Development and Evaluation of a High-Throughput Single-Nucleotide Polymorphism Array for Large Yellow Croaker (Larimichthys crocea)

Zhou, Tao; Chen, Baohua; Ke, Qiaozhen; Zhao, Ji; Pu, Fei; Wu, Yidi; Lin, Chen; Zhou, Zhixiong; Bai, Yulin; Pan, Ying; Gong, Jie; Zheng, Weiqiang; Xu, Peng

doi:10.3389/fgene.2020.571751

Cited by 18 publications

(2 citation statements)

References 52 publications

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“…A similar number of 9.6M SNPs were identified for the development of a 700 K SNP chip in catfish ( Zeng et al, 2017 ). Recently, a set of 82 fish were collected from six different locations of China and re-sequenced to identify 9.3M SNPs to design a 600K SNP chip for large yellow croaker ( Zhou et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Development of a High-Density 665 K SNP Array for Rainbow Trout Genome-Wide Genotyping

et al. 2022

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Single nucleotide polymorphism (SNP) arrays, also named « SNP chips », enable very large numbers of individuals to be genotyped at a targeted set of thousands of genome-wide identified markers. We used preexisting variant datasets from USDA, a French commercial line and 30X-coverage whole genome sequencing of INRAE isogenic lines to develop an Affymetrix 665 K SNP array (HD chip) for rainbow trout. In total, we identified 32,372,492 SNPs that were polymorphic in the USDA or INRAE databases. A subset of identified SNPs were selected for inclusion on the chip, prioritizing SNPs whose flanking sequence uniquely aligned to the Swanson reference genome, with homogenous repartition over the genome and the highest Minimum Allele Frequency in both USDA and French databases. Of the 664,531 SNPs which passed the Affymetrix quality filters and were manufactured on the HD chip, 65.3% and 60.9% passed filtering metrics and were polymorphic in two other distinct French commercial populations in which, respectively, 288 and 175 sampled fish were genotyped. Only 576,118 SNPs mapped uniquely on both Swanson and Arlee reference genomes, and 12,071 SNPs did not map at all on the Arlee reference genome. Among those 576,118 SNPs, 38,948 SNPs were kept from the commercially available medium-density 57 K SNP chip. We demonstrate the utility of the HD chip by describing the high rates of linkage disequilibrium at 2–10 kb in the rainbow trout genome in comparison to the linkage disequilibrium observed at 50–100 kb which are usual distances between markers of the medium-density chip.

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Section: Discussionmentioning

confidence: 99%

Development of a High-Density 665 K SNP Array for Rainbow Trout Genome-Wide Genotyping

et al. 2022

View full text Add to dashboard Cite

show abstract

“…A similar number of 9.6M SNPs were identified for the development of a 700K SNP chip in catfish (Zeng et al, 2017). Recently, a set of 82 fish were collected from six different locations of China and re-sequenced to identify 9.3M SNPs to design a 600K SNP chip for large yellow croaker (Zhou et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

Development of a high-density 665 K SNP array for rainbow trout genome-wide genotyping

Bernard

Dehaullon

Gao

et al. 2022

Preprint

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Single nucleotide polymorphism (SNP) arrays, also named "SNP chips", enable very large numbers of individuals to be genotyped at a targeted set of thousands of genome-wide identified markers. We used preexisting variant datasets from USDA, a French commercial line and 30X-coverage whole genome sequencing of INRAE isogenic lines to develop an Affymetrix 665 K SNP array (HD chip) for rainbow trout. In total, we identified 32,372,492 SNPs that were polymorphic in the USDA or INRAE databases. A subset of identified SNPs were selected for inclusion on the chip, prioritizing SNPs whose flanking sequence uniquely aligned to the Swanson reference genome, with homogenous repartition over the genome and the highest Minimum Allele Frequency in both USDA and French databases. Of the 664,531 SNPs which passed the Affymetrix quality filters and were manufactured on the HD chip, 65.3% and 60.9% passed filtering metrics and were polymorphic in two other distinct French commercial populations in which, respectively, 288 and 175 sampled fish were genotyped. Only 576,118 SNPs mapped uniquely on both Swanson and Arlee reference genomes, and 12,071 SNPs did not map at all on the Arlee reference genome. Among those 576,118 SNPs, 38,948 SNPs were kept from the commercially available medium-density 57K SNP chip. We demonstrate the utility of the HD chip by describing the high rates of linkage disequilibrium at 2 kb to 10 kb in the rainbow trout genome in comparison to the linkage disequilibrium observed at 50 kb to 100 kb which are usual distances between markers of the medium-density chip.

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Decoding the fish genome opens a new era in important trait research and molecular breeding in China

Zhou,

Wang,

et al. 2024

Sci. China Life Sci.

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Development and Evaluation of a High-Throughput Single-Nucleotide Polymorphism Array for Large Yellow Croaker (Larimichthys crocea)

Cited by 18 publications

References 52 publications

Development of a High-Density 665 K SNP Array for Rainbow Trout Genome-Wide Genotyping

Development of a High-Density 665 K SNP Array for Rainbow Trout Genome-Wide Genotyping

Development of a high-density 665 K SNP array for rainbow trout genome-wide genotyping

Decoding the fish genome opens a new era in important trait research and molecular breeding in China

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