Investigation of pseudoautosomal and bordering regions in avian Z and W chromosomes with the use of large insert genomic BAC clones

Blagoveschensky, I Yu; Sazanova, Anna L; Stekol'nikova, V A; Фомичев, К А; Barkova, Olga; Romanov, Michael N; Sazanov, Alexei A

doi:10.1134/s1022795411020050

Cited by 4 publications

(11 citation statements)

References 15 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The FISH experiments were performed following the protocol as specified elsewhere (e.g., Sazanov et al 2006;Blagoveschensky et al 2011; see also Online resource 3 for further detail). In short, the 96-h Brown Leghorn chick embryo cells were used to generate preparations of mitotic chromosomes using hypotonic treatment, fixation, and colchicine incubation.…”

Section: Fish Proceduresmentioning

confidence: 99%

“…Others, other six clones shown in this table and included in this contig. 3 BAC clones that were also positive for, and FISH mapped to, UBAP2L2 (or UBAP2W; Sazanov et al 2006;Blagoveschensky et al 2011). 4 BAC clone that was also positive for UBE2R2L and UBAP2L2 but not tested (NT) by FISH in the previous (Sazanov et al 2006;Blagoveschensky et al 2011 Out of these seven BACs, there were four clones, CH261-105E16, CH261-114G22, CH261-019I23 and CH261-053P09, that also hybridized to the UBAP2L2 (or UBAP2W) specific overgo probe.…”

Section: Overgo Design and Hybridization Using Chicken Bac Librarymentioning

confidence: 99%

“…3 BAC clones that were also positive for, and FISH mapped to, UBAP2L2 (or UBAP2W; Sazanov et al 2006;Blagoveschensky et al 2011). 4 BAC clone that was also positive for UBE2R2L and UBAP2L2 but not tested (NT) by FISH in the previous (Sazanov et al 2006;Blagoveschensky et al 2011 Out of these seven BACs, there were four clones, CH261-105E16, CH261-114G22, CH261-019I23 and CH261-053P09, that also hybridized to the UBAP2L2 (or UBAP2W) specific overgo probe. These appeared to overlap with both the UBE2R2L and UBAP2L2 genes that can be confirmed by their close localization in the chicken genome assembly GRCg6a (Fig.…”

Section: Overgo Design and Hybridization Using Chicken Bac Librarymentioning

confidence: 99%

See 2 more Smart Citations

A pair of gametologous genes provides further insights into avian comparative cytogenomics

Sazanov

Sazanova

Nefedov³

et al. 2023

Biologia

View full text Add to dashboard Cite

Exploration of avian gametologous genes, i.e., homologous genes located on both the Z and W chromosomes, provides a crucial information about the underlying mechanism pertaining to the evolution of these chromosomes. The domestic chicken (Gallus gallus (Linnaeus 1758); GGA) traditionally serves as the primary reference subject of these comparative cytogenomic studies. Using bioinformatic, molecular (overgo BAC library scanning), and cytogenetic (BAC-based FISH) techniques, we have investigated in detail a pair of UBE2R2/UBE2R2L gametologs. By screening a gridded genomic jungle fowl BAC library, CHORI-261, with a short labeled UBE2R2L gene fragment called overgo probe, we detected seven specific clones. For three of them, CH261-019I23, CH261-105E16, and CH261-114G22, we identified their precise cytogenetic location on the Gallus gallus W chromosome (GGAW). They also co-localized with the UBAP2L2 gene on the, as was shown previously, along with the CH261-053P09 BAC clone also containing the GGAW-specific UBE2R2L DNA sequence. The fine mapping of the UBE2R2/UBE2R2L homologs in the chicken genome also shed the light on comparative cytogenetic aspects in birds. Our findings provided further evidence that bird genomes moderately changed only during evolution and are suitable for successful use of interspecies hybridization using both overgo-based BAC library screen and BAC-based FISH.

show abstract

Section: Fish Proceduresmentioning

confidence: 99%

Section: Overgo Design and Hybridization Using Chicken Bac Librarymentioning

confidence: 99%

Section: Overgo Design and Hybridization Using Chicken Bac Librarymentioning

confidence: 99%

See 1 more Smart Citation

A pair of gametologous genes provides further insights into avian comparative cytogenomics

Sazanov

Sazanova

Nefedov³

et al. 2023

Biologia

View full text Add to dashboard Cite

show abstract

“…If these can be reliably identified, they can be treated as an artificial autosomal chromosome in AlphaImpute. Compared to chromosome Z, chromosome W is very small, contains only a handful of known genes [5] and has very few known SNP reported in Assembly 2 of the chicken genome.…”

Section: Resultsmentioning

confidence: 99%

“…Males receive one copy of Z from each of their parents, while females receive one copy of Z only from their male parent and none from their female parent. Chromosome Z has a small pseudo-autosomal region that recombines with chromosome W [5], which can be treated as an autosomal chromosome in AlphaImpute.…”

Section: Chromosome Z Inheritancementioning

confidence: 99%

Extending long-range phasing and haplotype library imputation methods to impute genotypes on sex chromosomes

Hickey

Kranis

2013

Genet Sel Evol

View full text Add to dashboard Cite

AlphaImpute is a flexible and accurate genotype imputation tool that was originally designed for the imputation of genotypes on autosomal chromosomes. In some species, sex chromosomes comprise a large portion of the genome. For example, chromosome Z represents approximately 8% of the chicken genome and therefore is likely to be important in determining genetic variation in a population. When breeding programs make selection decisions based on genomic information, chromosomes that are not represented on the genotyping platform will not be subject to selection. Therefore imputation algorithms should be able to impute genotypes for all chromosomes. The objective of this research was to extend AlphaImpute so that it could impute genotypes on sex chromosomes. The accuracy of imputation was assessed using different genotyping strategies in a real commercial chicken population. The correlation between true and imputed genotypes was high in all the scenarios and was 0.96 for the most favourable scenario. Overall, the accuracy of imputation of the sex chromosome was slightly lower than that of autosomes for all scenarios considered.

show abstract

Sex Differences in Response to Marek’s Disease: Mapping Quantitative Trait Loci Regions (QTLRs) to the Z Chromosome

Lipkin¹,

Smith²,

Soller³

et al. 2022

Preprint

View full text Add to dashboard Cite

Marek’s Disease (MD) has a significant impact on both the global poultry economy and animal welfare. The disease pathology can include neurological damage and tumour formation. Sexual dimorphism in immunity and known higher susceptibility of females to MD makes the chicken Z chromosome (GGZ) a particularly attractive target to study the chicken MD response. Previously, we used a Hy-Line F6 population from a full-sib advanced intercross line to map MD QTL regions (QTLRs) on all chicken autosomes. Here we mapped MD QTLRs on GGZ in the previously utilized F6 population with individual genotypes and phenotypes, and in eight elite commercial egg production lines with daughter-tested sires and selective DNA pooling (SDP). Four MD QTLRs were found from each analysis. Some of these QTLRs overlap regions from previous reports. All QTLRs were tested by indiviuals from the same eight lines used in the SDP and genotyped with markers located within and around the QTLRs. All QTLRs were confirmed. The results exemplify the complexity of MD resistance in chickens and the complex distribution of P-values and LD pattern and their effect on localization of the causative elements. Considering the fragments and interdigitated LD blocks while using LD to aid localization of causative elements, one must look beyond the insignificant markers, for possible distant markers and blocks in high LD with the significant block. The QTLRs found here may explain at least part of the gender differences in MD tolerance, and provide targets for mitigating the effects of MD.

show abstract

Investigation of pseudoautosomal and bordering regions in avian Z and W chromosomes with the use of large insert genomic BAC clones

Cited by 4 publications

References 15 publications

A pair of gametologous genes provides further insights into avian comparative cytogenomics

A pair of gametologous genes provides further insights into avian comparative cytogenomics

Extending long-range phasing and haplotype library imputation methods to impute genotypes on sex chromosomes

Sex Differences in Response to Marek’s Disease: Mapping Quantitative Trait Loci Regions (QTLRs) to the Z Chromosome

Contact Info

Product

Resources

About