Signatures of positive selection on the hepatic lipase gene in human populations.
Abstract The hepatic lipase plays a central role in the lipid metabolism, catalyzing the hydrolysis of phospholipids, monoglycerides, diglycerides, and triglycerides, and acyl-CoA. It is also implied in the conversion of very low-density lipoprotein and intermediate density lipoprotein to low density lipoproteins. As a consequence, the gene encoding the hepatic lipase (LIPC) is associated with several diseases derived from the imbalance of lipids that are in general derived from the interaction between life styles and genetic architecture. Therefore, it is interesting to understand more about the characteristics o...
Source: Journal of Genetics - February 26, 2020 Category: Genetics & Stem Cells Authors: Flores SV, Olivari CF, Prado LF Tags: J Genet Source Type: research
Role of MMP-1, MMP-8 and MMP-9 gene polymorphisms in preterm birth.
This study, which is a hospital-based case-control study, aims to investigate the association of MMP-1, MMP-8 and MMP-9 polymorphisms, and levels of MMP-9 in preterm birth. Increased level of MMP-9 was reported in cases as compared to control. The significant association of MMP-9 (-1562) CT (P = 0.001; OR = 1.44(CI = 0.97-2.14)) and TTgenotype (P = 0.05;OR = 2.6 (CI = 1.46-4.69)) were reported in preterm birth. Our findings suggest that the MMP-9 plays an important role in contributing preterm labour and this can be used as a diagnostic tool during pregnancy. PMID: 32089521 [PubMed - in process] (Source: Journal of Genetics)
Source: Journal of Genetics - February 26, 2020 Category: Genetics & Stem Cells Authors: Pandey M, Awasthi S Tags: J Genet Source Type: research
Gene coexpression network analysis reveals the role of SRS genes in senescence leaf of maize (Zea mays L.).
This study provides valuable information for understanding the functions of the SRS genes in maize. PMID: 32089522 [PubMed - in process] (Source: Journal of Genetics)
Source: Journal of Genetics - February 26, 2020 Category: Genetics & Stem Cells Authors: He B, Shi P, Lv Y, Gao Z, Chen G Tags: J Genet Source Type: research
A novel DNAH5 variant in a Tunisian patient with primary ciliary dyskinesia.
Abstract Primary ciliary dyskinesia (PCD) is a genetically heterogeneous hereditary disease caused by the structural abnormalities and dysfunction of motile cilia. The DNAH5 is the most frequently mutated gene in PCD patients and hot spot exons were reported in this gene. Here, we aim to screen mutations in a set of five hot spot exons of DNAH5 gene in a cohort of 10 clinically diagnosed Tunisian PCD patients using an optimized polymerase chain reaction-single-strand conformational polymorphism screening technique. Only one patient harboured a novel heterozygous variant in exon 63 (c.10767A>G), which was inheri...
Source: Journal of Genetics - February 26, 2020 Category: Genetics & Stem Cells Authors: Mani R, Bouguila J, Ameur SB, Hachicha M, Soua Z, Mabrouk I Tags: J Genet Source Type: research
Variation of grain quality characters and marker-trait association in rice (Oryza sativa L.).
Abstract A set of 24 genotypes were studied for 17 grain quality characters and validated with the reported associated rice microsatellite markers with grain quality characters. Using 23 polymorphic markers distributed across 11 chromosomes marker-trait associations were studied. The percentage of polymorphism information content (PIC) of the markers ranged between 54.0 and 86.7. Eight markers with>80% and seven markers with>70% of PIC were found to be efficient in differentiating the studied grain quality characters. A total of 37 significant marker-trait associations (P ≤ 0.09) were found with R2 rangin...
Source: Journal of Genetics - February 26, 2020 Category: Genetics & Stem Cells Authors: Suman K, Madhubabu P, Rathod R, Sanjeeva Rao D, Rojarani A, Prashant S, Subbarao LV, Ravindrababu V, Neeraja CN Tags: J Genet Source Type: research
Assessment of FMR1 triplet repeats in patients affected with mental retardation, fragile X syndrome and primary ovarian insufficiency.
In this study, the CGG repeats in the FMR1 gene were studied in 449 males and 207 females using traditional polymerase chain reaction and triplet repeat primed PCR methods, also 18 CVS samples (six males and 12 females) were tested for prenatal diagnosis. Further, methylation sensitive multiplexed ligation dependent probe amplification was performed on some samples to confirm the results. Regarding the male patients, 1.1% and 9.7% had premutation (PM) and full mutation (FM) alleles, respectively. Also three (0.66%) male patients were mosaic for PM and FM alleles. Among females, 1.9% were GZ carriers and 5.8% were PM carrie...
Source: Journal of Genetics - February 26, 2020 Category: Genetics & Stem Cells Authors: Salimy Z, Akbari MT, Deilamani FK Tags: J Genet Source Type: research
A novel de novo mutation in the PURA gene associated with a new clinical finding: large brainstem.
In conclusion, our data expand both geneticand phenotypic spectrum associated with PURA gene mutations. PMID: 32089526 [PubMed - in process] (Source: Journal of Genetics)
Source: Journal of Genetics - February 26, 2020 Category: Genetics & Stem Cells Authors: Rodríguez-García ME, Cotrina-Vinagre FJ, Arranz-Canales E, Aragón AM, Hernández-Sánchez L, Rodríguez-Fornés F, Carnicero-Rodríguez P, Morales-Conejo M, Martín-Hernández E, Martínez-Azorín F Tags: J Genet Source Type: research
Codon usage by chloroplast gene is bias in Hemiptelea davidii.
In this study, the codon usage pattern of the chloroplast protein coding genes of H. davidii provides us with a better understanding of the expression of chloroplast genes, and may advice the future molecular breeding programmes. PMID: 32089527 [PubMed - in process] (Source: Journal of Genetics)
Source: Journal of Genetics - February 26, 2020 Category: Genetics & Stem Cells Authors: Liu H, Lu Y, Lan B, Xu J Tags: J Genet Source Type: research
Two-phase SSU and SKAT in genetic association studies.
Abstract The sum of squared score (SSU) and sequence kernel association test (SKAT) are the two good alternative tests for genetic association studies in case-control data. Both SSU and SKAT are derived through assuming a dose-response model between the risk of disease and genotypes. However, in practice, the real genetic mode of inheritance is impossible to know. Thus, these two tests might losepower substantially as shown in simulation results when the genetic model is misspecified. Here, to make both the tests suitable in broad situations, we propose two-phase SSU (tpSSU) and two-phase SKAT (tpSKAT), where the ...
Source: Journal of Genetics - February 26, 2020 Category: Genetics & Stem Cells Authors: Xue Y, Ding J, Wang J, Zhang S, Pan D Tags: J Genet Source Type: research
Genomewide analysis of the CIII peroxidase family in sweet orange (Citrus sinensis) and expression profiles induced by Xanthomonas citri subsp. citri and hormones.
Abstract Class III peroxidase (CIII prx) is a plant-specific multigene family that regulates the physiological and stress responses. This research aimed to exhaustively annotate and analyse the CIII prx family in sweet orange and to explore the regulated expression profiles by Xanthomonas citri subsp. citri (Xcc) and plant hormones. We further assessed the relationship between CIII prxs and citrus bacterial canker. The phylogeny, gene structure, conserved motifs, gene duplications and microsynteny of the CIII prx family were analysed. Expression profiles of specific CsPrxs induced by Xanthomonas citri subsp. citri...
Source: Journal of Genetics - February 26, 2020 Category: Genetics & Stem Cells Authors: Li Q, Dou W, Qi J, Qin X, Chen S, He Y Tags: J Genet Source Type: research
Mining genes associated with furanocoumarin biosynthesis in an endangered medicinal plant, Glehnia littoralis.
The objective of this study was to mine the putative candidate genes involved in the biosynthesis pathwayof furanocoumarin and provide references for gene identification, and functional genomics of G. littoralis. We carried out the transcriptome analysis of leaves and roots in G. littoralis, which provided a dataset for gene mining. Psoralen, imperatorin and isoimperatorin were detected in G. littoralis by high performance liquid chromatography analysis. Candidate key genes were mined based on the annotations and local BLAST with homologous sequences using BioEdit software. The relative expression of genes was analysed usi...
Source: Journal of Genetics - February 26, 2020 Category: Genetics & Stem Cells Authors: Song J, Luo H, Xu Z, Zhang Y, Xin H, Zhu D, Zhu X, Liu M, Wang W, Ren H, Chen H, Gao T Tags: J Genet Source Type: research
Drosophila ananassae: a species characterized by spontaneous male recombination in appreciable frequency.
Abstract Mutation and recombination are primarily responsible for generating the genetic variability in natural populations of microorganisms, plant and animal species including humans. Upon such genetic variations, elemental forces of evolution such as natural selection, random genetic drift and migration operate to bring about micro-evolutionary changes. Recombination or crossing-over produces new combinations of genes due to interchange of corresponding segments between nonsister chromatids of homologous chromosomes, thus, it is an important evolutionary factor. Since the time of T. H. Morgan, Drosophila has be...
Source: Journal of Genetics - February 26, 2020 Category: Genetics & Stem Cells Authors: Singh BN Tags: J Genet Source Type: research
Complete chloroplast genome of Sophora alopecuroides (Papilionoideae): molecular structures, comparative genome analysis and phylogenetic analysis.
This study provided an essential data for the understanding of phylogenetic status of S. alopecuroides. PMID: 32089532 [PubMed - in process] (Source: Journal of Genetics)
Source: Journal of Genetics - February 26, 2020 Category: Genetics & Stem Cells Authors: Zha X, Wang X, Li J, Gao F, Zhou Y Tags: J Genet Source Type: research
Genomic marker assisted identification of genetic loci and genes associated with variation of grain zinc concentration in rice.
Abstract A study was conducted to examine the genetic divergence and to determine the genetic loci and genes associated with natural variation of grain zinc (Zn) concentration among 28 landraces, improved varieties and advanced breeding lines of rice using candidate gene specific primers. Field evaluation of the experimental material was conducted in randomized block design with three replications and Zn content in unpolished grains of the entries was determined by addition of nitric acid and perchloric acid (1:3) following the procedure of diacid digestion method. Statistical analysis revealed the exploitable ext...
Source: Journal of Genetics - December 1, 2019 Category: Genetics & Stem Cells Authors: Kumari K, Kumar P, Sharma VK, Singh SK Tags: J Genet Source Type: research
Cataloguing of blast resistance genes in landraces and breeding lines of rice from India.
Abstract The rice blast caused by the fungus Magnaporthe oryzae is one of the most devastating diseases of rice and can lead to complete failure of the crop under severe cases. The first step in breeding for blast resistance in rice is therefore to identify the novel sources of resistance and cataloguing different blast resistant genes in these genotypes. In the present study, a set of 37 rice genotypes comprising of landraces, advanced breeding lines and released varieties were first characterized for blast resistance under epiphytotic conditions and subsequently different blast resistant genes were catalogued wi...
Source: Journal of Genetics - December 1, 2019 Category: Genetics & Stem Cells Authors: Gavhane DB, Kulwal PL, Kumbhar SD, Jadhav AS, Sarawate CD Tags: J Genet Source Type: research
An in silico approach to characterize nonsynonymous SNPs and regulatory SNPs in human TOX3 gene.
In this study, we have examined the potentially damaging nonsynonymous SNPs(nsSNPs) in TOX3 gene using in silico tools, namely PolyPhen2, SNP&GO, PhD-SNP and PROVEAN, which were further confirmed by I-Mutant, MutPred1.2 and ConSurf for their stability, functional and structural effects. nsSNPs rs368713418 (A266D), rs751141352 (P273S, P273T), rs200878352 (A275T) have been found to be the most deleterious that may have a vital role in breast cancer. Premature stop codon producing SNPs (Q527STOP), rs1259790811 (G495STOP), rs1294465822 (S395STOP) and rs1335372738 (G8STOP) were also found having prime importance in truncate...
Source: Journal of Genetics - December 1, 2019 Category: Genetics & Stem Cells Authors: Akhtar M, Jamal T, Din JU, Hayat C, Rauf M, Ul Haq SM, Sher Khan R, Shah AA, Jamal M, Jalil F Tags: J Genet Source Type: research
Mitogenome analysis of dwarf pufferfish (Carinotetraodon travancoricus) endemic to southwest India and its implications in the phylogeny of Tetraodontidae.
Abstract The Tetraodontidae (pufferfishes), is primarily a family of marine and estuarine fishes with a limited number of freshwater species. Freshwater invasions can be observed in South America, Southeast Asia and central Africa. In the present study, we have analysed the complete mitogenome of freshwater pufferfish, Carinotetraodon travancoricus (dwarf pufferfish or Malabar pufferfish) endemic to southwest India. The genome is 16487 bp in length and consist of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one control region like all the other vertebrate mitogenomes. The protein-cod...
Source: Journal of Genetics - December 1, 2019 Category: Genetics & Stem Cells Authors: Sathyajith C, Yamanoue Y, Yokobori SI, Thampy S, Vattiringal Jayadradhan RK Tags: J Genet Source Type: research
Hypermethylation of NRG1 gene correlates with the presence of heart defects in Down's syndrome.
Abstract Congenital heart defects can decrease the quality of life and life expectancy in affected individuals, and constitute a major burden for the health care systems. Endocardial cushion defects are among the most prevalent heart malformations in the general population, and are extremely frequent (approximately a 100-fold higher prevalence) in children with Down syndrome. Several genes have been proposed to be involved in the pathogenesis of these malformations, but no common pathogenic DNA variants have been identified so far. Here, we focussed on constitutive, epigenetic alterations of function of selected g...
Source: Journal of Genetics - December 1, 2019 Category: Genetics & Stem Cells Authors: Dobosz A, Grabowska A, Bik-Multanowski M Tags: J Genet Source Type: research
Evolutionary analysis of genus Channa based on karyological and 16S rRNA sequence data.
In this study, the karyological information was superimposed on the evolutionary tree generated by 16S rRNA mitochondrial gene sequences. Here, the metaphase chromosome complements stained with Giemsa, AgNO3 and CMA3 were prepared from six snakehead murrel fish species collected from northeast India. The diploid chromosome numbers and the fundamental arms of C. aurantimaculata (2n = 52, NF = 98), C. gachua (2n = 56, NF = 84), C. marulius (2n = 44, NF = 58), C. orientalis (2n = 52, NF = 74), C. punctata (2n = 32, NF = 60) and C. striata (2n = 40, NF = 48) were calculated by the analysis of metaphase chromosome complements. ...
Source: Journal of Genetics - December 1, 2019 Category: Genetics & Stem Cells Authors: Kumar R, Baisvar VS, Kushwaha B, Waikhom G, Singh M Tags: J Genet Source Type: research
Beadex, a homologue of the vertebrate LIM domain only protein, is a novel regulator of crystal cell development in Drosophila melanogaster.
This study describes the role of Beadex, a Drosophila homologue of LIM domain only 2 (LMO2), in haematopoiesis. Mutants of Beadex were analysed for blood cell abnormalities. Crystal cells, a subset of haemocytes, were significantly more in Beadex hypermorphic flies. Similarly, Beadex misexpression in prohemocytes altered the crystal cell numbers. Stage-specific misexpression analyses demonstrated that Beadex functions after the prohemocytes enter the crystal cell lineage. We also discovered that Pannier-U-shaped complex is a negative regulator of the crystal cell differentiation and is possibly negatively regulated by Bead...
Source: Journal of Genetics - December 1, 2019 Category: Genetics & Stem Cells Authors: Chatterjee A, Aavula K, Nongthomba U Tags: J Genet Source Type: research
Genetics of novel brown planthopper Nilaparvata lugens (St ål) resistance genes in derived introgression lines from the interspecific cross O. sativa var. Swarna × O. nivara.
In this study, we show the introgression line RPBio4918-230S was identified as BPH resistant after five years of rigorous screening at seedling stage and two years at tillering and reproductive stages. The inheritance of resistance indicated that two recessive genes are involved at seedling and reproductive stages. The allelic relation with known genes using linked reported markers suggested that the genes present in RPBio4918-230S are different. We report here the genetics of the two newly introgressed BPH resistance genes from O. nivara in the background of Swarna which are effective at all the important growth stages. T...
Source: Journal of Genetics - December 1, 2019 Category: Genetics & Stem Cells Authors: Akanksha S, Jhansi Lakshmi V, Singh AK, Deepthi Y, Chirutkar PM, Ramdeen, Balakrishnan D, Sarla N, Mangrauthia SK, Ram T Tags: J Genet Source Type: research
A de novo truncating mutation in ASXL1 associated with segmental overgrowth.
Abstract Mutations in genes involved in chromatin remodelling have been implicated in broad phenotypes of congenital abnormalities and neurodevelopment. However, limited genotype-phenotype correlations are available for some of the rarest genetic disorders that affect chromatin regulation. We hereby describe a 12-year-old girl presented at birth with severe hypotonia, developmental delay, a mid-line capillary malformation and distinctive craniofacial features. During the natural history of her disease, the girl developed severe spasticity and drug-resistant seizures, leading to a diagnosis of Bohring-Opitz syndrom...
Source: Journal of Genetics - December 1, 2019 Category: Genetics & Stem Cells Authors: Efthymiou S, Salpietro V, Pironti E, Bonsignore M, Ferrazzoli V, Rosa GD, Houlden H Tags: J Genet Source Type: research
Complete plastid genome of Suriana maritima L. (Surianaceae) and its implications in phylogenetic reconstruction of Fabales.
Abstract The present paper reports for the first time the characteristics of the complete plastid genome of Surianaceae (Suriana maritima L.) in the order Fabales. The circular complete plastid genome is 163,747 bp in length with a typical quadripartite organization containing 115 unique genes, of which 80 are protein-coding genes, 31 tRNA genes and four rRNA genes. The plastid genome of S. maritima is characterized by absence of intron in the atpF gene, which has never been reported for any other species of the Fabales. The gene content and their orders in the plastid genome of Surianaceae are similar to the basa...
Source: Journal of Genetics - December 1, 2019 Category: Genetics & Stem Cells Authors: Lai Q, Zhu C, Gu S, Tu T, Zhang D Tags: J Genet Source Type: research
A review on the conservation genetic studies of Indian amphibians and their implications on developing strategies for conservation.
In this study, were view the overall trend on amphibian studies in India with the specific focus on conservation genetics. Overall, of the 173 studies, only 14 dealt with the conservation of amphibians through genetic tools and five studies estimated the genetic diversity or gene structure. Here, we discuss the gaps and provide future directions on how genetic studies can be helpful in Indian amphibian conservation. PMID: 31819027 [PubMed - in process] (Source: Journal of Genetics)
Source: Journal of Genetics - December 1, 2019 Category: Genetics & Stem Cells Authors: Hebbar P, Ravikanth G, Aravind NA Tags: J Genet Source Type: research
Correction to: Roles of the troponin isoforms during indirect flight muscle development in Drosophila.
PMID: 31819028 [PubMed - in process] (Source: Journal of Genetics)
Source: Journal of Genetics - December 1, 2019 Category: Genetics & Stem Cells Authors: Singh SH, Kumar P, Ramachandra NB, Nongthomba U Tags: J Genet Source Type: research
Connection between polymorphisms in HTR2A, TPH2, BDNF, TOMM40 genes and the successful mastering of human-computer interfaces.
Abstract The development of human-computer interfaces in different individuals occur with different efficiencies, this is due to the individual characteristics of the genotype determined by the single-nucleotide polymorphism (SNP) of a person. Here, we checked the connection between the success of the acquisition of the brain-computer, eye-tracking, electromyographic, and respiratory interfaces and SNP of the TOMM40, BDNF, HTR2A and TPH2 genes. Here, we show that the T-allele in rs6313 of the HTR2A gene is associated with an increase in the number of correctly submitted commands of the electromyographic and eye-tr...
Source: Journal of Genetics - November 1, 2019 Category: Genetics & Stem Cells Authors: Turovsky YA, Gureev AP, Vitkalova IY, Popov VN Tags: J Genet Source Type: research
Complete mitogenome sequencing of Andaman buffalo: an endangered germplasm of Andaman and Nicobar Islands, India.
Abstract Andaman buffalo is an indigenous buffalo of Andaman and Nicobar Islands, India. Over the last decade, it has witnessed a rapid decline in population, necessitating its immediate characterization and conservation. The present study reports the complete mitogenome profile of Andaman buffalo which is 16,359 bp in length and comprised of 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNAs and two ribosomal RNAs. In addition, one A + T rich region (D-loop) was also present. A biasness towards A and T base was observed in all the genes. All the PCGs except ND6 were present on heavy strand. Star...
Source: Journal of Genetics - November 1, 2019 Category: Genetics & Stem Cells Authors: Kumar De A, Ponraj P, Malakar D, Muthiyan R, Kundu A, Bhattacharya D Tags: J Genet Source Type: research
Molecular characterization of PgUFGT gene and R2R3-PgMYB transcription factor involved in flavonoid biosynthesis in four tissues of wild pomegranate (Punica granatum L.).
Abstract The diversity on fruit colouration in plants directly depends on the flavonoids that explain the development of different pigmentation patterns. Anthocyanins are the major class of flavonoid pigments that are synthesized through flavonoid biosynthetic pathway. In the present study, two genes: PgUFGT gene and R2R3-PgMYB gene, involved in anthocyanin biosynthesis were analysed in four tissues of wild pomegranate. The structural genes, UDP-glucose: flavonoid-3-O-glucosyl transferase (PgUFGT; GenBank accession number: MK058491) and its myeloblastosis transcription factor (R2R3-PgMYB; GenBank accession number:...
Source: Journal of Genetics - November 1, 2019 Category: Genetics & Stem Cells Authors: Kaur R, Kapoor N, Aslam L, Mahajan R Tags: J Genet Source Type: research
The utility of NBS-profiling for characterization of yellow rust resistance in an F6 durum wheat population.
t M Abstract Seedling and adult plant (field) resistance to yellow rust in the durum wheat (Triticum turgidum ssp. durum) cross Kunduru-1149 x Cham-1 was characterized using a functionally-targeted DNA marker system, NBS-profiling. Chi-squared analysis indicated a four gene model conferring seedling yellow rust resistance against Puccinia striiformis f. sp. tritici isolate WYR85/22 (virulent on Yr2, Yr6, Yr7 and Yr9). Interval mapping located two QTL for yellow rust resistance on the long arm of chromosome 1B, while Kruskal-Wallis single marker regression identified a number of additional marker loci associated wi...
Source: Journal of Genetics - November 1, 2019 Category: Genetics & Stem Cells Authors: Tufan HA, Taşkin BG, Maccormack R, Boyd LA, Kaya Z, Türet M Tags: J Genet Source Type: research
Utilizing bioinformatics to detect genetic similarities between African honey bee subspecies.
This study presents insights into the genetic aspects of African bee subspecies and highlights similarity and dissimilarity aspects. Also, Africanized honey bees derived from A. m. scutellata showed high genetic similarities to other African bees, especially A. m. capensis. Additionally, specific primers to identify these subspecies were designed and tested. PMID: 31767817 [PubMed - in process] (Source: Journal of Genetics)
Source: Journal of Genetics - November 1, 2019 Category: Genetics & Stem Cells Authors: Abou-Shaara HF Tags: J Genet Source Type: research
Development of EST-SSR markers in Cenchrus ciliaris and their applicability in studying the genetic diversity and cross-species transferability.
Abstract Most of the grasses of the genus Cenchrus (20-25 species) and Pennisetum (80-140 species) are distributed throughout the tropical and subtropical regions of the world and reproduce both by sexual and apomictic modes. However, the relationships among the Cenchrus-Pennisetum species are not very clear yet. Molecular markers like expressed sequence tag-simple sequence repeats (EST-SSRs) have been reported to be a better choice for resolving the phylogenetic relationships and to estimate the genetic diversity. The present study describes the identification of EST-SSR markers based on the transcriptome data of...
Source: Journal of Genetics - November 1, 2019 Category: Genetics & Stem Cells Authors: Abdi S, Dwivedi A, Shashi, Kumar S, Bhat V Tags: J Genet Source Type: research
X-chromosome genetic association test incorporating X-chromosome inactivation and imprinting effects.
Abstract Studies have shown that many complex diseases are sex-determined. When conducting genetic association studies on X-chromosome, there are two important epigenetic factors which should be considered simultaneously: X-chromosome inactivation and genomic imprinting. Currently, there have been several association tests accounting for the information on X-chromosome inactivation. However, these tests do not take the imprinting effects into account. In this paper, we propose a novel association test simultaneously incorporating X-chromosome inactivation and imprinting effects based on case-parent trios and contr...
Source: Journal of Genetics - November 1, 2019 Category: Genetics & Stem Cells Authors: Liu W, Wang BQ, Liu-Fu G, Fung WK, Zhou JY Tags: J Genet Source Type: research
Narrow gene pool can threaten the survival of Calamus nagbettai R. R. Fernald & Dey: a highly, endemic dioecious rattan species in the Western Ghats of India.
Narrow gene pool can threaten the survival of Calamus nagbettai R. R. Fernald & Dey: a highly, endemic dioecious rattan species in the Western Ghats of India. J Genet. 2019 Nov;98: Authors: Dev SA, Balakrishnan S, Kurian A, Sreekumar VB Abstract Rattans, the spiny climbing palms of Arecaceae (Palmae) family exhibit high endemism to the biodiversity hot spots in India. Of the five rattan genera, Calamus is the only genus found in peninsular India with 15 of 21 species, endemic to the Western Ghats. The extensive utilization of rattans owing to their strength, durability and huge demand has resulted...
Source: Journal of Genetics - November 1, 2019 Category: Genetics & Stem Cells Authors: Dev SA, Balakrishnan S, Kurian A, Sreekumar VB Tags: J Genet Source Type: research
Comparison of parametric, semiparametric and nonparametric methods in genomic evaluation.
Abstract Access to dense panels of molecular markers has facilitated genomic selection in animal breeding. The purpose of this study was to compare the nonparametric (random forest and support vector machine), semiparametric reproducing kernel Hilbert spaces (RKHS), and parametric methods (ridge regression and Bayes A) in prediction of genomic breeding values for traits with different genetic architecture. The predictive performance of different methods was compared in different combinations of distribution of QTL effects (normal and uniform), two levels of QTL numbers (50 and 200), three levels of heritability (0...
Source: Journal of Genetics - November 1, 2019 Category: Genetics & Stem Cells Authors: Sahebalam H, Gholizadeh M, Hafezian H, Farhadi A Tags: J Genet Source Type: research
Language impairment in primary progressive aphasia and other neurodegenerative diseases.
Abstract Primary progressive aphasia (PPA) is a progressive neurodegenerative disease that disrupts the language capacity of an individual by selectively affecting the language network of brain. Although aphasic literature is replete with reports of brain damage responsible for various types of PPA, it does not provide a comprehensive understanding of whether PPA is an independent pathological condition or an atypical syndrome of neurodegenerative diseases (NDD). To address this ambiguity, we provide a detailed description of PPA, its variants and their brain anatomy. Subsequently, we unravel the relationship betw...
Source: Journal of Genetics - November 1, 2019 Category: Genetics & Stem Cells Authors: Rahul DR, Joseph Ponniah R Tags: J Genet Source Type: research
African elephant genetics: enigmas and anomalies.
Abstract During the last two decades, our understanding of the genetics of African elephant populations has greatly increased. Strong evidence, both morphological and genetic, supports recognition of two African elephant species: the savanna elephant (Loxodonta africana) and the forest elephant (L. cyclotis). Among elephantids, phylogeographic patterns for mitochondrial DNA are highly incongruent with those detected using nuclear DNA markers, and this incongruence is almost certainly due to strongly male-biased geneflow in elephants. As our understanding of elephant population genetics has grown, a number of obser...
Source: Journal of Genetics - September 1, 2019 Category: Genetics & Stem Cells Authors: Roca AL Tags: J Genet Source Type: research
Association between the SNPs in trace element-related metabolic genes and the risk of gastric cancer: a case-control study in Xianyou of China.
This study aims to analyse the potential relationship between single-nucleotide polymorphism (SNPs) in trace element related metabolic genes GSTM3, GSTP1, GPX1 and NKG2D and the risk of gastric cancer. A case-control study was conducted in the hospital of Xianyou, Fujian, China. In this study, a total of 299 patients with histopathological diagnosis in gastric cancer and 295 healthy control subjects were involved. Association between the SNPs in trace element-related metabolic genes and gastric cancer risk was analysed using the unconditional logistic regression model. No relationship was found between the SNPs of GSTM3 an...
Source: Journal of Genetics - September 1, 2019 Category: Genetics & Stem Cells Authors: Zheng W, Li H, Liu B, Wu C Tags: J Genet Source Type: research
Genetic variation and population structure of different geographical populations of Meretrix petechialis based on mitochondrial gene COI.
In this study, the genetic diversity and differentiation of nine populations of M. petechialis were assessed using the mitochondrial cytochrome oxidase subunit I (mtCOI) gene. A total of 90 COI sequences were obtained and each COI sequence was 699 bp in length. Fifty-one haplotypes were identified with 10 haplotypes shared among populations. The haplotype diversity was highest in Fujian, Panjin and Jiangsu (0.9778 ± 0.0540) and lowest in Dalian (0.7778 ± 0.1374). The nucleotide diversity was highest in Panjin (0.453401 ± 0.240463) and lowest in Jiangsu (0.006213 ± 0.004141). Neutral test (Fu's F...
Source: Journal of Genetics - September 1, 2019 Category: Genetics & Stem Cells Authors: Zheng JH, Nie HT, Yang F, Yan XW Tags: J Genet Source Type: research
Genetic dissection of grain iron and zinc concentrations in lentil (Lens culinaris Medik.).
Abstract Iron (Fe) and zinc (Zn) deficiencies are wide spread in South Asia and Africa. Biofortification of food crops is a viable means of addressing micronutrient deficiencies. Lentil is an important pulse crop that provides affordable source of proteins, minerals, fibre and carbohydrates for micronutrient deficient countries. An association mapping (AM) panel of 96 diverse lentil genotypes from India and Mediterranean region was evaluated for three seasons and genotyped using 80 polymorphic simple-sequence repeat (SSR) markers for identification of the markers associated with grain Fe and Zn concentrations. A B...
Source: Journal of Genetics - September 1, 2019 Category: Genetics & Stem Cells Authors: Kumar H, Singh A, Dikshit HK, Mishra GP, Aski M, Meena MC, Kumar S Tags: J Genet Source Type: research
Physical information of 2705 PCR-based molecular markers and the evaluation of their potential use in wheat.
This study facilitates the integration of physical and genetical information of molecular markers, which could be of value for use in genetics and genomics research such as gene/QTL map-based cloning and marker-assisted selection. PMID: 31544776 [PubMed - in process] (Source: Journal of Genetics)
Source: Journal of Genetics - September 1, 2019 Category: Genetics & Stem Cells Authors: Zhao C, Sun H, Guan C, Cui J, Zhang Q, Liu M, Zhang M, Guo Q, Hou Y, Xiang M, Jiang X, Luo X, Han D, Wu Y, Cui F Tags: J Genet Source Type: research
Candidate screening of blast resistance donors for rice breeding.
In this study, a panel of 80 released varieties from National Rice Research Institute, Cuttack was genotyped with 36 molecular markers that were linked to 36 different blast resistance genes, to investigate the varietal genetic diversity and molecular marker-trait association with blast resistance. The polymorphism information content of 36 loci varied from 0.11 to 0.37 with an average of 0.34. The cluster analysis and population structure categorized the 80 National Rice Research Institute released varieties (NRVs) into three major genetic groups. The principal co-ordinate analysis displays the distribution of resistant a...
Source: Journal of Genetics - September 1, 2019 Category: Genetics & Stem Cells Authors: Yadav MK, Aravindan S, Ngangkham U, Prabhukarthikeyan SR, Keerthana U, Raghu S, Pramesh D, Banerjee A, Roy S, Sanghamitra P, Adak T, Priyadarshinee P, Jena M, Kar MK, Rath PC Tags: J Genet Source Type: research
Myotonia congenita: mutation spectrum of CLCN1 in Spanish patients.
, Molano Mateos J Abstract Myotonia congenita (MC) is a Mendelian inherited genetic disease caused by the mutations in the CLCN1 gene, encoding the main skeletal muscle ion chloride channel (ClC-1). The clinical diagnosis of MC should be suspected in patients presenting myotonia, warm-up phenomenon, a characteristic electromyographic pattern, and/or family history. Here, we describe the largest cohort of MC Spanish patients including their relatives (up to 102 individuals). Genetic testing was performed by CLCN1 sequencing and multiplex ligation-dependent probe amplification (MLPA). Analysis of selected exons of t...
Source: Journal of Genetics - September 1, 2019 Category: Genetics & Stem Cells Authors: Milla CP, De Castro CP, Gómez-González C, Martínez-Montero P, Pascual Pascual SI, Molano Mateos J Tags: J Genet Source Type: research
Assessment of genetic diversity and relationships among Salvia species using gene targeted CAAT box-derived polymorphism markers.
In conclusion, because the CBDP markers are derived from the gene containing regions of the genome, consequently, the high genetic diversity among studied Salvia species would be more useful for crop improvement programmes, such as hybridization between species and QTL mapping. The potential of CBDPs for analysing the phylogeny and genetic diversity of Salvia species is another key result with practical implications. PMID: 31544779 [PubMed - in process] (Source: Journal of Genetics)
Source: Journal of Genetics - September 1, 2019 Category: Genetics & Stem Cells Authors: Fabriki-Ourang S, Karimi H Tags: J Genet Source Type: research
Genes involved in the deformations of the shoot apical meristem in somatic embryos of Capsicum chinense Jacq.
Pérez-Pastrana J, Santana-Buzzy N Abstract Somatic embryos (SE) of habanero pepper (Capsicum chinense Jacq.) represent persistent deformations in the shoot apical meristem (SAM), which inhibits their capacity to form organs and subsequently plants. In dicotyledonous plants, SAM is formed in the apex, between cotyledons and it plays a central role in postembryonic shoot organ formation. Based on the previous knowledge on the role of some families of gene in the formation, organization and maintenance of the SAM, the expression patterns of WUS, WOX2, NAM, STM, PIN1 and PIN7 genes were analysed, which would a...
Source: Journal of Genetics - September 1, 2019 Category: Genetics & Stem Cells Authors: Regla-Márquez CF, Avilés-Viñas SA, Canto-Flick A, Muñoz-Ramírez LS, Peña-Yam LP, Valle-Gough RE, Osorio-Montalvo PM, Pérez-Pastrana J, Santana-Buzzy N Tags: J Genet Source Type: research
Identification of genomewide single-nucleotide polymorphisms associated with presummer, summer and autumn bolls in upland cotton.
In this study, we developed an association analysis panel consisting of 169 upland cotton accessions. The panel was phenotyped for PSB, SB and AB across four environments and genotyped using a Cotton SNP80K array. Single-nucleotide polymorphisms (SNPs) associated with these three traits were identified by a genomewide association study. A total of 53,848 high-quality SNPs were screened, and 91 significant trait-associated SNPs were detected. Of the 91 SNPs 33 were associated with PSB, 21 with SB and 37 with AB. Three SNPs for PSB (TM10410, TM13158 and TM21762) and five for AB (TM13730, TM13733, TM13834, TM29666 and TM43214...
Source: Journal of Genetics - September 1, 2019 Category: Genetics & Stem Cells Authors: Feng GL, Zhai FY, Liu HL, Ai NJ Tags: J Genet Source Type: research
Developmental retardation due to paternal 5q/11q translocation in a Chinese infant: clinical, chromosomal and microarray characterization.
This study aims to investigate the genetic factors of a Chinese infant with multiple malformations and severe postnatal development retardation. In this study, the routine cytogenetic analysis, chromosomal microarray analysis (CMA) and fluorescence in situ hybridization (FISH) analysis were performed. Conventional karyotype analyses revealed normal karyotypes of all family members. CMA of the DNA of the proband revealed a 8.3 Mb duplication of 5q35.1-qter and a 6.9 Mb deletion of 11q24.3-qter. FISH analyses verified a paternal tiny translocation between the long arm of chromosomes 5 and 11. Our investigation serves to prov...
Source: Journal of Genetics - September 1, 2019 Category: Genetics & Stem Cells Authors: Zhao X, Xu H, Zhao C, Li L Tags: J Genet Source Type: research
Molecular markers and phenotypic characterization of adult plant resistance genes Lr 34, Lr 46, Lr 67 and Lr 68 and their association with partial resistance to leaf rust in wheat.
Abstract Thirty-nine wheat genotypes were studied to estimate their partial resistance levels to leaf rust at Behira governortae during three growing seasons, i.e. 2016/2017, 2017/2018 and 2018/2019. In these genotypes, partial resistance was characterized using final leaf rust severity (FRS %) and area under disease progress curve (AUDPC). Of the tested genotypes, only three wheat varieties; Giza 171, Misr 3 and Sohag 5 showed complete resistance. Further, 28 of the 39 genotypes had partial resistance as they revealed low and/or moderate values of FRS (%) and AUDPC (not exceeding 30% and 300, respectively). The o...
Source: Journal of Genetics - September 1, 2019 Category: Genetics & Stem Cells Authors: El-Orabey WM, Hamwieh A, Ahmed SM Tags: J Genet Source Type: research
Genetic diversity of Indo-China rice varieties using ISSR, SRAP and InDel markers.
The objective of this study was to evaluate the genetic relationship of Indochina rice varieties using intersimple sequence repeat (ISSR), sequence-related amplified polymorphism (SRAP) and insertion-deletion (InDel) markers. Forty-six rice varieties, including 16, 4,11 and 15 from Thailand, China, Laos and Vietnam, respectively were used in this study. Seventeen of the 20 ISSR primers showed 82.96% polymorphism. At the same time, 17 of the 30 primer pairs of SRAP marker showed clear DNA amplification, which resulted in 84.79% polymorphism. Ninety-seven of 133 InDel markers have about 99.47% polymorphism. Three markers sho...
Source: Journal of Genetics - September 1, 2019 Category: Genetics & Stem Cells Authors: Moonsap P, Laksanavilat N, Sinumporn S, Tasanasuwan P, Kate-Ngam S, Jantasuriyarat C Tags: J Genet Source Type: research
Expression of the cassava nitrate transporter NRT2.1 enables Arabidopsis low nitrate tolerance.
Abstract The cassava grows well on low-nutrient soils because of its high-affinity to absorb nitrate. However, the molecular mechanisms by which cassava adapts itself to this environment remain elusive, although we have cloned a putative gene named MeNRT2.1 which has a crucial role in high-affinity nitrate transporter from cassava seeding. Here, the expression pattern of MeNRT2.1 was further assessed using the GUS activity driven by MeNRT2.1 promoter in Arabidopsis transformation plants. The GUS activity was monitored over time following the reduction of nitrate supply. The GUS gene expression not only peaked in r...
Source: Journal of Genetics - September 1, 2019 Category: Genetics & Stem Cells Authors: Zou L, Qi D, Sun J, Zheng X, Peng M Tags: J Genet Source Type: research
Development of KASP marker for cytoplasmic male sterility in Nicotiana tabacum and utilization in trait introgression.
In this study, three mutations in ATPase subunit 6 were identified and their cosegregation with male sterility was established using tobacco male sterile hybrids and Nicotiana suvaolensis. A breeder friendly Kompetitive allele specific polymerase chain reaction (KASP) SNP marker was developed for high throughput and quick genotyping. Introgression of this trait into selected germplasm lines (n = 9) was achieved based on foreground for CMS and background selection for recurrent parent using KASP marker and 50K custom tobacco SNP array, respectively. Analysis of genotyping data from SNP array revealed the presence of 88-99% ...
Source: Journal of Genetics - September 1, 2019 Category: Genetics & Stem Cells Authors: Priya BNV, Venkata Reddy T, Chidanand U, Saiprasad GVS Tags: J Genet Source Type: research