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Fulltext The Effects of Feed Restriction and Isolated or Group Rearing on the Measurement of Individual Feed Intake and Estimation of Feed Conversion Ratio in Juvenile Nile Tilapia (Oreochromis niloticus) for Selective Breeding Purposes

Rodde C, Vandeputte M, Trinh TQ, Douchet V, Canonne M, Benzie JAH, et al.

Front Genet, 2020;11:596521.
PMID: 33519898 DOI: 10.3389/fgene.2020.596521

Accurately measuring the phenotype at the individual level is critical to the success of selective breeding programs. Feed efficiency is a key sustainability trait and is typically approached through feed conversion ratio (FCR). This requires measurements of body weight gain (BWG) and feed intake (FI), the latter being technically challenging in fish. We assessed two of the principal methods for measuring feed intake in fish over consecutive days: (1) group rearing 10 fish per group and video recording the meals and (2) rearing fish individually on a restricted ration. Juvenile Nile tilapia (Oreochromis niloticus) from the Genetically Improved Farmed Tilapia (GIFT) strain and the Cirad strain were entered into the study (128 GIFT and 109 Cirad). The GIFT strain were reared over three consecutive periods of 7 days each under different feeding, recording, and rearing scenarios (i) in groups fed an optimal ration (g100) or (ii) fed a 50% restricted ration (g50) both with video records of all meals and (iii) reared in isolation and fed a 50% restrictive ration. The Cirad strain were tested similarly but only for scenarios (i) and (iii). All fish were fed twice daily with a calculated ration. Correlations showed the same trends for the GIFT and the Cirad strains. For the GIFT strain, correlations were positive and significant for BWG and FI measured in scenarios (i) and (ii), 0.49 and 0.63, respectively, and FI measured in scenarios (i) and (iii) (0.50) but not for BWG measured in scenarios (i) and (iii) (0.29, NS). The phenotypic correlation estimated for FCR between scenarios (i) and (ii) with fish fed an optimal or a 50% restricted ration was low and not significant (0.22). Feed Conversion Ratio for GIFT fish reared in groups or in isolation and fed with a restricted ration [scenarios (ii) and (iii)] were not significantly correlated either. Social interactions between fish, potentially impacting their efficiency, may explain the results. Therefore, selective breeding programs seeking to improve feed efficiency will need to carefully plan the feeding rate and the rearing system used to estimate FCR in order to optimize selection for the targeted production system.

Matched MeSH terms: Phenotype
Effect of HbE trait on measurement of HbA1c by three different methods

Azizi A, Sthaneshwar P, Shanmugam H, Arumugam S

Pathology, 2015 Aug;47(5):495-7.
PMID: 26126045 DOI: 10.1097/PAT.0000000000000286
Matched MeSH terms: Phenotype
The brave new world of genetic testing in the management of the dyslipidaemias

Nawawi HM, Chua YA, Watts GF

Curr Opin Cardiol, 2020 05;35(3):226-233.
PMID: 32097179 DOI: 10.1097/HCO.0000000000000721

PURPOSE OF REVIEW: With the exception of familial hypercholesterolaemia, the value of genetic testing for managing dyslipidaemias is not established. We review the genetics of major dyslipidaemias in context of clinical practice.
RECENT FINDINGS: Genetic testing for familial hypercholesterolaemia is valuable to enhance diagnostic precision, cascade testing, risk prediction and the use of new medications. Hypertriglyceridaemia may be caused by rare recessive monogenic, or by polygenic, gene variants; genetic testing may be useful in the former, for which antisense therapy targeting apoC-III has been approved. Familial high-density lipoprotein deficiency is caused by specific genetic mutations, but there is no effective therapy. Familial combined hyperlipidaemia (FCHL) is caused by polygenic variants for which there is no specific gene testing panel. Familial dysbetalipoproteinaemia is less frequent and commonly caused by APOE ε2ε2 homozygosity; as with FCHL, it is responsive to lifestyle modifications and statins or/and fibrates. Elevated lipoprotein(a) is a quantitative genetic trait whose value in risk prediction over-rides genetic testing; treatment relies on RNA therapeutics.
SUMMARY: Genetic testing is not at present commonly available for managing dyslipidaemias. Rapidly advancing technology may presage wider use, but its worth will require demonstration of cost-effectiveness and a healthcare workforce trained in genomic medicine.

Matched MeSH terms: Phenotype
Fulltext Review of functional markers for improving cooking, eating, and the nutritional qualities of rice

Lau WC, Rafii MY, Ismail MR, Puteh A, Latif MA, Ramli A

Front Plant Sci, 2015;6:832.
PMID: 26528304 DOI: 10.3389/fpls.2015.00832

After yield, quality is one of the most important aspects of rice breeding. Preference for rice quality varies among cultures and regions; therefore, rice breeders have to tailor the quality according to the preferences of local consumers. Rice quality assessment requires routine chemical analysis procedures. The advancement of molecular marker technology has revolutionized the strategy in breeding programs. The availability of rice genome sequences and the use of forward and reverse genetics approaches facilitate gene discovery and the deciphering of gene functions. A well-characterized gene is the basis for the development of functional markers, which play an important role in plant genotyping and, in particular, marker-assisted breeding. In addition, functional markers offer advantages that counteract the limitations of random DNA markers. Some functional markers have been applied in marker-assisted breeding programs and have successfully improved rice quality to meet local consumers' preferences. Although functional markers offer a plethora of advantages over random genetic markers, the development and application of functional markers should be conducted with care. The decreasing cost of sequencing will enable more functional markers for rice quality improvement to be developed, and application of these markers in rice quality breeding programs is highly anticipated.

Matched MeSH terms: Phenotype
Identifying a Long QTL Cluster Across chrLG18 Associated with Salt Tolerance in Tilapia Using GWAS and QTL-seq

Jiang DL, Gu XH, Li BJ, Zhu ZX, Qin H, Meng ZN, et al.

Mar Biotechnol (NY), 2019 Apr;21(2):250-261.
PMID: 30737627 DOI: 10.1007/s10126-019-09877-y

Understanding the genetic mechanism of osmoregulation is important for the improvement of salt tolerance in tilapia. In our previous study, we have identified a major quantitative trait locus (QTL) region located at 23.0 Mb of chrLG18 in a Nile tilapia line by QTL-seq. However, the conservation of these QTLs in other tilapia populations or species is not clear. In this study, we successfully investigated the QTLs associated with salt tolerance in a mass cross population from the GIFT line of Nile tilapia (Oreochromis niloticus) using a ddRAD-seq-based genome-wide association study (GWAS) and in a full-sib family from the Malaysia red tilapia strain (Oreochromis spp) using QTL-seq. Our study confirmed the major QTL interval that is located at nearly 23.0 Mb of chrLG18 in Nile tilapia and revealed a long QTL cluster across chrLG18 controlling for the salt-tolerant trait in both red tilapia and Nile tilapia. This is the first GWAS analysis on salt tolerance in tilapia. Our finding provides important insights into the genetic architecture of salinity tolerance in tilapia and supplies a basis for fine mapping QTLs, marker-assisted selection, and further detailed functional analysis of the underlying genes for salt tolerance in tilapia.

Matched MeSH terms: Phenotype
Evaluating Frugivore-fruit Interactions Using Avian Eye Modelling

Fadzly N, Burns KC, Zuharah WF

Trop Life Sci Res, 2013 Dec;24(2):31-50.
PMID: 24575247 MyJurnal

Fruit phenotypes are often hypothesised to be affected by selection by frugivores. Here, we tested two hypotheses concerning frugivore-fruit interactions from the perspective of fruit colours. We measured the spectral properties of 26 fruits and the associated leaves of plants from 2 islands in New Zealand. Visual observations were also performed to record the birds that fed on the fruits. First, we tested the fruit-foliage hypothesis, where fruit colours are assumed to be evolutionarily constrained by their own leaf colour to maximise colour contrast and fruit conspicuousness. We ran a null model analysis comparing fruit colour contrast using an avian eye model. Second, we tested the frugivore specificity hypothesis, where specific fruit colours are thought to be connected with a specific bird frugivore. We performed a regression on the number of bird visits against the fruit colour in tetrahedral colour space based on an avian eye calculation using Mantel's test. The results show that fruit colours are not constrained by their own leaf colours. There is also no relationship or pattern suggesting a link between a specific fruit colour and specific bird visitors. We suggest that although fruit colour is one of the most highly discussed components, it is not the most important single deciding factor in frugivore fruit selection.

Matched MeSH terms: Phenotype
Fulltext Establishment and analysis of the 3-dimensional (3D) spheroids generated from the Nasopharyngeal Carcinoma cell line HK1

Muniandy, Kalaivani, Sankar, Prabu Siva, Lian, Benedict Shi Xiang, Khoo, Alan Soo-Beng, Balakrishnan, Venugopal, Mohana-Kumaran, Nethia

Trop Life Sci Res, 2016;27(11):125-130.
MyJurnal

Spheroids have been shown to recapitulate the tumour in vivo with properties
such as the tumour microenvironment, concentration gradients, and tumour phenotype. As
such, it can serve as a platform for determining the growth and invasion behaviour pattern
of the cancer cells as well as be utilised for drug sensitivity assays; capable of exhibiting
results that are closer to what is observed in vivo compared to two-dimensional (2D) cell
culture assays. This study focused on establishing a three-dimensional (3D) cell culture
model using the Nasopharyngeal Carcinoma (NPC) cell line, HK1 and analysing its growth
and invasion phenotypes. The spheroids will also serve as a model to elucidate their
sensitivity to the chemotherapeutic drug, Flavopiridol. The liquid overlay method was
employed to generate the spheroids which was embedded in bovine collagen I matrix for
growth and invasion phenotypes observation. The HK1 cells formed compact spheroids
within 72 hours. Our observation from the 3 days experiments revealed that the spheroids
gradually grew and invaded into the collagen matrix, showing that the HK1 spheroids are
capable of growth and invasion. Progressing from these experiments, the HK1 spheroids
were employed to perform a drug sensitivity assay using the chemotherapeutic drug,
Flavopiridol. The drug had a dose-dependent inhibition on spheroid growth and invasion.

Matched MeSH terms: Phenotype
Fulltext Morphological Variability Identification of Harumanis Mango (Mangifera indica L.) Harvested from Different Location and Tree Age

Yusuf SNA, Rahman AMA, Zakaria Z, Subbiah VK, Masnan MJ, Wahab Z

Trop Life Sci Res, 2020 Jul;31(2):107-143.
PMID: 32922671 DOI: 10.21315/tlsr2020.31.2.6

Harumanis is one of the main signatures of Perlis with regards to its delightful taste, pleasant aroma and expensive price. Harumanis authenticity and productivity had become the remarks among the farmers, entrepreneurs, consumers and plant breeders due to the existence of morphological characteristics variation among the fruits and high production cost. Assessment of Harumanis morphological characteristics of natural population and different tree ages may represent a possible source of important characteristics for development and breeding purposes of Harumanis. The aim of this study is to evaluate the morphological variation of Harumanis collected from different location in Perlis and tree age. A total of 150 Harumanis fruits from 50 trees with three different stages of development (young, middle-aged and old) were characterised using 11 traits; 10 quantitative and one qualitative morphological trait. The ANOVA analyses in combination with Dunn's pairwise and Kruskal-Wallis multiple comparison test able to point out the existence of environmental factor and age influence towards the significant different of identified morphological traits except for Total Soluble Solid (TSS) and pulp percentage. Five clusters of 50 Harumanis accessions reflect a grouping pattern which not according to neither geographical region nor age. The result of Principal Component Analysis (PCA) using the first two principal components (PCs) provided a good approximation of the data explaining 84.09% of the total variance which majorly contributed by parameters of weight, fruit dimensional characteristics, peel percentage and hue angle, h. Preliminary screening of important morphological characteristics which contribute to the phenotypic diversity of Harumanis is successfully achieved. The findings can be employed by the plant breeders and farmers for the establishment of standard grading of Harumanis and advancement of breeding crop of Harumanis in future.

Matched MeSH terms: Phenotype
von Willebrand disease: Diagnosis and treatment, treatment of women, and genomic approach to diagnosis

Laffan M, Sathar J, Johnsen JM

Haemophilia, 2021 Feb;27 Suppl 3:66-74.
PMID: 32578345 DOI: 10.1111/hae.14050

von Willebrand disease (VWD) is the most common inherited bleeding disorder. VWD is caused by deficiencies in von Willebrand factor (VWF), a critical adhesive haemostatic protein. This review provides an overview of VWD diagnosis and treatment, special considerations in treating women with VWD, and current genomic approaches to VWD. For diagnosis and treatment in VWD, an accurate diagnosis is critical to providing effective treatments, determining appropriate laboratory monitoring and for counselling the patient and family. Diagnosis of VWD begins with the clinical assessment for the bleeding phenotype, which is usually characterized by mucocutaneous and provoked bleeding. The diagnosis of VWD is then made by laboratory investigation. Multiple assays are used to assess VWF levels and functions. The mainstays of VWD treatment are tailored by VWD type and symptoms, and can include antifibrinolytic treatment, desmopressin and VWF replacement treatment. Women with VWD are also at risk for excessive uterine bleeding, such as with menses and childbirth. In addition to standard VWD treatments, heavy menstrual bleeding can be treated with hormones. Interdisciplinary management of childbirth and prophylaxis in the postpartum period are needed to reduce the risk of postpartum haemorrhage. Genomic approaches to VWD can inform VWD diagnosis, treatment, test assay selection, reproductive planning and family counselling. Most VWD patients have an identifiable VWF gene DNA variant. Next-generation sequencing is rapidly being adopted to provide more comprehensive VWF sequence information for patients with known or suspected VWD.

Matched MeSH terms: Phenotype
Fulltext Revisiting asthma phenotype in children

Fahisham Taib

Malaysian Journal of Paediatrics and Child Health, 2011;17(1):0-0.
MyJurnal

Asthma is considered as heterogeneous multidimensional disorder due to variable phenotypic presentation. Phenotype is defined as a cluster of either clinical or pathologic features, which tends to be associated with the understanding the mechanisms of the disease. Asthma is typically characterized by airway inflammation, variable airway obstruction, bronchial hyper-reactivity, smooth muscle hypertrophy and apparent reversible airflow obstruction by bronchodilators. ‘Asthma syndrome’ is a term to describe complex pathophysiology of the condition which is not exclusive to allergen triggered episodes. Diagnosing childhood asthma is difficult, due to the similarity of symptoms and overlapping with other wheezing conditions. The precise mechanism for asthma exacerbation, for each individual phenotype is not fully understood. However, it is influenced by genetic interaction with variety of external environmental stimuli. The current understanding on asthma phenotypes were interpreted based on age of onset, associated triggers, clinical aspects, physiologic parameters and type of inflammation (Table 1). Due to the illdefined of the current phenotypic definition and disagreement among the respirologists, it is becoming a challenge to label specific phenotype with certainty. Accurate definition of each phenotype should therefore be helpful to provide better understanding of different mechanistic pathways and focusing on targeted therapy for individual phenotype. (Copied from article).

Matched MeSH terms: Phenotype
The aetiology of Turner's syndrome

Boon WH

Med J Malaya, 1969 Jun;23(4):272-81.
PMID: 4242175
Matched MeSH terms: Phenotype
Fulltext The relevance of micrornas in vascular aging

Wong PF, Jong HL

JUMMEC, 2014;17(2):1-6.
MyJurnal

MicroRNAs (miRNAs) are short, single-stranded non-coding RNAs that control gene expression by annealing to complementary sequences in mRNAs. They are estimated to regulate at least one third of human transcripts and hence, manipulation of these miRNAs can profoundly affect the proteome and ultimately cellular phenotypes. A substantial amount of work has shed light on the crucial roles of miRNAs in diseases. miRNA expression profiles between normal and diseased tissues have identified miRNA signature patterns that correlate to disease development and progression. This review discusses some of the important miRNAs that are involved in endothelial cell senescence and dysfunction that contribute to the development and progression of cardiovascular diseases.

Matched MeSH terms: Phenotype
Fulltext Haemolytic Disease of Foetus and Newborn and Haemolytic Transfusion Reaction Due to Kidd antibody in Hospital Umum Sarawak, Malaysia

Irni Mohd Yasin, Narazah Mohd Yusoff, Afifah Hassan, Muhammad Masrin Md. Zahrin

Journal of Biomedical and Clinical Sciences, 2017;2(202):26-27.
MyJurnal

Haemolytic Disease of Foetus and Newborn (HDFN) and Haemolytic Transfusion Reaction (HTR) may occur due to antibodies against Kidd antigen. In Malaysia, the prevalence of RBC alloimmunization due to Kidd antibody for cases of HDFN and HTR have been reported [1-2] however there is insufficient data in Hospital Umum Sarawak (HUS).The aim of this study is to determine whether Kidd alloimmunization causes HDFN and HTR. Indirectly categorize Kidd phenotype blood in regular blood donors.

Matched MeSH terms: Phenotype
Fulltext Molecular Genetic Characterization of Patients With Focal Epilepsy Using a Customized Targeted Resequencing Gene Panel

Tsai MH, Chan CK, Chang YC, Lin CH, Liou CW, Chang WN, et al.

Front Neurol, 2018;9:515.
PMID: 30034362 DOI: 10.3389/fneur.2018.00515

Objective: Focal epilepsy is the most common subtype of epilepsies in which the influence of underlying genetic factors is emerging but remains largely uncharacterized. The purpose of this study is to determine the contribution of currently known disease-causing genes in a large cohort (n = 593) of common focal non-lesional epilepsy patients. Methods: The customized focal epilepsy gene panel (21 genes) was based on multiplex polymerase chain reaction (PCR) and sequenced by Illumina MiSeq platform. Results: Eleven variants (1.85%) were considered as pathogenic or likely pathogenic, including seven novel mutations. There were three SCN1A (p.Leu890Pro, p.Arg1636Ter, and p.Met1714Val), three PRRT2 (two p.Arg217Profs*8 and p.Leu298Pro), two CHRNA4 (p.Ser284Leu, p.Ile321Asn), one DEPDC5 (p.Val516Ter), one PCDH19 (p.Asp233Asn), and one SLC2A1 (p.Ser414Ter) variants. Additionally, 16 other rare variants were classified as unknown significance due to inconsistent phenotype or lack of segregation data. Conclusion: Currently known focal epilepsy genes only explained a very small subset of focal epilepsy patients. This indicates that the underlying genetic architecture of focal epilepsies is very heterogeneous and more novel genes are likely to be discovered. Our study highlights the usefulness, challenges and limitations of using the multi-gene panel as a diagnostic test in routine clinical practice in patients with focal epilepsy.

Matched MeSH terms: Phenotype
Fulltext The modified Gompertz model demonstrates a variable growth rate between two Centella asiatica phenotypes

Hussein, S., Halmi, M.I.E., Ling, A.P.K.

Journal of Biochemistry, Microbiology and Biotechnology, 2017;5(1):18-20.
MyJurnal

Centella asiatica, a weakly aromatic plant that flourishes in wet tropical and sub-tropical areas as
a medicinal species since ancient times. It contained important terpenoids that impart important
medicinal values. Currently, studies on the terpenoid content of various Centella asiatica
phenotypes have shown not only variable content but variable growth rates of different
phenotypes that can affect future selection of phenotypes. The use of mathematical growth
modelling can reveal important growth constants and discriminate between faster and slower
growth phenotypes. Two Centella asiatica phenotypes from South Africa is modelled using the
modified Gompertz model and the results showed that the C. asiatica Type-1 exhibited a faster
growth rates and a shorter lag period at 0.152 day-1 and 2.313 day than another phenotype; C.
asiatica Type 2 with a growth rate and a lag period of 0.067 day-1 and 3.363 day, respectively.
The data indicates that different phenotypes of C. asiatica can have different growth rates and
lag period and this can be important for selection of phenotypes to be used as the best bioactive
peptides producer.

Matched MeSH terms: Phenotype
Fulltext Genotypic and Phenotypic Relationship among Yield Components in Rice under Tropical Conditions

Oladosu Y, Rafii MY, Magaji U, Abdullah N, Miah G, Chukwu SC, et al.

Biomed Res Int, 2018;2018:8936767.
PMID: 30105259 DOI: 10.1155/2018/8936767

The associations among yield-related traits and the pattern of influence on rice grain yield were investigated. This evaluation is important to determine the direct and indirect effects of various traits on yield to determine selection criteria for higher grain yield. Fifteen rice genotypes were evaluated under tropical condition at five locations in two planting seasons. The experiment was laid out in a randomized complete block design with three replications across the locations. Data were collected on vegetative and yield components traits. The pooled data based on the analysis of variance revealed that there were significant differences (p < 0.001) among the fifteen genotypes for all the characters studied except for panicle length and 100-grain weight. Highly significant and positive correlations at phenotypic level were observed in grain weight per hill (0.796), filled grains per panicle (0.702), panicles per hill (0.632), and tillers per hill (0.712) with yield per hectare, while moderate positive correlations were observed in flag leaf length to width ratio (0.348), days to flowering (0.412), and days to maturity (0.544). By contrast, unfilled grains per panicle (-0.225) and plant height (-0.342) had a negative significant association with yield per hectare. Filled grains per panicle (0.491) exhibited the maximum positive direct effect on yield followed by grain weight per hill (0.449), while unfilled grain per panicle (-0.144) had a negative direct effect. The maximum indirect effect on yield per hectare was recorded by the tillers per hill through the panicles per hill. Therefore, tillers per hill, filled grains per panicle, and grain weight per hill could be used as selection criteria for improving grain yield in rice.

Matched MeSH terms: Phenotype
Fulltext Opportunistic Bacteria Dominate the Soil Microbiome Response to Phenanthrene in a Microcosm-Based Study

Storey S, Ashaari MM, Clipson N, Doyle E, de Menezes AB

Front Microbiol, 2018;9:2815.
PMID: 30519226 DOI: 10.3389/fmicb.2018.02815

Bioremediation offers a sustainable approach for removal of polycyclic aromatic hydrocarbons (PAHs) from the environment; however, information regarding the microbial communities involved remains limited. In this study, microbial community dynamics and the abundance of the key gene (PAH-RHDα) encoding a ring hydroxylating dioxygenase involved in PAH degradation were examined during degradation of phenanthrene in a podzolic soil from the site of a former timber treatment facility. The 10,000-fold greater abundance of this gene associated with Gram-positive bacteria found in phenanthrene-amended soil compared to unamended soil indicated the likely role of Gram-positive bacteria in PAH degradation. In contrast, the abundance of the Gram-negative PAHs-RHDα gene was very low throughout the experiment. While phenanthrene induced increases in the abundance of a small number of OTUs from the Actinomycetales and Sphingomonadale, most of the remainder of the community remained stable. A single unclassified OTU from the Micrococcaceae family increased ~20-fold in relative abundance, reaching 32% of the total sequences in amended microcosms on day 7 of the experiment. The relative abundance of this same OTU increased 4.5-fold in unamended soils, and a similar pattern was observed for the second most abundant PAH-responsive OTU, classified into the Sphingomonas genus. Furthermore, the relative abundance of both of these OTUs decreased substantially between days 7 and 17 in the phenanthrene-amended and control microcosms. This suggests that their opportunistic phenotype, in addition to likely PAH-degrading ability, was determinant in the vigorous growth of dominant PAH-responsive OTUs following phenanthrene amendment. This study provides new information on the temporal response of soil microbial communities to the presence and degradation of a significant environmental pollutant, and as such has the potential to inform the design of PAH bioremediation protocols.

Matched MeSH terms: Phenotype
Fulltext Whole exome sequencing identifies compound heterozygous variants of CR2 gene in monozygotic twin patients with common variable immunodeficiency

Mat Ripen A, Ghani H, Chear CT, Chiow MY, Syed Yahya SNH, Kassim A, et al.

SAGE Open Med, 2020;8:2050312120922652.
PMID: 32547748 DOI: 10.1177/2050312120922652

Objectives: A pair of female Malay monozygotic twins who presented with recurrent upper respiratory tract infections, hepatosplenomegaly, bronchiectasis and bicytopenia were recruited in this study. Both patients were suspected with primary immunodeficiency diseases. However, the definite diagnosis was not clear due to complex disease phenotypes. The objective of this study was to identify the causative gene mutation in these patients.
Methods: Lymphocyte subset enumeration test and whole exome sequencing were performed.
Results: We identified a compound heterozygous CR2 mutation (c.1916G>A and c.2012G>A) in both patients. These variants were then confirmed using Sanger sequencing.
Conclusion: Whole exome sequencing analysis of the monozygotic twins revealed compound heterozygous missense mutations in CR2.

Matched MeSH terms: Phenotype
Fulltext Data on genome resequencing of pigmented and non-pigmented Malaysian rice varieties

Zainal-Abidin RA, Zainal Z, Mohamed-Hussein ZA, Sew YS, Simoh S, Ab Razak S, et al.

Data Brief, 2020 Aug;31:105806.
PMID: 32566707 DOI: 10.1016/j.dib.2020.105806

The genomics and genetic data of pigmented and non-pigmented Malaysian rice varieties are still limited. Hence, we performed the genome resequencing of two black rice varieties (Bali, Pulut Hitam 9), two red rice varieties (MRM16, MRQ100) and two white rice varieties (MR297 and MRQ76) using Illumina HiSeq 4000 platform with 30x sequencing coverage. We aimed to identify and annotate single nucleotide polymorphisms (SNPs) from the genome of these four pigmented and two non-pigmented rice varieties. The potential SNPs will be used in developing the functional SNP markers related to nutritional (i.e. antioxidant, folate, amylose) and quality (i.e. aromatic) traits. Raw data of the pigmented and non-pigmented rice varieties have been deposited into the European Nucleotide Archive (ENA) database with accession number PRJEB29070 and PRJEB32344, respectively.

Matched MeSH terms: Phenotype
Bisphenol A exposure modulates reproductive and endocrine system, mitochondrial function and cellular senescence in female adult rats: A hallmarks of polycystic ovarian syndrome phenotype

Prabhu NB, Adiga D, Kabekkodu SP, Bhat SK, Satyamoorthy K, Rai PS

Environ Toxicol Pharmacol, 2022 Nov;96:104010.
PMID: 36334871 DOI: 10.1016/j.etap.2022.104010

Bisphenol A (BPA) mimics estrogen and consequently suspected to be detrimental to female reproductive system. Biomonitoring confirms the BPA burden in body leading to a complex condition called polycystic ovarian syndrome (PCOS) which is frequently attributed to female infertility. Due to unclear precise molecular pathomechanisms of BPA in PCOS, we intend to examine the molecular mechanisms of the reproductive, endocrine, mitochondrial features, and cellular senescence in BPA-treated rats. We analyzed vaginal smears and ovarian follicles using microscope, assessed sex hormones by ELISA, analyzed BPA target gene expression by semi-quantitative RT-PCR, assessed senescence induction by β-galactosidase staining and immunofluorescence in BPA-treated rats. Our data showed hormonal imbalance, impaired folliculogenesis, abnormal expression patterns of target genes, CDKN2A overexpression and enhanced ROS levels in BPA-treated rats. This study provides insights on the effects of BPA exposure on ovulatory, hormonal, mitochondrial dysfunction, and senescence that benefit in better understanding of PCOS induced by BPA.

Matched MeSH terms: Phenotype

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