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

Fine-tuning GBS data with comparison of reference and mock genome approaches for advancing genomic selection in less studied farmed species

BACKGROUND

Diversifying animal cultivation demands efficient genotyping for enabling genomic selection, but non-model species lack efficient genotyping solutions. The aim of this study was to optimize a genotyping-by-sequencing (GBS) double-digest RAD-sequencing (ddRAD) pipeline. Bovine data was used to automate the bioinformatic analysis. The application of the optimization was demonstrated on non-model European whitefish data.

RESULTS

DdRAD data generation was designed for a reliable estimation of relatedness and is scalable to up to 384 samples. The GBS sequencing yielded approximately one million reads for each of the around 100 assessed samples. Optimizing various strategies to create a de-novo reference genome for variant calling (mock reference) showed that using three samples outperformed other building strategies with single or very large number of samples. Adjustments to most pipeline tuning parameters had limited impact on high-quality data, except for the identity criterion for merging mock reference genome clusters. For each species, over 15k GBS variants based on the mock reference were obtained and showed comparable results with the ones called using an existing reference genome. Repeatability analysis showed high concordance over replicates, particularly in bovine while in European whitefish data repeatability did not exceed earlier observations.

CONCLUSIONS

The proposed cost-effective ddRAD strategy, coupled with an efficient bioinformatics workflow, enables broad adoption of ddRAD GBS across diverse farmed species. While beneficial, a reference genome is not obligatory. The integration of Snakemake streamlines the pipeline usage on computer clusters and supports customization. This user-friendly solution facilitates genotyping for both model and non-model species.

Development of DNA Markers for Acute Hepatopancreatic Necrosis Disease Tolerance in Litopenaeus vannamei through a Genome-Wide Association Study

Shrimp aquaculture is facing a serious disease, acute hepatopancreatic necrosis disease (AHPND), caused by Vibrio paraheamolyticus (VpAPHND). For sustainable shrimp aquaculture, massive losses of shrimp infected with VpAPHND must be prevented. Research and selection of shrimp tolerant to VpAPHND infection is a sustainable approach to reducing the risk of AHPND. This study focused on the identification and development of potential DNA markers associated with AHPND using DArT sequencing (DArTSeq) and a genome-wide association study. Three populations of post-larval Litopenaeus vannamei were immersed in VpAPHND to collect susceptible (D) and tolerant (S) samples. The 45 D and 48 S shrimp had their genotypes analyzed using DArTSeq. A total of 108,983 SNPs and 17,212 InDels were obtained from the DArTseq data, while the biallelic 516 SNPs and 2293 InDels were finally filtered with PIC < 0.1, MAF < 0.05, and a call rate ≥ 80%. The filtered variants were analyzed for their association with AHPND tolerance. Although there were no significantly associated SNPs and InDels above the Bonferroni correction threshold, candidate variants, four SNPs and 17 InDels corresponding to p < 0.01, were provided for further validation of the AHPND tolerance trait. The candidate SNPs are located on an exon of the zinc finger protein 239-like gene, an intron of an uncharacterized gene, and in intergenic regions. Most of the candidate InDels are in the intergenic regions, with fewer in the intronic and exonic regions. This study provides information on SNPs and InDels for white shrimp. These markers will support the variant database of shrimp and be useful in shrimp aquaculture for breeding selection.

Characterization of Eighty-Eight Single-Nucleotide Polymorphism Markers in the Manila Clam Ruditapes philippinarum Based on High-Resolution Melting (HRM) Analysis

Single-nucleotide polymorphisms (SNPs) are the most commonly used DNA markers in population genetic studies. We used the Illumina HiSeq4000 platform to develop single-nucleotide polymorphism (SNP) markers for Manila clam Ruditapes philippinarum using restriction site-associated DNA sequencing (RAD-seq) genotyping. Eighty-eight SNP markers were successfully developed by using high-resolution melting (HRM) analysis, with a success rate of 44%. SNP markers were analyzed for genetic diversity in two clam populations. The observed heterozygosity per locus ranged from 0 to 0.9515, while the expected heterozygosity per locus ranged from 0.0629 to 0.4997. The value of FIS was estimated to be from -0.9643 to 1.0000. The global Fst value was 0.1248 (p < 0.001). After Bonferroni correction, 15 loci deviated significantly from the Hardy-Weinberg equilibrium (p < 0.0006). These SNP markers provide a valuable resource for population and conservation genetics studies in this commercially important species.

Single nucleotide polymorphism SNP19140160 A > C is a potential breeding locus for fast-growth largemouth bass (Micropterus salmoides)

BACKGROUND

Largemouth bass (Micropterus salmoides) has significant economic value as a high-yielding fish species in China's freshwater aquaculture industry. Determining the major genes related to growth traits and identifying molecular markers associated with these traits serve as the foundation for breeding strategies involving gene pyramiding. In this study, we screened restriction-site associated DNA sequencing (RAD-seq) data to identify single nucleotide polymorphism (SNP) loci potentially associated with extreme growth differences between fast-growth and slow-growth groups in the F1 generation of a largemouth bass population.

RESULTS

We subsequently identified associations between these loci and specific candidate genes related to four key growth traits (body weight, body length, body height, and body thickness) based on SNP genotyping. In total, 4,196,486 high-quality SNPs were distributed across 23 chromosomes. Using a population-specific genotype frequency threshold of 0.7, we identified 30 potential SNPs associated with growth traits. Among the 30 SNPs, SNP19140160, SNP9639603, SNP9639605, and SNP23355498 showed significant associations; three of them (SNP9639603, SNP9639605, and SNP23355498) were significantly associated with one trait, body length, in the F1 generation, and one (SNP19140160) was significantly linked with four traits (body weight, height, length, and thickness) in the F1 generation. The markers SNP19140160 and SNP23355498 were located near two growth candidate genes, fam174b and ppip5k1b, respectively, and these candidate genes were closely linked with growth, development, and feeding. The average body weight of the group with four dominant genotypes at these SNP loci in the F1 generation population (703.86 g) was 19.63% higher than that of the group without dominant genotypes at these loci (588.36 g).

CONCLUSIONS

Thus, these four markers could be used to construct a population with dominant genotypes at loci related to fast growth. These findings demonstrate how markers can be used to identify genes related to fast growth, and will be useful for molecular marker-assisted selection in the breeding of high-quality largemouth bass.

Innovative Advances in Plant Genotyping

Over the past decade, advances in plant genotyping have been critical in enabling the identification of genetic diversity, in understanding evolution, and in dissecting important traits in both crops and native plants. The widespread popularity of single-nucleotide polymorphisms (SNPs) has prompted significant improvements to SNP-based genotyping, including SNP arrays, genotyping by sequencing, and whole-genome resequencing. More recent approaches, including genotyping structural variants, utilizing pangenomes to capture species-wide genetic diversity and exploiting machine learning to analyze genotypic data sets, are pushing the boundaries of what plant genotyping can offer. In this chapter, we highlight these innovations and discuss how they will accelerate and advance future genotyping efforts.

Genetic analysis of digital image derived morphometric traits of black tiger shrimp (Penaeus monodon) by incorporating G × E investigations

The black tiger shrimp, Penaeus monodon, is the second most economically important aquaculture shrimp species in the world, and in Australia it is one of the most commonly farmed shrimp species. Despite its economic significance, very few studies have reported the genetic evaluation of economically important morphological size and shape traits of shrimp grown in commercial grow-out environments. In this study we obtained genetic parameter estimates and evaluated genotype-by-environment interaction (GxE) for nine body morphological traits of shrimp derived from images. The data set contained image and body weight (BW) records of 5,308 shrimp, from 64 sires and 54 dams, reared in eight grow-out ponds for an average of 133 days. From the images, landmark based morphological distances were computed from which novel morphological traits associated with size and shape were derived for genetic evaluation. These traits included body weight (BW), body length (BL), body size (BS), head size (HS), Abdominal size (AS), abdominal percentage (AP), tail tip (TT), front by back ratio (FBR), condition factor (CF) and condition factor length (CFL). We also evaluated G×E interaction effects of these traits for shrimp reared in different ponds. The heritability estimates for growth related morphological and body weight traits were moderately high (BW: h² = 0.32 ± 0.05; BL: h² = 0.36 ± 0.06; BS: h² = 0.32 ± 0.05; HS: h² = 0.31 ± 0.05; AS: h² = 0.32 ± 0.05; and TT: h² = 0.28 ± 0.05) and low for abdominal percentage and body shape traits (AP: h² = 0.09 ± 0.02; FBR: h² = 0.08 ± 0.02; CF: h² = 0.06 ± 0.02; and CFL: h² = 0.003 ± 0.004). G × E interaction were negligible for all traits for shrimp reared in different ponds, suggesting re-ranking is not prevalent for this population. Genetic correlations among growth related morphological traits were high ranging from 0.36 to 0.99, suggesting these traits can be simultaneously improved through indirect genetic selection. However, negative genetic correlations were observed for FBR & CF shape traits with major growth traits (ranged −0.08 to −0.95), suggesting genetic selection for rapid growth will likely result in thick/fatty shrimp over generations. Our study showed image-based landmark data can be successfully employed for genetic evaluation of complex morphological traits of shrimp and is potentially amenable to machine-learning derived parameters in semi-automated high volume phenotyping systems needed under commercial conditions.

Genetics reveals shifts in reproductive behaviour of the invasive bird parasite Philornis downsi collected from Darwin’s finch nests

Due to novel or dynamic fluctuations in environmental conditions and resources, host and parasite relationships can be subject to diverse selection pressures that may lead to significant changes during and after invasion of a parasite. Genomic analyses are useful for elucidating evolutionary processes in invasive parasites following their arrival to a new area and host. Philornis downsi (Diptera: Muscidae), the avian vampire fly, was introduced to the Galápagos Islands circa 1964 and has since spread across the archipelago, feeding on the blood of developing nestlings of endemic land birds. Since its discovery, there have been significant changes to the dynamics of P. downsi and its novel hosts, such as shifting mortality rates and changing oviposition behaviour, however no temporal genetic studies have been conducted. We collected P. downsi from nests and traps from a single island population over a 14-year period, and genotyped flies at 469 single nucleotide polymorphisms (SNPs) using restriction-site associated DNA sequencing (RADSeq). Despite significant genetic differentiation (FST) between years, there was no evidence for genetic clustering within or across four sampling years between 2006 and 2020, suggesting a lack of population isolation. Sibship reconstructions from P. downsi collected from 10 Darwin’s finch nests sampled in 2020 showed evidence for shifts in reproductive behaviour compared to a similar genetic analysis conducted in 2004–2006. Compared with this previous study, females mated with fewer males, individual females oviposited fewer offspring per nest, but more unique females oviposited per nest. These findings are important to consider within reproductive control techniques, and have fitness implications for both parasite evolution and host fitness.

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

Black tiger shrimp (Penaeus monodon) is the second most important aquaculture species of shrimp in the world. In addition to growth traits, uncooked and cooked body color of shrimp are traits of significance for profitability and consumer acceptance. This study investigated for the first time, the phenotypic and genetic variances and relationships for body weight and body color traits, obtained from image analyses of 838 shrimp, representing the progeny from 55 sires and 52 dams. The color of uncooked shrimp was subjectively scored on a scale from 1 to 4, with “1” being the lightest/pale color and “4” being the darkest color. For cooked shrimp color, shrimp were graded firstly by subjective scoring using a commercial grading score card, where the score ranged from 1 to 12 representing light to deep coloration which was subsequently found to not be sufficiently reliable with poor repeatability of measurement (r = 0.68–0.78) Therefore, all images of cooked color were regraded on a three-point scale from brightest and lightest colored cooked shrimp, to darkest and most color-intense, with a high repeatability (r = 0.80–0.92). Objective color of both cooked and uncooked color was obtained by measurement of RGB intensities (values range from 0 to 255) for each pixel from each shrimp. Using the “convertColor” function in “R”, the RGB values were converted to L*a*b* (CIE Lab) systems of color properties. This system of color space was established in 1976, by the International Commission of Illumination (CIE) where “L*” represents the measure of degree of lightness, values range from 0 to 100, where 0 = pure black and 100 = pure white. The value “a*” represents red to green coloration, where a positive value represents the color progression towards red and a negative value towards green. The value “b*” represents blue to yellow coloration, where a positive value refers to more yellowish and negative towards the blue coloration. In total, eight color-related traits were investigated. An ordinal mixed (threshold) model was adopted for manually (subjectively) scored color phenotypes, whereas all other traits were analyzed by linear mixed models using ASReml software to derive variance components and estimated breeding values (EBVs). Moderate to low heritability estimates (0.05–0.35) were obtained for body color traits. For subjectively scored cooked and uncooked color, EBV-based selection would result in substantial genetic improvement in these traits. The genetic correlations among cooked, uncooked and body weight traits were high and ranged from −0.88 to 0.81. These suggest for the first time that 1) cooked color can be improved indirectly by genetic selection based on color of uncooked/live shrimp, and 2) intensity of coloration is positively correlated with body weight traits and hence selection for body weight will also improve color traits in this population.

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

Shrimp are a valuable aquaculture species globally; however, disease remains a major hindrance to shrimp aquaculture sustainability and growth. Mechanisms mediated by endogenous viral elements have been proposed as a means by which shrimp that encounter a new virus start to accommodate rather than succumb to infection over time. However, evidence on the nature of such endogenous viral elements and how they mediate viral accommodation is limited. More extensive genomic data on Penaeid shrimp from different geographical locations should assist in exposing the diversity of endogenous viral elements. In this context, reported here is a PacBio Sequel-based draft genome assembly of an Australian black tiger shrimp (Penaeus monodon) inbred for 1 generation. The 1.89 Gbp draft genome is comprised of 31,922 scaffolds (N50: 496,398 bp) covering 85.9% of the projected genome size. The genome repeat content (61.8% with 30% representing simple sequence repeats) is almost the highest identified for any species. The functional annotation identified 35,517 gene models, of which 25,809 were protein-coding and 17,158 were annotated using interproscan. Scaffold scanning for specific endogenous viral elements identified an element comprised of a 9,045-bp stretch of repeated, inverted, and jumbled genome fragments of infectious hypodermal and hematopoietic necrosis virus bounded by a repeated 591/590 bp host sequence. As only near complete linear ∼4 kb infectious hypodermal and hematopoietic necrosis virus genomes have been found integrated in the genome of P. monodon previously, its discovery has implications regarding the validity of PCR tests designed to specifically detect such linear endogenous viral element types. The existence of joined inverted infectious hypodermal and hematopoietic necrosis virus genome fragments also provides a means by which hairpin double-stranded RNA could be expressed and processed by the shrimp RNA interference machinery.

Population Structure of Macaca fascicularis aurea, and their Genetic Relationships with M. f. fascicularis and M. mulatta Determined by 868 RADseq-Derived Autosomal SNPs-A consideration for biomedical research

BACKGROUND

This study examined the population structure of Macaca fascicularis aurea and their genetic relationships with M. f. fascicularis and M. mulatta.

METHODS

The study analyzed 868 RADseq-derived SNPs from samples representing the entire distribution range of M. f. aurea, including their inter- and intraspecific hybrid zones.

RESULTS

The study supports a M. mulatta/Indochinese M. f. fascicularis, Sundaic M. f. fascicularis, and M. f. aurea trichotomy; M. f. aurea was genetically distinct from both forms of M. f. fascicularis and M. mulatta. Hybridization between M. f. aurea and M. f. fascicularis occurred in two directions: south-north (8°25' to 15°56') and west-east (98°28' to 99°02'). Low levels of M. mulatta introgression were also detected in M. f. aurea.

CONCLUSION

This study showcases a complicated scenario of genetic relationships between the M. fascicularis subspecies and between M. fascicularis and M. mulatta and underscores the importance of these taxa's population structure and genetic relationships for biomedical research.

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

The composition and stability of microbial communities in aquaculture water are crucial for the healthy growth of shrimp and present considerable risk to aquatic ecosystems. The modified clay (MC) method has been proposed as an efficient and safe solution for the mitigation of harmful algal blooms (HABs). Currently, the effects of MC on microbial communities in aquaculture water remain unknown. Here, we adopted the MC method to regulate shrimp-culture water quality and evaluated the effects of MC on the composition and stability of phytoplankton together with bacteria communities through high-throughput sequencing. On the one hand, a prominent change in the composition of microbial community was observed, with green algae becoming the most abundant genera and pathogens being infrequent in the MC-treated pond, which was more conducive to the growth of shrimp than that in the control pond. Moreover, MC could increase the diversity and stability of the microbial community structure in the water column, which had a higher anti-interference ability, as demonstrated by the analysis of the diversity and molecular ecological network. Taken together, MC could reduce the possibility for the occurrence of HABs and maintain a stable microbial community, which is beneficial for the health and high yield of shrimp.

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

Genotypic errors, conflict between recorded genotype and the true genotype, can lead to false or biased population genetic parameters. Here, the effect of genotypic errors on accuracy of genomic predictions and genomic relationship matrix are investigated using a simulation study based on population and genomic structure comparable to black tiger prawn, Penaeus monodon. Fifty full-sib families across five generations with phenotypic and genotypic information on 53 K SNPs were simulated. Ten replicates of different scenarios with three heritability estimates, equal and unequal family contributions were generated. Within each scenario, four SNP densities and three genotypic error rates in each SNP density were implemented. Results showed that family contribution did not have a substantial impact on accuracy of predictions across different datasets. In the absence of genotypic errors, 3 K SNP density was found to be efficient in estimating the accuracy, whilst increasing the SNP density from 3 to 20 K resulted in a marginal increase in accuracy of genomic predictions using the current population and genomic parameters. In addition, results showed that the presence of even 10% errors in a 10 and 20 K SNP panel might not have a severe impact on accuracy of predictions. However, below 10 K marker density, even a 5% error can result in lower accuracy of predictions.