A genetic linkage map of the soybean cyst nematode <Emphasis Type="Italic">Heterodera glycines</Emphasis>

A genetic linkage map of the soybean cyst nematode (SCN) Heterodera glycines was constructed using a population of F2 individuals obtained from matings between two highly inbred SCN lines, TN16 and TN20. The AFLP fingerprinting technique was used to genotype 63 F2 progeny with two restriction enzyme combinations (EcoRI/MseI and PstI/TaqI) and 38 primer combinations. The same F2 population was also genotyped for Hg-cm-1 (H. glycines chorismate mutase-1), a putative virulence gene, using real-time quantitative PCR. Some of the markers were found to be distributed non-randomly. Even so, of the 230 markers analyzed, 131 could be mapped onto ten linkage groups at a minimum LOD of 3.0, for a total map distance of 539 cM. The Hg-cm-1 locus mapped to linkage group III together with 16 other markers. The size of the H. glycines genome was estimated to be in the range of 630-743 cM, indicating that the current map represents 73-86% of the genome, with a marker density of one per 4.5 cM, and a physical/genetic distance ratio of between 124 kb/cM and 147 kb/cM. This genetic map will be of great assistance in mapping H. glycines markers to genes of interest, such as nematode virulence genes and genes that control aspects of nematode parasitism.     

High-resolution melt analysis to identify and map sequence-tagged site anchor points onto linkage maps: a white lupin (Lupinus albus) map as an exemplar

* The provision of sequence-tagged site (STS) anchor points allows meaningful comparisons between mapping studies but can be a time-consuming process for nonmodel species or orphan crops. * Here, the first use of high-resolution melt analysis (HRM) to generate STS markers for use in linkage mapping is described. This strategy is rapid and low-cost, and circumvents the need for labelled primers or amplicon fractionation. * Using white lupin (Lupinus albus, x = 25) as a case study, HRM analysis was applied to identify 91 polymorphic markers from expressed sequence tag (EST)-derived and genomic libraries. Of these, 77 generated STS anchor points in the first fully resolved linkage map of the species. The map also included 230 amplified fragment length polymorphisms (AFLP) loci, spanned 1916 cM (84.2% coverage) and divided into the expected 25 linkage groups. * Quantitative trait loci (QTL) analyses performed on the population revealed genomic regions associated with several traits, including the agronomically important time to flowering (tf), alkaloid synthesis and stem height (Ph). Use of HRM-STS markers also allowed us to make direct comparisons between our map and that of the related crop, Lupinus angustifolius, based on the conversion of RFLP, microsatellite and single nucleotide polymorphism (SNP) markers into HRM markers.     

A linkage map of an F2 hybrid population of Antirrhinum majus and A. molle

To increase the utility of Antirrhinum for genetic and evolutionary studies, we constructed a molecular linkage map for an interspecific hybrid A. majus x A. molle. An F(2) population (n = 92) was genotyped at a minimum of 243 individual loci. Although distorted transmission ratios were observed at marker loci throughout the genome, a mapping strategy based on a fixed framework of codominant markers allowed the loci to be placed into eight robust linkage groups consistent with the haploid chromosome number of Antirrhinum. The mapped loci included 164 protein-coding genes and a similar number of unknown sequences mapped as AFLP, RFLP, ISTR, and ISSR markers. Inclusion of sequences from mutant loci allowed provisional alignment of classical and molecular linkage groups. The total map length was 613 cM with an average interval of 2.5 cM, but most of the loci were aggregated into clusters reducing the effective distance between markers. Potential causes of transmission ratio distortion and its effects on map construction were investigated. This first molecular linkage map for Antirrhinum should facilitate further mapping of mutations, major QTL, and other coding sequences in this model genus.     

Linkage Map of the Honey Bee, Apis Mellifera, Based on Rapd Markers

A linkage map was constructed for the honey bee based on the segregation of 365 random amplified polymorphic DNA (RAPD) markers in haploid male progeny of a single female bee. The X locus for sex determination and genes for black body color and malate dehydrogenase were mapped to separate linkage groups. RAPD markers were very efficient for mapping, with an average of about 2.8 loci mapped for each 10-nucleotide primer that was used in polymerase chain reactions. The mean interval size between markers on the map was 9.1 cM. The map covered 3110 cM of linked markers on 26 linkage groups. We estimate the total genome size to be ~3450 cM. The size of the map indicated a very high recombination rate for the honey bee. The relationship of physical to genetic distance was estimated at 52 kb/cM, suggesting that map-based cloning of genes will be feasible for this species.     

花椰菜遗传图谱的构建及NBS-LRR类抗性同源基因在图谱中的定位

利用AFLP和NBS profiling技术, 以花椰菜自交系“AD白花”与高代自交不亲和系“C-8”杂交得到的F1代自交产生的F2代分离群体为材料, 构建了第一个花椰菜遗传连锁图谱。该图谱由234个AFLP标记和21个NBS标记构成了9个连锁群, 总图距为668.4 cM, 标记间平均距离为2.9 cM。每个连锁群包含的位点数从12到47个, 相邻两标记之间的距离范围是0~14.9 cM。NBS标记分布在8个连锁群中, 这些标记大部分聚在一起。本研究为今后的基因定位及重要农艺性状的分析提供框架图。此外, 研究NBS profiling 方法在花椰菜中的稳定性和有效性以及NBS-LRR类RGA在花椰菜基因组中的分布和特点。     

Regulation of Arabidopsis defense responses against Spodoptera littoralis by CPK-mediated calcium signaling

Background

Genetic markers and linkage mapping are basic prerequisites for marker-assisted selection and map-based cloning. In the case of the key grassland species Lolium spp., numerous mapping populations have been developed and characterised for various traits. Although some genetic linkage maps of these populations have been aligned with each other using publicly available DNA markers, the number of common markers among genetic maps is still low, limiting the ability to compare candidate gene and QTL locations across germplasm.

Results

A set of 204 expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers has been assigned to map positions using eight different ryegrass mapping populations. Marker properties of a subset of 64 EST-SSRs were assessed in six to eight individuals of each mapping population and revealed 83% of the markers to be polymorphic in at least one population and an average number of alleles of 4.88. EST-SSR markers polymorphic in multiple populations served as anchor markers and allowed the construction of the first comprehensive consensus map for ryegrass. The integrated map was complemented with 97 SSRs from previously published linkage maps and finally contained 284 EST-derived and genomic SSR markers. The total map length was 742 centiMorgan (cM), ranging for individual chromosomes from 70 cM of linkage group (LG) 6 to 171 cM of LG 2.

Conclusions

The consensus linkage map for ryegrass based on eight mapping populations and constructed using a large set of publicly available Lolium EST-SSRs mapped for the first time together with previously mapped SSR markers will allow for consolidating existing mapping and QTL information in ryegrass. Map and markers presented here will prove to be an asset in the development for both molecular breeding of ryegrass as well as comparative genetics and genomics within grass species.     

A microsatellite-based, gene-rich linkage map for the AA genome of Arachis (Fabaceae)

Cultivated peanut (Arachis hypogaea) is an important crop, widely grown in tropical and subtropical regions of the world. It is highly susceptible to several biotic and abiotic stresses to which wild species are resistant. As a first step towards the introgression of these resistance genes into cultivated peanut, a linkage map based on microsatellite markers was constructed, using an F₂ population obtained from a cross between two diploid wild species with AA genome (A. duranensis and A. stenosperma). A total of 271 new microsatellite markers were developed in the present study from SSR-enriched genomic libraries, expressed sequence tags (ESTs), and by “data-mining” sequences available in GenBank. Of these, 66 were polymorphic for cultivated peanut. The 271 new markers plus another 162 published for peanut were screened against both progenitors and 204 of these (47.1%) were polymorphic, with 170 codominant and 34 dominant markers. The 80 codominant markers segregating 1:2:1 (P<0.05) were initially used to establish the linkage groups. Distorted and dominant markers were subsequently included in the map. The resulting linkage map consists of 11 linkage groups covering 1,230.89 cM of total map distance, with an average distance of 7.24 cM between markers. This is the first microsatellite-based map published for Arachis, and the first map based on sequences that are all currently publicly available. Because most markers used were derived from ESTs and genomic libraries made using methylation-sensitive restriction enzymes, about one-third of the mapped markers are genic. Linkage group ordering is being validated in other mapping populations, with the aim of constructing a transferable reference map for Arachis.Electronic supplementary material is available for this at     

A consensus map for <Emphasis Type="Italic">Cucurbita pepo</Emphasis>

Using random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), simple sequence repeats (SSR), and morphological traits, the first genetic maps for Cucurbita pepo (2n=2x=40) were constructed and compared. The two mapping populations consisted of 92 F₂ individuals each. One map was developed from a cross between an oil-seed pumpkin breeding line and a zucchini accession, into which genes for resistance to Zucchini Yellow Mosaic Virus (ZYMV) from a related species, C. moschata, had been introgressed. The other map was developed from a cross between an oil-seed pumpkin and a crookneck variety. A total of 332 and 323 markers were mapped in the two populations. Markers were distributed in each map over 21 linkage groups and covered an average of 2,200 cM of the C. pepo genome. The two maps had 62 loci in common, which enabled identification of 14 homologous linkage groups. Polyacrylamide gel analyses allowed detection of a high number of markers suitable for mapping, 10% of which were co-dominant RAPD loci. In the Pumpkin-Zucchini population, bulked segregant analysis (BSA) identified seven markers less than 7 cM distant from the locus n, affecting lignification of the seed coat. One of these markers, linked to the recessive hull-less allele (AW11-420), was also found in the Pumpkin-Crookneck population, 4 cM from n. In the Pumpkin-Zucchini population, 24 RAPD markers, previously introduced into C. pepo from C. moschata, were mapped in two linkage groups (13 and 11 markers in LGpz1 and LGpz2, respectively), together with two sequence characterized amplified region (SCAR) markers linked to genes for resistance to ZYMV.     

AFLP linkage map of the Japanese quail Coturnix japonica

The quail is a valuable farm and laboratory animal. Yet molecular information about this species remains scarce. We present here the first genetic linkage map of the Japanese quail. This comprehensive map is based solely on amplified fragment length polymorphism (AFLP) markers. These markers were developed and genotyped in an F2 progeny from a cross between two lines of quail differing in stress reactivity. A total of 432 polymorphic AFLP markers were detected with 24 TaqI/EcoRI primer combinations. On average, 18 markers were produced per primer combination. Two hundred and fifty eight of the polymorphic markers were assigned to 39 autosomal linkage groups plus the ZW sex chromosome linkage groups. The linkage groups range from 2 to 28 markers and from 0.0 to 195.5 cM. The AFLP map covers a total length of 1516 cM, with an average genetic distance between two consecutive markers of 7.6 cM. This AFLP map can be enriched with other marker types, especially mapped chicken genes that will enable to link the maps of both species and make use of the powerful comparative mapping approach. This AFLP map of the Japanese quail already provides an efficient tool for quantitative trait loci (QTL) mapping.     

New markers and map sequences inNeurospora crassa,with a description of mapping by duplication coverage,and of multiple translocation stocks for testing linkage

Thirty previously unmapped markers have been located; 13 are at newly designated loci. Numerous sequences for previously mapped genes have also been determined. A revised map of linkage group I is presented. The order from conventional mapping has been confirmed by testing recessive markers in IL for coverage by duplications. Assignment of new mutants to linkage groups is greatly facilitated by using gene-tagged multiple translocation strains for linkage detection; these “alcoy” tester strains and procedures for using them are described. Recent mapping data of other workers are compiled. Distal markers are now known for all but one of the 14 chromosome arms, but extensive map segments are still devoid of markers.     

Genetic linkage mapping of an annual × perennial ryegrass population

Annual (Lolium multiflorum Lam.) and perennial (L. perenne L.) ryegrass are two common forage and turfgrass species grown throughout the world. Perennial ryegrass is most commonly used for turfgrass purposes, and contamination by annual ryegrass, through physical seed mixing or gene flow, can result in a significant reduction in turfgrass quality. Seed certifying agencies in the United States currently use a test called seedling root fluorescence (SRF) to detect contamination between these species. The SRF test, however, can be inaccurate and therefore, the development of additional markers for species separation is needed. Male and female molecular-marker linkage maps of an interspecific annual × perennial ryegrass mapping population were developed to determine the map location of the SRF character and to identify additional genomic regions useful for species separation. A total of 235 AFLP markers, 81 RAPD markers, 16 comparative grass RFLPs, 106 SSR markers, 2 isozyme loci and 2 morphological characteristics, 8-h flowering, and SRF were used to construct the maps. RFLP markers from oat and barley and SSR markers from tall fescue and other grasses allowed the linkage groups to be numbered, relative to the Triticeae and the International Lolium Genome Initative reference population P150/112. The three-generation population structure allowed both male and female maps to be constructed. The male and female maps each have seven linkage groups, but differ in map length with the male map being 537 cm long and the female map 712 cm long. Regions of skewed segregation were identified in both maps with linkage groups 1, 3, and 6 of the male map showing the highest percentage of skewed markers. The (SRF) character mapped to linkage group 1 in both the male and female maps, and the 8-h flowering character was also localized to this linkage group on the female map. In addition, the Sod-1 isozyme marker, which can separate annual and perennial ryegrasses, mapped to linkage group 7. These results indicate that Lolium linkage groups 1 and 7 may provide additional markers and candidate genes for use in ryegrass species separation.Communicated by C. Möllers     

A human genome map of comparative anchor tagged sequences.

Effective comparative mapping inference utilizing developing gene maps of animal species requires the inclusion of anchored reference loci that are homologous to genes mapped in the more "gene-dense" mouse and human maps. Nominated anchor loci, termed comparative anchor tagged sequences (CATS), have been ordered in the mouse linkage map, but due to the dearth of common polymorphisms among human coding genes have not been well represented in human linkage maps. We present here an ordered framework map of 314 comparative anchor markers in humans based on mapping analysis in the Genebridge 4 panel of radiation hybrid cell lines, plus empirically optimized CATS PCR primers which detect these markers. The ordering of these homologous gene markers in human and mouse maps provides a framework for comparative gene mapping of representative mammalian species.     

Comparative AFLP mapping in two hexaploid oat populations

Amplified fragment length polymorphisms (AFLPs) can be used to quickly develop linkage maps in plant species and are especially useful for crops with large genomes like oat (Avena sativa L., 2n=6x=42). High reproducibility and consistency are crucial if AFLP linkage maps are employed for comparative mapping. We mapped AFLP markers in combination with restriction fragment length polymorphism (RFLP) markers in two recombinant inbred populations of hexaploid oat in two laboratories to test the consistency of AFLP markers in a polyploid crop. Eight primer combinations produced 102 and 121 scoreable AFLP markers in the respective populations. In a population from the cross Kanota×Ogle, AFLP markers were placed onto a RFLP reference map consisting of 32 linkage groups. Nineteen linkage groups from another population from the cross Kanota×Marion were assigned to the reference map using AFLP and RFLP markers homologous to those used in the Kanota× Ogle cross. Reproducibility of AFLP assays was high in both laboratories and between laboratories. The AFLP markers were well-distributed across the genome in both populations. Many AFLP markers tended to extend the distance between adjacent RFLP markers in linkage analysis. Of the 27 polymorphic AFLPs common in both populations, 20 mapped to homologous linkage groups, 4 were unlinked in at least one population, and 3 mapped to different linkage groups in the two crosses. We believe that 1 of the 3 markers that mapped to a different linkage group in the two populations mapped to homoeologous linkage groups. The linkage map of hexaploid oat is not yet complete, and genomic rearrangements such as translocations exist among cultivars and are likely to account for the remaining two non-syntenous mapping results. AFLPs provide not only a fast and powerful tool for mapping but could be useful in characterizing genomic structural variations among germplasms in hexaploid oat. Received: 17 December 1999 / Accepted: 28 July 2000     

A microsatellite-based genetic linkage map of the cichlid fish, Astatotilapia burtoni (Teleostei): a comparison of genomic architectures among rapidly speciating cichlids

Cichlid fishes compose an astonishingly large number of species and formed species flocks in record-breaking time. To facilitate efficient genome scans and comparisons of cichlid genomes, we constructed a medium-density genetic linkage map of microsatellite markers of Astatotilapia burtoni. The mapping cross was derived from two inbred laboratory lines to obtain F₂ progeny by intercrossing. The map revealed 25 linkage groups spanning 1249.3 cM of the genome (size ~950 Mb) with an average marker spacing of 6.12 cM. The seven Hox clusters, ParaHox C1, and two paralogs of Pdgfrβ were mapped to different linkage groups, thus supporting the hypothesis of a teleost-specific genome duplication. The A. burtoni linkage map was compared to the other two available maps for cichlids using shared markers that showed conservation and synteny among East African cichlid genomes. Interesting candidate genes for cichlid speciation were mapped using SNP markers.     

Comparison off genetic distance and order off DNA markers in five populations of rice.

A group of about 300 evenly distributed DNA markers from a high density RFLP linkage map of rice constructed using an F2 population derived from a japonica variety, Nipponbare, and an indica variety, Kasalath, were used to evaluate gene order and genetic distance in four other rice mapping populations. The purpose of this study was to determine the degree to which information gained from the high density linkage map could be applied to other mapping populations, particularly with regard to its utility in bridging quantitative traits and molecular and physical mapping information. The mapping populations consisted of two F2 populations derived from Dao Ren Qiao/Fl-1084 and Kinandangputi/Fl-1007, recombinant inbred lines from Asominori/IR24, and a backcross population from Sasanishiki/Habataki//Sasanishiki. All DNA markers commonly mapped in the four populations showed the same linkage groups as in the Nipponbare/Kasalath linkage map with conserved linkage order. The genetic distance between markers among the different populations did not vary to a significant level in any of the 12 chromosomes. The differences in some markers could be attributed to the size of the population used in the construction of the linkage maps. Furthermore, the conservation of linkage order found in the distal region of chromosomes 11 and 12 was also confirmed in the RFLP maps based on the four populations of rice. These suggest that any major genetic information from the Nipponbare/Kasalath map can be expected to be approximately the same in other crosses or populations. This high density RFLP linkage map, which is being utilized in constructing a physical map of rice, can be very useful in interpreting genome structure with great accuracy in other populations. Key words : linkage map, japonica, indica, gene order, genetic distance.     

A microsatellite linkage map of Barramundi, Lates calcarifer

Barramundi (Lates calcarifer) is an important farmed marine food fish species. Its compact genome (approximately 700 Mb) is among the smallest genomes of food fish species. We established a first-generation genetic linkage map of Barramundi with a mapping panel containing three parents (two males and one female) and 93 progeny. A total of 240 microsatellite markers were mapped into 24 linkage groups. Among these markers, 10 were located in ESTs and known genes. The total lengths of the female and male maps were 873.8 and 414.5 cM with an average marker spacing of 6.20 and 4.70 cM, respectively. Comparing the flanking sequences of the 240 Barramundi microsatellites with the assembled whole-genome sequences of Tetraodon nigrovidiris revealed 55 homologous sequences located in 19 of the 21 chromosomes of T. nigrovidiris. The map will not only enable the mapping of quantitative trait loci, but also provide new resources for understanding the evolution of fish genomes.     

Genetic mapping of EST-derived simple sequence repeats (EST-SSRs) to identify QTL for leaf morphological characters in a Quercus robur full-sib family

The availability of genomic resources such as expressed sequence tag-derived simple sequence repeat (EST-SSR) markers in adaptive genes with high transferability across related species allows the construction of genetic maps and the comparison of genome structure and quantitative trait loci (QTL) positions. In the present study, genetic linkage maps were constructed for both parents of a Quercus robur × Q. robur ssp. slavonica full-sib pedigree. A total of 182 markers (61 AFLPs, 23 nuclear SSRs, 98 EST-SSRs) and 172 markers (49 AFLPs, 21 nSSRs, 101 EST-SSRs, 1 isozyme) were mapped on the female and male linkage maps, respectively. The total map length and average marker spacing were 1,038 and 5.7 cM for the female map and 998.5 and 5.8 cM for the male map. A total of 68 nuclear SSRs and EST-SSRs segregating in both parents allowed to define homologous linkage groups (LG) between both parental maps. QTL for leaf morphological traits were mapped on all 12 LG at a chromosome-wide level and on 6 LG at a genome-wide level. The phenotypic effects explained by each single QTL ranged from 4.0 % for leaf area to 15.8 % for the number of intercalary veins. QTL clusters for leaf characters that discriminate between Q. robur and Quercus petraea were mapped reproducibly on three LG, and some putative candidate genes among potentially many others were identified on LG3 and LG5. Genetic linkage maps based on EST-SSRs can be valuable tools for the identification of genes involved in adaptive trait variation and for comparative mapping.     

Extension of the core map of common bean with EST-SSR,RGA, AFLP,and putative functional markers

Microsatellites and gene-derived markers are still underrepresented in the core molecular linkage map of common bean compared to other types of markers. In order to increase the density of the core map, a set of new markers were developed and mapped onto the RIL population derived from the ‘BAT93’ × ‘Jalo EEP558’ cross. The EST-SSR markers were first characterized using a set of 24 bean inbred lines. On average, the polymorphism information content was 0.40 and the mean number of alleles per locus was 2.7. In addition, AFLP and RGA markers based on the NBS-profiling method were developed and a subset of the mapped RGA was sequenced. With the integration of 282 new markers into the common bean core map, we were able to place markers with putative known function in some existing gaps including regions with QTL for resistance to anthracnose and rust. The distribution of the markers over 11 linkage groups is discussed and a newer version of the common bean core linkage map is proposed.     

Characterization,development and mapping of Unigene-derived microsatellite markers in sorghum [<Emphasis Type="Italic">Sorghum bicolor</Emphasis> (L.) Moench]

Molecular variation within known genes controlling specific functions provide candidate gene-based markers which are tightly linked with the trait of interest. Unigene-derived microsatellite markers, with their unique identity and positions, offer the advantage of unraveling variation in the expressed component of the genome. We characterized ≥12-bp-long microsatellite loci from 13,899 unique sequences of sorghum [Sorghum bicolor (L.) Moench] available in the NCBI unigene database for their abundance and possible use in sorghum breeding. Analysis of 12,464 unigenes (≥200-bp) using MISA software identified 14,082 simple sequence repeats (SSRs) in 7,370 unigenes, from which 1,519 unigene SSR markers were developed. The average frequency of SSR was 1 per1.6 kb and 1.0 per 1.1 unigene; hexamers followed by trimers were found in abundance, of which 33.3% AT-rich and CCG repeats were the most abundant. Of the 302 unigene SSRs tested, 60 (19.8%) were polymorphic between the two parents, M35-1 and B35 of a recombinant inbred line (RIL) mapping population. A mapping population consisting of 500 RILs was developed using the above two parents, and a subset of random 245 RILs was used for genotyping with polymorphic SSRs. We developed a linkage map containing 231 markers, of which 228 (174 genomic and 54 genic) were microsatellites and three were morphological markers. Markers were distributed over 21 linkage groups, and spanned a genetic distance of 1235.5 cM. This map includes 81 new SSRs, of which 35 (21 unigene and 14 genomic) were developed in the present study and 46 from other studies. The order of the SSR markers mapped in the present study was confirmed physically by BLAST search against the whole-genome shotgun sequence of sorghum. Many unigene sequences used for marker development in this study include genes coding for important regulatory proteins and functional proteins that are involved in stress-related metabolism. The unigene SSR markers used together with other SSR markers to construct the sorghum genetic map will have applications in studies on comparative mapping, functional diversity analysis and association mapping, and for quantitative trait loci detection for drought and other agronomically important traits in sorghum.