Tissue expression and bioinformatics analysis of the vitellogenin gene of Asian arowana (Scleropages formosus)

The RACE technique was used to clone the full‐length vitellogenin (VTG) cDNA sequence of Asian arowana (Scleropages formosus). The full‐length sequence was 5,550 bp with an open reading frame of 5,238 bp, encoding 1,745 amino acids, and 5′ and 3′ UTRs (untranslated regions) of 45 bp and 267 bp, respectively. Phylogenetic analysis showed that S. formosus and silver arowana (Osteoglossum bicirrhosum) share a close evolutionary relationship (bootstrap 100%). The quantitative real‐time PCR results showed that vtg expression was significantly higher in liver and gonads of male and female fish compared with its expression in the other tissues tested (p < 0.01). The relative expression levels of vtg in liver, gland, kidney, heart, head kidney, and brain of female fish were significantly higher than in the corresponding tissues of male fish (p < 0.05).     

Developing microsatellite markers from cDNA: a tool for adding expressed sequence tags to the genetic linkage map of the chicken

A chicken embryonic cDNA library was screened with a (TG)₁₃ probe in order to develop polymorphic microsatellite markers. The redundancy of the embryonic cDNA library with a chicken brain cDNA library, which was used for microsatellite development in a previous study, was extremely high. Of the 300 (TG)₁₃ positive clones, only 80 were unique for the embryonic cDNA library. Still, nine expressed sequences derived from the embryonic cDNA library were mapped in the Wageningen (WAU) resource population. In addition seven microsatellite markers from the chicken brain cDNA library, which were monomorphic or unlinked in the two international reference families in the previous study, were also mapped in the WAU population. Three of the 16 mapped chicken expressed sequence tags (ESTs) showed relatively high percentages of sequence similarity to sequences found in other species. As two of these genes, RAB6 and ZFX/ZFY, have been mapped in humans, they contribute to the comparative map of the chicken.     

Construction of a genetic linkage map for silver carp (Hypophthalmichthys molitrix)

For silver carp (Hypophthalmichthys molitrix), a combined microsatellite (or simple sequence repeat) and amplified fragment length polymorphism (AFLP) sex average linkage map was constructed. A total of 483 markers (245 microsatellites and 238 AFLPs) were assigned to 33 linkage groups. The map spanned 1352.2 cM, covering 86.4% of the estimated genome size of silver carp. The maximum and average spaces between 420 loci were 21.5 cM and 3.2 cM, respectively. The length of linkage groups ranged from 3.6 cM to 98.5 cM with an average of 41.0 cM. The number of markers per group varied from 2 to 44 with an average of 14.6. The AFLP markers significantly improved the integrity of microsatellite-based linkage groups and increased the genome coverage and marker evenness. A genome-wide recombination suppression was observed in male. In an extreme case, six microsatellites co-segregated in male, but spanned a 45.1 cM region in female.     

A genetic linkage map of durum wheat

 A genetic linkage map of tetraploid wheat [Triticum turgidum (L.) Thell.] was constructed using segregation data from a population of 65 recombinant inbred lines (RILs) derived from a cross between the durum wheat cultivar Messapia and accession MG4343 of T. turgidum (L.) Thell. ssp dicoccoides (Korn.) Thell. A total of 259 loci were analysed, including 244 restriction fragment length polymorphisms (RFLPs), one PCR (polymerase chain reaction) marker (a sequence coding for a LMW (low-molecular-weight) glutenin subunit gene located at the Glu-B3 locus), seven biochemical (six seed-storage protein loci and one isozyme locus) and seven morphological markers. A total of 213 loci were mapped at a LOD≥3 on all 14 chromosomes of the A and B genomes. The total length of the map is 1352 cM and the average distance between adjacent markers is 6.3 cM. Forty six loci could not be mapped at a LOD≥3. A fraction (18.6%) of the markers deviated significantly from the expected Mendelian ratios; clusters of loci showing distorted segregation were found on chromosomes 1B, 3AL, 4AL, 6AL and 7AL. The durum wheat map was compared with the published maps of bread wheat using several common RFLP markers and general features are discussed. The markers detected the known structural rearrangements involving chromosomes 4A, 5A and 7B as well as the translocation between 2B-6B, but not the deletion on 2BS. This map provides a useful tool for analysing and breeding economically important quantitative traits and for marker-assisted selection, as well as for studies of genome organisation in small grain cereal species. Received: 5 January 1998 / Accepted: 31 March 1998     

The first genetic linkage map of Eucommia ulmoides

In accordance with pseudo-testcross strategy, the first genetic linkage map of Eucommia ulmoides Oliv. was constructed by an F₁ population of 122 plants using amplified fragment length polymorphism (AFLP) markers. A total of 22 AFLP primer combinations generated 363 polymorphic markers. We selected 289 markers segregating as 1:1 and used them for constructing the parent-specific linkage maps. Among the candidate markers, 127 markers were placed on the maternal map LF and 108 markers on the paternal map Q1. The maternal map LF spanned 1116.1 cM in 14 linkage groups with a mean map distance of 8.78 cM; the paternal map Q1 spanned 929.6 cM in 12 linkage groups with an average spacing of 8.61 cM. The estimated coverage of the genome through two methods was 78.5 and 73.9% for LF, and 76.8 and 71.2% for Q1, respectively. This map is the first linkage map of E. ulmoides and provides a basis for mapping quantitative-trait loci and breeding applications.     

A second‐generation genetic linkage map for bighead carp (Aristichthys nobilis) based on microsatellite markers

Bighead carp (Aristichthys nobilis) is an important aquaculture fish worldwide. Genetic linkage maps for the species were previously reported, but map resolution remained to be improved. In this study, a second‐generation genetic linkage map was constructed for bighead carp through a pseudo‐testcross strategy using interspecific hybrids between bighead carp and silver carp. Of the 754 microsatellites genotyped in two interspecific mapping families (with 77 progenies for each family), 659 markers were assigned to 24 linkage groups, which were equal to the chromosome numbers of the haploid genome. The consensus map spanned 1917.3 cM covering 92.8% of the estimated bighead carp genome with an average marker interval of 2.9 cM. The length of linkage groups ranged from 52.2 to 133.5 cM with an average of 79.9 cM. The number of markers per linkage group varied from 11 to 55 with an average of 27.5 per linkage group. Normality tests on interval distances of the map showed a non‐normal marker distribution; however, significant correlation was found between the length of linkage group and the number of markers below the 0.01 significance level (two‐tailed). The length of the female map was 1.12 times that of the male map, and the average recombination ratio of female to male was 1.10:1. Visual inspection showed that distorted markers gathered in some linkage groups and in certain regions of the male and female maps. This well‐defined genetic linkage map will provide a basic framework for further genome mapping of quantitative traits, comparative mapping and marker‐assisted breeding in bighead carp.     

Construction of a genetic linkage map of Japanese quail (Coturnix japonica) based on AFLP and microsatellite markers

The Japanese quail (Coturnix japonica) is a notably valuable egg and meat producer but has also been used as a laboratory animal. In the present study, we constructed a Japanese quail linkage map with 1735 polymorphic amplified fragment length polymorphisms markers, and nine chicken microsatellite (MS) markers, as well as sex and phenotypes of two genetic diseases; a muscular disorder (LWC) and neurofilament-deficient mutant (Quv). Linkage analysis revealed 578 independent loci. The resulting linkage map contained 44 multipoint linkage groups covering 2597.8 cM and an additional 218.2 cM was contained in 21 two-point linkage groups. The total map was 2816 cM in length with an average marker interval of 5.5 cM. The Quv locus was located on linkage group 5, but linkage was not found between the LWC locus and any of the markers. Comparative mapping with chicken using orthologous markers revealed chromosomal assignments of the quail linkage group 1 to chicken chromosome 2 (GGA2), 5 to GGA22, 2 to GGA5, 8 to GGA7, 27 to GGA11, 29 to GGA1 and 45 to GGA4.     

A SNP/microsatellite genetic linkage map of the Atlantic cod (Gadus morhua)

A first genetic linkage map of the Atlantic cod ( Gadus morhua ) was produced, based on segregation data from 12 full-sib families of Norwegian origin. The map contained 174 single nucleotide polymorphism markers and 33 microsatellites, distributed on 25 linkage groups and had a length of 1225 cM. A significant difference in recombination rates between sexes was found, the average ratio of female:male recombination rates being 1.78 ± 1.62 (SD).     

A genetic linkage map for coho salmon (Oncorhynchus kisutch)

Construction of genetic linkage maps is an important first step for a variety of genomic applications, such as selective breeding in aquaculture, comparative studies of chromosomal evolution and identification of loci that have played key roles in the evolution of a species. Here we present a sex-specific linkage map for coho salmon. The map was constructed using 148 AFLP markers, 133 microsatellite loci and the phenotypic locus SEX . Twenty-four linkage groups spanning 287.4 cM were mapped in males, and 33 linkage groups spanning 429.7 cM were mapped in females. Several male linkage groups corresponded to two female linkage groups. The combination of linkage groups across both sexes appeared to characterize regions of 26 chromosomes. Two homeologous chromosomes were identified based on information from duplicated loci. Homologies between the coho and rainbow trout maps were examined. Eighty-six loci were found to form common linkage relationships between the two maps; these relationships provided evidence for whole-arm fissions, fusions and conservation of chromosomal regions in the evolution of these two species.     

A first-generation microsatellite linkage map of the Japanese quail

A linkage map of the Japanese quail (Coturnix japonica) genome was constructed based upon segregation analysis of 72 microsatellite loci in 433 F(2) progeny of 10 half-sib families obtained from a cross between two quail lines of different genetic origins. One line was selected for long duration of tonic immobility, a behavioural trait related to fearfulness, while the other was selected based on early egg production. Fifty-eight of the markers were resolved into 12 autosomal linkage groups and a Z chromosome-specific linkage group, while the remaining 14 markers were unlinked. The linkage groups range from 8 cM (two markers) to 206 cM (16 markers) and cover a total map distance of 576 cM with an average spacing of 10 cM between loci. Through comparative mapping with chicken (Gallus gallus) using orthologous markers, we were able to assign linkage groups CJA01, CJA02, CJA05, CJA06, CJA14 and CJA27 to chromosomes. This map, which is the first in quail based solely on microsatellites, is a major step towards the development of a quality molecular genetic map for this valuable species. It will provide an important framework for further genetic mapping and the identification of quantitative trait loci controlling egg production and fear-related behavioural traits in quail.     

中国植物遗传连锁图谱构建研究进展

遗传连锁图谱构建是基因组研究中的重要环节,是基因定位与克隆乃至基因组结构与功能研究的基础上。近十几年来,分子生物学特别是分子标记技术的飞速发展,为构建高饱和的植物遗传连锁图谱和利用分子标记进行辅助育种奠定了基础。综述了我国在植物遗传连锁图谱构建研究方面的进展及发展动态,列举了我国利用DNA分子标记构建的34张植物遗传连锁图谱实例,且讨论了当前我国在该领域研究中存在的问题并提出了解决途径。     

A genetic linkage map for Eucalyptus globulus with candidate loci for wood,fibre, and floral traits

A genetic linkage map containing potential candidate loci for wood, fibre and floral traits has been constructed for Eucalyptus globulus (Labill.) based on the segregation of 249 codominant loci in an outbred F₁ population of 148 individuals. The map contains 204 RFLP loci, including 31 cambium-specific expressed sequence tags (ESTs) and 14 known function genes, and 40 microsatellite and five isozyme loci. Independent male and female maps were constructed, and the 98 loci (39%) that segregated in both parents were used to combine the parental maps into an integrated map. The 249 loci mapped to 11 major linkage groups (n=11 in eucalypts) and a 12th small linkage group containing three loci that segregated in the male parent only. Total map distance is 1375 cM with an average interval of 6 cM. Forty one of the mapped loci identify known proteins (five isozymes) or sequences with known function (14 genes and 22 ESTs). The mapped genes include enzymes involved in lignin and cell-wall polysaccharide biosynthesis, and floral-development genes. This map will be used to locate quantitative trait loci for wood, fibre, and other traits in Eucalyptus. Received: 30 August 2000 / Accepted: 23 March 2001     

Interspecific genetic linkage map, segregation distortion and genetic conversion in coffee (Coffea sp.)

An interspecific partial genetic linkage map of Coffea sp. based on 62 backcross hybrids is presented. F₁ hybrids were generated by a cross between the wild C. pseudozanguebariae and the anciently cultivated C. liberica var. dewevrei (DEW); progeny were then derived from a backcross between F₁ hybrid and DEW. The map construction consisted of a two-step strategy using 5.5 and 3.1 LOD scores revealed by simulation file. The map consisted of 181 loci: 167 amplified fragment length polymorphism (AFLP) and 13 random fragment length polymorphism (RFLP) loci. The markers were assembled into 14 linkage groups, each with 4–31 markers covering 1,144 cM. Segregation distortion was observed for 30% of all loci, in particular 3:1 and 1:3 ratios equally favouring each of the two parents. The existence of such ratios suggests genetic conversion events. This map also represents an initial step towards the detection of quantitative trait loci. Received: 4 Janaury 2000 / Accepted: 17 January 2000     

A sequence-anchored genetic linkage map for the moss, Physcomitrella patens

The moss Physcomitrella patens is a model for the study of plant cell biology and, by virtue of its basal position in land plant phylogeny, for comparative analysis of the evolution of plant gene function and development. It is ideally suited for 'reverse genetic' analysis by virtue of its outstanding ability to undertake targeted transgene integration by homologous recombination. However, gene identification through mutagenesis and map-based cloning has hitherto not been possible, due to the lack of a genetic linkage map. Using molecular markers [amplified fragment length polymorphisms (AFLP) and simple sequence repeats (SSR)] we have generated genetic linkage maps for Physcomitrella. One hundred and seventy-nine gene-specific SSR markers were mapped in 46 linkage groups, and 1574 polymorphic AFLP markers were identified. Integrating the SSR- and AFLP-based maps generated 31 linkage groups comprising 1420 markers. Anchorage of the integrated linkage map with gene-specific SSR markers coupled with computational prediction of AFLP loci has enabled its correspondence with the newly sequenced Physcomitrella genome. The generation of a linkage map densely populated with molecular markers and anchored to the genome sequence now provides a resource for forward genetic interrogation of the organism and for the development of a pipeline for the map-based cloning of Physcomitrella genes. This will radically enhance the potential of Physcomitrella for determining how gene function has evolved for the acquisition of complex developmental strategies within the plant kingdom.     

The first linkage map of the American mink (Mustela vison)

Described herein, the first microsatellite linkage map for the American mink consists of 85 microsatellite markers resolved into 17 linkage groups. The map was constructed using 92 F(1) progeny from five sire families created by crossing mink with different colour types. The linkage groups ranged from 0 to 137 cM. These linkage groups were assigned to 12 of the 14 mink autosomes using a somatic cell hybrid panel. The total map covered 690 sex-averaged Kosambi units with an average marker spacing of 8 cM. This map will facilitate further genetic mapping of monogenic characters and QTL.     

A combined AFLP and microsatellite linkage map and pilot comparative genomic analysis of European sea bass Dicentrarchus labrax L

European sea bass (Dicentrarchus labrax L., Moronidae, Teleostei) sustains a regional fishery and is commonly farmed in the Mediterranean basin, but has not undergone much long-term genetic improvement. An updated genetic linkage map of the European sea bass was constructed using 190 microsatellites, 176 amplified fragment length polymorphisms and two single nucleotide polymorphisms. From the 45 new microsatellite markers (including 31 type I markers) reported in this study, 28 were mapped. A total of 368 markers were assembled into 35 linkage groups. Among these markers, 28 represented type I (coding) markers, including those located within the peptide Y, SOX10, PXN1, ERA and TCRB genes (linkage groups 1, 7, 16, 17 and 27 respectively). The sex-averaged map spanned 1373.1 centimorgans (cM) of the genome. The female map measured 1380.0 cM, whereas the male map measured 1046.9 cM, leading to a female-to-male (F:M) recombination rate ratio of 1.32:1. The intermarker spacing of the second-generation linkage map of the European sea bass was 3.67 cM, which is smaller than that of the first-generation linkage map (5.03 cM). Comparative mapping of microsatellite flanking regions was performed with five model teleosts and this revealed a high percentage (33.6%) of evolutionarily conserved regions with the three-spined stickleback.     

大粒裸燕麦(Avena nuda L.)遗传连锁图谱的构建

以“元莜麦”和“555”杂交得到的281个F2单株为作图群体,利用20对AFLP引物、3对SSR引物和1个穗型性状构建了一张大粒裸燕麦遗传连锁图。该图谱全长1544.8cM,包含19个连锁群,其上分布有92个AFLP标记、3个SSR标记和1个穗型形态标记,不同连锁群标记数为2-14个,长度在23.7-276.3cM之间,平均长度为81.3cM,标记间平均距离为20.1cM。穗型标记分离比符合3：1,11个AFLP标记表现为偏分离,偏分离比为11.5%。该图谱符合遗传连锁框架图的要求,为今后大粒裸燕麦的QTL定位、分子标记辅助育种和比较基因组学等研究奠定基础。     

Paternal phylogeography and genetic diversity of East Asian goats

This study was a first analysis of paternal genetic diversity for extensive Asian domestic goats using SRY gene sequences. Sequencing comparison of the SRY 3′‐untranslated region among 210 Asian goats revealed four haplotypes (Y1A, Y1B, Y2A and Y2B) derived from four variable sites including a novel substitution detected in this study. In Asian goats, the predominant haplotype was Y1A (62%) and second most common was Y2B (30%). Interestingly, the Y2B was a unique East Asian Y chromosomal variant, which differentiates eastern and western Eurasian goats. The SRY geographic distribution in Myanmar and Cambodia indicated predominant the haplotype Y1A in plains areas and a high frequency of Y2B in mountain areas. The results suggest recent genetic infiltration of modern breeds into South‐East Asian goats and an ancestral SRY Y2B haplotype in Asian native goats.     

Preliminary linkage map of the turkey (Meleagris gallopavo) based on microsatellite markers

The turkey is an agriculturally important species for which, until now, there is no published genetic linkage map based on microsatellite markers--still the markers most used in the chicken and other farm animals. In order to increase the number of markers on a turkey genetic linkage map we decided to map new microsatellite sequences obtained from a GT-enriched turkey genomic library. In different chicken populations more than 35-55% of microsatellites are polymorphic. In the turkey populations tested here, 43% of all turkey primers tested were found to be polymorphic, in both commercial and wild type turkeys. Twenty linkage groups (including the Z chromosome) containing 74 markers have been established, along with 37 other unassigned markers. This map will lay the foundations for further genetic mapping and the identification of genes and quantitative trait loci in this economically important species. Genome comparisons, based on genetic maps, with related species such as the chicken would then also be possible. All primer information, polymerase chain reaction (PCR) conditions, allele sizes and genetic linkage maps can be viewed at http://roslin.thearkdb.org/. The DNA is also available on request through the Roslin Institute.