scholarly journals Assigning the Sex-Specific Markers via Genotyping-by-Sequencing onto the Y Chromosome for a Torrent Frog Amolops mantzorum

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 727 ◽  
Author(s):  
Wei Luo ◽  
Yun Xia ◽  
Bisong Yue ◽  
Xiaomao Zeng
Keyword(s):  
Sex Differences ◽  
Sex Determination ◽  
Candidate Gene ◽  
Y Chromosome ◽  
Light Microscope ◽  
Whole Genome Amplification ◽  
Genotyping By Sequencing ◽  
Whole Genome ◽  
Promoter Regions ◽  
Male Heterogamety

We used a genotyping-by-sequencing (GBS) approach to identify sex-linked markers in a torrent frog (Amolops mantzorum), using 21 male and 19 female wild-caught individuals from the same population. A total of 141 putatively sex-linked markers were screened from 1,015,964 GBS-tags via three approaches, respectively based on sex differences in allele frequencies, sex differences in heterozygosity, and sex-limited occurrence. With validations, 69 sex-linked markers were confirmed, all of which point to male heterogamety. The male specificity of eight sex markers was further verified by PCR amplifications, with a large number of additional individuals covering the whole geographic distribution of the species. Y chromosome (No. 5) was microdissected under a light microscope and amplified by whole-genome amplification, and a draft Y genome was assembled. Of the 69 sex-linked markers, 55 could be mapped to the Y chromosome assembly (i.e., 79.7%). Thus, chromosome 5 could be added as a candidate to the chromosomes that are particularly favored for recruitment in sex-determination in frogs. Three sex-linked markers that mapped onto the Y chromosome were aligned to three different promoter regions of the Rana rugosa CYP19A1 gene, which might be considered as a candidate gene for triggering sex-determination in A. mantzorum.

scholarly journals The Snakeskin Gourami (Trichopodus pectoralis) Tends to Exhibit XX/XY Sex Determination

Fishes ◽  
2021 ◽  
Vol 6 (4) ◽  
pp. 43
Author(s):  
Thitipong Panthum ◽  
Nararat Laopichienpong ◽  
Ekaphan Kraichak ◽  
Worapong Singchat ◽  
Dung Ho My Nguyen ◽  
...  
Keyword(s):  
Sex Differences ◽  
Sex Determination ◽  
Y Chromosome ◽  
Cytogenetic Analysis ◽  
Genotyping By Sequencing ◽  
Sexually Dimorphic ◽  
Determination System ◽  
Sex Determination System ◽  
Male Specific ◽  
Determination Mechanism

The snakeskin gourami (Trichopodus pectoralis) has a high meat yield and is one of the top five aquaculture freshwater fishes in Thailand. The species is not externally sexually dimorphic, and its sex determination system is unknown. Understanding the sex determination system of this species will contribute to its full-scale commercialization. In this study, a cytogenetic analysis did not reveal any between-sex differences in chromosomal patterns. However, we used genotyping-by-sequencing to identify 4 male-linked loci and 1 female-linked locus, indicating that the snakeskin gourami tends to exhibit an XX/XY sex determination system. However, we did not find any male-specific loci after filtering the loci for a ratio of 100:0 ratio of males:females. This suggests that the putative Y chromosome is young and that the sex determination region is cryptic. This approach provides solid information that can help identify the sex determination mechanism and potential sex determination regions in the snakeskin gourami, allowing further investigation of genetic improvements in the species.

scholarly journals High fusibility and chimera prevalence in an invasive colonial ascidian

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Maria Casso ◽  
Davide Tagliapietra ◽  
Xavier Turon ◽  
Marta Pascual
Keyword(s):  
Genetic Diversity ◽  
Whole Genome Amplification ◽  
Genetic Relatedness ◽  
Genotyping By Sequencing ◽  
Whole Genome ◽  
Didemnum Vexillum ◽  
Colonial Ascidian ◽  
Mediterranean Populations ◽  
Colony Fusion ◽  
Modular Organisms

Abstract The formation of chimeric entities through colony fusion has been hypothesized to favour colonisation success and resilience in modular organisms. In particular, it can play an important role in promoting the invasiveness of introduced species. We studied prevalence of chimerism and performed fusion experiments in Mediterranean populations of the worldwide invasive colonial ascidian Didemnum vexillum. We analysed single zooids by whole genome amplification and genotyping-by-sequencing and obtained genotypic information for more than 2,000 loci per individual. In the prevalence study, we analysed nine colonies and identified that 44% of them were chimeric, composed of 2–3 different genotypes. In the fusion experiment 15 intra- and 30 intercolony pairs were assayed but one or both fragments regressed and died in ~45% of the pairs. Among those that survived for the length of the experiment (30 d), 100% isogeneic and 31% allogeneic pairs fused. Fusion was unlinked to global genetic relatedness since the genetic distance between fused or non-fused intercolony pairs did not differ significantly. We could not detect any locus directly involved in allorecognition, but we cannot preclude the existence of a histocompatibility mechanism. We conclude that chimerism occurs frequently in D. vexillum and may be an important factor to enhance genetic diversity and promote its successful expansion.

scholarly journals Genomic data shed light on sex-determination in Australian freshwater Percichthyid fish species: Many ways to be a male

2021 ◽  
Author(s):  
Alexandra Pavlova ◽  
Katherine Harrisson ◽  
Rustam Turakulov ◽  
Yin Peng Lee ◽  
Brett Ingram ◽  
...  
Keyword(s):  
Sex Differences ◽  
Sex Determination ◽  
Fish Species ◽  
Amplicon Sequencing ◽  
Molecular Sexing ◽  
Whole Genome ◽  
Genome Wide ◽  
Freshwater Biota ◽  
Whole Genome Resequencing ◽  
Australian Freshwater

Understanding sex-specific biology can aid conservation management. But understanding genomic sex differences of monomorphic fish species and developing molecular sexing assays is challenged by their diverse sex-determination systems. To facilitate research on Percichthyid fish, predominant in the Australian freshwater biota, we report whole genome sequences and annotations of the endangered Macquarie perch Macquaria australasica and its sister species, the golden perch M. ambigua. To identify sex-linked loci, we conducted whole genome resequencing on 100 known-sex Macquarie perch. In-silico pool-seq comparisons revealed few sex differences, but a 275-Kb SOX-containing scaffold was enriched for gametologous loci- homozygous in females, heterozygous in males. Within this scaffold we reconstructed X- and Y-linked 146-bp haplotypes containing 5 sex-linked SNPs, ~38 Kb upstream of SOX, and developed a PCR-RFLP sexing assay targeting the Y-linked allele of one SNP. We tested this assay in a panel of known-sex Macquarie perch, and smaller panels of three other confamilial species. Amplicon sequencing of 400 bp encompassing the 146-bp region revealed that the few sex-linked positions differ interspecifically, and within Macquarie perch such that its sexing test approached 100% reliability only for the populations used in assay development. Similarly, Macquarie- and golden perch genome-wide DArTseq SNPs revealed different sex-linked loci across non-homologous scaffolds. Overall, we identified 22 sex-linked SNPs in Macquarie perch in a predominantly XX/XY system in which females are homozygous at all 22, and males are heterozygous at 2 or more. The resources here will facilitate multi-locus sexing assays for both species and research on Percichthyid biology.

Sex determination and Y chromosome constitutive heterochromatin

2019 ◽  
Vol 1 (1) ◽  
pp. 1-5
Author(s):  
Abyt Ibraimov
Keyword(s):  
Sex Determination ◽  
Y Chromosome ◽  
Constitutive Heterochromatin ◽  
Sex Differentiation ◽  
Secondary Sexual Characteristics ◽  
Biological Meaning ◽  
Heterochromatin Block ◽  
Sexual Characteristics ◽  
Open Question ◽  
Efficient Elimination

In many animals, including us, the genetic sex is determined at fertilization by sex chromosomes. Seemingly, the sex determination (SD) in human and animals is determined by the amount of constitutive heterochromatin on Y chromosome via cell thermoregulation. It is assumed the medulla and cortex tissue cells in the undifferentiated embryonic gonads (UEG) differ in vulnerability to the increase of the intracellular temperature. If the amount of the Y chromosome constitutive heterochromatin is enough for efficient elimination of heat difference between the nucleus and cytoplasm in rapidly growing UEG cells the medulla tissue survives. Otherwise it doomed to degeneration and a cortex tissue will remain in the UEG. Regardless of whether our assumption is true or not, it remains an open question why on Y chromosome there is a large constitutive heterochromatin block? What is its biological meaning? Does it relate to sex determination, sex differentiation and development of secondary sexual characteristics? If so, what is its mechanism: chemical or physical? There is no scientifically sound answer to these questions.

scholarly journals Quantifying genome DNA during whole-genome amplification via quantitative real-time multiple displacement amplification

RSC Advances ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 4617-4621
Author(s):  
Jing Tu ◽  
Yi Qiao ◽  
Yuhan Luo ◽  
Naiyun Long ◽  
Zuhong Lu
Keyword(s):  
Real Time ◽  
Whole Genome Amplification ◽  
Multiple Displacement Amplification ◽  
Whole Genome ◽  
Genome Amplification

Monitoring multiple displacement amplification by fluorescence signals.

scholarly journals Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Michael Abrouk ◽  
Naveenkumar Athiyannan ◽  
Thomas Müller ◽  
Yveline Pailles ◽  
Christoph Stritt ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Candidate Gene ◽  
Population Genomics ◽  
Genotyping By Sequencing ◽  
Wheat Cultivars ◽  
Structural Variations ◽  
High Quality ◽  
Diversity Panel ◽  
Haplotype Variation ◽  
Single Region

AbstractThe cloning of agriculturally important genes is often complicated by haplotype variation across crop cultivars. Access to pan-genome information greatly facilitates the assessment of structural variations and rapid candidate gene identification. Here, we identified the red glume 1 (Rg-B1) gene using association genetics and haplotype analyses in ten reference grade wheat genomes. Glume color is an important trait to characterize wheat cultivars. Red glumes are frequent among Central European spelt, a dominant wheat subspecies in Europe before the 20th century. We used genotyping-by-sequencing to characterize a global diversity panel of 267 spelt accessions, which provided evidence for two independent introductions of spelt into Europe. A single region at the Rg-B1 locus on chromosome 1BS was associated with glume color in the diversity panel. Haplotype comparisons across ten high-quality wheat genomes revealed a MYB transcription factor as candidate gene. We found extensive haplotype variation across the ten cultivars, with a particular group of MYB alleles that was conserved in red glume wheat cultivars. Genetic mapping and transient infiltration experiments allowed us to validate this particular MYB transcription factor variants. Our study demonstrates the value of multiple high-quality genomes to rapidly resolve copy number and haplotype variations in regions controlling agriculturally important traits.

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