Sequencing a Shrimp Diversity Panel

Eighty-six shrimp (eighty Pacific White, six Tiger shrimp) from ten different geographic regions were sequenced with a twofold goal: first, to better understand and document the genetic makeup of the species, and second, to discover genetic differences between shrimp lines that may facilitate the breeding of shrimp with better performance trait

Genetic Marker Discovery for Gene Map Construction in the Pacific White Shrimp (Litopenaeus vannamei)

The Pacific White Shrimp (Litopenaeus vannamei) is important to the aquaculture industry and as a food source, but only limited genome information exists. The demand for specific shrimp broodstocks with high disease resistance and growth rate is increasing so the construction of a genetic map with easily usable genetic markers is a high priority. Using all the available public genomics information, a largescale discovery effort for single nucleotide polymorphism (SNP) genetic markers has produced the identification of 1,576 SNPs in 545 unique contigs. The genotyping work will be performed on the standardized Sequenom TM platform on a ready-to-use shrimp resource family, which will be used to develop a shrimp genetic map, as well as facilitate the mapping of quantitative trait locus (QTL) for growth rate and disease resistance

Candidate Gene Discovery for Retained Testicles in Dogs

Cryptorchidism, or retained testicles, is one of the most common congenital developmental defects in purebred dogs. DNA markers called single nucleotide polymorphisms (SNPs) are being used to investigate the associations between 21 candidate genes and cryptorchidism in Siberian huskies. We found the genes COL2A1, HOXA10, INSL3 and TIMP1 tended to be associated with cryptorchidism in Siberian huskies. The results will help to find the causative mutations in the future and will be useful in dog breeding programs to reduce the incidence of cryptorchidism

A SNP Genetic Map for Pacific White Shrimp (Litopenaeus vannamei)

Pacific white shrimp are of particular economic importance to the global shrimp aquaculture industry. We utilized the limited public sequence information, mainly genetic markers called single nucleotide polymorphisms (SNPs) and expressed sequence tags, to discover markers for the construction of the first SNP genetic map for Pacific white shrimp. In total, 1344 putative SNPs were discovered, and out of 825 SNPs genotyped, 418 SNP markers from 347 contigs were mapped onto 45 sex-averaged linkage groups, with approximate coverage of 2071 and 2130 cM for the female and male maps, respectively. Comparative mapping to model organisms, Daphnia pulex and Drosophila melanogaster, revealed extensive rearrangement of genome architecture for L. vannamei, and that L. vannamei was more related to Daphnia pulex. This SNP genetic map lays the foundation for future shrimp genomics studies, especially the identification of genetic markers or regions for economically important traits

Investigation of effects of three candidate genes on leg action and fat deposition traits in pigs

Data from 188 sows were used in the current study to examine the effects of high mobility group AT-hook1 (HMGA1), transcription factor 7-like-2 (TCF7L2) and insulin-like growth factor binding protein 3 (IGFBP3) genes on leg action and fat deposition traits, and further to explore the possible relationships between these genes on both traits. The candidate genes used in the study are known for their roles in fat deposition and growth. Overall leg action was scored on a scale of 1 (good movement) to 9 (leg weakness). Fatness traits included 10th rib backfat (BF10), adjusted 10th rib backfat to 125 kg (adjBF10) and last rib backfat (last BF), measured by ultrasonic imaging approach. The association analyses between single nucleotide polymorphisms (SNPs) and traits were performed using PROC MIXED procedures of SAS. The results showed that the associations between HMGA1, TCF7L2 and IGFBP3 genotypes with fat deposition traits were mostly suggestive in this limited data set. Leg action was also suggestively associated with IGFBP3 gene effects but was not associated with HMGA1 and TCF7L2 genes. Thus, IGFBP3 AA homozygote individuals tended to have had better movements (5.40), and were fatter when compared to GG homozygotes (5.84). The results from this study suggest a possible association between the IGFBP3 gene effects on both leg action and fatness. Therefore, further studies must be carried out in several populations, and using larger data to demonstrate these results conclusively

Short communication. SNP analyses of the 5HT1R and STAT genes in Pacific white shrimp, Litopenaeus vannamei

Shrimp aquaculture is one of the growing animal industries. Breeding stocks with high disease-resistance and growth rate are of particular interest to shrimp breeders. Association studies are useful to find genetic markers for marker assisted selection of animals. Using six Litopenaeus vannamei individuals from a sample population, four single nucleotide polymorphisms (SNPs) were found in the 5HT1R (5-hydroxytryptamine receptor1) gene and one SNP in the STAT (signal transducer and activator of transcription) gene. However, the SNP in the STAT gene was homozygous in a different population used for association analyses. The association analyses revealed that allele C of two SNPs, C109T and C395G in 5HT1R, tended to be associated with increased body weight. Further studies need to be conducted using a large and diverse population sample

Assessing the African Union Concerns about Article 16 of the Rome State of the International Criminal Court

This article assesses the African Union’s (AU) concerns about Article 16 of the Rome Statute of the International Criminal Court (ICC). It seeks to articulate a clearer picture of the law and politics of deferrals within the context of the AU’s repeated calls to the United Nations Security Council (UNSC, or the Council) to invoke Article 16 to suspend the processes initiated by the ICC against President Omar Al Bashir of Sudan. The UNSC’s failure to accede to the AU request led African States to formally withhold cooperation from the ICC in respect to the arrest and surrender of the Sudanese leader. Given the AU’s continued concerns, and the current impasse, fundamental questions have arisen about the Council’s authority to exercise, or not exercise, its deferral power. This culminated into a November 2009 African proposal for an amendment to the Rome Statute to empower the UN General Assembly to act should the UNSC fail to act on a deferral request after six months. Although ICC States Parties have so far shown limited public support for the AU’s proposed amendment to the deferral provision, this article examines its merits because a failure to engage the “Article 16 problem” could impact international accountability efforts in the Sudan, and further damage the ICC’s credibility in Africa. This unresolved issue also has wider significance given that the matters underlying the tension – how ICC prosecutions may be reconciled with peacemaking initiatives and the role and power of the Council in ICC business – will likely arise in future situations from around the world

Designing Software to Locate Differences in the Shrimp Genome

In order to determine where important differences in the genomic sequence of Pacific White Shrimp occur, many copies each of multiple regions of DNA sequence are needed. Then similar sequences can be aligned so that almost all of the bases are identical between the sequences and differences are easy to notice. One of the major issues with predicting single base position differences (SNPs) in this manner is that DNA sequencing techniques are not 100% consistent in most cases. Consequently, it needs to be determined whether a particular base is different because the true genetic sequence is variable at that position or because the sequencing process resulted in the base position being incorrectly called. SNPidentifier is a newly developed computer program that takes into account the unreliability of sequence data and tries to use only the more reliable sequences to predict where true SNPs are located. The goal of locating SNPs in Pacific White Shrimp is to identify base positions that can possibly be used in the future as molecular markers for traits of interest to shrimp breeders