Relationships between quantitative and reproductive fitness traits in animals

Genomic architecture of phenotypic extremes in a wild cervid

Identifying the genes underlying fitness-related traits such as body size and male ornamentation can provide tools for conservation and management and are often subject to various selective pressures. Here we performed high-depth whole genome re-sequencing of pools of individuals representing the phenotypic extremes for antler and body size in white-tailed deer (Odocoileus virginianus). Samples were selected from a tissue repository containing phenotypic data for 4,466 male white-tailed deer from Anticosti Island, Quebec, with four pools representing the extreme phenotypes for antler and body size after controlling for age. Our results revealed a largely homogenous population but detected highly divergent windows between pools for both traits, with the mean allele frequency difference of 14% for and 13% for antler and body SNPs in outlier windows, respectively. Genes in outlier antler windows were enriched for pathways associated with cell death and protein metabolism and some of the most differentiated windows included genes associated with oncogenic pathways and reproduction, processes consistent with antler evolution and growth. Genes associated with body size were more nuanced, suggestive of a highly complex trait. Overall, this study revealed the complex genomic make-up of both antler morphology and body size in free-ranging white-tailed deer and identified target loci for additional analyses.

Insertion/deletion variants within the IGF2BP2 gene identified in reported genome-wide selective sweep analysis reveal a correlation with goat litter size

Insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2, also called IMP2) plays an essential role in the development and maturation of germ cells and embryos and is a candidate gene for goat litter size, based on a previous genome-wide selective sweep analysis. In this study, the mRNA expression level of IGF2BP2 was found to be significantly higher in a single-lamb group than in a multi-lamb group. Insertions/deletions (indels) within the goat IGF2BP2 gene, including P4-Ins-13bp and P5-Del-12bp, were verified in 918 Shaanbei White Cashmere (SBWC) female goats. The minor allelic frequencies (MAFs) of P4-Ins-13bp and P5-Del-12bp loci were 0.349 and 0.295, respectively. Analysis using the Chi-square (χ²) test showed that the genotype (χ²=14.479, P=0.006) distribution of P4-Ins-13bp was significantly different between the single-lamb and multi-lamb groups. Correlation analysis demonstrated that P4-Ins-13bp was significantly associated with goat litter size (P=0.022), and individual goats with the homozygous deletion/deletion (DD) genotype produced more litters than other goats. Therefore, considered as a potential molecular marker significantly related to lambing traits, the P4-Ins-13bp mutation of the goat IGF2BP2 gene can be used in goat breeding with practical molecular marker-assisted selection (MAS) to optimize female reproduction and improve economic efficiency in the goat industry.

Relationship between litter size at birth and within-litter birth weight characteristics in laboratory mice as pilot animal for pig

We investigated the relationship between litter size at birth and within-litter birth weight (BW) characteristics of laboratory mice as a pilot mammal for pig. We obtained records of number born alive (NBA) and total and mean litter BW (LWB, MWB), and maximum and minimum values of within-litter BW (MaxIWB, MinIWB), range and standard deviation (Range, SDIWB), skewness (Skew), and kurtosis (Kurt) of within-litter BW for 656 litters at first parity. Pearson's correlations of NBA were highly positive with LWB (0.92), weakly negative with MWB (-0.31), MaxIWB (-0.19), and MinIBW (-0.33), and those of MWB were negligible with Range, SDIWB, Skew, and Kurt (-0.10 to 0.06). Estimated heritabilities, treated as dam traits, were 0.32 for NBA, 0.39 for LWB, 0.24 for MWB, 0.28 for MaxIWB, 0.05 for MinIWB, 0.16 for Range, 0.17 for SDIWB, and 0.00 for Skew and Kurt. Estimated genetic correlation between NBA and LWB was high (0.95). Therefore, LWB could be promising for efficiently improving NBA. The estimated genetic correlation of NBA was negligible with MWB (0.00), positive with MaxIWB (0.10), Range (0.48), and SDIWB (0.36), and negative with MinIWB (-0.36), suggesting that selection for increased NBA brings larger SDIWB and lighter MinIWB.

Quantitative Genetic Assessment of Female Reproductive Traits in a Domesticated Pacific White Shrimp (Penaeus vannamei) Line in China

Seed production can be improved if genetic selection is applied to key reproductive traits when a substantial amount additive genetic variation is present that can be exploited in a selective breeding program. Despite the commercial importance of reproductive traits to the seed production sector currently, few quantitative genetic studies have been conducted to address these traits in farmed penaeid shrimp culture lines. Here, we investigated genetic parameters for a number of key reproductive traits that directly impact nauplii production in Pacific white shrimp (P. vannamei) hatcheries in China. Our objectives were to determine the additive genetic variance associated with reproductive traits, and to anticipate any potential impacts on reproductive performance when selecting for increased body weight by assessing genetic correlations between post-spawning body weight and specific female reproductive traits. Data were collected on 595 females from 78 full-sib families over 30 days, with a total of 1,113 spawning events recorded. Traits studied included: body weight after spawning (WAS), number of eggs per spawn (NE), number of nauplii per spawn (NN), egg hatching rate per spawn (HR), number of eggs produced relative to female weight (g) (FE), and spawn frequency over 30 days (SF). Estimated heritability was high  for WAS (h² = 0.64 ± 0.10) and moderate for NE (0.26 ± 0.07), NN (0.18 ± 0.06), and SF (0.15 ± 0.06), respectively. In contrast, h² for HR (0.04 ± 0.03) and FE (0.05 ± 0.04) were low. The genetic correlations between growth trait (WAS) with NE, NN and SF were 0.93 ± 0.10, 0.84 ± 0.10, and 0.57 ± 0.18, respectively. While the genetic correlation between WAS and HR was low (0.02 ± 0.33), a negative genetic correlation was found between WAS and FE (-0.50 ± 0.27). Overall, we concluded that it is possible to improve the key female reproductive traits (i.e. NE, NN, and SF) in cultured white shrimp lines via genetic selection, but not for HR or FE. The genetic relationship between the growth trait and reproductive traits predicts that selection on fast growth would increase the production in the seed sector, with little or no compromise on the eggs quality.

Whole-genome sequence analysis reveals candidate genomic footprints and genes associated with reproductive traits in Thoroughbred horse

The primary objective of most horse breeding operations was to maximize reproductive efficiency and minimize the cost of producing live foals. Here, we compared individual horses from the Thoroughbred population (n = 17), known as a horse breed with poor reproductive performance, with other six horse populations (n = 28), to detect genomic signatures of positive selection underlying of reproductive traits. A number of protein-coding genes with significant (p-value <.01) higher F_ST values (616 genes) and a lower value for nucleotide diversity (π) (310 genes) were identified. The results of our study revealed some candidate genes such as IGFBP2, IGFBP5, GDF9, BRINP3 and GRID1 are possibly associated with functions influencing reproductive traits. These genes may have been under selection due to their essential roles in reproduction performance in horses. The candidate selected genes identified in this work should be of great interest for future research into genetic architecture of traits relevant to horse breeding programmes.

An Evolutionary Genomic Perspective on the Breeding of Dwarf Chickens

The evolutionary history for dwarfism in chickens remains an enigma. Herein, we explore the evolution of the Serama, the smallest breed of chicken. Leveraging comparative population genomics, analyses identify several genes that are potentially associated with the growth and development of bones and muscles. These genes, and in particular both POU1F1 and IGF1, are under strong positive selection. Three allopatric dwarf bantams (Serama, Yuanbao, and Daweishan) with different breeding-histories, form distinct clusters and exhibit unique population structures. Parallel genetic mechanisms underlay their variation in body size. These findings provide insights into the multiple and complex pathways, depending on genomic variation, that chicken can take in response to aviculture selection for dwarfism.

Effect of restricted feeding under rearing on reproduction, body condition and blood metabolites of rabbit does selected for growth rate

Young rabbit females selected for growth rate can have nutritional needs which may not be met by the common practice of feed restriction during rearing in commercial rabbit production. The aim of this study was to analyse the effect of two different feeding programmes: restricted and ad libitum feeding, applied in young rabbit females for one month at the end of rearing, on reproductive performance, body condition and circulating metabolic hormones and metabolites in a rabbit line selected by growth rate in 3 consecutive reproductive cycles. Thus, twenty-four 16-week-old does were randomly assigned to a group in which the daily recommended nutrient intakes were satisfied (fed restricted: 130 g/day, n=13) or a group fed to satiety (ad libitum: 235.5 g/day, n=11) during one month. Then, all does were inseminated in 3 consecutive cycles using a 42-day reproductive cycle. Measurements of does’ body weight, perirenal fat thickness and plasma leptin, non-esterified-fatty-acids (NEFA), beta-hydroxybutyrate (BOHB) and fructosamine were performed at artificial insemination (AI), parturition and weaning time in 3 consecutive cycles. Reproductive performance of does was evaluated based on fertility, litter size at parturition, prolificacy and productivity. Differences in body weight were found only in the 1^st cycle, ad libitum fed females being heavier than restricted ones. Nevertheless, body weight variances disappeared in later cycles. No differences were found in perirenal fat thickness. Finally, in ad libitum fed females slight differences were found in plasma levels of NEFAs (452 vs. 258 μekv/L and 527 vs. 306 μekv/L for 1^st and 2^nd cycles) and BOHB (0.26 vs. 0.03 mM for 2^nd cycle), but disappeared in the 3^rd reproductive cycle. Fertility, prolificacy and productivity was not significantly affected by the feeding programme. Nevertheless, total litter size showed to be higher in ad libitum fed females at second parturition (8.7 vs. 5.9 kits). Therefore, the evaluated feeding programmes until first AI in females selected by growth rate had no effect on their reproductive outcomes, as the global reproductive performance was not affected.

Genetic variation and correlated changes in reproductive performance of a red tilapia line selected for improved growth over three generations

The present study examines genetic variation and correlated changes in reproductive performance traits in a red tilapia (Oreochromis spp.) population selected over three generations for improved growth. A total of 328 breeding females (offspring of 111 sires and 118 dams) had measurements of body weight prior to spawning (WBS), number of fry at hatching (NFH), total fry weight (TFW) and number of dead fry (NDF) or mortality of fry including unhatched eggs at hatching (MFH). Restricted maximum likelihood (REML) analysis in a multi-trait model showed that there are heritable genetic components for all traits studied. The heritability for WBS was very high (0.80). The estimates for traits related to fecundity (NFH, TFW) and survival (NDF) were low and they were associated with high standard errors. Genetic correlations of WBS with other reproductive performance traits (NFH, TFW and NDF) were generally positive. However, NFH was negatively correlated genetically with TFW. As expected, body measurements during growth stage exhibited strong positive genetic correlations with WBS. The genetic correlations between body traits and reproductive performance (NFH, TFW, NDF) were not significant. Correlated responses in reproductive traits were measured as changes in least squares means between generations or spawning years. Except for WBS that increased with the selection programs, the phenotypic changes in other reproductive traits observed were not statistically significant (P>0.05). It is concluded that the selection program for red tilapia has resulted in very little changes in reproductive performance of the animals after three generations. However, periodic monitoring of genetic changes in fecundity and fitness related traits such as NDF or MFH should be made in selective breeding programs for red tilapia.

Metabolic adaptations in the liver of born long-distance running mice

PURPOSE

Long-distance runners have increased needs of energy supply. To unravel genetically based mechanisms required for efficient energy supply, we have analyzed hepatic metabolism of mice characterized by the inborn capacity to perform as long-distance runners.

METHODS

The mouse model had been established by phenotypic selection for high treadmill performance for 90 generations and was characterized by approximately 3.8-fold higher running capacities (Dummerstorf high Treadmill Performance mouse line [DUhTP]) compared with unselected and also untrained controls (Dummerstorf Control mouse line [DUC]). From 7-wk-old male mice, serum and liver samples were collected and analyzed for messenger RNA, protein, and metabolite levels, respectively.

RESULTS

In livers from DUhTP mice, we identified significantly higher messenger RNA transcript levels of peroxisome proliferator-activated receptor delta and higher protein levels of sirtuin-1, acetyl-CoA-synthetase, acetyl-CoA-carboxylase, phosphoenolpyruvate carboxykinase, and glutamate-dehydrogenase, suggesting higher gluconeogenesis and lipogenesis in DUhTP mice. In fact, higher hepatic levels of glycogen and triglycerides as well as higher concentrations of carbohydrate, fatty acid, and cholesterol metabolites were found in DUhTP mice. In parallel, in DUhTP mice, which did not have access to running wheels, a marked hyperlipidemia (cholesterol = 160% ± 8%, triglycerides = 174% ± 14% of controls, respectively), and abdominal obesity (DUhTP = 0.396 ± 0.019 g, DUC = 0.291 ± 0.019 g) were found.

CONCLUSIONS

From our data, we conclude that the physiological basis of genetically fixed higher endurance-running performance in DUhTP marathon mouse is related to increased hepatic gluconeogenesis and lipogenesis. Expression of sirtuin 1 as well as of gluconeogenic and lipogenic key enzymes may be related to peroxisome proliferator-activated receptor delta. Metabolic adaptations presented in our study represent inborn features of superior endurance-running performance.

Parental experience of a risky environment leads to improved offspring growth rate

Parasites (or diseases) are major selective force for the evolution of life history traits and parasite-host evolution. Mothers can show a variety of responses to parasites during pregnancy with different consequences for them or their offspring. However, whether information in the maternal environment before pregnancy can cause a change in the phenotype of the offspring is unknown. To avoid the confounding effect of pathogens and to reduce the risk of direct effect of mother's immune activation, we injected female laboratory mice with lipopolysaccharides (LPS) before mating. In order to provide a constant information on the potential infectious risk of the environment, females were mated with males that were also exposed to LPS before mating. Offspring from immune-challenged parents were larger and grew at a faster rate than offspring from control parents (injected with PBS). Additionally, offspring from immune-challenged parents that suffered the most from inflammation grew at a faster rate than offspring from low suffering parents. Producing heavier offspring that will reach sexual maturity earlier is likely to have fitness benefit for parents and offspring through improved reproductive success.

Body weight and body condition of breeding rabbits in commercial units

Live BW and BCS data were collected from 2,775 breeding rabbits (644 males and 2,131 females) of 34 genetic types and sorted according to their specialization (maternal, paternal, and others). Data were gathered on 66 visits to 43 commercial farms in Spain between 2009 and 2011. Mean BW was 4.72 kg (range of 2.87 to 8.13 kg, with a median BW of 4.60 kg) and mean BCS was 4.6 (range of 1.0 to 9.0, with a median BCS of 5.0). females had heavier (P < 0.05) BW than males and paternal lines of rabbits had greater (P < 0.05) BW than maternal lines and other breeds/lines not selected for meat production. Between 69.3% and 75.4% of the rabbits were deemed healthy by a veterinarian and, as expected, healthy rabbits were heavier (P < 0.05) than sick rabbits diagnosed with rhinitis, mastitis, sore hocks, and several other diseases. Among purebred, maternal lines of rabbits, Hyplus GD24, UPV A, and UPV V were heavier (P < 0.05) than hyplus GD14 and Hyla HL-D lines, and line UPV R had the greatest (P < 0.05) BW among the purebred, paternal lines. Additionally, A×H, A×V, PS19, and P×A crossbreds had greater (P < 0.05) BW than HE-C×D, HL-C×D, H×V, LP×V, and V×P crossbreds among the maternal lines, whereas HE-SL were the heaviest (P < 0.05) crossbred paternal line of rabbits. Additionally, females received greater (P < 0.05) BCS than males and BCS were greater (P < 0.05) in healthy than sick rabbits. Moreover, maternal lines had smaller (P < 0.05) BCS than either paternal lines or other lines/breeds not selected for meat production. Results also indicated a moderate relationship between BCS and BW (r = 0.32), with a 1-point change in BCS equivalent to an ~ 245-g change in BW. results from this study can be used as baseline figures for breeding rabbits in spain and are essential factors in several decisions concerning housing, feeding, reproduction, health, and welfare of breeding rabbits.

mRNA expression in rabbit blastocyst and endometrial tissue of candidate gene involved in gestational losses

Gestation is a complex process that involves different growth factors, cytokines and adhesion proteins related with embryo development, cellular differentiation and proliferation, embryo-endometrium interaction, angiogenesis, maternal-embryonic recognition and growth development of placenta and embryos. In this study, we examine pre-implantational (at 6 days of gestation) and gestational (at 12 days and total from ovulation to birth) losses in two rabbit lines selected by different criteria (post-weaning daily gain and litter size) and the pattern of a set of candidate transcripts, at 6 days of gestation, related with embryo development and implantation process, such as Oct-4, epidermal growth factor receptor 3 (erbB3), Transforming Growth Factor β2, Vascular Endothelial Growth Factor and Interferon γ and related with insulin-like growth factors signalling as insulin growth factors I and II and their receptors in rabbit blastocysts and endometrial tissue. Similar pre-implantational losses were obtained in both lines. However, the gestational losses of the line selected by post-weaning daily gain clearly mirrored an increase in losses by 50% at 12 days and at birth (22.4 vs 9.5 and 50.2 vs 25.4, respectively, between line selected by post-weaning daily gain and line selected by litter size). In blastocysts and endometrial tissue at 6 days of gestation qRT-PCR assays indicated that the mean insulin-like growth factor (IGF)-IIR mRNA expression was down-regulated in line selected by post-weaning daily gain. Dysregulation of the IGF-IIR could be potential reasons for induced gestational losses. We conclude that IGF-IIR gene expression in blastocyst and endometrial tissue at 6th day of gestation tends to decline in line selected by post-weaning daily gain. The functional significance related with gestational losses is uncertain.

Can more be learned from selection experiments of value in animal breeding programmes? Or is it time for an obituary?

Selection experiments in laboratory animals and livestock have provided a wealth of information on genetic parameters of quantitative traits and on the effectiveness of selection in the short and long term on both directly selected and correlated traits. They have stimulated developments in theory and tests of it, and extreme selected lines continue to be source material for biological study. Some of the main questions and findings are briefly reviewed. Yet much of successful animal breeding practice has been based essentially on statistical methods, assuming where necessary the infinitesimal model, and new developments such as genomic selection are similarly not based on selection experiments. Information on the genetic architecture of quantitative traits is provided by selection experiments, but new methods for deeper studies of the biology are available. I discuss the future role for selection experiments in view of changes in funding streams and technology and conclude that there is little case for starting new experiments, but retention of existing long-term lines is desirable and DNA should be collected from all lines on a continuing basis.

Study of smell and reproductive organs in a mouse model for CHARGE syndrome

CHARGE syndrome is a multiple congenital anomaly syndrome characterised by Coloboma, Heart defects, Atresia of choanae, Retardation of growth and/or development, Genital hypoplasia, and Ear anomalies often associated with deafness. It is caused by heterozygous mutations in the CHD7 gene and shows a highly variable phenotype. Anosmia and hypogonadotropic hypogonadism occur in the majority of the CHARGE patients, but the underlying pathogenesis is unknown. Therefore, we studied the ability to smell and aspects of the reproductive system (reproductive performance, gonadotropin-releasing hormone (GnRH) neurons and anatomy of testes and uteri) in a mouse model for CHARGE syndrome, the whirligig mouse (Chd7^Whi/+). We showed that Chromodomain Helicase DNA-binding protein 7 (Chd7) is expressed in brain areas involved in olfaction and reproduction during embryonic development. We observed poorer performance in the smell test in adult Chd7^Whi/+ mice, secondary either to olfactory dysfunction or to balance disturbances. Olfactory bulb and reproductive organ abnormalities were observed in a proportion of Chd7^Whi/+ mice. Hypothalamic GnRH neurons were slightly reduced in Chd7^Whi/+ females and reproductive performance was slightly less in Chd7^Whi/+ mice. This study shows that the penetrance of anosmia and hypogonadotropic hypogonadism is lower in Chd7^Whi/+ mice than in CHARGE patients. Interestingly, many phenotypic features of the Chd7 mutation showed incomplete penetrance in our model mice, despite the use of inbred, genetically identical mice. This supports the theory that the extreme variability of the CHARGE phenotype in both humans and mice might be attributed to variations in the fetal microenvironment or to purely stochastic events.