Visualization of the conservation of synteny between humans and pigs by heterologous chromosomal painting

448

382

We report the highest density genetic linkage map for a livestock species produced to date. Three published maps for Sus scrofa were merged by genotyping virtually every publicly available microsatellite across a single reference population to yield 1042 linked loci, 536 of which are novel assignments, spanning 2286.2 cM (average interval 2.23 cM) in 19 linkage groups 08 autosomal and X chromosomes, n = 19). Linkage groups were constructed de novo and mapped by locus content to avoid propagation of errors in older genotypes. The physical and genetic maps were integrated with 123 informative loci assigned previously by fluorescence in situ hybridization {FISH). Fourteen linkage groups span the entire length of each chromosome. Coverage of chromosomes 11, 12, 15, and 18 will be evaluated as more markers are physically assigned. Marker-deficient regions were identified only on Ilql.7-qter and 14 cen-ql.2. Recombination rates [cM/Mbp) varied between and within chromosomes. Short chromosomal arms recombined at higher rates than long arms, and recombination was more frequent in telomeric regions than in pericentric regions. The high-resolution comprehensive map has the marker density needed to identify quantitative trait loci [QTL), implement marker-assisted selection or introgression and YAC contig construction or chromosomal microdissection.

Section: Genome Research ~ 379supporting

confidence: 79%

A comprehensive map of the porcine genome.

Rohrer¹,

Alexander²,

Hu³

et al. 1996

448

382

“…The mammalian X chromosome is considered to have retained the original genetic constitution of a common ancestor of the eutherian mammals (Graves and Watson 1991). This is evident from the almost identical banding patterns, morphology (with the exception of ruminantia), and gene content (Ohno et al 1964;O'Brien et al 1993;Gallagher et al 1994;Morizot 1994;Hayes 1995;Rettenberger et al 1995a;Chowdhary et al 1996). Notwithstanding the high degree of conservation, the rearranged order of genes on the X chromosome suggests intrachromosomal rearrangements (Nadeau 1989;Farr and Goodfellow 1992).…”

Section: Conservation Of Whole Chromosome Syntenymentioning

confidence: 88%

“…To date, comparative chromosomal maps of eight mammalian species of three different orders (excluding Primates) have been generated by Zoo-FISH. (1) Artiodactyla: pig (Rettenberger et al 1995a;Goureau et al 1996;Milan et al 1996), cattle (Hayes 1995;Solinas-Toldo et al 1995;Chowdhary et al 1996), Indian muntjac deer (Scherthan et al 1994(Scherthan et al , 1995Yang et al 1997). (2) Carnivora: cat (Rettenerger et al 1995b;, American mink (Hameister et al 1997), and harbor seal .…”

mentioning

confidence: 99%

Emerging Patterns of Comparative Genome Organization in Some Mammalian Species as Revealed by Zoo-FISH

Chowdhary¹,

Raudsepp²,

Frönicke³

et al. 1998

212

143

Although gene maps for a variety of evolutionarily diverged mammalian species have expanded rapidly during the past few years, until recently it has been difficult to precisely define chromosomal segments that are homologous between species. A solution to this problem has come from the development of Zoo-FISH, also known as cross-species chromosome painting. The use of Zoo-FISH to identify regions of chromosomal homology has allowed the transfer of information from map-rich species such as human and mouse to a wide variety of other species. From a Zoo-FISH analysis spanning four mammalian orders (Primates, Artiodactyla, Carnivora, and Perissodactyla), and involving eight species (human, pig, cattle, Indian muntjac, cat, American mink, harbor seal, and horse), three distinct classes of synteny conservation have been designated: (1) conservation of whole chromosome synteny, (2) conservation of large chromosomal blocks, and (3) conservation of neighboring segment combinations. This analysis has also made it possible to identify a set of chromosome segments (based on human chromosome equivalents) that probably made up the karyotype of the common ancestor of the four orders. This approach provides a basis for developing a picture of the ancestral mammalian karyotype, but a full understanding will depend on studies encompassing more diverse combinations of mammalian orders.

“…RH mapping of LGALS8 and CHRM3, both from Hsa1q42-Hsa1q43, to feline chromosome D2, confirms the presence of a small fragment of Hsa1q in association with Hsa10q on cat chromosome D2 identified previously (Murphy et al 2000;Yang et al 2000). This small syntenic segment has also been observed in another carnivore, the dog (Yang et al 2000;Breen et al 1999), and in cetartiodactyls, represented by the cow (Band et al 2000) and the pig (Rettenberger et al 1995;Frönicke et al 1996). It is likely that due to the small size of the Hsa1 fragment, this association may have gone undetected in other carnivores and cetartiodactyls examined in previous chromosome-painting studies using human probes.…”

Section: Comparative Gene Mappingmentioning

confidence: 91%

The Origin of Human Chromosome 1 and Its Homologs in Placental Mammals

Murphy

Frönicke²,

O’Brien³

et al. 2003

Developing ordered gene maps from multiple mammalian species coupled with chromosome-painting data provide a powerful resource for resolving the evolutionary history of chromosomes and whole genomes. In this work, we recapitulate the evolutionary history of human chromosome 1 and its homologs in placental mammals, putatively the largest physical unit in the ancestral placental genome. Precise definition of translocation exchange breakpoints in human, carnivore, cetartiodactyl, and rodent-ordered gene maps demonstrate that chromosome breakpoints, previously considered as equivalent, actually represent distinct chromosome positions and exchange events. Multidirectional chromosome painting, using probes from homologs to chromosome 1 in seven mammal species from six orders of placental mammals, confirm the gene-mapping results and indicate that the multiple human chromosome 1 homologs in these species are derived from independent fissions of a single ancestral chromosome. Chromosome painting using human chromosome 1 probes identifies a single human chromosome 1 homolog in phylogenetically distant taxa, the two-toed sloth, cetaceans, and higher primates. The diverse phylogenetic occurrence of a single Hsa1 synteny among the major clades of placental mammals suggests that human chromosome 1 represents an intact ancestral chromosome, which was variously fissioned in the majority of placental species. We find that the number of human chromosome 1 fissions in a specific lineage reflects its general rate of genomic evolution. Further, historic chromosome exchange appears to have been disproportionately clustered in two breakpoint hotspots on the long arm.