Whole-genome resequencing reveals recent signatures of selection in five populations of largemouth bass (<i>Micropterus</i> <i>salmoides</i>)

Abstract

Largemouth bass ( Micropterus salmoides ) is an economically important fish species in North America, Europe, and China. Various genetic improvement programs and domestication processes have modified its genome sequence through selective pressure, leaving nucleotide signals that can be detected at the genomic level. In this study, we sequenced 149 largemouth bass fish, including protospecies (imported from the US) and improved breeds (four domestic breeding populations from China). We detected genomic regions harboring certain genes associated with improved traits, which may be useful molecular markers for practical domestication, breeding, and selection. Subsequent analyses of genetic diversity and population structure revealed that the improved breeds have undergone more rigorous genetic changes. Through selective signal analysis, we identified hundreds of putative selective sweep regions in each largemouth bass line. Interestingly, we predicted 103 putative candidate genes potentially subjected to selection, including several associated with growth (p sst1 and grb10 ), early development ( klf9 , sp4 , and sp8 ), and immune traits ( pkn2 , sept2 , bcl6 , and ripk2 ). These candidate genes represent potential genomic landmarks that could be used to improve important traits of biological and commercial interest. In summary, this study provides a genome-wide map of genetic variations and selection footprints in largemouth bass, which may benefit genetic studies and accelerate genetic improvement of this economically important fish.

Mitogenomic Characterization and Phylogenetic Placement of African Hind, Cephalopholis taeniops: Shedding Light on the Evolution of Groupers (Serranidae: Epinephelinae)

“…The resulting molecular data have been instrumental in estimating phylogeographic patterns, demographic history [31][32][33][34], gaining insights into population dynamics and adaptive radiation [35], detecting biological invasions [36], and contributing to the improvement of fisheries management and grouper conservation [37]. Subsequent advancements in molecular tools have further facilitated the exploration of phylogenomics and population genomics within this fish group, unveiling intraspecific variation, adaptation differentiation, physiological changes, radiations, and the intricate processes of speciation [38][39][40].…”