David Morrice

The dynamics of chromosome evolution in birds and mammals.

Comparative mapping, which compares the location of homologous genes in different species, is a powerful tool for studying genome evolution. Comparative maps suggest that rates of chromosomal change in mammals can vary from one to ten rearrangements per million years. On the basis of these rates we would expect 84 to 600 conserved segments in a chicken comparison with human or mouse. Here we build comparative maps between these species and estimate that numbers of conserved segments are in the lower part of this range. We conclude that the organization of the human genome is closer to that of the chicken than the mouse and by adding comparative mapping results from a range of vertebrates, we identify three possible phases of chromosome evolution. The relative stability of genomes such as those of the chicken and human will enable the reconstruction of maps of ancestral vertebrates.

Gene homologs on human chromosome 15q21-q26 and a chicken microchromosome identify a new conserved segment

The genes for insulin-like growth factor 1 receptor (IGF1R), aggrecan (AGC1), β2-microglobulin (B2M), and an H6-related gene have been mapped to a single chicken microchromo-some by genetic linkage analysis. In addition, a second H6-related gene was mapped to chicken macrochromosome 3. The Igf1r and Agc1 loci are syntenic on mouse Chr 7, together with Hmx3, an H6-like locus. This suggests that the H6-related locus, which maps to the chicken microchromosome in this study, is the homolog of mouse Hmx3. The IGF1R, AGC1, and B2M loci are located on human Chr 15, probably in the same order as found for this chicken microchromosome. This conserved segment, however, is not entirely conserved in the mouse and is split between Chr 7 (Igf1r-Age) and 2 (B2m). This comparison also predicts that the HMX3 locus may map to the short arm of human Chr 15. The conserved segment defined by the IGF1R-AGC1-HMX3—B2M loci is approximately 21–35 Mb in length and probably covers the entire chicken microchromosome. These results suggest that a segment of human Chr 15 has been conserved as a chicken micro-chromosome. The significance of this result is discussed with reference to the evolution of the avian and mammalian genomes.

Identification of chromosomal regions associated with growth and carcass traits in an F3 full sib intercross line originating from a cross of chicken lines divergently selected on body weight.

An F(3) resource population originating from a cross between two divergently selected lines for high (D+ line) or low (D- line) body weight at 8-weeks of age (BW55) was generated and used for Quantitative Trait Locus (QTL) mapping. From an initial cross of two founder F(0) animals from D(+) and D(-) lines, progeny were randomly intercrossed over two generations following a full sib intercross line (FSIL) design. One hundred and seventy-five genome-wide polymorphic markers were employed in the DNA pooling and selective genotyping of F(3) to identify markers with significant effects on BW55. Fifty-three markers on GGA2, 5 and 11 were then genotyped in the whole F(3) population of 503 birds, where interval mapping with GridQTL software was employed. Eighteen QTL for body weight, carcass traits and some internal organ weights were identified. On GGA2, a comparison between 2-QTL vs. 1-QTL analysis revealed two separate QTL regions for body, feet, breast muscle and carcass weight. Given co-localization of QTL for some highly correlated traits, we concluded that there were 11 distinct QTL mapped. Four QTL localized to already mapped QTL from other studies, but seven QTL have not been previously reported and are hence novel and unique to our selection line. This study provides a low resolution QTL map for various traits and establishes a genetic resource for future fine-mapping and positional cloning in the advanced FSIL generations.

Expression of exogenous DNA during the early development of the chick embryo

SummaryA plasmid construct containing the reporter gene,lacZ, under the control of the cytomegalovirus immediate early promoter, was injected into the germinal disc of fertilised chick ova. The distribution of cells expressing β-galactosidase was examined in the embryos after periods of from 3 h to 7 days in culture. β-galacto-sidase-positive cells were first observed at mid-cleavage (250–500 closed cells) in the centre of the blastodisc. After one day, they were prominent in large segments of the blastoderm and, at later stages, in proportionately smaller segments of the extra-embryonic membranes, notably in the endodermal layer. In the embryonic regions, positive cells were scattered in the vicinity of the primitive streak of most cultures, but after gastrulation they were present in the embryonic tissue of only 7% of surviving embryos. The results provide supportive evidence for transcriptional activity during the cleavage stages of avian development. They also confirm previous findings on the loss of exogenous DNA during the early development of the chick.

Quantitative trait loci for bone traits segregating independently of those for growth in an F2 broiler × layer cross

An F2 broiler–layer cross was phenotyped for 18 skeletal traits at 6, 7 and 9 weeks of age and genotyped with 120 microsatellite markers. Interval mapping identified 61 suggestive and significant QTL on 16 of the 25 linkage groups for 16 traits. Thirty-six additional QTL were identified when the assumption that QTL were fixed in the grandparent lines was relaxed. QTL with large effects on the lengths of the tarsometatarsus, tibia and femur, and the weights of the tibia and femur were identified on GGA4 between 217 and 249 cM. Six QTL for skeletal traits were identified that did not co-locate with genome wide significant QTL for body weight and two body weight QTL did not coincide with skeletal trait QTL. Significant evidence of imprinting was found in ten of the QTL and QTL × sex interactions were identified for 22 traits. Six alleles from the broiler line for weight- and size-related skeletal QTL were positive. Negative alleles for bone quality traits such as tibial dyschondroplasia, leg bowing and tibia twisting generally originated from the layer line suggesting that the allele inherited from the broiler is more protective than the allele originating from the layer.

A QTL for osteoporosis detected in an F2 population derived from White Leghorn chicken lines divergently selected for bone index

Osteoporosis, resulting from progressive loss of structural bone during the period of egg-laying in hens, is associated with an increased susceptibility to bone breakage. To study the genetic basis of bone strength, an F(2) cross was produced from lines of hens that had been divergently selected for bone index from a commercial pedigreed White Leghorn population. Quantitative trait loci (QTL) affecting the bone index and component traits of the index (tibiotarsal and humeral strength and keel radiographic density) were mapped using phenotypic data from 372 F(2) individuals in 32 F(1) families. Genotypes for 136 microsatellite markers in 27 linkage groups covering approximately 80% of the genome were analysed for association with phenotypes using within-family regression analyses. There was one significant QTL on chromosome 1 for bone index and the component traits of tibiotarsal and humeral breaking strength. Additive effects for tibiotarsal breaking strength represented 34% of the trait standard deviation and 7.6% of the phenotypic variance of the trait. These QTL for bone quality in poultry are directly relevant to commercial populations.

Microsatellite polymorphism and its association with body weight and selected morphometrics of farm red fox (Vulpes vulpes L.)

Polymorphism of 30 canine-derived microsatellites was studied in a group of 200 red foxes kept on 2 Polish farms. 22 out of 30 microsatellites were selected to study association between marker genotypes and body weight (BW), body length (BL), body circumference (BC), tail length (TL), ear height (EH), length of the right front limb (FRLL), length of the right rear limb (RRLL), length of the right front foot (FRFL) and length of the right rear foot (RRFL). A total of 112 alleles and 243 genotypes were found at 22 autosomal microsatellite loci. Three monomorphic loci deemed as uninformative were excluded from the study. The association between marker genotypes and the studied traits was analysed using general linear model (GLM) procedure and least squares means (LSM). Linkage disequilibrium (LD) was estimated to assess non-random association between microsatellite loci. Out of 19 microsatellites studied four markers showed no association with the studied traits, three markers had a significant effect on one trait, and another three markers had significant effect on two traits. Among ten microsatellites with significant effect on four economically important traits (BW, BL, BC, TL) four were associated with two characters: marker FH2613 with BW and BC, marker FH2097withBL and BC, marker ZUBECA6 with BW and BC, whereas marker REN75M10 was associated with BL and TL. The strongest LD (r2 ranged from 0.15 to 0.33) was estimated between nine loci with significant effect on economically important traits (BW, BL, BC, TL).

Expression of transcription factor c-Rel and apoptosis occurrence in polydactylous and syndactylous limb buds of the talpid3 mutant chick embryo.

The chicken proto-oncogene c-rel encodes a transcription factor of the Rel/NF-κB family. We have previously shown that c-rel mRNAs accumulate in different types of apoptotic cells of the chick embryo, especially in mesenchymal cells within the four cell death areas of the limb bud: the anterior and posterior necrotic zones, the opaque patch and the interdigital necrotic zones. This study aimed to further establish the involvement of c-Rel in apoptosis of the developing limb by investigating its expression in the talpid3 mutant which was originally shown to be defective in apoptosis. However, our preliminary examinations highlighted the apparent presence of apoptotic cells in talpid3 embryos. Hence, we performed a systematic study of the occurence of apoptosis in mutant and control embryos by the TUNEL method. The results revealed that apoptosis does occur in talpid3 embryos but with altered spatial and temporal patterns. This suggests that the talpid3 mutation does not affect a gene involved in apoptosis per se but rather in the determination of the pattern of apoptosis. Neither the expression of c-Rel nor that of its IκBα inhibitor are grossly modified in talpid3 limb buds, suggesting that the talpid3 mutation does not affect any of these genes. They are mostly expressed in epidermal, endodermal and striated muscle cells in control and in talpid3 limb buds as well. C-Rel was also detected in some scarce mesenchymal cells that could be apoptotic, in both control and mutant embryos. The only slight difference between control and talpid3 limbs lies in the perichondrium which is not fully differentiated in talpid3 embryos: c-Rel and IκBα are only faintly expressed in talpid3 perichondrial cells, whereas they are both detected in control perichondrial cells. Taken together, these results suggest that c-Rel could participate in several developmental processes, especially in the differentiation of perichondrial cells, besides its already documented involvement in apoptosis and haematopoeisis.

Genomic evaluation, breed identification, and population structure of Guernsey cattle in North America, Great Britain, and the Isle of Guernsey

As of December 2015, 2,376 Guernsey bulls and cows had genotypes from collaboration between the United States, Canada, the United Kingdom, and the Isle of Guernsey. Of those, 439 bulls and 504 cows had traditional US evaluations, which provided sufficient data to justify investigation of the possible benefits of genomic evaluation for the Guernsey breed. Evaluation accuracy was assessed using a traditional 4-yr cutoff study. Twenty-two traits were analyzed (5 yield traits, 3 functional traits, and 14 conformation traits). Mean reliability gain over that for parent average was 16.8 percentage points across traits, which compares with 8.2, 18.5, 20.0, and 32.6 percentage points reported for Ayrshires, Brown Swiss, Jerseys, and Holsteins, respectively. Highest Guernsey reliability gains were for rump width (44.5 percentage points) and dairy form (40.5 percentage points); lowest gains were for teat length (1.9 percentage points) and rear legs (side view) (2.3 percentage points). Slight reliability losses (1.5 to 4.5 percentage points) were found for udder cleft, final score, and udder depth as well as a larger loss (13.6 percentage points) for fore udder attachment. Twenty-one single nucleotide polymorphisms were identified for Guernsey breed determination and can be used in routine genotype quality control to confirm breed and identify crossbreds. No haplotypes that affect fertility were identified from the current data set. Principal component analysis showed some divergence of US and Isle of Guernsey subpopulations. However, the overlap of US, Canadian, UK, and Isle of Guernsey subpopulations indicated the presence of gene flow, and the similarities in the subpopulations supports a common genomic evaluation system across the regions.

A genome-wide linkage study in families with major depression and co-morbid unexplained swelling†

Major depressive disorder (MDD) is a common heritable condition. The diversity of the phenotype coupled with aetiological and genetic heterogeneity present formidable obstacles in the search for causative genetic loci. Studies of large families with many affected individuals, and the selection of well‐defined clinical subgroups of depression, are two ways to reduce this complexity. Unexplained swelling symptoms (USS) are common in women and many patients give a strong personal and family history of depression. Co‐morbid depression and swelling symptoms define a useful sub‐phenotype for investigating genetic factors in depression. We have completed a genome‐wide linkage analysis using 371 microsatellite markers in four families where MDD is co‐morbid with USS. Of 47 affected individuals, 28 had both MDD and unexplained swelling, 11 had symptoms of swelling alone, and 8 had MDD alone. Parametric marker‐specific analysis identified one suggestive locus, D8S260 (LOD = 2.02) and non‐parametric multipoint variance component analysis identified a region on 7p (LOD = 2.10). A 47 cM suggestive linkage region on chromosome 14q (identified by both parametric and non‐parametric methods) was identified and investigated further with fine‐mapping markers but the evidence for linkage to this region decreased with increased marker information content.