水稻ILP标记遗传图谱的构建

内含子长度多态性(ILP)是一种基于PCR的新型分子标记, 具有许多突出的优点。我们先前利用已公布的籼稻品种93-11和粳稻品种日本晴的基因组序列数据, 已开发了172个水稻ILP标记。为了检验这些ILP标记的可靠性及其在遗传作图中的可用性, 利用一个BC1F1(日本晴/93-11//日本晴)群体, 构建了一张含172个ILP标记座位和13个SSR标记座位的水稻遗传图谱, 总长度为1 905.7 cM。比较显示, 图谱上所有标记的顺序与其物理顺序完全一致, 证明了利用ILP标记进行遗传作图的可行性和有效性。文中还对标记偏分离现象进行了分析, 发现在第6号染色体短臂上存在一个严重偏分离的区域。     

Construction of a cytogenetically anchored microsatellite map in rabbit

Rabbit (Oryctolagus cuniculus) represents a valuable source of biomedical models and corresponds to a small but active economic sector in Europe for meat and fur. The rabbit genome has not been thoroughly studied until recently, and high-resolution maps necessary for identification of genes and quantitative trait loci (QTL) are not yet available. Our aim was to isolate over 300 new and regularly distributed (TG)n or (TC)n rabbit microsatellites. To achieve this purpose, 164 microsatellite sequences were isolated from gene-containing bacterial artificial chromosome (BAC) clones previously localized by fluorescence in situ hybridization (FISH) on all the rabbit chromosomes. In addition, 141 microsatellite sequences were subcloned from a plasmid genomic library, and for 41 of these sequences, BAC clones were identified and FISH-mapped. TC repeats were present in 62% of the microsatellites derived from gene-containing BAC clones and in 22% of those from the plasmid genomic library, with an average of 42.9% irrespective of the microsatellite origin. These results suggest a higher proportion of (TC)n repeats and a nonhomogeneous distribution of (TG)n and (TC)n repeats in the rabbit genome compared to those in man. Among the 305 isolated microsatellites, 177 were assigned to 139 different cytogenetic positions on all the chromosomes except rabbit Chromosome 21. Sequence similarity searches provided hit locations on the Human Build 35a and hypothetical assignments on rabbit chromosomes for ten additional microsatellites. Taken together, these results report a reservoir of 305 new rabbit microsatellites of which 60% have a cytogenetic position. This is the first step toward the construction of an integrated cytogenetic and genetic map based on microsatellites homogeneously anchored to the rabbit genome.     

Construction of a genetic linkage map in tetraploid species using molecular markers

This article presents methodology for the construction of a linkage map in an autotetraploid species, using either codominant or dominant molecular markers scored on two parents and their full-sib progeny. The steps of the analysis are as follows: identification of parental genotypes from the parental and offspring phenotypes; testing for independent segregation of markers; partition of markers into linkage groups using cluster analysis; maximum-likelihood estimation of the phase, recombination frequency, and LOD score for all pairs of markers in the same linkage group using the EM algorithm; ordering the markers and estimating distances between them; and reconstructing their linkage phases. The information from different marker configurations about the recombination frequency is examined and found to vary considerably, depending on the number of different alleles, the number of alleles shared by the parents, and the phase of the markers. The methods are applied to a simulated data set and to a small set of SSR and AFLP markers scored in a full-sib population of tetraploid potato.     

Construction of a genetic linkage map in celery using DNA-based markers.

A F2 population of two celery cultivated types (Apium graveolens L. var. rapaceum and A. graveolens L. var. secalinum) was used to construct a linkage map consisting of 29 RFLP (restriction fragment length polymorphism), 100 RAPD (random amplified polymorphic DNA), four isozyme, one disease resistance, and one growth habit markers. The map contains 11 major groups and 9 small groups and has a total length of 803 cM with an average distance of 6.4 cM between two adjacent loci. Ten percent of the RAPDs segregated as codominant markers and their allelic homologies were tested by Southern hybridization. One-quarter of the dominant RAPDs were linked in repulsion phase, whereas the majority of them were linked to either codominant or dominant markers in coupling phase. About 10% of the markers showed significant segregation distortion. The detectable level of duplications in the celery genome was relatively low.     

Construction of a genetic linkage map in Fenneropenaeus chinensis using SNP markers

Genetic linkage maps of Fenneropenaeus chinensis were constructed using a “double pseudo-testcross” strategy with 200 single nucleotide polymorphisms (SNPs) markers. This study represents the first SNP genetic linkage map for F. chinensis. The parents and F ₁ progeny of 100 individuals were used as mapping populations. 21 genetic linkage groups in the male and female maps were identified. The male linkage map was composed of 115 loci and spanned 879.7 cM, with an average intermarker spacing of 9.4 cM, while the female map was composed of 119 loci and spanned 876.2 cM, with an average intermarker spacing of 8.9 cM. The estimated coverage of the linkage maps was 51.94% for the male and 53.77% for the female, based on two estimates of genome length. The integrated map contains 180 markers distributed in 16 linkage groups, and spans 899.3 cM with an average marker interval of 5.2 cM. This SNP genetic map lays the foundation for future shrimp genomics and genetic breeding studies, especially the discovery of gene or regions for economically important traits in Chinese shrimp.     

Integration of gene-based markers in a pearl millet genetic map for identification of candidate genes underlying drought tolerance quantitative trait loci

Background  

Identification of genes underlying drought tolerance (DT) quantitative trait loci (QTLs) will facilitate understanding of molecular mechanisms of drought tolerance, and also will accelerate genetic improvement of pearl millet through marker-assisted selection. We report a map based on genes with assigned functional roles in plant adaptation to drought and other abiotic stresses and demonstrate its use in identifying candidate genes underlying a major DT-QTL.     

Construction of a genetic linkage map for roses using RAPD and AFLP markers

A segregating population of diploid rose hybrids (2n = 2x = 14) was used to construct the first linkage maps of the rose genome. A total of 305 RAPD and AFLP markers were analysed in a population of 60 F₁ plants based on a so-called ”double-pseudotestcross” design. Of these markers 278 could be located on the 14 linkage groups of the two maps, covering total map lengths of 326 and 370 cM, respectively. The average distances between markers in the maps for 93/1–117 and 93/1–119 is 2.4 and 2.6 cM, respectively. In addition to the molecular markers, genes controlling two phenotypic characters, petal number (double versus single flowers) and flower colour (pink versus white), were mapped on linkage groups 3 and 2, respectively. The markers closest to the gene for double flowers, Blfo, and to the gene for pink flower colour, Blfa, cosegregated without recombinants. The maps provide a tool for further genetic analyses of horticulturally important genes as, for example, resistance genes and a starting point for marker-assisted breeding in roses. Received: 22 September 1998 / Accepted: 12 March 1999     

Construction of a rat genetic map by using randomly amplified microsatellite polymorphism (RAMP) markers

Many rat strains have been employed in the genetic study of quantitative traits such as blood pressure. In such genetic studies, it is essential to prepare rat genetic maps fine enough to identify the genes regulating quantitative traits. However, it is not an easy task to isolate a sufficient number of genetic markers polymorphic between a particular pair of rat strains. In this study, we applied the randomly amplified microsatellite polymorphism (RAMP) method, a simple method to identify co-dominant markers (Wu et al. Nucleic Acids Res 22, 3257, 1994), to isolate markers polymorphic between the stroke-prone spontaneously hypertensive rat and the Wistar-Kyoto rat, a genetically hypertensive strain and its normotensive control strain, which share a common genetic background. We successfully identified 111 RAMP markers distributed throughout the rat genome after screening 3046 sets of primers. We also showed that we could isolate ordinary simple-sequence-length-polymorphism markers by cloning RAMP markers. The RAMP method is a simple and efficient way to identify co-dominant genetic markers on mammalian genomes. Received: 10 October 1997 / Accepted: 16 March 1998     

A framework genetic map of Muscadinia rotundifolia

This study presents a framework linkage map based on microsatellite markers for Muscadinia rotundifolia (1n?=?20). The mapping population consisted of 206 progeny generated from a cross of two M. rotundifolia varieties, 'Fry' and 'Trayshed'. A total of 884 primers were tested for their ability to amplify markers: 686 amplified and 312 simple sequence repeat (SSR) primer pairs generated 322 polymorphic markers for either one or both parents. The map for the female parent 'Fry' consisted of 212 markers and covered 879?cM on 18 chromosomes. The average distance between the markers was 4.1?cM and chromosome 6 was not represented due to a lack of polymorphic markers. The map for the male parent 'Trayshed' consisted of 191 markers and covered 841?cM on 19 chromosomes. The consensus map consisted of 314 markers on 19 chromosomes with a total distance of 1,088?cM, which represented 66?% of the distance covered by the Vitis vinifera reference linkage map. Marker density varied greatly among chromosomes from 5 to 35 mapped markers. Relatively good synteny was observed across 19 chromosomes based on markers in common with the V. vinifera reference map. Extreme segregation distortion was observed for chromosome 8 and 14 on the female parent map, and 4 on the male parent map. The lack of mapping coverage for the 20th M. rotundifolia chromosome is discussed in relation to possible evolutionary events that led to the reduction in chromosome number from 21 to 19 in the ancestral genome.     

A gene-based RFLP map of petunia

Due in large part to the data accumulated from years of classic genetic analysis, petunia (Petunia hybrida Vilm) has remained a useful model system, particularly for studies of gene regulation and genome structure. We have used three segregating populations of petunia, including those serving as the source of an earlier actin gene RFLP map, for RFLP mapping of several additional genes. Twenty-seven loci have been merged with 11 previously mapped morphological and biochemical markers. Our results contribute additional evidence to reports of a high degree of genome plasticity and segregation distortion in this species and suggest that petunia may be a useful plant system for detailed analysis of plant genome organization, activity and evolution. Received 14 July 1999 / Accepted: 30 July 1999     

Construction of a 10,000-marker ultradense genetic recombination map of potato: providing a framework for accelerated gene isolation and a genomewide physical map

An ultradense genetic linkage map with >10,000 AFLP loci was constructed from a heterozygous diploid potato population. To our knowledge, this is the densest meiotic recombination map ever constructed. A fast marker-ordering algorithm was used, based on the minimization of the total number of recombination events within a given marker order in combination with genotyping error-detection software. This resulted in "skeleton bin maps," which can be viewed as the most parsimonious marker order. The unit of distance is not expressed in centimorgans but in "bins." A bin is a position on the genetic map with a unique segregation pattern that is separated from adjacent bins by a single recombination event. Putative centromeres were identified by a strong clustering of markers, probably due to cold spots for recombination. Conversely, recombination hot spots resulted in large intervals of up to 15 cM without markers. The current level of marker saturation suggests that marker density is proportional to physical distance and independent of recombination frequency. Most chromatids (92%) recombined once or never, suggesting strong chiasma interference. Absolute chiasma interference within a chromosome arm could not be demonstrated. Two examples of contig construction and map-based cloning have demonstrated that the marker spacing was in accordance with the expected physical distance: approximately one marker per BAC length. Currently, the markers are used for genetic anchoring of a physical map of potato to deliver a sequence-ready minimal tiling path of BAC contigs of specific chromosomal regions for the potato genome sequencing consortium (http://www.potatogenome.net).     

Construction of a genetic map for arabica coffee

We have used AFLPs to construct a genetic linkage map on a pseudo-F₂ population of arabica coffee (Coffea arabica L.) derived from a cross between the cultivars Mokka hybrid and Catimor. Sixty trees from this population were selected on the basis of plant height distribution to construct a linkage map. A total of 456 dominant markers and eight co-dominant markers were generated from 288 AFLP primer combinations. Of the total number of markers generated, 68% were from cv. Catimor, 30% from cv. Mokka hybrid, and 2% were co-dominant. This distribution suggests that the heterozygosity within the cv. Catimor sub-genomes was twice that within the cv. Mokka hybrid sub-genomes. Linkage groups were constructed using MAPMAKER version 3.0, resulting in 16 major linkage groups containing 4–21 markers, and 15 small linkage groups consisting of 2–3 linked markers each. The total length of the map was 1,802.8 cM, with an average distance of 10.2 cM between adjacent markers. This genetic map will serve as the framework for mapping QTL controlling source-sink traits in the same population.Communicated by H.F. Linskens     

Construction of a framework map in Pinus contorta subsp. latifolia using random amplified polymorphic DNA markers.

We report on the construction of the first random amplified polymorphic DNA (RAPD) framework map in Pinus contorta subsp. latifolia. Genomic DNA of haploid megagametophytes from 90 open-pollinated seeds originating from a single tree were amplified with 840 random decamer oligonucleotide primers by the polymerase chain reaction. Three-hundred twenty-eight RAPD markers with fragment sizes that ranged between 260 and 3080 base pairs were found segregating at 110 random decamer oligonucleotide primers. Of these 328 RAPD markers, 148 were mapped to 16 framework linkage groups and 77 were mapped as accessory markers onto the framework linkage groups, on a support interval of minimal LOD score of 3. The 16 framework maps cover a distance of 2287 cM. The estimate of genome size was 2407 cM with a 95% confidence interval of 2304-2459 cM.     

Construction of a genetic linkage map in the wild plant Mimulus using RAPD and isozyme markers.

As a first step to mapping quantitative trait loci for mating system differences, a genetic linkage map was generated from an interspecific backcross between Mimulus guttatus and Mimulus platycalyx. The linkage map consists of 99 RAPD and two isozyme markers. Eighty-one of these markers were mapped to 15 linkage groups, spanning 1437 contiguous centiMorgans, and covering 58% of the estimated genome. The genome length of Mimulus is estimated at 2474 +/- 35 cM; bootstrapping indicates that only ca. 40 markers are needed to give an accurate estimate of genome length. Further statistical analyses indicate that many RAPD markers cannot be ordered with certainty and that uncertain linkage groups tend to map nonlinearly even under commonly used mapping functions. Strategies for speeding up the mapping process for a wild species and possible applications of a partial linkage map in evolutionary studies are discussed. Key words : linkage map, mating system, Mimulus, RAPD.     

Cosmid-derived markers anchoring the bovine genetic map to the physical map

The mapping strategy for the bovine genome described in this paper uses large insert clones as a tool for physical mapping and as a source of highly polymorphic microsatellites for genetic typing, and was one objective of the BovMap Project funded by the European Union (UE). Eight-three cosmid and phage clones were characterized and used to physically anchor the linkage groups defining all the bovine autosomes and the X Chromosome (Chr). By combining physical and genetic mapping, clones described in this paper have led to the identification of the linkage groups corresponding to Chr 9, 12, 16, and 25. In addition, anchored loci from this study were used to orient the linkage groups corresponding to Chr 3, 7, 8, 9, 13, 16, 18, 19, and 28 as identified in previously published maps. Comparison of the estimated size of the physical and linkage maps suggests that the genetic length of the bovine genome may be around 4000 cM. Received: 1 July 1996 / Accepted: 13 September 1996     

Construction of a basic genetic map for alfalfa using RFLP, RAPD, isozyme and morphological markers

The genetic map for alfalfa presented here has eight linkage groups representing the haploid chromosome set of the Medicago species. The genetic map was constructed by ordering the linkage values of 89 RFLP, RAPD, isozyme and morphological markers collected from a segregating population of 138 individuals. The segregating population is self-mated progeny of an F1 hybrid plant deriving from a cross between the diploid (2n=2x=16) yellow-flowered Medicago sativa ssp. quasifalcata and the diploid (2n=2x=16) blue-flowered M. sativa ssp. coerulea. The inheritance of many traits displayed distorted segregation, indicating the presence of lethal loci in the heterozygotic parent plants. In spite of the lack of uniform segregation, linkage groups could be assigned and the order of the markers spanning > 659 centimorgans could be unambiguously determined. This value and the calculated haploid genome size for Medicago (1n=1x=1.0 x 10⁹ bp) gives a ratio of < 1500 kb per centimorgan.     

Construction of a genetic map of Pseudomonas mendocina bacteria

Based on the results of matings with interrupted conjugation and analysis of marker joint inheritance frequencies, distances between 26 genetic determinants were estimated and a genetic map of Pseudomonas mendocina bacteria was constructed.     

Construction of a genetic map for Caulobacter crescentus.

RP4-mediated conjugation has been used to transfer large fragments of chromosomal material in Caulobacter crescentus. In this system, conjugation proceeds from multiple origins, and haploid recombinants are recovered at frequencies of 10(-6) and 10(-7) per donor cell. The data from five-factor crosses were subjected to computer-assisted crossover analyses as a rapid method to determine marker order. Using this information and data from additional two- and three-factor crosses mediated by RP4 or the generalized transducing bacteriophage phi Cr30, we constructed the first genetic map for C. crescentus.     

Construction of an oilseed rape (Brassica napus L.) genetic map with SSR markers

We constructed a Brassica napus genetic map with 240 simple sequence repeats (SSR) primer pairs from private and public origins. SSR, or microsatellites, are highly polymorphic and efficient markers for the analysis of plant genomes. Our selection of primer pairs corresponded to 305 genetic loci that we were able to map. In addition, we also used 52 sequence-characterized amplified region primer pairs corresponding to 58 loci that were developed in our lab. Genotyping was performed on six F2 populations, corresponding to a total of 574 F2 individual plants, obtained according to an unbalanced diallel cross design involving six parental lines. The resulting consensus map presented 19 linkage groups ranging from 46.2 to 276.5 cM, which we were able to name after the B. napus map available at , thus enabling the identification of the A genome linkage groups originating from the B. rapa ancestor and the C genome linkage groups originating from the B. oleracea ancestor in the amphidiploid genome of B. napus. Some homoeologous regions were identified between the A and the C genomes. This map could be used to identify more markers, which would eventually be linked to genes controlling important agronomic characters in rapeseed. Furthermore, considering the good genome coverage we obtained, together with an observed homogenous distribution of the loci across the genome, this map is a powerful tool to be used in marker-assisted breeding. Electronic Supplementary Material Supplementary material is available for this article at     

Soybean genetic map of RAPD markers assigned to an existing scaffold RFLP map

A 356-marker linkage map of Glycine max (L.) Merr. (2n = 20) was established by anchoring 106 RAPD markers to an existing RFLP map built with a large recombinant inbred line population (330 RILs). This map comprises 24 major and 11 minor linkage groups for this genome which is estimated to be approximately 3,275 cM. The RAPD markers show similar distribution throughout the genome and identified similar levels of polymorphism as the RFLP markers used in the framework. By using a subset population to anchor the RAPD markers, it was possible to enhance the throughput of selecting and adding reliable marker loci to the existing map. The procedures to generate a dependable genetic linkage map are also described in this report.