scholarly journals Identification and QTL Analysis of Flavonoids and Carotenoids in Tetraploid Roses Based on an Ultra-High-Density Genetic Map

2021 ◽  
Vol 12 ◽  
Author(s):  
Bixuan Cheng ◽  
Huihua Wan ◽  
Yu Han ◽  
Chao Yu ◽  
Le Luo ◽  
...  
Keyword(s):  
Qtl Analysis ◽  
Average Distance ◽  
Flower Color ◽  
Snp Markers ◽  
High Density ◽  
Linkage Groups ◽  
Genome Wide ◽  
Final Length ◽  
Ssr And Snp Markers ◽  
Whole Genome Resequencing

Roses are highly valuable within the flower industry. The metabolites of anthocyanins, flavonols, and carotenoids in rose petals are not only responsible for the various visible petal colors but also important bioactive compounds that are important for human health. In this study, we performed a QTL analysis on pigment contents to locate major loci that determine the flower color traits. An F1 population of tetraploid roses segregating for flower color was used to construct an ultra-high-density genetic linkage map using whole-genome resequencing technology to detect genome-wide SNPs. Previously developed SSR and SNP markers were also utilized to increase the marker density. Thus, a total of 9,259 markers were mapped onto seven linkage groups (LGs). The final length of the integrated map was 1285.11 cM, with an average distance of 0.14 cM between adjacent markers. The contents of anthocyanins, flavonols and carotenoids of the population were assayed to enable QTL analysis. Across the 33 components, 46 QTLs were detected, explaining 11.85–47.72% of the phenotypic variation. The mapped QTLs were physically clustered and primarily distributed on four linkage groups, namely LG2, LG4, LG6, and LG7. These results improve the basis for flower color marker-assisted breeding of tetraploid roses and guide the development of rose products.

scholarly journals Development of an SNP Marker Set for Marker-Assisted Backcrossing Using Genotyping-By-Sequencing in Tetraploid Perilla

2021 ◽  
Author(s):  
Yun-Joo Kang ◽  
Bo-Mi Lee ◽  
Jangmi Kim ◽  
Moon Nam ◽  
Myoung-Hee Lee ◽  
...  
Keyword(s):  
Recurrent Selection ◽  
Diploid Species ◽  
Genotyping By Sequencing ◽  
Snp Markers ◽  
Genetic Maps ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Genome Wide ◽  
A Genome ◽  
Marker Assisted Backcrossing

Abstract High-quality molecular markers are essential for marker-assisted selection to accelerate breeding progress. Compared with diploid species, recently diverged polyploid crop species tend to have highly similar homeologous subgenomes, which is expected to limit the development of broadly applicable locus-specific single-nucleotide polymorphism (SNP) assays. Furthermore, it is particularly challenging to make genome-wide marker sets for species that lack a reference genome. Here, we report the development of a genome-wide set of kompetitive allele specific PCR (KASP) markers for marker-assisted recurrent selection (MARS) in the tetraploid minor crop perilla. To find locus-specific SNP markers across the perilla genome, we used genotyping-by-sequencing (GBS) to construct linkage maps of two F2 populations. The two resulting high-resolution linkage maps comprised 2,326 and 2,454 SNP markers that spanned a total genetic distance of 2,133 cM across 16 linkage groups and 2,169 cM across 21 linkage groups, respectively. We then obtained a final genetic map consisting of 22 linkage groups with 1,123 common markers from the two genetic maps. We selected 96 genome-wide markers for MARS and confirmed the accuracy of markers in the two F2 populations using a high-throughput Fluidigm system. We confirmed that 91.8% of the SNP genotyping results from the Fluidigm assay were the same as the results obtained through GBS. These results provide a foundation for marker-assisted backcrossing and the development of new varieties of perilla.

scholarly journals Whole genome resequencing data enables a targeted SNP panel for conservation and aquaculture of Oreochromis cichlid fishes

2021 ◽  
Author(s):  
Adam Ciezarek ◽  
Antonia Ford ◽  
Graham Etherington ◽  
Kasozi Nasser ◽  
Milan Malinsky ◽  
...  
Keyword(s):  
Native Species ◽  
Cichlid Fish ◽  
Snp Markers ◽  
Whole Genome ◽  
The Novel ◽  
Genome Resequencing ◽  
Genome Wide ◽  
In The Wild ◽  
Snp Panel ◽  
Whole Genome Resequencing

Cichlid fish of the genus Oreochromis form the basis of the global tilapia aquaculture and fisheries industry. Non-native farmed tilapia populations are known to be widely distributed across Africa and to hybridize with native Oreochromis species. However, many species are difficult to distinguish morphologically, hampering attempts to maintain good quality farmed strains or to identify pure populations of native species. Here, we describe the development of a single nucleotide polymorphism (SNP) genotyping panel from whole-genome resequencing data that enables targeted species identification in Tanzania. We demonstrate that an optimized panel of 96 genome-wide SNPs based on FST outliers performs comparably to whole genome resequencing in distinguishing species and identifying hybrids. We also show this panel outperforms microsatellite-based and phenotype-based classification methods. Case studies indicate several locations where introduced aquaculture species have become established in the wild, threatening native Oreochromis species. The novel SNP markers identified here represent an important resource for assessing broodstock purity and helping to conserve unique endemic biodiversity, and in addition potentially for assessing broodstock purity in hatcheries.

Genome-wide linkage mapping of yield-related traits in three Chinese bread wheat populations using high-density SNP markers

2018 ◽  
Vol 131 (9) ◽  
pp. 1903-1924 ◽  
Author(s):  
Faji Li ◽  
Weie Wen ◽  
Zhonghu He ◽  
Jindong Liu ◽  
Hui Jin ◽  
...  
Keyword(s):  
Bread Wheat ◽  
Linkage Mapping ◽  
Snp Markers ◽  
High Density ◽  
Genome Wide

scholarly journals Genome-Wide Identification of SSR and SNP Markers Based on Whole-Genome Re-Sequencing of a Thailand Wild Sacred Lotus (Nelumbo nucifera)

PLoS ONE ◽  
2015 ◽  
Vol 10 (11) ◽  
pp. e0143765 ◽  
Author(s):  
Jihong Hu ◽  
Songtao Gui ◽  
Zhixuan Zhu ◽  
Xiaolei Wang ◽  
Weidong Ke ◽  
...  
Keyword(s):  
Snp Markers ◽  
Nelumbo Nucifera ◽  
Whole Genome ◽  
Sacred Lotus ◽  
Genome Wide ◽  
Ssr And Snp Markers

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 Mapping Quantitative Trait Loci onto Chromosome-scale Pseudomolecules in Flax

2019 ◽  
Author(s):  
Frank M. You ◽  
Sylvie Cloutier
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Quantitative Traits ◽  
Snp Markers ◽  
Genetic Maps ◽  
Genome Wide ◽  
Trait Loci ◽  
Ssr And Snp Markers ◽  
Gene Scanning ◽  
Genomic Regions

Quantitative trait loci (QTL) are genomic regions associated with phenotype variation of quantitative traits in a population. To date, a total of 267 QTL for 29 quantitative traits have been reported in 13 studies on flax. Of these, 200 QTL from 12 studies were identified based on genetic maps, scaffold sequences, or pre-released chromosome-scale pseudomolecules. Molecular markers for QTL identification differed across studies but were mainly based on simple sequence repeat (SSR) or single nucleotide polymorphism (SNP) markers. This article provides methods with software tools and database files to uniquely map SSR and SNP markers from different references onto the recently released chromosome-scale pseudomolecules. Using these methods, 195 QTL were successfully sorted onto the 15 flax chromosomes and grouped into 133 co-located QTL clusters. Mapping of QTL from different studies to the same reference enables comparisons and facilitates genome-wide QTL analysis, candidate gene scanning, and breeding applications.

scholarly journals Construction of a High-Density Genetic Map for Pitaya Using the Whole Genome Resequencing Approach

Horticulturae ◽  
2021 ◽  
Vol 7 (12) ◽  
pp. 534
Author(s):  
Zhijiang Wu ◽  
Haiyan Deng ◽  
Guidong Liang ◽  
Xiaoying Ye ◽  
Yonghua Qin ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Map ◽  
Snp Markers ◽  
High Density ◽  
Genetic Maps ◽  
Fleshy Fruit ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Hylocereus Undatus ◽  
Whole Genome Resequencing

Pitaya (Hylocereus undatus) is one of the most economic fleshy fruit tree crops. This study aimed at producing a high-density linkage genetic map of pitaya based on the whole genome resequencing (WGrS) approach. For this purpose, a bi-parental F1 population of 198 individuals was generated and genotyped by WGrS. High-quality polymorphic 6434 single polymorphism nucleotide (SNP) markers were extracted and used to construct a high-density linkage map. A total of 11 linkage groups were resolved as expected in accordance with the chromosome number. The map length was 14,128.7 cM with an average SNP interval of 2.2 cM. Homology with the sequenced reference genome was described, and the physical and genetic maps were compared with collinearity analysis. This linkage map in addition to the available genomic resources will help for quantitative trait mapping, evolutionary studies and marker-assisted selection in the important Hylocereus species.

PSVIII-31 Genome-wide estimation of linkage disequilibrium using American mink genotyping-by-sequencing data

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 267-267
Author(s):  
Karim Karimi ◽  
A Hossain Farid ◽  
Mehdi Sargolzaei ◽  
Sean Myles ◽  
Younes Miar
Keyword(s):  
Linkage Disequilibrium ◽  
Association Studies ◽  
Average Distance ◽  
American Mink ◽  
Genotyping By Sequencing ◽  
Snp Markers ◽  
Genome Wide Association Studies ◽  
Sequencing Data ◽  
Single Nucleotide ◽  
Genome Wide

Abstract Linkage disequilibrium (LD) has been defined as the correlation between alleles at different loci in the genome. The LD levels can be influenced by the evolutionary processes and historical events in populations. The main objective of this study was to estimate the LD levels at different distances of American mink genome using genotyping-by-sequencing (GBS) data. A total of 285 American mink (Neovison vison) were sequenced based on GBS libraries prepared by digesting the genomic DNA with the restriction enzyme ApeKI. After quality control, 13,321 single nucleotide polymorphism (SNP) markers located on 46 Scaffolds were used to determine the extension of LD in the genome. The average r2 was computed for all syntenic SNP pairwise at inter-marker distances from 0 up to 1 Mb. The average r2 between adjacent SNPs was 0.29, ranged from 0.18 to 0.53 across all scaffolds. In addition, the average distance between adjacent markers was 51 kb. The average r2 above 0.3 was observed in less than 1 kb distances and declined with increase in distances between markers. The average r2 was estimated to be less than 0.2 for markers more than 10 kb apart. Furthermore, the average LD level was decreased to 0.08 for inter-marker distances between 0.9 and 1 Mb. The results of this study can be used to determine the optimum maker density required for obtaining enough accuracy and power in both genomic selection and genome-wide association studies.

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