First identification of two co-existing genome-wide significant sex quantitative trait loci (QTL) in red tilapia using integrative QTL mapping

Abstract

Red tilapia ( Oreochromis spp . ) is one of the most popular fish in China due to its bright red appearance, fast growth rate, and strong adaptability. Understanding the sex determination mechanisms is of vital importance for the selection of all-male lines to increase aquacultural production of red tilapia. In this research, the genetic architecture for sex from four mapping populations ( n =1 090) of red tilapia was analyzed by quantitative trait loci (QTL)-seq, linkage-based QTL mapping, and linkage disequilibrium (LD)-based genome-wide association studies. Two genome-wide significant QTL intervals associated with sex were identified on ChrLG1 (22.4–23.9 Mb) and ChrLG23 (32.0–35.9 Mb), respectively. The QTL on ChrLG1 was detected in family 1 (FAM1), FAM2, and FAM4, and the other QTL on ChrLG23 was detected in FAM3 and FAM4. Four microsatellite markers located within the QTL were successfully developed for marker-assisted selection. Interestingly, three ( lpp , sox14 , and amh ) of the 12 candidate genes located near or on the two QTL intervals were abundantly expressed in males, while the remaining genes were more highly expressed in females. Seven genes ( scly , ube3a , lpp , gpr17 , oca2 , cog4 , and atp10a ) were significantly differentially expressed between the male and female groups. Furthermore, LD block analysis suggested that a cluster of genes on ChrLG23 may participate in regulating sex development in red tilapia. Our study provides important information on the genetic architecture of sex in red tilapia and should facilitate further exploration of sex determination mechanisms in this species.

Status of conventional and molecular breeding of salinity‐tolerant tilapia

“…101 In red tilapia, QTL mapping of sex-determining loci in four mapping families with 1090 fish identified two QTL for sex in LG1 and LG23. 102 A QTL on LG1 was detected in three families, and the other QTL on LG23 was detected in two of the four families. Interestingly, three (lpp: lipoma-preferred partner, sox14: sry-related hmg-box 14 and amh: anti-mullerian hormone) of the 12 candidate genes localized to these QTL were highly expressed in males, and the remaining genes were highly expressed in females.…”

“…Sex‐linked DNA markers were also identified in LG14 and in LG3 in O. mossambicus 101 . In red tilapia, QTL mapping of sex‐determining loci in four mapping families with 1090 fish identified two QTL for sex in LG1 and LG23 102 . A QTL on LG1 was detected in three families, and the other QTL on LG23 was detected in two of the four families.…”

Research progress and applications of genome‐wide association study in farm animals

“…Therefore, a fine mapping result can be obtained using GWAS [73]. Zhu et al detected four SNPs associated with sex development using QTL mapping, while only one plausible SNP within the region was found by GWAS [74]. In fact, most causative GWAS loci have a relative small effect size and could only explain a low proportion of heritability, which confused researchers and decreased motivation for exploring underlying genetic mechanisms [75].…”

<i>ZR</i> and <i>ZRDC</i> embrace a new era

“…( 2022 ) provided insights into the underlying assembly mechanisms of mountain amphibians, integrating multidimensional diversity; Zhu et al. ( 2022 ) presented important information on the genetic architecture of sex in red tilapia, facilitating further exploration of sex determination mechanisms in this species; Yu et al. ( 2022 ) updated the checklist of butterflies (Lepidoptera, Papilionoidea) of Yunnan Province, China; Ma et al.…”