1. Complex population structure and haplotype patterns in the Western European honey bee from sequencing a large panel of haploid dronesDavid Wragg, Sonia E. Eynard, Benjamin Basso, Kamila Canale-Tabet, Emmanuelle Labarthe, Olivier Bouchez, Kaspar Bienefeld, Małgorzata Bieńkowska, Cecilia Costa, Aleš Gregorc, Per Kryger, Melanie Parejo, Alice M. Pinto, Jean-Pierre Bidanel, Bertrand Servin, Yves Le Conte, Alain Vignal, 2022, original scientific article Abstract: Honey bee subspecies originate from specific geographical areas in Africa, Europe and the Middle East, and beekeepers interested in specific phenotypes have imported genetic material to regions outside of the bees' original range for use either in pure lines or controlled crosses. Moreover, imported drones are present in the environment and mate naturally with queens from the local subspecies. The resulting admixture complicates population genetics analyses, and population stratification can be a major problem for association studies. To better understand Western European honey bee populations, we produced a whole genome sequence and single nucleotide polymorphism (SNP) genotype data set from 870 haploid drones and demonstrate its utility for the identification of nine genetic backgrounds and various degrees of admixture in a subset of 629 samples. Five backgrounds identified correspond to subspecies, two to isolated populations on islands and two to managed populations. We also highlight several large haplotype blocks, some of which coincide with the position of centromeres. The largest is 3.6 Mb long and represents 21% of chromosome 11, with two major haplotypes corresponding to the two dominant genetic backgrounds identified. This large naturally phased data set is available as a single vcf file that can now serve as a reference for subsequent populations genomics studies in the honey bee, such as (i) selecting individuals of verified homogeneous genetic backgrounds as references, (ii) imputing genotypes from a lower-density data set generated by an SNP-chip or by low-pass sequencing, or (iii) selecting SNPs compatible with the requirements of genotyping chips.
Keywords: genome, haplotype, honey bee, population genetics, SNP
Published in DKUM: 08.07.2024; Views: 109; Downloads: 7
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2. MTHFR C677T and A1298C genotypes and haplotypes in Slovenian couples with unexplained infertility problems and in embryonic tissues from spontaneous abortionsŠpela Stangler Herodež, Boris Zagradišnik, Alenka Erjavec Škerget, Andreja Zagorac, Iztok Takač, Veljko Vlaisavljević, Lidija Lokar, Nadja Kokalj-Vokač, 2013, original scientific article Abstract: The objective of this study was to analyze the methylenetetrahydrofolate reductases (MTHFRs) C677T and A1298C genotype distributions in couples with unexplained fertility problems (UFP) and healthy controls, and to analyze the genotype and haplotype distribution in spontaneously aborted embryonic tissues (SAET) using allele specific polymerase chain reaction (PCR) in 200 probands with UFP, 353 samples of SAET and 222 healthy controls. The analysis revealed a significant overall representation of the 677T allele in male probands from couples with UFP (p = 0.036). The combined genotype distribution for both MTHFR polymorphisms was also significantly altered (χ2 21.73, p <0.001) although female probands made no contribution (c2 1.33, p = 0.72). The overall representation of the 677T allele was more pronounced in SAET (0.5 vs. 0.351 in controls, p <0.001) regardless of the karyotype status (aneuploidy vs. normal karyotype). In addition, the frequencies of the CA and CC haplotypes were significantly lower than in the control group (p = 0.021 and p = 0.001, respectively), whereas the frequency of the TC haplotype was significantly higher than in controls (p <0.0001). The presented findings indicate that only male probands contribute to the association of MTHFR mutations with fertility problems in grown adults and demonstrate a high prevalence of mutated MTHFR genotypes in SAET.
Keywords: methylenetetrahydrofolate reductase (MTHFR), genotype, haplotype, infertility, miscarriage
Published in DKUM: 30.03.2017; Views: 1469; Downloads: 306
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