Construction Of Genetic Linkage Map Research Articles

A review of catfish genomics: progress and perspectives

Catfish is one of the lower teleosts whose genome research is important for evolutionary genomics. As the major aquaculture species in the USA, its genome research also has practical and economical implications. Much progress has been made in recent years, including the development of large numbers of molecular markers, the construction of framework genetic linkage maps, the identification of putative markers involved in performance traits, and the development of genomic resources. Repetitive elements have been identified and characterized in the catfish genome that should facilitate physical analysis of the catfish genome. A large number of genes or full-length cDNAs have been analysed using genomic approaches, providing information on gene structure, gene evolution and gene expression in relation to functions. Catfish genome research has come to a stage when physical mapping through BAC contig construction is greatly demanded, in order to develop regional markers for QTL analysis and for large-scale comparative mapping. The current effort in large-scale EST analysis and type I marker mapping should further enhance research efficiency through comparative mapping. Candidate gene identification is being accelerated through the use of cDNA microarrays.

Effects of genotyping errors, missing values and segregation distortion in molecular marker data on the construction of linkage maps.

A simulation study was performed to investigate the effects of missing values, typing errors and distorted segregation ratios in molecular marker data on the construction of genetic linkage maps, and to compare the performance of three locus-ordering criteria (weighted least squares, maximum likelihood and minimum sum of adjacent recombination fractions criteria) in the presence of such effects. The study was based upon three linkage groups of 10 loci at 2, 6, and 10 cM spacings simulated from a doubled-haploid population of size 150. Criteria performance were assessed using the number of replicates with correctly estimated orders, the mean rank correlation between the estimated and the true order and the mean total map length. Bootstrap samples from replicates in the maximum likelihood analysis produced a measure of confidence in the estimated locus order. The effects of missing values and/or typing errors in the data are to reduce the proportion of correctly ordered maps, and this problem worsens as the distances between loci decreases. The maximum likelihood criterion is most successful at ordering loci correctly, but gives estimated map lengths, which are substantially inflated when typing errors are present. The presence of missing values in the data produces shorter map lengths for more widely spaced markers, especially under the weighted least-squares criterion. Overall, the presence of segregation distortion has little effect on this population.

RAPD 마커를 이용한 무의 유전자지도 작성

작물의 신품종 육성 과정에 있어서 선발은 육종의 성패를 좌우하는 중요한 과정이다. 하지만 개체가 나타내는 표현형은 유전적 요인과 환경적 요인이 동시에 작용하여 나타나기 때문에 유전적인 효과만 구분하여 선발하는 것은 매우 어렵다. 최근에 분자생물학 분야의 연구가 급속도로 발전함에 따라 분자 수준의 표지 인자를 유용 유전자의 간접선발 지표로 활용하여 선발 효율을 높일 수 있게 되었다. 작물의 유전자 지도 및 분자 표지인자는 작물 육종에 매우 유용하게 활용될 수 있다. 따라서 본 연구에서는 무에서 양친인 '835'와 'B<TEX>$_2$</TEX>'에서 유래한 여교잡 집단 82개체를 이용하여 RAPD 유전자군 지도를 작성하고 관련 마커를 탐색하여 육종에 이용하고자 연구를 수행하였다. Primer 375종류를 이용하여 양친, 835와 B<TEX>$_2$</TEX> 사이의 다형화 밴드 128개를 찾았다. BC<TEX>$_1$</TEX>F<TEX>$_1$</TEX>집단 조사를 통해 MAPMAK ER/EXP를 이용하여 연관군 지도를 작성하였다. 분리 분석된 RAPD 표지인자 128개 중 126개는 멘델의 이론 분리비 1:1에 적합하였으며. 2개는 동형접합체 (모본형) 쪽으로 편중되어 분리되었다. LOD 3.0 수준에서 128개의 표지인자가 9개의 연관군으로 나뉘어졌고 전체거리는 1,688.3 cM이었으며, 표지인자 간 평균거리는 13.8 cM으로 Lefebvre 등 (1996)이 발표한 자료를 참고하여 무 genome 전체의 유전적 거리를 계산한 결과 무의 유전자지도는 무 genome전체의 68.7%~80.1%를 포함하는 것으로 추정할 수 있었다. RAPD 마커에서 문제시되는 재현성 문제를 검정하기 위해 이를 STS 마커로 변환하고자 OPE10 primer에 의해 증폭된 특정 밴드를 클로닝하고 염기서열을 분석한 다음 얻어진 염기서열을 기본으로 하여 primer를 제작하여 PCR 하였다. 그 결과 10mer인 OPE10을 이용하여 분석했을 때와 동일하였으며 목적 밴드 외 다른 밴드는 생성되지 않아 앞으로 분자 마커로서 충분히 이용될 수 있음을 보여주었다. Genetic map and molecular marker have a great importance in improving and facilitating crop breeding program as well as in genome analysis and map-based cloning of genes representing desirable characters. This study aimed at developing RAPD markers and constructing a genetic linkage map using 82 BC<TEX>$_1$</TEX>F<TEX>$_1$</TEX>individuals originated from the cross between '835' and B<TEX>$_2$</TEX>in radish (Raphanus sativus L.). One of the parents for genetic linkage map construction, '835'(P<TEX>$_1$</TEX>) of egg type is susceptible to Fusarium wilt and have medium resistance to virus infection and the other parent, B<TEX>$_2$</TEX>(P<TEX>$_2$</TEX>) of round type, is susceptible to Fusarium wilt and virus, Screening of 394 RAPD primers in BC<TEX>$_1$</TEX>F<TEX>$_1$</TEX>) population resulted in selecting 128 polymorphic markers which displayed 1:1 segregation pattern. Two markers failed to display 1:1 segregation and showed the segregation ratio skewed to maternal genotype. Selected markers were categorized into 14 linkage group based on LOD score represented by MAPMAKER/EXP program. Five groups composed of single marker among them were excluded from the linkage map, and consequently, the remaining groups are well matched with the number of radish chromosome (n＝9). The linkage map constructed with 128 markers covers 1,688.3 cM and the average distance between markers was 13.8 cM. For developing STS marker, we determined the partial nucleotide sequence of OPE10 marker at both ends and designed a oligonucleotide primer pair based on this sequence. STS PCR using the primer pair displayed a single, clear band of which segregation is perfectly matched with that of OPE10 marker. This implies that RAPD markers could readily convert into clear and reliable STS markers.

Genetic mapping of the black tiger shrimp Penaeus monodon with amplified fragment length polymorphism

We report construction of an initial genetic linkage map for the black tiger shrimp, Penaeus monodon. Mapping was carried out using polymorphic markers derived from 23 Amplified Fragment Length Polymorphism (AFLP) primer pairs. These were analysed on three reference families of known pedigree. A total of 673 polymorphic AFLP loci that conformed to expected Mendelian segregation ratios were scored in three families, and these were used to construct separate male and female linkage maps for each family. AFLP markers that consisted of a segregating fragment of the same size, amplified with the same primer pair in two or more of the reference families, were considered to be common markers. 116 such common AFLP markers were used to construct a common linkage map across the three families. This linkage map has 20 linkage groups covering a total genetic distance of 1412 cM. Future directions for genetic mapping in P. monodon are discussed in light of these initial data.

Constructing dense genetic linkage maps

This paper describes a novel combination of techniques for the construction of dense genetic linkage maps. The construction of such maps is hampered by the occurrence of even small proportions of typing errors. Simulated annealing is used to obtain the best map according to the optimality criterion: the likelihood or the total number of recombination events. Spatial sampling of markers is used to obtain a framework map. The construction of a framework map is essential if the steps used for simulated annealing are required to be simple. For missing-data imputation the Gibbs sampler is used. Map construction using simulated annealing and missing-data imputation are used in an iterative way. In order to obtain some measure of precision of the genetic linkage map obtained, the Metropolis-Hastings algorithm is used to obtain posterior intervals for the positions of markers. The process of map construction is embedded in a framework of pre-mapping and post-mapping diagnostics. The techniques described are illustrated using a practical application.

Molecular phylogeny of Gossypium species by DNA fingerprinting

Total genomic DNA from 31 available Gossypium species, three subspecies and one interspecific hybrid, were analysed to evaluate genetic diversity by RAPD, using 45 random decamer primers. A total of 579 amplified bands were observed, with 12.9 bands per primer, of which 99.8% were polymorphic. OPJ-17 produced the maximum number of fragments while the minimum number of fragments was produced with primer OPA-08. Cluster analysis by the unweighted paired group method of arithmetic means (UPGMA) showed six main clusters. Cluster ’A’ consisted of two species and one subspecies of the A-genome, with a 0.78–0.92 Nei’s similarity range. Cluster B, composed of all available tetraploid species and one interspecific hybrid, showed the same sister cluster. Nei’s similarity ranged from 0.69 to 0.84. The B-genome formed the UPGMA sister cluster to the E-genome species. Cluster ’C’ consisted of five Gossypium species of which three belong to the B-genome, with Nei’s similarity values of 0.81 to 0.86. Although there was considerable disagreement at lower infra-generic ranks, particularly among the D- genome (diploid New World species) and C-genome (diploid Australian species) species. The sole F-genome species Gossypium longicalyx was resolved as a sister group to the D-genome species. Gossypium herbaceum and G. herbaceum Africanum showed the maximum Nei’s similarity (0.93). Minimum similarity (0.29) was observed between Gossypium trilobum and Gossypium nelsonii. The average similarity among all studied species was 50%. The analysis revealed that the interspecific genetic relationship of several species is related to their centre of origin. As expected, most of the species have a wide genetic base range. The results also revealed the genetic relationships of the species Gossypium hirsutum to standard cultivated Gossypium barbadense, G. herbaceum and Gossypium arboreum. These results correspond well with previous reported results. The level of variation detected in closely related genotypes by RAPD analysis indicates that it may be a more efficient marker than morphological marker, isozyme and RFLP technology for the construction of genetic linkage maps.

A male bovine linkage map for the ADR granddaughter design

SummaryThe aim of this paper is to present the construction of a male genetic linkage map as a result of the bovine genome mapping project, which is a common effort of the German cattle breeding federation (ADR), four animal breeding institutes, three blood group laboratories and two animal data and breeding value evaluation centres. In total 20 grandsires with 1074 sires were provided from the German cattle population as reference families, 16 of these paternal half‐sib groups are German Holstein families (DH), three are German Simmental (ST) families, and one is a Brown Swiss family (BS). Of 265 markers included in the linkage map, 248 were microsatellite markers, five were bovine blood group systems, eight SSCP markers and four proteins and enzymes. More than 239 000 genotypes resulted from typing the offspring for the respective markers and these were used for the construction of the map. On average 478 informative meioses were provided from each marker of the map. The summarized map length over all chromosomes was 3135.1 cM with an average interval size of 13.34 cM. About 17, 35.7 and 79.1% of the map intervals showed a maximum genetic distance between the adjacent markers of 5, 10 and 20 cM, respectively. The number of loci ranged from two (pseudoautosomal region of the sex chromosome, BTAY) to 15 (BTA23) with an average of 8.8 markers per chromosome. Comparing the length of the chromosomes shows variation from 49.6 cM for BTA26 to 190.5 cM for BTA1 with a mean of 107.7 cM for all autosomes of the genetic linkage map. It was possible to identify chromosomal discrepancies in locus order and map intervals by comparison with other published maps. The map provided sufficient marker density to serve as a useful tool for a scan of segregating quantitative trait loci.

Genetic linkage mapping in Acacia mangium 1. Evaluation of restriction endonucleases, inheritance of RFLP loci and their conservation across species

Random genomic probes were used to assess levels of restriction fragment length polymorphism (RFLP) in two 2-generation outbred pedigrees of Acacia mangium Willd. Probes were evaluated for their ability to detect polymorphic loci in each pedigree and to determine the relative efficiency of different restriction enzymes in revealing polymorphisms. Sixty two percent of the probes which detected single- or low-copy number sequences revealed polymorphisms with at least one restriction enyzme. HpaII was the most efficient in detecting polymorphism among first-generation individuals. The recognition sequence of HpaII contains a CpG dimer, suggesting that cytosines in the CpG sequence may be hotspots for mutation in plant genomes, as previously reported in bacterial and mammalian genomes. Mendelian inheritance of 230 loci was demonstrated based on single-locus segregation in second-generation individuals. Less than 5% of loci showed evidence of segregation distortion. The proportion of fully informative loci (15%) was lower than previously reported in eucalypts reflecting the lower level of genetic diversity in A. mangium. The RFLP probes are suitable for the construction of a high-density genetic linkage map in A. mangium. Cross-hybridisation of the A.mangium RFLPs to DNA from species representing the three subgenera of the genus Acacia indicates that these markers could be used in breeding programs of other diploid acacias, for comparative studies of genome organisation, and for phylogenetic studies.

Detection of Polymorphic DNA and Taxonomic Relationships Among 10 Wild Perennial Soybean Species Using Specific and Arbitrary Nucleotide Primers

Polymorphic DNA in complex genomes of agronomic crops can be detected using specific nucleotide and arbitrary primers and the polymerase chain reaction (PCR). Nineteen accessions representing 10 species of the wild perennial soybean were evaluated using 4 sets of specific primers and 3 sets of random amplified polymorphic DNAs (RAPD) primers. The potential of the RAPD assays was further increased by combining two primers in a single PCR. The fragments generated by the two assays discriminated 10 wild species by banding profiles. The size of the amplified DNA fragments ranged from 100 to 2100 base pairs. The resolved PCR products yielded highly characteristic and homogeneous DNA fingerprints. The fingerprints were useful not only for investigating genetic variability but also for further characterizing the wild soybean species by detecting inter- and intra-specific polymorphisms, constructing dendrograms defining the phylogenetic relationships among these species, and identifying molecular markers for the construction of genetic linkage maps. Furthermore, unique markers distinguishing particular species were also identified. Thus, it is expected that PCR will have great relevance for taxonomic studies.

A Genomewide Analysis Provides Evidence for Novel Linkages in Inflammatory Bowel Disease in a Large European Cohort

Inflammatory bowel disease (IBD) is characterized by a chronic relapsing intestinal inflammation, typically starting in early adulthood. IBD is subdivided into two subtypes, on the basis of clinical and histologic features: Crohn disease and ulcerative colitis (UC). Previous genomewide searches identified regions harboring susceptibility loci on chromosomes 1, 3, 4, 7, 12, and 16. To expand our understanding of the genetic risk profile, we performed a 9-cM genomewide search for susceptibility loci in 268 families containing 353 affected sibling pairs. Previous linkages on chromosomes 12 and 16 were replicated, and the chromosome 4 linkage was extended in this sample. New suggestive evidence for autosomal linkages was observed on chromosomes 1, 6, 10, and 22, with LOD scores of 2.08, 2.07, 2.30, and 1.52, respectively. A maximum LOD score of 1.76 was observed on the X chromosome, for UC, which is consistent with the clinical association of IBD with Ullrich-Turner syndrome. The linkage finding on chromosome 6p is of interest, given the possible contribution of human leukocyte antigen and tumor necrosis-factor genes in IBD. This genomewide linkage scan, done with a large family cohort, has confirmed three previous IBD linkages and has provided evidence for five additional regions that may harbor IBD predisposition genes.

Brief communication. High levels of conservation at microsatellite loci among ictalurid catfishes

Abstract The potential of microsatellite sequences as genetic markers in channel catfish (Ictalurus punctatus) was investigated with respect to their variability, inheritance, and usefulness in related species. Six small insert genomic DNA libraries enriched for six families of microsatellites of channel catfish were constructed. We describe here the isolation, characterization, and PCR amplification of 32 microsatellites from channel catfish. The flanking primer regions of microsatellite loci were highly conserved between channel catfish and blue catfish (I. furcatus). Of the 32 loci, 29 were amplified from blue catfish using primers designed from channel catfish, indicating conservation of primer binding sequences. Most of the amplified alleles from channel catfish and blue catfish were polymorphic. White catfish (Ameiurus catus) and flathead catfish (Pylodictus olivaris) loci were also amplified. The microsatellite markers are highly polymorphic for all catfish species tested and are inherited as codominant markers. They should be highly useful for construction of genetic linkage maps of catfish and for marker-assisted selection.

Evaluation of AFLP for genetic mapping in Pinus radiata D. Don

Efficient construction of reasonable density genetic linkage maps is an essential component of QTL detection programmes. The AFLP technique has been used to produce genetic linkage maps in a range of species. We have developed protocols to generate reproducible AFLP profiles in Pinus radiata and have evaluated the inheritance and informativeness of AFLP markers in this important timber species. The large genome size of P. radiata necessitated increased levels of selection at both the pre-amplification and selective amplification steps of the AFLP protocol to generate reproducible AFLP profiles. Once optimised ca. 41.3 scorable AFLP bands were resolvable through denaturing gels, of which 48.4% were polymorphic in a screen of eight unrelated trees. This level of polymorphism is ca. three times higher than with RAPD markers. The total number of bands and the number of polymorphismic bands per PCR were ca. halved when AFLPs were electrophoresed on non-denaturing gels and stained with ethidium bromide. Using the protocols developed, AFLP is an efficient method for generating the DNA markers required for genetic linkage map construction in P. radiata.

Designs of reference families for the construction of genetic linkage maps

The reference family panel is the foundation of a gene mapping program because it affects the cost and quality of the genetic linkage maps, and should be designed to yield reliable linkage detection and locus ordering at minimal gene mapping cost. A map cost function was defined as the number of genotypes required per marker per unit of genome coverage and was used to obtain optimal designs with respect to linkage detection. An ordering reliability function was defined as the likelihood ratio of the most likely order to the second most likely order of genetic markers and was used to find optimal designs with respect to locus ordering. Optimum levels of recombination frequency were found to be in the neighborhood of 0.11‐0.15 for linkage detection and were in the region of 0.05‐0.20 for locus ordering. Therefore, recombination frequencies optimal for linkage detection are also optimal for locus ordering. Based on the optimal detection levels, sample size (number of offspring) and map cost requirements were derived for six representative designs, assuming gender‐specific linkage maps and two alleles with equal frequency for each marker. The sample size required for linkage detection ranged from 168 to 432 offspring for full‐sib designs and ranged from 350 to 600 offspring for half‐sib designs depending on the family size and the target LOD score, with corresponding minimal map costs of 10‐20 genotypes per marker per centiMorgan map coverage. Locus ordering generally requires more genotypes than linkage detection. For full‐sib designs, meioses from both genders should be used for locus ordering even when the maps are gender‐specific. For half‐sib designs, additional families may be needed for locus ordering. Sample size for ordering closely linked loci as required by positional cloning were provided. Effects of family size, grandparents, and marker polymorphism on design efficiency were analyzed.

Inheritance of RAPD markers in channel catfish (Ictalurus punctatus), blue catfish (I. furcatus), and their F1, F2 and backcross hybrids

The channel catfish (Ictalurus punctatus) has become the most important aquaculture species in the USA. A genetic linkage map in catfish is needed to improve efficiency of breeding by marker‐assisted selection (MAS) and for identification of economically important genes such as disease resistance genes. To identify DNA‐based genetic polymorphism, the present authors tested 42 randomly amplified polymorphic DNA (RAPD) primers for their utility in identifying genetic polymorphism in catfish. Out of these primers, 22 generated 171 highly reproducible RAPD markers, producing almost eight polymorphic bands per primer. The remaining 20 primers produced an additional 20 polymorphic bands. The RAPD markers were highly reproducible, transmitted to F1 hybrids, and segregated in F2 or backcross progeny in ratios that did not differ from Mendelian expectations. Because the interspecific hybrids of channel catfish and blue catfish are fertile, RAPD markers using the interspecific hybrid system will be useful for rapid construction of genetic linkage maps of catfish and for analysis of important quantitative trait loci.

Construction of a genetic linkage map and identification of AFLP markers for resistance to root-knot nematodes in peach rootstocks

Construction of a genetic linkage map and identification of AFLP markers for resistance to root-knot nematodes in peach rootstocks

Genetic Linkage of Randomly Amplified Polymorphic DNA (RAPD) Markers in Sweetpotato

RAPD marker analyses were completed on parents and progeny of two sweetpotato [Ipomoea batatas (L.) Lam.] crosses to determine the feasibility of genetic linkage map construction. A total of 100 primers was tested and 96 produced amplified genomic DNA fragments. The average number of polymorphisms per primer was 0.69. A total of 134 polyphorphic markers was observed and 74 (60%) segregated 1 band present : 1 band absent as needed for use in genetic linkage mapping of polyploids. The 60% of RAPD markers that segregated 1:1 shows that genetic linkage mapping of the hexaploid sweetpotato by RAPD marker analysis is feasible. Linkage was determined for all markers that segregated 1:1 and five pairs of linked markers were found. These were the first linked molecular markers found in sweetpotato and they show that construction of a genetic linkage map is feasible. A genetic linkage map will be a valuable tool to assist in genetic improvements.

An incremental algorithm for efficient multipoint linkage analysis.

While much effort has gone into developing efficient algorithms for calculating multipoint likelihoods, these calculations still form a significant bottleneck in the construction of genetic linkage maps. Our approach to this problem is based on incremental processing techniques, which attempt to reduce the time required to perform iterative computations by storing intermediate results during the initial iteration, so that they may be reused with little extra computation in subsequent iterations. We have developed an incremental program which provides a more efficient substitute for the CMAP program of the LINKAGE package. Our incremental approach stores intermediate results of the computations in the form of a rational function. Thus, computing the likelihood for one position of an unmapped marker locus requires only the reevaluation of the rational function. Timing data suggest that when pedigrees are fully or nearly fully typed, our program runs about 3-fold faster than CMAP to compute the likelihood for one position of a marker locus. Additional positions do not add any appreciable time to our program; thus, speedups become more pronounced as more marker locus positions are considered.

Phytophthora sojae avirulence genes, RAPD, and RFLP markers used to construct a detailed genetic linkage map.

Two crosses between different races of Phytophthora sojae were established using one race as a common parent in both crosses. F2 populations comprising over 200 individuals were generated for each cross. A subset of 53 F2 individuals from each cross was selected at random for genetic analysis of virulence/avirulence and molecular markers, and finally the construction of a detailed genetic linkage map. The linkage map developed for P. sojae is based on a total of 257 markers (22 RFLP, 228 RAPD, and 7 avirulence genes). The linkage map comprises 10 major and 12 minor linkage groups covering a total of 830.5 cM. Close linkage was observed between Avr4 and Avr6 (0.0 cM), Avr1b and Avr1k (0.0 cM), and Avr3a and Avr5 (4.6 cM). Coupling phase linkage of RFLP and RAPD markers to all seven avirulence genes was identified at the minimum and maximum distances of 0.0 and 14.7 cM, respectively.

A genetic linkage map of the laboratory rat, Rattus norvegicus

We report the construction of the first complete genetic linkage map of the laboratory rat. By testing 1171 simple sequence length polymorphisms (SSLPs), we have identified 432 markers that show polymorphisms between the SHR and BN rat strains and mapped them in a single (SHR x BN) F2 intercross. The loci define 21 large linkage groups corresponding to the 21 rat chromosomes, together with a pair of nearby markers on chromosome 9 that are not linked to the rest of the map. Because 99.5% of the markers fall into one of the 21 large linkage groups, the maps appear to cover the vast majority of the rat genome. The availability of the map should facilitate whole genome scans for genes underlying qualitative and quantitative traits relevant to mammalian physiology and pathobiology.

Correction: Corrigendum: Automated construction of genetic linkage maps using an expert system (MultiMap): a human genome linkage map

Correction: Corrigendum: Automated construction of genetic linkage maps using an expert system (MultiMap): a human genome linkage map