Genetic improvement of Pacific white shrimp [Penaeus (Litopenaeus) vannamei]: perspectives for genomic selection

Castillo‐Juárez, Héctor; Campos-Montes, Gabriel R.; Caballero-Zamora, Alejandra; Montaldo, Hugo H.

doi:10.3389/fgene.2015.00093

Cited by 58 publications

(36 citation statements)

References 18 publications

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“…We provide the first genome sequence for the major yield‐limiting shrimp pathogen E. hepatopenaei . This genomic data in conjunction with previously‐published information on the parasite's transmission cycle (Tangprasittipap et al ., ; Tangprasittipap et al ., ), a growing body of genomic data for host shrimp species (You et al ., ; Baranski et al ., ; Castillo‐Juarez et al ., ; Yu et al ., ) and the capacity to study this pathogen in the shrimp host (Salachan et al ., ) will undoubtedly underpin the development of new tools to diagnose, monitor and potentially mitigate the negative impacts of E. hepatopenaei . As a whole our data provide resounding evidence of the consistent loss of glycolysis into the Enterocytozoonidae and closest relatives.…”

Section: Resultsmentioning

confidence: 98%

Decay of the glycolytic pathway and adaptation to intranuclear parasitism within Enterocytozoonidae microsporidia

Boakye

Jaroenlak

Prachumwat

et al. 2017

Environmental Microbiology

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Glycolysis and oxidative phosphorylation are the fundamental pathways of ATP generation in eukaryotes. Yet in microsporidia, endoparasitic fungi living at the limits of cellular streamlining, oxidative phosphorylation has been lost: energy is obtained directly from the host or, during the dispersive spore stage, via glycolysis. It was therefore surprising when the first sequenced genome from the Enterocytozoonidae - a major family of human and animal-infecting microsporidians - appeared to have lost genes for glycolysis. Here, we sequence and analyse genomes from additional members of this family, shedding new light on their unusual biology. Our survey includes the genome of Enterocytozoon hepatopenaei, a major aquacultural parasite currently causing substantial economic losses in shrimp farming, and Enterospora canceri, a pathogen that lives exclusively inside epithelial cell nuclei of its crab host. Our analysis of gene content across the clade suggests that Ent. canceri's adaptation to intranuclear life is underpinned by the expansion of transporter families. We demonstrate that this entire lineage of pathogens has lost glycolysis and, uniquely amongst eukaryotes, lacks any obvious intrinsic means of generating energy. Our study provides an important resource for the investigation of host-pathogen interactions and reductive evolution in one of the most medically and economically important microsporidian lineages.

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Section: Resultsmentioning

confidence: 98%

Decay of the glycolytic pathway and adaptation to intranuclear parasitism within Enterocytozoonidae microsporidia

Boakye

Jaroenlak

Prachumwat

et al. 2017

Environmental Microbiology

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“…Due to the decrease in genotyping costs, genomic selection is becoming the standard tool in many plant and animal breeding programs (Bernardo, 2008;González-Camacho et al, 2012;Crossa et al, 2013b;Meuwissen et al, 2013;Wiggans et al, 2017). There is an increasing number of successful applications of genomic selection in diploid and polyploid organisms where its use has generated important genetic gains by improving the accuracy of breeding value prediction and dramatically reducing generation intervals (Crossa et al, 2013a;Castillo-Juárez et al, 2015;Duangjit et al, 2016;Juliana et al, 2019;de Bem Oliveira et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Exploring Deep Learning for Complex Trait Genomic Prediction in Polyploid Outcrossing Species

et al. 2020

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“…The increase in selection accuracy by utilising GRMs has been well studied in terrestrial agriculture species [62] and has seen increasing attention in aquaculture breeding programs [40,[63][64][65]. When compared to mass selection approaches that are currently available for the black tiger shrimp aquaculture industry, utilising GRMs simultaneously allows increased accuracy of selection [66], and further mitigation of inbreeding [e.g. optimised contribution selection; [67]].…”

Section: Genomic Relationship Calculationsmentioning

confidence: 99%

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

Guppy

Jones

Kjeldsen

et al. 2020

Preprint

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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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Genetic improvement of Pacific white shrimp [Penaeus (Litopenaeus) vannamei]: perspectives for genomic selection

Cited by 58 publications

References 18 publications

Decay of the glycolytic pathway and adaptation to intranuclear parasitism within Enterocytozoonidae microsporidia

Decay of the glycolytic pathway and adaptation to intranuclear parasitism within Enterocytozoonidae microsporidia

Exploring Deep Learning for Complex Trait Genomic Prediction in Polyploid Outcrossing Species

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

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