that panicle length (PL) and thousand-grain weight (TGW) were controlled by a pleiotropic locus OsGRb23906 on chromosome 1 at 10,116,371 cM. The loci OsGRb25803 and OsGRb15974 on chromosomes 4 and 8 at the position of 14,321,111 cM and 6,205,816 cM respectively, showed pleiotropic effects for seed setting % (SS) and unfilled grain per panicle (UG/P). A locus OsGRb09180 on chromosome 4 at 19,850,601 cM was significantly linked with SS and yield/ha. Furthermore, gene annotation was performed, and results indicated that the 190 candidate genes or QTLs that closely linked with studied traits. These candidate genes and novel significant markers could be useful in marker-assisted gene selection and QTL pyramiding to improve rice yield and the selection of potential parents, recombinants and MTAs which could be used in rice breeding programs to develop high-yielding rice varieties for sustainable food security.

Genome-Wide Identification, and In-Silico Expression Analysis of YABBY Gene Family in Response to Biotic and Abiotic Stresses in Potato (Solanum tuberosum).

YABBY is among the specific transcription factor (TF) gene family in plants and plays an important role in the development of the leaves and floral organs. Its specific roles include lateral organ development, the establishment of dorsoventral polarity, and response to abiotic stress. Potato is an important crop worldwide and YABBY genes are not still identified and characterized in potato. So, little has been known about YABBY genes in potato until now. This study was carried out to perform genome-wide analysis, which will provide an in-depth analysis about the role of YABBY genes in potato. There have been seven StYAB genes identified, which are found to be located on seven different chromosomes. Through multiple sequence analyses, it has been predicted that the YABBY domain was present in all seven genes while the C2-C2 domain was found to be absent only in StYAB2. With the help of cis-element analysis, the involvement of StYAB genes in light, stress developmental, and hormonal responsiveness has been found. Furthermore, expression analysis from RNA-seq data of different potato organs indicated that all StYAB genes have a role in the vegetative growth of the potato plant. In addition to this, RNA-seq data also identified StYAB3, StYAB5, and StYAB7 genes showing expression during cadmium, and drought stress, while StYAB6 was highly expressed during a viral attack. Moreover, during the attack of Phytophthora infestans on a potato plant StYAB3, StYAB5, StYAB6, and StYAB7 showed high expression. This study provides significant knowledge about the StYAB gene structures and functions, which can later be used for gene cloning, and functional analysis; this information may be utilized by molecular biologists and plant breeders for the development of new potato lines.

Genome wide association mapping of yield and various desirable agronomic traits in Rice.

BACKGROUND: Rice (Oryza sativa L.) is one of the staple foods worldwide. To feed the growing population, the improvement of rice cultivars is important. To make the improvement in the rice breeding program, it is imperative to understand the similarities and differences of the existing rice accessions to find out the genetic diversity. Previous studies demonstrated the existence of abundant elite genes in rice landraces. A genome-wide association study (GWAS) was performed for yield and yield related traits to find the genetic diversity. DESIGN: Experimental study. METHODS AND RESULTS: A total of 204 SSRs markers were used among 17 SSRs found to be located on each chromosome in the rice genome. The diversity was analyzed using different genetic characters i.e., the total number of alleles (TNA), polymorphic information content (PIC), and gene diversity by Power markers, and the values for each genetic character per marker ranged from 2 to 9, 0.332 to 0.887 and 0.423 to 0.900 respectively across the whole genome. The results of population structure identified four main groups. MTA identified several markers associated with many agronomically important traits. These results will be very useful for the selection of potential parents, recombinants, and MTAs that govern the improvements and developments of new high yielding rice varieties. CONCLUSIONS: Analysis of diversity in germplasm is important for the improvement of cultivars in the breeding program. In the present study, the diversity was analyzed with different methods and found that enormous diversity was present in the studied rice germplasm. The structure analysis found the presence of 4 genetic groups in the existing germplasm. A total of 129 marker-trait associations (MTAs) have been found in this study.

Expression of Arabidopsis Ornithine Aminotransferase (AtOAT) encoded gene enhances multiple abiotic stress tolerances in wheat.

KEY MESSAGE: The drought and salt tolerances of wheat were enhanced by ectopic expression of the Arabidopsis ornithine aminotransferase (AtOAT) encoded gene. The OAT was confirmed to play a role in proline biosynthesis in wheat. Proline (Pro) accumulation is a common response to both abiotic and biotic stresses in plants. Ornithine aminotransferase (OAT) is pyridoxal-5-phosphate dependent enzyme involved in plant proline biosynthesis. During stress condition, proline is synthesized via glutamate and ornithine pathways. The OAT is the key enzyme in ornithine pathway. In this study, an OAT gene AtOAT from Arabidopsis was expressed in wheat for its functional characterization under drought, salinity, and heat stress conditions. We found that the expression of AtOAT enhanced the drought and salt stress tolerances of wheat by increasing the proline content and peroxidase activity. In addition, it was confirmed that the expression of AtOAT also played a partial tolerance to heat stress in the transgenic wheat plants. Moreover, quantitative real-time PCR (qRT-PCR) analysis showed that the transformation of AtOAT up-regulated the expression of the proline biosynthesis associated genes TaOAT, TaP5CS, and TaP5CR, and down-regulated that of the proline catabolism related gene TaP5CDH in the transgenic plants under stress conditions. Moreover, the genes involved in ornithine pathway (Orn-OAT-P5C/GSA-P5CR-Pro) were up-regulated along with the up-regulation of those genes involved in glutamate pathway (Glu-P5CS-P5C/GSA-P5CR-Pro). Therefore, we concluded that the expression of AtOAT enhanced wheat abiotic tolerance via modifying the proline biosynthesis by up-regulating the expression of the proline biosynthesis-associated genes and down-regulating that of the proline catabolic gene under stresses condition.

UPLC-Tandem Mass Spectrometry for Quantification of Busulfan in Human Plasma: Application to Therapeutic Drug Monitoring.

Busulfan (Bu) is an alkylating agent commonly used in preparative regimens for hematologic malignant and non-malignant patients undergoing hematopoietic stem cell transplantation (HSCT). The objective of the present study was to develop an UPLC-MS/MS method for quantification of Bu in human plasma. A total of 55 patients with hematologic malignancies (n = 34) and non- malignancies (n = 21) received myeloablative Bu therapy prior to HSCT. A tandem mass spectrometric method was developed and validated to quantify Bu levels in these patients. The method was fully validated over the concentration range of 25-2000 ng/mL (r > 0.99). The assay method demonstrated good precision and accuracy. Stability studies indicated that the drug was stable in various conditions. Incurred sample reanalysis findings were within acceptable ranges (<15% of the nominal concentration). Based on the 1st dose AUC results, one third of hematologic malignant patients and half of non-malignant patients needed dose adjustment. However, in subsequent doses (5th, 9th, and 13th), 77%, 82% and 82%, respectively, of hematologic malignant patients and 71%, 67% and 86%, respectively, of non-malignant patients achieved the target range of Bu AUC. The suitability of the developed method for routine TDM of Bu in HSCT patients was demonstrated. The study suggests that the pharmacokinetic profile of Bu varies in both groups.

Cloning and molecular characterization of Triticum aestivum ornithine amino transferase (TaOAT) encoding genes.

BACKGROUND: Ornithine aminotransferase (OAT, EC:2.6.1.13), alternatively known as ornithine delta aminotransferase (δOAT), is a pyridoxal phosphate (PLP)-dependent enzyme involved in the conversion of ornithine into glutamyl-5-semi-aldehyde (GSA) and vice versa. Up till now, there has been no study on OAT in wheat despite the success of its isolation from rice, maize, and sorghum. This study focuses on identification and molecular characterization of OAT in wheat. RESULTS: In total, three homeologous OAT genes in wheat genome were found on chromosome group 5, named as TaOAT-5AL, TaOAT-5BL, and TaOAT-5DL. Sequence alignment between gDNA and its corresponding cDNA obtained a total of ten exons and nine introns. A phylogenetic tree was constructed and results indicated that OATs shared highly conserved domains between monocots and eudicots, which was further illustrated by using WebLogo to generate a sequence logo. Further subcellular localization analysis indicated that they functioned in mitochondria. Protein-protein interactions supported their role in proline biosynthesis through interactions with genes, such as delta 1-pyrroline-5-carboxylate synthetase (P5CS) and pyrroline-5-carboxylate reductase (P5CR), involved in the proline metabolic pathway. Promoter analysis exposed the presence of several stress responsive elements, implying their involvement in stress regulation. Expression profiling illustrated that TaOAT was highly induced in the wheat plants exposed to drought or salt stress condition. Upregulated expression of TaOATs was observed in stamens and at the heading stage. A potential role of TaOAT genes during floret development was also revealed. Furthermore, the transgenic plants overexpressing TaOAT showed enhanced tolerance to drought stress by increasing proline accumulation. In addition, salt tolerance of the transgenic plants was also enhanced. CONCLUSION: TaOATs genes were involved in proline synthesis and nitrogen remobilization because they interacted with genes related to proline biosynthesis enzymes and arginine catabolism. In addition, TaOAT genes had a role in abiotic stress tolerance and a potential role in floret development. The results of this study may propose future research in the improvement of wheat resistance to abiotic stresses.

Biological Roles of Ornithine Aminotransferase (OAT) in Plant Stress Tolerance: Present Progress and Future Perspectives.

Plant tolerance to biotic and abiotic stresses is complicated by interactions between different stresses. Maintaining crop yield under abiotic stresses is the most daunting challenge for breeding resilient crop varieties. In response to environmental stresses, plants produce several metabolites, such as proline (Pro), polyamines (PAs), asparagine, serine, carbohydrates including glucose and fructose, and pools of antioxidant reactive oxygen species. Among these metabolites, Pro has long been known to accumulate in cells and to be closely related to drought, salt, and pathogen resistance. Pyrroline-5-carboxylate (P5C) is a common intermediate of Pro synthesis and metabolism that is produced by ornithine aminotransferase (OAT), an enzyme that functions in an alternative Pro metabolic pathway in the mitochondria under stress conditions. OAT is highly conserved and, to date, has been found in all prokaryotic and eukaryotic organisms. In addition, ornithine (Orn) and arginine (Arg) are both precursors of PAs, which confer plant resistance to drought and salt stresses. OAT is localized in the cytosol in prokaryotes and fungi, while OAT is localized in the mitochondria in higher plants. We have comprehensively reviewed the research on Orn, Arg, and Pro metabolism in plants, as all these compounds allow plants to tolerate different kinds of stresses.

Genome-wide association for grain yield under rainfed conditions in historical wheat cultivars from Pakistan.

Genome-wide association studies (GWAS) were undertaken to identify SNP markers associated with yield and yield-related traits in 123 Pakistani historical wheat cultivars evaluated during 2011-2014 seasons under rainfed field conditions. The population was genotyped by using high-density Illumina iSelect 90K single nucleotide polymorphism (SNP) assay, and finally 14,960 high quality SNPs were used in GWAS. Population structure examined using 1000 unlinked markers identified seven subpopulations (K = 7) that were representative of different breeding programs in Pakistan, in addition to local landraces. Forty four stable marker-trait associations (MTAs) with -log p > 4 were identified for nine yield-related traits. Nine multi-trait MTAs were found on chromosomes 1AL, 1BS, 2AL, 2BS, 2BL, 4BL, 5BL, 6AL, and 6BL, and those on 5BL and 6AL were stable across two seasons. Gene annotation and syntey identified that 14 trait-associated SNPs were linked to genes having significant importance in plant development. Favorable alleles for days to heading (DH), plant height (PH), thousand grain weight (TGW), and grain yield (GY) showed minor additive effects and their frequencies were slightly higher in cultivars released after 2000. However, no selection pressure on any favorable allele was identified. These genomic regions identified have historically contributed to achieve yield gains from 2.63 million tons in 1947 to 25.7 million tons in 2015. Future breeding strategies can be devised to initiate marker assisted breeding to accumulate these favorable alleles of SNPs associated with yield-related traits to increase grain yield. Additionally, in silico identification of 454-contigs corresponding to MTAs will facilitate fine mapping and subsequent cloning of candidate genes and functional marker development.

Comparative analysis of the effects of hubble-bubble (Sheesha) and cigarette smoking on respiratory and metabolic parameters in hubble-bubble and cigarette smokers.

OBJECTIVES AND BACKGROUND: Hazard of smoking tobacco is believed to be minimized by smoking hubble-bubble (HB) instead of cigarettes. Our aims were to (i) develop an assay for estimating nicotine and cotinine; and (ii) evaluate the effect of smoking on respiratory and metabolic parameters in cigarette and HB smokers. METHODS: Urine samples were collected from 152 volunteer smokers (75 cigarette and 77 HB) as well as from 16 healthy controls. We optimized an HPLC method for the determination of nicotine and cotinine. Subjects were asked to complete a chronic respiratory symptoms questionnaire and to undergo spirometry. Fasting blood samples were collected for the determination of their lipid profile. RESULTS: The intra-assay coefficients of variation for nicotine and cotinine were 16.6% and 6.6%, respectively. The mean of cotinine in cigarette smokers (1321.4 ng/mL) was significantly (P = 0.008) higher than the mean cotinine (677.6 ng/mL) in HB smokers. The mean nicotine level in cigarette smokers (1487.3 ng/mL) was significantly (P < 0.0001) higher than the mean nicotine (440.5 ng/mL) in HB smoker. The urinary cotinine and nicotine levels of the control subjects were lower than the detection levels of the assay. The mean high-density lipoprotein cholesterol was lower in cigarette smokers (0.99 mmol/L) compared with HB smoker smokers (1.02 mmol/L) but this was not significant (P = 0.28). Spirometric values were comparable among the three groups but the chronic respiratory symptoms in the smoking groups appeared at an earlier age in the HB smokers compared with the cigarettes smokers (P < 0.05). CONCLUSION: Smoking HB does not reduce the risk of tobacco exposure and it's potentially harmful metabolites on health.