scholarly journals Exploring the genomic resources of seven domestic Bactrian camel populations in China through restriction site-associated DNA sequencing

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0250168
Author(s):  
Chenmiao Liu ◽  
Huiling Chen ◽  
Xuejiao Yang ◽  
Chengdong Zhang ◽  
Zhanjun Ren
Keyword(s):  
Dna Sequencing ◽  
Signaling Pathways ◽  
Restriction Site ◽  
Reference Population ◽  
Mapk Signaling ◽  
Snp Markers ◽  
Bactrian Camel ◽  
Transport Pathways ◽  
Target Populations ◽  
Arid Desert

The domestic Bactrian camel is a valuable livestock resource in arid desert areas. Therefore, it is essential to understand the roles of important genes responsible for its characteristics. We used restriction site-associated DNA sequencing (RAD-seq) to detect single nucleotide polymorphism (SNP) markers in seven domestic Bactrian camel populations. In total, 482,786 SNPs were genotyped. The pool of all remaining others were selected as the reference population, and the Nanjiang, Sunite, Alashan, Dongjiang, Beijiang, Qinghai, and Hexi camels were the target populations for selection signature analysis. We obtained 603, 494, 622, 624, 444, 588, and 762 selected genes, respectively, from members of the seven target populations. Gene Ontology classifications and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed, and the functions of these genes were further studied using Genecards to identify genes potentially related to the unique characteristics of the camel population, such as heat resistance and stress resistance. Across all populations, cellular process, single-organism process, and metabolic process were the most abundant biological process subcategories, whereas cell, cell part, and organelle were the most abundant cellular component subcategories. Binding and catalytic activity represented the main molecular functions. The selected genes in Alashan camels were mainly enriched in ubiquitin mediated proteolysis pathways, the selected genes in Beijiang camels were mainly enriched in MAPK signaling pathways, the selected genes in Dongjiang camels were mainly enriched in RNA transport pathways, the selected genes in Hexi camels were mainly enriched in endocytosis pathways, the selected genes in Nanjiang camels were mainly enriched in insulin signaling pathways, while the selected genes in Qinghai camels were mainly enriched in focal adhesion pathways; these selected genes in Sunite camels were mainly enriched in ribosome pathways. We also found that Nanjiang (HSPA4L and INTU), and Alashan camels (INO80E) harbored genes related to the environment and characteristics. These findings provide useful insights into the genes related to the unique characteristics of domestic Bactrian camels in China, and a basis for genomic resource development in this species.

scholarly journals High-Density Genetic Linkage Map Construction and White Rot Resistance Quantitative Trait Loci Mapping for Genus Vitis Based on Restriction Site-Associated DNA Sequencing

2021 ◽  
pp. PHYTO-12-19-048
Author(s):  
Kai Su ◽  
Yinshan Guo ◽  
Weihao Zhong ◽  
Hong Lin ◽  
Zhendong Liu ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Dna Sequencing ◽  
Quantitative Trait ◽  
Restriction Site ◽  
Genetic Distances ◽  
Snp Markers ◽  
High Density ◽  
White Rot ◽  
Phenotypic Variance ◽  
Trait Locus

Grape white rot (Coniothyrium diplodiella) is a major fungal disease affecting grape yield and quality. Quantitative trait locus (QTL) analysis is an important method for studying important horticultural traits of grapevine. This study was conducted to construct a high-density map and conduct QTL mapping for grapevine white rot resistance. A mapping population with 177 genotypes was developed from interspecific hybridization of a white rot-resistant cultivar (Vitis vinifera × V. labrusca ‘Zhuosexiang’) and white rot-susceptible cultivar (V. vinifera ‘Victoria’). Single-nucleotide polymorphism (SNP) markers were developed by restriction site-associated DNA sequencing. The female, male, and integrated maps contained 2,501, 4,110, and 6,249 SNP markers with average genetic distances of adjacent markers of 1.25, 0.77, and 0.50 cM, respectively. QTL mapping was conducted based on white rot resistance identification of 177 individuals in July and August of 2017 and 2018. Notably, one stable QTL related to white rot resistance was detected and located on linkage group LG14. The phenotypic variance ranged from 12.93 to 13.43%. An SNP marker (chr14_3929380), which cosegregated with white rot resistance, was discovered and shows potential for use in marker-assisted selection to generate new grapevine cultivars with resistance to white rot.

Development and characterization of 26 SNP markers in Ochetobius elongatus based on restriction site-associated DNA sequencing (RAD-seq)

2018 ◽  
Vol 12 (1) ◽  
pp. 53-55 ◽  
Author(s):  
Jiping Yang ◽  
Yuefei Li ◽  
Shuli Zhu ◽  
Weitao Chen ◽  
Jie Li ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Restriction Site ◽  
Snp Markers

scholarly journals Development of SNP markers derived from RAD sequencing for Atlantic salmon (Salmo salar L.) inhabiting the rivers of southern England

2021 ◽  
Author(s):  
R. Andrew King ◽  
Jamie R. Stevens
Keyword(s):  
Atlantic Salmon ◽  
Restriction Site ◽  
Snp Markers ◽  
Rad Sequencing ◽  
Effective Management ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Southern England ◽  
Target Populations ◽  
The Uk

AbstractThe rivers of the Hampshire Basin, southern England contain a genetically unique group of Atlantic salmon that have suffered dramatic declines in numbers over the last 40 years. Knowledge of levels and patterns of genetic diversity is essential for effective management of these vulnerable populations. Using restriction site-associated DNA sequencing (RADseq) data, we describe the development and characterisation of a panel of 94 single nucleotide polymorphism (SNP) loci for salmon from this region and investigate their applicability and variability in both target (i.e. southern English) and non-target populations. The SNP loci will be useful for population genetic and assignment studies on Atlantic salmon within the UK and beyond.

scholarly journals Mapping of Quantitative Trait Loci Controlling Egg-Quality and -Production Traits in Japanese Quail (Coturnix japonica) Using Restriction-Site Associated DNA Sequencing

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 735
Author(s):  
Mohammad Ibrahim Haqani ◽  
Shigeru Nomura ◽  
Michiharu Nakano ◽  
Tatsuhiko Goto ◽  
Atsushi J. Nagano ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Dna Sequencing ◽  
Japanese Quail ◽  
Quantitative Trait ◽  
Restriction Site ◽  
Snp Markers ◽  
Egg Weight ◽  
Second Stage ◽  
Trait Loci ◽  
Egg Shell

This research was conducted to identify quantitative trait loci (QTL) associated with egg-related traits by constructing a genetic linkage map based on single nucleotide polymorphism (SNP) markers using restriction-site associated DNA sequencing (RAD-seq) in Japanese quail. A total of 138 F2 females were produced by full-sib mating of F1 birds derived from an intercross between a male of the large-sized strain with three females of the normal-sized strain. Eggs were investigated at two different stages: the beginning stage of egg-laying and at 12 weeks of age (second stage). Five eggs were analyzed for egg weight, lengths of the long and short axes, egg shell strength and weight, yolk weight and diameter, albumen weight, egg equator thickness, and yolk color (L*, a*, and b* values) at each stage. Moreover, the age at first egg, the cumulative number of eggs laid, and egg production rate were recorded. RAD-seq developed 118 SNP markers and mapped them to 13 linkage groups using the Map Manager QTX b20 software. Markers were spanned on 776.1 cM with an average spacing of 7.4 cM. Nine QTL were identified on chromosomes 2, 4, 6, 10, 12, and Z using the simple interval mapping method in the R/qtl package. The QTL detected affected 10 egg traits of egg weight, lengths of the long and short axes of egg, egg shell strength, yolk diameter and weight, albumen weight, and egg shell weight at the beginning stage, yellowness of the yolk color at the second stage, and age at first egg. This is the first report to perform a quail QTL analysis of egg-related traits using RAD-seq. These results highlight the effectiveness of RAD-seq associated with targeted QTL and the application of marker-assisted selection in the poultry industry, particularly in the Japanese quail.

scholarly journals Development of 30 SNP Markers for the Daphnia Magna based on Restriction Site-associated DNA Sequencing (RAD-seq)

2021 ◽  
Author(s):  
Shengman Zhang ◽  
Wenhui He ◽  
Haisu Zheng ◽  
Yiran Xiong ◽  
Meng Tan ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Daphnia Magna ◽  
Restriction Site ◽  
Snp Markers ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genetics Research ◽  
Expected Heterozygosity ◽  
Water Ecosystem ◽  
Hardy Weinberg Equilibrium

Abstract Daphnia magna belongs to the Cladocera and plays an important role in the water ecosystem. With the intensification of water pollution, the wild population of D. magna has declined rapidly in recent years, and insufficient molecular markers have limited effective research and conservation of this species. In this research, 30 novel single nucleotide polymorphism (SNP) markers were developed in a cultivar of Daphnia magna and 12 wild Daphnia magna using restriction site-associated DNA sequencing (RAD-seq). The minor allele frequency, observed heterozygosity, and expected heterozygosity ranged from 0.115 to 0.721, 0.073 to 0.800, and 0.077 to 0.520, respectively. The PIC ranged from 0.071 to 0.403. Six loci showed significant deviations from the Hardy-Weinberg equilibrium after Bonferroni correction (p < 0.05).These newly developed polymorphic SNP markers for D. magna are of great significance in terms of the genetic breeding of D. magna, identification of wild and artificially domesticated species and conservation genetics research.

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