Genome-wide genetic analysis of cultured rainbow trout (Oncorhynchus mykiss) populations in China

Authors: ZHAO, ZIXIA - Chinese Academy Of Sciences; XU, JIAN - Chinese Academy Of Sciences; BAI, QINGLI - Chinese Academy Of Sciences; YANG, SHIYONG - Sichuan Agricultural University; JIANG, LIKUN - Chinese Academy Of Sciences; CHEN, BAOHUA - Chinese Academy Of Sciences; Palti, Yniv; Gao, Guangtu; XU, PENG - Chinese Academy Of Sciences

Submitted to: Journal of Fishery Sciences of China (JFSC)
Publication Type: Trade Journal
Publication Acceptance Date: 6/27/2018
Publication Date: 6/27/2018
Citation: Zhao, Z., Xu, J., Bai, Q., Yang, S., Jiang, L., Chen, B., Palti, Y., Gao, G., Xu, P. 2018. Genome-wide genetic analysis of cultured rainbow trout (Oncorhynchus mykiss) populations in China. Journal of Fishery Sciences of China (JFSC). 25(3):485-493.
DOI: https://doi.org/10.3724/SP.J.1118.2018.17340

Interpretive Summary:

Technical Abstract: The present study aimed to perform a genome-wide genetic evaluation of representative aquaculture populations of rainbow trout (Oncorhynchus mykiss) in China. A 57K single nucleotide polymorphism (SNP) array that was designed by the National Center for Cool and Cold Water Aquaculture (NCCCWA) was used to genotype 48 individuals from six aquaculture populations, which included the Heilongjiang rainbow trout (1HLJ), Heilongjiang golden trout (2gHLJ), Sichuan rainbow trout (3SC), Sichuan golden trout (4gSC), Beijing rainbow trout (5BJ), and Beijing golden trout (6gBJ). A total of 50,201 SNPs were successfully genotyped using a greater than 97% call rate threshold, and the overall rate of polymorphism was 97.7%, which indicated that the SNP array was suitable for analyzing the Chinese rainbow trout populations, even though it was designed using USA and Norwegian populations. The average minor allele frequency of each population was between 0.240 and 0.267, which is similar to that reported for other major aquaculture populations. Genetic diversity was high in the 1HLJ, 3SC, and 5BJ populations, with rates of polymorphism ranging from 83.6 to 84.9%, which is similar to reported for other major aquaculture populations. However, genetic diversity was relatively low in the 2gHLJ, 4gSC, and 6gBJ populations, with rates of polymorphism ranging from 60.2 to 76.9%. Phylogenetic, principal components, and STRUCTURE analyses, which were performed using genotype data from the six Chinese populations and two USA populations, indicated that the eight populations could be clustered into three groups. The three golden trout groups and the 1HLJ and 5BJ populations formed respective clusters, whereas the 3SC population was placed in a third cluster with the two USA populations. Outliers were identified for the 3SC, 4gSC, and 6gBJ populations, which suggested that the populations possessed inhomogeneous genetic backgrounds. Together, these results demonstrate the promising potential of high-density SNP arrays for the genetic analysis of Chinese rainbow trout populations and that such analyses could provide genomic data for plasm resource evaluation, localized strain breeding, high-quality fry production, and reasonable foreign strain introduction.