scholarly journals Genome-wide variations analysis of special waxy sorghum cultivar Hongyingzi for brewing Moutai liquor

2019 ◽  
Author(s):  
Can Wang ◽  
Lingbo Zhou ◽  
Xu Gao ◽  
Yanqing Ding ◽  
Bin Cheng ◽  
...  
Keyword(s):  
Chalcone Synthase ◽  
Reference Genome ◽  
Copy Number Variations ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Structural Variations ◽  
Genome Resequencing ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Whole Genome Resequencing

AbstractsHongyingzi is a special waxy sorghum (Sorghum bicolor L. Moench) cultivar for brewing Moutai liquor. For an overall understanding of the whole genome of Hongyingzi, we performed whole-genome resequencing technology with 56.10 X depth to reveal its comprehensive variations. Compared with the BTx623 reference genome, 2.48% of genome sequences were altered in the Hongyingzi genome. Among these alterations, there were 1885774 single nucleotide polymorphisms (SNPs), 309381 small fragments insertions and deletions (Indels), 31966 structural variations (SVs), and 217273 copy number variations (CNVs). These alterations conferred 29614 genes variations. It was also predicted that 35 genes variations were related to the multidrug and toxic efflux (MATE) transporter, chalcone synthase (CHS), ATPase isoform 10 (AHA10) transporter, dihydroflavonol-4-reductase (DFR), the laccase 15 (LAC15), flavonol 3′-hydroxylase (F3′H), flavanone 3-hydroxylase (F3H), O-methyltransferase (OMT), flavonoid 3′5′ hydroxylase (F3′5′H), UDP-glucose:sterol-glucosyltransferase (SGT), flavonol synthase (FLS), and chalcone isomerase (CHI) involved in the tannin synthesis. These results would provide theoretical supports for the molecular markers developments and gene function studies related to the liquor-making traits, and the genetic improvement of waxy sorghum based on the genome editing technology.

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 Genome-wide identifying of G-quadruplex structures directly by whole-genome resequencing

2021 ◽  
Author(s):  
Jing Tu ◽  
Mengqin Duan ◽  
Wenli Liu ◽  
Na Lu ◽  
Xiao Sun ◽  
...  
Keyword(s):  
Individual Differences ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Single Nucleotide ◽  
Genome Wide ◽  
G Quadruplex ◽  
Sequencing Quality ◽  
Single Nucleotide Variations ◽  
Whole Genome Resequencing ◽  
The Given

Abstract We present a convenient genome-wide DNA G-quadruplex (G4) profiling method that identifies G4 structures from ordinary whole-genome resequencing data by seizing the slight fluctuation of sequencing quality. We identified 736,689 G4 structures within human genome, in which 44.9% of all predicted canonical G4-froming sequences were contained. We observed that some of the single nucleotide variations (SNVs) influenced the formation of G4 structures, including homozygous SNVs and heterozygous SNVs. Due to SNVs contain individual differences, the given approach is available to identify and characterize G4s genome-wide for specific individuals.

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.

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