Retraction Note to: Inferring Phylogenetic Relationships of Indian Citron ( Citrus medica L.) Based on rbcL and matK Sequences of Chloroplast DNA The Editor-in-Chief and the publisher have retracted this article [1] because of significant overlap with previously published articles [2–5]. Ajit Uchoi, Surendra Kumar Malik, Ravish Chaudhary, Susheel Kumar, M.R. Rohini, Digvender Pal, and Sezai Ercisli disagree with the retraction. The publisher was not able to get in contact with Rekha Chaudhury, she did not respond to any correspondence about this retraction.

Association of the Variant rs7561317 Downstream of the TMEM18 Gene with Overweight/Obesity and Related Anthropometric Traits in a Sample of Pakistani Population Abstract Obesity is a multifactorial disorder and requires favorable environment for its expression. However, some individuals are more prone to weight gain than others in an obesogenic environment. Thus, at individual level, who becomes overweight or obese is mostly determined by genetic factors. The current study was undertaken to explore for the first time the association of the TMEM18 rs7561317 variant with overweight/obesity and related anthropometric, metabolic, physical, and behavioral traits in a sample of Pakistani population with association between the rs7561317 and many traits was not investigated before in any population. The current study involved a total of 612 subjects including 306 overweight/obese and equal number of age- and sex-matched normal weight individuals. Obesity-related parameters were determined and the variant was genotyped by allelic discrimination assay. All the aforementioned associations were assessed by regression analyses adjusted for covariates and corrected for multiple comparisons. The results revealed a significant association of the TMEM18 rs7561317 with overweight/obese phenotype in more than one genetic model. Therefore, h-index (degree of dominance) was calculated, which indicated the recessive mode of inheritance for the above-said association. Similarly, a significant association of the rs7561317 with obesity-related anthropometric traits and clinical surrogate markers of visceral adiposity was observed. Thus, GG genotype of the rs7561317 was found to increase 1.74 times the risk of overweight/obesity in Pakistani population (OR = 1.74, 95% CI 1.210–2.496, p = 0.003) while low physical activity seemed to accentuate the TMEM18 rs7561317-associated risk of overweight/obesity (OR = 2.696, 95% CI 1.485–4.896, p = 0.004).

Expression of Concern: AFLP-Based Analysis of Genetic Diversity, Population Structure, and Relationships with Agronomic Traits in Rice Germplasm from North Region of Iran and World Core Germplasm Set

Correction to: Morphological Characterization and Gene Expression Patterns for Melanin Pigmentation in Rex Rabbit The original article has been published with an incorrect grant number in the Funding section.

Association of the IL6 Gene Polymorphism with Component Features of Metabolic Syndrome in Obese Subjects Abstract Metabolic syndrome (MetS) is a risk factor for type 2 diabetes mellitus and cardiovascular disease. Obesity is a component of the metabolic syndrome. Several genetic variants are reported to be associated with obesity and hypo adiponectinemia, including ars1800796 polymorphism of the interleukin-6 (IL-6) gene. Since obesity is associated with inflammatory factors, the aim of this study was to investigate the association between this polymorphism and MetS and its related features. Obese patients with body mass index (BMI) ≥ 30 (n = 182) were recruited into this study and divided into two groups; 110 patients with MetS, based on the International Diabetes Federation (IDF) criteria, and 72 subjects without MetS. The anthropometric and biochemical data for the groups were compared. Genotyping was carried out using RT-PCR. The association of the genetic polymorphism with MetS and its components were assessed using univariate and multivariate analyzes. There was an association between the presence of the rs1800796polymorphism of the IL-6 gene, with BMI (P = 0.031), high-density lipoprotein (HDL) (P = 0.010) and low-density lipoprotein (LDL) (P = 0.037), while this genetic variant did not show any significant association with the presence of MetS as defined by the IDF. We demonstrate an association between the rs1800796 genetic variant of the IL-6 gene with components of MetS including BMI, and HDL-cholesterol, but not the MetS itself. Therefore, supporting further studies are warranted to investigate this point in a larger population.

Discovery and Utilization of EST-SSR Marker Resource for Genetic Diversity and Population Structure Analyses of a Subtropical Bamboo, Dendrocalamus hamiltonii Abstract Dendrocalamus hamiltonii is a giant bamboo species native to Indian subcontinent with high economic importance. Nevertheless, highly outcross nature and flowering once in decades impose severe limitation in its propagation. Identification and mixed cultivation of genetically diverse genotypes may assist successful breeding and natural recombination of desirable traits. Characterization of existing genetic diversity and population structure are indispensable for efficient implementation of such strategies, which is facing a major challenge due to non-availability of sequence-based markers for the species. In this study, 8121 EST-SSR markers were mined from D. hamiltonii transcriptome data. Among all, tri-repeats were most represented (52%), with the abundance of CCG/CGG repeat motif. A set of 114 polymorphic markers encompassing epigenetic regulators, transcription factors, cell cycle regulators, signaling, and cell wall biogenesis, detected polymorphism and interaction (in silico) with important genes, that might have role in bamboo growth and development. Genetic diversity and population structure of the three D. hamiltonii populations (72 individuals) revealed moderate to high-level genetic diversity (mean alleles per locus: 5.8; mean PIC: 0.44) using neutral EST-SSR markers. AMOVA analysis suggests maximum diversity (59%) exists within population. High genetic differentiation (Gst = 0.338) and low gene flow (Nm = 0.49) were evident among populations. Further, PCoA, dendrogram, and Bayesian STRUCTURE analysis clustered three populations into two major groups based on geographical separations. In future, SSR marker resources created can be used for systematic breeding and implementation of conservation plans for sustainable utilization of bamboo complex.

Genome-Wide Identification of the Aux/IAA Family Genes ( MdIAA ) and Functional Analysis of MdIAA18 for Apple Tree Ideotype Abstract The Aux/IAA (auxin/indole-3-acetic acid) gene family is one of the early auxin-responsive gene families, which play a central role in auxin response. Few reports are involved in Aux/IAA genes in fruit trees, especially in apple (Malus × domestica Borkh.). A total of 33 MdIAA members were identified, of which 27 members contained four conserved domains, whereas the others lost one or two conserved domains. Several cis-elements in promoters of MdIAAs were predicted responsive to hormones and abiotic stress. Tissue-specific expression patterns of MdIAAs in different apple tree ideotypes were investigated by quantitative real-time PCR. A large number of MdIAAs were highly expressed in leaf buds and reproductive organs, and MdIAAs clustered in same group showed similar expression profiles. Overexpression of MdIAA18 in Arabidopsis resulted in compact phenotype. These results indicated that MdIAA genes may be involved in vegetative and reproductive growth of apple. Taken together, the results provide useful clues to reveal the function of MdIAAs in apple and control apple tree architecture by manipulation of MdIAAs.

IGF2 is Deregulated During the Development of Uterine Cervical Carcinoma in Indian Patients Abstract Uterine cervical carcinoma (CACX) is one of the leading causes of deaths in Indian women. Chromosomal alterations including 11p15.5 locus were reported in CACX. Consequently, we strived for the first time to understand the molecular status of the candidate gene Insulin-like growth factor 2, IGF2 (11p15.5) in Indian CACX patients (n = 128). DNA copy number (CN) analysis using CGH-SNP analysis showed no genetic alteration and it was further validated by comparison with publicly available CN datasets. But promoter hypo-methylation during the progression of CACX was observed and also found to be concordant with publicly available DNA methylation datasets. Interestingly, we found diverse expression of IGF2 transcript in both normal cervical epithelium (NCE) and CACX tumors. Similar heterogeneous expression pattern was seen in publicly available expression datasets as well. Finally, protein expression analysis in NCE showed concordance with transcript expression but tumors showed frequent low expression. Log-rank test showed a difference (p-value = 0.057) in overall survival between cases with and without alteration for IGF2 in Indian CACX patients. Collectively, our study proposes that regulation of IGF2 expression in NCE appeared to be multifaceted and deregulation during the development of CACX resulted in the differential expression.

Morphological Characterization and Gene Expression Patterns for Melanin Pigmentation in Rex Rabbit Abstract Animal melanin has an important role in the formation of animal fur and skin, which is determined by its quantities, character, and distribution. To identify the effect of melanin on the formation of multi-colored Rex rabbits (Black, Chinchilla, Beaver, Protein cyan, Protein yellow, White), the structure of hair follicles and melanin content in multi-colored Rex rabbit skins were observed by Hematoxylin and Eosin (H&E) staining and melanin staining, respectively. The melanin granules were primarily found in the epidermis and hair follicle roots. The melanin content of skin was measured by extracting melanin from skin tissue. The results demonstrated that the melanin content was the highest in the skin of black Rex rabbit. Additionally, we measured the mRNA and protein expression levels of melanin-related key genes (MITF and TYR) in the skin of different hair color by quantitative real-time PCR and Wes assay, respectively. The results revealed that the mRNA expression levels in the skin of black Rex rabbit was highly expressed when as compared with other Rex rabbit skin (P < 0.01), and they were the lowest in the skin of white Rex rabbit. Finally, correlation analysis was conducted between melanin content and the expression levels of mRNA and protein. The results indicated a significant correlation between melanin content and the mRNA expression of MITF (P < 0.05), but it was not correlated with the mRNA expression of TYR (P > 0.05). In summary, melanin deposition has important economic value, and the coat color of fur-bearing animals is partly determined by the melanin-related genes.

De Novo Assembled Transcriptome Analysis and Identification of Genic SSR Markers in Red-Flowered Strawberry Abstract Red-flowered strawberry is a new ornamental flower derived from intergeneric hybridization (Fragaria × Potentilla). To date, few molecular markers have been reported for this plant. RNA sequencing provides a relatively fast and low-cost approach for large-scale detection of simple sequence repeats (SSRs). In the present study, we profiled the transcriptome of red-flowered strawberry by Illumina HiSeq 2500 to identify SSRs related to petal color. Based on 2 million clean reads of red and white flowers from red-flowered strawberry hybrids, we assembled 91,835 unigenes with an average length of 717 bp. After functional annotation and prediction, there were 47,058 unigenes; of these, 26,861 had a gene ontology annotation, with 14,264 SSR loci. Mononucleotide SSRs were the predominant repeat type (47.20%, n = 6724), followed by di- (32.50%, n = 4641), tri- (19.10%, n = 2729), tetra- (0.90%, n = 132), hexa- (0.2%, n = 21), and penta- (0.10%, n = 16) nucleotide repeats. The most frequent di-, tri-, and tetra-nucleotide repeats were AG/CT, AAG/CTT, and AAAG/CTTT, respectively. PCR amplification with 105 SSR primer pairs yielded four bands specific to red flowers, namely UgRFsr57622, UgRFsr94149, UgRFsr40142, and UgRFsr54608; corresponding 4 trait-specific markers were found to co-segregate with white and red flower color in hybrid population, demonstrating that the genic SSR marker is useful to discriminate between white and red flowers in strawberry. Markers to discriminate flower color in red-flowered strawberry will be useful for early selection of progeny and for breeding management.