scholarly journals Whole Genome Resequencing of Arkansas Progressor and Regressor Line Chickens to Identify SNPs Associated with Tumor Regression

Genes ◽  
2018 ◽  
Vol 9 (10) ◽  
pp. 512
Author(s):  
Bhuwan Khatri ◽  
Ashley M. Hayden ◽  
Nicholas B. Anthony ◽  
Byungwhi C. Kong
Keyword(s):  
Network Analysis ◽  
Genetic Factors ◽  
Tumor Regression ◽  
Read Depth ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Genome Resequencing ◽  
Synonymous Mutations ◽  
Regression Property ◽  
Whole Genome Resequencing

Arkansas Regressor (AR) chickens, unlike Arkansas Progressor (AP) chickens, regress tumors induced by the v-src oncogene. To better understand the genetic factors responsible for this tumor regression property, whole genome resequencing was conducted using Illumina Hi-Seq 2 × 100 bp paired-end read method (San Diego, CA, USA) with AR (confirmed tumor regression property) and AP chickens. Sequence reads were aligned to the chicken reference genome (galgal5) and produced coverage of 11× and 14× in AR and AP, respectively. A total of 7.1 and 7.3 million single nucleotide polymorphisms (SNPs) were present in AR and AP genomes, respectively. Through a series of filtration processes, a total of 12,242 SNPs were identified in AR chickens that were associated with non-synonymous, frameshift, nonsense, no-start and no-stop mutations. Further filtering of SNPs based on read depth ≥ 10, SNP% ≥ 0.75, and non-synonymous mutations identified 63 reliable marker SNPs which were chosen for gene network analysis. The network analysis revealed that the candidate genes identified in AR chickens play roles in networks centered to ubiquitin C (UBC), phosphoinositide 3-kinases (PI3K), and nuclear factor kappa B (NF-kB) complexes suggesting that the tumor regression property in AR chickens might be associated with ubiquitylation, PI3K, and NF-kB signaling pathways. This study provides an insight into genetic factors that could be responsible for the tumor regression property.

scholarly journals Development a Set of 46 SNP Markers for the Yellow Catfish (Tachysurus Fulvidraco)

2021 ◽  
Author(s):  
Huaxing Zhou ◽  
Tingshuang Pan ◽  
Huan Wang ◽  
He Jiang ◽  
Jun Ling ◽  
...  
Keyword(s):  
Snp Markers ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Yellow Catfish ◽  
Genome Resequencing ◽  
Single Nucleotide ◽  
Expected Heterozygosity ◽  
Hardy Weinberg Equilibrium ◽  
Whole Genome Resequencing ◽  
Tachysurus Fulvidraco

Abstract The whole genome resequencing was used to develop single nucleotide polymorphisms (SNP) markers for the yellow catfish (Tachysurus fulvidraco). A total of 46 SNP markers were selected from 5550676 genotyping markers which distributed on 26 chromosomes. Of the 46 SNPs analyzed, 35 SNPs conformed to Hardy-Weinberg equilibrium. The observed and expected heterozygosity of these markers ranged from 0.2519 to 0.771 and from 0.265 to 0.5018, respectively. This set of markers will be of great useful for population genetics of the yellow catfish.

scholarly journals Genetic diversity analysis of Chinese plum (Prunus salicina L.) based on whole-genome resequencing

2021 ◽  
Vol 17 (3) ◽  
Author(s):  
Xiao Wei ◽  
Fei Shen ◽  
Qiuping Zhang ◽  
Ning Liu ◽  
Yuping Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Principal Component ◽  
Private Allele ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Genome Resequencing ◽  
Cultivar Group ◽  
Prunus Salicina ◽  
Whole Genome Resequencing

AbstractChinese plum (Prunus salicina L.), also known as Japanese plum, is gaining importance because of its extensive genetic diversity and nutritional attributes that are beneficial for human health. Single-nucleotide polymorphisms (SNPs) are the most abundant form of genomic polymorphisms and are widely used in population genetics research. In this study, we constructed high-quality SNPs through whole-genome resequencing of 67 Prunus accessions with a depth of ~20× to evaluate the genome-level diversity and population structure. Phylogenetic analysis, principal component analysis, and population structure profiling indicated that the 67 plum accessions could be classified into four groups corresponding to their origin location, the southern cultivar group (SCG), the northern cultivar group (NCG), the foreign cultivar group (FG), and the mixed cultivar group (MG). Some cultivars from South China clustered with the other three groups. The genetic diversity indices including private allele number, observed heterozygosity, expected heterozygosity, and the nucleotide diversity of the SCG were higher than those of the NCG. Gene flow from the SCG to FG was also detected. Based on the distribution of wild resources, we concluded that the domestication center of origin of the Chinese plum was southwestern China. This study also provided genetic variation features and the population structure of Chinese plum cultivars, laying a foundation for breeders to use diverse germplasm and allelic variants to improve Chinese plum varieties.

scholarly journals Whole-genome resequencing of three Coilia nasus population reveals genetic variations in genes related to immune, vision, migration, and osmoregulation

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jun Gao ◽  
Gangchun Xu ◽  
Pao Xu
Keyword(s):  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Genome Resequencing ◽  
Coilia Nasus ◽  
Expression Levels ◽  
Different Populations ◽  
Genome Level ◽  
Whole Genome Resequencing

Abstract Background Coilia nasus is an important anadromous fish, widely distributed in China, Japan, and Korea. Based on morphological and ecological researches of C. nasus, two ecotypes were identified. One is the anadromous population (AP). The sexually mature fish run thousands of kilometers from marine to river for spawning. Another one is the resident population which cannot migrate. Based on their different habitats, they were classified into landlocked population (LP) and sea population (SP) which were resident in the freshwater lake and marine during the entire lifetime, respectively. However, they have never been systematically studied. Moreover, C. nasus is declining sharply due to overfishing and pollution recently. Therefore, further understandings of C. nasus populations are needed for germplasm protection. Results Whole-genome resequencing of AP, LP, and SP were performed to enrich the understanding of different populations of C. nasus. At the genome level, 3,176,204, 3,307,069, and 3,207,906 single nucleotide polymorphisms (SNPs) and 1,892,068, 2,002,912, and 1,922,168 insertion/deletion polymorphisms (InDels) were generated in AP, LP, and SP, respectively. Selective sweeping analysis showed that 1022 genes were selected in AP vs LP; 983 genes were selected in LP vs SP; 116 genes were selected in AP vs SP. Among them, selected genes related to immune, vision, migration, and osmoregulation were identified. Furthermore, their expression profiles were detected by quantitative real-time PCR. Expression levels of selected genes related to immune, and vision in LP were significantly lower than AP and SP. Selected genes related to migration in AP were expressed significantly more highly than LP. Expression levels of selected genes related to osmoregulation were also detected. The expression of NKAα and NKCC1 in LP were significantly lower than SP, while expression of NCC, SLC4A4, NHE3, and V-ATPase in LP was significantly higher than SP. Conclusions Combined to life history of C. nasus populations, our results revealed that the molecular mechanisms of their differences of immune, vision, migration, and osmoregulation. Our findings will provide a further understanding of different populations of C. nasus and will be beneficial for wild C. nasus protection.

scholarly journals Revealing Distinctions in Genetic Diversity and Adaptive Evolution Between Two Varieties of Camellia sinensis by Whole-Genome Resequencing

2020 ◽  
Vol 11 ◽  
Author(s):  
Yanlin An ◽  
Xiaozeng Mi ◽  
Shiqi Zhao ◽  
Rui Guo ◽  
Xiaobo Xia ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Adaptive Evolution ◽  
Camellia Sinensis ◽  
Balancing Selection ◽  
Genetic Research ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Synonymous Mutations ◽  
Indel Markers ◽  
Whole Genome Resequencing

Camellia sinensis var. sinensis (CSS) and C. sinensis var. assamica (CSA) are the two most economically important tea varieties. They have different characteristics and geographical distribution. Their genetic diversity and differentiation are unclear. Here, we identified 18,903,625 single nucleotide polymorphisms (SNPs) and 7,314,133 insertion–deletion mutations (indels) by whole-genome resequencing of 30 cultivated and three wild related species. Population structure and phylogenetic tree analyses divided the cultivated accessions into CSS and CSA containing 6,440,419 and 6,176,510 unique variations, respectively. The CSS subgroup possessed higher genetic diversity and was enriched for rare alleles. The CSA subgroup had more non-synonymous mutations and might have experienced a greater degree of balancing selection. The evolution rate (dN/dS) and KEGG enrichment indicated that genes involved in the synthesis and metabolism of flavor substances were positively selected in both CSS and CSA subpopulations. However, there are extensive genome differentiation regions (2959 bins and approximately 148 M in size) between the two subgroups. Compared with CSA (141 selected regions containing 124 genes), the CSS subgroup (830 selected regions containing 687 genes) displayed more selection regions potentially related to environmental adaptability. Fifty-three pairs of polymorphic indel markers were developed. Some markers were located in hormone-related genes with distinct alleles in the two cultivated subgroups. These identified variations and selected regions provide clues for the differentiation and adaptive evolution of tea varieties. The newly developed indel markers will be valuable in further genetic research on tea plants.

Whole-genome resequencing of Ujumqin sheep to investigate the determinants of the multi-vertebral trait

Genome ◽  
2018 ◽  
Vol 61 (9) ◽  
pp. 653-661 ◽  
Author(s):  
Shuo Li ◽  
Rongsong Luo ◽  
Defang Lai ◽  
Min Ma ◽  
Fei Hao ◽  
...  
Keyword(s):  
Nucleotide Polymorphisms ◽  
Genome Resequencing ◽  
Single Nucleotide ◽  
Frameshift Mutations ◽  
Synonymous Mutations ◽  
Coding Regions ◽  
Homozygous Mutations ◽  
Vertebral Development ◽  
Whole Genome Resequencing ◽  
Genomic Regions

The Ujumqin sheep is one of the most profitable breeds in China, with unique multi-vertebral characteristics. We performed high-throughput genome resequencing of five multi-vertebral and three non-multi-vertebral sheep in an Ujumqin population. We identified the genomic regions that correlated with the germplasm characteristics to establish the cause of the “multi-vertebral” phenotype in this breed. Sequencing generated a total of 314 952 000 000 bp of raw data. The alignment rate of all the samples was between 98.53% and 99.11%, and the mean depth of coverage relative to the reference genome was between 11.58× and 14.92×. After comparing the differences between the two groups, we identified 21 homozygous single nucleotide polymorphisms (SNPs) in the mutant exons of 14 genes. Nineteen loci of 10 genes contained nonsynonymous mutations, while two loci contained synonymous mutations. Resequencing revealed homozygous mutations comprised of 44 indels located within exons of 19 genes. These indels included 37 frameshift mutations, 6 non-frameshift mutations, and 1 stopgain single nucleotide variation (SNV). Finally, comparisons of genotypic variations revealed 17 genes with homozygous mutations in their coding regions, 5 of which have previously been associated with vertebral development and the remaining 12 genes were newly identified in this study.

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.

Detection of Genomic Variation and Tepal Shape Related Genes Between Broad and Narrow Tepal Lotus (Nelumbo Adans.) by whole Genome Resequencing

2021 ◽  
Author(s):  
Feng-Luan Liu ◽  
Mi Qin ◽  
Shuo Li ◽  
Da-Sheng Zhang ◽  
Qing-Qing Liu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genomic Variation ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Wild Type ◽  
Genome Resequencing ◽  
Pollinator Attraction ◽  
Water Lily ◽  
Epidermal Growth ◽  
Whole Genome Resequencing

Abstract Background: The shape, color, and size of petals or tepals are vital attributes of flowering plants, as they affect the pollinator attraction ability, environmental stress adaptation, and ornamental value of plants. Compared with rose, chrysanthemum, and water lily, the tepal shapes of lotus (Nelumbo Adans.) exhibit low variation, and the absence of short-broad and long-narrow tepals limits the commercial value of lotus flowers. Therefore, this study aimed to uncover the genomic variation underlying the broad and narrow tepal phenotypes of lotus flowers, and to screen candidate genes associated with different tepal shapes.Results: Whole genome resequencing of two groups of lotus, NL (comprising three American lotus genotypes: broad tepal mutant, narrow tepal mutant, and wild type) and WSH (comprising two Asian lotus genotypes: narrow tepal mutant and wild type), generated 9.23–12.85 Gb clean data. A total of 716,656 single nucleotide polymorphisms (SNPs) and 221,688 insertion-deletion mutations (Indels) were obtained in the NL group, while 639,953 SNPs and 134,6118 Indels were obtained in the WSH group. Only a small proportion of these SNPs and Indels was mapped to exonic regions of genome: 1.92% and 0.47%, respectively, in the NL group, and 1.66% and 0.48%, respectively, in the WSH group. Gene Ontology (GO) analysis showed that out of 4,890 (NL group) and 1,272 (WSH group) annotated variant genes, 125 and 62 genes were enriched (Q < 0.05), respectively. Additionally, in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, 104 genes (NL group) and 35 genes (WSH group) were selected (P < 0.05). Finally, 41 genes were filtered and predicted to be associated with tepal shape in lotus.Conclusions: This is the first comprehensive report of genomic variation controlling tepal shape in lotus. Significant genetic variation was detected between the wild-type and mutant lotus genotypes, and varying levels of differentiation between groups NL and WSH. Candidate genes containing epidermal growth factor (EGF) and wall-associated receptor kinase (WAK) domains are considered important targets for further research on tepal development. Overall, the genomic data and candidate genes obtained in this study are essential references for future identification of tepal-shaped control genes in lotus combined with transcriptome analysis and quantitative trait loci (QTL) mapping.

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