Genome survey and high-resolution genetic map provide valuable genetic resources for Fenneropenaeus chinensis

Abstract

Fenneropenaeus chinensis is one of the most important aquaculture species in China. Research on its genomic and genetic structure not only helps us comprehend the genetic basis of complex economic traits, but also offers theoretical guidance in selective breeding. In the present study, a genome survey sequencing was performed to generate a rough reference genome utilized for groping preliminary genome characteristics and facilitate linkage and quantitative trait locus (QTL) mapping. Linkage mapping was conducted using a reduced-representation sequencing method 2b-RAD. In total, 36,762 SNPs were genotyped from 273 progenies in a mapping family, and a high-resolution linkage map was constructed. The consensus map contained 12,884 markers and spanned 5257.81 cM with an average marker interval of 0.41 cM, which was the first high-resolution genetic map in F. chinensis to our knowledge. QTL mapping and association analysis were carried out in 29 characters including body size, sex and disease resistance. 87 significant QTLs were detected in several traits and they were also evaluated by association analysis. Results of this study provide us valuable suggestions in genetic improvement and breeding of new varieties and also lay a basic foundation for further application of cloning of economic genes in selective breeding program and marker-assisted selection.

Penaeid Shrimp Chromosome Studies Entering the Post-Genomic Era

“…Over the past twenty years, genetic maps with hundreds and thousands of markers have been constructed in economic shrimp species such as L. vannamei, P. monodon, F. chinensis, and M. japonicus. Their marker density on chromosome linkage groups has also increased (average inter-marker distances of 0.7, 0.39, 0.9, and 0.41 cM, respectively) [61][62][63][64][65][66]. Quantitative trait loci (QTLs) associated with some important economic traits, such as sex, body length, body weight, and disease resistance, have been mapped.…”

“…The triploids of F. chinensis and M. japonicus have been identified as having a female preference, suggesting that females have heterogametic (ZW) sex determination in penaeid shrimps [44,51,92]. Genetic maps also show that shrimp are female heterogamety and possess a stable mechanism of sexual inheritance [61][62][63][64][65][66].…”

Improved genome assembly of Chinese shrimp (Fenneropenaeus chinensis) suggests adaptation to the environment during evolution and domestication

“…A high‑resolution linkage map was constructed in F. chinensis , providing a valuable genetic resource for selective breeding programme and marker‑assisted selection (Meng et al., 2021). Because of their structural complexity and high heterozygosity (Yu et al., 2015), only a few crustacean genomes have been completely characterized.…”

“…A high-resolution linkage map was constructed in F. chinensis, providing a valuable genetic resource for selective breeding programme and marker-assisted selection (Meng et al, 2021).…”

Evidences of Z- and W-Linked Regions on the Genome of Fenneropenaeus chinensis

“…However, even some closely related species have different SD loci (Phillip et al, 2001;Miura, 2007;Mank and Avise, 2009;Pucholt et al, 2017). For F. chinensis, several sexrelated markers have been identified by QTL mapping, but no direct evidence of their connection with SD was found (Meng et al, 2021). We therefore studied the SD mechanism of F. chinensis to improve our knowledge of the sex differentiation mechanism in crustaceans and facilitate the study of sexcontrolling technologies, and provide sex-linked markers to identify the sexes at early developmental stages.…”