Correction: The fodder grass resources for ruminants: A indigenous treasure of local communities of Thal desert Punjab, Pakistan.

[This corrects the article DOI: 10.1371/journal.pone.0224061.].

Genetic predisposition of SNPs in miRNA-149 (rs2292832) and FOXE1 (rs3758249) in thyroid Cancer.

BACKGROUND: Many efforts have been made in recent years to investigate the alterations in protein-coding genes as well as non-coding RNAs that are playing an emerging role in the development and progression of cancers. These miRNAs are short non-coding functional RNAs that are involved in the regulation of transcriptome. In different studies, it was found that human miRNA-149 is an important microRNA that is functioning either as onco-miRNAs or acting as tumor suppressors, in different conditions. RATIONALE: Many of the miRNAs are regulating different SNPs of FOXE1 in different studies which are causing low-to-moderate penetrance of genes that initiates the development of thyroid cancer. The involvement of SNPs in miRNA-149 gene rs2292832 and FOXE1 rs3758249 with PTC for better disease prognosis and management was determined in this study and the relation between these SNPs at the genotypic level was also evaluated. MATERIALS AND METHODS: PTC patients with age and gender-matched controls were recruited in the present study. Blood samples were collected in EDTA vacutainer followed by DNA extraction by the organic method. Genotyping of rs2292832 and rs3758249 was done by ARMS-PCR and PCR- RFLP respectively. Statistical analyses were carried out by using SPSS software (version 20). RESULTS: The mutation T>C in miRNA-149 rs2292832 was significantly associated with thyroid cancer (p-value 0.0004, < 0.05) while rs3758249 G>C did not show significant association with the disease (p-value 0.124244, > 0.05). Moreover, no correlation of rs2292832 at the genotype level was observed with rs3758249. CONCLUSIONS: miRNA-149 gene SNP rs2292832 was observed in strong association with thyroid cancer. Lack of genetic association of rs3758249 of FOXE1 gene has been ruled for the disease. The statistically significant association of rs2292832 with thyroid cancer depicts its mechanistic involvement at the cellular level in Papillary Thyroid Carcinoma.

The fodder grass resources for ruminants: A indigenous treasure of local communities of Thal desert Punjab, Pakistan.

Indigenous people have been using local grasses for rearing their animals for centuries. The present study is the first record of traditional knowledge of grasses and livestock feeding system from the Thal desert in Pakistan. A snowball sampling method was used to identify key participants. Information was collected from the respondents from six districts of Thal Desert through semi-structural questionnaire and site visits. The data was analyzed through Smith's salience index and Composite Salience using ANTHROPAC package in R software. On the whole 61 grasses were recorded from the study area: most of them belong to the Poaceae family (52 species). Based on palatability grasses were categorized into three major groups i.e. (A) High priority, (B) Medium priority and (C) Low priority. Species in Group A, abundantly present in the study area represent a source of highly palatable forage for all ruminants. 232 (141M +91W) local participants were interviewed. Participants were grouped into three major age categories: 20-35 (48 participants), 36-50 (116 participants) and 51-67 years old (68 participants). ANTHROPAC frequency analysis confirmed the Smith's salience index and Composite Salience; Cynodon dactylon was the favorite species (6.46 SI, 0.6460 CS) followed by Cymbopogon jwarancusa (5.133 SI, 0.5133 CS) and Sorghum sp. was the third most salient species (5.121 SI, 0.5121 CS). Grasses were mostly available during the months of August and October and had also ethnoveterinary importance. This document about the traditional feeding of livestock in Thal Desert can underline the importance of conserving a traditional knowledge, which was poorly documented before.

Effects of Pre-Anthesis Drought, Heat and Their Combination on the Growth, Yield and Physiology of diverse Wheat (Triticum aestivum L.) Genotypes Varying in Sensitivity to Heat and drought stress.

Independent and combined drought and heat stress negatively affect wheat yield and physiology. The present study was aimed to quantify effects of Drought [D], heat [H] and combined heat and drought [HD] during reproductive stage on wheat yield and to identify physio-biochemical traits which were strongly associated with improved yield and tolerance of wheat under stressful conditions. One hundred and eight elite diverse wheat genotypes were exposed to [H], [D] and [HD] treatments from heading till maturity. Grain yield was reduced by 56.47%, 53.05% and 44.66% under [HD], [H] and [D] treatment, respectively. The [HD] treatment affects the grain yield by reducing metabolism and mobilization of reserves to developing grains and leaves. Disintegration of membrane structure, chlorophyll and protein molecules was higher under [H] stress than [D] stress while water status of genotypes and sink strength was more affected by [D] than [H] stress. Multivariate analysis showed a strong correlation of chlorophyll content before and after anthesis, water-soluble carbohydrates (WSC), proline content (PC) and all other studies agronomic and physiological traits with grain yield while days to anthesis (DTA) and days to maturity (DTM) were negatively associated with grain yield under stress showing advantage of early maturity during stress. Traits having a major contribution in the first two principal components under different stress treatments may lead to improved varieties with heat and drought stress tolerance. To best of over knowledge, the present study is the first detailed study which used physiological and biochemical traits to explain the variation in grain yield and related traits in diverse wheat germplasm.

Genome-wide association analyses for yield and yield-related traits in bread wheat (Triticum aestivum L.) under pre-anthesis combined heat and drought stress in field conditions.

Understanding the genetic basis of heat and drought stress tolerance in wheat is prerequisite for wheat breeding program. In the present study, a wheat panel comprising of 192 elite bread wheat genotypes was phenotyped in eight environments for yield and related traits in field conditions. Four stress environments were created by implying four different treatments differing in sowing date and water availability, panel was evaluated for two years in field conditions. The panel was genotyped with 15K Illumina chip and 9236 polymorphic markers concentrated on B genome were employed in GWAS analysis. Consistent, fast LD decay was observed on D genome and structure analysis germplasm divided panel into three major populations. GWAS was performed using BLUEs values of combined environment data in R package GAPIT using log10(P) = 3.96 as significance threshold. The significance of association was further checked using FDR<0.05 threshold. The GWAS identified 487 loci associated with the traits and were significant at log10(p) threshold out of these 350 loci were significant at FDR threshold. For two stress indices 108 associations were significant at FDR threshold. Nine genomic regions were shared among all treatment, while multiple pleiotropic regions were present on chromosome 7D followed by unmapped chromosome. The present study validated many marker trait associations for yield and other traits, MTAs significant under combined drought and heat stress were novel. These regions are important and can be used for fine mapping and marker assisted selection to discover new genes responsible for heat and drought tolerance in wheat.

Genome-wide association mapping in bread wheat subjected to independent and combined high temperature and drought stress.

Most investigations to date aiming to identify the genetic basis of the stress response of wheat (Triticum aestivum L.) have focused on the response to single stress agents such as high temperature or drought, even though in the natural situation, these stresses tend often to occur together. Here, a panel of 108 spring type bread wheat cultivars was phenotyped for 15 yield and yield related traits for two years (2014/15 and 2015/16) under non-stressed conditions, under high temperature stress, under drought and under a combined high temperature and drought regime. The mean loss in grain yield caused by all stress regimes was 51.33%. Analysis of variance (ANOVA) of yield trait showed significant differences among genotypes environments and their interactions (G×E). All the studied traits had higher heritability values which ranged from 0.35-0.94 under [C], 0.58-0.95 under [D], 0.62-0.93 under [H] and 0.60-0.95 under [HD]. GWAS was performed by using 9,646 informative SNP markers and based on these polymorphic SNPs population structure analysis divided whole germplasm into five major sub-populations. Mixed model association analysis detected 503 marker-trait associations (MTAs) at P ≤0.001 while 329 MTAs crossed FDR ≤ 0.05 for all traits with phenotypic variances (R2) ranged from 24.83% to 12.51%. Seven new pleiotropic SNPs on chromosome 7D and IAAV8258 (86.91cM) and wsnp_Ex_c7168_12311649 (57.93cM) on chromosome 5A were most stable association in present study. Furthermore, candidate genes Psy and Sr25 (TG0040) were also significant in present study, these genes were previously mapped on 7A and 7D. The region on 7D was assiociated with 7DL.7Ag translocation from Lophopyrum carring rust resistance Yr16 and many other genes. Similarly region on chromosome 7A which was associated with Psy gene was linked with grain yellow pigment content QTLs. Favourable alleles controlling grain yield were of vital importance and incorporation of these alleles after validation through marker assisted selection and fine mapping could be helpful in wheat yield improvement stress and non-stress conditions.

Exploration of ethno-medicinal knowledge among rural communities of Pearl Valley; Rawalakot, District Poonch Azad Jammu and Kashmir.

BACKGROUND: Medicinal plants are the basic source of health care in the Pearl Valley District Poonch, Azad Jammu, and Kashmir. The basic aim of present study was to record information about the use of plants in herbal preparation and quantification of recorded data. MATERIALS AND METHODS: The research was conducted with the null hypothesis that there was no differential distribution of knowledge among the communities between genders and among different age groups in the study area and across cultural medicinal uses of the plants are similar. To check these hypotheses information about medicinal plants was collected from 46 laypeople and 18 herbalists by using an open ended and semistructured questionnaire. Different ethnobotanical indices were calculated in order to quantify the knowledge on the medicinal plants reported in the study. RESULTS: Our study recorded 136 species of medicinal plants belonging to 45 families with Asteraceae (14 species) as the dominant family of the area. Decoction (26 species), juice and powder (24 species each) were most common methods of preparation. Spearman's correlation analysis showed that age and gender had the significant effect on both numbers of mentioned species and different uses. A number of known medicinal plants and the number of different uses (H: 38.51; p < 0.001) differ significantly as indicated by Kruskal-Wallis tests. These results showed that the knowledge about the plant varies among different age groups, which were the first hypothesis of the present study. The highest use values (UVs) were reported for Berberis lyceum and Ajuga bracteosa (1.13 each) followed by Abies pindrow (1.03). Highest informant consensus factor (ICF) values were recorded for digestive system diseases (ICF = 0.90) and muscular and skeletal system diseases (ICF = 0.89). The value of Jaccarad index ranged from 6.11 to 32.97 with an average value of 19.84, percentage of similarity was highest between study area and Pir Lasura National Park (34.62%). CONCLUSION: High similarity might be due to the fact that the communities living in these areas have same sociocultural values and have more opportunities to exchange their traditional knowledge. The present study provides practical evidence about the use of medicinal plants among the inhabitants of the Pearl Valley.

Correction: Descriptive study of plant resources in the context of the ethnomedicinal relevance of indigenous flora: A case study from Toli Peer National Park, Azad Jammu and Kashmir, Pakistan.

[This corrects the article DOI: 10.1371/journal.pone.0171896.].

Descriptive study of plant resources in the context of the ethnomedicinal relevance of indigenous flora: A case study from Toli Peer National Park, Azad Jammu and Kashmir, Pakistan.

BACKGROUND: This paper presents the first quantitative ethnobotanical study of the flora in Toli Peer National Park of Azad Jammu and Kashmir, Pakistan. Being a remote area, there is a strong dependence by local people on ethnobotanical practices. Thus, we attempted to record the folk uses of the native plants of the area with a view to acknowledging and documenting the ethnobotanical knowledge. The aims of the study were to compile an inventory of the medicinal plants in the study area and to record the methods by which herbal drugs were prepared and administered. MATERIALS AND METHODS: Information on the therapeutic properties of medicinal plants was collected from 64 local inhabitants and herbalists using open ended and semi-structured questionnaires over the period Aug 2013-Jul 2014. The data were recorded into a synoptic table comprising an ethnobotanical inventory of plants, the parts used, therapeutic indications and modes of application or administration. Different ethnobotanical indices i.e. relative frequencies of citation (RFC), relative importance (RI), use value (UV) and informant consensus factor (Fic), were calculated for each of the recorded medicinal plants. In addition, a correlation analysis was performed using SPSS ver. 16 to check the level of association between use value and relative frequency of citation. RESULTS: A total of 121 species of medicinal plants belonging to 57 families and 98 genera were recorded. The study area was dominated by herbaceous species (48%) with leaves (41%) as the most exploited plant part. The Lamiaceae and Rosaceae (9% each) were the dominant families in the study area. Among different methods of preparation, the most frequently used method was decoction (26 species) of different plant parts followed by use as juice and powder (24 species each), paste (22 species), chewing (16 species), extract (11 species), infusion (10 species) and poultice (8 species). The maximum Informant consensus factor (Fic) value was for gastro-intestinal, parasitic and hepatobiliary complaints (0.90). Berberis lycium Ajuga bracteosa, Prunella vulgaris, Adiantum capillus-veneris, Desmodium polycarpum, Pinus roxburgii, Albizia lebbeck, Cedrella serrata, Rosa brunonii, Punica granatum, Jasminum mesnyi and Zanthoxylum armatum were the most valuable plants with the highest UV, RFC and relative importance values. The Pearson correlation coefficient between UV and RFC (0.881) reflects a significant positive correlation between the use value and relative frequency of citation. The coefficient of determination indicated that 77% of the variability in UV could be explained in terms of RFC. CONCLUSION: Systematic documentation of the medicinal plants in the Toli Peer National Park shows that the area is rich in plants with ethnomedicinal value and that the inhabitants of the area have significant knowledge about the use of such plants with herbal drugs commonly used to cure infirmities. The results of this study indicate that carrying out subsequent pharmacological and phytochemical investigations in this part of Pakistan could lead to new drug discoveries.

Inventory of medicinal flora from Thal Desert, Punjab, Pakistan.

BACKGROUND: This article reports the preliminary findings of an ethno-botanical survey that was carried out in the Thal Desert, Punjab, Pakistan during 2010 to 2013. The aim of this study was to document the traditional use of medicinal plants from the study area. MATERIALS AND METHODS: The whole area was surveyed for inventorying medicinal flora by using a semi-structured questionnaire. RESULTS: The people of the study area are extremely knowledgeable, hence reported 120 plants which are being used in treating various human diseases. The detailed inventory including botanical name, parts used, method of preparation and diseases treated is provided in this paper. CONCLUSION: This study revealed that the inhabitants possessed empirical knowledge of medicinal plants which would be useful in developing health care products and preserving traditional cultures as well as phyto-diversity.