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Chili pepper (Capsicum annuum L.) is one of the oldest and most phenotypically diverse pre-Columbian crops of the Americas. Despite the abundance of genetic resources, the use of wild germplasm and landraces in chili pepper breeding is limited. A better understanding of the evolutionary history in chili peppers, particularly in the context of traits of agronomic interest, can contribute to future improvement and conservation of genetic resources. In this study, an F2:3 mapping population derived from a cross between a C. annuum wild accession (Chiltepin) and a cultivated variety (Puya) was used to identify genomic regions associated with 19 domestication and agronomic traits. A genetic map was constructed consisting of 1023 single nucleotide polymorphism (SNP) markers clustered into 12 linkage groups and spanning a total of 1,263.87 cM. A reciprocal translocation that differentiates the domesticated genome from its wild ancestor and other related species was identified between chromosomes 1 and 8. Quantitative trait locus (QTL) analysis detected 20 marker-trait associations for 13 phenotypes, from which 14 corresponded to previously identified loci, and six were novel genomic regions related to previously unexplored domestication-syndrome traits, including form of unripe fruit, seedlessness, deciduous fruit, and growth habit. Our results revealed that the genetic architecture of Capsicum domestication is similar to other domesticated species with few loci with large effects, the presence of QTLs clusters in different genomic regions, and the predominance of domesticated recessive alleles. Our analysis indicates the domestication process in chili pepper has also had an effect on traits not directly related to the domestication syndrome. The information obtained in this study provides a more complete understanding of the genetic basis of Capsicum domestication that can potentially guide strategies for the exploitation of wild alleles.
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In general population, it is estimated that 1/560 -1/1100 of the individuals are carriers of a balanced structural alteration and, in general, do not present an abnormal phenotype. For patients who have balanced rearrangements, a family planning alternative is to perform an In Vitro Fertilization (IVF) cycle with the embryonic analysis by Preimplantation Genetic Testing for Chromosomal Structural Rearrangements (PGT-SR). This test aims to reduce the time to obtain a healthy chromosomally pregnancy, to minimize the risk of miscarriage and a live birth with a chromosomopathy. The present work reports a case in which the couple had a history of implantation failure and biochemical pregnancy. They had not performed the karyotype exam to verify the parents' chromosomal content. After two embryo transfers without achieving pregnancy, the couple was directed to the Preimplantation Genetic Testing for Aneuploidies (PGT-A). The result presented in PGT-A in the couple's first cycle using the embryo selection technique showed recurrent segmental aneuploidies the trophectoderm biopsies. The couple was given genetic counselling, and they decided to investigate their karyotype, which showed a balanced chromosomal rearrangement in one of the parents. With this investigation and genetic counselling, it was possible to apply the correct embryonic analysis strategy, which contributed to a healthy pregnancy and birth with a living child.
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BACKGROUND: Since 2011, screening maternal blood for cell-free foetal DNA (cffDNA) fragments has offered a robust clinical tool to classify pregnancy as low or high-risk for Down, Edwards, and Patau syndromes. With recent advances in molecular biology and improvements in data analysis algorithms, the screening's scope of analysis continues to expand. Indeed, screening now encompassess additional conditions, including aneuploidies for sex chromosomes, microdeletions and microduplications, rare autosomal trisomies, and, more recently, segmental deletions and duplications called copy number variations (CNVs). Yet, the ability to detect CNVs creates a new challenge for cffDNA analysis in couples in which one member carries a structural rearrangement such as a translocation or inversion. CASE PRESENTATION: We report a segmental duplication of the long arm of chromosome 3 and a segmental deletion of the short arm of chromosome 5 detected by cffDNA analysis in a 25-year-old pregnant woman. The blood sample was sequenced on a NextSeq 550 (Illumina) using the VeriSeq NIPT Solution v1 assay. G-band karyotyping in amniotic fluid only detected an abnormality in chromosome 5. Next-generation sequencing in amniocytes confirmed both abnormalities and identified breakpoints in 3q26.32q29 and 5p13.3p15. The foetus died at 21 weeks of gestation due to multiple abnormalities, and later G-band karyotyping in the parents revealed that the father was a carrier of a balanced reciprocal translocation [46,XY,t(3;5)(q26.2;p13)]. Maternal karyotype appeared normal. CONCLUSION: This case provides evidence that extended cffDNA can detect, in addition to aneuploidies for whole chromosomes, large segmental aneuploidies. In some cases, this may indicate the presence of chromosomal rearrangements in a parent. Such abnormalities are outside the scope of standard cffDNA analysis targeting chromosomes 13, 18, 21, X, and Y, potentially leading to undiagnosed congenital conditions.
Assuntos
Ácidos Nucleicos Livres/genética , Cromossomos Humanos Par 3/genética , Doenças Fetais/genética , Feto/metabolismo , Trissomia/genética , Adulto , Biomarcadores/sangue , Cromossomos Humanos Par 3/metabolismo , Variações do Número de Cópias de DNA , Feminino , Doenças Fetais/diagnóstico , Doenças Fetais/metabolismo , Testes Genéticos , Humanos , Cariotipagem , Gravidez , Trissomia/diagnósticoRESUMO
BACKGROUND: Turner syndrome is a genetic disorder that affects women. It is caused by an absent or incomplete X chromosome, which can be presented in mosaicism or not. There are 12 cases of Turner syndrome patients who present structural alterations in autosomal chromosomes. CASE PRESENTATION: The present case report describes a patient with a reciprocal, maternally inherited translocation between chromosomes 2 and 12 with a mosaicism of X monosomy 45,X,t(2;12)(p13;q24)[95]/46,XX,t(2;12)(p13;q24)[5]. Through genetic mapping arrays, altered genes in the patient were determined within the 23 chromosome pairs. These genes were associated with the patient's clinical features using a bioinformatics tool. CONCLUSION: To our knowledge, this is the first case in which a translocation (2;12) is reported in a patient with Turner syndrome and confirmed by conventional cytogenetics, FISH and molecular genetics. Clinical features of our patient are closely related with the loss of one X chromosome, however mild intellectual disability can be likely explained by autosomal genes. The presence of familial translocations was a common finding, thus emphasizing the need for familiar testing for further genetic counselling.
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Several patients with 5p duplication or 15q deletion have been reported in the literature, involving different chromosome regions and clinical features. Here, we describe a family in which we identified a 30-Mb 5p15.33p13.3 gain and a 2.5-Mb 15q26.3 loss in 3 individuals, due to a balanced familial translocation between chromosomes 5p and 15q. They presented a similar combination of clinical findings related to their genetic imbalances, but there were also phenotypic differences between them. Our analyses show that their clinical picture is mostly caused by the loss in 15q and not the gain in 5p, despite its much larger size. Our findings suggest that other genes, besides the IGF1R gene, in the 15q26.3 region, such as the CHSY1 gene, may have a great impact on the clinical picture of the syndrome. Our data emphasize the importance of detailed cytogenomic and clinical analyses for an accurate diagnosis, prognosis, and genetic counseling, providing an opportunity to improve genotype-phenotype correlations of patients with partial 5p duplication and 15q deletion syndromes.
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Reciprocal translocations are one of themost common structural rearrangements with a frequency of 1:500 and occur when there is an exchange of distal segments to breakpoints between non-homologous chromosomes. Two or three independent, simple reciprocal or Robertsonian translocations co-exist in the same carrier were classified as complex chromosome rearrangements (CCRs). Structural chromosome rearrangements are considered balanced when there is no apparent gain or loss of chromosome material. In majority of cases, apparently balanced structural chromosome rearrangements (ABCR) are not associated with abnormal phenotypes, although these have been described in 6% of de novo ABCR and 23% of apparently balanced CCR. Here we report a patient with de novo two apparently balanced reciprocal translocations and two partial monosomies, one of these involving an independent chromosome characterized by microarray. Structural rearrangement investigations can improve the knowledge about human genome architecture and correlation of genomic imbalances to abnormal phenotype.
Assuntos
Monossomia , Translocação Genética , Humanos , Hibridização in Situ Fluorescente , Cariotipagem , MasculinoRESUMO
OBJECTIVE: To map the X-chromosome and autosome breakpoints in women with balanced X-autosome translocations and primary amenorrhea, searching candidate genomic loci for female infertility. DESIGN: Retrospective and case-control study. SETTING: University-based research laboratory. PATIENT(S): Three women with balanced X-autosome translocation and primary amenorrhea. INTERVENTION(S): Conventional cytogenetic methods, genomic array, array painting, fluorescence in situ hybridization, and quantitative reverse transcription-polymerase chain reaction. MAIN OUTCOME MEASURE(S): Karyotype, copy number variation, breakpoint mapping, and gene expression levels. RESULT(S): All patients presented with breakpoints in the Xq13q21 region. In two patients, the X-chromosome breakpoint disrupted coding sequences (KIAA2022 and ZDHHC15 genes). Although both gene disruptions caused absence of transcription in peripheral blood, there is no evidence that supports the involvement of these genes with ovarian function. The ZDHHC15 gene belongs to a conserved syntenic region that encompasses the FGF16 gene, which plays a role in female germ line development. The break in the FGF16 syntenic block may have disrupted the interaction between the FGF16 promoter and its cis-regulatory element. In the third patient, although both breakpoints are intergenic, a gene that plays a role in the DAX1 pathway (FHL2 gene) flanks distally the autosome breakpoint. The FHL2 gene may be subject to position effect due to the attachment of an autosome segment in Xq21 region. CONCLUSION(S): The etiology of primary amenorrhea in balanced X-autosome translocation patients may underlie more complex mechanisms than interruption of specific X-linked candidate genes, such as position effect. The fine mapping of the rearrangement breakpoints may be a tool for identifying genetic pathogenic mechanisms for primary amenorrhea.
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Amenorreia/genética , Cromossomos Humanos X , Translocação Genética , Amenorreia/diagnóstico , Amenorreia/fisiopatologia , Pontos de Quebra do Cromossomo , Coloração Cromossômica , Hibridização Genômica Comparativa , Proteínas de Ligação a DNA/genética , Feminino , Fertilidade/genética , Fatores de Crescimento de Fibroblastos/genética , Regulação da Expressão Gênica , Estudos de Associação Genética , Predisposição Genética para Doença , Humanos , Hibridização in Situ Fluorescente , Proteínas com Homeodomínio LIM/genética , Proteínas Musculares/genética , Proteínas do Tecido Nervoso/genética , Fenótipo , Estudos Retrospectivos , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Fatores de Risco , Fatores de Transcrição/genéticaRESUMO
Las translocaciones reciprocas balanceadas ocurren con una incidencia de 1 por cada 500 nacimientos. Un porcentaje de ellas es diagnosticado en adultos que consultan por problemas reproductivos, otras descubiertas de manera fortuita y muchas pasan desapercibidas porque los portadores no tienen sintomatología, ni problemas al concebir y tienen descendencia normal. Solo un 5%, cursa con anomalías fenotípicas, con o sin retardo mental, atribuible a una inactivación o pérdida de genes. Se reporta el caso de una niña de 3 años y 6 meses de edad, portadora de una translocación balanceada reciproca entre los cromosomas 2 y 11, que consulta al servicio de Genética por retardo del desarrollo sicomotor y convulsiones. Al examen físico la paciente presentaba: CC: 46,5cm. (2DS), talla de 87 cm. percentil 3, clinodactilia de ambos quintos dedos, hipertricosis y un soplo sistólico debido a una insuficiencia tricúspides y una válvula aórtica bicúspide. La niña es el producto del tercer embarazo de un matrimonio joven, no consanguíneo, tiene dos hermanos varones, el mayor de 8 años, con la misma cardiopatía y en el otro hermano de 6 años se ausculta un soplo sistólico, de etiología a confirmar. El estudio cromosómico de la propósita, ambos padres y los dos hermanos, se llevó a cabo a través de las técnicas de cultivo de sangre periférica. Las láminas se analizaron con coloración convencional y Bandas G y C. Se examinaron treinta células por individuo. En la paciente se encontró una translocación reciproca balanceada, no así en los padres y hermanos, por lo cual se la considero de novo. Cariotipo: 46, XX,rcp (2;11)(p11;p11). Se reporta este caso por ser de interés ya que las características clínicas de la niña son atribuibles a la anomalía cromosómica pero no así la cardiopatía y también porque el número de portadores de translocaciones reciprocas balanceadas afectados es bajo.
The incidence of balanced reciprocal translocations is 1 for every 500 births. A percentage of them is diagnosed in adults consulting for reproductive problems, other are discovered fortuitously and many pass unnoticed because the carriers do not have either symptomatology or problems on conception and have normal descents. Only 5% of them deal with phenotypic anomalies, with or without mental retardation, attributable to an inactivation or loss of genes. Here we report the case of a 3yearold girl and 6 months of age, carrier of a balanced reciprocal translocation between chromosomes 2 and 11, who consulted the service of Genetics for retardation of the psychomotor development and convulsion. To the physical examination the patient presented: CC: 46.5cm.(2DS), size of 87 cm, percentile 3, clinodactyly of both fifth fingers, hypertrichosis and a systolic breath due to an tricuspid insufficiency and bicuspid aortic valves. The girl is the product of the third pregnancy of a young, nonconsanguineous couple. She has and older brother who was 8 years old and presented the same cardiopathy and a 6yearold brother with a systolic breath of unknown aetiology detected by auscultation. The chromosomal study of the patient, both parents and both brothers, was made by culture of peripheral blood. The slides were analyzed by conventional coloration and G and C bands. Thirty cells were examined per patient and a balanced reciprocal translocation balanced was found in the girl but not in the parents and brothers. Due to this, it was considered a de novo translocation. Karyotype: 46, XX, rcp (2; 11) (p11; p11). This case is reported for being of interest since the clinical characteristics of the girl are attributable to the chromosomal anomaly but not the cardiopathy and because the number of carriers of balanced reciprocal translocations affected is low.