Correlated responses to long-term divergent selection for eight-week body weight in chickens: growth, sexual maturity, and egg production

Differing Expression and Potential Immunological Role of C-Type Lectin Receptors of Two Different Chicken Breeds against Low Pathogenic H9N2 Avian Influenza Virus

Diverse immune responses in different chicken lines can result in varying clinical consequences following avian influenza virus (AIV) infection. We compared two widely used layer breeds, Lohmann Brown (LB) and Lohmann White (LW), to examine virus replication and immune responses against H9N2 AIV infection. The transcription profile in the spleen of H9N2-infected chickens was compared using a microarray. Confirmatory real-time RT-PCR was used to measure the expression of C-type lectin, OASL, and MX1 genes. Additionally, to investigate the role of chicken lectin receptors in vitro, two C-type lectin receptors (CLRs) were expressed in DF-1 cells, and the early growth of the H9N2 virus was evaluated. The LB chickens shed a lower amount of virus from the cloaca compared with the LW chickens. Different expression levels of C-type lectin-like genes were observed in the transcription profile, with no significant differences in OASL or MX gene expression. Real-time RT-PCR indicated a sharp decrease in C-type lectin levels in the spleen of H9N2-infected LW chickens. In vitro studies demonstrated that cells overexpressing CLR exhibited lower virus replication, while silencing of homeostatic CLR had no effect on AIV replication. This study demonstrated distinct immune responses to H9N2 avian influenza in LB and LW chickens, particularly with differences in C-type lectin expression, potentially leading to lower virus shedding in LB chickens.

Elucidation of the genetic determination of clutch traits in Chinese local chickens of the Laiwu Black breed

BACKGROUND

Egg laying rate (LR) is associated with a clutch, which is defined as consecutive days of oviposition. The clutch trait can be used as a selection indicator to improve egg production in poultry breeding. However, little is known about the genetic basis of clutch traits. In this study, our aim was to estimate genetic parameters and identify quantitative trait single nucleotide polymorphisms for clutch traits in 399 purebred Laiwu Black chickens (a native Chinese breed) using a genome-wide association study (GWAS).

METHODS

In this work, after estimating the genetic parameters of age at first egg, body weight at first egg, LR, longest clutch until 52 week of age, first week when the longest clutch starts, last week when the longest clutch ends, number of clutches, and longest number of days without egg-laying until 52 week of age, we identified single nucleotide polymorphisms (SNPs) and potential candidate genes associated with clutch traits in Laiwu Black chickens. The restricted maximum likelihood method was used to estimate genetic parameters of clutch pattern in 399 Laiwu Black hens, using the GCTA software.

RESULTS

The results showed that SNP-based heritability estimates of clutch traits ranged from 0.06 to 0.59. Genotyping data were obtained from whole genome re-sequencing data. After quality control, a total of 10,810,544 SNPs remained to be analyzed. The GWAS revealed that 421 significant SNPs responsible for clutch traits were scattered on chicken chromosomes 1-14, 17-19, 21-25, 28 and Z. Among the annotated genes, NELL2, SMYD9, SPTLC2, SMYD3 and PLCL1 were the most promising candidates for clutch traits in Laiwu Black chickens.

CONCLUSION

The findings of this research provide critical insight into the genetic basis of clutch traits. These results contribute to the identification of candidate genes and variants. Genes and SNPs potentially provide new avenues for further research and would help to establish a framework for new methods of genomic prediction, and increase the accuracy of estimated genetic merit for egg production and clutch traits.

Interacting Networks of the Hypothalamic-Pituitary-Ovarian Axis Regulate Layer Hens Performance

Egg production is a vital biological and economic trait for poultry breeding. The 'hypothalamic-pituitary-ovarian (HPO) axis' determines the egg production, which affects the layer hens industry income. At the organism level, the HPO axis is influenced by the factors related to metabolic and nutritional status, environment, and genetics, whereas at the cellular and molecular levels, the HPO axis is influenced by the factors related to endocrine and metabolic regulation, cytokines, key genes, signaling pathways, post-transcriptional processing, and epigenetic modifications. MiRNAs and lncRNAs play a critical role in follicle selection and development, atresia, and ovulation in layer hens; in particular, miRNA is known to affect the development and atresia of follicles by regulating apoptosis and autophagy of granulosa cells. The current review elaborates on the regulation of the HPO axis and its role in the laying performance of hens at the organism, cellular, and molecular levels. In addition, this review provides an overview of the interactive network regulation mechanism of the HPO axis in layer hens, as well as comprehensive knowledge for successfully utilizing their genetic resources.

Genomic signatures of 60 years of bidirectional selection for 8-week body weight in chickens

Sixty years, constituting 60 generations, have passed since the founding of the Virginia body weight lines, an experimental population of White Plymouth Rock chickens. Using a stringent breeding scheme for divergent 8-week body weight, the lines, which originated from a common founder population, have responded to bidirectional selection with an approximate 15-fold difference in the selected trait. They provide a model system to study the genetics of complex traits in general and the influences of artificial selection on quantitative genetic architectures in particular. As we reflect on the 60th anniversary of the initiation of the Virginia body weight lines, there is opportunity to discuss the findings obtained using different analytical and experimental genetic and genomic strategies and integrate them with a recent pooled genome resequencing dataset. Hundreds of regions across the genome show differentiation between the 2 lines, reinforcing previous findings that response to selection relied on standing variation across many genes and giving insights into the haplotype complexity underlying regions associated with body weight.

Correlated responses to long-term divergent selection for 8-week body weight in female White Plymouth Rock chickens: Sexual maturity

Reported here are correlated responses for reproductive traits to long-term divergent selection (54 generations) for 8-week body weight (BW8). Comparisons involved both selected and relaxed lines. Traits measured were age at first egg (AFE), body weight at first egg (WFE), and ratio of body weight and age at first egg (WAFE). Although sexual maturity was delayed in the selected lines, the effect was more pronounced in the low than high selected and relaxed lines. Selection for low BW resulted in decreases in WFE and WAFE. Correlated responses to selection for high BW were increased WFE and WAFE. Minimum AFE, WFE, and WAFE in relation to sexual maturity were line specific and influenced by selection for BW8. WAFE provided a "yardstick" for target body weights that were optimum for successful attainment of sexual maturity and higher reproductive rates. Such may be line specific. There was opposition between relaxed and artificial selection, resulting in a higher reproductive performance and fitness for the former.

Detection of genomic signatures of recent selection in commercial broiler chickens

Background

Identification of the genomic signatures of recent selection may help uncover causal polymorphisms controlling traits relevant to recent decades of selective breeding in livestock. In this study, we aimed at detecting signatures of recent selection in commercial broiler chickens using genotype information from single nucleotide polymorphisms (SNPs). A total of 565 chickens from five commercial purebred lines, including three broiler sire (male) lines and two broiler dam (female) lines, were genotyped using the 60K SNP Illumina iSelect chicken array. To detect genomic signatures of recent selection, we applied two methods based on population comparison, cross-population extended haplotype homozygosity (XP-EHH) and cross-population composite likelihood ratio (XP-CLR), and further analyzed the results to find genomic regions under recent selection in multiple purebred lines.

Results

A total of 321 candidate selection regions spanning approximately 1.45 % of the chicken genome in each line were detected by consensus of results of both XP-EHH and XP-CLR methods. To minimize false discovery due to genetic drift, only 42 of the candidate selection regions that were shared by 2 or more purebred lines were considered as high-confidence selection regions in the study. Of these 42 regions, 20 were 50 kb or less while 4 regions were larger than 0.5 Mb. In total, 91 genes could be found in the 42 regions, among which 19 regions contained only 1 or 2 genes, and 9 regions were located at gene deserts.

Conclusions

Our results provide a genome-wide scan of recent selection signatures in five purebred lines of commercial broiler chickens. We found several candidate genes for recent selection in multiple lines, such as SOX6 (Sex Determining Region Y-Box 6) and cTR (Thyroid hormone receptor beta). These genes may have been under recent selection due to their essential roles in growth, development and reproduction in chickens. Furthermore, our results suggest that in some candidate regions, the same or opposite alleles have been under recent selection in multiple lines. Most of the candidate genes in the selection regions are novel, and as such they should be of great interest for future research into the genetic architecture of traits relevant to modern broiler breeding.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-016-0430-1) contains supplementary material, which is available to authorized users.

Selection for divergent body size alters rates of embryonic skeletal muscle formation and muscle gene expression patterns

The impact of divergent selection for body size on embryogenesis is poorly understood. The objective of this experiment was to document skeletal muscle development during embryogenesis in two lines of chickens that display divergent growth as adults. Results reveal that after 54 generations of opposing selection from a common founder population, the embryos from the low weight select (LWS) line develop more rapidly during early embryogenesis than those from the high weight select (HWS) line. Muscle formation during the late embryonic period is more rapid and extensive in the HWS embryo than in the LWS contemporary. Isolated muscle progenitors from embryonic day 10 HWS embryos proliferated more rapidly, forming fibers sooner with a larger size than the LWS cells. The limited myogenic capacity of the LWS progenitor cells is not attributed to altered patterns of expression of Pax7, Pax3 or the myogenic regulatory factor genes. Members of the fibroblast growth factor family are potent mitogens and inhibitors of myoblast differentiation. Transcript abundance of FGF2 and FGF4 was measured in cultures of HWS and LWS progenitors as a function of time. The pattern of expression of FGF4 was similar between HWS and LWS with a large increase between days 1 and 3 followed by a reduction at day 5 of culture. Expression of FGF2 in LWS muscle cells did not change while a significant reduction in FGF2 expression was observed by day 5 in the HWS. Our results indicate that divergent selection for postnatal growth has altered embryonic development.

Effects of Long-term Graded L-arginine Supply on Growth Development, Egg Laying and Egg Quality in Four Genetically Diverse Purebred Layer Lines

The present study was conducted to examine effects of long-term graded L-arginine supply on growth development, egg laying and egg quality in four genetically diverse purebred layer lines. The study comprised a rearing trial from hatch to week 16 and a following laying performance trial from week 17 to 41. After hatch 150 one-day-old female chicks of each genotype were distributed to three diets. The experimental diets were equivalent to 70, 100 and 200% L-arginine of age-specific recommended level (National Research Council, 1994) and were offered ad libitum to chicks (hatch to week 7), pullets (week 8 to 16) and hens (week 17 to 41). However, hens' diets were quite low in crude protein. After a pre-laying period from week 17 to 21 thirty-six pullets of each group were used further in the laying performance trial. Independent of chicken's genetic background, insufficient L-arginine supply caused lower body weight, daily weight gain and daily feed intake during the rearing (p<0.001) and induced lower laying intensity and daily egg mass production in the laying period (p<0.05). Parameters fitted to Gompertz function suggested higher adult body weight in L-arginine supplemented birds compared to insufficient supplied ones (p<0.01). Groups fed with insufficient L-arginine reached age of maximum daily weight gain later and showed lowest maximum daily weight gain (p<0.001). As a consequence of limitations in dietary L-arginine and crude protein, high performing genotypes decreased strongly in body weight, daily feed intake and performance compared to the low performing genotypes. In conclusion, L-arginine modified the amount of weight gain and feed intake, especially in growing chicks and pullets independent of genetic background. The high performing hens were more nutritionally stressed than the low performing ones, because concentrations of dietary crude protein were relatively low.

The relationship between feed efficiency traits and fertility in young beef bulls

Awda, B. J., Miller, S. P., Montanholi, Y. R., Vander Voort, G., Caldwell, T., Buhr, M. M. and Swanson, K. C. 2013. The relationship between feed efficiency traits and fertility in young beef bulls. Can. J. Anim. Sci. 93: 185–192. Great efforts have been taken in recent years for improving feed efficiency in beef cattle. Despite there being several studies on biological factors associated with this trait, little is known about the potential relationships between fertility and feed efficiency in beef cattle. The objective of this study was to examine the relationship between feed efficiency traits and bull fertility traits [sperm motility, viability and scrotal circumference (SC)]. From a total of 328 crossbred beef bulls that were subjected to a performance test (112 d in each of 6 yr), SC was measured and semen collected from 110 bulls using the electroejaculation method (average age±SE=417±2.5 d). Sperm were extended, cooled, and frozen in liquid nitrogen. Two residual feed intake (RFI) measures were considered with different prediction models for dry matter intake (DMI), RFIKoch included size and growth rate and RFIbkft included the additional adjustment for backfat thickness (BKFT). Sperm viability, motility and progressive motility of the 10 bulls with the greatest RFIKoch (Hi-RFIKoch) were greater than those of the 10 bulls with the lowest RFIKoch (Lo-RFIKoch; P<0.05, 0.01, and 0.05, respectively). Sperm motility (P<0.01), progressive motility and SC (P<0.05) of the 10 bulls with the greatest RFIbkft (Hi-RFIbkft) were greater than those of the 10 bulls with the lowest RFIbkft (Lo-RFIbkft). In summary, these data indicate that young beef bulls with greater feed efficiency have decreased sperm motility, sperm viability and SC, which is an undesirable effect of selection for improved feed efficiency that needs to be addressed through multiple trait selection.

The GTPase activating Rap/RanGAP domain-like 1 gene is associated with chicken reproductive traits

Background

Abundant evidence indicates that chicken reproduction is strictly regulated by the hypothalamic-pituitary-gonad (HPG) axis, and the genes included in the HPG axis have been studied extensively. However, the question remains as to whether any other genes outside of the HPG system are involved in regulating chicken reproduction. The present study was aimed to identify, on a genome-wide level, novel genes associated with chicken reproductive traits.

Methodology/Principal Finding

Suppressive subtractive hybridization (SSH), genome-wide association study (GWAS), and gene-centric GWAS were used to identify novel genes underlying chicken reproduction. Single marker-trait association analysis with a large population and allelic frequency spectrum analysis were used to confirm the effects of candidate genes. Using two full-sib Ningdu Sanhuang (NDH) chickens, GARNL1 was identified as a candidate gene involved in chicken broodiness by SSH analysis. Its expression levels in the hypothalamus and pituitary were significantly higher in brooding chickens than in non-brooding chickens. GWAS analysis with a NDH two tail sample showed that 2802 SNPs were significantly associated with egg number at 300 d of age (EN300). Among the 2802 SNPs, 2 SNPs composed a block overlapping the GARNL1 gene. The gene-centric GWAS analysis with another two tail sample of NDH showed that GARNL1 was strongly associated with EN300 and age at first egg (AFE). Single marker-trait association analysis in 1301 female NDH chickens confirmed that variation in this gene was related to EN300 and AFE. The allelic frequency spectrum of the SNP rs15700989 among 5 different populations supported the above associations. Western blotting, RT-PCR, and qPCR were used to analyze alternative splicing of the GARNL1 gene. RT-PCR detected 5 transcripts and revealed that the transcript, which has a 141 bp insertion, was expressed in a tissue-specific manner.

Conclusions/Significance

Our findings demonstrate that the GARNL1 gene contributes to chicken reproductive traits.

Gene expression of nutrient transporters in the small intestine of chickens from lines divergently selected for high or low juvenile body weight

Nutrient transporters in the small intestine are responsible for dietary nutrient assimilation; therefore, the expression of these transporters can influence overall nutrient status as well as the growth and development of the animal. This study examined correlated responses to selection in the developmental gene expression of PepT1, EAAT3, SGLT1, and GLUT5 in the small intestine of chickens from lines divergently selected for 48 generations for high (HH) or low (LL) 56-d BW and their reciprocal crosses (HL and LH). Duodenum, jejunum, and ileum were collected from male and female chicks on embryonic d 20, day of hatch with no access to feed, and d 3, 7, and 14 posthatch. Total RNA was extracted, and nutrient transporter expression was assayed by real-time PCR using the relative quantification method. In comparing male and female HH and LL chicks, there was a mating combination x age x sex interaction for PepT1 expression (P < 0.001), a main effect of sex for EAAT3 (P < 0.05) and SGLT1 (P < 0.001) expression, and an age x sex interaction for SGLT1 expression (P < 0.001). These results demonstrate a sexual dimorphism in the capacity to absorb nutrients from the intestine, which has implications for the poultry industry with regard to diet formulations for straight-run and sex-separate grow-out operations. Results from comparing male LL, LH, HL, and HH chicks indicate that selection for high or low juvenile BW may have influenced the gene expression profiles of these nutrient transporters in the small intestine, which may contribute to the overall differences in the growth and development of these lines of chickens.

Phenotypic evolution from genetic polymorphisms in a radial network architecture

Background

The genetic architecture of a quantitative trait influences the phenotypic response to natural or artificial selection. One of the main objectives of genetic mapping studies is to identify the genetic factors underlying complex traits and understand how they contribute to phenotypic expression. Presently, we are good at identifying and locating individual loci with large effects, but there is a void in describing more complex genetic architectures. Although large networks of connected genes have been reported, there is an almost complete lack of information on how polymorphisms in these networks contribute to phenotypic variation and change. To date, most of our understanding comes from theoretical, model-based studies, and it remains difficult to assess how realistic their conclusions are as they lack empirical support.

Results

A previous study provided evidence that nearly half of the difference in eight-week body weight between two divergently selected lines of chickens was a result of four loci organized in a 'radial' network (one central locus interacting with three 'radial' loci that, in turn, only interacted with the central locus). Here, we study the relationship between phenotypic change and genetic polymorphism in this empirically detected network. We use a model-free approach to study, through individual-based simulations, the dynamic properties of this polymorphic and epistatic genetic architecture. The study provides new insights to how epistasis can modify the selection response, buffer and reveal effects of major loci leading to a progressive release of genetic variation. We also illustrate the difficulty of predicting genetic architecture from observed selection response, and discuss mechanisms that might lead to misleading conclusions on underlying genetic architectures from quantitative trait locus (QTL) experiments in selected populations.

Conclusion

Considering both molecular (QTL) and phenotypic (selection response) data, as suggested in this work, provides additional insights into the genetic mechanisms involved in the response to selection. Such dissection of genetic architectures and in-depth studies of their ability to contribute to short- or long-term selection response represents an important step towards a better understanding of the genetic bases of complex traits and, consequently, of the evolutionary properties of populations.

Heritabilities and genetic correlations of economic traits in Iranian native fowl and estimated genetic trend and inbreeding coefficients

1. Genetic parameters were estimated in a base population of a closed experimental strain of fowl. Data were obtained on 21 245 Iranian native hens (breeding centre for Fars province) subject to 8 successive generations of selection. This population had been selected for body weight at 12 weeks of age (BW12) and egg number during the first 12 weeks of the laying period (EN), mean egg weight (EW) at weeks 28, 30 and 32, and age at sexual maturity (ASM). 2. The method of multi-traits restricted maximum likelihood with an animal model was used to estimate genetic parameters. Resulting heritabilities for BW12, EN, EW and ASM were 0.68 +/- 0.02, 0.40 +/- 0.02, 0.64 +/- 0.02 and 0.49 +/- 0.02, respectively. 3. Genetic correlations between BW12 and EN, EW and ASM were 0.11 +/- 0.33, 0.54 +/- 0.21 and -0.12 +/- 0.03, respectively. Genetic correlations between EN and EW and ASM were -0.09 +/- 0.03 and -0.85 +/- 0.01, respectively, while between EW and ASM, it was 0.05 +/- 0.03. 4. The overall predicted genetic gains, after 7 generations of selection, estimated by the regression coefficients of the breeding value on generation number were equal to 22.7, 0.17, 0.04 and -1.38, for BW12, EN, EW and ASM, respectively. 5. A pedigree file of 21 245 female and male birds was used to calculate inbreeding coefficients and their influence on production and reproduction traits. Average inbreeding coefficients for all birds, inbred birds, female birds and male birds were 0.048, 0.673, 0.055 and 0.047%, respectively. Regression coefficients of BW12, ASM, EN and EW on inbreeding coefficient for all birds were equal to 0.51 +/- 0.001, 0.31 +/- 0.003, -0.51 +/- 0.003 and 0.03 +/- 0.001, respectively.

Variance components for live weight, body measurements and reproductive traits of pair-mated ostrich females

Estimates of genetic parameters for reproductive traits, live weight and body measurements were obtained using data from a pair-mated ostrich flock at Oudtshoorn in South Africa. Reproductive traits included total egg and chick production, along with hatchability percentage. Live weight, chest circumference and tail circumferences were recorded at the commencement and cessation of breeding. Heritability estimates (h(2)) were 0.23 for egg production, 0.20 for chick production, 0.10 for hatchability, 0.20 to 0.34 for live weight, 0.12 for chest circumference and 0.30 to 0.38 for tail circumference. Female permanent environmental effects (c(2)) amounted to 0.18 for egg production, 0.18 for chick production, 0.21 for hatchability, 0.32 to 0.36 for live weight and 0.23 to 0.32 for chest circumference. Service sire exerted significant effects only on hatchability (0.22) and subsequently chick production (0.09). Genetic correlations of reproductive traits with live weight were low to moderate, variable in sign, and did not differ significantly from zero. Correlations between live weight recorded at the beginning and end of the breeding season were unity for additive genetic and permanent environmental effects. Egg and chick production were highly correlated genetically and phenotypically, with the genetic correlation exceeding the theoretical limit. In unconstrained analyses, hatchability was positively related to chick production, including at the service sire level. Selection gains in the current flock and future generations are likely. No significant adverse relationships were found between live weight, body measurements and reproductive traits.

Influence of genetic selection for antibody production against sheep blood cells on energy metabolism in laying hens

Genetic selection in chickens has been utilized to enhance immune responses that may influence resistance to diseases. It is important, however, to investigate the effects of this selection on other physiological processes. Therefore, this study was conducted to determine whether selection for antibody (Ab) production against SRBC has an effect on energy metabolism. Laying hens from three lines were used in this study, two of which were selected for 15 generations for Ab response against SRBC, and the third was nonselected and randombred. The hens used were from four different groups. The first two groups were from the lines that were selected for either high (SH) or low (SL) Ab production. The second two groups were control birds (nonselected) that had either high (CH) or low (CL) Ab titers that were similar to those in the SH and SL lines, respectively. The birds were housed in climate-respiration chambers. Body weights and energy metabolism were measured. Body weights of SL hens were significantly (P < 0.05) higher than those of SH hens. However, the BW for the two nonselected groups were similar but significantly less than the SL group. Energy partitioning was similar in all groups; however, ME for maintenance for the selected groups (119 kcal x kg(-0.75 x d(-1)) was numerically, but not significantly (P < 0.09), higher than that of the nonselected groups (112 kcal x kg(-0.75) x d(-1)). These results suggest that divergent selection for Ab may result in an increase in the requirements of energy for maintenance, which is not directly related to the amount of Ab produced. Furthermore, these results support previous findings of the presence of a negative correlation between BW and the levels of Ab in selected lines.

Hematocrit values in weight-selected and relaxed lines of White Rock chickens

Hematocrits (PCV) were measured at 29 and 106 d of age (PCV1 and PCV2, respectively) in male and female White Plymouth Rocks. Four lines were used, two of which had undergone 40 generations of divergent selection for 8-wk BW (HWS, LWS), and two respective sublines (HWR, LWR), in which selection had been relaxed for five generations. At both ages, males and females did not differ for PCV in lines HWR, LWR, and LWS. For line HWS there was an age by sex interaction that resulted from an age effect for males but not for females, and from a sex effect at each age. At both ages, PCV was higher for the HW than the LW lines. Initially, there was no difference between the selected and their respective relaxed lines, but by 106 d, HWR chickens had a higher PCV than HWS chickens. In lines HWR and LWR, PCV increased with age. There was a negative correlation in HWS males for PCV1 with 28 and 56 d BW. The HWR males also had a negative correlation for PCV1 with BW at 28 d, but not between PCV2 and BW. The correlation for PCV1 with PCV2 was high and positive for HWR males and females.

Long-term divergent selection for eight-week body weight in white Plymouth rock chickens

This paper provides an overview of results from a long-term (38 generations) selection experiment. Lines were developed from individual phenotypic selection for high or low body weight at 8 wk of age. Included are data for the selected lines, sublines in which selection was relaxed, crosses of the selected lines, and sublines in which the sex-linked dw gene was introduced. Periodically (and in some cases every generation) data were obtained for unselected traits. These unselected traits included feed consumption and intake behavior, reproduction, allomorphic relationships, and metabolic, immunological, endocrine, and molecular factors. These responses have been integrated into a resource allocation paradigm.