Selection In Breeding Programs Research Articles

Morphology and metabolic traits related to swimming performance in Australasian snapper (Chrysophrys auratus) selected for fast growth.

Changes in body shape are linked to swimming performance and become relevant for selective breeding programmes in cultured finfish. We studied how the selection for fast growth could affect phenotypes by investigating the relationship between swimming performance and body shape. We also investigated how swimming might affect plasma metabolite concentrations. Critical swimming speed (UCrit), body traits (e.g., BW, body weight; BL, body length; K, condition factor), and plasma lactate and glucose concentrations were evaluated in two cohorts of Australasian snapper (Chrysophrys auratus): one derived from wild broodstock (F1), and the other selected for fast growth (F4). UCrit tests (n = 8) were applied in groups of 10 snapper of similar BW (71.7 g) and BL (14.6 cm). The absolute or relative UCrit values of both cohorts were similar (0.702 m⋅s-1 and 4.795 BL⋅s-1, respectively), despite the F4 cohort displaying a higher K. A positive correlation between K and absolute UCrit (Pearson's r = 0.414) was detected in the F4 cohort, but not in the F1 cohort, which may be linked to differences in body shape. A negative correlation between relative UCrit and body size (Pearson's r between -0.682 and -0.501), but no correlation between absolute UCrit and body size, was displayed in both cohorts. Plasma lactate and glucose concentrations were higher in the F4 cohort at UCrit. Whether a longer selective breeding programme could result in more changes in body shape, potentially affecting swimming performance, should be explored, along with the potential outcomes of the differences in metabolic traits detected.

Fiber characteristics of the dromedary camel in the Arabian Peninsula

Dromedary camel fibers have long been utilized to make clothes, tents, ropes, mats, and carpets, however, only a minority of these fibers are currently used to produce textiles. Dromedary fiber classification based on quality traits is essential to investigate its textile potential. Therefore, the objectives of this study were to (1) develop a classification protocol for dromedary camel fibers based on crimp (i.e., shape), (2) investigate the characteristics of each fiber class using length, diameter, and medulla (i.e., the innermost hair layer) and (3) determine which fiber class is most suitable for the textile industry. Fiber samples were obtained from the mid-torso of 32 Arabian Peninsula camels of different types. Five crimp categories were identified (straight, C-shaped, wavy, ringed, and kinky). Across all crimp categories, the average length ranged from 20.20 – 43.93 mm whereas the mean fiber diameter ranged from 29.74 – 72.11 μm. Percent medullation extended from 68% to 100% with noticeable variation between crimp categories. Overall, fiber traits significantly differed between the crimp categories. Kinky hair was particularly distinct from the other crimp categories. The kinky crimp category is the most suitable dromedary fiber for the textile industry because its fibers are long, fine, and has the lowest percentage of medullated fibers. Hence, we recommend that selective breeding programs and genetic studies focus on the production of dromedaries with kinky hair fibers.

Assessment of body metrics, weight, and carcass yields in dusky grouper (Epinephelus marginatus) through correlation and path analysis: Implications for optimizing genetic breeding programs

One of the objectives of aquaculture selective breeding programs is to enhance body conformation traits, often by using indirect criteria like correlation between live body measurements and carcass traits. This research investigated the relationship between live body measurements and carcass traits in dusky grouper (Epinephelus marginatus). We assessed the relationship between body measurements and carcass traits in 150 farmed dusky groupers with an average weight of 680 ± 221 g. The fish were measured for length, width, height, and length of head, and then processed to obtain weights (body, fillet, steaks, head, and residues) and yields (carcass, fillet, steaks, head, and residues). Path analysis was employed to estimate direct and indirect effects, with body part weight and yields as dependent variables and morphometric measurements and relationships as explanatory variables. The findings indicate that morphometric measurements can be used to estimate farmed dusky grouper body weights and carcass yields. Among the morphometric measurements and relationships examined, fish body height and standard length were identified as the main factors influencing variation in body weights and carcass yields.

Resistance of juvenile Nile tilapia Oreochromis niloticus from Brazilian populations to Streptococcus agalactiae (serotype Ib and ST-NT)

Nile tilapia is the main farmed fish in Brazilian aquaculture. Streptococcus agalactiae (GBS) is responsible for high mortality rates in fish farms. Genetic improvement is considered an effective alternative for producing resistant animals in aquaculture. The objective of this study was to estimate genetic parameters for resistance to GBS infection in a breeding population of Nile tilapia from Brazil, based on disease challenge using a circulating serotype (Ib and ST-NT). Furthermore, genetic correlations between resistance to GBS and average daily gain (ADG) were estimated to determine whether these traits can be included in selective breeding programs. Survival (SS) and time until death (TD) were the evaluated traits. The survival of the most resistant families was approximately 30%, indicating high phenotypic variation in resistance to the infection. Low to moderate heritability values for resistance traits in the Nile tilapia population were estimated, ranging from 0.14 to 0.27. Heritability for ADG was moderate to high (0.40) based on a growth trial involving 43 families (735 animals). Phenotypic correlations between the resistance traits (SS and TD) and ADG were positive and low, ranging from 0.09 to 0.18, whereas genetic correlations were close to zero. Phenotypic and genetic correlations between SS and TD were considered high and positive, ranging from 0.38 to 0.72. The results suggest that selection for resistance against GBS does not negatively affect juvenile weight gain in Nile tilapia.

Comparative analysis on growth performance, survival and harvest traits between offspring from wild and mass-selected populations of Crassostrea nippona

Crassostrea nippona has recently been recognized as a preferred alternative to C. gigas in summer due to its firm flesh and high glycogen content. To promote industrial development, the mass selective breeding program was initiated to improve growth performance of C. nippona in 2014. Although a steady genetic gain of approximately 10% for growth traits was achieved in each of the first three generations of the selected strains, little is known about the cumulative genetic progress in desired traits contributed by the selective breeding in the genetic improvement program. In this study, the aquaculture performance of the selected population was comprehensively evaluated by comparing the production performance and reproductive traits of the progeny (WF1 and SF4) from the wild population and the third-generation selected line in commercial farming environments. The results showed that the diameters of eggs from both populations were at similar levels, but the fertilization and hatching rates of the progeny from the selected lines were significantly higher than those of the wild population (P < 0.05). At larval stages, the shell height and cumulative survival rate (CSR) of individuals from SF4 were consistently superior to that of WF1, especially on day 6 post-fertilization, in which CSR of the improved C. nippona was increased by 25.08% compared to that of wild oysters. Meanwhile, a significant 12.10% enhancement in the metamorphosis rate was observed in SF4 when compared with WF1. During the grow-out stage, SF4 displayed distinct advantages in growth performance and survival compared to the wild strain, with 23.19, 33.48, 34.18 and 79.11% improvement in shell height, body weight, CSR and final yield at harvest on day 800, respectively. Meanwhile, relative brood amount (RBA) associated with initial development of offspring was found to be significantly higher in SF4 compared with WF1 (P < 0.05). Remarkably, the gonadal development, sex ratios and biochemical composition of oysters from both populations were at similar levels at final harvest, implying that high-intensity artificial selection had no significant effect on reproductive characteristics and nutritional quality of C. nippona. The encouraging results in the present study suggest that the overall genetic progress contributed by genetic breeding is considerable in the fast-growing strain of C. nippona, and such gains are expected to continue to increase with further selective breeding.

Genetic diversity of common carp Cyprinus carpio in the base population of a selective breeding programme in India

A selective breeding program for developing a suitable strain of Cyprinus carpio (Linnaeus, 1758) for inland saline aquaculture in India is in progress. At ICAR-CIFE, various geographical populations of common carp of India, viz. Madhya Pradesh (MP), Haryana (HR), Tripura (TR), Andhra Pradesh (AP), Manipur (MN), and Maharashtra (MH) formed the base population for selective breeding. The present study assesses the genetic diversity of these stocks using truss morphometry and mitochondrial DNA D loop marker analysis. The images of 600 fish were captured and digitized. The landmarks were identified, and an image network was constructed for truss analysis using tpsDig2 and PAST software. The data was subjected to scale transformation and factor analysis using SAS for Academics. The top 3 factors could explain 85.40% of the total variation. The results indicate stock-wise and sex-wise groupings. The mitochondrial DNA (D-loop) sequence analysis was conducted on 169 samples using MEGA6 software. The overall average haplotype and nucleotide diversity of the population were 0.08129 and 0.01134, respectively. Among stocks, the MP stock had a maximum of four haplotypes. The AMOVA results reveal that the stock AP is unique, and the other stocks form a single grouping. The information generated from the present study delineates genetic diversity among stocks and will aid in designing breeding plans.

Farmers’ Perception on Contribution of Community-Based Breeding Program to Sheep Flock Performance and Income of Producers in Hula and Dara Districts, Southern Ethiopia

Community-based breeding programs (CBBP) have been viewed as attractive breeding strategies, resulting in significant improvements in the performance of small ruminants and the income of producers in many parts of the world. As part of these interventions, a community-based breeding program was implemented on Abera sheep mostly reared in the region since 2013. An interview was conducted with 188 sheep producers (91 CBBP members) and 97 non-CBBP members) to know the contribution of CBBP in terms of sheep flock performance improvement and income of sheep producers in the Hula and Dara districts of Sidama region. Focused group discussions with 6–8 individuals in each breeder cooperative were separately made to complement the survey results. CBBP households owned significantly (p&lt;0.05) larger sheep heads (7.28 versus 4.99) than non-CBBP members. CBBP households further had more market participation, sold significantly (p&lt;0.05) higher average sheep (2.4 versus 1.3), and consequently earned significantly (p&lt;0.05) higher annual income (ETB 3877) than non-participating (ETB 2007) households. The majority of CBBP households (85%) observed a better twining rate for their sheep flocks since they joined the breeding program. The average age of 8.63 months of a lambing interval, 7.9 months of ram maturity for breeding, and 10.42 months needed for a ram to achieve market age before implementation of the breeding program were significantly (p&lt;0.05) reduced to 7.31 months, 6.2 months, and 7.69 months, respectively, after sheep producers started a selective breeding program. Low market integration (0.28), sheep mortality (0.21), feed shortage (0.20), low institutional support and coordination (0.17), and managerial problems of the committee (0.13) were major problems with the ranking index in parenthesis. Despite the significant contribution of the breeding program to sheep producers, the current study found weak and unsustainable institutional support for proper breeding ..........

Farmer perspectives on desired catfish attributes in aquaculture systems in Nigeria. An exploratory focus group study

As a first step to determine the focus of potential genetic improvement programs for African catfish in Nigeria, we conducted a study to identify the preferred attributes among catfish producers across three states renowned for aquaculture production, in December 2022. Employing a qualitative approach, data were collected through 11 focus group discussions involving 123 participants. The findings indicate that farmers prioritize a range of catfish attributes related to both consumption and production. The top five production-related attributes identified by farmers include stress tolerance, disease resistance, fast growth, robustness, and high survival rates. For consumption-related attributes, preferences were for large, long, heavy catfish, with abundant flesh and thickness. Notably, the prioritization of these attributes varied among catfish farmers both between and within states, reflecting diverse farming objectives and market dynamics. Future research is essential to define precise objectives and scope for selective breeding program design, considering the investment necessary for the success of such programs and how they can accommodate the diverse preferences identified.

Molecular Parentage Analysis in Aquaculture: Principles, Applications, and Challenges: A Review

Molecular parentage analysis is a powerful tool for reconstructing pedigrees and estimating genetic parameters in aquaculture species. It is based on the comparison of DNA marker genotypes between offspring and potential parents. This review provides a concise overview of molecular parentage analysis in aquaculture, covering its principles, methods, applications, challenges, and limitations. It describes common DNA markers, including microsatellites and single nucleotide polymorphisms (SNPs), used in parentage analysis and the criteria for their selection. The software and statistical methods for assigning parentage and evaluating the accuracy and power of the assignment are also discussed. This review demonstrates applications for estimating genetic parameters, investigating inbreeding, evaluating reproductive success, and improving selective breeding programs. In conclusion, while molecular parentage analysis is a valuable tool for improving genetic management in aquaculture, careful planning, implementation, and interpretation are essential.

Genetic analysis of phenotypic indicators for heat tolerance in crossbred dairy cattle

Climate change-induced rise in global temperatures has intensified heat stress on dairy cattle and is contributing to the generally observed low milk productivity. Selective breeding aimed at enhancing animals’ ability to withstand rising temperatures while maintaining optimal performance is crucial for ensuring future access to dairy products. However, phenotypic indicators of heat tolerance are yet to be effectively factored into the objectives of most selective breeding programs. This study investigated the response of milk production to changing heat load as an indication of heat tolerance and the influence of calving season on this response in multibreed dairy cattle performing in three agroecological zones Kenya. First-parity 7-day average milk yield (65 261 milk records) of 1 739 cows were analyzed. Based on routinely recorded weather data that were accessible online, the Temperature-Humidity Index (THI) was calculated and used as a measure of heat load. THI measurements used represented averages of the same 7-day periods corresponding to each 7-day average milk record. Random regression models, including reaction norm functions, were fitted to derive two resilience indicators: slope of the reaction norm (Slope) and its absolute value (Absolute), reflecting changes in milk yield in response to the varying heat loads (THI 50 and THI 80). The genetic parameters of these indicators were estimated, and their associations with average test-day milk yield were examined. There were no substantial differences in the pattern of milk yield response to heat load between cows calving in dry and wet seasons. Animals with ≤50% Bos taurus genes were the most thermotolerant at extremely high heat load levels. Animals performing in semi-arid environments exhibited the highest heat tolerance capacity. Heritability estimates for these indicators ranged from 0.06 to 0.33 and were mostly significantly different from zero (P < 0.05). Slope at THI 80 had high (0.64–0.71) negative correlations with average daily milk yield, revealing that high-producing cows are more vulnerable to heat stress and vice versa. A high (0.63–0.74) positive correlation was observed between Absolute and average milk yield at THI 80. This implied that low milk-producing cows have a more stable milk production under heat-stress conditions and vice versa. The study demonstrated that the slope of the reaction norms and its absolute value can effectively measure the resilience of crossbred dairy cattle to varying heat load conditions. The implications of these findings are valuable in improving the heat tolerance of livestock species through genetic selection.

Evidence of subpopulation diversification and traces of introgression within Canarian camel breed zoometric standard: scope and opportunities for selection

Extant diversity for phenotypic traits is an essential criterion to be considered when ordering priorities for conservation and improvement of animal genetic resources. Concretely, the characterisation of the distinctive body morphometry of a particular group of animals can aid in the design of selective breeding programs, given the strong correlation between body morphology and productive function. The present research aims to characterise an endangered autochthonous camel breed (Canarian camel), mainly relegated to leisure riding, for its body morphology, with a double objective: to explore the phenotypic diversity and structure of the breed for zoometric traits and assess the zoometric profile of this genetic resource that supports its differentiation from other camel breeds. Overall, the results highlight the existence of a high degree of diversity, which may be linked to genetic factors for zoometric traits in an endangered autochthonous breed with traditional in situ breeding schemes, which predicts the success of the implementation of genetic improvement schemes for such functional characteristics. This phenotypic diversity in body morphology could also be a tool for the evaluation of new functional niches within the efforts of functional valorisation of this camel breed for its sustainable conservation. Body morphology traits in the studied camel breed are significantly influenced by sex, physiological status and coat colour.

Optimal open nucleus breeding system for long-term genetic gain in the Pacific white shrimp using genomic selection

The open nucleus breeding system (ONBS) has been widely employed in livestock breeding and has demonstrated a desirable genetic gain compared to the traditional closed nucleus breeding system (CNBS). However, no related study and application for ONBS exist on aquatic animal breeding. The present investigation simulates the family-based ONBS with different proportions of introduced multiplier individuals used as parents of the nucleus population (NP) and CNBS schemes for the harvest body weight of the Pacific white shrimp (Litopenaeus vannamei). The multiplier population (MP) comprised progenies from eight families with high estimated breeding value (EBV) or genomic EBV (GEBV) of NP of the previous generation. ONBS was assigned three proportions (10%, 30%, and 50%) of the introduced MP individuals. The short-term selection (G0 to G10) and long-term selection (G0 to G20) were performed for CNBS and ONBS schemes using pedigree-based best linear unbiased prediction (PBLUP) with the A relationship matrix from the pedigree or single-step genomic BLUP (ssGBLUP) with the H relationship matrix integrating SNP markers and pedigree. The genetic gain of body weight and inbreeding coefficient of NP for eight breeding schemes with CNBS_PBLUP (CP), CNBS_ssGLUP (CS), ONBS_PBLUP (OP10, OP30, OP50), and ONBS_ssGBLUP (OS10, OS30, OS50) with three proportions of the introduced MP individuals were calculated. Compared to CP, genetic gains for the three OP schemes increased by 7.68 to 11.27% after short-term selection, and by 2.51 to 5.79% after long-term selection. In comparison to CS, genetic gains for the three OS schemes increased by 8.21 to 8.96% after short-term selection, and from 4.46 to 5.87% after long-term selection. The ONBS schemes achieved higher genetic gains than the corresponding CNBS schemes whether using genomic or pedigree information. The advantage of ONBS over CNBS is reduced after long-term selection. Genetic gains for the three OS schemes increased by 9.77 to 14.06% after long-term selection compared with the corresponding OP schemes. Furthermore, no significant difference (P > 0.05) in genetic gain was revealed among the ONBS schemes after either pedigree-based or genomic selection. Inbreeding coefficients for the three OP schemes increased from 59.45 to 70.98% compared with CP, whereas inbreeding coefficients for the three OS schemes increased from 24.72 to 32.22% compared with CS. Besides, after long-term selection, inbreeding coefficients for the three OS schemes decreased from 13.13 to 14.79% compared with the corresponding OP schemes. In a nutshell, ONBS using introduced MP individuals has great promise in the selective breeding program of L. vannamei. Genomic information has more potential to improve selection response and control inbreeding level than pedigree information when applying ONBS.

Influence of ploidy, genetic and environment on production traits of the Pacific oyster Crassostrea gigas

Pacific oysters, Crassostrea gigas, are one of the most widely farmed shellfish. To meet demand, the advantages of growth and increased sterility are currently being exploited in the commercial culture of triploid C. gigas. However, the extent of the triploid advantage can vary, environmental conditions and rearing methods. In the present study, the performance of diploid and triploid oysters was compared at two sites (Rongcheng and Rushan) to determine whether the triploidization would result in any advantage on production traits that could be utilized for aquaculture of this species. Triploid oysters were also produced using the wild broodstock and selected line to verify whether selectively bred oysters maintain their improved traits after triploidization. In this study, we found that the survival advantage of triploid is “site-dependent” and that Rongcheng's triploids did not exhibit significantly higher cumulative survival than diploids. Notably, incremental survival of triploid oysters was consistently higher than that of diploids during the second summer, which may be related to gonad development and spawning in diploids. At both sites, growth traits (shell height and individual weight) were always higher for triploids than in diploids in both the selected and control groups, which is strong evidence of a superior growth advantage for triploids. In addition, we found that the production performance (growth, survival and yield) of the selected group was consistently better than that of the control group (either diploid or triploid), suggesting that the superior traits of diploids can be converted to triploids through ploidy manipulation. Our results support the notion that yield can be further optimized by reducing mortality through a selective breeding program coupled with triploid production to increase growth rates. This study provides meaningful information on the potential of triploid C. gigas for oyster culture in northern China.

Signaling pathways and regulatory networks in quail skeletal muscle development: insights from whole transcriptome sequencing

Quail, as an advantageous avian model organism due to its compact size and short reproductive cycle, holds substantial potential for enhancing our understanding of skeletal muscle development. The quantity of skeletal muscle represents a vital economic trait in poultry production. Unraveling the molecular mechanisms governing quail skeletal muscle development is of paramount importance for optimizing meat and egg yield through selective breeding programs. However, a comprehensive characterization of the regulatory dynamics and molecular control underpinning quail skeletal muscle development remains elusive. In this study, through the application of HE staining on quail leg muscle sections, coupled with preceding fluorescence quantification PCR of markers indicative of skeletal muscle differentiation, we have delineated embryonic day 9 (E9) and embryonic day 14 (E14) as the start and ending points, respectively, of quail skeletal muscle differentiation. Then, we employed whole transcriptome sequencing to investigate the temporal expression profiles of leg muscles in quail embryos at the initiation of differentiation (E9) and upon completion of differentiation (E14). Our analysis revealed the expression patterns of 12,012 genes, 625 lncRNAs, 14,457 circRNAs, and 969 miRNAs in quail skeletal muscle samples. Differential expression analysis between the E14 and E9 groups uncovered 3,479 differentially expressed mRNAs, 124 lncRNAs, 292 circRNAs, and 154 miRNAs. Furthermore, enrichment analysis highlighted the heightened activity of signaling pathways related to skeletal muscle metabolism and intermuscular fat formation, such as the ECM-receptor interaction, focal adhesion, and PPAR signaling pathway during E14 skeletal muscle development. Conversely, the E9 stage exhibited a prevalence of pathways associated with myoblast proliferation, exemplified by cell cycle processes. Additionally, we constructed regulatory networks encompassing lncRNA‒mRNA, miRNA‒mRNA, lncRNA‒miRNA-mRNA, and circRNA-miRNA‒mRNA interactions, thus shedding light on their putative roles within quail skeletal muscle. Collectively, our findings illuminate the gene and non-coding RNA expression characteristics during quail skeletal muscle development, serving as a foundation for future investigations into the regulatory mechanisms governing non-coding RNA and quail skeletal muscle development in poultry production.

Characterization of sperm quality in captive-bred barramundi (Lates calcarifer): Effect on spawning performance and paternal contribution in mass-spawning events

Barramundi (Asian sea bass, Lates calcarifer) is a species with a mass-spawning reproductive strategy whereby adults synchronously release their gametes into the water column. In captivity, this reproductive strategy usually results in uneven paternal contributions to each cohort of progeny, creating skews in family size that hinder the effectiveness of selective breeding programs. As sperm quality influences fertilization success and early larval development, we investigated the relationship between sperm quality and spawning performance. Accordingly, we assessed three established breeding cohorts. Sperm samples (n = 22) were collected by cannulation. Sperm motility was assessed using CASA, and sperm viability and DNA integrity were evaluated using dual-fluorescence stains by flow cytometry. Broodstock were induced to spawn across two consecutive nights, and offspring were collected at 2.5 h and 12 h post-fertilization (hpf) and 24 h and 48 h post-hatching (hph). Offspring were assessed for morphological abnormalities, and key morphological parameters were recorded. Offspring collected at 2.5 hpf and 24 hph were genotyped to determine their parentage and examine the relationship between sperm quality of individual males and offspring survival. Results highlighted that male condition factor (K) and sperm quality were highly variable within each breeding cohort. Males with a lower condition factor showed lower sperm motility and velocity. In contrast, males with a higher condition factor showed higher sperm motility and velocity but also higher levels of sperm DNA damage. While all males were capable of fertilization, males with a lower condition factor had greater paternal contribution. In this study, a reduction in skewed paternity was also found on Night 2 of spawning compared to Night 1. Moreover, males from Tank B, which had the lowest level of sperm DNA damage, had the most even paternal contribution. Conversely, highly skewed maternal contributions were reported across all spawning events. The results of this study suggest that additional complex dynamics and further unmeasured variables, such as spawning behavior, social hierarchy, and the spawning induction procedure, may also skew family sizes. Therefore, further development of artificial reproductive technology is recommended to gain greater control over individual contribution and overcome current breeding bottlenecks.

VARIATION IN THE ASIP AND DUN GENES RESPONSIBLE FOR COAT COLOUR IN BOSNIAN MOUNTAIN HORSE

Within the Bosnian Mountain Horse Registry (BMH), some specific coat colours are permitted. Accurate determination of coat colours can be challenging as there are variations in coat colour shades and several dun dilution variants occur. The previously found single nucleotide polymorphisms (SNPs) within two coat colour loci, T-box 3 (TBX3) and Agouti Signalling Protein (ASIP), were genotyped in 313 BMH individuals. The obtained genotypes were then compared to the predicted phenotypes by using the observed coat colour types from the International Association of Bosnian Mountain Horse Breeders (IABMHB) database. It was found that the dark bay and black coat colours were the most representative coat colours both phenotypically and genotypically. The frequency of the dominant Dun (D) dilution allele is (0.09), and this frequency is higher than the previously predicted frequency recorded in the available BMH registers, as also demonstrated. Among the identified alleles, there was a discrepancy or inconsistency between the predicted coat colour based on genotypes and the observed coat colour in 73 horses (23%). The most frequent error concerned the misclassification of horses with genotypes aa and Aa at the ASIP gene, non-dun1/non-dun1 (nd1/nd1) and non-dun2/non-dun1 (nd1/nd2) at the TBX3 gene, which can be associated with the occurrence of slight dilution phenotypes in these individuals. In contrast to the Konik and Hucul breeds, no homozygosity of the D allele was found in the BMH. The D allele can be easily overlooked or not recognised in different phenotypic groups, such as dark bay and black horses. Therefore, the hypothesis that Dun dilution effects itself is not as strongly epistatic in the BMH as described in other horse breeds. This could be the result of an additional genetic modifier suppressing the phenotypic effect of the D allele. It also suggests that there has been a persistent selection pressure in favour of dark base colours, which may have contributed to the observed differences in BMH. Finally, a significant proportion (35%) of BMH individuals with genetically black coat colour were officially classified as dark bay. We hypothesise that the difficulty in visually distinguishing these two phenotypes is due to an independent locus upstream of the ASIP gene. This locus was recently identified as a factor that darkens the typical pigmentation in dark bay horses. The results of the study confirm the importance of molecular testing in accurately determining the coat colour of horses. This would help to avoid errors in coat colour descriptions in official breeding records and provide valuable information for selective breeding programmes aimed at producing specific and desired coat colours.

Effect of low-salt on the survival of mussel Mytilus coruscus and its molecular responses to chronic prolonged low-salt stress

Mussel Mytilus coruscus is a coastal economic culture species. However, massive mortalities associated with low-salt environments caused by persistent rainfall and freshwater inflow threaten its development. Herein, we examined its survival under different low-salt conditions. The survival rate of umbo and eyed larvae significantly decreased with the decline in salinity or prolonged stress time. The umbo larvae were more tolerant to low-salt stress than the eyed larvae. When the salinity levels dropped suddenly, the adults could not survive below 16‰ salinity, and their survival rate decreased faster with the increase in salinity span or the decrease in final stress salinity. However, the adults could tolerate a lower salinity levels when it dropped slowly, and their low-salt tolerance limit was 10‰. Therefore, mussel M. coruscus could adapt to a lower salinity only when the salinity levels dropped gradually. We also explored the physiological and adaptive responses of the foot in response to chronic prolonged low-salt stress by transcriptome analysis. We found that most genes in the “calcium ion binding” term and the osmoregulation-related genes were significantly induced in the salt 12 and 14 groups, suggesting the strong positive response in calcium signal transduction and osmoregulation under prolonged low-salt stress. The HSP70 and IAP genes were upregulated, suggesting that mussel M. coruscus protects itself from low-salt environments by inhibiting apoptosis. The cytoskeleton and cell cycle were inhibited, and the byssus attachment-related genes, such as tyrosinase and foot-protein genes, were suppressed, suggesting a negative response of cell division and byssus thread attachment during prolonged low-salt stress. The enhancement of carbohydrate metabolism indicated its positive role in maintaining energy homeostasis during prolonged low-salt stress. Our findings contribute to the improvement of culture technology and the guidance of selective breeding program for mussel M. coruscus and enhance our understanding of low-salt adaptation mechanism.

Integrated alternative approaches to select feed-efficient rainbow trout families to enhance the plant protein utilization

Improving feed utilization efficiency is a challenge in aquaculture. Therefore, we developed an indirect benchmark to use in selecting trout for improved efficiency of feed utilization on plant protein (soy)-based diets, with the long-term goal of reducing the cost of commercial trout production. We used a four-part integrative approach to identify feed efficient individuals among 1595 fish coming from 12 genetically selected families by establishing the phenotypic relationship between feed conversion ratio (FCR) and body weight variations using compensatory feeding regimes. Additionally, we examined the nutritional composition of fish filet for each efficiency phenotype during the compensatory regimen. Our findings showed that the fish with the lowest weight loss during a feed deprivation period and the highest weight gain during the refeeding period (FD−/RF +) demonstrated the lowest FCR (FCR = 0.99) and consisted of individuals from several lines. This finding confirms the possibility of improving feed efficiency in mixed lines. Although feeding period has an effect on nutritional composition of fillet, such selection criteria did not show an effect on groups. Overall, successful selection for the improvement of feed efficiency will have a broad application to commercial fish selective breeding programs, leading to increased aquaculture sustainability in the long run.

Genetic diversity of three consecutive selective breeding generations in Pseudobagrus vachellii (Actinopterygii: Siluriformes: Bagridae)

Pseudobagrus vachellii (Richardson, 1846) is a commercially important freshwater fish species in China. To understand the effects of artificial breeding on the genetic diversity of three consecutive P. vachellii breeding populations (F1, F2, and F3) since 2012, a genetic analysis was conducted using polymorphic microsatellite markers. The mean allele number, expected heterozygosity, observed heterozygosity, and the polymorphic information content from generation F1 to F3 decreased from 7.75 to 5.63, from 0.77 to 0.63, from 0.83 to 0.77, and from 0.72 to 0.58, respectively. Analysis of molecular variance showed greater genetic divergence within the three generations (93.67%) than that among the generations (6.33%), and the overall differentiation level was moderate. Additionally, the lowest genetic differentiation was between F2 and F3 (Fst = 0.0484), and the highest was between F1 and F3 (Fst = 0.12864). Inbreeding occurred in each generation and was the highest in generation F3. Structural analysis showed that the three P. vachellii generations were most likely divided into two different genetic clusters. Although genetic diversity declined slightly in the mass selection lines after three breeding generations, overall genetic diversity was maintained at a relatively high level. To minimize the loss of genetic diversity and inbreeding in the subsequent breeding process, a moderate number of parents can be used for each generation. Information regarding the genetic diversity and structure of the selective P. vachellii breeding generations obtained in this study will be useful for future broodstock management and selective breeding programs.

Optimizing aquaculture-scale common carp artificial reproduction: a novel approach to sperm cryopreservation using large-volume containers and elevated thawing temperatures

IntroductionThe successful cryopreservation of common carp sperm is crucial for its application in aquaculture and selective breeding programs. This study investigates the efficacy of cryopreserving sperm in large containers (5 mL) with a low dilution rate (1:1) in three different cryoprotective media and thawing in different conditions.MethodsThe developed method utilizes a low-ionic (hypotonic) cryoprotective medium, freezing with a controlled cooling rate, and high-temperature sperm thawing (60°C). The investigation employs a detailed spermatozoon motility assessment.ResultsPost-thaw motility of 32.3% ± 14% and initial curvilinear velocity of 89 ± 20 μm/s across 30 males were observed. Principal component analysis of sperm kinematic characteristics revealed distinct populations of sperm cells exhibiting varying responses to cryopreservation. The developed method achieved successful fertilization comparable to that of the non-frozen control group using sperm from a single cryotube (2.5 mL, approximately 50 * 109 spermatozoa) to fertilize 200 g of eggs (1:120,000 egg:spz).DiscussionThis novel approach demonstrates an effective cryopreservation protocol for common carp sperm in large-volume cryo-containers in combination with low-ionic cryomedia and high thawing temperature, providing methods well-suited for fisheries practices and selective breeding programs. Future studies of the biological properties of different sperm subpopulations in post-thaw sperm samples can contribute to a deeper understanding of sperm biology, improve cryopreservation techniques, and enhance the success rates of assisted reproductive technologies.