Comparative Linkage Mapping Research Articles

Identification of simple sequence repeat markers for utilizing wide-compatibility genes in inter-subspecific hybrids in rice (Oryza sativa L.)

Although pronounced heterosis in inter-subspecific hybrids was known in rice for a long time, its utilization for hybrid rice breeding has been limited due to their hybrid sterility (HS). For the last two decades, however, a few inter-subspecific hybrids have been developed by incorporating wide-compatibility genes (WCG) that resolve HS, into parental lines of these inter-subspecific hybrids. For effective use of WCG, it is necessary to find convenient markers linked to WCG of practical importance. In this paper, initially a set of simple sequence repeat (SSR) markers in the vicinity of known WCG loci identified based on comparative linkage maps have been surveyed in a population derived from the three-way cross- IR36/Dular//Akihikari, where a known donor of WCG Dular was crossed to a representative indica and japonica cultivar. Of the five parental polymorphic markers, RM253 and RM276 were found to be closely linked to the WCG locus S5 at a distance of 3.0 and 2.8 cM, respectively. Later, loci for HS were examined in three F(2) populations derived from inter-subspecific crosses, with same set of SSR markers. The locus S8 was confirmed to have major influence on HS in the F(2 )population derived from CHMRF-1/Taichung65 since two SSR markers in its vicinity, RM412 and RM141, co-segregated with HS at a map distance of 7.6 and 4.8 cM, respectively. In the F(2) population derived from the cross BPT5204/Taipei309, three SSR markers in the vicinity of S5, RM50, RM276 and RM136 co-segregated with HS at a map distance of 4.2, 3.2 and 7.8 cM, respectively. In the third F(2 )population derived from Swarna/Taipei309, the SSR markers in the vicinity of S5, RM225, RM253, RM50, RM276 and RM136 were identified to co-segregate with HS at a map distance of 3.2, 2.6, 3.4, 2.6 and 6.6 cM, respectively. These results indicated a clear picture of WCG in Dular as well as the predominant role of HS alleles at S5 locus. The identified SSR markers are expected to be used for incorporation of WCG into parental lines in hybrid rice breeding to solve HS in inter-subspecific hybrids.

Comparative linkage mapping of the Grey coat colour gene in horses1

Grey horses are born coloured, turn progressively grey and often develop melanomas late in life. Grey shows an autosomal dominant inheritance and the locus has previously been mapped to horse chromosome 25 (ECA25), around the TXN gene. We have now developed eight new single nucleotide polymorphisms (SNPs) associated with genes on ECA25 using information on the linear order of genes on human chromosome 9q, as well as the human and mouse coding sequences. These SNPs were mapped in relation to the Grey locus using more than 300 progeny from matings between two Swedish Warmblood grey stallions and non-grey mares. Grey was firmly assigned to an interval with flanking markers NANS and ABCA1. This corresponds to a region of approximately 6.9 Mb on human chromosome 9q. Furthermore, no recombination was observed between Grey, TGFBR1 and TMEFF1, the last two being 1.4 Mb apart in human. There are no obvious candidate genes in this region and none of the genes has been associated with pigmentation disorders or melanoma development, suggesting that the grey phenotype is caused by a mutation in a novel gene.

Genomic tools and cDNA derived markers for butterflies

The Lepidoptera have long been used as examples in the study of evolution, but some questions remain difficult to resolve due to a lack of molecular genetic data. However, as technology improves, genomic tools are becoming increasingly available to tackle unanswered evolutionary questions. Here we have used expressed sequence tags (ESTs) to develop genetic markers for two Müllerian mimic species, Heliconius melpomene and Heliconius erato. In total 1363 ESTs were generated, representing 330 gene objects in H. melpomene and 431 in H. erato. User-friendly bioinformatic tools were used to construct a nonredundant database of these putative genes (available at http://www.heliconius.org), and annotate them with blast similarity searches, InterPro matches and Gene Ontology terms. This database will be continually updated with EST sequences for the Papilionideae as they become publicly available, providing a tool for gene finding in the butterflies. Alignments of the Heliconius sequences with putative homologues derived from Bombyx mori or other public data sets were used to identify conserved PCR priming sites, and develop 55 markers that can be amplified from genomic DNA in both H. erato and H. melpomene. These markers will be used for comparative linkage mapping in Heliconius and will have applications in other phylogenetic and genomic studies in the Lepidoptera.

Congenital and idiopathic scoliosis: clinical and genetic aspects.

Genetic and environmental factors influencing spinal development in lower vertebrates are likely to play a role in the abnormalities associated with human congenital scoliosis (CS) and idiopathic scoliosis (IS). An overview of the molecular embryology of spinal development and the clinical and genetic aspects of CS and IS are presented. Utilizing synteny analysis of the mouse and human genetic databases, likely candidate genes for human CS and IS were identified. Review and synteny analysis. A search of the Mouse Genome Database was performed for "genes," "markers" and "phenotypes" in the categories Neurological and neuromuscular, Skeleton, and Tail and other appendages. The Online Mendelian Inheritance in Man was used to determine whether each mouse locus had a known human homologue. If so, the human homologue was assigned candidate gene status. Linkage maps of the chromosomes carrying loci with possibly relevant phenotypes, but without known human homologues, were examined and regions of documented synteny between the mouse and human genomes were identified. Searching the Mouse Genome Database by phenotypic category yielded 100 mutants of which 66 had been mapped. The descriptions of each of these 66 loci were retrieved to determine which among these included phenotypes of scoliosis, kinky or bent tails, other vertebral abnormalities, or disturbances of axial skeletal development. Forty-five loci of interest remained, and for 27 of these the comparative linkage maps of mouse and human were used to identify human syntenic regions to which plausible candidate genes had been mapped. Synteny analysis of mouse candidate genes for CS and IS holds promise due to the close evolutionary relationship between mice and human beings. With the identification of additional genes in animal model systems that contribute to different stages of spine development, the list of candidate genes for CS and IS will continue to grow.

Comparative linkage map of the Solanum lycopersicoides and S. sitiens genomes and their differentiation from tomato.

The wild nightshades Solanum lycopersicoides and Solanum sitiens are closely affiliated with the tomatoes (Lycopersicon spp.). Intergeneric hybridization with cultivated tomato (Lycopersicon esculentum) is impeded by strong reproductive barriers including hybrid sterility and suppressed recombination. Conservation of genome structure between these nightshades and tomato was studied by construction of a genetic map from F2 S. sitiens x S. lycopersicoides and comparison with existing maps of tomato. Owing to self-incompatibility of the F1, two hybrid plants were crossed to obtain a population of 82 F2 individuals. Using 166 previously mapped RFLP markers and 5 restriction enzymes, 101 loci polymorphic in the S. sitiens x S. lycopersicoides population were identified. Analysis of linkage between the markers resulted in a map with 12 linkage groups covering 1192 cM and one unlinked marker. Recombination rates were similar to those observed in tomato; however, significant segregation distortion was observed for markers on 7 out of the 12 chromosomes. All chromosomes were colinear with the tomato map, except for chromosome 10, where a paracentric inversion on the long arm was detected. In this region, S. sitiens and S. lycopersicoides share the same chromosomal configuration previously reported for potato (S. tuberosum) and pepper (Capsicum), suggesting that of tomato is derived. The 10L inversion explains the lack of recombination detected among homeologous chromosomes of intergeneric hybrids in this region. On this basis, we recognize two principle genomes, designated L for the Lycopersicon spp., and S for S. lycopersicoides and S. sitiens, the first examples of structural differentiation between tomato and its cross-compatible wild relatives.

Linkage assignment of eleven genes to the porcine genome.

We report comparative linkage mapping of eleven genes in the swine genome by RFLP analysis. These genes include: Acid phosphatase type 5 (ACP5), Cholecystokinin Type B Receptor (CCKBR), Antibiotic Peptide (FALL39), Insulin-like Growth Factor 1 Receptor (IGF1R), Integrin Alpha M (ITGAM), Integrin Beta 2 (ITGbeta2), Opioid Receptor Mu-1 (OPRM1), Pro-hormone Converter (PC1/3), Retinol Binding Protein 3 (RBP3), Ribosomal DNA (RNR1), and Zona Pellucida Glycoprotein 1 (ZP1). The CCKBR and ITGbeta2 loci define the ends of the linkage groups on Chromosomes (Chro) (SSC) 9p and 13qter, respectively.

Comparative Linkage Mapping of Human Chromosome 13 and Bovine Chromosome 12

A comparative linkage map of human chromosome 13 and bovine chromosome 12 was constructed using eight polymorphic microsatellite markers associated with six specific genes. Linkage of these was also examined relative to five previously mapped anonymous microsatellite markers. Seven gene-linked markers were developed from bovine large-insert genomic clones containing one of five genes of interest (serotonin receptor subtype 2, fms-related tyrosine kinase, coagulation factor 10, retinoblastoma susceptibility gene, collagen type IV alpha 1), and one additional marker was developed from a microsatellite resident within an intron of the bovine dopachrome tautomerase gene. Four of these loci were previously assigned to bovine chromosome 12 by analysis of a somatic cell hybrid panel. This study provides linkage information for examining gene order in this conserved synteny group. The comparative linkage mapping results indicate that the q arm of human chromosome 13 is almost entirely conserved in bovine chromosome 12. One intrachromosomal rearrangement was detected in this linkage group relative to human, and this rearrangement was confirmed by fluorescencein situhybridization results.

Chromosomal Assignment of Four Testis-Expressed Mouse Genes from a New Family of Transmembrane Proteins (ADAMs) Involved in Cell–Cell Adhesion and Fusion

A new gene family of multidomain membrane proteins (ADAMs) that includeADisintegrinAndMetalloprotease domain comprises an increasing number of identified members. Two members of this family, fertilin α and fertilin β, form a heterodimeric protein that is required for sperm–egg fusion. Most recently, it has been shown that a third family member, meltrin α, is involved in myoblast fusion (Yagami-Hiromasaet al.,1995,Nature377: 652–656). Using restriction fragment length polymorphism analysis of a DNA panel from an interspecific backcross, we have determined the chromosomal locations of four mouse genes of this family that are expressed in testis: fertilin α, fertilin β, ADAM 4, and ADAM 5. These genes have been given the locus symbolsFtna(fertilin α),Ftnb(fertilin β),Adam4(ADAM 4), andAdam5(ADAM 5). They were mapped to chromosomes 5, 14, 9, and 8, respectively, revealing a dispersed localization. Human chromosome locations of these genes are predicted on the basis of the mapping results using the information provided by comparative linkage maps. Because all four of these ADAM genes are expressed in testis and fertilin α and β have been found to be important for fertilization, we compared their chromosomal locations with known mouse mutations affecting spermatogenesis and fertility.

Analysis of the barley and rice genomes by comparative RFLP linkage mapping

Analysis of the barley and rice genomes by comparative RFLP linkage mapping

Analysis of the barley and rice genomes by comparative RFLP linkage mapping

Comparative genetic mapping of rice and barley, both major crop species with extensive genetic resources, offers the possibility of uniting two well-established and characterized genetic systems. In the present study, we screened 229 molecular markers and utilized 110 polymorphic orthologous loci to construct comparative maps of the rice and barley genomes. While extensive chromosomal rearrangements, including inversions and intrachromosomal translocations, differentiate the rice and barley genomes, several syntenous chromosomes are evident. Indeed, several chromosomes and chromosome arms appear to share nearly identical gene content and gene order. Seventeen regions of conserved organization were detected, spanning 287 cM (24%) and 321 cM (31%) of the rice and barley genomes, respectively. The results also indicate that most (72%) of the single-copy sequences in barley are also single copy in rice, suggesting that the large barley genome arose by unequal crossing over and amplification of repetitive DNA sequences and not by the duplication of single-copy sequences. Combining these results with those previously reported for comparative analyses of rice and wheat identified nine putatively syntenous chromosomes among barley, wheat and rice. The high degree of gene-order conservation as detected by comparative mapping has astonishing implications for interpreting genetic information among species and for elucidating chromosome evolution and speciation.

Homology among RAPD fragments in interspecific comparisons

AbstractThe use of RAPDs for comparative purposes relies on the assumption that similarity of fragment size is a dependable indicator of homology. To test the validity of this assumption, homology among 220 pairs of comigrating fragments from three wild sunflower species was determined. Ninety‐one per cent cross‐hybridized and/or displayed congruent restriction fragment profiles suggestive of homology. However, comparative linkage mapping data indicated that 13% of the homologous loci mapped to genomic locations that were incongruent with the majority of loci, suggestive of paralogous rather than orthologous relationships. Thus, of the 220 pairwise comparisons, only 174 (79.1%) identified loci that are useful for comparative genetic studies. These problems, as well as several other factors discussed in the text, will introduce noise into RAPD data sets and thereby reduce the probability of generating accurate estimates of genetic relationships. Recommended methods for reducing noise in RAPD data sets include increasing gel resolution and/or testing fragment homology. However, implementation of these approaches will not eliminate all uncertainties, and it is also recommended that RAPD data sets be tested for structure and reliability.

Comparative linkage maps for the mosquitoes, Aedes albopictus and Ae. aegypti, based on common RFLP loci

Aedes albopictus and Aedes aegypti are members of the mosquito family Culicidae and share a haploid chromosome complement of three. Although a genetic linkage map based on restriction fragment length polymorphism (RFLP), markers exists for Ae. aegypti, the extent of synteny and linkage order conservation between the two species was unknown. A comparative linkage map for Ae. albopictus was constructed based mainly on cDNA clones from Ae. aegypti. Nearly all Ae. aegypti probes hybridized to Ae. albopictus DNA at high stringency. For eighteen RFLP markers tested, the linkage group and linear order appears to be identical for the two species. 78% of the loci tested exhibited significant deviations from the expected segregation ratio in at least one of the test crosses. An excess of heterozygote genotypes was recovered with most loci. This probably reflects the effects of lethal loci on survival of F2 progeny homozygous for the parental genotypes. These results demonstrate that comparative linkage maps based on common DNA markers provide a basis for rapidly developing linkage maps for various mosquito species, and the opportunity to examine the significance and function of orthologous quantitative trait loci associated with mosquito vector competence for disease transmission.

The bovine B and C blood group systems are not likely to be the orthologues of human RH: an interesting twist in the comparative map

SummaryWe tested the hypothesis that either the bovine B or C blood group system is the orthologue of human RH. A comparative linkage mapping strategy was applied, using blood typing and restriction fragment length polymorphism (RFLP) analysis of four loci linked to RH on HSA1; PGD, FGR, ALPL and FUCA1. Four sires with a total of 255 half‐sib offspring were used for the linkage analysis. Strong support for linkage between ALPL, FUCA1 and FGR was obtained for all sire families (lod scores >11 for all pairwise comparisons). This new linkage group was assigned to bovine synteny group U17 based on previous somatic cell mapping of the FGR locus. The most favoured order is ALPL—FUCA1—FGR (2·18:1), with ALPL and FGR 5·4 cm and 6·3 cm, respectively, from FUCA1. The B and C blood group systems and PGD were genetically independent of each other and all other markers, indicating that neither B nor C is likely to be the bovine orthologue of human RH. However, given available comparative mapping data, there is some chance that the bovine orthologue of RH is on bovine synteny group U6. Although gene order appears to be conserved with humans, the differences in recombination rates between these three loci in cattle, humans and mice strongly suggest that it is not possible to use human map distances to predict map distances in cattle, making it imperative that bovine gene mappers continue to emphasize adding type I markers to the bovine linkage map.

Comparative Genetic Linkage Mapping in Insects

Genomics is the study of the structure and organization of entire genomes. The recent coinage of this term (46) reflects the comparative youth of this emerging field. The nuclear genome of eukaryotic organisms is the collection of all DNA sequ ences in the nucleus that are transmitted through cell lineages by the orthodox processes of mitosis and meiosis. Eukaryotic genomes are organized into discrete units, the chromosomes , whose uniqueness is defined by their DNA base sequences . The genome includes sequences specifying information for chromosome replication, maintenance, packaging, and trans­ mission; other sequences that with their coding and control regions represent expressed genes; still other sequence families often regarded as parasitic because of methods of duplication, transposition, and recombination that allow nonorthodox methods of transmission; and many other sequences of unknown function and significance. Comparative genomics examines properties of genomes from different species. It represents an extension of the classical tradition of the comparative approach in evolutionary biology to questions of genome structure and function. One property of genomes is their complexity spectrum, which describes the distribution of DNA sequences into different copy number classes (single copy, moderately repeated, or highly repeated). A related