Genetic variability of the cytosolic phosphoenolpyruvate carboxykinase gene in white leghorn chickens

Transcriptome assembly and identification of genes and SNPs associated with growth traits in largemouth bass (Micropterus salmoides)

Growth is one of the most crucial economic traits of all aquaculture species, but the molecular mechanisms involved in growth of largemouth bass (Micropterus salmoides) are poorly understood. The objective of this study was to screen growth-related genes of M. salmoides by RNA sequencing and identify growth-related single-nucleotide polymorphism (SNP) markers through a growth association study. The muscle transcriptomes of fast- and slow-growing largemouth bass were obtained using the RNA-Seq technique. A total of 54,058,178 and 54,742,444 qualified Illumina read pairs were obtained for the fast-growing and slow-growing groups, respectively, giving rise to 4,865,236,020 and 4,926,819,960 total clean bases, respectively. Gene expression profiling showed that 3,530 unigenes were differentially expressed between the fast-growing and slow-growing phenotypes (false discovery rate ≤0.001, the absolute value of log₂ (fold change) ≥1), including 1,441 up-regulated and 2,889 down-regulated unigenes in the fast-growing largemouth bass. Analysis of these genes revealed that several signalling pathways, including the growth hormone-insulin-like growth factor 1 axis and signalling pathway, the glycolysis pathway, and the myostatin/transforming growth factor beta signalling pathway, as well as heat shock protein, cytoskeleton, and myofibril component genes might be associated with muscle growth. From these genes, 10 genes with putative SNPs were selected, and 17 SNPs were genotyped successfully. Marker-trait analysis in 340 individuals of Youlu No. 1 largemouth bass revealed three SNPs associated with growth in key genes (phosphoenolpyruvate carboxykinase 1, FOXO3b, and heat shock protein beta-1). This research provides information about key genes and SNPs related to growth, providing new clues to understanding the molecular basis of largemouth bass growth.

Restriction fragment length and single strand conformational polymorphisms in chicken mitochondrial phosphoenol-pyruate carboxykinase gene and its association with egg production

This study analysed mitochondrial phosphoenol-pyruate carboxykinase (PEPCK-M) gene as a candidate QTL for egg production traits in chickens. Single Strand Conformational Polymorphism (SSCP) of a 300 bp DNA fragment, from exon 9 of samples from an egg laying North American commercial White Leghorn stock, revealed a total of 6 different single strand conformers, indicative of 3 alleles. Subsequent DNA sequencing found a total of 4 base changes in this fragment between these alleles (called A1, A2 and A3) when compared to the reference sequence published online. The A1 allele had one transition mutation of T to C at position 1700. The A2 allele had accumulated three transition mutations: T to C at position 1578, A to G at position 1647 and T to C at position 1650. Transition mutation of T to C at position 1578 of the A2 allele results in the loss of an AccI site, hence, producing a de novo RFLP. Analysis of 358 female individuals from this strain showed that the population is highly polymorphic at this site. The effect of PEPCK-M genotypes at this site, namely AccI -/-, AccI +/- and AccI +/+, was tested on three traits, age at first egg, egg production rate and egg number. Least square analysis showed that exon 9 RFLP significantly affects age at first egg (p < 0.05). Egg production rate and egg number traits were not affected by different genotypes at this position. The data also indicates an over-dominance effect for the associated trait.

High Diversity of the Chicken Growth Hormone Gene and Effects on Growth and Carcass Traits

The chicken growth hormone (cGH) gene plays a crucial role in controlling growth and metabolism, leading to potential correlations between cGH polymorphisms and economic traits. In this study, DNA from four divergent chicken breeds were screened for single nucleotide polymorphisms (SNPs) in the cGH gene using denaturing high-performance liquid chromatography and sequencing. A total of 46 SNPs were identified, of which 4 were in the 5' untranslated region, 1 in the 3' untranslated region, 5 in exons (two of which are nonsynonymous), with the remaining 36 in introns. The nucleotide diversity in the cGH gene ( theta = 2.7 x 10(-3)) was higher than that reported for other chicken genes, even within the same breeds. The associations of five of these SNPs and their haplotypes with chicken growth and carcass traits were determined using polymerase chain reaction-restriction fragment length polymorphism analysis in a F2 resource population cross of two of the four chicken breeds (White Recessive Rock and Xinghua). This analysis shows that, among other correlations, G+1705A was significantly associated with body weight at all ages measured, shank length at three of four ages measured, and average daily gain within weeks 0 to 4. Thus, this cGH polymorphism, or another polymorphism that is in linkage disequilibrium with G+1705A, appears to correspond to a significant growth-related quantitative trait locus difference between the two breeds used to construct the resource population.

Reduced variation on the chicken Z chromosome

Understanding the population genetic factors that shape genome variability is pivotal to the design and interpretation of studies using large-scale polymorphism data. We analyzed patterns of polymorphism and divergence at Z-linked and autosomal loci in the domestic chicken (Gallus gallus) to study the influence of mutation, effective population size, selection, and demography on levels of genetic diversity. A total of 14 autosomal introns (8316 bp) and 13 Z-linked introns (6856 bp) were sequenced in 50 chicken chromosomes from 10 highly divergent breeds. Genetic variation was significantly lower at Z-linked than at autosomal loci, with one segregating site every 39 bp at autosomal loci (theta(W) = 5.8 +/- 0.8 x 10(-3)) and one every 156 bp on the Z chromosome (theta(W) = 1.4 +/- 0.4 x 10(-3)). This difference may in part be due to a low male effective population size arising from skewed reproductive success among males, evident both in the wild ancestor-the red jungle fowl-and in poultry breeding. However, this effect cannot entirely explain the observed three- to fourfold reduction in Z chromosome diversity. Selection, in particular selective sweeps, may therefore have had an impact on reducing variation on the Z chromosome, a hypothesis supported by the observation of heterogeneity in diversity levels among loci on the Z chromosome and the lower recombination rate on Z than on autosomes. Selection on sex-linked genes may be particularly important in organisms with female heterogamety since the heritability of sex-linked sexually antagonistic alleles advantageous to males is improved when fathers pass a Z chromosome to their sons.

Ornithine decarboxylase: haplotype structure and trait associations in White Leghorn chickens

Sequence analysis of 4,230 bp of the 3' end of the ornithine decarboxylase gene of 20 chickens from a noninbred White Leghorn strain revealed a total of 62 polymorphisms. Of these 61% were transitions, 24% were transversions, and 16% were deletions or insertions. Despite the high number of polymorphisms, only 3 haplotypes were present among the 40 alleles analyzed. Based on the genetic distances between haplotypes they segregated early during domestication of the chicken. Ornithine decarboxylase is a pivotal enzyme in regulating the synthesis of polyamines, cations that are important regulators of cell division, differentiation, and apoptosis. Variants of ornithine decarboxylase are, therefore, expected to affect many different traits. Association analyses between genotypes and the major egg production traits in female chickens of the same strain revealed significant effects on the onset of sexual maturity, BW at sexual maturity, eggshell thickness (a measure of calcium deposition), and residual feed consumption (a measure of the metabolic rate). Further, comparisons of the genotypes indicated that the 3 haplotypes differ in their phenotypic properties. Our results show that variations in a gene that is ubiquitously expressed in all cells of an organism may nevertheless contribute to distinct phenotypic properties of the organism as a whole.

Alleles of cytosolic phosphoenolpyruvate carboxykinase (PEPCK): trait association and interaction with mitochondrial PEPCK in a strain of White Leghorn chickens

White Leghorn chickens from a nonselected closed population were typed for two RFLP located in the 3' end of the gene coding for cytosolic phosphoenol-pyruvate carboxykinase (PEPCK-C), a major control gene of gluconeogenesis. The two RFLP gave rise to three alleles (or haplotype classes), thus defining six genotypes. Feed efficiency (FE) and residual feed consumption (RFC) varied significantly among the genotypes and indicated that all three haplotypes differed from each other. FE is the ratio between feed consumption and egg mass produced, whereas RFC is the feed consumption after correcting for BW and egg production. There was significant interaction between PEPCK-C genotypes and mitochondrial PEPCK (PEPCK-M) genotypes defined by a single RFLP. The latter enzyme catalyzes the same reaction but is located in the matrix of the mitochondria and is encoded by a different nuclear gene. Interaction was evident from an analysis of the egg weight and egg specific gravity in the early phase of egg laying. It was such that the effect of the variation in one gene depended entirely on the genotype of the second gene. In addition, significant genotypic disequilibria were observed between two of the three alleles of PEPCK-C and between one of these alleles and the two RFLP alleles of PEPCK-M. This finding indicates variations of genes in the gluconeogenesis pathway may affect feed utilization and egg production traits, as well as reproductive fitness.

The dynamics of the genotype-phenotype association

The integrity of an organism is maintained by networks of interacting genes. Such networks predict that genetic variants affect phenotypes in a nonadditive fashion. That is, the effect of an allelic variation in one gene is dependent on the variations in other genes. We summarize the analyses of a series of genes in a White Leghorn strain that support the existence of such gene networks: 1) genes are pleiotropic, 2) genes affect trait correlations, 3) genes affect trait distributions in a nonadditive fashion, 4) genes interact with each other, and 5) genes are at linkage disequilibrium, even when located on different chromosomes. The latter observation indicated that certain gene combinations lead to reduced reproductive fitness. Each candidate genes we analyzed segregated for multiple alleles that affected production traits. This finding was surprising, even for a strain with a large effective population size. The shapes of trait distributions appear to be a better descriptor of gene effects than measures of central tendency. Despite this complexity, it is feasible to conduct DNA-based selection, starting from any of several different genes that affect a trait. Gene networks may be altered in many different ways to improve a particular phenotype, but networks may differ in their effects on other traits.