Identification and developmental expression of a novel embryonic myosin heavy-chain gene in chicken

A survey of functional genomic variation in domesticated chickens

BACKGROUND

Deleterious genetic variation can increase in frequency as a result of mutations, genetic drift, and genetic hitchhiking. Although individual effects are often small, the cumulative effect of deleterious genetic variation can impact population fitness substantially. In this study, we examined the genome of commercial purebred chicken lines for deleterious and functional variations, combining genotype and whole-genome sequence data.

RESULTS

We analysed over 22,000 animals that were genotyped on a 60 K SNP chip from four purebred lines (two white egg and two brown egg layer lines) and two crossbred lines. We identified 79 haplotypes that showed a significant deficit in homozygous carriers. This deficit was assumed to stem from haplotypes that potentially harbour lethal recessive variations. To identify potentially deleterious mutations, a catalogue of over 10 million variants was derived from 250 whole-genome sequenced animals from three purebred white-egg layer lines. Out of 4219 putative deleterious variants, 152 mutations were identified that likely induce embryonic lethality in the homozygous state. Inferred deleterious variation showed evidence of purifying selection and deleterious alleles were generally overrepresented in regions of low recombination. Finally, we found evidence that mutations, which were inferred to be evolutionally intolerant, likely have positive effects in commercial chicken populations.

CONCLUSIONS

We present a comprehensive genomic perspective on deleterious and functional genetic variation in egg layer breeding lines, which are under intensive selection and characterized by a small effective population size. We show that deleterious variation is subject to purifying selection and that there is a positive relationship between recombination rate and purging efficiency. In addition, multiple putative functional coding variants were discovered in selective sweep regions, which are likely under positive selection. Together, this study provides a unique molecular perspective on functional and deleterious variation in commercial egg-laying chickens, which can enhance current genomic breeding practices to lower the frequency of undesirable variants in the population.

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.

Associations of MYH3 gene copy number variations with transcriptional expression and growth traits in Chinese cattle

Copy number variations (CNVs) have been recently recognized as another important genetic variability complementary to single nucleotide polymorphisms (SNPs). Compelling evidence has indicated that CNVs are responsible for phenotypic traits by changing the copy numbers of functional genes. Myosin heavy chain 3 (MYH3) gene is a critical regulatory factor in skeletal muscle development, and has been detected in the CNVs region by comparative genomic hybridization (CGH) array. This study was conducted to validate and detect the distribution of MYH3 copy numbers (relative to Angus cattle) in four Chinese cattle breeds (NY, QC, LX, and CY), and further to investigate the associations of the copy number changes with its transcriptional expression and cattle growth traits. Substantial genetic differences of MYH3 copy numbers were identified between NY and the other three breeds (P<0.01). The copy numbers of MYH3 gene presented the positive correlations with the transcript level of MYH3 gene in both fetal and adult skeletal muscles (P<0.05). Statistical analysis revealed that CNVs of MYH3 gene were significantly associated with growth traits of NY cattle, and the individuals with copy number gain showed better phenotypes than the loss and/or median groups (P<0.05). This study firstly attempted to establish the correlations between CNVs of candidate genes and growth traits, and our results suggested that the CNVs of MYH3 gene may be utilized as the potential markers for economic traits in selection breeding programs of Chinese cattle.

Single nucleotide polymorphisms, haplotypes and combined genotypes in MYH₃ gene and their associations with growth and carcass traits in Qinchuan cattle

MYH₃ is a major contractile protein which converts chemical energy into mechanical energy through the ATP hydrolysis. MYH₃ is mainly expressed in the skeletal muscle in different stages especially embryonic period, and it has a role in the development of skeletal muscle and heart. In this study, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was applied to analyze the genetic variations of the MYH₃ gene and verify the effect on growth and carcass traits in a total of 365 Qinchuan cattles. The PCR product was digested with some restriction enzyme and demonstrated the polymorphism in the population, the single nucleotide polymorphisms (SNPs) at nucleotides g. +1215T>C, g. +3377C>T, and g. +28625C>T were in linkage disequilibrium with each other. The result of haplotype analysis showed that nineteen different haplotypes were identified among the five SNPs. The statistical analyses indicated that the five SNPs were significant association with growth and carcass traits (P < 0.05, N = 365); whereas the five SNPs were no significant association between 18 combined genotypes of MYH₃ gene and growth and carcass traits. Taken together, our results provide the evidence that polymorphisms in MYH₃ are associated with growth and carcass traits in Qinchuan cattle, and may be used as a possible candidate for marker-assisted selection and management in beef cattle breeding program.

Heavy and light roles: myosin in the morphogenesis of the heart

Myosin is an essential component of cardiac muscle, from the onset of cardiogenesis through to the adult heart. Although traditionally known for its role in energy transduction and force development, recent studies suggest that both myosin heavy-chain and myosin light-chain proteins are required for a correctly formed heart. Myosins are structural proteins that are not only expressed from early stages of heart development, but when mutated in humans they may give rise to congenital heart defects. This review will discuss the roles of myosin, specifically with regards to the developing heart. The expression of each myosin protein will be described, and the effects that altering expression has on the heart in embryogenesis in different animal models will be discussed. The human molecular genetics of the myosins will also be reviewed.

Knockdown of embryonic myosin heavy chain reveals an essential role in the morphology and function of the developing heart

The expression and function of embryonic myosin heavy chain (eMYH) has not been investigated within the early developing heart. This is despite the knowledge that other structural proteins, such as alpha and beta myosin heavy chains and cardiac alpha actin, play crucial roles in atrial septal development and cardiac function. Most cases of atrial septal defects and cardiomyopathy are not associated with a known causative gene, suggesting that further analysis into candidate genes is required. Expression studies localised eMYH in the developing chick heart. eMYH knockdown was achieved using morpholinos in a temporal manner and functional studies were carried out using electrical and calcium signalling methodologies. Knockdown in the early embryo led to abnormal atrial septal development and heart enlargement. Intriguingly, action potentials of the eMYH knockdown hearts were abnormal in comparison with the alpha and beta myosin heavy chain knockdowns and controls. Although myofibrillogenesis appeared normal, in knockdown hearts the tissue integrity was affected owing to apparent focal points of myocyte loss and an increase in cell death. An expression profile of human skeletal myosin heavy chain genes suggests that human myosin heavy chain 3 is the functional homologue of the chick eMYH gene. These data provide compelling evidence that eMYH plays a crucial role in important processes in the early developing heart and, hence, is a candidate causative gene for atrial septal defects and cardiomyopathy.

Molecular and cellular mechanisms involved in the generation of fiber diversity during myogenesis

Skeletal muscles have a characteristic proportion and distribution of fiber types, a pattern which is set up early in development. It is becoming clear that different mechanisms produce this pattern during early and late stages of myogenesis. In addition, there are significant differences between the formation of muscles in head and those found in rest of the body. Early fiber type differentiation is dependent upon an interplay between patterning systems which include the Wnt and Hox gene families and different myoblast populations. During later stages, innervation, hormones, and functional demand increasingly act to determine fiber type, but individual muscles still retain an intrinsic commitment to form particular fiber types. Head muscle is the only muscle not derived from the somites and follows a different development pathway which leads to the formation of particular fiber types not found elsewhere. This review discusses the formation of fiber types in both head and other muscles using results from both chick and mammalian systems.

Protein and mRNA analysis of myosin heavy chains in the developing avian pectoralis major muscle

While the existence of post-hatch and adult myosin heavy chain isoforms in the large, avian type IIB pectoralis major muscle has been clearly established, the number and nature of fast myosin heavy chains during in ovo development and the perihatch period have not been resolved. In the present study, developmental fast heavy chain proteins purified by high resolution anion-exchange have been characterized by sequence analysis of a unique CNBr peptide and by complementary mRNA analysis. The four proteins present at 15/16 days in ovo are shown to differ uniquely in primary structure. They correlate with heavy chains II, IV, VI and VII, characterized recently as major or minor species in adult fast muscles using similar methods. These four heavy chains are expressed in a time-dependent fashion from 8 to 16 days in ovo. At the mRNA level, heavy chain VI predominates until 12 days in ovo. Heavy chain IV mRNA is upregulated dramatically at 16 days in ovo preparatory to its protein's predominance in the peri-hatch period. Heavy chains II, IV and V (the post-hatch isoform which replaces heavy chain IV) have major roles in adult fast muscles.

Expression of fast myosin heavy chain transcripts in developing and dystrophic chicken skeletal muscle

The expression of fast myosin heavy chain (MyHC) genes was examined in vivo during fast skeletal muscle development in the inbred White Leghorn chicken (line 03) and in adult muscles from the genetically related dystrophic White Leghorn chicken (line 433). RNA dotblot and northern hybridization was employed to monitor MyHC transcript levels utilizing specific oligonucleotide probes. The developmental pattern of MyHC gene expression in the pectoralis major (PM) and the gastrocnemius muscles was similar during embryonic development with three embryonic MyHC isoform genes, Cemb1, Cemb2, and Cemb3, sequentially expressed. Following hatching, MyHC expression patterns in each muscle differed. The expression of MyHC genes was also studied in muscle cell cultures derived from 12-day embryonic pectoralis muscles. In vitro, Cvent, Cemb1, and Cemb2 MyHC genes were expressed; however, little if any Cemb3 MyHC gene expression could be detected, even though Cemb3 was the predominant MyHC gene expressed during late embryonic development in vivo. In most adult muscles other than the PM and anterior latissimus dorsi (ALD), the Cemb3 MyHC gene was the major adult MyHC isoform. In addition, two general patterns of expression were identified in fast muscle. The fast muscles of the leg expressed neonatal (Cneo) and Cemb3 MyHC genes, while other fast muscles expressed adult (Cadult) and Cemb3 MyHC genes. MyHC gene expression in adult dystrophic muscles was found to reflect the expression patterns found in corresponding normal muscles during the neonatal or early post-hatch developmental period, providing additional evidence that avian muscular dystrophy inhibits muscle maturation.

The evolutionary relationship of avian and mammalian myosin heavy-chain genes

Sequence comparisons of avian and mammalian skeletal and cardiac myosin heavy-chain isoforms are used to examine the evolutionary relationships of sarcomeric myosin multigene families. Mammalian fast-myosin heavy-chain isoforms from different species, with comparable developmental expression, are more similar to each other than they are to other fast isoforms within the same genome. In contrast, the developmentally regulated chicken fast isoforms are more similar to each other than they are to myosin heavy-chain isoforms in other species. Extensive regions of nucleotide identity among the chicken fast myosin heavy chains and in the mouse and rat alpha- and beta-cardiac myosin heavy-chain sequences suggest that gene-conversion-like mechanisms have played a major role in the concerted evolution of these gene families. We also conclude that the chicken fast myosin heavy-chain multigene family has undergone recent expansion subsequent to the divergence of birds and mammals and that both the developmental regulation and the specialization of myosin isoforms have likely developed independently in birds and mammals.

Developmental modulation of myosin expression by thyroid hormone in avian skeletal muscle

It is well established that a rise in circulating thyroid hormone during the second half of chick embryo development significantly influences muscle weight gain and bone growth. We studied thyroid influence on differentiation in slow anterior latissimus dorsi (ALD) and fast posterior latissimus dorsi (PLD) muscles of embryos rendered hypothyroid by hypophysectomy or administration of an anti-thyroid drug. The expression of native myosins and myosin light chains (MLCs) was studied by electrophoretic analysis, and the myosin heavy chain (MHC) was characterized by immunohistochemistry. The first effects of hypothyroid status were observed at day 21 of embryonic development (stage 46 according to Hamburger and Hamilton). Analysis of myosin isoform expression in PLD muscles of hypothyroid embryos showed persistence of slow migrating native myosins and slow MLCs as well as inhibition of neonatal fast MHC expression, indicating retarded differentiation of this muscle. In ALD muscle, hypothyroidism maintained fast embryonic MHC and induced noticeable amounts of fast MLCs, thus delaying slow muscle differentiation. Our results suggest that thyroid hormones play a role in modulating the appearance of neonatal fast MHC and the disappearance of isomyosins transiently present during embryogenesis. However, T3 supplemental treatment would seem to compensate in part for the effects of hypothyroidism induced by hypophysectomy, suggesting that thyroid hormone might interfere with other factors also accounting for the observed effects.

Analysis of the chicken fast myosin heavy chain family. Localization of isoform-specific antibody epitopes and regions of divergence

cDNAs encoding the rod region of four different fast myosin heavy chains (MYCHs) in the chicken were identified, using anti-MYCH monoclonal antibodies, in two expression libraries prepared from 19-day embryonic and adult chicken muscle. These clones were used to determine the amino acid sequences that encompass the epitopes of five anti-MYHC monoclonal antibodies. Additionally, the amino acid sequences were compared to each other and to a full length embryonic MYHC. Although there is extensive homology in the chicken fast myosin rods, sequences within the hinge, within the central portion of the light meromyosin fragment, and at the carboxy terminus exhibit the largest number of amino acid substitutions. We propose that divergence within these subdomains may contribute to isoform-specific properties associated with skeletal myosin rods.

Myoblasts from fetal and adult skeletal muscle regulate myosin expression differently

We compared the expression of myosin heavy chains in myogenic cultures prepared from fetal (embryonic Day 10) and adult (12-16 weeks) chicken pectoralis muscle using immunofluorescence with isoform-specific monoclonal antibodies. We found that the majority of fetal myocytes (differentiated myoblasts) and myotubes coexpressed ventricular and embryonic myosin heavy chains in culture. Also, when fetal cells were plated at a clonal density most clones coexpressed both ventricular and embryonic isoforms. In contrast, all adult myocytes and newly formed adult myotubes expressed just ventricular myosin, whether plated at mass or clonal densities. Within 12-24 hr of the onset of fusion, adult myotubes began to express embryonic myosin as well. Eventually, the majority of adult myotubes coexpressed both ventricular and embryonic myosin. The delay of embryonic myosin expression until after fusion was also seen in passaged adult myoblasts and in myoblasts isolated from regenerating adult muscle. The expression of embryonic myosin can be abolished by inhibiting fusion with EGTA in adult but not in fetal cultures. We conclude that both fetal and adult myotubes express ventricular and embryonic myosins but only fetal myocytes express the embryonic isoform prior to fusion. This difference in the regulation of embryonic myosin expression between fetal and adult myoblasts supports the hypothesis that these cells may represent two distinct populations of myogenic precursors.

Expression of embryonic myosin heavy chain mRNA in stretched adult chicken skeletal muscle

Chronic stretch of the chicken fast-twitch patagialis muscle increases the rate of growth and percentage of fast-twitch oxidative fibers. We have analyzed the effects of stretch on the expression of two previously identified "embryonic" myosin heavy chain (MHC) mRNAs (p251 and p110). Both MHC mRNAs were expressed in the patagialis at their highest levels in the embryo and 1 wk after hatching. During posthatch development (7-52 wk), the p110 mRNA was expressed in only trace quantities while the p251 mRNA was not detectable. After 2 wk of stretch of the patagialis in 7- or 38-wk-old birds, the p110 mRNA was increased to levels similar to that found in patagialis of newly hatched chicks, whereas expression of the p251 transcript was not affected. The existence of two other MHC mRNAs homologous to the p110 mRNA was suggested by the S1 mapping analysis, one of which was expressed at dramatically reduced levels in the stretched patagialis. It is concluded that stretch can cause selective alterations in the expression of developmentally regulated MHC isoforms in chicken fast-twitch muscle.

Effects of electrically induced contractile activity on cultured embryonic chick breast muscle cells

Development of chicken breast muscle is characterized by the sequential appearance of six electrophoretically distinct myosin heavy chain (HC) isoforms. Cultured secondary myotubes, derived from 12-day embryonic chick breast muscle, mainly express the early embryonic HC isoform HCemb/e, normally present in 8-day embryonic breast muscle, and the two fast light chain isoforms LC1f and LC2f. Direct low-frequency (2.5 Hz) stimulation of these myotubes via platinum electrodes leads to a shift in myosin HC expression with increases in the late embryonic HC isoform HCemb/l amounting to 35% of total HC in 19-day-stimulated cultures. Measurements of 35S-methionine incorporation and immunohistochemical analyses demonstrate increases in LC3f. This increase is also seen at the mRNA level. These results indicate that induced contractile activity promotes myotube maturation in vitro. The observation that chronic stimulation enhances the expression of the slow isoform LC2s at the RNA, as well as the protein level, suggests an additional effect consisting of a fast-to-slow change in phenotype expression. In view of the fact that muscle maturation and phenotype expression is under neural control during development in vivo, our results on directly stimulated, aneural myotubes indicate that neurally transmitted contractile activity may be an important factor in modulating phenotype expression of secondary myotubes.

Silkmoth chorion antisense RNA. Structural characterization, developmental regulation and evolutionary conservation

Choriogenic follicular cells of the silkmoth Bombyx mori contain significant quantities of antisense RNA transcribed from chorion genes. Antisense RNA derived from a chorion gene with a high content of cysteine, HcB.12, was characterized in detail. The antisense transcripts are initiated downstream from the 3' end of HcB.12 mRNA and extend over 75% of the length of the gene, comprising its entire second exon and part of its intervening sequence. The antisense RNA is devoid of any significant open reading frames and is not polyadenylated. These features, combined with the presence of specific sequence motifs within its transcribed and upstream region, suggest that antisense RNA may be transcribed by RNA polymerase III. Chorion antisense RNA is detectable only in choriogenic follicular cells and appears to be co-ordinately regulated with chorion mRNA. Its cytoplasmic accumulation during choriogenesis parallels that of the corresponding mRNA. Although chorion mRNA is at least five times more abundant than antisense RNA, the latter is present as a single-stranded entity in follicular cytoplasm but can form perfect duplexes with its mRNA complement upon annealing in vitro. The possible involvement of antisense RNA transcription in the pathway that controls the programmed expression of chorion genes at the level of transcription initiation or post-transcriptional processing is discussed.