scholarly journals Genome-wide assessment of genetic diversity and population structure insights into admixture and introgression in Chinese indigenous cattle

BMC Genetics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Wengang Zhang ◽  
Xue Gao ◽  
Yang Zhang ◽  
Yumin Zhao ◽  
Jiabao Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Indigenous Cattle ◽  
Genome Wide

scholarly journals Genome-wide genetic diversity, population structure and admixture analysis in Eritrean Indigenous Cattle

2020 ◽  
Vol 49 (6) ◽  
pp. 1083-1092
Author(s):  
S Goitom ◽  
M.G. Gicheha ◽  
F.K. Njonge ◽  
N Kiplangat
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variability ◽  
Population Differentiation ◽  
Principal Component ◽  
Vital Role ◽  
Group Method ◽  
Indigenous Cattle ◽  
Ecological Zones ◽  
Genome Wide

Indigenous cattle play a vital role in subsistence and livelihood of pastoral producers in Eritrea. In order to optimally utilize and conserve these valuable indigenous cattle genetic resources, the need to carry out an inventory of their genetic diversity was recognized. This study assessed the genetic variability, population structure and admixture of the indigenous cattle populations (ICPs) of Eritrea using a genotype by sequencing (GBS) approach. The authors genotyped 188 animals, which were sampled from 27 cattle populations in three diverse agro-ecological zones (western lowlands, highlands and eastern lowlands). The genome-wide analysis results from this study revealed genetic diversity, population structure and admixture among the ICPs. Averages of the minor allele frequency (AF), observed heterozygosity (HO), expected heterozygosity (HE), and inbreeding coefficient (FIS) were 0.157, 0.255, 0.218, and -0.089, respectively. Nei’s genetic distance (Ds) between populations ranged from 0.24 to 0.27. Mean population differentiation (FST) ranged from 0.01 to 0.30. Analysis of molecular variance revealed high genetic variation between the populations. Principal component analysis and the distance-based unweighted pair group method and arithmetic mean analyses revealed weak substructure among the populations, separating them into three genetic clusters. However, multi-locus clustering had the lowest cross-validation error when two genetically distinct groups were modelled. This information about genetic diversity and population structure of Eritrean ICPs provided a basis for establishing their conservation and genetic improvement programmes. Keywords: genetic variability, molecular characterization, population differentiation

scholarly journals Genetic Diversity and Population Structure in South African, French and Argentinian Angora Goats from Genome-Wide SNP Data

PLoS ONE ◽  
2016 ◽  
Vol 11 (5) ◽  
pp. e0154353 ◽  
Author(s):  
Carina Visser ◽  
Simon F. Lashmar ◽  
Este Van Marle-Köster ◽  
Mario A. Poli ◽  
Daniel Allain
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
South African ◽  
Snp Data ◽  
Genome Wide ◽  
Angora Goats

scholarly journals Genome-wide DNA Variants Identify Genetic Diversity and Population Structure of Leptosphaeria maculans in Western Canada

2020 ◽  
Author(s):  
Qilin Chen ◽  
Gary Peng ◽  
Randy Kutcher ◽  
Fengqun Yu
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genome Wide Association Study ◽  
Leptosphaeria Maculans ◽  
Western Canada ◽  
Effective Management ◽  
Genome Wide ◽  
Population Structure Analysis ◽  
Dna Variants ◽  
Genomic Regions

Abstract Background: Leptosphaeria maculans is a serious concern for canola production in Canada. For effective management, knowledge of the pathogen’s genetic variability and population structure is a prerequisite. Despite some information on race dynamics of the western Canadian L. maculans population in recent years, genetic diversity based on a large number of genome-wide DNA variants has not been investigated.Results: From 1,590 L. maculans isolates collected from 23 field sites in three provinces: Manitoba, Saskatchewan and Alberta, Canada, in the years 2007-2008 and 2012-2014, 150 representative isolates were selected and whole-genome sequenced, and 31,870 polymorphic DNA variants (SNPs and InDels) were used to study L. maculans genetic diversity and population structure. Cluster analysis showed that the genetic diversity levels and isolate groupings varied with the number and genomic regions of the variants involved; isolates collected in 2012-2014 were more genetically diverse than those collected in 2007-2008 when genome-wide variants were considered. The genome wide association study (GWAS) detected variants in egn4_Lema_T86290 (AvrLm4-7), egn4_Lema_T86300 and egn4_Lema_T86310 associated with the year of collection, but no variants was found to be associated with the province or specific location from which the isolates were collected. Population structure analysis indicated the presence of three distinct sub-populations in western Canada. While isolates from Saskatchewan were mainly of one sub-population (sub-pop1), the Alberta isolates comprised two sub-populations (sub-pop1 and sub-pop2), and all the 3 subpopulations were found in Manitoba.Conclusion: The genetic diversity of the western Canadian L. maculans population varied among provinces. It was highly admixed in Manitoba, followed by that in Alberta. The Saskatchewan population had the lowest genetic diversity. Significant genome variation between 2007-2008 and 2012-2014 occurred in the genes egn4_Lema_T86290 (AvrLm4-7), egn4_Lema_T86300 and egn4_Lema_T86310), with AvrLm4-7 becoming much more common in the L. maculans population in the later period.

scholarly journals Genetic Diversity, Population Structure, and Andean Introgression in Brazilian Common Bean Cultivars after Half a Century of Genetic Breeding

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1298
Author(s):  
Caléo Panhoca de Almeida ◽  
Jean Fausto de Carvalho Paulino ◽  
Sérgio Augusto Morais Carbonell ◽  
Alisson Fernando Chiorato ◽  
Qijian Song ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Common Bean ◽  
Gene Diversity ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Association Mapping Approach

Brazil is the largest consumer and third highest producer of common beans (Phaseolus vulgaris L.) worldwide. Since the 1980s, the commercial Carioca variety has been the most consumed in Brazil, followed by Black and Special beans. The present study evaluates genetic diversity and population structure of 185 Brazilian common bean cultivars using 2827 high-quality single-nucleotide polymorphisms (SNPs). The Andean allelic introgression in the Mesoamerican accessions was investigated, and a Carioca panel was tested using an association mapping approach. The results distinguish the Mesoamerican from the Andean accessions, with a prevalence of Mesoamerican accessions (94.6%). When considering the commercial classes, low levels of genetic differentiation were seen, and the Carioca group showed the lowest genetic diversity. However, gain in gene diversity and allelic richness was seen for the modern Carioca cultivars. A set of 1060 ‘diagnostic SNPs’ that show alternative alleles between the pure Mesoamerican and Andean accessions were identified, which allowed the identification of Andean allelic introgression events and shows that there are putative introgression segments in regions enriched with resistance genes. Finally, genome-wide association studies revealed SNPs significantly associated with flowering time, pod maturation, and growth habit, showing that the Carioca Association Panel represents a powerful tool for crop improvements.

scholarly journals Genomic analysis reveals the genetic diversity, population structure, evolutionary history and relationships of Chinese pepper

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Shijing Feng ◽  
Zhenshan Liu ◽  
Yang Hu ◽  
Jieyun Tian ◽  
Tuxi Yang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Demographic History ◽  
Genomic Analysis ◽  
Genotyping By Sequencing ◽  
Gansu Province ◽  
Climatic Oscillations ◽  
Genome Wide ◽  
A Genome ◽  
Wild Accessions

Abstract Chinese pepper, mainly including Zanthoxylum bungeanum and Zanthoxylum armatum, is an economically important crop popular in Asian countries due to its unique taste characteristics and potential medical uses. Numerous cultivars of Chinese pepper have been developed in China through long-term domestication. To better understand the population structure, demographic history, and speciation of Chinese pepper, we performed a comprehensive analysis at a genome-wide level by analyzing 38,395 genomic SNPs that were identified in 112 cultivated and wild accessions using a high-throughput genome-wide genotyping-by-sequencing (GBS) approach. Our analysis provides genetic evidence of multiple splitting events occurring between and within species, resulting in at least four clades in Z. bungeanum and two clades in Z. armatum. Despite no evidence of recent admixture between species, we detected substantial gene flow within species. Estimates of demographic dynamics and species distribution modeling suggest that climatic oscillations during the Pleistocene (including the Penultimate Glaciation and the Last Glacial Maximum) and recent domestication events together shaped the demography and evolution of Chinese pepper. Our analyses also suggest that southeastern Gansu province is the most likely origin of Z. bungeanum in China. These findings provide comprehensive insights into genetic diversity, population structure, demography, and adaptation in Zanthoxylum.

Genetic diversity and population structure of pear (Pyrus spp.) collections revealed by a set of core genome-wide SSR markers

2015 ◽  
Vol 11 (6) ◽  
Author(s):  
Qingwen Liu ◽  
Yue Song ◽  
Lun Liu ◽  
Mingyue Zhang ◽  
Jiangmei Sun ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Core Genome ◽  
Genome Wide
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