Investigation of the molecular genetic causes of non-syndromic primary ovarian ınsufficiency by next generation sequencing analysis

ABSTRACT Objective: The aim of this study is to investigate the molecular genetic causes of non-syndromic primary ovarian insufficiency (POI) cases with the gene panel based on next generation sequencing analysis and to establish the relationship between genotype and phenotype. Subjects and methods: Twenty three cases aged 14-40 years followed up with POI were included. Patients with a karyotype of 46, XX, primary or secondary amenorrhea before the age of 40, with elevated FSH (>40 IU/mL) and low AMH levels (<0.03 ng/mL) were included in the study. Molecular genetic analyzes were performed by the next generation sequencing analysis method targeted with the TruSightTM Exome panel. Results: Median age of the cases was 17.8 (14.0-24.3) years, and 12 (52%) cases admitted before the age of 18. Fifteen (65%) patients had consanguineous parents. In 2 (8.6%) cases, variants detected were in genes that have been previously proven to cause POI. One was homozygous variant in FIGLA gene and the other was homozygous variant in PSMC3IP gene. Heterozygous variants were detected in PROK2, WDR11 and CHD7 associated with hypogonadotropic hypogonadism, but these variants are insufficient to contribute to the POI phenotype. Conclusion: Genetic panels based on next generation sequencing analysis technologies can be used to determine the molecular genetic diagnosis of POI, which has a highly heterogeneous genetic basis.

Mapping of QTL associated with rice cooking quality and candidate gene analysis / 生物工程学报

Excavating the quantitative trait locus (QTL) associated with rice cooking quality, analyzing candidate genes, and improving cooking quality-associated traits of rice varieties by genetic breeding can effectively improve the taste of rice. In this study, we used the indica rice HZ, the japonica rice Nekken2 and 120 recombinant inbred lines (RILs) populations constructed from them as experimental materials to measure the gelatinization temperature (GT), gel consistency (GC) and amylose content (AC) of rice at the maturity stage. We combined the high-density genetic map for QTL mapping. A total of 26 QTLs associated with rice cooking quality (1 QTL associated with GT, 13 QTLs associated with GC, and 12 QTLs associated with AC) were detected, among which the highest likelihood of odd (LOD) value reached 30.24. The expression levels of candidate genes in the localization interval were analyzed by quantitative real-time polymerase chain reaction (qRT-PCR), and it was found that the expression levels of six genes were significantly different from that in parents. It was speculated that the high expression of LOC_Os04g20270 and LOC_Os11g40100 may greatly increase the GC of rice, while the high expression of LOC_Os01g04920 and LOC_Os02g17500 and the low expression of LOC_Os03g02650 and LOC_Os05g25840 may reduce the AC. The results lay a molecular foundation for the cultivation of new high-quality rice varieties, and provide important genetic resources for revealing the molecular regulation mechanism of rice cooking quality.

Gene co-expression network analysis provides a novel insight into the dynamic response of wheat to powdery mildew stress

Powdery mildew (Blumeria graminis f. sp. Tritici, (Bgt)) is an important worldwide fungal foliar disease of wheat (Triticum aestivum) responsible for severe yield losses. The development of resistance genes and dissection of the resistance mechanism will therefore be beneficial in wheat breeding. The Bgt resistance gene PmAS846 was transferred to the hexaploid wheat lines N9134 from Triticum dicoccoides, and it is still one of the most effective resistance genes. Here, by RNA sequencing, we identified three co-expressed gene modules using pairwise comparisons and weighted gene co-expression network analysis during wheat–Bgt interactions compared with mock-infected plants. Hub genes of stress-specific modules were significantly enriched in spliceosomes, phagosomes, the mRNA surveillance pathway, protein processing in the endoplasmic reticulum, and endocytosis. Induced module genes located on chromosome 5BL were selected to construct a protein–protein interaction network. Several proteins were predicted as the key hub node, including Hsp70, DEAD/DEAH box RNA helicase PRH75, elongation factor EF-2, cell division cycle 5, ARF guanine-nucleotide exchange factor GNOM-like, and protein phosphatase 2C 70 protein, which interacted with several disease resistance proteins such as RLP37, RPP13 and RPS2 analogues. Gene ontology enrichment results showed that wheat could activate binding functional genes via an mRNA transcription mechanism in response to Bgt stress. Of these node genes, GNOM-like, PP2C isoform X1 and transmembrane 9 superfamily member 9 were mapped onto the genetic fragment of PmAS846 with a distance of 4.8 Mb. This work provides the foundations for understanding the resistance mechanism and cloning the resistance gene PmAS846

Reminiscencing the Genetics of Orofacial Clefting.

Cleft lip with or without cleft palate is the most common craniofacial birth defect (1/1000 live births), caused by a complex interaction of chromosome rearrangements, genemutations as well as environmental influences. The frequent occurrence of orofacial clefting, along with their extensive psychological, surgical, speech and dental involvement emphasize the importance of identifying the underlying etiology. Rare cleft forms, where they occur as a component ofmultiple congenital anomaly syndromes, haveMendelian or Teratogenic origins; the non-syndromic forms of orofacial clefts are more common and are probably due to secondary geneenvironment interactions. The purpose of our review is to provide a short summary of the vast spectrum of genetic architecture of orofacial clefting covering both syndromic as well as nonsyndromic forms of clefting .Although the gene identification process for orofacial clefting in humans is in an early stage (especially in India); the research pace is rapidly accelerating worldwide. Ongoing human genomewide linkage studies have identified regions that are likely to contain genes that when mutated cause orofacial clefting .Our main aim is to bring together a discussion of new and previously identified candidate genes to create a more cohesive picture of interacting pathways that shape the human craniofacial region. In addition, sequencing of protein coding regions in candidate genes and screening for genetic variation in noncoding regulatory elements, will help in the area of advanced research. Furthermore, statistical geneticists are developing new methods to characterize both gene-gene and gene-environment inter-actions, for explaining the pathology of this common birth defect. The ultimate goal of these studies is to provide knowledge for more accurate risk counseling and the development of preventive therapies. Though India has an estimated population of one million untreated cleft patients, facilities for its treatment have been limited and are not evenly distributed across the country. Paucity of committed cleft surgeons, poverty, illiteracy, superstitions, poor connectivity in some remote areas; severely limit the chances of an average cleft lip Indian child from receiving rational and effective treatment for his malady. The Oscar winning documentary film “Smile Pinki” highlighted the plight of cleft patients in our country. The film stood testimony to the passion of dedicated doctors, social workers and paramedical staffs toiling in the Indian heartland as they treated unfortunate cleft children with the support of the “Smile Train Project”.

Advances in Transcriptomic Studies and Ginsenoside Biosynthesis of American Ginseng / 中草药·英文版

American ginseng (. Panax quinquefolius L.), belonging to the Araliaceae family, is one of the most widely used traditional herbs in the world. Its major bioactive constituents are triterpene saponins known as ginsenosides. Up to date, it is still a big challenge to sequence and assemble the large and repeat-enriched genome of tetraploid American ginseng, using whole genome shotgun (WGS) sequencing strategy. The lack of American ginseng genome information has significantly impeded its genetic and functional genomic studies. With the development of next-generation sequencing (NGS) technologies, sequencing and analysis of transcriptomes have become powerful tools for the discovery of novel genes and elucidation of specific biosynthetic pathways of secondary metabolites. Here we summarized the recent advances in the transcriptomic studies of American ginseng, including high-throughput transcriptome sequencing, assembly, and functional gene annotation and classification. Based on the results of transcriptomic data mining and co-expression analyses, many candidate genes possibly involved in the biosynthetic pathway of ginsenosides have been found, thereby providing an unparalleled opportunity to fully understand the mechanism of ginsenoside biosynthesis and its regulations in American ginseng. Advances in transcriptomic studies will contribute to the molecular breeding and planting management of American ginseng and to the development of novel ginsenoside-type drugs.

Estudios sobre las bases genéticas de la hipertensión arterial / Studies about the genetic bases of high blood pressure

Entre las causas determinantes para el incremento de los valores de la presión arterial, se sabe que tanto las de origen genético como las ambientales desempeñan un importante papel, clasificando como una enfermedad multifactorial. Las bases genéticas de la enfermedad están firmemente establecidas y el desarrollo en el campo de la genética molecular ha sido vertiginoso por lo que el avance en el conocimiento de las alteraciones genéticas causantes de la hipertensión arterial resulta de gran importancia. Se realizó una revisión sobre los diferentes estudios efectuados recientemente en relación con las bases genéticas de la hipertensión arterial. La información aportada por estos análisis en el futuro, resulta muy importante para la selección de pacientes de alto riesgo, puesta en marcha de medidas preventivas adecuadas, así como el desarrollo de nuevos fármacos y terapia individualizada

It is known that among the main causes of the increase in high blood pressure levels, the causes of both genetic origin and environmental origin play an important role, thus classifying it as a multifactor disease. The genetic bases are well established in the disease and the development in the field of molecular genetics has been vertiginous. That is the reason why the advances in the knowledge of the genetic alterations that cause high blood pressure are of paramount importance. A review about the different studies that were carried out recently in relation to the genetic basis of high blood pressure was made. The information shown for the future in these analyses is of great importance for high-risk patients' selection, the implementation of adequate preventive measures and the development of both new drugs and individualized therapy

LINKAGE MAPPING OF CANDIDATE GENES FOR INDUCE RESISTANCE AND GROWTH PROMOTION BY Trichoderma koningiopsis (Th003) IN TOMATO Solanum lycopersicum / Mapeo de genes candidatos relacionados con inducción de resistencia sistemica y promoción de crecimiento por Trichoderma koningiopsis (Th003) en tomate Solanum lycopersicum

Induced systemic resistance (ISR) is a mechanism by which plants enhance defenses against any stress condition. ISR and growth promotion are enhanced when tomato (Solanum lycopersicum) is inoculated with several strains of Trichoderma ssp. This study aims to genetically map tomato candidate genes involved in ISR and growth promotion induced by the Colombian native isolate Trichoderma koningiopsis Th003. Forty-nine candidate genes previously identified on tomato plants treated with Th003 and T. hamatum T382 strains were evaluated for polymorphisms and 16 of them were integrated on the highly saturated genetic linkage map named “TOMATO EXPEN 2000”. The location of six unigenes was similar to the location of resistance gene analogs (RGAs), defense related ESTs and resistance QTLs previously reported, suggesting new possible candidates for these quantitative trait loci (QTL) regions. The candidate gene-markers may be used for future ISR or growth promotion assisted selection in tomato.

La resistencia sistémica inducida (ISR) es un mecanismo mediante el cual las plantas aumentan sus defensas frente a cualquier condición de estrés. El objetivo de este trabajo fue localizar en el mapa genético de tomate, genes candidatos involucrados en ISR y promoción de crecimiento inducidos por la cepa colombiana nativa Th003 de Trichoderma koningiopsis. Se realizó una búsqueda de polimorfismos en cuarenta y nueve genes candidatos previamente identificados en plantas de tomate inoculadas con Th003 y la cepa T382 de T. hamatum. Diez y seis de estos genes candidatos fueron integrados en el mapa genético de tomate altamente saturado, llamado “TOMATO EXPEN 2000”. La ubicación de seis unigenes fue similar a la localización de genes análogos de resistencia (RGAs), ESTs relacionados con defensa y QTLs de resistencia previamente identificados, sugiriendo posibles nuevos candidatos para estas regiones de QTLs. Los genes candidatos o marcadores pueden ser usados en futuros programas de selección asistida relacionados con ISR o promoción de crecimiento en tomate.

Update on Genetic Studies of Functional Gastrointestinal Disorders / 대한소아소화기영양학회지

Childhood functional gastrointestinal disorders are defined as a variable combination of often age-dependent, chronic, or recurrent gastrointestinal symptoms not explained by structural or biochemical abnormalities. A better understanding of genetic background of these disorders would help to better identify their complex biology and make it possible to identify subgroups of patients who respond to customized therapies. Family and twin studies have shown a genetic component in irritable bowel syndrome. Candidate gene studies have identified a few genetic polymorphisms that may be associated with functional dyspepsia and irritable bowel syndrome. Studies of associations of spontaneous genetic variations and altered functions may provide novel insights of the mechanisms contributing to the disease.

Assessment of the association between SMAD1 and HHIP gene variation and non-syndromic cleft-lip palate in Chilean case-parent trios

Nonsyndromic cleft lip/palate (NSCLP) is a congenital malformation with features of a complex genetic trait. Several studies have reported positive association and linkage between NSCLP and microsatellite markers in the 4q28-4q33 region particularly with the D4S192 (4q31) marker. We hypothesized that the candidate genes SMAD1 and HHIP (4q31) could be involved in the etiology of NSCLP based on previous positive linkage results and their important role in maxillofacial development. We evaluated the possible association between microsatellite markers located at less than 1 cM from these genes and NSCLP using a sample of 58 Chilean case-parent trios. Microsatellite markers were analyzed using the polymerase chain reaction (PCR) with fluorescent labeled primers. Electrophoresis of the PCR products was performed on a laser-fluorescent automatic DNA sequencer. The extended transmission disequilibrium test (ETDT) was used to analyze allelic transmissions from the parents to their affected progeny. No significant association due to linkage disequilibrium was detected between both markers and NSCLP.

Genetics of cleft lip and palate: A review

Orofacial clefts, particularly non-syndromic cleft lip with or without cleft palate (CL/P) are the most common craniofacial deformities, affecting one in every 700 to 1000 newborns worldwide. Numerous efforts have been made to understand the etiology of CL/P so as to predict its occurrence and to prevent it from occurring in the future. In the recent years, advances in genetics and molecular biology have begun to reveal the basis of craniofacial development. Various genetic approaches, including genome-wide and candidate gene association studies as well as linkage analysis, have been undertaken to identify aetiologic factors, but results have often been inconclusive or contradictory. These results may support the presence of aetiologic heterogeneity among populations and the presence of multiple genes involved in the aetiology of CL/P. Despite these difficulties, several different genes have been implicated in harbouring genes that contribute to the aetiology of CL/P. In conclusion, the genetic basis of CL/P is still controversial because of genetic complexity of clefting.

Efecto de genes candidatos sobre características reproductivas de hembras porcinas / Effect of Candidate Genes on Reproductive Traits of Sows

Se estudiaron genes candidatos para tamaño de la camada en 300 hembras porcinas Yorkshire-Landrace; ESR, PRLR, RBP4 y FUT1. Las hembras fueron agrupadas en dos niveles de producción (NP): nivel alto (NA) y nivel bajo (NB). Utilizando Ji cuadrado se analizaron las frecuencias génicas y genotípicas. Empleando análisis de varianza con un modelo de efectos mixtos, para lechones nacidos totales (LNT), nacidos vivos (LNV), peso de la camada al nacimiento (PNAC) y destete (PAJ21), lechones destetados (LD) y valor de cría de la progenie de la cerda (BVSP), se compararon las medias con contrastes ortogonales. Las hembras con alta productividad se asociaron con una mayor frecuencia del alelo B del gen ESR (P < 0,05). Las diferencias fueron de 0,4 LNV, 0,3 LD, 2,9 Kg de PAJ21 y 8,6 puntos de BVSP a favor del genotipo AB del gen ESR (P < 0,05) sin considerar el NP, no se detectaron animales homocigotos BB. Las frecuencias génicas y genotípicas del gen PRLR no se relacionaron con el NP (P > 0,05), no hubo diferencias (P > 0,05) entre los genotipos AA, AB y BB sin considerar el NP ni dentro del mismo NP. En el gen RBP4 la frecuencia del alelo A y del genotipo AA fue más alta en hembras con NA (P < 0,05), no se detectaron animales con genotipo BB. Las hembras con genotipos AA tuvieron más 0,5 LNT; 0,5 LNV; 0,6 Kg de PNAC; 2,6 Kg de PAJ21 y 3,2 puntos de BVSP que el genotipo AB (P < 0,05), sin considerar el NP. La frecuencia del alelo G y del genotipo GG del gen FUT1 fue mayor en el nivel de productividad alto (P < 0,05). El genotipo GG fue superior al genotipo AG con más 0,6 LNV; 0,8 Kg de PNAC; 3 Kg de PAJ21 y 3,9 puntos de BVSP (P < 0,05) sin considerar el NP.

Candidate genes were studied for litter size in 300 sows Yorkshire-Landrace; ESR, PRLR, RBP4 y FUT1. The sows were grouped in two levels of production (LP): high level (HL) and low level (LL). Using Chi-Square test the alleles and genotypic frequencies were analyzed. Employing analysis of variance with an mixed model effects for the total number born (TNB), number of piglets born alive (NBA), number of piglets alive at weaning (NW), total weight of piglets born (WTNB), total weight of piglets alive at weaning (WNW) and breeding value sow productivity (BVSP). The means were compared by orthogonal contrasts. The sows with high production were associated with a higher frequency of B allele of ESR gene (P < 0.05). The differences were of 0.04 NBA, 0.3 NW, 2.9 WNW kg and 8.6 BVSP points to favor of AB genotype of ESR gene (P < 0.05) without considering the LP and no homozygous BB animal was detected. The alleles and genotypic frequencies of PRLR gene were not related with the LP (P > 0.05), did not have differences (P > 0.05) between the genotypes AA, AB and BB without considering the LP, neither within of same LP. In the RBP4 gene the frequency of A allele and the AA genotype was higher in sows with HL (P < 0.05), no homozygous BB animals were detected. The sows with AA genotype had 0.5 TNB, 0.5 NBA, 0.6 WTNB kg, 2.6 WNW kg and 3.2 BVSP points more than sows with AB genotype (P < 0.05), without considering the LP. The frequency of G allele and GG genotype of FUT1 gene was higher in the HL (P < 0.05). The GG genotype was higher than AG genotype with 0.6 TNB, 0.8 WTNB kg, 3.0 WNW kg and 3.9 BVSP points more (P < 0.05), without considering the LP.

DGAT1 K232A polymorphism in Brazilian cattle breeds

Recent reports identified DGAT1 (EC 2.3.1.20) harboring a lysine to alanine substitution (K232A) as a candidate gene with a strong effect on milk production traits. Our objective was to estimate the frequency of the DGAT1 K232A polymorphism in the main Zebu and Taurine breeds in Brazil as well as in Zebu x Taurine crossbreds as a potential QTL for marker-assisted selection. Samples of 331 animals from the main Brazilian breeds, Nellore, Guzerat, Red Sindhi, Gyr, Holstein, and Gyr x Holstein F1 were genotyped for DGAT1 K232A polymorphism (A and K alleles) using the PCR-RFLP technique. The highest frequency of the A allele was found in the Holstein sample (73%) followed by Gyr x Holstein F1 (39%). Gyr and Red Sindhi showed low frequencies of A alleles (4 and 2.5%, respectively). The A allele was not found in the Nellore and Guzerat samples. Our results could be used to guide association studies between this locus and milk traits in these breeds.

Genética de la esquizofrenia: avances en el estudio de genes candidatos: [revisión] / Genetics of schizophrenia: advances in the study of candidate genes: [review]

Schizophrenia is one of the most severe mental disorders that affect 1% of the population worldwide. It is clear that both genetic and environmental factors participate in its etiology. Nonetheless, the effort to identify susceptibility genes has been difficult and there are no unequivocal findings until now. Notwithstanding this, during the last couple of years, a group of candidate genes has been identified because of their possible role in the physiopathology or by association and linkage studies. In this article, the role of these genes is summarized as well as the results of the studies conducted in Costa Rica by our group.

Association of TGF? and TGF?3 polymorphisms with nonsyndromic cleft lip and cleft palate / 实用口腔医学杂志

Objective:To study TGF? and TGF?3 polymorphisms in patients with nonsyndromic cleft lip with or without cleft palate(NSCLP,CLP or CL)and cleft palate only(CPO).Methods:TGF? and TGF?3 DNA was extracted and amplified from peripheral leukocytes of 56 cases of NSCLP(40 of CLP and 16 of CL),26 of CPO and 28 of unrelated controls.The primers were designed according to the 3'untranslated region of TGF? and 5th exon of TGF?3 published in the Internet.The PCR products were analyzed by single-stranded conformation polymorphism(SSCP).The aim fragments were further conformed by DNA sequencing after being cloned into pGEM-T vector.Results:The 345 bp fragment of TGF? and 193 bp of TGF?3 were amplified from NSCLP,CPO and control samples.In SSCP analysis,three alleles of TGF? and two of TGF?3 were found.Sequencing results showed three DNA polymorphic sites in TGF? and one in TGF?3 which were all base shifts.There was no difference of each genome between patients and controls.Conclusion:There are no direct association between 3'UTR of TGF? or 5th exon of TGF?3 and NSCLP or CPO in Chinese.