Single Nucleotide Polymorphism Discovery and Genetic Differentiation Analysis of Geese Bred in Poland, Using Genotyping-by-Sequencing (GBS)

Grzegorczyk, Joanna; Gurgul, Artur; Oczkowicz, Maria; Szmatoła, Tomasz; Fornal, Agnieszka; Bugno‐Poniewierska, Monika

doi:10.3390/genes12071074

Cited by 8 publications

(8 citation statements)

References 27 publications

(37 reference statements)

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“…This was because the nucleotides of the protein-coding gene that cause mutations were under less natural selection pressure at the codon site. This was consistent with the results reported by Grzegorczyk et al [ 33 ]. Haplotype (Hd) and nucleotide (Pi) diversity are important indicators of the genetic diversity of a population [ 34 ].…”

Section: Discussionsupporting

confidence: 94%

Genetic Diversity Analysis and Breeding of Geese Based on the Mitochondrial ND6 Gene

Zhang

Liu

et al. 2023

Genes

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To explore the differences in body-weight traits of five goose breeds and analyze their genetic diversity and historical dynamics, we collected body-weight data statistics and used Sanger sequencing to determine the mitochondrial DNA of 100 samples of five typical goose breeds in China and abroad. The results indicated that Lion-Head, Hortobagy, and Yangzhou geese have great breeding potential for body weight. Thirteen polymorphic sites were detected in the corrected 505 bp sequence of the mitochondrial DNA (mtDNA) ND6 gene, accounting for approximately 2.57% of the total number of sites. The guanine-cytosine (GC) content (51.7%) of the whole sequence was higher than the adenine-thymine (AT) content (48.3%), showing a certain GC base preference. There were 11 haplotypes among the five breeds, including one shared haplotype. We analyzed the differences in the distribution of base mismatches among the five breeds and conducted Tajima’s D and Fu’s Fs neutral tests on the historical dynamics of the populations. The distribution of the mismatch difference presented an unsmooth single peak and the Tajima’s D value of the neutral test was negative (D < 0) and reached a significant level, which proves that the population of the three species had expanded; the Lion-Head goose population tends to be stable. The genetic diversity of Lion-Head, Zhedong White, Yangzhou, and Taihu geese was equal to the average diversity of Chinese goose breeds. The Hortobagy goose is a foreign breed with differences in mating line breeding and hybrid advantage utilization.

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Section: Discussionsupporting

confidence: 94%

Genetic Diversity Analysis and Breeding of Geese Based on the Mitochondrial ND6 Gene

Zhang

Liu

et al. 2023

Genes

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“…To apply genomics in population studies (of multiple individuals), methods were developed to reduce the genomic complexity of data, such as "Genotyping by Sequencing -GBS" 29 . GBS methods have been used to genotype thousands of single nucleotide polymorphisms (SNPs) scattered around unknown genomes of many of individuals of different plants 30,31 and animals 32,33 .…”

Section: Introductionmentioning

confidence: 99%

Population genomics of the critically endangered Brazilian merganser

Santos

Campos

Júnior

et al. 2023

Preprint

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The Brazilian merganser (Mergus octosetaceus) is one of the most endangered bird species in South America that comprises less than 250 mature individuals in the wild environments. This is a species extremely sensitive to environmental disturbances and restricted to few “pristine” freshwater habitats in Brazil, and it has been classified as Critically Endangered on the IUCN Red List since 1994. Understanding its current genetic diversity to promote in situ and ex situ management strategies was considered urgent for conservation of the remaining populations. To understand the evolutionary dynamics of remaining Brazilian merganser populations we have used "Genotyping by Sequencing" approach to characterize 923 SNPs in 31 individuals from all known areas of occurrence. The remaining populations of the Brazilian merganser present a low genetic diversity and high inbreeding levels likely due to recent population decline associated to habitat loss. Furthermore, it revealed a moderate level of genetic differentiation between all populations located in four separated areas of the highly threatened Cerrado biome. The results indicate that urgent actions for conservation of the species should be accompanied by a careful genetic monitoring to allow appropriate in situ and ex situ management to increase the long-term species survival in its natural environment.

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“…However, Poland is also the largest European geese producer and is second, just behind China, in the global geese production. The production of geese is an important and growing branch of the Polish poultry industry [ 3 , 4 ]. The most significant commercial goose is the White Kołuda breed, representing approximately 90% of the country’s goose population [ 4 , 5 ].…”

Section: Introductionmentioning

confidence: 99%

“…The production of geese is an important and growing branch of the Polish poultry industry [ 3 , 4 ]. The most significant commercial goose is the White Kołuda breed, representing approximately 90% of the country’s goose population [ 4 , 5 ]. The production of broiler and breeding geese is seasonal and the breeding cycle begins early spring and ends in the autumn [ 3 ].…”

Section: Introductionmentioning

confidence: 99%

Isolation and characterization of multidrug resistant Gallibacterium anatis biovar haemolytica strains from Polish geese and hens

Karwańska,

Wieliczko,

Bojesen

et al. 2023

Vet Res

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Gallibacterium anatis biovar haemolytica is a bacterium that is frequently associated with infections of the reproductive tract and respiratory system in poultry. To assess the current prevalence and resistance profile of these bacteria in Poland, we collected and investigated 63 strains of Gallibacterium from diseased domestic poultry flocks including geese, laying hens, breeding hens and an ornamental hen. Detailed characterization of the isolates included the analysis of phenotypic antimicrobial resistance profiles and biofilm formation ability. Furthermore, the genetic background of 40 selected isolates regarding the presence of virulence and antimicrobial resistance genes and mobile genetic elements was determined. All investigated isolates were multidrug resistant, most prominently to β-lactams, fluoroquinolones, sulfonamides and macrolides. A total of 48 different resistance profiles were detected. Of all isolates, 50.8% formed a strong biofilm, where strains isolated from geese appeared to be better at biofilm formation than strains isolated from laying and breeding hens. Single-nucleotide polymorphism genotyping revealed that G. anatis bv. haemolytica strains are restricted in host and geographical distribution, and the geese isolates showed greater phylogenetic similarity. Whole genome sequencing enabled identification of 25 different antimicrobial resistance determinants. The most common resistance genes were tetB, blaROB-1, and blaTEM-1 which may be located on mobile genetic elements. All isolates possessed the toxin gene gtxA, and the fimbrial gene flfA was identified in 95% of strains. Our results indicated that all G. anatis bv. haemolytica isolates showed multidrug resistant phenotypes. Strains isolated from geese were characterized by the highest percentage of isolates resistant to selected antimicrobials, probably reflecting host-related adaptations.

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Single Nucleotide Polymorphism Discovery and Genetic Differentiation Analysis of Geese Bred in Poland, Using Genotyping-by-Sequencing (GBS)

Cited by 8 publications

References 27 publications

Genetic Diversity Analysis and Breeding of Geese Based on the Mitochondrial ND6 Gene

Genetic Diversity Analysis and Breeding of Geese Based on the Mitochondrial ND6 Gene

Population genomics of the critically endangered Brazilian merganser

Isolation and characterization of multidrug resistant Gallibacterium anatis biovar haemolytica strains from Polish geese and hens

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