Application of Familial Y-STR Haplotype Mismatch Tolerance in Genealogy Inference / 法医学杂志

OBJECTIVES@#To provide a guideline for genealogy inference and family lineage investigation through a study of the mismatch tolerance distribution of Y-STR loci in Chinese Han male lineage.@*METHODS@#Three Han lineages with clear genetic relationships were selected. YFiler Platinum PCR amplification Kit was used to obtain the typing data of 35 Y-STR loci in male samples. The variation of Y-STR haplotypes in generation inheritance and the mismatch tolerance at 1-7 kinship levels were statistically analyzed.@*RESULTS@#Mutations in Y-STR were family-specific with different mutation loci and numbers of mutation in different lineages. Among all the mutations, 66.03% were observed on rapidly and fast mutating loci. At 1-7 kinship levels, the number of mismatch tolerance ranged from 0 to 5 on all 35 Y-STR loci, with a maximum step size of 6. On medium and slow mutant loci, the number of mismatch tolerance ranged from 0 to 2, with a maximum step size of 3; on rapidly and fast mutant loci, the number of mismatch tolerance ranged from 0 to 3, with a maximum step size of 6.@*CONCLUSIONS@#Combined use of SNP genealogy inference and Y-STR lineage investigation, both 0 and multiple mismatch tolerance need to be considered. Family lineage with 0-3 mismatch tolerance on all 35 Y-STR loci and 0-1 mismatch tolerance on medium and slow loci can be prioritized for screening. When the number of mismatch tolerance is eligible, family lineages with long steps should be carefully excluded. Meanwhile, adding fast mutant loci should also be handled with caution.

Primary Ovarian Small Cell Carcinoma of Pulmonary Type: Analysis of 6 Cases and Review of 31 Cases in the Literatures / 中国医学科学杂志(英文版)

Objective Primary ovarian small cell carcinoma of pulmonary type (SCCOPT) is a rare ovarian tumor with a poor prognosis. The platinum-based chemotherapy is the standard treatment. However, there is little research on the clinical characteristics of SCCOPT and the potential benefits of other treatments due to its low incidence. The study aims to investigate clinicopathological characteristics and treatment of SCCOPT.Methods We summarized the clinical, imaging, laboratorical and pathological characteristics of 37 SCCOPT cases, in which 6 cases were admitted to the Gansu Provincial Hospital from the year of 2008 to 2022 and 31 cases reported in 17 English and 3 Chinese literatures.Results The median age of the studied SCCOPT cases (n=37) was 56.00 (range, 22-80) years. Almost 80% of them had a stage Ⅲ or Ⅳ tumor. All patients underwent an operation and postoperative chemotherapy. Nevertheless, all cases had a poor prognosis, with a median overall survival time of 12 months. Immunohistochemically, the SCCOPT of all patients showed positive expressions of epithelial markers, such as CD56 and sex-determining region of Y chromosome-related high-mobility-group box 2 (SOX-2), and negative expressions of estrogen receptor, progesterone receptor, vimentin, Leu-7, and somatostatin receptor 2. The tumor of above 80% cases expressed synaptophysin. Only a few cases expressed neuron-specific enolase, chromogranin A, and thyroid transcription factor-1. Conclusions SCCOPT had a poor prognosis. SOX-2 could be a biomarker to be used to diagnose SCCOPT.

Forensic Application of Next Generation Sequencing Technology in the Typing of Y Chromosome Genetic Markers / 法医学杂志

The paternal inheritance characteristics of Y chromosome have been widely used in the forensic genetics field to detect the genetic markers in the non-recombining block, and used in the studies such as, genetic relationship identification, mixed stain detection, pedigree screen and ethnicity determination. At present, capillary electrophoresis is still the most common detection technology. The commercial detection kits and data analysis and processing system based on this technology are very mature. However, the disadvantages of traditional detection technology have gradually appeared with the rapid growth of bio-information amount, which promotes the renewal of forensic DNA typing technology. In recent years, next generation sequencing （NGS） technology has developed rapidly. This technology has been applied to various fields including forensic genetics and has provided new techniques for the detection of Y chromosome genetic markers. This article describes the current situation and application prospects of the NGS technology in forensic Y chromosome genetic markers detection in order to provide new ideas for future judicial practice.

Development and Forensic Application of EX20+30Y Kit / 法医学杂志

OBJECTIVES@#To develop a multiplex PCR amplification system (EX20+30Y for short) of 19 autosomes, 30 Y-STR loci plus the gender indicator, and evaluate its forensic application value.@*METHODS@#With the six-color fluorescence labeling technology, a multiplex amplification system of 19 autosomal STR loci and 30 Y-STR loci plus the gender indicator was constructed. Blood samples from 210 unrelated individuals, 69 daily case samples and standard samples 9948 and 9947A were collected for loci detection and analysis. The EX20+30Y multiplex amplification system was evaluated by its sensitivity, mixed sample detection ability, species specificity, balance, direct amplification ability, sample applicability and anti-inhibition ability.@*RESULTS@#Multiplex amplification of blood samples from 210 unrelated individuals by the detection system obtained accurate genotyping results. The detection sensitivity of standard samples was 0.125 ng and the species specificity was high. The 69 samples from daily cases were genotyped correctly. Moreover, standard sample 9948 could be accurately genotyped even if the samples contained a certain concentration of inhibitors.@*CONCLUSIONS@#The multiplex amplification system established in this study can conduct combined examination of 19 autosomes, 30 Y-STR loci plus the gender indicator with accurate genotyping and high sensitivity. It has a good forensic application prospect.

46XX pure gonadal dysgenesis with dysgerminoma along with leydig cells: a unique presentation

Authors report a unique case of 46XX gonadal dysgenesis, with dysgerminoma in one ovary and other streak ovary with hilar nests of leydig cells. It is exceptionally rare to find dysgerminoma in a dysgenetic gonad with no Y chromosome and so is the presence of leydig cells in the contralateral streak ovary in a patient with 46XX pure gonadal dysgenesis.

Ascertaining the paternal lineage in crossbred calves

Karyotyping is one among the culling parameter used for taking up culling decisions. Cytogenetic screening of breeding bulls has been recommended to screen for chromosomal abnormalities before semen production in artificial insemination. The chromosomal analysis of a Holstein Friesian crossbred bull revealed the presence of acrocentric Y-chromosome, which was further confirmed by CBGbanding. The shape of the Y-chromosome determining that male line used for crossbreeding was from indigenous origin. Karyotyping is a best and reliable technique for the identification of crossbred calves born to the indigenous bulls.

Karyomorphological Studies of Kangayam, Pulikulam, Crossbred Jersey and Crossbred Holstein Friesian Bulls

The present study was carried out in four genetic groups of cattle, viz. Kangayam, Pulikulam, crossbred Jersey and crossbred Holstein Friesian, to compare the karyomorphological pattern between Bos indicus and Bos taurus x indicus bull calves. Metaphase chromosomal spreads obtained by short term lymphocyte culture technique revealed chromosomal complement (2n) of 60, with 29 pairs of autosomes and one pair of sex chromosomes in four groups. All the autosomes were acrocentric, X-chromosome was sub-metacentric and Y-chromosome was acrocentric in Bos indicus and metacentric in crossbred bulls. There was no significant difference in relative length, arm ratio, centromeric index and morphological index of autosomes and X-chromosome between indicine and taurine groups; but Y-chromosome differed significantly (P˂0.01) in relative length between Bos indicus and Bos taurus x indicus crosses. Y-chromosome polymorphism could help in the determination of breed origin and male lines used in the breeding programmes in order to prevent the possible interferences in the process of reproduction

Prevalence of Y chromosome microdeletion in azoospermic infertile males of Iraqi population

In human gamete development, the important period is spermatogenesis, which is organized by specific genes on Y chromosome. In some cases, the infertile men have shown microdeletions on Y chromosome, which seemed as if the structural chromosome variance is linked to the reduction of sperm count. This study aimed to determine the frequency and patterns of Y chromosome microdeletions in azoospermia factor (AZF) of Iraqi infertile males. Here, 90 azoospermic infertile males as a study group and 95 normal fertile males as control group were investigated for the microdeletion of AZF loci using numerous sequence-tagged sites. Of these 90 infertile male patients, 43 (47.8%) demonstrated Y chromosome microdeletions, in which AZFb region was the most deleted section in azoospermia patients (33.3%) followed by deletions in the AZFc region (23%), while there were no microdeletion in the AZFa region. The largest microdeletion involved in both AZFb and AZFc was detected in six azoospermic patients (6.7%). The present study demonstrated a high frequency of Y chromosome microdeletions in the infertile Iraqi patients which is not reported previously. The high frequency of deletions may be due to the association of ethnic and genetic factors. PCR-based Y chromosome screening for microdeletions has a potential to be used in infertility clinics for genetic counselling and assisted reproduction.

Single molecule sequencing of nucleic acids in real time (SMRT) to characterize transcriptomes and mRNA isoforms / Secuenciación de moléculas individuales de ácidos nucleicos en tiempo real (SMRT) para caracterizar transcriptomas e isoformas de ARNm

Abstract Our efforts are oriented to assess bovine Y-chromosome gene expression patterns. One set of genes that are of interest are the so-called X-degenerate Y-chromosome genes that are located in the male-specific region of the Y-chromosome (MSY). This region contains 95% of the DNA of the Y chromosome. These genes are single copy and have an X-chromosome homolog. Both, the Y-encoded and X-encoded homologs have ubiquitous expression profiles. However, some genes, like SRY that regulates male sex determination, have functions that are more specific. Identifying DNA sequence differences between these homologs will allow evaluation of their spatial and temporal expression patterns. Identification of the Y-encoded mRNAs and their isoforms will allow our understanding of tissue specific expression of isoforms in male tissues. The latter will facilitate our evaluation of gene function in male sex differentiation and fertility. Hence, we hypothesized that each of these X-degenerate gene homologs generate isoforms and that differential expression patterns exist between sexes and across tissues. To investigate the latter we used a new generation sequencing (NGS) technology that generates long sequencing reads with a range between 1000 to 10,000 base pairs in length. Single molecule real time (SMRT) isoform sequencing (IsoSeq) of several tissues (liver, lung, adipose, muscle, hypothalamus and testis) was carried out. Transcript sequences were used for bioinformatics analysis and isoform characterization. Given the focus of this manuscript the SMRT technology we are only presenting results obtained with the analysis of the bUTY and bUTX genes.

Resumen Nuestros esfuerzos están orientados a evaluar patrones de expresión génica del cromosoma Y bovino. Los genes de interés son los denominados genes X-degenerados que se encuentran en la región específica masculina del cromosoma Y (MSY). Esta región contiene el 95% del ADN del cromosoma Y. Estos genes son de copia única y tienen un homólogo en el cromosoma X. Ambos homólogos tienen perfiles amplios de expresión. Sin embargo, algunos genes, como el SRY que regula la determinación del sexo masculino, tienen funciones más específicas. La identificación de las diferencias de secuencia de ADN entre estos homólogos permitirá evaluar sus patrones de expresión espacial y temporal. La identificación de los ARNm codificados en el cromosoma Y y de sus isoformas permitirán analizar la expresión específica de sus isoformas en tejidos masculinos. Esto último facilitará nuestra evaluación de función génica en la diferenciación sexual masculina y la fertilidad. Por lo tanto, planteamos la hipótesis de que cada uno de estos genes homólogos degenerados del X genera isoformas y que existen patrones de expresión diferencial entre sexos y tejidos. Para investigar esto último, utilizamos una tecnología de secuenciación de nueva generación (NGS) que genera lecturas de secuenciación largas con un rango de longitud de 1000 a 10,000 pares de bases. Se secuenciaron los transcriptomas en varios tejidos (hígado, pulmón, adiposo, muscular, hipotálamo y testículo). Se utilizaron las secuencias generadas para el análisis bioinformático y la caracterización de isoformas. Siendo el foco de este manuscrito la tecnología SMRT, solo presentamos los resultados obtenidos con el análisis de los genes bUTY y bUTX.

Polymorphism and Forensic Application of 11 Y-SNP in Guizhou Shui Ethnic Group / 法医学杂志

Objective To investigate the frequency distribution features of 11 Y-SNP of Guizhou Shui ethnic group, explore its genetic relationship with other ethnic groups and evaluate its forensic application value. Methods Multiplex amplification of the 11 Y-SNP of samples of 180 unrelated male individuals from Guizhou Shui ethnic group was performed with microsequencing technique. The frequency of haplogroup was calculated by direct counting method, and principal component analysis （PCA） of Guizhou Shui ethnic group and reference ethnic groups was performed by using Multi-variate statistical package （MVSP）. The Fst genetic distance between Guizhou Shui ethnic group and other ethnic groups was calculated with Arlequin v3.5. The phylogenetic tree was established with MEGA 4.0 software according to the Fst value. Results Six types of Y chromosome haplogroups were observed in total. Among which, the distribution frequency of O-M175 haplogroup was the highest （71.11%）, followed by C-M130 （25.00%）, and D-M174 （3.89%）. O1b-M268 （31.11%） and O2a2-IMS-JST021354 （28.33%） had a relatively high distribution frequency in O haplogroup. The paternal relationship between Guizhou Shui ethnic group and Guizhou Gelao ethnic group in the same language group was the closest. Conclusion The distribution of Y-SNP haplogroup of the Shui ethnic group in Guizhou has certain specificity, which can provide basic data for forensic biogeographic inference.

Genetic Structure Analysis of Y Chromosome STR and SNP in Population of Changshu / 法医学杂志

Objective To provide a theoretical basis for building a Y chromosome database in specific regions by analyzing the pedigree specific core haplogroup and region specific genetic structure in Changshu. Methods One thousand seven hundred and two samples from unrelated Han male individuals in Changshu were collected. Then 27 Y-STR were genotyped through YfilerTM Plus PCR Amplification Kit, Y-SNP haplogroup of each sample was speculated using Y-Predictor software and some samples were verified by amplification refractory mutation system-polymerase chain reaction （ARMS-PCR）. Results A total of 1 556 haplotypes were found on the 27 Y-STR genetic markers of the 1 702 samples. The haplotype diversity （HD） value was 0.999 827. DYS385 （0.933） had the highest gene diversity （GD） value while DYS438 （0.409） had the lowest. By the Y-Predictor software, all samples were confirmed to be from 162 sub-haplogroups of C, D, N, O, Q and R. Samples were randomly selected to verify the prediction results by the software and the prediction accuracy of Y-Predictor software was as high as 95.74%. Conclusion This study found that 27 Y-STR genetic markers have relatively high polymorphisms in the Changshu population, and have good forensic individual identification and paternity testing ability.

Preliminary study between Y chromosome haplogroups and chagasic cardiomyopathy manifestations in patients with Chagas disease

Abstract INTRODUCTION: Among patients with Chagas disease, men have a higher risk of worse pathological symptoms than women. We aimed to explore the role of the Y chromosome in men diagnosed with Chagas disease and assess the relationship between their ancestry and disease status. METHODS In this comparative study, we analyzed 150 men with unrelated non-chagasic disease (nCD) and 150 men with unrelated chagasic disease (CD). We assessed the serological diagnosis of Chagas disease, biochemical parameters, thoracic X-rays, electrocardiogram, and transthoracic echocardiography and determined the haplogroup by analyzing a set of 17 microsatellites from the Y chromosome. We examined the associations between common Y chromosome haplogroups and the clinical parameters of risk by logistic regression. RESULTS For all patients, the most common haplogroups were R1b (43%), G2a (9%), and E1b1b (9%). The R1b and G2a haplogroup was more frequent in men with nCD and CD, respectively. As expected, we observed a high proportion of symptomatic patients in the CD group independent of the haplogroups. Men from both groups classified as having the R1b haplogroup showed less clinical evidence of disease. Multivariate analysis showed that CD patients without R1b were about five times more likely to have a cardio-thorax index >0.5% (OR [odds ratio] = 5.1, 95% CI [confidence interval] = 3.31-8.17). Men without the R1b haplogroup were 2.5 times more likely to show EcoCG alterations (OR = 2.50, 95% CI = 0.16-3.94). CONCLUSIONS: Our results provided evidence that the R1b haplogroup may have a potential protective cardiovascular effect for its carriers.

High frequency of Y chromosome microdeletions in male infertility patients with 45,X/46, XY mosaicism

The mosaic 45,X/46,XY karyotype is a common sex chromosomal abnormality in infertile men. Males with this mosaic karyotype can benefit from assisted reproductive therapies, but the transmitted abnormalities contain 45,X aneuploidy as well as Y chromosome microdeletions. The aim of this study was to investigate the clinical and genetic characteristics of infertile men diagnosed with 45,X/46,XY mosaicism in China. Of the 734 infertile men found to carry chromosomal abnormalities, 14 patients were carriers of 45,X/46,XY mosaicism or its variants, giving a prevalence of 0.27% (14/5269) and accounting for 1.91% (14/734) of patients with a chromosomal abnormality. There were ten cases (71.43%, 10/14) of 45,X mosaicism exhibiting AZF microdeletions. Case 1 and Case 4 had AZFc deletions, and the other eight cases had AZFb+c deletions. A high frequency of Y chromosome microdeletions were detected in male patients with 45,X/46,XY mosaicism. Preimplantation genetic diagnosis should be offered to men having intracytoplasmic sperm injection for hypospermatogenesis caused by 45,X/46,XY mosaicism, to avoid the risk of transfering AZF microdeletions in addition to X monosomy in male offspring.

The association between the two more common genetic causes of spermatogenic failure: a 7-year retrospective study / 亚洲男科学杂志(英文版)

Chromosomal abnormalities and Y chromosome microdeletions are considered to be the two more common genetic causes of spermatogenic failure. However, the relationship between chromosomal aberrations and Y chromosome microdeletions is still unclear. This study was to investigate the incidence and characteristics of chromosomal aberrations and Y chromosome microdeletions in infertile men, and to explore whether there was a correlation between the two genetic defects of spermatogenic failure. A 7-year retrospective study was conducted on 5465 infertile men with nonobstructive azoospermia or oligozoospermia. Karyotype analysis of peripheral blood lymphocytes was performed by standard G-banding techniques. Y chromosome microdeletions were screened by multiplex PCR amplification with six specific sequence-tagged site (STS) markers. Among the 5465 infertile men analyzed, 371 (6.8%) had Y chromosome microdeletions and the prevalence of microdeletions in azoospermia was 10.5% (259/2474) and in severe oligozoospermia was 6.3% (107/1705). A total of 4003 (73.2%) infertile men underwent karyotyping; 370 (9.2%) had chromosomal abnormalities and 222 (5.5%) had chromosomal polymorphisms. Karyotype analysis was performed on 272 (73.3%) patients with Y chromosome microdeletions and 77 (28.3%) had chromosomal aberrations, all of which involved sex chromosomes but not autosomes. There was a significant difference in the frequency of chromosomal abnormalities between men with and without Y chromosome microdeletions (P< 0.05).

Y chromosome microdeletion screening using a new molecular diagnostic method in 1030 Japanese males with infertility / 亚洲男科学杂志(英文版)

The azoospermia factor (AZF) region is important for spermatogenesis, and deletions within these regions are a common cause of oligozoospermia and azoospermia. Although several studies have reported this cause, the present research, to the best of our knowledge, is the first large-scale study assessing this factor in Japan. In this study, 1030 male patients with infertility who were examined for Y chromosome microdeletion using the polymerase chain reaction-reverse sequence-specific oligonucleotide (PCR-rSSO) method, a newly developed method for Y chromosome microdeletion screening, were included. The study enrolled 250 patients with severe oligospermia and 717 patients with azoospermia. Among the 1030 patients, 4, 4, 10, and 52 had AZFa, AZFb, AZFb+c, and AZFc deletions, respectively. The sperm recovery rate (SRR) of microdissection testicular sperm extraction in patients with AZFc deletions was significantly higher than that in those without AZF deletions (60.0% vs 28.7%, P = 0.04). In patients with gr/gr deletion, SRR was 18.7%, which was lower than that in those without gr/gr deletion, but was not statistically significant. In conclusion, our study showed that the frequency of Y chromosome microdeletion in male patients in Japan was similar to that reported in patients from other countries, and SRR was higher in patients with AZFc deletion.

Gonadoblastoma bilateral em paciente com mosaicismo de síndrome de Turner: relato de caso e revisão de literatura / Bilateral gonadoblastoma in patient with Turner syndrome mosaicism: case report and literature review

A síndrome de Turner decorre de uma anomalia dos cromossomos sexuais, afetando cerca de 1:2.500 nascidos vivos. A síndrome caracteriza-se principalmente por atraso do e denvolvimento dos caracteres sexuais e/ou amenorreia e baixa estatura. Entretanto, uma diversidade de estigmas também pode estar presente. O diagnóstico pode ser realizado com base nos estigmas da síndrome associados a um quadro de hipogonadismo hipergonadotrófico e confirmado por meio do cariótipo ­ sendo esse classicamente 45,X (monossomia do cromossomo X). Entretanto, os mosaicos (45,X/46,XY ou 45,X/46,XX) podem representar 34% a 75% dos casos, dependendo do método de análise utilizado. Trata-se de uma condição rara correspondendo a 5% das disgenesia gonadais e apresenta um amplo espectro fenotípico. A importância da identificação de mosaicos, especialmente a presença do cromossomo Y, reside no manejo adequado da gônada disgenética para a prevenção da ocorrência de tumor gonadal, principalmente o gonadoblastoma, com considerável potencial maligno.(AU)

Turner's syndrome results from a sex chromosomes anomaly, affecting about 1:2,500 live births. The syndrome is characterized mainly by delayed development of sexual characteristics and/or amenorrhea and short stature. However, a variety of stigmas may also be presented. The diagnosis can be made based on the stigmas of the syndrome associated with a hypergonadotrophic hypogonadism and confirmed by the karyotype ­ this being classically 45, X (monosomy of the X chromosome). However, mosaics (45,X/46,XY or 45,X/46, XX) may represent 34% to 75% of cases depending on the method of analysis used. It is a rare condition, corresponding to 5% of gonadal dysgenesis and presents a broad phenotypic spectrum. The importance of mosaic identification, especially the presence of the Y chromosome, lies in the proper management of the dysgenetic gonad for the prevention of the occurrence of gonadal tumor, especially gonadoblastoma, with considerable malignant potential.(AU)

Identification and expression profiling of MSY genes of yak for bull fertility

Yak (Bos grunniens) is a unique bovine species and considered as lifeline of highlanders. The male subfertility in yak is a matter of concern that causes huge economic loses. The spermatogenesis and male reproduction machinery are critically governed by Y-linked genes which tend to acquire necessary information in the course of evolution. The Y-linked fertility genes are present in multiple copies with testis-limited expression. To understand this novel complexity, 12 male-specific region of Y chromosome (MSY) genes have been studied in the yak. Targeted genes are amplified in male and female genomic DNA and confirmed the male derived specificity. Moreover, testis and sperm-specific expressions of MSY genes are distinct among different tissues. The quantitative polymerase chain reaction results validate the expression pattern of these genes in various tissues with predominant expression intestis and sperm. The sequencing of resultant yak MSY genes gives significant result and shows similarity with cattle (Bos indicus), but few nucleotide mismatches define the proposition of infertile male in the F1 hybrid of cattle and yak. The identified MSY genes can be used to establish male-specific characteristics and to differentiate male and female yak genotypically. Further, these genes may act as valuable resources to understand the capacity of spermatogenesis, embryogenesis, cellular growth, azoospermia and malesubfertility in the yak.

Y-chromosomal STR variation in Kurds and Arabs population in Iraqi Kurdistan

Background: The Iraqi Kurdistan local population involves more than eight gatherings of tenants. The Muslim Kurds make up most of the population and after that the Yezidi Kurds. Alternate gatherings incorporate Armenians, Assyrian, Chaldea, Syriacs, and little minority of Arab and Turkmen individuals.Methods: A total of 36 unrelated males from the two population groups in Iraqi Kurdistan: Kurds and Arabs were analyzed for eight Y-chromosome STRs (DYS19, DYS392, DYS437, DYS448, DYS456, DYS458, DYS635 and Y-GATA-H4). Total DNA from blood cells was extracted using DNA extraction Kit.Results: A number of genetic parameters such as mean number of alleles, allele frequency, gene diversity, polymorphic information content (PIC), and genetic distance were calculated using Power Marker V3.25 software. The DYS458 had the highest diversity (GD: 0.883), while loci DYS456 and Y-GATA-H4 had the lowest (GD: 0.574). The Dendrogram separated the populations into two main clades, the Kurd group and the Arab group except in one case only from the whole population.Conclusions: This study confirms the discriminating power of high-resolution Y-STR typing and provides first primary dataset on Iraqi Kurdistan samples. The comparison of Kurdish and Arab datasets reveals an interesting overall picture of isolation of Kurdish group. The primers DYS19, DYS448, DYS458, and DYS635 can be considered the best for their high PIC power.

Establishing gene Amelogenin as sex-specific marker in yak by genomic approach

Yak, an economically important bovine species considered as lifeline of the Himalaya. Indeed, this gigantic bovine is neglected because of the scientific intervention for its conservation as well as research documentation for a long time. Amelogenin is an essential protein for tooth enamel which eutherian mammals contain two copies in both X and Y chromosome each. In bovine, the deletion of a fragment of the nucleotide sequence in Y chromosome copy of exon 6 made Amelogenin an excellent sex-specific marker. Thus, an attempt was made to use the gene as an advanced molecular marker of sexing of the yak to improve breeding strategies and reproduction. The present study confirmed that the polymerase chain reaction amplification of the Amelogenin gene with a unique primer is useful in sex identification of the yak. The test is further refined with qPCR validation by quantifying the DNA copy number of the Amelogenin gene in male and female. We observed a high level of sequence polymorphisms of AMELX and AMELY in yak considered as novel identification. These tests can be further extended into several other specialized fields includingforensics, meat production and processing, and quality control.

Genetic Structure Analysis of Y-Chromosome STR and SNP in Population of Wujiang Area, Suzhou City / 法医学杂志

Objective To analyze the genetic phenotypes of Y-chromosome STR and SNP in Han male population of Wujiang area, Suzhou City and explore the genetic structure of population of Wujiang area for further examination of regional-specific Y-SNP genetic markers ancestor haplogroups. Methods Blood samples of 472 Wujiang area Han males were randomly collected and genotyped by YfilerTM Plus PCR Amplification Kit. The allele frequencies and haplotype frequencies of each locus were obtained using the direct calculation method. Y-SNP haplogroups of each sample were estimated using Y-Predictor software and verified through experiments by amplification refractory mutation system-polymerase chain reaction （ARMS-PCR）. Results A total of 453 haplotypes were found in the 27 Y-STR genetic markers in 472 Han males of Wujiang area. The haplotype diversity （HD） was 0.997 696 93, among which, the highest gene diversity （GD） value was DYF387S1a/b （GD=0.953 1） and the lowest was DYS438 （GD=0.321 8）. Based on genotyping data of 27 Y-STRs and 472 samples, 132 haplogroups from C, D, N, O and Q, etc downstream Y-SNP haplogroups were estimated and then verified through experiments. Conclusion This study is based on Y-chromosome STR haplotypes, and predicts Y-SNP haplogroups by Y-Predictor software, then uses ARMS-PCR to verify. Y-SNP genetic markers were introduced to achieve precise analysis of the genetic structure of male families in population of three towns in Wujiang area.