Detection of genetic divergence among putative ethyl methane sulfonate mutants of super basmati using microsatellite markers.

BACKGROUND: Seeds of super basmati were mutagenized with different ethyl methane sulphonate (EMS) doses for creating genetic variability. METHODS AND RESULTS: A total of 48 randomly selected putative EMS mutants of super basmati were analyzed to dissect the genetic diversity by using 25 SSR primers located on twelve chromosomes of rice. SSRs analysis revealed that wide-range of genetic diversity is present among mutants of super basmati. A sum of 91 alleles were identified, out of these, 82 alleles were polymorphic and the rest of nine alleles were monomorphic in nature. The range of allele number was 2-10 with mean of 3.64 alleles/locus. The value of polymorphic information content was range between 0.039 (RM5) and 0.878 (RM44) with mean of 0.439 for each locus. A number of polymorphic markers showed unique bands of various sizes ranges from 75 to 1000 bp, during genetic dissection of mutant population. Dendrogram divided whole mutant population into four major groups. Phylogenic analyses revealed that 40-96%genetic similarity is present among individuals of mutant population. CONCLUSION: It is concluded that EMS induced genetic variability and SSRs markers (RM44, RM154, RM1, RM252, RM334, RM487, RM110 and RM257) could be handy for the selection of rice mutants as parents for functional genomic and molecular breeding program.

Genetic variants of CSN1S1, CSN2, CSN3, and BLG genes and their association with dairy production traits in Sahiwal cattle and Nili-Ravi buffaloes.

Milk protein genes are associated with milk yield and composition in dairy animals. The present study aimed to identify milk protein genes (CSN1S1, CSN2, CSN3, and BLG) genetic variants and their association with milk yield in Sahiwal cattle and Nili-Ravi buffaloes. One hundred animals from each species were selected to collect blood samples and milk production records. Primers were designed for these milk protein genes for PCR amplification. Sequencing of resultant PCR products revealed a higher number of SNPs (13 vs. 7, 5 vs. 1, and 6 vs. 2) in Sahiwal as compared to Nili-Ravi animals in CSN1S1, CSN2, and CSN3 genes, respectively. However, a single SNP was observed in BLG gene of both species. Association analysis revealed that one SNP in BLG gene of Nili-Ravi was associated (p < 0.05) with 305-day milk yield. Two SNPs at CSN1S1 gene in Sahiwal were associated with dry-period. Similarly, one SNP at CSN1S1 and two SNPs at CSN3 gene showed significant association (p < 0.05) with average calving-interval in Sahiwal while two SNPs in CSN1S1 gene were associated (p < 0.05) with this trait in Nili-Ravi. These SNPs could be helpful as candidate variants for marker-assisted selection in cattle and buffaloes for improvement of lactation performance.

Identification and lead-in characterization of novel B3 metallo-ß-lactamases.

Metallo-ß-lactamases (MBLs) are zinc ion dependent enzymes that are responsible for the emergence and spread of ß-lactam resistance among bacterial pathogens. There are uncharacterized putative MBLs in the environment and their emergence is major interference in the generation of universal MBL inhibitors so it is important to identify and characterize novel MBLs. In this study two novel MBLs from Luteimonas sp. J29 and Pseudoxanthomonas mexicana were identified using B3 MBLs as query in BLAST database search. 3D models of putative MBLs generated by SWISS-MODEL server taking AIM-1 as a structural template were verified using web based structure assessment and validation programs. Multiple sequence alignment revealed that residues important for substrate binding were conserved and loop region residues (156-162 and 223-230) important for catalysis are variable in these novel MBLs. Homology models showed typical MBL α/ß/ß/α sandwich fold containing six α helices, twelve ß strands and metal interacting residues are conserved in similar way as with other B3 MBLs. We report promising putative B3 MBLs with some variations and substrate docking studies revealed that novel MBLs have attributes close to acquired B3 MBLs.

Human cancer risk due to chromium and its bioaccumulation in physids in Central Punjab, Pakistan.

The present study aims to assess the ecological risk of chromium [Cr(VI)] in the water and soil of Central Punjab and its natural bioremediation through physids. Members of the genus Physa are cosmopolitan as they are resistant to various pollutants. The snails of the genus Physa were sampled from October through March. Three species, i.e., P. acuta, P. fontinalis, and P. gyrina, were identified. The foot, shell, water, and soil samples were tested for the presence of the hexavalent chromium, using ICP-MS. The maximum mean concentration of chromium in soil was found in GB(R8), i.e., 2.66 ppb. The maximum mean concentration of chromium in water was found in RB(R4), 1.627 ppb. The highest maximum average daily dose (ADD) was found in RB:R6, with a hazard quotient (HQ) of 32.32 and a carcinogenic risk (CR) of approximately 20 in every 100 children as a result of water pollution which is quite similar to RB:R5 showing these are extremely polluted area due to chromium. The pollution level of chromium in soil of Faisalabad is less than zero and safe while water is unsuitable for drinking as the value of water quality index (WQI) is higher than 100. No significant difference among the three species was found regarding bioaccumulation of chromium, in the snail shell and body. Physids play an active role in the bioremediation of soil and water yet may become cancer-causing tablets in the food chains of the region.

De novo transcriptome assembly of Dalbergia sissoo Roxb. (Fabaceae) under Botryodiplodia theobromae-induced dieback disease.

Dalbergia sissoo Roxb. (Shisham) is a timber-producing species of economic, cultural, and medicinal importance in the Indian subcontinent. In the past few decades, Shisham's dieback disease caused by the fungus Botryodiplodia theobromae has become an evolving issue in the subcontinent endangering its survival. To gain insights into this issue, a standard transcriptome assembly was deployed to assess the response of D. sissoo at the transcriptomic level under the stress of B. theobromae infection. For RNA isolation, the control and infected leaf tissue samples were taken from 1-year-old greenhouse-grown D. sissoo plants after 20 days of stem-base spore inoculation. cDNA synthesis was performed from these freshly isolated RNA samples that were then sent for sequencing. About 18.14 Gb (Giga base) of data was generated using the BGISEQ-500 sequencing platform. In terms of Unigenes, 513,821 were identified after a combined assembly of all samples and then filtering the abundance. The total length of Unigenes, their average length, N50, and GC-content were 310,523,693 bp, 604 bp, 1,101 bp, and 39.95% respectively. The Unigenes were annotated using 7 functional databases i.e., 200,355 (NR: 38.99%), 164,973 (NT: 32.11%), 123,733 (Swissprot: 24.08%), 142,580 (KOG: 27.75%), 139,588 (KEGG: 27.17%), 99,752 (GO: 19.41%), and 137,281 (InterPro: 26.72%). Furthermore, the Transdecoder detected 115,762 CDS. In terms of SSR (Simple Sequence Repeat) markers, 62,863 of them were distributed on 51,508 Unigenes and on the predicted 4673 TF (Transcription Factor) coding Unigenes. A total of 16,018 up- and 19,530 down-regulated Differentially Expressed Genes (DEGs) were also identified. Moreover, the Plant Resistance Genes (PRGs) had a count of 9230. We are hopeful that in the future, these identified Unigenes, SSR markers, DEGs and PRGs will provide the prerequisites for managing Shisham dieback disease, its breeding, and in tree improvement programs.

Mass-Producible 2D Nanocomposite-Based Temperature-Independent All-Printed Relative Humidity Sensor.

Relative humidity sensors are widely studied under the categories of both environmental and biosensors owing to their vast reaching applications. The research on humidity sensors is mainly divided into two concentration areas including novel material development and novel device structure. Another approach focuses on the development of printed sensors with performance comparable to the sensors fabricated via conventional techniques. The major challenges in the research on relative humidity sensors include the range of detection, sensitivity (especially at lower %RH), transient response time, and dependence on temperature. Temperature dependence is one of the least studied parameters in relative humidity sensor development. In this work, relative humidity sensors were fabricated using all-printed approaches that are also compatible with mass production, resulting in low cost and easy development. Laser-induced graphene (LIG)-based printed electrodes were used as the transducers, while the 2D MoS2 and graphene nanocomposite was used as the active layer material with the built-in property of temperature independence. The exfoliation process of 2D MoS2 was based on wet grinding, while graphene for the active layer was obtained by scratching the graphene grown on the polyimide (PI) surface via laser ablation. The resulting sensors showed an excellent output response for a full range of 0%RH to 100%RH, having no dependence on the surrounding temperature, and excellent response and recovery times of 4 and 2 s, respectively. The developed sensors can be confidently employed for a wide range of humidity sensing applications where the temperature of the surrounding environment is not constant.

Genome-wide association studies of seedling quantitative trait loci against salt tolerance in wheat.

Salinity is one of the significant factors in decreasing wheat yield and quality. To counter this, it is necessary to develop salt-tolerant wheat varieties through conventional and advanced molecular techniques. The current study identified quantitative trait loci in response to salt stress among worldwide landraces and improved varieties of wheat at the seedling stage. A total of 125 landraces and wheat varieties were subjected to salt treatment (50, 100, and 150 mM) with control. Morphological seedling traits, i.e., shoot length, root length, and fresh and dry shoot and root weights for salinity tolerance were observed to assess salt tolerance and genetic analysis using SNP data through DArT-seq. The results showed that, at the seedling stage, 150 mM NaCl treatment decreased shoot length, root length, and fresh and dry weights of the shoot and root. The root length and dry root weight were the most affected traits at the seedling stage. Effective 4417 SNPs encompassing all the chromosomes of the wheat genome with marker density, i.e., 37%, fall in genome B, genome D (32%), and genome A (31%). Five loci were found on four chromosomes 6B, 6D, 7A, and 7D, showing strong associations with the root length, fresh shoot weight, fresh root weight, and dry root weight at the p < 0.03 significance level. The positive correlation was found among all morphological traits under study.

Genome-Wide Association Mapping for Stripe Rust Resistance in Pakistani Spring Wheat Genotypes.

Stripe rust caused by the pathogen Puccinia striiformis f. sp. tritici (Pst) is a major threat for wheat, resulting in low yield and grain quality loss in many countries. Genetic resistance is a prevalent method to combat the disease. Mapping the resistant loci and their association with traits is highly exploited in this era. A panel of 465 Pakistani spring wheat genotypes were evaluated for their phenotypic response to stripe rust at the seedling and adult plant stages. A total of 765 single nucleotide polymorphism (SNP) markers were applied on 465 wheat genotypes to evaluate their stripe rust response against nine races during the seedling test and in three locations for the field test. Currently, twenty SNPs dispersed on twelve chromosomal regions (1A, 1B, 1D, 2A, 2B, 4A, 4B, 5B, 6A, 6B, 6D and 7B) have been identified that were associated with rust race-specific resistance at the seedling stage. Thirty SNPs dispersed on eighteen chromosomal regions (1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 3D, 4B, 5A, 5B, 6A, 6B, 6D, 7A, 7B and 7D) are associated with adult plant resistance. SNP loci IWB3662 was linked with all three Pakistani races, and likewise IWA2344 and IWA4096 were found to be linked with three different USA races. The present research findings can be applied by wheat breeders to increase their resistant capability and yield potential of their cultivars, through marker-assisted selection.

Gender Identification in Date Palm Using Molecular Markers.

Breeding of date palm is complicated because of its long life cycle and heterozygous nature. Sexual propagation of date palm does not produce true-to-type plants. Sex of date palms cannot be identified until the first flowering stage. Molecular markers such as random amplified polymorphic DNA (RAPD), sequence-characterized amplified regions (SCAR), and simple sequence repeats (SSR) have successfully been used to identify the sex-linked loci in the plant genome and to isolate the corresponding genes. This chapter highlights the use of three molecular markers including RAPD, SCAR, and SSR to identify the gender of date palm seedlings.

Development of molecular method for sex identification in date palm (Phoenix dactylifera L.) plantlets using novel sex-linked microsatellite markers.

Microsatellite markers containing simple sequence repeats (SSRs) are a valuable tool for genetic analysis. Date palm is a dioecious and slow flowering and is very difficult to identify the gender of the trees until it reaches the reproductive age (5-10 years). A total of 12 microsatellite primers were used with 30 date palm samples, 14 parents (8 male + 6 females) and 16 progeny (developed from parents breeding) which showed that microsatellites were highly polymorphic, having a great number of alleles. A total of 124 alleles were characterized in 12 SSR loci. On average, there are 9.08 alleles per locus, with a range from 5 to 16 alleles, for primers mpdCIR15 and mpdCIR57, respectively. These primers produced 15 polymorphic loci specifically in male date palm samples and the seedlings harboring the unique fragments were further characterized as male plants. Increasingly, 38.46 % of these loci were scored as homozygous alleles while 61.53 % heterozygous allelic loci were determined. Primer mpdCIR48 produced a specific locus (250/250) in all male samples whereas the same locus was absent in female samples. Similarly, a locus of 300/310 bp reoccurred in 5 date palm male samples using marker DP-168 which indicated that these are the promising candidate marker to detect the sex in date palm seedlings at early stage. The data resulted from combination of 12 primers enabled the 16 seedling samples progeny (developed from parents breeding) of date palm cultivars to divide into two groups i.e., male and female regarding their sex expression comparative to the parents (male + female) using the principle coordinate analysis.