STUDYING THE STRUCTURE OF A GENE POOL POPULATION OF THE RUSSIAN WHITE CHICKEN BREED BY GENOME-WIDE SNP SCAN

We have previously shown that linkage disequilibrium (LD) in the elite cultivated barley ( Hordeum vulgare ) gene pool extends, on average, for <1–5 cM. Based on this information, we have developed a platform for whole genome association studies that comprises a collection of elite lines that we have characterized at 3060 genome-wide single nucleotide polymorphism (SNP) marker loci. Interrogating this data set shows that significant population substructure is present within the elite gene pool and that diversity and LD vary considerably across each of the seven barley chromosomes. However, we also show that a subpopulation comprised of only the two-rowed spring germplasm is less structured and well suited to whole genome association studies without the need for extensive statistical intervention to account for structure. At the current marker density, the two-rowed spring population is suited for fine mapping simple traits that are located outside of the genetic centromeres with a resolution that is sufficient for candidate gene identification by exploiting conservation of synteny with fully sequenced model genomes and the emerging barley physical map.

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Population-based biobank for analyzing the frequencies of clinically relevant DNA markers in the Russian population: bioinformatic aspects

CARDIOVASCULAR THERAPY AND PREVENTION ◽

10.15829/1728-8800-2020-2732 ◽

2020 ◽

Vol 19 (6) ◽

pp. 2732

Author(s):

I. O. Gorin ◽

V. S. Petrushenko ◽

Yu. S. Zapisetskaya ◽

S. M. Koshel ◽

O. P. Balanovsky

Keyword(s):

Genetic Markers ◽

Gene Pool ◽

Population Based ◽

Russian Population ◽

Northern Eurasia ◽

Medical Genetic ◽

Equal Distribution ◽

Genome Wide ◽

Genome Wide Data ◽

Components Analysis

One of the tasks of population-based biobanks is to determine the frequencies of clinically relevant genetic polymorphisms in the population. The population of Russia is very heterogeneous both ethnically and genetically. Therefore, the frequencies of genetic markers are in demand not in one sample, but in a series of samples reflecting the heterogeneity of the gene pool of different peoples and regions.Aim. To divide the population of Russia and neighboring countries into population groups meeting certain conditions, as well as having a representative sample in existing data and biobanks.Material and methods. We developed a method for combining populations into larger groups with maintaining intragroup homogeneity based on the principal components analysis with K-means clustering, followed by refinement of clustering for higher homogeneity and a more equal distribution of group sizes using FST distances. The technology has been adjusted using the example of the Biobank of Northern Eurasia. Therefore, the material was the genome-wide data on 4.5 million genetic markers for 1,883 samples representing 247 populations of Russia and neighboring countries from this biobank. The developed approach, the resulting set of populations and related map can be applied for other collections of biomaterials from Russian populations.Results. Application of this approach made it possible to divide the entire population of Russia and neighboring countries into 29 ethnogeographic groups, characterized by relative genetic homogeneity. This set of populations is recommended as a baseline for population screenings to identify the frequency of any genetic markers among the population of Russia. A map has been constructed showing the division of population into 29 ethnogeographic areas.Conclusion. On the basis of a reliable genome-wide data, the zoning of gene pool of the Russian population was carried out. We identified ethnogeographic groups with intergroup contrasting allele frequencies, but at the same time with relatively homogeneous intragroup parameters. The resulting map and register of groups can be used in population genetic, medical genetic and pharmacogenetic studies.

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Genome-wide Copy Number Variation in a Korean Native Chicken Breed

Korean Journal of Poultry Science ◽

10.5536/kjps.2014.41.4.305 ◽

2014 ◽

Vol 41 (4) ◽

pp. 305-311 ◽

Cited By ~ 4

Author(s):

Eun-Seok Cho ◽

Won-Hyong Chung ◽

Jung-Woo Choi ◽

Hyun-Jun Jang ◽

Mi-Na Park ◽

...

Keyword(s):

Copy Number Variation ◽

Copy Number ◽

Chicken Breed ◽

Genome Wide ◽

Native Chicken ◽

Number Variation ◽

Korean Native Chicken

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Lifetime productivity in gilts previously selected for decreased age at puberty

Animal Science ◽

10.1017/s135772980001359x ◽

1995 ◽

Vol 61 (1) ◽

pp. 115-121 ◽

Cited By ~ 15

Author(s):

R. B. Holder ◽

W. R. Lamberson ◽

R. O. Bates ◽

T. J. Safranski

Keyword(s):

Weight Loss ◽

Birth Weight ◽

Food Consumption ◽

Litter Size ◽

Reproductive Performance ◽

Gene Pool ◽

Ovulation Rate ◽

Age At Puberty ◽

Line P ◽

Pool Population

AbstractA study was conducted to evaluate the effect of decreasing age of puberty on lifetime productivity in sows. Two lines of gilts from the Nebraska Gene Pool population were used in this study: a line that had been selected for decreased age at puberty (AP) and a line in which selection had been random (RS). The study was conducted in two parts. In part one, 75 gilts were mated at second oestrus and the productivity measured over five parities. A second experiment utilizing 68 gilts was conducted to provide further data for comparing litter size at parity 1, and also to compare ovulation rates in the two lines at second oestrus. Results showed that litter size was similar in both lines across parities. After five parities the percentage of sows farrowing relative to parity 1 was 58-8% for the AP line but only 39·4% for the RS line (P = 0·17). Litter birth weight, litter size and weight at 21 days, number weaned, and lactation food consumption were similar for both lines. Lactation weight loss was not significantly different between the two lines (60·9 (s.e. 5·9) v. 527 (s.e. 5·0) kg, for RS and AP gilts, respectively) but was consistent with the slightly longer weaning to remating intervals in the RS line (7·8 (s.e. 0·7) v. 6·6 (s.e. 0·7) days, P = 0·22). Ovulation rate at second oestrus did not differ between the two lines (14·1 (s.e. 0·9) v. 14·3 (s.e. 0·5), for RS and AP gilts, respectively). The regression of mean accumulative productivity on time was in favour of the AP line (P = 0·05). These results suggest that reproductive performance is not impaired in gilts which have been selected to reach puberty at earlier ages, and productivity at a specific age may be enhanced.

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Genome-wide genotyping elucidates the geographical diversification and dispersal of the polyploid and clonally propagated yam (Dioscorea alata)

Annals of Botany ◽

10.1093/aob/mcaa122 ◽

2020 ◽

Vol 126 (6) ◽

pp. 1029-1038

Author(s):

Bilal Muhammad Sharif ◽

Concetta Burgarella ◽

Fabien Cormier ◽

Pierre Mournet ◽

Sandrine Causse ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Pool ◽

Genotyping By Sequencing ◽

Caribbean Region ◽

Gene Pools ◽

Dioscorea Alata ◽

Allele Frequency Distribution ◽

Low Genetic Diversity ◽

Genome Wide ◽

Greater Yam

Abstract Background and Aims Inferring the diffusion history of many human-dispersed species is still not straightforward due to unresolved past human migrations. The centre of diversification and routes of migration of the autopolyploid and clonally propagated greater yam, Dioscorea alata, one of the oldest edible tubers, remain unclear. Here, we address yam demographic and dispersal history using a worldwide sample. Methods We characterized genome-wide patterns of genetic variation using genotyping by sequencing 643 greater yam accessions spanning four continents. First, we disentangled the polyploid and clonal components of yam diversity using allele frequency distribution and identity by descent approaches. We then addressed yam geographical origin and diffusion history with a model-based coalescent inferential approach. Key Results Diploid genotypes were more frequent than triploids and tetraploids worldwide. Genetic diversity was generally low and clonality appeared to be a main factor of diversification. The most likely evolutionary scenario supported an early divergence of mainland Southeast Asian and Pacific gene pools with continuous migration between them. The genetic make-up of triploids and tetraploids suggests that they have originated from these two regions before westward yam migration. The Indian Peninsula gene pool gave origin to the African gene pool, which was later introduced to the Caribbean region. Conclusions Our results are congruent with the hypothesis of independent domestication origins of the two main Asian and Pacific gene pools. The low genetic diversity and high clonality observed suggest a strong domestication bottleneck followed by thousands of years of widespread vegetative propagation and polyploidization. Both processes reduced the extent of diversity available for breeding, and this is likely to threaten future adaptation.

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Genome-Wide Diversity Analysis of Valeriana officinalis L. Using DArT-seq Derived SNP Markers

Agronomy ◽

10.3390/agronomy10091346 ◽

2020 ◽

Vol 10 (9) ◽

pp. 1346

Author(s):

Maja Boczkowska ◽

Katarzyna Bączek ◽

Olga Kosakowska ◽

Anna Rucińska ◽

Wiesław Podyma ◽

...

Keyword(s):

Population Structure ◽

Gene Pool ◽

Natural Populations ◽

Snp Markers ◽

Valeriana Officinalis ◽

Wild Populations ◽

Relaxant Effect ◽

Genome Wide ◽

Array Technology ◽

Outcrossing Species

Common valerian (Valeriana officinalis L.) is one of the most important medicinal plants, with a mild sedative, nervine, antispasmodic and relaxant effect. Despite a substantial number of studies on this species, the genetic diversity and population structure have not yet been analyzed. Here, we use a next-generation sequencing-based Diversity Array Technology sequencing (DArT-seq) technique to analyze Polish gene bank accessions that originated from wild populations and cultivars. The major and, also, the most astounding result of our work is the low level of observed heterozygosity of individual plants from natural populations, despite the fact that the species is widespread in the studied area. Inbreeding in naturally outcrossing species such as valerian decreases reproductive success. The analysis of the population structure showed the potential presence of a metapopulation in the central part of Poland and the formation of a distinct gene pool in the Bieszczady Mountains. The results also indicate the presence of the cultivated gene pool within wild populations in the region where the species is cultivated for the needs of the pharmaceutical industry, and this could lead to structural and genetic imbalances in wild populations.

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Interactions between gene pools of russian and finnish-speaking populations from Tver region: analysis of 4 million SNP markers

Bulletin of Russian State Medical University ◽

10.24075/brsmu.2020.072 ◽

2020 ◽

Cited By ~ 1

Author(s):

OP Balanovsky ◽

IO Gorin ◽

YuS Zapisetskaya ◽

AA Golubeva ◽

ES Kostryukova ◽

...

Keyword(s):

Gene Flow ◽

Gene Pool ◽

Population Decline ◽

Principal Component ◽

Genetic Admixture ◽

Gene Pools ◽

Genome Wide ◽

A Genome ◽

Tver Region ◽

Snp Panel

This study explored the gene pools of Russian and Karelian populations of Tver region. Forty-one samples representing Tver Karels (n = 11) and Russians residing in the Western, Central and Eastern districts of Tver region (n = 30) were genotyped using a genome-wide panel of 4,559,465 SNPs. In order to investigate the phenomenon of genetic admixture between Slavic and Finnish-speaking populations, the obtained results were compared to the data on the Russian populations inhabiting the neighboring territories, Karels from Karelia and other North Eastern Europeans. Studying the gene pools of Russian populations with a genome-wide SNP panel is essential for cataloging their genetic diversity and identifying the distinct features of regional gene pools; in addition, it provides valuable data for practical pharmacogenomics and forensics. Using the principal component analysis, the ADMIXTURE method and D- and f3-statistics, we demonstrated that the gene pool of Tver Karels is closest to the gene pool of Karelian Karels, despite a long (300 to 500 years) history of living among the larger Russian population and the twentyfold population decline during the 20th century. At the same time, the gene pool of Tver Karels exhibits more pronounced similarity to the gene pool of the studied Russian populations than does any other Karelian population. The genetic admixture between Tver Russians and Tver Karels occurred due to a more intense gene flow from Russians to Karels whereas the gene flow from Karels to Russians was much weaker: Tver Russians turned out to be as genetically different from Karels as Pskov Russians. The genetic similarity of Tver Karels to Karelian Karels assessed with the autosomal SNP panel exhibits a slight shift towards the Russian gene pool and is consistent with the previously published analysis of Y-chromosome lineages in these populations that detected no admixture between Tver Karels and Russians.

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Genome-Wide Association Study of Resistance to Bean Fly and Population Structure of Market Classes of Common Bean

10.1101/633545 ◽

2019 ◽

Author(s):

Pascal P. Okwiri Ojwang ◽

Tilly Eldridge ◽

Pilar Corredor-Moreno ◽

Vincent Njung'e

Keyword(s):

Population Structure ◽

Common Bean ◽

Southern Africa ◽

Gene Pool ◽

Association Studies ◽

Genome Wide Association ◽

Chromosome 1 ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Bean Fly

Common bean (Phaesolus vulgaris L.) distribution across eastern, central and southern Africa region is widely driven by choice of grain types, which is affecting the genetic composition and adaptation to target production environments for biotic and abiotic constraints. Two bean fly species, Ophiomyia spencerella and Ophiomyia phaseoli are harmful insect pests of beans causing significant yield losses. Our objectives were to assess the population structure of common bean germplasm of different market classes and to identify polymorphic loci associated with resistance to O. spencerella. The study was carried out on a diversity panel of 284 genotypes using 9040 SNP markers. The genotypes were differentiated in to 14 distinct clusters. The mean FST of 0.4849, revealed major differentiation among the populations. Andean gene pool was more diverse compared to Mesoamerica gene pool which could be attributed to preference for large seeded cultivars. Multi-dimensional scaling and structure analyses revealed admixture among seed types. From genome wide association studies (GWAS), major genomic regions associated with O. spencerella resistance were identified on chromosome 1 (Pv01). The most significant SNP on Pv01 was aligned to gene PHAVU_001G075500g that is related to the Interleukin-1 receptor-associated kinase (IRAK) pathway, critical in regulating inherent immune responses to disease infection and insect herbivore attack. The diversity uncovered on the basis of market classes of beans and the presence of QTL regions associated with resistance to bean fly could serve as a valuable genetic resource for improvement of beans of different seed types in eastern and southern Africa region.

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