scholarly journals A New Single Nucleotide Polymorphism Database for Rainbow Trout Generated Through Whole Genome Resequencing

2018 ◽  
Vol 9 ◽  
Author(s):  
Guangtu Gao ◽  
Torfinn Nome ◽  
Devon E. Pearse ◽  
Thomas Moen ◽  
Kerry A. Naish ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Rainbow Trout ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Genome Resequencing ◽  
Single Nucleotide ◽  
Single Nucleotide Polymorphism Database ◽  
Whole Genome Resequencing

scholarly journals Construction of A High-Density Genetic Map and Mapping of Fruit Traits in Watermelon (Citrullus Lanatus L.) Based on Whole-Genome Resequencing

2018 ◽  
Vol 19 (10) ◽  
pp. 3268 ◽  
Author(s):  
Bingbing Li ◽  
Xuqiang Lu ◽  
Junling Dou ◽  
Ali Aslam ◽  
Lei Gao ◽  
...  
Keyword(s):  
Genetic Map ◽  
Citrullus Lanatus ◽  
Snp Markers ◽  
High Density ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Genome Resequencing ◽  
Single Nucleotide ◽  
Parental Lines ◽  
Whole Genome Resequencing

Watermelon (Citrullus lanatus L.) is an important horticultural crop that is grown worldwide and has a high economic value. To dissect the loci associated with important horticultural traits and to analyze the genetic and genomic information of this species, a high-density genetic map was constructed based on whole-genome resequencing (WGR), a powerful high-resolution method for single-nucleotide polymorphism (SNP) marker development, genetic map construction, and gene mapping. Resequencing of both parental lines and 126 recombinant inbred lines (RIL) resulted in the detection of 178,762 single-nucleotide polymorphism (SNP) markers in the parental lines at a sequencing depth greater than four-fold. Additionally, 2132 recombination bin markers comprising 103,029 SNP markers were mapped onto 11 linkage groups (LGs). Substantially more SNP markers were mapped to the genetic map compared with other recent studies. The total length of the linkage map was 1508.94 cM, with an average distance of 0.74 cM between adjacent bin markers. Based on this genetic map, one locus for fruit bitterness, one locus for rind color, and one locus for seed coat color with high LOD scores (58.361, 18.353, 26.852) were identified on chromosome 1, chromosome 8, and chromosome 3, respectively. These prominent loci were identified in a region of 6.16 Mb, 2.07 Mb, and 0.37 Mb, respectively. On the basis of current research, the high-density map and mapping results will provide a valuable tool for identifying candidate genes, map-based gene cloning, comparative mapping, and marker-assisted selection (MAS) in watermelon breeding.

scholarly journals Whole-Genome Single-Nucleotide-Polymorphism Analysis for Discrimination of Clostridium botulinum Group I Strains

2014 ◽  
Vol 80 (7) ◽  
pp. 2125-2132 ◽  
Author(s):  
Narjol Gonzalez-Escalona ◽  
Ruth Timme ◽  
Brian H. Raphael ◽  
Donald Zink ◽  
Shashi K. Sharma
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Clostridium Botulinum ◽  
Toxin Gene ◽  
Polymorphism Analysis ◽  
Snp Analysis ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Content Type ◽  
Group I

ABSTRACTClostridium botulinumis a genetically diverse Gram-positive bacterium producing extremely potent neurotoxins (botulinum neurotoxins A through G [BoNT/A-G]). The complete genome sequences of three strains harboring only the BoNT/A1 nucleotide sequence are publicly available. Although these strains contain a toxin cluster (HA+OrfX−) associated with hemagglutinin genes, little is known about the genomes of subtype A1 strains (termed HA−OrfX+) that lack hemagglutinin genes in the toxin gene cluster. We sequenced the genomes of three BoNT/A1-producingC. botulinumstrains: two strains with the HA+OrfX−cluster (69A and 32A) and one strain with the HA−OrfX+cluster (CDC297). Whole-genome phylogenic single-nucleotide-polymorphism (SNP) analysis of these strains along with other publicly availableC. botulinumgroup I strains revealed five distinct lineages. Strains 69A and 32A clustered with theC. botulinumtype A1 Hall group, and strain CDC297 clustered with theC. botulinumtype Ba4 strain 657. This study reports the use of whole-genome SNP sequence analysis for discrimination ofC. botulinumgroup I strains and demonstrates the utility of this analysis in quickly differentiatingC. botulinumstrains harboring identical toxin gene subtypes. This analysis further supports previous work showing that strains CDC297 and 657 likely evolved from a common ancestor and independently acquired separate BoNT/A1 toxin gene clusters at distinct genomic locations.

Sign in / Sign up

Export Citation Format

Share Document