Development of a 690 K SNP array in catfish and its application for genetic mapping and validation of the reference genome sequence

Qifan Zeng, Qiang Fu, Yun Li, Geoff Waldbieser, Brian Bosworth, Shikai Liu, Yujia Yang, Lisui Bao, Zihao Yuan, Ning Li, Zhanjian "John" Liu

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

Single nucleotide polymorphisms (SNPs) are capable of providing the highest level of genome coverage for genomic and genetic analysis because of their abundance and relatively even distribution in the genome. Such a capacity, however, cannot be achieved without an efficient genotyping platform such as SNP arrays. In this work, we developed a high-density SNP array with 690,662 unique SNPs (herein 690 K array) that were relatively evenly distributed across the entire genome, and covered 98.6% of the reference genome sequence. Here we also report linkage mapping using the 690 K array, which allowed mapping of over 250,000 SNPs on the linkage map, the highest marker density among all the constructed linkage maps. These markers were mapped to 29 linkage groups (LGs) with 30,591 unique marker positions. This linkage map anchored 1,602 scaffolds of the reference genome sequence to LGs, accounting for over 97% of the total genome assembly. A total of 1,007 previously unmapped scaffolds were placed to LGs, allowing validation and in few instances correction of the reference genome sequence assembly. This linkage map should serve as a valuable resource for various genetic and genomic analyses, especially for GWAS and QTL mapping for genes associated with economically important traits.

Original languageEnglish (US)
Article number40347
JournalScientific Reports
Volume7
DOIs
StatePublished - Jan 12 2017
Externally publishedYes

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Catfishes
Single Nucleotide Polymorphism
Genome
Chromosome Mapping
Genome-Wide Association Study

ASJC Scopus subject areas

  • General

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Development of a 690 K SNP array in catfish and its application for genetic mapping and validation of the reference genome sequence. / Zeng, Qifan; Fu, Qiang; Li, Yun; Waldbieser, Geoff; Bosworth, Brian; Liu, Shikai; Yang, Yujia; Bao, Lisui; Yuan, Zihao; Li, Ning; Liu, Zhanjian "John".

In: Scientific Reports, Vol. 7, 40347, 12.01.2017.

Research output: Contribution to journalArticle

Zeng, Qifan ; Fu, Qiang ; Li, Yun ; Waldbieser, Geoff ; Bosworth, Brian ; Liu, Shikai ; Yang, Yujia ; Bao, Lisui ; Yuan, Zihao ; Li, Ning ; Liu, Zhanjian "John". / Development of a 690 K SNP array in catfish and its application for genetic mapping and validation of the reference genome sequence. In: Scientific Reports. 2017 ; Vol. 7.
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