흰다리새우(Litopenaeus vannamei)의 유전체 기반 Microsatellite 마커 개발
Development of Genome-Based Microsatellite Markers for Whiteleg Shrimp Litopenaeus vannamei
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The aim of this studywas to develop genome-wide microsatellite (SSR) markers for whiteleg shrimp Litopenaeus vannamei using a reference genome-based in silico approach and evaluate their applicability for genetic analysis in L. vannamei populations. A total of 9,123,781 perfect SSRs were identified from the reference genome (ASM378908v1) using the Krait software, and 96 candidate loci were initially selected. After PCR amplification and genotyping, eight polymorphic SSR markers were validated and selected. These markers were evaluated using broodstock samples (n=82) that were collected from three L. vannamei farms. The number of alleles (NA) per locus ranged from 6 to 12 (mean=8.6), while the average observed heterozygosity (HO) and expected heterozygosity (HE) were 0.737 and 0.738, respectively. All markers exhibited polymorphism information content (PIC) values above 0.5 (mean = 0.685) and null allele frequencies below 0.1, indicating high informativeness and low bias. Genetic diversity analysis across the three broodstock populations revealed consistently high heterozygosity, minimal inbreeding coefficients and no significant deviation from the Hardy-Weinberg equilibrium. These results demonstrate that the developed SSR markers are reliable and effective tools for population genetics studies and selective breeding programs for L. vannamei.
Abstract
The aim of this studywas to develop genome-wide microsatellite (SSR) markers for whiteleg shrimp Litopenaeus vannamei using a reference genome-based in silico approach and evaluate their applicability for genetic analysis in L. vannamei populations. A total of 9,123,781 perfect SSRs were identified from the reference genome (ASM378908v1) using the Krait software, and 96 candidate loci were initially selected. After PCR amplification and genotyping, eight polymorphic SSR markers were validated and selected. These markers were evaluated using broodstock samples (n=82) that were collected from three L. vannamei farms. The number of alleles (NA) per locus ranged from 6 to 12 (mean=8.6), while the average observed heterozygosity (HO) and expected heterozygosity (HE) were 0.737 and 0.738, respectively. All markers exhibited polymorphism information content (PIC) values above 0.5 (mean = 0.685) and null allele frequencies below 0.1, indicating high informativeness and low bias. Genetic diversity analysis across the three broodstock populations revealed consistently high heterozygosity, minimal inbreeding coefficients and no significant deviation from the Hardy-Weinberg equilibrium. These results demonstrate that the developed SSR markers are reliable and effective tools for population genetics studies and selective breeding programs for L. vannamei.