Delayed somite formation in a quail line exhibiting myofiber hyperplasia is accompanied by delayed expression of myogenic regulatory factors and myosin heavy chain

Genome-wide detection of CNVs and their association with performance traits in broilers

Background

Copy number variations (CNVs) are a major type of structural genomic variants that underlie genetic architecture and phenotypic variation of complex traits, not only in humans, but also in livestock animals. We identified CNVs along the chicken genome and analyzed their association with performance traits. Genome-wide CNVs were inferred from Affymetrix® high density SNP-chip data for a broiler population. CNVs were concatenated into segments and association analyses were performed with linear mixed models considering a genomic relationship matrix, for birth weight, body weight at 21, 35, 41 and 42 days, feed intake from 35 to 41 days, feed conversion ratio from 35 to 41 days and, body weight gain from 35 to 41 days of age.

Results

We identified 23,214 autosomal CNVs, merged into 5042 distinct CNV regions (CNVRs), covering 12.84% of the chicken autosomal genome. One significant CNV segment was associated with BWG on GGA3 (q-value = 0.00443); one significant CNV segment was associated with BW35 (q-value = 0.00571), BW41 (q-value = 0.00180) and BW42 (q-value = 0.00130) on GGA3, and one significant CNV segment was associated with BW on GGA5 (q-value = 0.00432). All significant CNV segments were verified by qPCR, and a validation rate of 92.59% was observed. These CNV segments are located nearby genes, such as KCNJ11, MyoD1 and SOX6, known to underlie growth and development. Moreover, gene-set analyses revealed terms linked with muscle physiology, cellular processes regulation and potassium channels.

Conclusions

Overall, this CNV-based GWAS study unravels potential candidate genes that may regulate performance traits in chickens. Our findings provide a foundation for future functional studies on the role of specific genes in regulating performance in chickens.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07676-1.

Identification of mRNA Degradome Variation Dependent on Divergent Muscle Mass in Different Pig Breeds

The search is still on for the molecular processes associated with the development and metabolism of skeletal muscles. Selection conducted in farm animals is focused on high muscle mass because it delivers higher economic profit. The present study aimed to shed light on mRNA degradome signals that could be characteristic for molecular processes associated with an abundance of muscle mass and to identify miRNA regulatory networks controlling these processes in pigs applying next-generation-sequencing (NGS). In the study, over 10,000 degraded transcripts were identified per sample, with the highest abundance for genes encoding mitochondrial proteins (COXs, NDs, CYTB, ATP6 and ATP8). Moreover, only 26% of the miRNA targets were found within this degraded transcript pool, which suggested for miRNAs other molecular mechanism at different level of gene expression than mRNA degradation. On the other hand, a small share of the identified degraded transcripts associated with miRNA regulation suggests a different mechanism of mRNA degradation for identified degraded transcropts. Subsequently, most of the miRNA gene degraded targets, such as ENO3, CKM, CRYAB and ADAM19 encode proteins involved in the muscle mass control. The present study showed an interesting dependence between miRNAs and their targets. Nevertheless, the complete view of the miRNA regulatory network could be a subject of further advanced research, which would employ a miRNA transfection procedure in skeletal muscle cell cultures.

Expression profiles and associations of muscle regulatory factor (MRF) genes with growth traits in Tibetan chickens

1. Muscle regulatory factors (MRFs), including Myf5, Myf6 (MRF4/herculin), MyoD and MyoG (myogenin), play pivotal roles in muscle growth and development. Therefore, they are considered as candidate genes for meat production traits in livestock and poultry. 2. The objective of this study was to investigate the expression profiles of these genes in skeletal muscles (breast muscle and thigh muscle) at 5 developmental stages (0, 81, 119, 154 and 210 d old) of Tibetan chickens. Relationships between expressions of these genes and growth and carcass traits in these chickens were also estimated. 3. The expression profiles showed that in the breast muscle of both genders the mRNA levels of MRF genes were highest on the day of hatching, then declined significantly from d 0 to d 81, and fluctuated in a certain range from d 81 to d 210. However, the expression of Myf5, Myf6 and MyoG reached peaks in the thigh muscle in 118-d-old females and for MyoD in 154-d-old females, whereas the mRNA amounts of MRF genes in the male thigh muscle were in a narrow range from d 0 to d 210. 4. Correlation analysis suggested that gender had an influence on the relationships of MRF gene expression with growth traits. The RNA levels of MyoD, Myf5 genes in male breast muscle were positively related with several growth traits of Tibetan chickens (P < 0.05). No correlation was found between expressions of MRF genes and carcass traits of the chickens. 5. These results will provide a base for functional studies of MRF genes on growth and development of Tibetan chickens, as well as selective breeding and resource exploration.

Associations of the variation in the porcine myogenin gene with muscle fibre characteristics, lean meat production and meat quality traits

Pig breeding is aimed at improving lean meat production ability as well as meat quality, and muscle fibre characteristics may be important for enhancing these traits. Therefore, new molecular markers have been demanded for selecting lean meat production ability and meat quality in live animals. Myogenin belongs to the MyoD gene family, and is a candidate gene responsible for muscle fibre characteristics. We identified a new single nucleotide polymorphism (SNP) site in the 5' upstream region of the myogenin gene (nucleotides C and T). A total of 252 pigs of three breeds were genotyped by polymerase chain reaction-restriction fragment length polymorphism using BspCNI. Additionally, they were genotyped for the previously detected MspI site in the 3'-flanking region (alleles A and B). The CCBB diplotype had the highest frequency over breeds, followed by TCBB and CCAB. The other diplotypes were not found in studied pigs. Association analysis performed for the markers found that the TCBB diplotype has desirable effects on the total number of fibres (p < 0.002), fibre cross-sectional area (p < 0.06), and loin eye area (p < 0.001) than the other diplotypes. Moreover, the diplotype had the highest muscle pH value (p < 0.07) and all meat quality traits were near the upper limit of the normal range as a reddish pink, firm and non-exudative (RFN) pork. Therefore, we suggest that selection for the myogenin diplotypes could improve total muscle fibre number, size and lean meat production ability with good meat quality.

Polymorphisms in coding and regulatory regions of the porcineMYF6 andMYOG genes and expression of theMYF6 gene inm. longissimus dorsi versus productive traits in pigs

MYOG and MYF6 belong to the MyoD gene family. They code for the bHLH transcription factors playing a key role in later stages of myogenesis: differentiation and maturation of myotubes. Three SNPs in porcine MYF6 and two in porcine MYOG were analysed in order to establish associations with chosen carcass quality and growth rate traits in Polish Landrace, Polish Large White and line 990 sows. No statistically significant effect of SNP in the promoter region of the MYF6 gene on its expression measured on mRNA level was found. Associations between the genotype at the MYF6 locus and carcass quality traits appeared to be breed-dependent. The C allele in the case of SNP in the promoter region and GC haplotype in exon 1 were advantageous for right carcass side weight in Polish Landrace sows and disadvantageous for this trait in Polish Large White sows. These gene variants were also the most advantageous for loin and ham weight in sows of line 990. The mutation in exon 1 of the MYOG gene had no statistically significant association with carcass quality traits and the mutation in the 3'-flanking region had the breed-dependent effect as well. These results suggest that SNPs analysed in this study are not causative mutations, but can be considered as markers of some other, still unrevealed genetic polymorphism that influences the physiological processes and phenotypic traits considered in this study.

A comparative study of embryonic development of Japanese quail selected for different patterns of postnatal growth

Patterns of early embryonic development have traditionally been viewed as invariant within vertebrate taxa. It has been argued that the specific differences which are found arise during the later stages of development. These differences may be a result of allometry, heterochrony or changes in relative growth rates. To test whether early embryonic development is indeed invariant, or whether selection of adult characteristics can alter embryonic growth, we compared embryonic development in birds selected for different patterns of postnatal growth. Using quail lines selected for high and low body mass, we compared somite formation, and muscle and feather development. We obtained data that showed changes in the rate of myotome formation in the brachial somites which contribute to muscle formation in the limbs and thorax. We think these observations are connected with intraspecific changes in adult morphology, ie., breast muscle size. Our findings suggest that selection for late ontogenetic/adult stages affects early embryonic development.

Comparison of prenatal muscle tissue expression profiles of two pig breeds differing in muscle characteristics1

The objective of this study was to compare purebred Duroc and Pietrain prenatal muscle tissue transcriptome expression levels at different stages of prenatal development to gain insight into the differences in muscle tissue development in these pig breeds. Commercial western pig breeds have been selected for muscle growth for the past 2 decades. Pig breeds differ for their muscle phenotypes (i.e., myofiber numbers and myofiber types). Duroc and Pietrain pig breeds are extremes; Duroc pigs have redder muscle fiber types with more intramuscular fat, and Pietrain pigs have faster-growing and whiter muscle fiber types. Pietrain pigs are more muscular than Duroc pigs, whereas Duroc pigs are fatter than Pietrain pigs. The genomic background underlying these breed-specific differences is poorly known. Myogenesis is a complex exclusive prenatal process involving proliferation and differentiation (i.e., fusion) of precursor cells called myoblasts. We investigated the difference in the prenatal muscle-specific transcriptome profiles of Duroc and Pietrain pigs using microarray technology. The microarray contained more than 500 genes affecting myogenesis, energy metabolism, muscle structural genes, and other genes from a porcine muscle cDNA library. The results indicated that the expression of the myogenesis-related genes was greater in early Duroc embryos than in early Pietrain embryos (14 to 49 d of gestation), whereas the opposite was found in late embryos (63 to 91 d of gestation). These findings suggest that the myogenesis process is more intense in early Duroc embryos than in Pietrain embryos but that myogenesis is more intense in late Pietrain fetuses than in Duroc fetuses. Transcriptomes of muscle structural genes followed that pattern. The energy metabolism genes were expressed at a higher level in prenatal Pietrain pigs than in prenatal Duroc pigs, except for d 35, when the opposite situation was found. Fatty acid metabolism genes were expressed at a higher level in early (14 to 49 d of gestation) Duroc embryos than in Pietrain embryos. Better understanding of the genomic regulation of tissue formation leads to improved knowledge of the genome under selection and may lead to directed breed-specific changes in the future.

Transcriptome expression profiles in prenatal pigs in relation to myogenesis

Myogenesis, the formation of muscle fibers, is a complex process. Pigs have been selected for efficient muscle growth for the past decades making them interesting to study myogenesis. We studied expression profiles of genes known to affect myogenesis, muscle structural proteins, and energy metabolism in prenatal pigs from 14 to 91 days of gestation. Primary and secondary muscle fiber formation takes place during days 30-60 and 54-90 of gestation, respectively. Differential expression and expression levels of the genes were studied using microarray technology. Gene activation and repression profiles were studied counting the number of spots with detectable signal. The number of spots for muscle tissue structural protein genes showing upregulated expression increased constantly from day 14 until day 91 of gestation indicating continued activation of genes during this period. The mRNA expression level of the genes showed a peak around day 35 of gestation. The expression levels of genes affecting myogenic differentiation (stimulating and inhibiting) showed a peak at day 35 of gestation. The number of spots for differentiation-stimulating genes showing differential expression reaches a first peak around day 35 of gestation and a nadir at day 49 of gestation while the number of spots for differentiation-inhibiting genes reaches a nadir at day 35 of gestation. Myogenic differentiation seems less a matter of the expression level of genes affecting differentiation, but depends on the balance between the number of significantly activated genes for stimulating and inhibiting differentiation. Genes stimulating myoblast proliferation showed a small peak expression prior to day 35 of gestation indicating myoblast proliferation before differentiation. The number of spots and the expression levels of genes for glycolysis and ATP-metabolism are at a nadir around days 35 and 49-63 of gestation suggesting that the energy metabolism is low during fusion of myoblasts into multinucleated muscle fibers.

A comparative study of embryonic development of some bird species with different patterns of postnatal growth

Some studies show that birds with high postnatal growth rates (e.g. altricial species) are characterized by a rapid early development of "supply" organs, such as digestive organs. Birds with low postnatal growth rates (e.g. precocial species) exhibit a slower early development of these organs and a more rapid early development of other "demand" organs, such as brain, muscles, skeleton and feathers. To test whether these differences can be traced back to early embryonic development and whether they can be associated with changes in developmental timing, i.e. heterochrony, we compared embryos of the precocial quail and the altricial fieldfare, two bird species with low and high postnatal growth rates, respectively. We used classical staging techniques that use developmental landmarks to categorize embryonic maturity as well as morphological measurements. These techniques were combined with immune detection of muscle specific proteins in the somites. Our data showed that the anlagen of the head, brain and eyes develop earlier in the quail than in the fieldfare in contrast to the gut which develops earlier in the fieldfare than in the quail. Our data also showed that the quail and the fieldfare displayed different rates of myotome formation in the somites which contribute to muscle formation in the limbs and thorax. We believe these observations are connected with important differences in neonatal characteristics, such as the size of the brain, eyes, organs for locomotion and digestion. This leads us to the conclusion that selection for late ontogenetic characteristics can alter early embryonic development and that growth rate is of fundamental importance for the patterning of avian embryonic development. It also appears that this comparative system offers excellent opportunities to test hypotheses about heterochrony.

Comparison of chicken genotypes: myofiber number in pectoralis muscle and myostatin ontogeny

This study was performed to evaluate breast muscle development in chicken genotypes divergently selected for muscularity. In the first experiment, 2 commercial broiler lines (a high breast yield, HBY, and a normal breast yield broiler strain-cross, NBY) and a Leghorn line were grown up to 35 d to evaluate BW, breast weight, and breast yield. At 7 and 21 d of age, pectoralis muscle was used to estimate myofiber density (MFD, number of myofibers per mm2) and total apparent myofiber number (MFN). In the second experiment, the ontogeny of myostatin was determined from broiler- and Leghorn-type chick embryos, at embryonic days 1 to 20 (E1 to E20), using reverse transcription (RT)-PCR. As expected, the Leghorn line had lower BW, breast weight, and breast yield than broiler lines. The HBY line showed higher breast yield at all ages evaluated, but lower BW at 21 and 35 d than the NBY line. The Leghorn line had 45% higher MFD than broilers, which indicates an increased cross-sectional area of the myofibers in broiler lines. No MFD difference was observed between the broiler strains (P > 0.05). The myofiber number of broilers was more than twice that of Leghorns and HBY had 10% higher MFN than the NBY line. Myofiber number was correlated to BW (r = 0.58), breast weight (r = 0.58), and breast yield (r = 0.69). Conversely, MFD showed negative correlation with BW, breast weight, and breast yield (r = -0.85, -0.83, and -0.88, respectively). No effect of genotype or interaction between genotype and embryonic age was observed for myostatin expression. This study showed that broilers have higher MFN in the breast muscles than Leghorn-type chickens, and that high breast yield of broiler strains may be due to increased MFN. Higher muscularity of broilers, as compared with Leghorns, was not attributed to lower expression of myostatin during embryonic development.

Influence of the neural tube/notochord complex on MyoD expression and cellular proliferation in chicken embryos

Important advances have been made in understanding the genetic processes that control skeletal muscle formation. Studies conducted on quails detected a delay in the myogenic program of animals selected for high growth rates. These studies have led to the hypothesis that a delay in myogenesis would allow somitic cells to proliferate longer and consequently increase the number of embryonic myoblasts. To test this hypothesis, recently segmented somites and part of the unsegmented paraxial mesoderm were separated from the neural tube/notochord complex in HH12 chicken embryos. In situ hybridization and competitive RT-PCR revealed that MyoD transcripts, which are responsible for myoblast determination, were absent in somites separated from neural tube/notochord (1.06 and 0.06 10(-3) attomol MyoD/1 attomol beta-actin for control and separated somites, respectively; P<0.01). However, reapproximation of these structures allowed MyoD to be expressed in somites. Cellular proliferation was analyzed by immunohistochemical detection of incorporated BrdU, a thymidine analogue. A smaller but not significant (P = 0.27) number of proliferating cells was observed in somites that had been separated from neural tube/notochord (27 and 18 for control and separated somites, respectively). These results confirm the influence of the axial structures on MyoD activation but do not support the hypothesis that in the absence of MyoD transcripts the cellular proliferation would be maintained for a longer period of time.

Satellite cell proliferation and differentiation during postnatal growth of porcine skeletal muscle

Age-related changes in satellite cell proliferation and differentiation during rapid growth of porcine skeletal muscle were examined. Satellite cells were isolated from hindlimb muscles of pigs at 1, 7, 14, and 21 wk of age (4 animals/age group). Satellite cells were separated from cellular debris by using Percoll gradient centrifugation and were adsorbed to glass coverslips for fluorescent immunostaining. Positive staining for neural cell adhesion molecule (NCAM) distinguished satellite cells from nonmyogenic cells. The proportion of NCAM-positive cells (satellite cells) in isolates decreased from 1 to 7 wk of age. Greater than 77% of NCAM-positive cells were proliferating cell nuclear antigen positive at all ages studied. Myogenin-positive satellite cells decreased from 30% at 1 wk to 14% at 7 wk of age and remained at constant levels thereafter. These data indicate that a high percentage of satellite cells remain proliferative during rapid postnatal muscle growth. The reduced proportion of myogenin-positive cells during growth may reflect a decrease in the proportion of differentiating satellite cells or accelerated incorporation of myogenin-positive cells into myofibers.

Improvement of hatchability of chicken eggs injected by blastoderm cells

In our first experiment, we studied the effect of injection method of blastoderm cells (BC) into the subgerminal cavity of White Leghorn embryos on hatchability of chicken chimeras. Freshly laid eggs were injected through a hole made in the equatorial plane of the eggshell (Method A). In Method B, eggs were stored pointed end down for 5 to 7 d prior to injection, and a hole was cut in the blunt end of the eggshell. An advantage of Method B was that the early embryonic mortality was reduced (P < or = 0.01) and resulted in higher hatchability (41.0%; 43/105) than Method A (9.8%; 14/143). In the second experiment, we studied chicken hatchabililty as influenced by windowing (no hole, Group 1; hole in the equatorial plane, Group 2; hole in the blunt end of egg, Groups 3 and 4) and egg turning (Groups 1 and 4) or not (Groups 2 and 3) during incubation. The hatchability percentages were as follows: 67.9 (Group 1) 0.0, (Group 2) 23.3, (Group 3), and 56.8 (Group 4). A statistically significant difference (P < or = 0.05) was noted between Group 1 or 4 and the other groups. We found no statistically significant differences in the weight changes (g) but did note certain differences in the egg weight loss (%) among different egg treatments. In the third experiment, we investigated the influence of origins of BC donors: Rhode Island Red (RIR), Barred Plymouth Rock (BPR), and Green-legged Partridgelike (GP) on hatchability of putative and somatic chimera chickens. The hatchability of chimeras was dependent on the adequate assortment of BC of the donor and ranged from 7.4% (RIR) to 56.1% (GP). In the case of BC injection of the GP breed, good hatchability was accompanied by very high percentage (86.9; 20/23) of somatic chimeras.

In situ detection of transcripts of the myogenic factor MyoD in whole chicken embryos

In situ hybridization has provided insights into the molecular basis of skeletal myogenesis during embryonic development. In situ detection of different muscle-specific regulatory factors in whole embryos has been described. Spatial and temporal expression patterns of these factors differed among species. The expression pattern of MyoD in whole chicken embryos was studied via in situ hybridization using a probe obtained by the reverse transcription - polymerase chain reaction (RT-PCR) technique. In newly formed somites (embryos of stage 12), MyoD mRNA transcripts were detected along the anterior to posterior axis of somites immediately adjacent to the neural tube, whereas in mature somites (embryos of stage 24), MyoD transcripts were detected throughout the entire somite. These results indicate that MyoD expression is important for initiating and maintaining the avian myogenic system.

Identification of a novel cardiac-specific transcript critical for cardiac myocyte differentiation

A novel cDNA, pCMF1, which is expressed exclusively and transiently in the myogenic cells of the differentiating chicken heart was isolated and characterized. The full-length cDNA of pCMF1 has one open reading frame encoding 1538 predicted amino acids. While computer analysis predicts the presence of specific structural motifs, the overall sequence of pCMF1 is unique. The pattern of pCMF1 gene expression during heart formation was determined by whole-mount in situ hybridization. pCMF1 is transiently expressed within the myogenic cells of the primitive heart tube from stages 9 to 18 and is not detected in the heart or any other tissue thereafter. A replication-deficient retrovirus was used to mediate pCMF1 antisense expression in cardiogenic mesoderm. These analyses determined that the presence of pCMF1 antisense sequences disrupted myosin heavy chain expression during cardiac mesoderm differentiation. pCMF1 antisense had no effect on myosin heavy chain expression in differentiated cardiac myocytes. These data suggest a potential function for pCMF1 during cardiac myogenesis.

Initiation of cardiac differentiation occurs in the absence of anterior endoderm

Anterior endoderm has been proposed to be a specific inducer of cardiac differentiation in vertebrates (reviewed in Jacobson and Sater, Development 104, 341–359, 1988). The ability of cardiogenic mesoderm to differentiate in a minimal culture system was examined using cardiac-specific gene expression as an assay. Anterior lateral plate mesoderm was explanted from chick embryos with and without associated endoderm at developmental stages from just after gastrulation (stage 4; Hamburger and Hamilton, J. Morph. 88, 49–67, 1951) to just prior to contraction (stage 9). At all stages examined, cardiogenic mesoderm expressed a profile of cardiac-specific mRNAs after two days in minimal medium independent of the presence of endoderm. Our studies indicate that endoderm is necessary for the generation of stable sarcomeric protein expression, organized myofibrils and beating tissue from stage 4–6. Subsequent to this stage, an interaction with anterior endoderm is no longer required. Examination of cardia bifida embryos from which anterior endoderm had been unilaterally removed also showed a stage-dependent effect of endoderm on beating, while cardiac gene expression and heart morphogenesis were unaffected. These results demonstrate that anterior endoderm does not induce or maintain cardiac gene expression, nor is it required for terminal differentiation. Endoderm does appear to be necessary for a short period of time between initiation of cardiac gene expression and the onset of contraction.

Analysis of the in vivo myogenic status of chick somites by desmin expression in vitro

Expression of the muscle specific intermediate filament protein, desmin, is an early marker for chick somitic myogenesis. Somites are transient, paired, mesodermal structures adjacent to the neural tube which are formed very uniformly in a cranial to caudal fashion. The developmental somitic expression of desmin in vivo has been reported previously (Holtzer et al. [1991] "Frontiers in Muscle Research." New York: Elsevier Science, pp 187-207; Borman and Yorde [1994] J. Histochem. Cytochem. 42:265-272). Here we explore the ability of those somitic cells which are desmin negative in vivo to successfully carry out a myogenic program of development in the absence of the surrounding embryonic microenvironment. Somites which are known to be overtly desmin negative in the embryo were explanted and cultured on collagen gels for 4 days. Immuno-detection of desmin identified a population of somites that could support desmin positive cells in vitro as well as a population of somites that could not. The cranially located somites must remain in the embryo for a greater length of time than the caudally positioned somites prior to each being able to express desmin in vitro. In embryos of many ages there is also a population of somites unable to support desmin expression in vitro. The rate at which this ability to support somitic desmin expression in vitro progresses caudally in the embryo is significantly greater than the rate at which somites form. Notably, the detected expression of desmin in somites in vitro is parallel to the rate at which overt expression of desmin in vivo is detected. The implication for these observations with regard to the regulation of somitic myogenesis is discussed.

Expression of the atrial-specific myosin heavy chain AMHC1 and the establishment of anteroposterior polarity in the developing chicken heart

A unique myosin heavy chain cDNA (AMHC1), which is expressed exclusively in the atria of the developing chicken heart, was isolated and used to study the generation of diversified cardiac myocyte cell lineages. The pattern of AMHC1 gene expression during heart formation was determined by whole-mount in situ hybridization. AMHC1 is first activated in the posterior segment of the heart when these myocytes initially differentiate (Hamburger and Hamilton stage 9+). The anterior segment of the heart at this stage does not express AMHC1 although the ventricular myosin heavy chain isoform is strongly expressed beginning at stage 8+. Throughout chicken development, AMHC1 continues to be expressed in the posterior heart tube as it develops into the diversified atria. The early activation of AMHC1 expression in the posterior cardiac myocytes suggests that the heart cells are diversified when they differentiate initially and that the anterior heart progenitors differ from the posterior heart progenitors in their myosin isoform gene expression. The expression domain of AMHC1 can be expanded anteriorly within the heart tube by treating embryos with retinoic acid as the heart primordia fuse. Embryos treated with retinoic acid prior to the initiation of fusion of the heart primordia express AMHC1 throughout the entire heart-forming region and fusion of the heart primordia is inhibited. These data indicate that retinoic acid treatment produces an expansion of the posterior (atrial) domain of the heart and suggests that diversified fates of cardiomyogenic progenitors can be altered.