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 660 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, 7,542 high-quality SNPs were retained. From these, 4,236 high-quality genome-wide loci were selected for bates-probe development and 4,194 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. Conclusion Importantly, this assay equips the P. monodon industry with the ability to simultaneously assign parentage of communally reared animals, undertake genomic relationship analysis, manage mate pairings between cryptic family lines, as well as undertake advance studies of genome and trait architecture. Critically this assay can be cost effectively applied as P. monodon breeding programs transition to undertake genomic selection at less than $15 AUD per sample.

Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a novel fragmented IHHNV EVE sequence

“…These tissues, as well as the remainder of each shrimp (archived source of tissue for sequencing) were snap frozen under dry ice pellets and stored at −80°C. Each shrimp was then genotyping using the 120-SNP panel ( Sellars et al 2014 ) and a genome-wide SNP assay based on DArTSeq ( Guppy et al 2020 ). After ranking the 50 males based on inbreeding coefficient (F) and multilocus heterozygosity (MLH) data from the 120-SNP panel, the individual (named Nigel) with the highest inbreeding coefficient was chosen for genomic sequencing.…”

“…Of the >50,000 known crustacean species, high-quality genome assemblies are only available for a select few taxa, driven primarily by the commercial or unique biological significance of certain species. Genome assemblies provide a reference base for functional transcriptomic studies ( Yue and Wang 2017 ; Chandhini and Rejish Kumar 2019 ), aid in the positioning of genetic markers used for selective breeding ( Zenger et al , 2018 ; Houston et al 2020 ) and provide an important resource for the examination and characterization of genomic regions of commercial or biological interest ( Hollenbeck and Johnston 2018 ; Guppy et al 2020 ). However, crustacean genomes have also proved immensely challenging to assemble due to their large (>2 Gbp), highly repetitive (>50%), and highly heterozygous genomes ( Yuan et al 2021a ).…”

Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a fragmented IHHNV EVE sequence

“…These tissues, as well as the remainder of each shrimp (archived source of tissue for sequencing) were snap frozen under dry ice pellets and stored at -80°C. Each shrimp was then genotyping using the 120-SNP panel (Sellars et al 2014) and a genome-wide SNP assay based on DArTSeq (Guppy et al 2020)…”

“…Of the >50,000 known crustacean species, high-quality genome assemblies are only available for a select few taxa, driven primarily by the commercial or unique biological significance of certain species. Genome assemblies provide a reference base for functional transcriptomic studies (Yue and Wang 2017;Chandhini and Rejish Kumar 2019), aid in the positioning of genetic markers used for selective breeding (Houston et al 2020;Zenger et al 2017) and provide an important resource for the examination and characterization of genomic regions of commercial or biological interest (Guppy et al 2020;Hollenbeck and Johnston 2018). However, crustacean genomes have also proved immensely challenging to assemble due to their large (>2 Gbp), highly repetitive (>50%), and highly heterozygous genomes (Yuan et al 2021a).…”