Genome-wide QTL and eQTL mapping reveal genes associated with growth rate trait of the Pacific white shrimp (Litopenaeus vannamei).

Growth rate is a crucial economic trait for farmed animals, but the genetic regulation of this trait is largely unknown in non-model organisms such as shrimp. In this study, we performed genome-wide phenotypic quantitative trait loci (QTL) and expression quantitative trait loci (eQTL) mapping analyses to identify genes affecting the growth rate of Pacific white shrimp (Litopenaeus vannamei), which is the most commercially-farmed crustacean worldwide. We used RNA-sequencing of 268 individuals in a mapping population, and subsequently validated our findings through gene silencing and shrimp growth experiments. We constructed a high-density genetic linkage map comprising 5533 markers spanning 44 linkage groups, with a total distance of 6205.75 cM and an average marker interval of 1.12 cM. Our analyses identified 11 QTLs significantly correlated with growth rate, and 117,525 eQTLs. By integrating QTL and eQTL data, we identified a gene (metalloreductase STEAP4) highly associated with shrimp growth rate. RNA interference (RNAi) analysis and growth experiments confirmed that STEAP4 was significantly correlated with growth rate in L. vannamei. Our results indicate that the comprehensive analysis of QTL and eQTL can effectively identify genes involved in complex animal traits. This is important for marker-assisted selection (MAS) of animals. Our work contributes to the development of shrimp breeding and available genetic resources.

Chen X ，Peng M ，Yang C ，Li Q ，Feng P ，Zhu W ，Zhang Y ，Zeng D ，Zhao Y ... -  《BMC GENOMICS》

Fine Mapping of the High-pH Tolerance and Growth Trait-Related Quantitative Trait Loci (QTLs) and Identification of the Candidate Genes in Pacific White Shrimp (Litopenaeus vannamei).

Huang W ，Cheng C ，Liu J ，Zhang X ，Ren C ，Jiang X ，Chen T ，Cheng K ，Li H ，Hu C ... -  《-》

Identification of a quantitative trait loci (QTL) associated with ammonia tolerance in the Pacific white shrimp (Litopenaeus vannamei).

Zeng D ，Yang C ，Li Q ，Zhu W ，Chen X ，Peng M ，Chen X ，Lin Y ，Wang H ，Liu H ，Liang J ，Liu Q ，Zhao Y ... -  《BMC GENOMICS》

Genetic map construction and quantitative trait locus (QTL) detection of growth-related traits in Litopenaeus vannamei for selective breeding applications.

Andriantahina F ，Liu X ，Huang H 《PLoS One》

Genome survey and high-density genetic map construction provide genomic and genetic resources for the Pacific White Shrimp Litopenaeus vannamei.

Yu Y ，Zhang X ，Yuan J ，Li F ，Chen X ，Zhao Y ，Huang L ，Zheng H ，Xiang J ... -  《Scientific Reports》