Variations in heterochromatin content reveal important polymorphisms for studies of genetic improvement in garlic (Allium sativum L. ) / Conteúdo de heterocromatina revela polimorfismos importantes para o melhoramento genético do alho (Allium sativum L. )

Abstract Allium sativum L. is an herb of the Alliaceae family with a specific taste and aroma and medicinal and nutraceutical properties that are widely marketed in several countries. Brazil is one of the largest importers of garlic in the world, despite of its production is restricted and limited to internal consumption. Thus, explore the genetic diversity of commercial garlic conserved at germplasm banks is essential to generate additional genetic information about its economically important crop. A suitable tool for this purpose is the cytogenetic characterisation of these accessions. This study aimed to characterise the cytogenetic diversity among seven accessions of garlic from a Germplasm Bank in Brazil. The karyotypes were obtained by conventional staining and with chromomycin A3 (CMA) and 4,6-diamidino-2-phenylindole (DAPI) fluorochromes. All accessions analysed showed chromosome number 2n = 16, karyotype formula 6M+2SM, symmetrical karyotypes, reticulate interphase nuclei, and chromosomes with uniform chromatin condensation from prophase to metaphase. The fluorochromes staining showed differences in the amount and distribution of heterochromatin along the chromosomes and between accessions studied. Based on the distribution pattern of these small polymorphisms, it was possible to separate the seven accessions into three groups. It was also possible to differentiate some of the accessions individually. One of the results obtained showed a heteromorphic distension of the nucleolar organiser region observed on the chromosome pairs 6 or 7 with peculiar characteristics. It was suggested for example, that the heteromorphic block of heterochromatin (CMA+++/DAPI-) on chromosome 6 of the "Branco Mineiro Piauí" accession can be used as a marker to identify this genotype or may be associated with some character of economic interest.

Resumo Allium sativum L. é uma erva da família Alliaceae com sabor e aroma específicos e propriedades medicinais e nutracêuticas amplamente comercializada em diversos países. O Brasil é um dos maiores importadores de alho do mundo, apesar da sua produção ser restrita e limitada ao consumo interno. Assim, explorar a diversidade genética do alho comercial conservado em bancos de germoplasma é essencial para fornecer informações genéticas adicionais acerca dessa cultura economicamente importante. Uma ferramenta adequada para esse fim é a caracterização citogenética desses acessos. Este estudo teve como objetivo caracterizar a diversidade citogenética entre sete acessos de alho de um Banco de Germoplasma no Brasil. Os cariótipos foram obtidos por coloração convencional e com os fluorocromos de cromomicina A3 (CMA) e 4,6-diamidino-2-fenilindol (DAPI). Todos os acessos analisados ​​apresentaram número cromossômico 2n = 16, fórmula cariotípica 6M + 2SM, cariótipos simétricos, núcleos reticulados em intérfase e cromossomos com condensação uniforme da cromatina da prófase para a metáfase. A coloração com fluorocromos mostrou diferenças na quantidade e distribuição de heterocromatina ao longo dos cromossomos e entre os acessos estudados. Com base no padrão de distribuição desses pequenos polimorfismos, foi possível separar os sete acessos em três grupos. Também foi possível diferenciar individualmente alguns dos acessos. Um dos resultados obtidos mostrou distensão heteromórfica da região organizadora nucleolar observada nos pares dos cromossomos 6 ou 7 com características peculiares. Foi sugerido, por exemplo, que o bloco heteromórfico de heterocromatina (CMA +++ / DAPI-) no cromossomo 6 do acesso "Branco Mineiro Piauí" pode ser usado como um marcador para identificar esse genótipo ou pode estar associado a algum caráter de interesse econômico.

Prenatal diagnosis and genetic analysis of a rare case with 8p deletion and duplication / 中华医学遗传学杂志

OBJECTIVE@#To explore the genetic etiology for a child featuring mental retardation, language delay and autism.@*METHODS@#G-banding chromosomal karyotyping and single nucleotide polymorphism array (SNP-array) were carried out for the child and her parents.@*RESULTS@#The child was found to have a 46,XX,dup(8p?) karyotype, for which both of her parents were normal. SNP-array revealed that the child has harbored a 6.8 Mb deletion in 8p23.3p23.1 and a 21.8 Mb duplication in 8p23.1p12, both of which were verified as de novo pathogenic copy number variants.@*CONCLUSION@#The clinical features of the child may be attributed to the 8p deletion and duplication. SNP-array can facilitate genetic diagnosis for children featuring mental retardation in conjunct with other developmental anomalies.

Comparison of detection rates of chromosome G-banding karyotype analysis and fluorescence in situ hybridization among children with sex chromosome mosaicisms / 中华医学遗传学杂志

OBJECTIVE@#To explore the coincidence rate of G-banding karyotype analysis and fluorescence in situ hybridization (FISH) for the diagnosis of children with sex chromosome mosaicisms.@*METHODS@#A retrospective analysis was carried out for 157 children with suspected sex chromosome abnormalities who had presented at Shenzhen Children's Hospital from April 2021 to May 2022. Interphase sex chromosome FISH and G-banding karyotyping results were collected. The coincidence rate of the two methods in children with sex chromosome mosaicisms was compared.@*RESULTS@#The detection rates of G-banding karyotype analysis and FISH were 26.1% (41/157) and 22.9% (36/157) , respectively (P > 0.05). The results of G-banding karyotype analysis showed that 141 cases (89.8%) were in the sex chromosome homogeneity group, of which only 5 cases (3.5%) were inconsistent with the results of FISH. There were 16 cases (10.2%) in the sex chromosome mosaicism group, of which 11 cases (68.8%) were inconsistent with the results of FISH. There was a statistical difference between the two groups in the coincidence rate of the results of the two methods (P < 0.05).@*CONCLUSION@#No significant difference was found between G-banding karyotype analysis and FISH in the detection rate of chromosome abnormalities. The coincidence rate in the mosaicism group was lower than that in the homogeneity group, and the difference was statistically significant. The two methods should be combined for clinical diagnosis.

Phenotypic and genetic analysis of a child with partial trisomy 7q / 中华医学遗传学杂志

OBJECTIVE@#To define the nature and origin of a chromosomal aberration in a child with unexplained growth and development retardation, and to analyze its genotype-phenotype correlation.@*METHODS@#A child who had presented at the Affiliated Children's Hospital of Zhengzhou University on July 9, 2019 was selected as the study subject. Chromosomal karyotypes of the child and her parents were determined with routine G-banding analysis. Their genomic DNA was also analyzed with single nucleotide polymorphism array (SNP array).@*RESULTS@#Karyotyping analysis combined with SNP array suggested that the chromosomal karyotype of the child was 46,XX,dup(7)(q34q36.3), whilst no karyotypic abnormality was found in either of her parents. SNP array has identified a de novo 20.6 Mb duplication at 7q34q36.3 [arr[hg19] 7q34q36.3(138335828_158923941)×3] in the child.@*CONCLUSION@#The partial trisomy 7q carried by the child was rated as a de novo pathogenic variant. SNP array can clarify the nature and origin of chromosomal aberrations. Analysis of the correlation between genotype and phenotype can facilitate the clinical diagnosis and genetic counseling.

A rare case of dicentric ring chromosome and derivative ring chromosome Chimera / 中华医学遗传学杂志

OBJECTIVE@#Utilize high-resolution chromosome analysis and microarray detection to determine the genetic etiology of infertility of a 32-year old female patient.@*METHODS@#The peripheral blood of the patient was cultured for high-resolution chromosome G and C banding karyotype analysis, and then 750K SNP-Array chip detection was performed.@*RESULTS@#Karyotype analysis results showed that the patient's karyotype was 45,XX,-13 [7]/46,XX,r(13) (p13q34) [185]/46,XX,dic r(13;13)(p13q34;p13q34) [14]/ 47,XX,+der(13;13;13;13) (p13q34;p13q34;p13q34; p13q34), dic r(13;13) [1]/ 46,XX [3]. The microarray results showed that the patient had a 3.3 Mb deletion in the 13q34 segment of chromosome 13, which may be related to infertility.@*CONCLUSION@#Infertility of the patient reported in this article may be related to the deletion of chromosome segment (13q34-qter).

Clinical genetic analysis of an infant with 1q21.3-qter duplication and Xpter-p11 deletion caused by maternal balanced chromosomal translocation / 中华医学遗传学杂志

OBJECTIVE@#To investigate the clinical phenotype and genetic diagnosis of an infant featuring multiple hair and hyperbilirubinemia.@*METHODS@#Conventional G-banding analysis, chromosomal microarray analysis (CMA) and fluorescence in situ hybridization (FISH) for the patient were conducted, G-banding analyses of peripheral blood for the infant's parents were also performed.@*RESULTS@#We investigated an infant who carries a unbalanced, maternally inherited karyotype 46, X, der (X) t (X;1) (p11.22; q21.3) in which CMA and FISH analyses disclosed a 1q21.3q44 duplication of 93.03 Mb and Xp22.33p11.22 deletion of 54.53 Mb.@*CONCLUSION@#The phenotypes of this infant can probably be attributed to the 1q21.3q44 duplication and Xp22.33p11.22 deletion, which were maternally inherited.

Genetic analysis and prenatal diagnosis of a fetus with Xq25 microduplication / 中华医学遗传学杂志

OBJECTIVE@#To explore the genetic basis for a fetus with structural brain abnormalities.@*METHODS@#The karyotypes of the fetus and its parents were analyzed by conventional G-banding. Chromosome microarray analysis (CMA) was carried out to detect chromosomal microdeletion and microduplication.@*RESULTS@#No kartotypic abnormality was detected in the fetus and its parents. CMA has identified a 194 kb microduplication at Xq25 in the fetus, which encompassed exons 4-35 of the STAG2 gene and was derived from its mother.@*CONCLUSION@#The Xq25 duplication encompassing part of the STAG2 gene probably underlay the brain malformation in the fetus.

Genetic analysis of a case with 2q37 microdeletion syndrome / 中华医学遗传学杂志

OBJECTIVE@#To diagnose and fine map a deletion in chromosome region 2q37.@*METHODS@#G-banded chromosomal karyotyping, multiplex ligation-dependent probe amplification (MLPA), single nucleotide polymorphism array (SNP-array), and fluorescence in situ hybridization (FISH) were carried out in conjunct for the analysis.@*RESULTS@#The patient was found to have karyotype of 46,XY,del(2)(q3?), MLPA revealed one copy number of both CAPN10-3 and ATG4B-7 genes from the 2q37.3 region, Both parents were found to be normal upon chromosome karyotyping and MLPA. SNP-array has found a 9.7 Mb deletion in the 2q37.1.37.3 region. FISH analysis has confirmed there is a single copy for 2q37.3.@*CONCLUSION@#Combination of MLPA, FISH and SNP-array have enabled accurate diagnosis for the patient, and also provided more clues for the correlation of genotype with the phenotype of the disease, and a basis for genetic counseling.

Phenotypic and genetic analysis of a boy with inv dup del(8p) / 中华医学遗传学杂志

OBJECTIVE@#To delineate the nature and origin of a chromosomal aberration detected in a boy with mental retardation.@*METHODS@#The proband and his parents were subjected to routine G-banded chromosomal karyotyping and single nucleotide polymorphism array (SNP-array) analysis.@*RESULTS@#The karyotype of the proband was determined as 46, XX, add(8)(p23). No karyotypic abnormality was detected in either of his parents. SNP-array has identified a 34.9 Mb duplication at 8p23.1q11.1 and a 6.78 Mb microdeletion at 8p23.1pter in the proband. No copy number variation was detected in either parent.@*CONCLUSION@#The child was diagnosed with 8p inverted duplication deletion syndrome, which might be induced by non-allelic homologous recombination between olfactory genes in the 8p23.1 region.

Genetic study of a child carrying a maternally derived unbalanced 46,Y,der(X)t(X;Y)(p22;q11) chromosomal translocation / 中华医学遗传学杂志

OBJECTIVE@#To explore the genetic basis for a child featuring short stature, saddle nose, cryptorchidism and mental retardation.@*METHODS@#The child and his parents were subjected to G-banded karyotyping and chromosomal microarray analysis (CMA).@*RESULTS@#The child was found to have a 46,Y,der(X)t(X;Y)(p22;q11)mat karyotype. CMA has revealed a 8.3 Mb deletion at Xp22.33p22.31 and a 43.3 Mb duplication at Yq11.221qter. His mother had a karyotype of 46,X,der(X)t(X;Y)(p22;q11). His father had a normal karyotype.@*CONCLUSION@#The child has carried an unbalanced translocation der(X)t(X;Y) (p22;q11) derived from his mother. His clinical phenotype has correlated with the size and position of X chromosome deletion. Compared with the females, abnormal phenotypes such as mental retardation and growth retardation of male carriers are more severe.

Cytogenetic and molecular genetic analysis of three cases with small supernumerary marker chromosomes / 中华医学遗传学杂志

OBJECTIVE@#To delineate the origin and structure of 3 cases of small supernumerary marker chromosomes (sSMCs) through cytogenetic and molecular genetic analysis.@*METHODS@#Conventional G, C and N banding were carried out to analyze the chromosomal karyotypes. Chromosomal microarray analysis (CMA) and fluorescence in situ hybridization (FISH) were used to delineate the origin and structure of the sSMCs.@*RESULTS@#In case 1, chromosomal karyotype of peripheral blood sample was 47,XY,+mar. This de novo sSMC was a dual-satellited dicentric inverted duplicated marker chromosome, for which CMA yielded a normal result. It was predicted to not increase the risk of offspring. In case 2, the fetal chromosomal karyotype was 47,XY,+mar[17]/46,XY[33]. Chromosomal banding suggested that this de novo segment contained euchromatin, and the result of CMA was arr[hg19] 5p12q11.1(45 694 574-49 475 697) × 3. FISH showed the sSMC to be a fragment derived from 5p12 containing the HCN1 gene. Case 3 was found to have a fetal karyotype of 45,XY,-13[25]/46,XY,r(13)[18]/46,XY,-13,+mar[7]. Both parents had refused further examination.@*CONCLUSION@#Conventional chromosomal banding combined with molecular methods can delineate the origin and structure of the sSMCs, which can help with prediction of their pathogenicity and facilitate genetic counseling.

Clinical characterization and genetic analysis of a newborn with chromosome 8q21.11 deletion syndrome / 中华医学遗传学杂志

OBJECTIVE@#To explore the genetic etiology for a newborn with corneal opacity.@*METHODS@#The neonate and her parents were subjected to routine G-banding chromosomal karyotyping analysis. Copy number variation (CNV) was analyzed with low-coverage whole-genome sequencing (WGS) and single nucleotide polymorphism microarray (SNP array).@*RESULTS@#No karyotypic abnormality was found in the newborn and her parents. Low-coverage WGS has identified a de novo 5.5 Mb microdeletion at chromosome 8q21.11-q21.13 in the neonate, which encompassed the ZFHX4 and PEX2 genes. The result was confirmed by SNP array-based CNV analysis.@*CONCLUSION@#The newborn was diagnosed with chromosome 8q21.11 deletion syndrome. ZFHX4 may be one of the key genes underlying this syndrome.

Genetic testing and prenatal diagnosis for a family with 10q22.3q23.2 microdeletion / 中华医学遗传学杂志

OBJECTIVE@#To carry out genetic testing for a pregnant woman with mild mental retardation, facial dysmorphism, and a history of adverse pregnancies and provide prenatal diagnosis for her.@*METHODS@#Routine G-banded karyotyping and single nucleotide polymorphism microarray (SNP-array) analysis were performed on the couple and amniotic fluid sample.@*RESULTS@#No karyotypic abnormality was found with the couple and amniotic fluid sample. SNP-array analysis showed that the woman has carried a 7.801 Mb microdeletion in 10q22.3q23.2, which involved 18 OMIM genes including CDHR1, BMPR1A, NRG3, GRID1 and LDB3, which are associated with facial abnormalities, developmental retardation, mental retardation and autism. The fetus also carried a 7.819 Mb deletion in the same region, while the father showed no abnormality.@*CONCLUSION@#Both the pregnant woman and her fetus have carried a 10q22.3q23.2 microdeletion, which has provided guidance for her subsequent pregnancy.

Genetic analysis of a pedigree with atypical partial 4q trisomy / 中华医学遗传学杂志

OBJECTIVE@#To explore the genetic basis for a Chinese pedigree affected with mental retardation.@*METHODS@#G-banded karyotyping analysis and single nucleotide polymorphism microarray (SNP array) were used to detect the genetic variants within the family, and the origin of the variants was analyzed using UPDtool Statistics software.@*RESULTS@#The patient, a 26-year-old female, was found to have a chromosomal karyotype of 46,XX,dup(4)(q28.2q31.3),and SNP array revealed a 25.71 Mb duplication at 4q28.2-q31.3. The duplication was inherited from her father, and her fetus was found to carry the same duplication.@*CONCLUSION@#The duplication of the patient probably underlay the mental retardation. The gender of the carrier and parental origin of the duplication might have led to the variation in their clinical phenotype.

Prenatal diagnosis and genetic analysis of a fetus with der(X)t(X;Y)(p22.3;q11.2) / 中华医学遗传学杂志

OBJECTIVE@#To explore the pathogenesis and genetic characteristics of a fetus with a der(X)t(X;Y)(p22.3;q11.2) karyotype.@*METHODS@#G-banding karyotyping analysis, BoBs (BACs-on-Beads) assay, and single nucleotide polymorphism array (SNP-array) were used to delineate the structural chromosomal aberration of the fetus. The parents of the fetus were also subjected to karyotyping analysis.@*RESULTS@#The fetus and its mother were both found to have a karyotype of 46,X,add(X)(p22), while the father was normal. BoBs assay indicated that there was a lack of Xp22 but a gain of Yq11 signal. SNP-array confirmed that the fetus and its mother both had a 7.13 Mb deletion at Xp22.33p22.31 (608 021-7 736 547) and gain of a 12.52 Mb fragment at Yq11.221q11.23 (16 271 151-28 788 643).@*CONCLUSION@#The fetus was determined to have a karyotype of 46,X,der(X)t(X;Y)(p22.3;q11.2)mat. The combined use of various methods has facilitated delineation of the fetal chromosomal aberration and prediction of the risk prediction for subsequent pregnancy.

Molecular genetic analysis of a child with de novo 16p11.2 microdeletion / 中华医学遗传学杂志

OBJECTIVE@#To explore the genetic basis for a child featuring developmental delay, intelligent disability and language deficit.@*METHODS@#Peripheral blood samples of the child and her parents were collected for routine G-banding karyotyping analysis and single nucleotide polymorphism array (SNP array) detection. Amniotic fluid was also sampled from the mother for karyotyping analysis and SNP array detection.@*RESULTS@#No karyotypic abnormality was found with the child and her parents. SNP array showed that the child has carried a 761.4 kb microdeletion at 16p11.2, while her mother has carried a 444.4 kb microduplication at 15q13.3. Her father's result was negative. Further analysis showed that the 15q13.3 microduplication was inherited from her maternal grandfather who was phenotypically normal. Prenatal diagnosis showed that the fetus has inherited the15q13.3 microduplication from its mother.@*CONCLUSION@#The child has carried a de novo 16p11.2 microdeletion, which overlaps with 16p11.2 microdeletion syndrome region, in addition with similar clinical phenotypes. The 16p11.2 microdeletion probably underlies her abnormal phenotype.

Prenatal diagnosis of a fetus with Miller-Dieker syndrome / 中华医学遗传学杂志

OBJECTIVE@#To carry out genetic diagnosis for a fetus.@*METHODS@#Chromosome G-banding and chromosomal microarray analysis (CMA) were carried out for a fetus with abnormal morphology of lateral cerebral fissure.@*RESULTS@#The karyotype of the fetus was normal, but CMA showed that it has carried a 1.4 Mb deletion at 17p13.3 region, which suggested a diagnosis of Miller-Dieker syndrome (MDS).@*CONCLUSION@#Familiarity with clinical features and proper selection of genetic testing method are crucial for the diagnosis of MDS. Attention should be paid to microdeletions and microduplications which can be missed by conventional chromosomal karyotyping.

Genetic analysis of three children with disorders of sex development caused by structural rearrangements of Y chromosome / 中华医学遗传学杂志

OBJECTIVE@#To explore the genetic basis of three children with disorders of sex development (DSD) in association with rare Y chromosome rearrangements.@*METHODS@#The three children, who all featured short stature and DSD, were subjected to G banding chromosomal karyotyping, multiplex PCR for Y chromosomal microdeletion, sequencing of the whole SRY gene, SNP-array analysis for genomic copy number variations, and fluorescence in situ hybridization (FISH).@*RESULTS@#The combined analysis revealed chromosomal abnormalities in all of the three children, including 46,X,t(X;Y)(p22.3;q11.2) in case 1, mos 45,X,der(7)pus dic(Y:7)(p11.3p22)del(7)(p21.2p21.3) del(7)(p12.3p14.3) [56]/45,X [44] in case 2, and mos 45,X [50]/46,X,idic(Y)(q11.22) [42]/47,X,idem×2 [4]/47,XYY [2] in case 3.@*CONCLUSION@#Combined use of genetic techniques can delineate complex rearrangements involving Y chromosome in patients featuring short stature and DSD. Above findings have enabled molecular diagnosis and genetic counseling for the patients.

Clinical and genetic study of a child with 15q11.2 microduplication / 中华医学遗传学杂志

OBJECTIVE@#To explore the genetic basis of a child with developmental delay and intellectual disability.@*METHODS@#Peripheral blood samples of the child and his parents were collected for routine G-band karyotyping analysis and single nucleotide polymorphism array (SNP array) assay. Amniotic fluid sample was collected during the next pregnancy for prenatal diagnosis.@*RESULTS@#No karyotypic abnormality was found in the child and his parents. SNP array showed that the child has carried a 855.3 kb microduplication in 15q11.2. His mother carried the same duplication but had no phenotypic anomaly. No microdeletion/microduplication was found in his father. Upon prenatal diagnosis, no abnormalities was found with the chromosomal karyotype and SNP array result of the fetus.@*CONCLUSION@#15q11.2 microduplication may result in developmental delay and intellectual disability, for which CYFIP1 may be a candidate gene. However, the duplication may increase the risk but with a low penetrance. This should attract attention during clinical consultation.

Genetic analysis of a child with atypical Williams-Beuren syndrome presenting as supravalvular aortic stenosis / 中华医学遗传学杂志

OBJECTIVE@#To explore the genetic basis for a child with supravalvular aortic stenosis.@*METHODS@#The child and his parents were subjected to conventional G-banding karyotyping, array comparative genomic hybridization (aCGH) and multiplex ligation-dependent probe amplification (MLPA) analysis.@*RESULTS@#No karyotypic abnormality was detected in the child and his parents. aCGH has identified a de novo 278 kb deletion encompassing the ELN gene in 7q11.23, which overlapped with the critical region of Williams-Beuren syndrome (WBS). MLPA has confirmed above findings.@*CONCLUSION@#The proband was diagnosed with atypical WBS. Deletion of the ELN gene may predispose to supravalvular aortic stenosis in the proband.