A major SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp (Litopenaeus vannamei)

Abstract

Bioinformatics and re-sequencing approaches were used for the discovery of sequence polymorphisms in Litopenaeus vannamei. A total of 1221 putative single nucleotide polymorphisms (SNPs) were identified in a pool of individuals from various commercial populations. A set of 211 SNPs were selected for further molecular validation and 88% showed variation in 637 samples representing three commercial breeding lines. An association analysis was performed between these markers and several traits of economic importance for shrimp producers including resistance to three major viral diseases. A small number of SNPs showed associations with test weekly gain, grow-out survival and resistance to Taura Syndrome Virus. Very low levels of linkage disequilibrium were revealed between most SNP pairs, with only 11% of SNPs showing an r(2)-value above 0.10 with at least one other SNP. Comparison of allele frequencies showed small changes over three generations of the breeding programme in one of the commercial breeding populations. This unique SNP resource has the potential to catalyse future studies of genetic dissection of complex traits, tracing relationships in breeding programmes, and monitoring genetic diversity in commercial and wild populations of L. vannamei.

Analysis of Litopenaeus vannamei Transcriptome Using the Next-Generation DNA Sequencing Technique

“…Because of its great economic value and important evolutionary status, more and more studies have been focused on breeding, growth, development, immunity, genetics and evolution of L. vannamei in recent twenty years [2]–[6]. The L. vannamei genome with higher recombination rates than other genomes of closely related penaeid prawns is predicted to be 2.0 Gigabases and has not been sequenced up to now [7], [8].…”

“…By May 2012, 162,993 ESTs from many organs and tissues have been released on Genbank. These data have been used for cloning functional genes, selecting genetic molecular markers, and designing cDNA microarrays [2], [9]–[11]. However, because of the limitations of the traditional methods used for ESTs sequencing, the now available transcriptome data of L. vannamei are still insufficient for research requirements relative to the size of its genome.…”

White spot syndrome virus (WSSV) and prevalence of disease resistance in a commercially cultured population of Penaeus monodon Fabricius, 1798 (Decapoda, Dendrobranchiata)

“…Recently, single nucleotide polymorphism (SNP) discovery and association analysis detected several SNP markers associ ated with resistance to taura syndrome virus (TSV) in L. vannamei (cf. Ciobanu et al, 2009). Currently most of the aquaculture in cultured farms depends on the wild unselected broodstocks of P. monodon for seed generation and, probably due to this, the emergence of viral diseases is rapidly increasing.…”

BAC end sequencing of Pacific white shrimp Litopenaeus vannamei: a glimpse into the genome of Penaeid shrimp

“…However, the shrimp industry has experienced great economic loss due to viral diseases, overfi shing, environmental contamination, and habitat destruction (Naylor et al, 2000;Kocher and Kole, 2008). To address these issues, a considerable body of research has advanced our knowledge of genetics, immunology, and breeding in shrimp (Gross et al, 2001;Cheng et al, 2005;Alcivar-Warren et al, 2007;Luo et al, 2007;Zhang et al, 2007;Ciobanu et al, 2010;Huan et al, 2010).…”