Passive integrated transponder (PIT) tagging black tiger shrimp, Penaeus monodon : Applications for 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.

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A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of novel growth-associated genes

10.1101/2020.05.14.096073 ◽

2020 ◽

Cited By ~ 1

Author(s):

Tanaporn Uengwetwanit ◽

Wirulda Pootakham ◽

Intawat Nookaew ◽

Chutima Sonthirod ◽

Pacharaporn Angthong ◽

...

Keyword(s):

Genome Assembly ◽

Penaeus Monodon ◽

High Quality ◽

High Molecular Weight Dna ◽

Breeding Programs ◽

Crustacean Species ◽

Black Tiger Shrimp ◽

Tiger Shrimp ◽

High Quality Genome ◽

Chromosome Level

AbstractThe black tiger shrimp (Penaeus monodon) is one of the most prominent farmed crustacean species with an average annual global production of 0.5 million tons in the last decade. To ensure sustainable and profitable production through genetic selective breeding programs, several research groups have attempted to generate a reference genome using short-read sequencing technology. However, the currently available assemblies lack the contiguity and completeness required for accurate genome annotation due to the highly repetitive nature of the genome and technical difficulty in extracting high-quality, high-molecular weight DNA in this species. Here, we report the first chromosome-level whole-genome assembly of P. monodon. The combination of long-read Pacific Biosciences (PacBio) and long-range Chicago and Hi-C technologies enabled a successful assembly of this first high-quality genome sequence. The final assembly covered 2.39 Gb (92.3% of the estimated genome size) and contained 44 pseudomolecules, corresponding to the haploid chromosome number. Repetitive elements occupied a substantial portion of the assembly (62.5%), highest of the figures reported among crustacean species. The availability of this high-quality genome assembly enabled the identification of novel genes associated with rapid growth in the black tiger shrimp through the comparison of hepatopancreas transcriptome of slow-growing and fast-growing shrimps. The results highlighted several gene groups involved in nutrient metabolism pathways and revealed 67 newly identified growth-associated genes. Our high-quality genome assembly provides an invaluable resource for accelerating the development of improved shrimp strain in breeding programs and future studies on gene regulations and comparative genomics.

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