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

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.

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Genome-Wide Analysis of Nucleotide-Binding Site (NBS) Disease Resistance (R) Genes in Sacred Lotus (Nelumbo nucifera Gaertn.) Reveals Their Transition Role During Early Evolution of Land Plants

Tropical Plant Biology ◽

10.1007/s12042-013-9122-4 ◽

2013 ◽

Vol 6 (2-3) ◽

pp. 98-116 ◽

Cited By ~ 4

Author(s):

Rui Zong Jia ◽

Ray Ming ◽

Yun J. Zhu

Keyword(s):

Disease Resistance ◽

Binding Site ◽

Nucleotide Binding ◽

Nucleotide Binding Site ◽

Nelumbo Nucifera ◽

Land Plants ◽

R Genes ◽

Genome Wide Analysis ◽

Sacred Lotus ◽

Genome Wide

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Genome-wide identification of SSR and SNP markers from the non-heading Chinese cabbage for comparative genomic analyses

BMC Genomics ◽

10.1186/s12864-015-1534-0 ◽

2015 ◽

Vol 16 (1) ◽

Cited By ~ 22

Author(s):

Xiaoming Song ◽

Tingting Ge ◽

Ying Li ◽

Xilin Hou

Keyword(s):

Chinese Cabbage ◽

Snp Markers ◽

Comparative Genomic ◽

Genome Wide ◽

Genomic Analyses ◽

Ssr And Snp Markers ◽

Heading Chinese Cabbage

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

Frontiers in Plant Science ◽

10.3389/fpls.2021.682305 ◽

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.

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Mapping Quantitative Trait Loci onto Chromosome-scale Pseudomolecules in Flax

10.20944/preprints201901.0126.v1 ◽

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.

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