Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs

Abstract

Background: The development of genome-wide genotyping resources has provided terrestrial livestock and crop industries with the unique ability to accurately assess genomic relationships between individuals, uncover the genetic architecture of commercial traits, as well as identify superior individuals for selection based on their specific genetic profile. Utilising recent advancements in de-novo genome-wide genotyping technologies, it is now possible to provide aquaculture industries with these same important genotyping resources, even in the absence of existing genome assemblies. Here, we present the development of a genome-wide SNP assay for the Black Tiger shrimp (Penaeus monodon) through utilisation of a reduced-representation whole-genome genotyping approach (DArTseq). Results: Based on a single reduced-representation library, 31,262 polymorphic SNPs were identified across 650 individuals obtained from Australian wild stocks and commercial aquaculture populations. After filtering to remove SNPs with low read depth, low MAF, low call rate, deviation from HWE, and non-Mendelian inheritance, 7542 highquality SNPs were retained. From these, 4236 high-quality genome-wide loci were selected for baits-probe development and 4194 SNPs were included within a finalized target-capture genotype-by-sequence assay (DArTcap). This assay was designed for routine and cost effective commercial application in large scale breeding programs, and demonstrates higher confidence in genotype calls through increased call rate (from 80.2 ± 14.7 to 93.0% ± 3.5%), increased read depth (from 20.4 ± 15.6 to 80.0 ± 88.7), as well as a 3-fold reduction in cost over traditional genotype-by-sequencing approaches.

Healthier Communities of Phytoplankton and Bacteria Achieved via the Application of Modified Clay in Shrimp Aquaculture Ponds

“…Shrimp aquaculture has grown rapidly over several decades to become an economically important global industry [ 1 ]. Currently, shrimp aquaculture is generally carried out at high density in order to ensure high yields.…”

Impact of genotypic errors with equal and unequal family contribution on accuracy of genomic prediction in aquaculture using simulation

“…This includes (1) genotype-by-sequencing (GBS); (2) fixed high-density SNP arrays; and (3) low-density SNP panels. GBS does not necessarily provide genotypic data for all the detected SNPs in the population 25 – 27 . There are situations in quantitative genetics where the analysis requires reliable allelic information of the same loci across all the samples.…”

Genetic parameters of color phenotypes of black tiger shrimp (Penaeus monodon)

“…For each cohort, broodstock were allowed to mate naturally within the tanks, with any unmated females then artificially inseminated following industry practices. Since tracing of broodstock contribution could not be done on farm, all potential broodstock were genotyped and parentage analysis was utilised to determine the contributing parents retrospectively as detailed by Guppy et al (2020) . Females were spawned in communal spawning tanks and spawned eggs were transferred hatching tanks, and hatched nauplii were then transferred into 20,000 L larval rearing tanks (LRTs) at a density from 100 to 125 nauplii/liter, and reared on a commercial diet until 30 DOC.…”

“…A genotype-by-sequence (GBS) based single nucleotide polymorphism (SNP) genotyping method was used for the brood stocks (DArTSeq) ( Sansaloni et al, 2011 ). This DArTSeq data set was used to derive a targeted 4 K DArTcap custom SNP panel (4,194 SNPs) for genotyping of the offspring ( Guppy et al, 2020 ). CERVUS version 3.0.7 ( Kalinowski et al, 2007 ) was used to perform family assignment, and Colony V2.0.6.4 ( Jones and Wang, 2010 ) was employed to allocate offspring to the appropriate genetic group.…”