Development of SNP markers for analysis of population structure in white perch (Morone americana) using double digest restriction site-associated DNA sequencing

2016 ◽  
Vol 8 (4) ◽  
pp. 403-406 ◽  
Author(s):  
Li Bian ◽  
Yong-quan Su ◽  
Patrick M. Gaffney
Keyword(s):  
Population Structure ◽  
Dna Sequencing ◽  
Restriction Site ◽  
White Perch ◽  
Snp Markers ◽  
Morone Americana

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 Analysis of Population Structure and Differentially Selected Regions in Guangxi Native Breeds by Restriction Site Associated with DNA Sequencing

2019 ◽  
Vol 10 (1) ◽  
pp. 379-386
Author(s):  
Zhuliang Yang ◽  
Jixian Deng ◽  
Dongfeng Li ◽  
Tiantian Sun ◽  
Li Xia ◽  
...  
Keyword(s):  
Population Structure ◽  
Dna Sequencing ◽  
Restriction Site ◽  
Genomic Information ◽  
Indigenous Chicken ◽  
Autosomal Snps ◽  
Tree Distribution ◽  
Go Enrichment ◽  
Significant Difference ◽  
Native Chickens

Guangxi indigenous chicken breeds play a very important role in promoting the high-quality development of the broiler industry in China. However, studies on genomic information of Guangxi indigenous chicken to date remain poorly explored. To decipher the population genetic structure and differentially selected regions (DSRs) in Guangxi indigenous chickens, we dug into numerous SNPs from seven Guangxi native chickens (GX) by employing the restriction site associated with DNA sequencing (RAD-seq) technology. Another three breeds, Cobb, White Leghorn, and Chahua (CH) chicken, were used as a control. After quality control, a total of 185,117 autosomal SNPs were kept for further analysis. The results showed a significant difference in population structure, and the control breeds were distinctly separate from the Guangxi native breeds, which was also strongly supported by the phylogenetic tree. Distribution of FST indicated that there were three SNPs with big genetic differentiation (FST value all reach to 0. 9427) in GX vs. CH group, which were located on chr1-96,859,720,chr4-86,139,601, and chr12-8,128,322, respectively. Besides, we identified 717 DSRs associated with 882 genes in GX vs. Cobb group, 769 DSRs with 476 genes in GX vs. Leghorn group, and 556 DSRs with 779 genes in GX vs. CH group. GO enrichment showed that there were two significant terms, namely GPI-linked ephrin receptor activity and BMP receptor binding, which were enriched in GX vs. Leghorn group. In conclusion, this study suggests that Guangxi native chickens have a great differentiation with Cobb and Leghorn. Our findings would be beneficial to fully evaluate the genomic information on Guangxi native chicken and facilitate the application of these resources in chicken breeding.

scholarly journals The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing

2013 ◽  
Vol 22 (11) ◽  
pp. 2864-2883 ◽  
Author(s):  
Julian Catchen ◽  
Susan Bassham ◽  
Taylor Wilson ◽  
Mark Currey ◽  
Conor O'Brien ◽  
...  
Keyword(s):  
Population Structure ◽  
Dna Sequencing ◽  
Restriction Site ◽  
Threespine Stickleback ◽  
Colonization History ◽  
History Of

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 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.

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