Genetic diversity and selection elimination analyses of farmed Micropterus salmoides populations by the whole-genome resequencing

Micropterus salmoides, commonly known as largemouth bass, was introduced to mainland China (Guangdong Province) in 1983. Due to long-term artificial breeding and inbreeding, its germplasm has degraded, making it necessary to monitor its genetic diversity. In order to realize the sustainable development of aquaculture, we try to develop a long-term, effective, and low-cost method for monitoring the genetic diversity of the breeding population in M.salmoides, an important freshwater breeding species in China. We applied a low-depth (10×) second-generation high-throughput technology to the genome resequencing of 55 individuals from 7 farmed populations respectively collected in Jiangsu, Anhui, Zhejiang, and Guangdong province. A total of 2 675 780 690 reads were generated in the resequencing, which identified 2 550,187 single nucleotide diversity (SNP) loci when they were compared with the reference genome. The constructed phylogenetic relationship and population structure indicated that the 7 populations probably originated from two provenances and the Zhaoqing, Suzhou, Taizhou and Jinhua populations were closer relationship to the provenances. We speculated that these 4 populations might migrate to Huzhou, Xuzhou and Lu 'an with the following artificial cultivation. It was observed that the Zhaoqing pupulation, closest to the ancestral population, had the lowest genetic diversity. Analyses of population structure and genetic diversity indexes also agreed with that these cultured populations derived from two provenances. The selection elimination analysis by the calculation of population differentiation index (F_st) and nucleotide diversity (Pi) compared Zhaoqing and each of another 3 control populations, Xuzhou, Huzhou or Lu 'an control populations, respectively, which detected strong selective signals on chromosomes 1 and 18 of Zhaoqing where 16 genes were localized. These genes were annotated to be involved in growth and immunity. The identified low genetic diversity (PIC less than 0.25) in most of the cultured populations reflected the risk of germplasm degradation. The data outputs will lay a foundation for molecular biology research in M. salmoides by providing fundamental reference data for the breeding.