Genetic Basis of Aerobically Supported Voluntary Exercise: Results from a Selection Experiment with House Mice

The biological basis of exercise behavior is increasingly relevant for maintaining healthy lifestyles. Various quantitative genetic studies and selection experiments have conclusively demonstrated substantial heritability for exercise behavior in both humans and laboratory rodents. In the "High Runner" selection experiment, four replicate lines of Mus domesticus were bred for high voluntary wheel running (HR), along with four nonselected control (C) lines. After 61 generations, the genomes of 79 mice (9-10 from each line) were fully sequenced and single nucleotide polymorphisms (SNPs) were identified. We used nested ANOVA with MIVQUE estimation and other approaches to compare allele frequencies between the HR and C lines for both SNPs and haplotypes. Approximately 61 genomic regions, across all somatic chromosomes, showed evidence of differentiation; 12 of these regions were differentiated by all methods of analysis. Gene function was inferred largely using Panther gene ontology terms and KO phenotypes associated with genes of interest. Some of the differentiated genes are known to be associated with behavior/motivational systems and/or athletic ability, including Sorl1, Dach1, and Cdh10 Sorl1 is a sorting protein associated with cholinergic neuron morphology, vascular wound healing, and metabolism. Dach1 is associated with limb bud development and neural differentiation. Cdh10 is a calcium ion binding protein associated with phrenic neurons. Overall, these results indicate that selective breeding for high voluntary exercise has resulted in changes in allele frequencies for multiple genes associated with both motivation and ability for endurance exercise, providing candidate genes that may explain phenotypic changes observed in previous studies.

The Evolutionary Fates of a Large Segmental Duplication in Mouse

Gene duplication and loss are major sources of genetic polymorphism in populations, and are important forces shaping the evolution of genome content and organization. We have reconstructed the origin and history of a 127-kbp segmental duplication, R2d, in the house mouse (Mus musculus). R2d contains a single protein-coding gene, Cwc22 De novo assembly of both the ancestral (R2d1) and the derived (R2d2) copies reveals that they have been subject to nonallelic gene conversion events spanning tens of kilobases. R2d2 is also a hotspot for structural variation: its diploid copy number ranges from zero in the mouse reference genome to >80 in wild mice sampled from around the globe. Hemizygosity for high copy-number alleles of R2d2 is associated in cis with meiotic drive; suppression of meiotic crossovers; and copy-number instability, with a mutation rate in excess of 1 per 100 transmissions in some laboratory populations. Our results provide a striking example of allelic diversity generated by duplication and demonstrate the value of de novo assembly in a phylogenetic context for understanding the mutational processes affecting duplicate genes.

R2d2 Drives Selfish Sweeps in the House Mouse

A selective sweep is the result of strong positive selection driving newly occurring or standing genetic variants to fixation, and can dramatically alter the pattern and distribution of allelic diversity in a population. Population-level sequencing data have enabled discoveries of selective sweeps associated with genes involved in recent adaptations in many species. In contrast, much debate but little evidence addresses whether “selfish” genes are capable of fixation—thereby leaving signatures identical to classical selective sweeps—despite being neutral or deleterious to organismal fitness. We previously described R2d2, a large copy-number variant that causes nonrandom segregation of mouse Chromosome 2 in females due to meiotic drive. Here we show population-genetic data consistent with a selfish sweep driven by alleles of R2d2 with high copy number (R2d2^HC) in natural populations. We replicate this finding in multiple closed breeding populations from six outbred backgrounds segregating for R2d2 alleles. We find that R2d2^HC rapidly increases in frequency, and in most cases becomes fixed in significantly fewer generations than can be explained by genetic drift. R2d2^HC is also associated with significantly reduced litter sizes in heterozygous mothers, making it a true selfish allele. Our data provide direct evidence of populations actively undergoing selfish sweeps, and demonstrate that meiotic drive can rapidly alter the genomic landscape in favor of mutations with neutral or even negative effects on overall Darwinian fitness. Further study will reveal the incidence of selfish sweeps, and will elucidate the relative contributions of selfish genes, adaptation and genetic drift to evolution.

A multi-megabase copy number gain causes maternal transmission ratio distortion on mouse chromosome 2

Significant departures from expected Mendelian inheritance ratios (transmission ratio distortion, TRD) are frequently observed in both experimental crosses and natural populations. TRD on mouse Chromosome (Chr) 2 has been reported in multiple experimental crosses, including the Collaborative Cross (CC). Among the eight CC founder inbred strains, we found that Chr 2 TRD was exclusive to females that were heterozygous for the WSB/EiJ allele within a 9.3 Mb region (Chr 2 76.9 - 86.2 Mb). A copy number gain of a 127 kb-long DNA segment (designated as responder to drive, R2d) emerged as the strongest candidate for the causative allele. We mapped R2d sequences to two loci within the candidate interval. R2d1 is located near the proximal boundary, and contains a single copy of R2d in all strains tested. R2d2 maps to a 900 kb interval, and the number of R2d copies varies from zero in classical strains (including the mouse reference genome) to more than 30 in wild-derived strains. Using real-time PCR assays for the copy number, we identified a mutation (R2d2WSBdel1) that eliminates the majority of the R2d2WSB copies without apparent alterations of the surrounding WSB/EiJ haplotype. In a three-generation pedigree segregating for R2d2WSBdel1, the mutation is transmitted to the progeny and Mendelian segregation is restored in females heterozygous for R2d2WSBdel1, thus providing direct evidence that the copy number gain is causal for maternal TRD. We found that transmission ratios in R2d2WSB heterozygous females vary between Mendelian segregation and complete distortion depending on the genetic background, and that TRD is under genetic control of unlinked distorter loci. Although the R2d2WSB transmission ratio was inversely correlated with average litter size, several independent lines of evidence support the contention that female meiotic drive is the cause of the distortion. We discuss the implications and potential applications of this novel meiotic drive system.

Temporal transcriptome analysis of the chicken embryo yolk sac

Background

The yolk sac (YS) is an extra-embryonic tissue that surrounds the yolk and absorbs, digests and transports nutrients during incubation of the avian embryo as well as during early term mammalian embryonic development. Understanding YS functions and development may enhance the efficient transfer of nutrients and optimize embryo development. To identify temporal large-scale patterns of gene expression and gain insights into processes and mechanisms in the YS, we performed a transcriptome study of the YS of chick embryos on embryonic days (E) E13, E15, E17, E19, and E21 (hatch).

Results

3547 genes exhibited a significantly changed expression across days. Clustering and functional annotation of these genes as well as histological sectioning of the YS revealed that we monitored two cell types: the epithelial cells and the erythropoietic cells of the YS. We observed a significant up-regulation of epithelial genes involved in lipid transport and metabolism between E13 and E19. YS epithelial cells expressed a vast array of lipoprotein receptors and fatty acid transporters. Several lysosomal genes (CTSA, PSAP, NPC2) and apolipoproteins genes (apoA1, A2, B, C3) were among the highest expressed, reflecting the intensive digestion and re-synthesis of lipoproteins in YS epithelial cells. Genes associated with cytoskeletal structure were down-regulated between E17 and E21 supporting histological evidence of a degradation of YS epithelial cells towards hatch.

Expression patterns of hemoglobin synthesis genes indicated a high erythropoietic capacity of the YS between E13 and E15, which decreased towards hatch. YS histological sections confirmed these results. We also observed that YS epithelial cells expressed high levels of genes coding for plasma carrier proteins (ALB, AFP, LTF, TTR), normally produced by the liver.

Conclusions

Here we expand current knowledge on developmental, nutritional and molecular processes in the YS. We demonstrate that in the final week of chick embryonic development, the YS plays different roles to support or replace the functions of several organs that have not yet reached their full functional capacity. The YS has a similar functional role as the intestine in digestion and transport of nutrients, the liver in producing plasma carrier proteins and coagulation factors, and the bone marrow in synthesis of blood cells.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-690) contains supplementary material, which is available to authorized users.

The viability and performance under hot conditions of featherless broilers versus fully feathered broilers

Hot conditions decrease the difference between ambient temperature (AT) and the average temperature of the body surface. A smaller difference reduces the rate of sensible heat loss of excessive internal heat, elevates the body temperature (BT), and may lead to mortality during heat waves. Under conditions of chronic heat, broilers avoid lethal BT elevation by reducing their feed intake; consequently, growth rate and meat yield are lower. Practices to avoid hot conditions are costly, whereas breeding for heat tolerance offers a sustainable approach. Being featherless was shown to provide heat tolerance; this was reevaluated in experimental broilers with a growth rate similar to that of contemporary commercial broilers. In experiment 1, 26 featherless birds and 49 feathered siblings (sibs) were reared at warm AT and exposed to moderate and acute heat waves. The featherless birds maintained normal BT under a moderate heat wave, with a slight elevation under an acute heat wave, and only 1 bird died. In contrast, the heat waves led to a significant elevation in BT of the feathered sibs, and 34% of them died. In experiment 2, featherless broilers were compared with feathered sibs and commercial broilers at 2 AT treatments: a constant temperature of 25°C (control AT) or a constant temperature of 35°C (hot AT). The birds were reared to 46 or 53 d at the control and hot AT, respectively, and the measured traits included BT, growth, and weight of the whole body and carcass parts (breast meat, legs, wings, and skin). At the hot AT, only the featherless broilers maintained a normal BT; their mean d 46 BW (2,031g) was significantly higher than that of birds maintained at the control AT, and it increased to 2,400 g on d 53, much higher than the corresponding means of all feathered broilers (approximately 1,700 g only). Featherless broilers had significantly higher breast meat yield (approximately 20% in both AT), lower skin weight, and supposedly better wing quality. These results confirmed that being featherless improved the livability and performance of fast-growing broilers in hot conditions and suggests that introduction of the featherless phenotype into commercial broiler stocks would facilitate highly efficient yet low-cost production of broiler meat under hot conditions.

Yolk sac nutrient composition and fat uptake in late-term embryos in eggs from young and old broiler breeder hens

In the present study, we examined the composition, amount, and uptake of yolk nutrients [fat, protein, water, and carbohydrates (COH)] during incubation of eggs from 30- and 50-wk-old broiler breeder hens. Eggs were sampled at embryonic d 0 (fresh eggs), 13, 15, 17, 19, and 21 (hatch). Egg, embryo, yolk content, and yolk sac membrane were weighed, and the yolk sac (YS; i.e., yolk content + yolk sac membrane) composition was analyzed. From 30 to 50 wk of age, the albumen weight increased by 13.3%, whereas the yolk increased by more than 40%. The proportion of fat in the fresh yolk of the 30-wk-old group was 23.8% compared with 27.4% in the 50-wk-old group, whereas the proportion of protein was 17.9% compared with 15.6%, respectively. During incubation, results indicated that water and protein infiltrated from other egg compartments to the YS. Accordingly, the calculated change in the content of water and protein between fresh yolk and sampled YS does not represent the true uptake of these components from the YS to the embryo, and only fat uptake from the YS can be accurately estimated. By embryonic d 15, fat uptake relative to embryo weight was lower in the 30-wk-old group than in the 50-wk-old group. However, by embryonic d 21, embryos of both groups reached similar relative fat uptake, suggesting that to hatch, embryos must attain a certain amount of fat as a source of energy for the hatching process. The amount of COH in the YS increased similarly during incubation in eggs from hens of both ages, reaching a peak at embryonic d 19, suggesting COH synthesis in the YS. At hatch, the amount of protein, water, and COH in the residual YS, relative to the weight of the yolk-free chick, was similar in eggs from young and old hens. However, chicks from the younger hens had less fat in the YS for their immediate posthatch nutrition compared with those from the older hens.