Evaluation of inter-simple sequence repeat analysis for mapping in Citrus and extension of the genetic linkage map

Inter-simple sequence repeat (ISSR) analysis was evaluated for its usefulness in generating markers to extend the genetic linkage map of Citrus using a backcross population previously mapped with restriction fragment length polymorphism (RFLP), random amplified polymorphic DNA (RAPD) and isozyme markers. ISSR markers were obtained through the simple technique of PCR followed by analysis on agarose gels, using simple sequence repeat (SSR) primers. Optimization of reaction conditions was achieved for 50% of the SSR primers screened, and the primers amplified reproducible polymorphic bands in the parents and progeny of the backcross population. Mendelian segregation of the polymorphic bands was demonstrated, with an insignificant number of skewed loci. Most of the SSR primers produced dominant loci; however co-dominance was observed with loci derived from three primers. A new genetic map was produced by combining the segregation data for the ISSR markers and data for the RFLP, RAPD and isozyme markers from the previous map and creating genetic linkages among all the markers using JoinMap 2.0 mapping software. The new map has an improved distribution of markers along the linkage groups with fewer gaps, and marker order showed partial or complete conservation in the linkage groups. The incorporation of ISSR markers into the genetic linkage map demonstrates that ISSR markers are suitable for genetic mapping in Citrus. Received: 3 February 2000 / Accepted: 12 May 2000     

A genetic linkage map of tef [Eragrostis tef (Zucc.) Trotter] based on amplified fragment length polymorphism

A genetic linkage map of tef was constructed with amplified fragment length polymorphism (AFLP) markers using F₅ recombinant inbred lines (RILs) derived by single seed descent from the intraspecific cross of ’Kaye Murri’×’Fesho’. A total of 192 EcoRI/MseI primer combinations were screened for parental polymorphism. Around three polymorphic fragments per primer combination were detected, indicating a low polymorphism level in tef. Fifty primer combinations were selected to assay the mapping population, and 226 loci segregated among 85 F₅ RILs. Most AFLP loci behaved as dominant markers (presence or absence of a band), but about 15% of the loci were codominant. Significant deviations from the expected Mendelian segregation ratio were observed for 26 loci. The genetic linkage map comprised 211 markers assembled into 25 linkage groups and covered 2,149 cM of genome. AFLP is an efficient marker system for mapping plant species with low polymorphism such as tef. This is the first genetic linkage map constructed for tef. It will facilitate the mapping of genes controlling agronomically important traits and cultivar improvement in tef. Received: 27 April 1998 / Accepted: 4 January 1999     

Integration of the feline radiation hybrid and linkage maps

The recent development of genome mapping resources for the domestic cat provides a unique opportunity to study comparative medicine in this companion animal which can inform and benefit both veterinary and human biomedical concerns. We describe here the integration and order comparison of the feline radiation hybrid (RH) map with the feline interspecies backcross (ISB) genetic linkage map, constructed by a backcross of F₁ hybrids between domestic cat (Felis catus) and the Asian leopard cat (Prionailurus bengalensis). Of 253 microsatellite loci mapped in the ISB, 176 equivalently spaced markers were ordered among a framework of 424 Type I coding markers in the RH map. The integration of the RH and ISB maps resolves the orientation of multiple linkage groups and singleton loci from the ISB genetic map. This integrated map provides the foundation for gene mapping assessments in the domestic cat and in related species of the Felidae family. Received: 10 July 2000 / Accepted: 01 February 2001     

Molecular mapping of the Oregon Wolfe Barleys: a phenotypically polymorphic doubled-haploid population

A phenotypically polymorphic barley (Hordeum vulgare L.) mapping population was developed using morphological marker stocks as parents. Ninety-four doubled-haploid lines were derived for genetic mapping from an F₁ using the Hordeum bulbosum system. A linkage map was constructed using 12 morphological markers, 87 restriction fragment length polymorphism (RFLP), five random amplified polymorphic DNA (RAPD), one sequence-tagged site (STS), one intron fragment length polymorphism (IFLP), 33 simple sequence repeat (SSR), and 586 amplified fragment length polymorphism (AFLP) markers. The genetic map spanned 1,387 cM with an average density of one marker every 1.9 cM. AFLP markers tended to cluster on centromeric regions and were more abundant on chromosome 1 (7H). RAPD markers showed a high level of segregation distortion, 54% compared with the 26% observed for AFLP markers, 27% for SSR markers, and 18% for RFLP markers. Three major regions of segregation distortion, based on RFLP and morphological markers, were located on chromosomes 2 (2H), 3 (3H), and 7 (5H). Segregation distortion may indicate that preferential gametic selection occurred during the development of the doubled-haploid lines. This may be due to the extreme phenotypes determined by alleles at morphological trait loci of the dominant and recessive parental stocks. Several molecular markers were found to be closely linked to morphological loci. The linkage map reported herein will be useful in integrating data on quantitative traits with morphological variants and should aid in map-based cloning of genes controlling morphological traits. Received: 23 August 2000 / Accepted: 15 December 2000     

A genetic linkage map of Guinea yam ( Dioscorea rotundata Poir.) based on AFLP markers

A genetic linkage map of the tetraploid white yam (Dioscorea rotundata Poir.) was constructed based on 341 co-dominantly scored amplified fragment length polymorphism (AFLP) markers segregating in an intraspecific F₁ cross. The F₁ mapping population was produced by crossing a landrace cultivar TDr 93-1 as female parent to a breeding line TDr 87/00211 as the male parent. The marker segregation data were split into maternal and paternal data sets, and separate genetic linkage maps were constructed since the mapping population was an F₁ cross between two presumed heterozygous parents. The markers segregated like a diploid cross-pollinator population suggesting that the D. rotundata genome is an allo-tetraploid (2n = 4x = 40). The maternal map comprised 155 markers mapped on 12 linkage groups with a total map length of 891 cM. Three linkage groups consisted of maternal parent markers only. The paternal map consisted of 157 markers mapped on 13 linkage groups with a total map length of 852 cM. Three and one quantitative trait loci (QTLs) with effects on resistance to Yam Mosaic Virus (YMV) were identified on the maternal and paternal linkage maps, respectively. Prospects for detecting more QTLs and using marker-assisted selection in white yam breeding appear good, but this is subject to the identification of additional molecular markers to cover more of the genome.     

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.     

GENETIC MAPPING OF THE LAMINARIA JAPONICA (LAMINARALES,PHAEOPHYTA) USING AMPLIFIED FRAGMENT LENGTH POLYMORPHISM MARKERS1

To establish a molecular‐marker‐assisted system of breeding and genetic study for Laminaria japonica Aresch., amplified fragment length polymorphism (AFLP) was used to construct a genetic linkage map of L. japonica featuring 230 progeny of F₂ cross population. Eighteen primer combinations produced 370 polymorphic loci and 215 polymorphic loci segregated in a 3:1 Mendelian segregation ratio (P ≤ 0.05). Of the 215 segregated loci, 142 were ordered into 27 linkage groups. The length of the linkage groups ranged from 6.7 to 90.3 centimorgans (cM) with an average length of 49.6 cM, and the total length was 1,085.8 cM, which covered 68.4% of the estimated 1,586.9 cM genome. The number of mapped markers on each linkage group ranged from 2 to 12, averaging 5.3 markers per group. The average density of the markers was 1 per 9.4 cM. Based on the marker density and the resolution of the map, the constructed linkage map can satisfy the need for quantitative trait locus (QTL) location and molecular‐marker‐assisted breeding for Laminaria.     

A Preliminary Genetic Linkage Map of the Pacific Abalone Haliotis discus hannai Ino

Preliminary genetic linkage maps were constructed for the Pacific abalone (Haliotis discus hannai Ino) using amplified fragment length polymorphism (AFLP), randomly amplified polymorphic DNA (RAPD), and microsatellite markers segregating in a F₁ family. Nine microsatellite loci, 41 RAPD, and 2688 AFLP markers were genotyped in the parents and 86 progeny of the mapping family. Among the 2738 markers, 384 (including 365 AFLP markers, 10 RAPD markers, and 9 microsatellite loci) were polymorphic and segregated in one or both parents: 241 in the female and 146 in the male. The majority of these markers, 232 in the female and 134 in the male, segregated according to the expected 1:1 Mendelian ratio (α = 0.05). Two genetic linkage maps were constructed using markers segregating in the female or the male parent. The female framework map consisted of 119 markers in 22 linkage groups, covering 1773.6 cM with an average intermarker space of 18.3 cM. The male framework map contained 94 markers in 19 linkage groups, spanning 1365.9 cM with an average intermarker space of 18.2 cM. The sex determination locus was mapped to the male map but not to the female map, suggesting a XY-male determination mechanism. Distorted markers showing excess of homozygotes were mapped in clusters, probably because of their linkage to a gene that is incompatible between two parental populations.     

An intraspecific genetic map of velvetbean (<Emphasis Type="Italic">Mucuna</Emphasis> sp.) based on AFLP markers

Velvetbean (Mucuna sp., n=11), a self-pollinated species, is an important legume used in tropical agricultural systems in rotation with other crops for nematode management and/or soil improvement. A genetic map of velvetbean was constructed in order to identify potential molecular markers linked to important morphological and agronomic traits that would be particularly useful for developing and improving the species. Traits such as seed coat color, pod color, and pod pubescence were among the main parameters observed in a process of genetic diversity estimation. Two slightly divergent velvetbean accessions, PI364362 and Edgar Farm White, a land race from Alabama, were used to make an intraspecific F₁ hybrid. Amplified fragment length polymorphism analysis (AFLP) detected an average of six polymorphic fragments per primer pair between the two parents. As expected for dominant markers, the sum of all AFLP bands from both parents was generally observed to be present in the AFLP profiles of the F₁ progeny, indicating full penetrance and the dominant nature of AFLP markers. An F₂ population was generated by self-pollinating a single F₁ plant. Using 37 AFLP primer pairs, we detected 233 polymorphic markers of which 164 (70.4%) segregated in 3:1 Mendelian ratios, while the remaining 69 (29.6%) both segregated and were scorable. The genetic linkage map constructed from this population comprised 166 markers, including two morphological traits (pod color and pod pubescence). Twenty linkage groups were found with an average distance between markers of 34.4 cM, covering a total of 687.9 cM. The linkage groups contained from 2 to 12 loci each and the distance between two consecutive loci ranged from 0 to 21.8 cM. The newly designated morphological traits pod color (pdc) and pod pubescence (pdp) co-segregated with each other at a distance of 4.2 cM. Two DNA markers designated ACGCAG2 and ACTCTG1 were located in the same group as pdc and pdp. The AFLP linkage map provides opportunities for use in marker-assisted selection and in the detection of loci controlling morphologically important traits.Communicated by J. Dvorak     

A genetic linkage map for tef [Eragrostis tef (Zucc.) Trotter]

Tef [Eragrostis tef (Zucc.) Trotter] is the major cereal crop in Ethiopia. Tef is an allotetraploid with a base chromosome number of 10 (2n = 4x = 40) and a genome size of 730 Mbp. Ninety-four F₉ recombinant inbred lines (RIL) derived from the interspecific cross, Eragrostis tef cv. Kaye Murri × Eragrostis pilosa (accession 30-5), were mapped using restriction fragment length polymorphisms (RFLP), simple sequence repeats derived from expressed sequence tags (EST–SSR), single nucleotide polymorphism/insertion and deletion (SNP/INDEL), intron fragment length polymorphism (IFLP) and inter-simple sequence repeat amplification (ISSR). A total of 156 loci from 121 markers was grouped into 21 linkage groups at LOD 4, and the map covered 2,081.5 cM with a mean density of 12.3 cM per locus. Three putative homoeologous groups were identified based on multi-locus markers. Sixteen percent of the loci deviated from normal segregation with a predominance of E. tef alleles, and a majority of the distorted loci were clustered on three linkage groups. This map will be useful for further genetic studies in tef including mapping of loci controlling quantitative traits (QTL), and comparative analysis with other cereal crops.Electronic Supplementary Material Supplementary material is available to authorised users in the online version of this article at .     

An integrative genetic linkage map of winter wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.)

We constructed a genetic linkage map based on a cross between two Swiss winter wheat (Triticum aestivum L.) varieties, Arina and Forno. Two-hundred and forty F₅ single-seed descent (SSD)-derived lines were analysed with 112 restriction fragment length polymorphism (RFLP) anonymous probes, 18 wheat cDNA clones coding for putative stress or defence-related proteins and 179 simple-sequence repeat (SSR) primer-pairs. The 309 markers revealed 396 segregating loci. Linkage analysis defined 27 linkage groups that could all be assigned to chromosomes or chromosome arms. The resulting genetic map comprises 380 loci and spans 3,086 cM with 1,131 cM for the A genome, 920 cM for the B genome and 1,036 cM for the D genome. Seventeen percent of the loci showed a significant (P < 0.05) deviation from a 1:1 ratio, most of them in favour of the Arina alleles. This map enabled the mapping of QTLs for resistance against several fungal diseases such as Stagonospora glume blotch, leaf rust and Fusarium head blight. It will also be very useful for wheat genetic mapping, as it combines RFLP and SSR markers that were previously located on separate maps. S. Paillard and T. Schnurbusch contributed equally to the work     

A RFLP-based linkage map of mustard [Brassica juncea (L.) Czern. and Coss.]

 A genetic linkage map of Brassica juncea was constructed based on restriction fragment length polymorphism (RFLP) detected by anonymous cDNA markers from B. napus, using a segregating F₁-derived doubled haploid (DH) progeny from a cross between a canola-quality mustard line (J90-4317) and a high-oil-content mustard line (J90-2733). The RFLP probes consisted of 229 cDNA probes from B. napus and a B. napus tandem repeat sequence, RDA2. The map consisted of 343 marker loci arranged in 18 major linkage groups plus five small segments with two to five marker loci, covering a total map distance of 2073 cM. Twenty-four percent of the markers were dominant in nature. Sixty-two percent of the marker loci were duplicated, and the majority were involved in inter-linkage group duplications, illustrating that complex duplications and subsequent rearrangements occurred after allopolyploidy. Deviation from the Mendelian segregation ratio for a DH population was observed for 27% of the markers. Two-thirds of these markers with a skewed segregation were clustered in 6 linkage groups and two unassigned segments. The overall average marker interval of the B. juncea map reported here was 6.6 cM, which would provide a marker density satisfactory for efficient use of the map in breeding applications, such as tagging of important agronomic traits and marker-assisted selection. Received: 14 May 1996 / Accepted: 11 October 1996     

Preliminary Study on Linkage Mapping Based on Microsatellite DNA and AFLP Markers Using Homozygous Clonal Fish in Ayu (<Emphasis Type="Italic">Plecoglossus altivelis</Emphasis>)

A mapping referential family (F₁) of ayu was produced by crossing a normal diploid male with a homozygous clonal female. A genetic linkage map was constructed using 191 amplified fragment length polymorphism (AFLP) and 4 microsatellite DNA markers. A total of 178 loci were mapped in 36 linkage groups comprising 1659.6 cM, which includes approximately 77.3% to 81.8% of the total genome. As the markers were randomly distributed over the genome, they showed high efficiency for the construction of a wide linkage map.     

Trigonelline inheritance in the interspecific Coffea pseudozanguebariae×C. liberica var. dewevrei cross

Trigonelline alkaloid is present in coffee beans, and during roasting it gives rise to the major coffee aroma compounds (several alkyl-pyridines and pyrroles). In this study we investigated the genetic inheritance of trigonelline accumulation in green beans in an interspecific cross between a wild east African species, Coffea pseudozanguebariae (PSE) and the west African species C. liberica var. dewevrei (DEW). Trigonelline content was measured by HPLC in both parental species, F₁ hybrids and the reciprocal backcross hybrids (BCDEW and BCPSE). The results showed that, on average, PSE accumulated twice as much trigonelline as DEW. No year effect or interaction (genotype×year) was recorded. Trigonelline showed high heritability (71%), which meant that the genotypic value could be easily estimated from the phenotypic value. However, the fact that this trait was not additive suggested the possibility of nucleo-cytoplasmic inheritance. This hypothesis was confirmed by: (1) similar levels of trigonelline content in the PSE, F₁, BCPSE and BCDEW groups, all having the same maternal cytoplasm, and (2) the location of one nuclear QTL on the G linkage group. Received: 2 May 2000 / Accepted: 19 June 2000     

The first genetic map of pigeon pea based on diversity arrays technology (DArT) markers

With an objective to develop a genetic map in pigeon pea (Cajanus spp.), a total of 554 diversity arrays technology (DArT) markers showed polymorphism in a pigeon pea F₂ mapping population of 72 progenies derived from an interspecific cross of ICP 28 (Cajanus cajan) and ICPW 94 (Cajanus scarabaeoides). Approximately 13% of markers did not conform to expected segregation ratio. The total number of DArT marker loci segregating in Mendelian manner was 405 with 73.1% (P > 0.001) of DArT markers having unique segregation patterns. Two groups of genetic maps were generated using DArT markers. While the maternal genetic linkage map had 122 unique DArT maternal marker loci, the paternal genetic linkage map has a total of 172 unique DArT paternal marker loci. The length of these two maps covered 270.0 cM and 451.6 cM, respectively. These are the first genetic linkage maps developed for pigeon pea, and this is the first report of genetic mapping in any grain legume using diversity arrays technology.     

Mapping quantitative trait loci using molecular marker linkage maps

Summary High-density restriction fragment length polymorphism (RFLP) and allozyme linkage maps have been developed in several plant species. These maps make it technically feasible to map quantitative trait loci (QTL) using methods based on flanking marker genetic models. In this paper, we describe flanking marker models for doubled haploid (DH), recombinant inbred (RI), backcross (BC), F₁ testcross (F₁TC), DH testcross (DHTC), recombinant inbred testcross (RITC), F₂, and F₃ progeny. These models are functions of the means of quantitative trait locus genotypes and recombination frequencies between marker and quantitative trait loci. In addition to the genetic models, we describe maximum likelihood methods for estimating these parameters using linear, nonlinear, and univariate or multivariate normal distribution mixture models. We defined recombination frequency estimators for backcross and F₂ progeny group genetic models using the parameters of linear models. In addition, we found a genetically unbiased estimator of the QTL heterozygote mean using a linear function of marker means. In nonlinear models, recombination frequencies are estimated less efficiently than the means of quantitative trait locus genotypes. Recombination frequency estimation efficiency decreases as the distance between markers decreases, because the number of progeny in recombinant marker classes decreases. Mean estimation efficiency is nearly equal for these methods.     

An RFLP linkage map for loblolly pine based on a three-generation outbred pedigree

A genetic linkage map for loblolly pine (Pinus taeda L.) was constructed using segregation data from a three-generation outbred pedigree consisting of four grandparents, two parents, and 95 F₂ progeny. The map was based predominantly on restriction fragment length polymorphism (RFLP) loci detected by cDNA probes. Sixty-five cDNA and three genomic DNA probes revealed 90 RFLP loci. Six polymorphic isozyme loci were also scored. One-fourth (24%) of the cDNA probes detected more than 1 segregating locus, an indication that multigene families are common in pines. As many as six alleles were observed at a single segregating locus among grandparents and it was not unusual for the progeny to segregate for three or four alleles per locus. Multipoint linkage analysis placed 73 RFLP and 2 isozyme loci into 20 linkage groups; the remaining 17 RFLP and 4 isozyme loci were unlinked. The mapped RFLP probes provide a new set of codominant markers for genetic analyses in loblolly pine.     

Linkage arrangement of restriction fragment length polymorphism loci in Brassica oleracea

Summary A detailed genetic linkage map of Brassica oleracea was constructed based on the segregation of 258 restriction fragment length polymorphism loci in a broccoli × cabbage F₂ population. The genetic markers defined nine linkage groups, covering 820 recombination units. A majority of the informative genomic DNA probes hybridized to more than two restriction fragments in the F₂ population. Duplicate sequences having restriction fragment length polymorphism were generally found to be unlinked for any given probe. Many of these duplicated loci were clustered non-randomly on certain pairs of linkage groups, and conservation of the relative linkage arrangement of the loci between linkage groups was observed. While these data support previous cytological evidence for the existence of duplicated regions and the evolution of B. oleracea from a lower chromosome number progenitor, no evidence was provided for the current existence of blocks of homoeology spanning entire pairs of linkage groups. The arrangement of the analyzed duplicated loci suggests that a fairly high degree of genetic rearrangement has occurred in the evolution of B. oleracea. Several probes used in this study were useful in detecting rearrangements between the B. oleracea accessions used as parents, indicating that genetic rearrangements have occurred in the relatively recent evolution of this species.     

Mapping unexplored genomes: a genetic linkage map of the woody sonchus alliance (Asteraceae: Sonchinae) in the Macaronesian Islands

As an initial step to mapping quantitative trait loci for species differences and adaptive radiation of insular endemics in Macaronesia, a genetic linkage map was constructed from an intergeneric backcross between Lactucosonchus webbii and Sonchus radicatus, core members of the tree lettuces in the Macaronesian Islands. A total of 152 amplified fragment length polymorphism markers were mapped into 10 major and 3 minor linkage groups for a total map length of 644 cM with an average distance of 4.53 cM for the 10 major groups. The genetic linkage map length is considerably less than the estimated, and this may reflect incomplete genomic coverage in the current study or reduced recombination, which is a common feature of maps for hybrids of divergent taxa. Segregation distortion occurred in 34% of the mapped markers, and they were located primarily in 4 linkage groups. Segregation distortion in the current BC(1) intergeneric population is slightly lower than average (40%) for BC(1) interspecific populations. This level of segregation distortion implies that unlike what we normally assume no to few reproductive barriers, oceanic island plant taxa do exhibit some degree of postmating reproductive isolation.     

Construction of integrated genetic linkage maps of the tiger shrimp (Penaeus monodon) using microsatellite and AFLP markers

The linkage maps of male and female tiger shrimp (P. monodon) were constructed based on 256 microsatellite and 85 amplified fragment length polymorphism (AFLP) markers. Microsatellite markers obtained from clone sequences of partial genomic libraries, tandem repeat sequences from databases and previous publications and fosmid end sequences were employed. Of 670 microsatellite and 158 AFLP markers tested for polymorphism, 341 (256 microsatellite and 85 AFLP markers) were used for genotyping with three F₁ mapping panels, each comprising two parents and more than 100 progeny. Chi‐square goodness‐of‐fit test (χ²) revealed that only 19 microsatellite and 28 AFLP markers showed a highly significant segregation distortion (P < 0.005). Linkage analysis with a LOD score of 4.5 revealed 43 and 46 linkage groups in male and female linkage maps respectively. The male map consisted of 176 microsatellite and 49 AFLP markers spaced every ～11.2 cM, with an observed genome length of 2033.4 cM. The female map consisted of 171 microsatellite and 36 AFLP markers spaced every ～13.8 cM, with an observed genome length of 2182 cM. Both maps shared 136 microsatellite markers, and the alignment between them indicated 38 homologous pairs of linkage groups including the linkage group representing the sex chromosome. The karyotype of P. monodon is also presented. The tentative assignment of the 44 pairs of P. monodon haploid chromosomes showed the composition of forty metacentric, one submetacentric and three acrocentric chromosomes. Our maps provided a solid foundation for gene and QTL mapping in the tiger shrimp.