Wild Genotype Research Articles

A Review – Some Approaches to Combat Salt Stress in Wheat Crop

Wheat constitutes a central position for ensuring food and nutritional security; however, rapidly rising soil and water salinity pose a serious threat to its production globally. Salinity stress is a universal dilemma that is happening due to climate change. It affects hectares of arable land. Main focus regarding improving salinity tolerance in plants has been given to Na+ exclusion/ Na+ compartmentalization and enhanced ROS system. Besides this, ameliorative activity of phytohormones, nutrients, amino acids and organic osmolytes has also been widely studied. Exploring traits in wild genotype aids search for better solutions. Based upon phenotype screening, novel genes involving salinity tolerance will be easily identified. Moreover, selected mutants can be used to validate the functions of salt genes. Wheat plants utilize a range of physiological biochemical and molecular mechanisms to adapt under salinity stress at the cell, tissue as well as whole plant levels to optimize the growth, and yield by off-setting the adverse effects of saline environment. Recently, various adaptation and management strategies have been developed to reduce the deleterious effects of salinity stress to maximize the production and nutritional quality of wheat. Thereby, this review highlights effects of salt tolerance, physiological mechanisms behind salt tolerance and transgenic wheat that are potential indicators of salinity stress tolerance.

Association between polymorphisms within the gene coding for tumor necrosis factor (TNF)-alpha with outcomes of treatment in a sample of Iraqi patients with ankylosing spondylitis taking etanercept: an observational study

Background: Ankylosing spondylitis (AS) is a progressive, chronic inflammatory illness with an unclear etiology that explicitly targets the vertebral column, peripheral joints, and extraarticular tissues. The purpose of this research was to investigate if the existence of single nucleotide polymorphisms (SNPs) in the promoter region of the tumor necrosis factor-alpha (TNF-α) gene at positions -1031T/C (rs199964), -857C/T (rs1799724) and -806C/T (rs4248158) in a sample of Iraqi AS patients could influence the patients' outcomes with etanercept. Methods: Sixty patients with established AS receiving only etanercept were selected to enroll in this study, with a mean age of 40.75±8.67 years; 51 patients were male. Patients were classed as "responders" if they obtained a Bath Ankylosing Spondylitis Disease Activity Index (BASDAI) 50 clinical response and as "non-responders" if they did not achieve a BASDAI 50 clinical improvement after at least six months of treatment. After polymerase chain reaction (PCR) product amplification of the purified blood DNA, the promoter region of TNF-α gene SNPs was established by Sanger sequencing. Results: This research found a significant difference in the TT genotype of rs1799964, P = 0.02, in the responder group, in contrast to the TC genotype of rs1799964, which was significantly more frequent in the non-responder group, P = 0.01. The wild TT genotype of rs1799964 seemed to enhance the probability of being a responder. Nevertheless, the heterozygote TC genotype of rs1799964 showed a negative and significant correlation for responsiveness to etanercept. Conclusion: The TT genotype of rs1799964 is associated with a higher likelihood of responding to ETN, suggesting that it is a valuable diagnostic for predicting response in Iraqi AS patients.

Search for the putative RNA thermometers in the genome of Hepatitis E virus

Currently, some temperature-sensitive elements in bacteria are known. Structurally and functionally different RNA thermometers control a variety of cellular processes in bacteria including virulence. Up-to-date experimental confirmation of RNA thermometers functioning in viruses was obtained only for West Nile virus. But other, unknown yet, types of RNA thermometers may exist in nature. The goal of this study was the determination of conservative stem-loop structures in the swine, wild boars’ hepatitis E virus (HEV) genome which may act as RNA thermometers. The search for putative RNA thermometers in the swine HEV which is a common pathogen in the pig population worldwide was executed. Bioinformatics analysis was used to predict the secondary structure of the linear RNA fragments and to determine the melting temperature of the potential hairpins in the HEV genome. 108 swine, wild boars genotype 3 and genotype 4 HEV isolates with complete genomes from the GenBank database were analyzed for the availability of stem-loop structures. Conservative hairpin with the putative thermoregulating function was found in genotype 3 HEV isolates from pig and wild boar for 64 HEV isolates from 108 analyzed ones. The stem of the hairpin with a length of 37 nt contains two AUG start codons of translation initiation and the melting temperature of the hairpin is equal to 38–42 °С for ionic strength of 0.165 M Na+. These hairpins contain a metastable element (one or two bulges) in the stem. Conservative secondary stem-loop structures with putative thermoregulating function for genomic RNA of 64 HEV isolates with complete genome were found by bioinformatics analysis. These hairpins contain a metastable element (one or two bulges) in the stem like an RNA thermometer of West Nile virus and satisfy the necessary and sufficient conditions of RNA thermometer formation. Determined stem-loop structures are proposed as putative thermoregulator elements because they are highly conservative uncanonical structures that are present in the genomes of 64 HEV isolates from 108 analyzed ones

Pharmacogenomic markers of glucocorticoid response in congenital adrenal hyperplasia.

Glucocorticoids (GC) replacement are the mainstay treatment for 21-hydroxylase deficiency (21-OHD), the most common cause of congenital adrenal hyperplasia (CAH), in its classical form. There are novel insights into the genetic basis of the GC action diversity that point to an important role for GC receptor (GR) gene polymorphisms, suggesting a possible modulation in occurrence of metabolic disorders, what may be relevant to clinical management of 21-OHD. The aim of this study was to investigate whether the five GR gene polymorphisms Tth111I, ER22, 23EK, BclI, 9β (rs10052957, rs6189, rs6190, rs41423247, rs6198) and their combination into haplotypes are associated to different GC response in a cohort of classic 21-OHD subjects. GR genotype-phenotype associations were explored after a dexamethasone suppression test using very low-doses (VLD-DST), 20 and 40 μg/m². The final sample (n = 28) was selected based on the 102 individuals' previous genotypes classification, according to literature data of GC sensitivity or resistance. Thus, only patients with GC increased resistance (n = 18) or increased sensitivity (n = 10) profiles were selected. Out of 28 subjects aged 12 (2-34) years enrolled in this study, 75% were females, 75% presented the salt-wasting form (SW) and 25% the simple virilizing form (SV). Subjects who carried Tth111I and 9β, associated or not to the ER22/23EK variants, showed an impaired DST response. Results did not differ significantly according to gender or body mass index. SV subjects with GC hypersensitivity-genotypes showed decreased average cortisol levels compared to those with GC resistance-genotypes (p = 0.0023). The Tth111I + 9β/ Wild or Tth111I + ER22/23EK + 9β/ Wild genotypes were associated to GC resistance in this population. This finding may be relevant given the challenges posed by therapeutic management with GC in CAH.

Genome-Wide Association Study Revealed the Effect of rs312715211 in ZNF652 Gene on Abdominal Fat Percentage of Chickens.

Abdominal fat percentage (AFP) is an important economic trait in chickens. Intensive growth selection has led to the over-deposition of abdominal fat in chickens, but the genetic basis of AFP is not yet clear. Using 520 female individuals from selection and control lines of Jingxing yellow chicken, we investigated the genetic basis of AFP using a genome-wide association study (GWAS) and fixation indices (FST). A 0.15 MB region associated with AFP was located on chromosome 27 and included nine significant single nucleotide polymorphisms (SNPs), which could account for 3.34-5.58% of the phenotypic variation. In addition, the π value, genotype frequency, and dual-luciferase results identified SNP rs312715211 in the intron region of ZNF652 as the key variant. The wild genotype was associated with lower AFP and abdominal fat weight (AFW), but higher body weight (BW). Finally, annotated genes based on the top 1% SNPs were used to investigate the physiological function of ZNF652. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis suggested that ZNF652 may reduce AFW and BW in broilers through the TGF-β1/SMad2/3 and MAPK/FoxO pathways via EGFR and TGFB1. Our findings elucidated the genetic basis of chicken AFP, rs312715211 on the ZNF652 gene, which can affect BW and AFW and was the key variant associated with AFP. These data provide new insight into the genetic mechanism underlying AF deposition in chickens and could be beneficial in breeding chickens for AF.

Genetic variants of the GLP-1R gene affect the susceptibility and glucose metabolism of gestational diabetes mellitus: a two-center nested case‒control study

BackgroundGestational diabetes mellitus (GDM) is the most common complication during pregnancy, occurring under the combined action of environmental and genetic factors. Genetic variants of glucagon-like peptide-1 receptor (GLP-1R) have been reported to affect insulin secretion and susceptibility to type 2 diabetes. This study aimed to explore the role of GLP-1R polymorphisms in GDM and glucose metabolism.MethodsA two-center nested case‒control study was designed, including 200 pregnant women with GDM and 200 pregnant women without GDM genotyped for five tag SNPs of GLP-1R using Sanger sequencing. Logistic regression was used to evaluate the relationship between GLP-1R polymorphisms and GDM risk. Glucose and insulin concentrations were measured based upon the 75 g oral glucose tolerance test (OGTT). Beta cell function of different genotypes was estimated with the 60 min insulinogenic index (IGI60) and OGTT-derived disposition index (DI).ResultsMutant genotype AG + GG of tag SNP rs6458093 nominally increased GDM risk (p = 0.049), especially among subjects younger than 35 years (p = 0.024) and with BMI no less than 24 (p = 0.041), after adjusting for confounders. Meanwhile, compared with subjects with wild genotype AA, subjects with genotype AG + GG of rs6458093 also showed nominally significantly lower IGI60 (p = 0.032) and DI (p = 0.029), as well as significantly higher 75 g OGTT-based 1 h glucose load plasma glucose levels (p = 0.045). Moreover, the mutant heterozygous genotype GA of tag SNP rs3765467 nominally decreased GDM risk among subjects older than 35 years (p = 0.037) but showed no association with insulin secretion and glucose homeostasis.ConclusionsTag SNP rs6458093 of GLP-1R was nominally associated with increased GDM risk and affected beta cell function and postprandial glucose metabolism, while tag SNP rs3765467 of GLP-1R was nominally associated with decreased GDM risk, providing evidence for molecular markers and etiological study of GDM.

De novo transcriptome assembly and functional analysis reveal a dihydrochalcone 3-hydroxylase(DHC3H) of wild Malus species that produces sieboldin in vivo.

Sieboldin is a specialised secondary metabolite of the group of dihydrochalcones (DHC), found in high concentrations only in some wild Malus species, closely related to the domesticated apple (Malus × domestica L.). To date, the first committed step towards the biosynthesis of sieboldin remains unknown. In this study, we combined transcriptomic analysis and a de novo transcriptome assembly to identify two putative 3-hydroxylases in two wild Malus species (Malus toringo (K. Koch) Carriere syn. sieboldii Rehder, Malus micromalus Makino) whose DHC profile is dominated by sieboldin. We assessed the in vivo activity of putative candidates to produce 3-hydroxyphloretin and sieboldin by de novo production in Saccharomyces cerevisiae. We found that CYP98A proteins of wild Malus accessions (CYP98A195, M. toringo and CYP98A196, M. micromalus) were able to produce 3-hydroxyphloretin, ultimately leading to sieboldin accumulation by co-expression with PGT2. CYP98A197-198 genes of M. × domestica, however, were unable to hydroxylate phloretin in vivo. CYP98A195-196 proteins exerting 3-hydroxylase activity co-localised with an endoplasmic reticulum marker. CYP98A protein model from wild accessions showed mutations in key residues close to the ligand pocket predicted using phloretin for protein docking modelling. These mutations are located within known substrate recognition sites of cytochrome P450s, which could explain the acceptance of phloretin in CYP98A protein of wild accessions. Screening a Malus germplasm collection by HRM marker analysis for CYP98A genes identified three clusters that correspond to the alleles of domesticated and wild species. Moreover, CYP98A isoforms identified in M. toringo and M. micromalus correlate with the accumulation of sieboldin in other wild and hybrid Malus genotypes. Taken together, we provide the first evidence of an enzyme producing sieboldin in vivo that could be involved in the key hydroxylation step towards the synthesis of sieboldin in Malus species.

The impact of pre-pregnancy folic acid intake on placental DNA methylation in a fortified cohort.

Folate plays an important role in the modulation of one-carbon metabolism and DNA methylation through a complex biosynthesis pathway. Folate deficiency during pregnancy has been associated with an increased risk for birth defects. This study investigates the extent to which the availability of folate and S-Adenosylmethionine (SAM) affects placental DNA methylation. We hypothesized that maintaining sufficient levels of folate and SAM is particularly important in individuals carrying the MTHFR C677T polymorphism. Maternal- and cord blood was analyzed to genotype the MTHFR rs1801133 SNP. Red blood cell (RBC) folate, vitamin B12, SAM, and S-Adenosylhomocysteine (SAH) were analyzed in cord blood. Epigenome-wide methylation analyses were performed on 90 placenta tissue samples isolated from the fetal side of the placenta; 45 originating from mother-infant dyads homozygous for the MTHFR C677T variant and 45 originating from mother-infant dyads with the homozygous wild type MTHFR677 genotype. Verification of the results was performed using pyrosequencing assays. Genome-wide placental DNA methylation patterns were relatively stable and not significantly affected by levels of one-carbon metabolites. MTHFR genotype was associated with DNA methylation of several loci, including a locus in the MTHFR region. RBC folate and particularly the SAM:SAH ratio did affect overall CpG DNA methylation in some CpG regions when the loci were split according to their CpG island relation. This was most evident in participants carrying the MTHFR C677T variant suggesting a stronger influence of the biosynthesis pathway on the overall placental DNA methylation in MTHFR TT individuals than in MTHFR CC individuals.

Farklı Olgunluk Evrelerine Göre Erik Çeşit ve Genotiplerine Ait Meyvelerin Agromorfolojik ve Biyokimyasal Özelliklerinin Belirlenmesi

This study was conducted on five commercial plum cultivars are grown in Iğdır province and five wild plum genotypes commonly found in the province. The pomological properties, vitamin C, organic acids contents and phenolic compounds contents of plum fruits were determined. As for the pomological properties, fruit weight was measured as 130.5 g in Autumn Giant cultivar, while fruit thickness was 56.4 mm, fruit length was 48.6 mm, and fruit width was 53.3 mm. The fruit stem length was 13.7 mm in Japanese cultivar. Among phytochemicals; in the highest titratable acidity was detected in Angelino cultivar (2.1%), while the highest soluble solid content was determined in Green Plum (21.4%), the pH in Type 5 genotype (3.7), vitamin C in Type 2 genotype (29.44 mg 100g-1); of organic acids, oxalic acid was determined to be the highest in Type 3 genotype (8.043 mg 100g-1), citric acid in Autumn Giant cultivar (27.142 mg 100g-1), malic acid in Black Splendor cultivar (5.121 mg 100g-1), succinic acid (5.541 mg 100g-1) and fumaric acid (7.071 mg 100g-1) was determined in Angelino cultivar. From phenolic compounds; gallic acid was determined to be the highest in Type 4 genotype (2.078 mg 100g-1), protocatechuic acid in Angelino cultivar (1.975 mg 100g-1), catechin in Type 4 genotype (6.971 mg 100g-1), chlorogenic acid (20.027 mg 100g-1) and vanillic acid (0.589 mg 100g-1) in Autumn Giant cultivar, caffeic acid in Type 4 genotype (1.016 mg 100g-1), syringic acid in Type 4 genotype (0.982 mg 100g-1), p-coumaric acid in Angelino cultivar (1.712 mg 100g-1), ferulic acid in Type 5 genotype (1,647 mg 100g-1), o-coumaric acid in Angelino cultivar (0.388 mg 100g-1), rutin in Black Splendor cultivar (0.981 mg 100g-1). It has been observed that there is a great diversity among the plum genotypes.

Morphological, Pomological, and Nutritional Value of Wild and Cultivated Rosehip (Rosa canina L.) Genotypes in Slavonia, Croatia

In this study, the morphological, pomological, and nutritional values of wild and cultivated rosehip fruits grown in the Slavonia region of eastern Croatia were studied. The results revealed significant differences in several morphological and pomological characteristics among the rosehip genotypes in terms of fruit weight, flesh weight, seed weight, and fruit flesh ratio, with no significant differences in fruit width, fruit length, fruit shape index, seed number per fruit, or seed length. The evaluated rosehip fruit genotypes differed significantly from each other in terms of hectoliter weight (kg), fruit bulk (cm3), and bulk density (kg/m3). For water–soluble extracts, ash, and pH, no statistical difference was found between naturally grown genotypes, but there was a significant difference between naturally grown and cultivated genotypes. Twenty-three major and trace elements were analyzed. The most abundant elements were K, Ca, Mg, and P in both cultivated and naturally grown fruits. The highest concentrations of microelements were Fe, Al, Mn, and Sr. The conventionally cultivated genotype L1 had the highest concentration of Fe and Na as essential elements for humans but also had the highest concentrations of Al, Sr, Ti, V, Cr, Pb, Co, Li, and As of all the genotypes studied. The naturally grown genotype L4 had the highest concentrations of S, Zn, Rb, and Cd and the lowest concentrations of Mg, K, and Ca among all studied genotypes. The data showed that the analyzed genotypes from eastern Croatia had good nutritional quality and variability, making them suitable as genetic resources and possibly leading to the detection of rosehip genotypes as potential sources of beneficial ingredients for human health.

The methylenetetrahydrofolate reductase C677T and A1298C genetic polymorphisms and plasma homocysteine in Alzheimer’s disease in an Algerian population

Background The etiology of Alzheimer’s disease (AD) is multifactorial. The most important challenge of research is the identification of potential biomarkers associated with AD pathogenesis that may significantly contribute to early diagnosis of the disease. We aim to explore an eventual association of the C677T and A1298C genetic polymorphisms in the MTHFR gene with AD risk in an Algerian population. Methods This case-control study involved comparing a group of 106 patients that had developed AD to another group of 104 non-demented individuals. The MTHFR genotypes were determined using PCR-RFLP method. Additionally, the homocysteine level was evaluated. Results Genotypes analysis did not show an association for both MTHFR677CT and 677TT variants with AD risk (OR = 1.12; p = 0.66; OR = 1.76; p = 0.09) respectively. As expected, the 677CC wild type genotype showed a protective role against AD (OR = 0.52; p = 0.03). For 1298AC MTHFR variant, the distribution of different genotypes did not show a statistical significant difference between the two cohorts. However the silmutaneous carrier, CT/AC presented association with AD (OR = 5.96; p = 0.05). On the other hand, carrier-state of MTHFR T allele showed a relationship with AD (OR = 1.98; p = 0.02). Additionally, hyperhomocysteinemia seems to be a risk factor for AD (OR = 1.08; p = 0.02). Conclusion Our exploration reveals that the silmutaneous carrier, CT/AC, carrier-state of MTHFR T allele, and hyperhomocysteinemia seem to be risk factors for AD.

Characterization of Solanum sp. Lycopersicon section for density and types of leaf trichomes and resistance to whitefly and tomato pinworm

Resistance genes to pests such as Bemisia tabaci and Tuta absoluta can be abundant in wild tomato genotypes. For breeding program initiatives, the characterization of the germplasm in terms of resistance to pests and related morphoanatomical characteristics is essential. Thus, the objective of this study was to evaluate the resistance of different accessions of species of Solanum sp., section Lycopersicon to B. tabaci and T. absoluta and establish a relationship with the types of trichomes present on the leaf surface. Whitefly oviposition, nymphs, and exuviae were investigated in 35 genotypes. On the leaf surface of the genotypes, glandular and non-glandular trichomes were identified and quantified. Based on the results, the genotypes were chosen for pinworm testing. Thirteen tomato genotypes were investigated, including Solanum lycopersicum var. cerasiforme, two accessions of S. lycopersicum, and ten wild accessions of Solanum sp., section Lycopersicon. At 7, 14, 21, and 28 days after infestation, eggs were counted on the abaxial surface of the leaflets, and the extent of damage caused by the tomato leafminer was determined using multivariate analysis and the area under the attack severity progress curve. Leaf trichomes of the 13 pre-selected genotypes were identified and quantified. The findings for the whitefly showed that wild genotypes were more resistant than the commercial ones due to the presence of trichomes, mainly glandular trichomes. According to principal component analysis, stronger materials in whitefly tests correlated more with the number of glandular trichomes. Finally, glandular trichomes positively correlate with the genotype's defense against pests. Solanum pennellii LA-716 and S. habrochaites var. hirsutum PI-127826 were the genotypes with the lowest number of oviposition and damage caused by the moth. This trait was also related to the higher density of glandular trichomes. The results show variability among accessions of the same species for trichome density and pest resistance. This information allows the choice of the best accessions among the species when defining the parents to be used in initial crosses of breeding programs.

Growth and Nutritional Responses of Juvenile Wild and Domesticated Cacao Genotypes to Soil Acidity

Cacao is an important tropical crop and requires high-fertility soils for better growth and productivity; nevertheless, soils where this crop is grown are, in general, acidic and low in fertility. Therefore, germplasm with tolerance to soil acidity is desirable for cacao genetic improvement. The objective of this study was to evaluate cacao germplasm for early growth, nutrient concentration, and potential tolerance to soil acidity. A greenhouse experiment was conducted to evaluate 60 cacao genotypes with diverse geographic origins. Cacao seedlings were grown for six months in acid soil with and without lime. Growth parameters and the total concentration of N, P, K, Ca, Mg, Fe, Cu, Mn, and Zn were measured in shoots after harvest. Our results indicate that the best early growth predictors of acid soil tolerance are the number of leaves and root area. N, Ca, Mg, and K uptake may have a potential role in tolerance to soil acidity. Finally, the results revealed a large difference among cacao genotypes in terms of their responses to acid soil stress, which led to the selection of ten genotypes: CCN-51, PH-21, CCN-10, PAS-91, ICT-1087, ICS-95, UF-667, TSH-565, PH-144, ICT-1189 that are potentially tolerant to soil acidity and could be used for breeding acid soil-tolerant cacao varieties.

The root transcriptome dynamics reveals new valuable insights in the salt-resilience mechanism of wild grapevine (Vitis vinifera subsp. sylvestris).

Most of elite cultivated grapevine varieties (Vitis vinifera L.), conventionally grafted on rootstocks, are becoming more and more affected by climate changes, such as increase of salinity. Therefore, we revisited the valuable genetic resources of wild grapevines (V. sylvestris) to elaborate strategies for a sustainable viticulture. Here, we compared physiological and biochemical responses of two salt-tolerant species: a wild grapevine genotype "Tebaba" from our previous studies and the conventional rootstock "1103 Paulsen". Interestingly, our physio-biochemical results showed that under 150mM NaCl, "Tebaba" maintains higher leaf osmotic potential, lower Na+/K+ ratio and a significant peaked increase of polyphenol content at the first 8h of salinity stress. This behavior allowed to hypothesis a drastic repatterning of metabolism in "Tebaba's" roots following a biphasic response. In order to deepen our understanding on the "Tebaba" salt tolerance mechanism, we investigated a time-dependent transcriptomic analysis covering three sampling times, 8h, 24h and 48h. The dynamic analysis indicated that "Tebaba" root cells detect and respond on a large scale within 8h to an accumulation of ROS by enhancing a translational reprogramming process and inducing the transcripts of glycolytic metabolism and flavonoids biosynthesis as a predominate non-enzymatic scavenging process. Afterwards, there is a transition to a largely gluconeogenic stage followed by a combined response mechanism based on cell wall remodeling and lignin biosynthesis with an efficient osmoregulation between 24 and 48 h. This investigation explored for the first time in depth the established cross-talk between the physiological, biochemical and transcriptional regulators contributing to propose a hypothetical model of the dynamic salt mechanism tolerance of wild grapevines. In summary, these findings allowed further understanding of the genetic regulation mechanism of salt-tolerance in V. sylvestris and identified specific candidate genes valuable for appropriate breeding strategies.

Influence of ecological factors on asiaticoside and madecassoside contents and biomass production in Centella asiatica from its natural habitats in south India

Centella asiatica (L.) Urban (CA) has high demand in traditional medicine, skin care, pharmaceutical industries and as a leafy vegetable. India and Madagascar are its key producers. Due to its ever growing demand, CA is collected at an uncontrolled rate from its natural habitats, and this results in destruction of its wild genotypes. Here we report the screening of 106 CA accessions collected from their natural habitats in a wide geographical area in south India for their ASI and MAD contents by HPTLC-densitometry. The edaphic-ecologic parameters of the collection locations of CA accessions were recorded and correlated with their saponin (ASI, MAD) contents. Multilocation trials of CA elite lines at four different agro-climatic locations in Kerala were conducted, and their saponin-biomass yields were determined. Crucially, of these 106 CA accessions, only 6 showed saponin contents above the elite benchmark of industries (ASI+MAD ≥ 4.0%), viz. , 45/Ca-55 (6.18 ± 0.26%), 46/Ca-56 (5.88 ± 0.11%), 48/Ca-58 (4.64 ± 0.15%), 49/Ca-59 (6.94 ± 0.23%), 53/Ca-63 (5.59 ± 0.20%), 55/Ca-65 (5.94 ± 0.18%). Multilocation trials of these elite lines revealed highest saponin contents in Plot 1, characterized by sandy soil (pH 6.0), organic carbon 2.71%, nitrogen 74.20 Kg/ha, phosphorous 100.70 Kg/ha and potassium 23.52 Kg/ha. GC-MS and ICP-MS analyses showed absence of pesticides in CA elite lines and heavy metal contents were within the permissible levels. Highest (ASI+MAD) content (7.55%, dry wt.) and biomass yield (7534.73 Kg/ha) at Plot 1 were shown by the elite line, 49/Ca-59. Average (ASI+MAD) content and biomass yield at Plot 1 were 5.38 ± 1.82% (dry wt.) and 3462.39 ± 2032.54 Kg/ha (n = 6). Noticeably, all six CA elite lines with high ASI, MAD and (ASI+MAD) contents were originally collected from high altitude (700–1700 m) locations. This ASI, MAD screening of CA accessions over a wide geographical area and multilocation trials of elite lines reveal its edaphic and ecological preferences. Our study discovered a hotspot of CA elite clones in south India. This and our previous two reports on a total of 216 accessions provide the range of ASI, MAD and (ASI+MAD) in CA accessions in south India. Further, these studies urge the restriction of random (uncontrolled) collections of CA from its natural habitats, and for the development of cultivation practices of the elite lines for commercial purposes. Overall, this study provides collection, cultivation and conservation strategies towards sustainable management of the resources of this high value medicinal herb. • Centella asiatica accessions (106) from south India were screened for ASI, MAD. • Of 106 CA accessions, only 6 satisfied the elite benchmark of ASI+MAD ≥ 4.0%. • In multilocation trials, elite line showed ASI+MAD 7.55%, biomass 7534.73 Kg/ha. • Altitudes of CA collection locations were correlated to ASI, MAD, ASI+MAD contents. • Discovered a hotspot of CA elite clones in a vast geographical area in south India.

Molecular assessment of wild and cultivated Cicer species using ISSR markers

Characterization of germplasm is one of the prerequisites for utilizing it in crop improvement programs and this requires understanding of genetic relationship between the wild and the cultivar genotypes. For this purpose, we investigated genetic relationships between 12 wild and cultivated accessions of chickpea using ISSR markers. ISSR amplification result shows 123 band out of the 250 bands i.e, (49.2%) bands were polymorphic. The dendrogram classified all twelve accessions into two distinct major clusters A and B, with about 21% of the similarity coefficient value. Based on 20 ISSR primers, Jaccard's similarity indices between pairs of accessions ranged from 0.119 to 1.00. UPGMA dendrogram revealed that the cultivar genotype ICC2210 (Kabuli) from Algeria and the wild genotype ICC17156 (Desi) from Turkey had the lowest similarity indices. According to Principal Component Analysis (PCA), the top three principal components, with Eigen values of 5.40, 3.35, and 2.61, are the most informative, accounting for 61.33% of overall genetic variation. All the accessions were divided into three groups, which covered seven (58.33%) of the total, although five (41.66%) were scattered on the plot. The PCA results resemble to the cluster and similarity coefficient analysis although some deviations have been observed. This information could be useful in breeding strategies for the improvement of chickpea accessions.

Resistant genotypes and biological control for the integrated management of Tetranychus evansi (Acari: Tetranychidae) on tomato

The tomato red spider mite, Tetranychus evansi Baker & Pritchard (Acari: Tetranychidae), is an invasive tomato pest in several countries, with the potential to reduce yield by up to 90% in Africa. Due to the high biotic potential of the pest, the management focused on the use of synthetic pesticides is often not efficient or unsustainable over time, requiring the integration with other control methods. Previous studies found in wild genotypes expressive source of resistance (glandular trichomes) that could be explored to increase resistance level of varieties of interest to this pest. Furthermore, Phytoseiulus longipes Evans (Phytoseiidae), found in South America, proved to be a promising predatory mite of T. evansi. However, the incorporation of this predatory mite into IPM programs requires detailed knowledge of its interactions with other management practices.

Genome-Wide In Silico Identification, Structural Analysis, Promoter Analysis, and Expression Profiling of PHT Gene Family in Sugarcane Root under Salinity Stress

The phosphate transporter (PHT) family of proteins plays an imperative role in regulating phosphorus (P) acquisition as well as in translocation from the soil into cells and organs. Phosphorus is an essential macronutrient required for plant life that is not readily available to crops, and resources are diminishing rapidly because of the huge needs of global agriculture. In this study, 23 ShPHT genes were identified in the sugarcane (Saccharum spp.) genome through a comprehensive genome-wide in silico analysis. Phylogeny, gene structure, and conserved motif analysis of PHT genes in sugarcane (ShPHTs) indicated five subfamilies (PHT1-4 and PHO1 subfamily). Gene ontology (GO) analysis revealed that the ShPHT genes were largely involved in phosphate ion transport, phosphate starvation, stimulus response, stress response, and symporter activity. Gene expression analysis under salinity stress confirmed strong induction of PHT genes in wild genotype sugarcane (IND99-907). PHT1-1, PHT1-2, and PHT1-3 members were notably up-regulated in roots under salt stress. The upstream region of PHT genes contained PHR1-binding sites (P1BS), MYB-type, and WRKY- type binding elements. Overall, the present study paves the way for a deeper understanding of the evolution of sugarcane PHT genes and their role in salinity and Pi stress tolerance in sugarcane.

Functional genetic variation in 3’UTR of PARP1 indicates a decreased risk and a better severity of ischemic stroke

Aim of the study: Polymorphisms of DNA repair enzyme gene may alter the ability of damage repair, ischemic stroke susceptibility and outcome. This study aimed to explore the association of polymorphisms in PARP1 and the effects of interactions between genes in Chinese.Materials and methods: A total of 500 patients and 500 healthy controls were enrolled for genotyping. Results: Clinical information analysis revealed higher levels of alcohol and smoking exposure in patients with ischemic stroke, as well as chronic conditions such as diabetes, hypertension, and higher serum triglycerides concentration. In addition, Polymorphism in PARP1 rs8679 was significantly associated with the decreased ischemic stroke risk. Patients harboring the PARP1 rs8679 AG/GG genotype had a better initial stroke, and as for the mRNA level of PARP1, it was suppressed with mutant genotype in comparison with the wild genotype. Finally, the suppressed of PARP1 was induced by gain-binding ability of miR-124-5p through 3’UTR directly binding.Conclusions: In conclusion, our study demonstrates that the SNP rs8679 in PARP1 3′-UTR might act as a protective factor for the outcome of patients with ischemic stroke.

Factors affecting in vitro regeneration in the model tree Populus trichocarpa: II. Heritability estimates, correlations among explant types, and genetic interactions with treatments among wild genotypes

To enhance the sensitivity of an ongoing Genome Wide Association Study (GWAS) for in vitro shoot regeneration and genetic transformation, a wide range of factors that can affect regeneration rate and, therefore, expression of genetic diversity were studied. Included were explant types and sources; direct versus indirect regeneration; nitrogen salts and micronutrient levels in basal medium; sucrose, auxin, and cytokinin types and levels; light intensity and quality; melatonin and serotonin; antibiotics (to exogenously control contaminants); antioxidants; and the ethylene-mitigating agent silver nitrate. Genotype was a statistically significant source of variance in response to nearly every treatment and for every measure of regeneration noted in shoots and roots, and initial generation of callus. Nonetheless, broad-sense heritability estimates varied widely as a result of variable degrees of environmental modification and statistical interactions with genotype. Compared to leaves, stem and petiole explants were highly correlated in their expression of genetic variation in response to treatments, a likely result of their functional similarity. Based on literature review, this study appears to be the most intensive analysis of plant natural genetic variation in response to in vitro manipulations published. It should help to guide development of improved and highly heritable treatments in other plant species that employ organogenic regeneration systems.