0175 - mGBS - Metagenomic Genotyping-by-Sequencing shedding light on genomic diversity in ocean microbiome

2018 ◽  
Author(s):  
Hoon Je Seong
Keyword(s):  
Genotyping By Sequencing ◽  
Genomic Diversity

Genotyping-by-sequencing reveals genomic homogeneity among overwintering Pacific Dunlin (Calidris alpina pacifica) aggregations along the Pacific coast of North America

The Condor ◽  
2019 ◽  
Vol 121 (3) ◽  
Author(s):  
Iva Popovic ◽  
David P L Toews ◽  
Carson C Keever ◽  
C Toby St. Clair ◽  
Blake A Barbaree ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Isolation By Distance ◽  
Spatial Scales ◽  
River Estuary ◽  
Genotyping By Sequencing ◽  
Genomic Diversity ◽  
Nucleotide Polymorphisms ◽  
Migratory Connectivity ◽  
Calidris Alpina ◽  
The Pacific

Abstract Information on how migratory populations are genetically structured during the overwintering season of the annual cycle can improve our understanding of the strength of migratory connectivity and help identify populations as units for management. Here, we use a genotype-by-sequencing approach to investigate whether population genetic structure exists among overwintering aggregations of the Pacific Dunlin subspecies (Calidris alpina pacifica) sampled at 2 spatial scales (within and among overwintering sites) in the eastern Pacific Flyway. Genome-wide analyses of 874 single nucleotide polymorphisms across 80 sampled individuals revealed no evidence for genetic differentiation among aggregations overwintering at 3 locations within the Fraser River Estuary (FRE) of British Columbia. Similarly, comparisons of aggregations in the FRE and those overwintering in southern sites in California and Mexico indicated no genetic segregation between northern and southern overwintering areas. These results suggest that Pacific Dunlin within the FRE, Sacramento Valley (California), and Guerrero Negro (Mexico) are genetically homogeneous, with no evident genetic structure between sampled sites or regions across the overwintering range. Despite no evidence for differentiation among aggregations, we identified a significant effect of geographical distance between sites on the distribution of individual genotypes in a redundancy analysis. A small proportion of the total genotypic variance (R2 =0.036, P = 0.011) was explained by the combined effect of latitude and longitude, suggesting weak genomic patterns of isolation-by-distance that are consistent with chain-like migratory connectivity between breeding and overwintering areas. Our study represents the first genome-scale investigation of population structure for a Dunlin subspecies and provides essential baseline estimates of genomic diversity and differentiation within the Pacific Dunlin.

scholarly journals Sorghum Association Panel Whole-Genome Sequencing Establishes Pivotal Resource for Dissecting Genomic Diversity

2021 ◽  
Author(s):  
Jon Lucas Boatwright ◽  
Sirjan Sapkota ◽  
Hongyu Jin ◽  
James Schnable ◽  
Zachary Brenton ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Phenotypic Diversity ◽  
Genotyping By Sequencing ◽  
Genomic Diversity ◽  
Evolutionary Divergence ◽  
Whole Genome ◽  
Linear Predictor ◽  
Association Panel ◽  
Genomic Marker

Association mapping panels represent foundational resources for understanding the genetic basis of phenotypic diversity and serve to advance plant breeding by exploring genetic variation across diverse accessions with distinct histories of evolutionary divergence and local adaptation. We report the whole-genome sequencing (WGS) of 400 sorghum [Sorghum bicolor (L.) Moench] accessions from the Sorghum Association Panel (SAP) at an average coverage of 38X (25X-72X), enabling the development of a high-density genomic-marker set of 43,983,694 variants including SNPs (~38 million), indels (~5 million), and CNVs (~170,000). We observe slightly more deletions among indels and a much higher prevalence of deletions among copy number variants compared to insertions. This new marker set enabled the identification of several putatively novel genomic associations for plant height and tannin content, which were not identified when using previous lower-density marker sets. WGS identified and scored variants in 5 kb bins where available genotyping-by-sequencing (GBS) data captured no variants, with half of all bins in the genome falling into this category. The predictive ability of genomic best unbiased linear predictor (GBLUP) models was increased by an average of 30% by using WGS markers rather than GBS markers. We identified 18 selection peaks across subpopulations that formed due to evolutionary divergence during domestication, and we found six Fst peaks resulting from comparisons between converted lines and breeding lines within the SAP that were distinct from the peaks associated with historic selection. This population has been and continues to serve as a significant public resource for sorghum research and demonstrates the value of improving upon existing genomic resources.

scholarly journals Genetic Diversity, Population Structure and Linkage Disequilibrium Assessment among International Sunflower Breeding Collections

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 283 ◽  
Author(s):  
Carla V. Filippi ◽  
Gabriela A. Merino ◽  
Juan F. Montecchia ◽  
Natalia C. Aguirre ◽  
Máximo Rivarola ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Linkage Disequilibrium ◽  
Genotyping By Sequencing ◽  
Optimal Number ◽  
Genomic Diversity ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
Germplasm Collections ◽  
K 12

Sunflower germplasm collections are valuable resources for broadening the genetic base of commercial hybrids and ameliorate the risk of climate events. Nowadays, the most studied worldwide sunflower pre-breeding collections belong to INTA (Argentina), INRA (France), and USDA-UBC (United States of America–Canada). In this work, we assess the amount and distribution of genetic diversity (GD) available within and between these collections to estimate the distribution pattern of global diversity. A mixed genotyping strategy was implemented, by combining proprietary genotyping-by-sequencing data with public whole-genome-sequencing data, to generate an integrative 11,834-common single nucleotide polymorphism matrix including the three breeding collections. In general, the GD estimates obtained were moderate. An analysis of molecular variance provided evidence of population structure between breeding collections. However, the optimal number of subpopulations, studied via discriminant analysis of principal components (K = 12), the bayesian STRUCTURE algorithm (K = 6) and distance-based methods (K = 9) remains unclear, since no single unifying characteristic is apparent for any of the inferred groups. Different overall patterns of linkage disequilibrium (LD) were observed across chromosomes, with Chr10, Chr17, Chr5, and Chr2 showing the highest LD. This work represents the largest and most comprehensive inter-breeding collection analysis of genomic diversity for cultivated sunflower conducted to date.

scholarly journals Genome-Wide Diversity, Population Structure and Demographic History of Dromedaries in the Central Desert of Iran

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 599 ◽  
Author(s):  
Morteza Bitaraf Sani ◽  
Javad Zare Harofte ◽  
Ahmad Bitaraf ◽  
Saeid Esmaeilkhanian ◽  
Mohammad Hossein Banabazi ◽  
...  
Keyword(s):  
Population Structure ◽  
Population Size ◽  
Balancing Selection ◽  
Demographic History ◽  
Genomic Analysis ◽  
Genotyping By Sequencing ◽  
Genomic Diversity ◽  
Nucleotide Polymorphisms ◽  
Effective Population ◽  
Genome Wide

The development of camel husbandry for good production in a desert climate is very important, thus we need to understand the genetic basis of camels and give attention to genomic analysis. We assessed genome-wide diversity, linkage disequilibrium (LD), effective population size (Ne) and relatedness in 96 dromedaries originating from five different regions of the central desert of Iran using genotyping-by-sequencing (GBS). A total of 14,522 Single Nucleotide Polymorphisms (SNPs) with an average minor allele frequency (MAF) of 0.19 passed quality control and filtering steps. The average observed heterozygosity in the population was estimated at 0.25 ± 0.03. The mean of LD at distances shorter than 40 kb was low (r2 = 0.089 ± 0.234). The camels sampled from the central desert of Iran exhibited higher relatedness than Sudanese and lower than Arabian Peninsula dromedaries. Recent Ne of Iran’s camels was estimated to be 89. Predicted Tajima’s D (1.28) suggested a bottleneck or balancing selection in dromedary camels in the central desert of Iran. A general decrease in effective and census population size poses a threat for Iran’s dromedaries. This report is the first SNP calling report on nearly the chromosome level and a first step towards understanding genomic diversity, population structure and demography in Iranian dromedaries.

scholarly journals Genomic Diversity and Climate Adaptation in Brachypodium

2015 ◽  
Author(s):  
Pip B Wilson ◽  
Jared Streich ◽  
Justin Borevitz
Keyword(s):  
Climate Adaptation ◽  
Phenotypic Diversity ◽  
Association Studies ◽  
Genotyping By Sequencing ◽  
Genomic Diversity ◽  
Bioenergy Crops ◽  
Genome Wide Association Studies ◽  
Climate Data ◽  
Landscape Genomics ◽  
Recent Developments

The Brachypodium genus contains the model grassesB. distachyon,B. staceiandB. hybridum, that are useful for molecular and physiological studies relevant to grain, pasture and bioenergy crops, as well as ecology. In this chapter we discuss the natural variation in climate/geography, genotypic and phenotypic diversity that exists within these species. We describe utilisation of this diversity via two methods, Genome Wide Association Studies and Landscape Genomics, to examine the interaction between specific genetic variants, phenotype, and environment. The aim is to identify adaptive loci that control specific traits in specific environments and understand the contribution of background polygenetic variation shaped by demographic processes. With recent developments in high throughput phenotyping, cheaper genotyping by sequencing and higher spatial/temporal resolution of climate data, these approaches can exploit the diversity of the Brachypodium. Experiments using this toolkit will reveal alleles, genes and pathways underlying agriculturally important and environmentally sensitive traits for use in grass breeding.

scholarly journals Complete genomes of two extinct New Zealand passerines show responses to climate fluctuations but no evidence for genomic erosion prior to extinction

2019 ◽  
Vol 15 (9) ◽  
pp. 20190491 ◽  
Author(s):  
Nicolas Dussex ◽  
Johanna von Seth ◽  
Michael Knapp ◽  
Olga Kardailsky ◽  
Bruce C. Robertson ◽  
...  
Keyword(s):  
Climate Change ◽  
New Zealand ◽  
Human Impacts ◽  
Oceanic Islands ◽  
Genomic Diversity ◽  
Climate Fluctuations ◽  
Forest Clearing ◽  
Mammalian Predators ◽  
Demographic Trajectories ◽  
Human Climate

Human intervention, pre-human climate change (or a combination of both), as well as genetic effects, contribute to species extinctions. While many species from oceanic islands have gone extinct due to direct human impacts, the effects of pre-human climate change and human settlement on the genomic diversity of insular species and the role that loss of genomic diversity played in their extinctions remains largely unexplored. To address this question, we sequenced whole genomes of two extinct New Zealand passerines, the huia ( Heteralocha acutirostris ) and South Island kōkako ( Callaeas cinereus ). Both species showed similar demographic trajectories throughout the Pleistocene. However, the South Island kōkako continued to decline after the last glaciation, while the huia experienced some recovery. Moreover, there was no indication of inbreeding resulting from recent mating among closely related individuals in either species. This latter result indicates that population fragmentation associated with forest clearing by Maōri may not have been strong enough to lead to an increase in inbreeding and exposure to genomic erosion. While genomic erosion may not have directly contributed to their extinctions, further habitat fragmentation and the introduction of mammalian predators by Europeans may have been an important driver of extinction in huia and South Island kōkako.

scholarly journals PSII-22 Comparison of the meat quality traits of crossbred pigs and the Large Black pigs

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 241-242
Author(s):  
Yongjie Wang ◽  
Keshari Thakali ◽  
Sarah Shelby ◽  
Jason Apple ◽  
Yan Huang
Keyword(s):  
Meat Quality ◽  
Genomic Diversity ◽  
Longissimus Dorsi ◽  
Rna Seq ◽  
Longissimus Dorsi Muscle ◽  
A Value ◽  
Dorsi Muscle ◽  
Body Weights ◽  
C Value ◽  
Crossbred Pigs

Abstract The purpose of this study was to compare the meat quality and genomic differences between cross-bred commercial pig (CP) and domestic Large Black pig (BP). Seven cross-bred commercial pigs and eight British Large Black pigs were assigned to CP group and BP group, with initial mean body weights of 18.82±1.412 kg for CP group and 23.31±1.935 kg for BP group, P = 0.061, and fed ad libitum. The final BW of the CP at d101 was similar to the BP (130.0±8.16 kg vs. 121.1±2.80 kg, P = 0.132). However, the BP group took 108 days to reach the final BW. The ADG in the CP was higher than BP (1.102±0.0599 kg vs. 0.905±0.0138 kg, P = 0.003). The hot carcass weight of CP was higher (P < 0.01) than BP, but the backfat of BP was higher (P < 0.01) than CP. The a* value of CP was higher (P < 0.05) than BP, and the c* value of CP was tended to be higher (P < 0.10) than BP. However, the h value of BP was higher (P < 0.05) than CP. The longissimus dorsi muscle fat content of BP was higher (P < 0.05) than CP. For the fatty acid composition, the SFA and MUFA of BP were higher (P < 0.05) than CP, but the PUFA of CP was higher (P < 0.05) than BP. The metmyoglobin content of CP was tended to be higher (P < 0.10) than BP. For the meat metabolism, the oxygen consumption of longissimus dorsi muscle of BP was higher (P < 0.01) than CP. The RNA-Seq data showed that the expression of the genes related to lipid metabolism is higher in BP (fold change > 3, P < 0.05). To conclude, BP has higher meat quality, while CP has its advantages in growth performance. And the differences between these two breeds may due to the genomic diversity.

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