Genetic linkage map construction by 2b-RAD technology and QTL mapping of Litopenaeus vannamei growth traits

【Objective】 To construct high-density genetic linkage map of Litopenaeus vannamei, to conduct quantitative trait loci(QTL) mapping for growth-related traits, and to screen candidate genes related to growth traits, so as to provide theoretical basis for molecular marker-assisted L. vannamei breeding, fine mapping of growth-related functional genes and other studies.【Method】 In this study, a low salt-tolerant breeding L. vannamei was used as the male parent, and a wild L. vannamei from Ecuador the female parent. With 2 parents and 150 F₁ individuals as the mapping population, a large number of SNP molecular markers were found through 2b-RAD sequencing to construct a genetic linkage map. According to phenotypic data of growth-related traits, QTLs of 13 growth traits including body mass, total length, body length, carapace length, carapace width and carapace height were mapped on the genetic linkage map constructed through MapQTL 6.0. The genes near SNPs in the QTL interval were screened out, and growth-related candidate genes were mined through GO functional annotation and KEGG signal pathway enrichment analysis to get candidate genes related to growth. The expression of candidate genes in different tissues and populations of L. vannamei was detected by quantitative realtime PCR(qRT-PCR).【Result】The genetic linkage map of L. vannamei had 3136 SNPs, distributed in 44 linkage groups. The total map length was 5430.54 cM, and the average map distance was 1.73 cM. A total of 79 growth trait-related QTLs were mapped, with LOD ranging from 3.00 to 11.04, and the range of phenotypic variation that could be explained was 9.0%-28.8%. According to GO function annotation and KEGG signal pathway enrichment analysis results, 4 growth-related candidate genes(TOB2, CRAT, CCT6, and KLF4) were screened. The 4 candidate genes were generally expressed in all tissues of L. vannamei, and the relative expression of CCT6, KLF4, and TOB2 genes in low salt-tolerant breeding families was higher than conventional L. vannamei populations, of which the expression difference of CCT6 gene reached a significant level(P<0.05).【Conclusion】 The genetic linkage map of L. vannamei based on 2b-RAD technology identifies 79 QTLs related to growth traits, and screens 4 candidate genes related to growth traits of L. vannamei(CCT6, KLF4, TOB2 and CRAT), indication 2b-RAD technology and QTL mapping together can efficiently and quickly discover candidate genes related to growth traits of L. vannamei, thus providing technical support for molecular marker-assisted breeding, and fine mapping of growth-related functional genes.