Linkage mapping of developmentally expressed cDNAS containing at-rich elements in shrimp (Litopenaeus vannamei) - Differential expression after challenge with Taura Syndrome virus (TSV)

To explore the possibility of finding interleukin-like gene(s) in Litopenaeus vannamei shrimp, we sought evidence for the presence of interleukin 1 (IL-1)-like genes, because the proteins encoded by these genes are evolutionarily conserved. RT-PCR performed with primers from conserved regions of vertebrate IL-1α genes amplified three bands of 954 bp (ShIL1-21; accession # U94689), 864 bp (ShIL1-28; U94690), and 182 bp (ShIL1-J17; U94691) from various tissues. The cDNA sequences were AT-rich (∼65%) and contained 1-5 copies of the "ATTTA" motif, a possible indicator of mRNA degradation. GenBank search indicated that similar AT-rich elements are present in the 3′-untranslated regions (UTR) of vertebrate cytokines, growth factors and other tissue-specific and developmentally expressed genes. Northern blot hybridization analysis using ShIL1-21 as probe detected mRNA transcripts of ∼1.8 kb and ∼2.9 whereas ShIL1-28 detected a ∼7.5 kb transcript. All transcripts showed tissue and developmental variations in their mRNA expression. The 1.8 kb transcript of ShIL1-21 was expressed at high levels in postlarvae stage 8 (PL8) but not in Zoea stage 2/3 or tail muscle of juvenile and adult shrimp. The 7.5 kb mRNA of SHIL1-28 was present in tail muscle of adult female shrimp but not in male tail muscle. In addition, all transcripts levels increased in juveniles at 24 h and 36 h after TSV challenge indicating that the expression of these genes is modulated during TSV infection. Primer sets flanking simple sequence repeats in ShIL1-21 and ShIL1-28 amplified polymorphic alleles in L. vannamei from various geographic regions, suggesting that these markers will be useful for genetic diversity analyses. ShIL1-21 and ShIL1-28 primers were used for genotyping with the entire international reference mapping family (IRMF) panel developed for construction of a linkage map for shrimp (ShrimpMap). CRIMAP analysis using a limits-of-detection (LOD) score of 5.0 placed ShIL1-21 in linkage group 14 of ShrimpMap whereas ShIL1-28 remained unlinked. The parental alleles segregated in a Mendelian fashion indicating that these genes are useful for pedigree tracing and population analysis.