Search results for "homozygosity"
showing 10 items of 42 documents
Genome-wide detection of signatures of selection in three Valdostana cattle populations
2020
International audience; The Valdostana is a local dual purpose cattle breed developed in Italy. Three populations are recognized within this breed, based on coat colour, production level, morphology and temperament: Valdostana Red Pied (VPR), Valdostana Black Pied (VPN) and Valdostana Chestnut (VCA). Here, we investigated putative genomic regions under selection among these three populations using the Bovine 50K SNP array by combining three different statistical methods based either on allele frequencies (F-ST) or extended haplotype homozygosity (iHS and Rsb). In total, 8, 5 and 8 chromosomes harbouring 13, 13 and 16 genomic regions potentially under selection were identified by at least tw…
Production of Haploid and Doubled Haploid Lines in Nut Crops: Persian Walnut, Almond, and Hazelnut
2021
This chapter deals with induction of haploidy via parthenogenesis in Persian walnut and via microspore embryogenesis in almond and hazelnut. Haploid induction through in situ parthenogenesis using pollination with irradiated pollen to stimulate the embryogenic development of the egg cell, followed by in vitro culture of the immature haploid embryos. Microspore embryogenesis allows the induction of immature pollen grains (microspores), to move away from the normal gametophytic developmental route in the direction of the sporophytic one, yielding homozygous organisms (embryos in this case). Unlike other fruit crops (such as Citrus), regeneration of entire plants has not yet been obtained in o…
Genome-Wide Patterns of Homozygosity Reveal the Conservation Status in Five Italian Goat Populations.
2021
The application of genomic technologies has facilitated the assessment of genomic inbreeding based on single nucleotide polymorphisms (SNPs). In this study, we computed several runs of homozygosity (ROH) parameters to investigate the patterns of homozygosity using Illumina Goat SNP50 in five Italian local populations: Argentata dell’Etna (N = 48), Derivata di Siria (N = 32), Girgentana (N = 59), Maltese (N = 16) and Messinese (N = 22). The ROH results showed well-defined differences among the populations. A total of 3687 ROH segments >
Genome-wide homozygosity and risk of four non-Hodgkin lymphoma subtypes
2021
Aim: Recessive genetic variation is thought to play a role in non-Hodgkin lymphoma (NHL) etiology. Runs of homozygosity (ROH), defined based on long, continuous segments of homozygous SNPs, can be used to estimate both measured and unmeasured recessive genetic variation. We sought to examine genome-wide homozygosity and NHL risk.Methods: We used data from eight genome-wide association studies of four common NHL subtypes: 3061 chronic lymphocytic leukemia (CLL), 3814 diffuse large B-cell lymphoma (DLBCL), 2784 follicular lymphoma (FL), and 808 marginal zone lymphoma (MZL) cases, as well as 9374 controls. We examined the effect of homozygous variation on risk by: (1) estimating the fraction o…
Ancient Haplotypes at the 15q24.2 Microdeletion Region Are Linked to Brain Expression of MAN2C1 and Children's Intelligence
2016
The chromosome bands 15q24.1-15q24.3 contain a complex region with numerous segmental duplications that predispose to regional microduplications and microdeletions, both of which have been linked to intellectual disability, speech delay and autistic features. The region may also harbour common inversion polymorphisms whose functional and phenotypic manifestations are unknown. Using single nucleotide polymorphism (SNP) data, we detected four large contiguous haplotype-genotypes at 15q24 with Mendelian inheritance in 2,562 trios, African origin, high population stratification and reduced recombination rates. Although the haplotype-genotypes have been most likely generated by decreased or abse…
Genome-wide identification of runs of homozygosity islands and associated genes in local dairy cattle breeds
2018
Runs of homozygosity (ROH) are widely used as predictors of whole-genome inbreeding levels in cattle. They identify regions that have an unfavorable effect on a phenotype when homozygous, but also identify the genes associated with traits of economic interest present in these regions. Here, the distribution of ROH islands and enriched genes within these regions in four dairy cattle breeds were investigated. Cinisara (71), Modicana (72), Reggiana (168) and Italian Holstein (96) individuals were genotyped using the 50K v2 Illumina BeadChip. The genomic regions most commonly associated with ROHs were identified by selecting the top 1% of the single nucleotide polymorphisms (SNPs) most commonly…
Genome-wide analysis in endangered populations: a case study in Barbaresca sheep
2017
Analysis of genomic data is becoming increasingly common in the livestock industry and the findings have been an invaluable resource for effective management of breeding programs in small and endangered populations. In this paper, with the goal of highlighting the potential of genomic analysis for small and endangered populations, genome-wide levels of linkage disequilibrium, measured as the squared correlation coefficient of allele frequencies at a pair of loci, effective population size, runs of homozygosity (ROH) and genetic diversity parameters, were estimated in Barbaresca sheep using Illumina OvineSNP50K array data. Moreover, the breed's genetic structure and its relationship with oth…
Signatures of selection in the genome of Swedish warmblood horses selected for sport performance
2019
Abstract Background A growing demand for improved physical skills and mental attitude in modern sport horses has led to strong selection for performance in many warmblood studbooks. The aim of this study was to detect genomic regions with low diversity, and therefore potentially under selection, in Swedish Warmblood horses (SWB) by analysing high-density SNP data. To investigate if such signatures could be the result of selection for equestrian sport performance, we compared our SWB SNP data with those from Exmoor ponies, a horse breed not selected for sport performance traits. Results The genomic scan for homozygous regions identified long runs of homozygosity (ROH) shared by more than 85%…
Early embryo achievement through isolated microspore culture in citrus clementina hort. Ex tan., cvs. 'Monreal Rosso' and 'nules'
2015
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Genome‐wide survey on three local horse populations with a focus on runs of homozygosity pattern
2022
Purosangue Orientale Siciliano, Sanfratellano and Siciliano represent the Sicilian equine genetic resource. This study aimed to investigate the genetic diversity, population structure and the pattern of autozygosity of Sicilian horse populations using genome-wide single-nucleotide polymorphism (SNP) data generated with the Illumina Equine SNP70 array. The genotyping data of 17 European and Middle East populations were also included in the study. The patterns of genetic differentiation, model-based clustering and Neighbour-Net showed the expected positioning of Sicilian populations within the wide analysed framework and the close connections between the Purosangue Orientale Siciliano and the…