Abstract
Larimichthys polyactis is a commercially important marine fish species in Eastern Asia, yet very few genetic resources exist. In particular, genetic linkage maps are critical tools for genetic breeding. In this study, we generated a high resolution linkage map from a family of 110 individuals and their parents by resequencing the individuals. 3,802 effective SNPs were mapped to 24 linkage groups (LGs). The map spanned 2,567.39 cm, with an average marker interval of 0.66 cm. We used the map to conduct QTL analysis for growth traits, and found 31 markers were significantly associated with growth-related traits. Specifically, three SNPs were identified for total length, nineteen SNPs for body length, and nine SNPs for body weight. The identified SNPs could explain 15.2–22.6% of the phenotypic variation. SNPs associated with growth traits were distributed on LG6 and LG11, and candidate genes included, kif26b, bat1, gna1, gbgt1, and amfr, which may regulate growth. The linkage map and mapped QTLs would be useful for improving the quality of L. polyactis via marker-assisted selection.
Highlights
Larimichthys polyactis is a commercially important marine fish species in Eastern Asia, yet very few genetic resources exist
We found three significant SNPs for total length with logarithm of odds (LOD) scores of 4.74, 4.73 and 4.61, and these SNPs were located at 51.77, 52.23 and 52.69 of LG11
Compared to microsatellites with long flanking DNA sequences, SNP markers that are most abundant in an organism have been more suitable for genetic studies[26], especially in high-density genetic linkage mapping[27], QTL mapping[28], population genetic analysis[29], and genome-wide association studies (GWAS)[30]
Summary
Larimichthys polyactis is a commercially important marine fish species in Eastern Asia, yet very few genetic resources exist. Genomic resources for L. polyactis are not well developed, limiting our understanding of genes that contribute to growth in this species. The first reference genome of L. polyactis was sequenced and assembled (Xie et al, unpublished), and genome-scale SNP markers can be identified through resequencing of the genome, which allows for the construction of high-density linkage maps. Genetic linkage maps are essential resources that can improve the quality of the genome and chromosomal assembly[24], and are essential for mapping QTLs. QTL mapping identifies genes that are related to phenotype variations within populations, and genes identified through QTL studies could be used to enhance breeding programs. The objectives of this study were: (1) large-scale identification of SNPs and construction of a high-density SNP-based linkage map using genotyping by resequencing individuals of L. polyactis; (2) QTL mapping to detect
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