scholarly journals Contrasting whole-genome and reduced representation sequencing for population demographic inference: an alpine mammal example

2022 ◽  
Author(s):  
Daria Martchenko ◽  
Aaron Shafer
Keyword(s):  
Isolation By Distance ◽  
Demographic History ◽  
Genomic Region ◽  
Whole Genome ◽  
Summary Statistics ◽  
Effective Population ◽  
Genome Resequencing ◽  
Reduced Representation ◽  
Whole Genome Resequencing ◽  
Population Demographic

Genomic approaches to the study of population demography rely on accurate SNP calling and by-proxy the site frequency spectrum (SFS). Two main questions for the design of such studies remain poorly investigated: do reduced genomic sequencing summary statistics reflect that of whole genome, and how do sequencing strategies and derived summary statistics impact demographic inferences? To address those questions, we applied the ddRAD sequencing approach to 254 individuals and whole genome resequencing approach to 35 mountain goat (Oreamnos americanus) individuals across the species range with a known demographic history. We identified SNPs with 5 different variant callers and used ANGSD to estimate the genotype likelihoods (GLs). We tested combinations of SNP filtering by linkage disequilibrium (LD), minor allele frequency (MAF) and the genomic region. We compared the resulting suite of summary statistics reflective of the SFS and quantified the relationship to demographic inferences by estimating the contemporary effective population size (Ne), isolation-by-distance and population structure, FST, and explicit modelling of the demographic history with δaδi. Filtering had a larger effect than sequencing strategy, with the former strongly influencing summary statistics. Estimates of contemporary Ne and isolation-by-distance patterns were largely robust to the choice of sequencing, pipeline, and filtering. Despite the high variance in summary statistics, whole genome and reduced representation approaches were overall similar in supporting a glacial induced vicariance and low Ne in mountain goats. We discuss why whole genome resequencing data is preferable, and reiterate support the use of GLs, in part because it limits user-determined filters.

scholarly journals QTL Mapping of Quality Related Traits in Peanut Using Whole-Genome Resequencing

2021 ◽  
Author(s):  
Ziqi Sun ◽  
Feiyan Qi ◽  
Hua Liu ◽  
Li Qin ◽  
Jing Xu ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Fatty Acid ◽  
Protein Content ◽  
Genomic Region ◽  
High Density ◽  
Whole Genome ◽  
Missense Mutations ◽  
Genome Resequencing ◽  
Phenotypic Effect ◽  
Whole Genome Resequencing

Abstract Background: Oil and protein content, as well as fatty acid composition, are important quality traits in peanut. Elucidating the genetic mechanisms underlying these traits may help researchers to obtain improved cultivars through molecular breeding techniques.Results: Whole-genome resequencing of an RIL population of 318 lines was performed to construct a high-density linkage map and identify QTLs for peanut quality. The map, containing 4561 bin markers, covered a length of 2032.39 cM with an average marker density of 0.45 cM. A total of 109 QTLs for oil content, protein content, and fatty acid compositions were mapped on the 18 peanut chromosomes. The QTL qA05.1 was detected in four different environments and exhibited a major phenotypic effect on the content of oil, proteins, and six fatty acids. The genomic region spanned by qA05.1, corresponding to a physical interval of approximately 1.50 Mb, contains two polymorphic SNPs between two parents that could cause missense mutations. The two SNP sites were employed as KASP markers and validated using lines with extremely high and low oil contents; these sites may be useful in the marker-assisted breeding of peanut varieties with high oil contents.Conclusions: A high-density genetic map with 4561 bin markers was constructed, and a major and pleiotropic QTL located on LG05 was stably detected for oil, protein and fatty acids across four different environments.

scholarly journals Whole-genome resequencing of 472 Vitis accessions for grapevine diversity and demographic history analyses

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Zhenchang Liang ◽  
Shengchang Duan ◽  
Jun Sheng ◽  
Shusheng Zhu ◽  
Xuemei Ni ◽  
...  
Keyword(s):  
Demographic History ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Whole Genome Resequencing

scholarly journals Whole genome resequencing data sets of different species from Pistacia genus

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Ali Tajabadi ◽  
Ali Esmailizadeh
Keyword(s):  
Genomic Dna ◽  
Demographic History ◽  
Data Sets ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Insert Size ◽  
Illumina Hiseq ◽  
Data Description ◽  
Sequence Read Archive ◽  
Whole Genome Resequencing

Abstract Objectives Pistacia genus belongs to the flowering plants in the cashew family and contains at least 11 species. The whole-genome resequencing data of different species from Pistacia genus are described herein. The data reported here will be useful for better understand the adaptive evolution, demographic history, genetic diversity, population structure, and domestication of pistachio. Data description Genomic DNA was isolated from fresh leaves and used to construct libraries with insert size of 350 bp. Sequence libraries were made and sequenced on the Illumina Hiseq 4000 platform to produce 150 bp paired-end reads. A total number of 4,851,118,730 billion reads (ranging from 33,305,900 to 34,990,618 reads per sample) were created across all samples. We produced a total of 727.67 Gbp data which have been deposited in the Genome Sequence Archive (GSA) database with the Accession of CRA000978. All of the data are also available as the sequence read archive (SRA) format in the National Center for Biotechnology Information (NCBI) with identifier of SRP189222, mirroring our deposited data in GSA.

scholarly journals Whole-Genome Resequencing of Near-Isogenic Lines Reveals a Genomic Region Associated with High Trans-Lycopene Contents in Watermelon

Plants ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 8
Author(s):  
Siyoung Lee ◽  
Girim Park ◽  
Yunseo Choi ◽  
Seoyeon Park ◽  
Hoytaek Kim ◽  
...  
Keyword(s):  
Genomic Region ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Near Isogenic Lines ◽  
Genome Resequencing ◽  
Isogenic Lines ◽  
Genome Wide ◽  
Donor Parent ◽  
Caps Markers ◽  
Whole Genome Resequencing

Trans-lycopene is a functional phytochemical abundant in red-fleshed watermelons, and its contents vary among cultivars. In this study, the genetic basis of high trans-lycopene contents in scarlet red flesh was evaluated. Three near-isogenic lines (NILs) with high trans-lycopene contents were derived from the scarlet red-fleshed donor parent DRD and three coral red-fleshed (low trans-lycopene contents) recurrent parents. The lycopene contents of DRD (589.4 ± 71.8 µg/g) were two times higher than that of the recurrent parents, and values for NILs were intermediate between those of the parents. Coral red-fleshed lines and F1 cultivars showed low trans-lycopene contents (135.7 ± 18.0 µg/g to 213.7 ± 39.5 µg/g). Whole-genome resequencing of two NILs and their parents and an analysis of genome-wide single-nucleotide polymorphisms revealed three common introgressed regions (CIRs) on chromosomes 6, 9, and 10. Twenty-eight gene-based cleaved amplified polymorphic sequence (CAPS) markers were developed from the CIRs. The CAPS markers derived from CIR6 on chromosome 6, spanning approximately 1 Mb, were associated (R2 = 0.45–0.72) with the trans-lycopene contents, particularly CIR6-M1 and CIR6-M4. Our results imply that CIR6 is a major genomic region associated with variation in the trans-lycopene contents in red-fleshed watermelon, and CIR6-M1 and CIR6-M4 may be useful for marker-assisted selection.

scholarly journals Author Correction: Whole-genome resequencing of 472 Vitis accessions for grapevine diversity and demographic history analyses

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Zhenchang Liang ◽  
Shengchang Duan ◽  
Jun Sheng ◽  
Shusheng Zhu ◽  
Xuemei Ni ◽  
...  
Keyword(s):  
Demographic History ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Whole Genome Resequencing

scholarly journals Comparing genomic-based estimates of relatedness for use in pedigree-based conservation management

2021 ◽  
Author(s):  
Samantha S Hauser ◽  
Stephanie J Galla ◽  
Tammy E Steeves ◽  
Emily K Latch
Keyword(s):  
Captive Breeding ◽  
Whole Genome ◽  
Allele Sharing ◽  
Pedigree Data ◽  
Data Types ◽  
Genome Resequencing ◽  
Data Set ◽  
Breeding Programs ◽  
Reduced Representation ◽  
Whole Genome Resequencing

Researchers have long debated which genomic estimator of relatedness best captures the degree of relationship between two individuals. In the genomics era, this debate continues, with relatedness estimates being sensitive to the method used to generate genomic markers (e.g., reduced-representation sequencing, whole genome resequencing), marker quality, and levels of diversity in sampled individuals. Here, we compare six commonly used relatedness estimators (kinship genetic distance (KGD), Wang Maximum Likelihood (TrioML), Queller and Goodnight (Rxy), KING-robust, RAB, allele-sharing coancestry) across five species bred in captivity - including three birds and two mammals with varying degrees of reliable pedigree data, using reduced-representation and whole genome resequencing data. Relatedness estimates varied widely across estimators, sequencing method, and species, yet the most consistent results with known pedigree data were found using KING-robust and to a lesser extent KGD. The allele-sharing estimator was sensitive to missing data and inbreeding, attributes that make this estimator ill-suited for use in captive breeding programs. Our combined results indicate there is not a single genomic based estimator that is ideal across different species and data types. To enable researchers to evaluate the most appropriate relatedness estimator for each new data set, we provide a structured workflow that is broadly applicable to conservation breeding programs, particularly where genomic estimates of relatedness can complement and complete poorly pedigreed populations. Given a growing interest in wild pedigrees, our results and workflow are also applicable to in situ wildlife management.

scholarly journals Whole-genome resequencing of large yellow croaker (Larimichthys crocea) reveals the population structure and signatures of environmental adaptation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tetsuo Kon ◽  
Liyi Pei ◽  
Ryota Ichikawa ◽  
Chunyan Chen ◽  
Ping Wang ◽  
...  
Keyword(s):  
Population Structure ◽  
Population Genomics ◽  
Living Environment ◽  
Large Yellow Croaker ◽  
Whole Genome ◽  
Effective Population ◽  
Genome Resequencing ◽  
Genetic Population ◽  
Whole Genome Resequencing ◽  
Sea Area

AbstractLarge yellow croaker is an economically important fish in China and East Asia. Despite its economic importance, genome-wide adaptions of domesticated large yellow croaker are largely unknown. Here, we performed whole-genome resequencing of 198 individuals of large yellow croaker obtained in the sea or from farmers in Zhoushan or Ningde. Population genomics analyses revealed the genetic population structure of our samples, reflecting the living environment. Each effective population size is estimated to be declining over generations. Moreover, we identified genetically differentiated genomic regions between the sea-captured population in the Zhoushan Sea area and that of the Ningde Sea area or between the sea-captured population and the farmed population in either area. Gene ontology analyses revealed the gene groups under selective sweep for the adaptation to the domesticated environment. All these results suggest that individuals of the large yellow croaker populations show genomic signatures of adaptation to different living environments.

scholarly journals Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Luciano Calderón ◽  
Nuria Mauri ◽  
Claudio Muñoz ◽  
Pablo Carbonell-Bejerano ◽  
Laura Bree ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Somatic Mutations ◽  
Clonal Propagation ◽  
Variant Calling ◽  
Vitis Vinifera L ◽  
Whole Genome ◽  
Single Nucleotide Variants ◽  
Genome Resequencing ◽  
Diversity Pattern ◽  
Whole Genome Resequencing

AbstractGrapevine cultivars are clonally propagated to preserve their varietal attributes. However, genetic variations accumulate due to the occurrence of somatic mutations. This process is anthropically influenced through plant transportation, clonal propagation and selection. Malbec is a cultivar that is well-appreciated for the elaboration of red wine. It originated in Southwestern France and was introduced in Argentina during the 1850s. In order to study the clonal genetic diversity of Malbec grapevines, we generated whole-genome resequencing data for four accessions with different clonal propagation records. A stringent variant calling procedure was established to identify reliable polymorphisms among the analyzed accessions. The latter procedure retrieved 941 single nucleotide variants (SNVs). A reduced set of the detected SNVs was corroborated through Sanger sequencing, and employed to custom-design a genotyping experiment. We successfully genotyped 214 Malbec accessions using 41 SNVs, and identified 14 genotypes that clustered in two genetically divergent clonal lineages. These lineages were associated with the time span of clonal propagation of the analyzed accessions in Argentina and Europe. Our results show the usefulness of this approach for the study of the scarce intra-cultivar genetic diversity in grapevines. We also provide evidence on how human actions might have driven the accumulation of different somatic mutations, ultimately shaping the Malbec genetic diversity pattern.

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