Design and Evaluation of Multi-Density HD-Marker Arrays for Litopenaeus vannamei
Pacific white shrimp(Litopenaeus vannamei)has emerged as the dominant farmed shrimp species globally with economic importance.However,it is cost-prohibitive for L.vannamei with so large a genome size(e.g.2.6 GB)in the breeding program which needs to deal with a large number of samples.Although gene chip has been developed for target-genotyping,it relies on expensive and pro-fessional scanning instruments,and the fixed arrays are non-flexible.In this study,we performed whole genomic resequencing of 180 Pacific white shrimps from two artificially selective breeds and four market-leading companies and detected whole genome-wide Single nucleotide polymorphisms(SNPs).Based on the whole-genome wide SNPs,HD-Marker array with different densities of 12k,46k and 92k SNPs loci were designed and evaluated.The results revealed that the majority of SNPs in three panels are located in genic region with 93.15％in 12k-plex,76.24％in 46k-plex and 70.80％in 92k-plex,covering ap-proximately 11 618,20 055 and 20 056 genes,respectively.The minor allele frequencies(MAF)were also evaluated,observing 0.27±0.11,0.34±0.12 and 0.27±0.12 in three panels,respectively.The loci in three panels were evenly distributed on the chromosome,among which 51.11％,76.63％and 93.87％of the loci have an average spacing between 1～50 kB.The three panels cover multiple signaling pathways involved in growth and immune function,such as MAPK,mTOR,Wnt,and NOD-like recep-tors signaling pathways.This study provided basis for the establishment of HD-Marker in Pacific white shrimp so that providing technical support for whole genome selection breeding,evaluation of germ-plasm resources,Quantitative trait locus(QTL)Location,and Genome wide association study(GWAS)for L.vannamei.
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维普
