A genetic linkage map of lentil (Lens sp.) based on RAPD and AFLP markers using recombinant inbred lines

 A genetic linkage map of Lens sp. was constructed with 177 markers (89 RAPD, 79 AFLP, six RFLP and three morphological markers) using 86 recombinant inbred lines (F_6:8) obtained from a partially interspecific cross. The map covered 1073 cM of the lentil genome with an average distance of 6.0 cM between adjacent markers. Previously mapped RFLP markers were used as anchor probes. The morphological markers, pod indehiscence, seed-coat pattern and flower-color loci were mapped. Out of the total linked loci, 8.4% showed segregation distortion. More than one-fourth of the distorted loci were clustered in one linkage group. AFLP markers showed more segregation distortion than the RAPD markers. The AFLP and RAPD markers were intermingled and clustering of AFLPs was seldom observed. This is the most extensive genetic linkage map of lentil to-date. The marker density of this map could be used for the identification of markers linked to quantitative trait loci in this population. Received: 6 November 1997 / Accepted: 10 February 1998     

Towards a saturated sorghum map using RFLP and AFLP markers

 A near-saturated sorghum genetic linkage map was produced using RFLP, AFLP and morphological markers. First a composite, essentially RFLP-based genetic linkage map was obtained from analyses of two recombinant inbred populations. This map includes 343 loci for 11 linkage groups spanning 1352 cM. Since this map was constructed with many previously mapped heterologous probes, it offers a good basis for synteny studies. Separately, an AFLP map was obtained from the analysis of 168 bands revealed from 12 primer pair combinations. It includes 137 loci for 11 linkage groups spanning 849 cM. Taking into account the different data sets, we constructed a combined genetic linkage map including 443 loci spanning 1899 cM. Two main features are to be noted: (1) the distribution of AFLPs along the genome is not uniform; (2) an important stretching of the former core map is induced after adding the AFLPs. Received: 10 May 1998 / Accepted: 13 July 1998     

A genetic linkage map of Lens sp. based on microsatellite and AFLP markers and the localization of fusarium vascular wilt resistance

Microsatellites have currently become the markers of choice for molecular mapping and marker-assisted selection for key traits such as disease resistance in many crop species. We report here on the mapping of microsatellites which had been identified from a genomic library of lentil (Lens culinaris Medik.). The majority of microsatellite-bearing clones contained imperfect di-nucleotide repeats. A total of 41 microsatellite and 45 amplified fragment length polymorphism (AFLP) markers were mapped on 86 recombinant inbred lines derived from the cross ILL 5588 × L 692-16-1(s), which had been previously used for the construction of a random amplified polymorphic DNA and AFLP linkage map. Since ILL 5588 was resistant to fusarium vascular wilt caused by the fungus Fusarium oxysporum Shlecht. Emend. Snyder & Hansen f.sp. lentis Vasud. & Srini., the recombinant inbreds were segregating for this character. The resulting map contained 283 markers covering about 751 cM, with an average marker distance of 2.6 cM. The fusarium vascular wilt resistance was localized on linkage group 6, and this resistance gene was flanked by microsatellite marker SSR59-2B and AFLP marker p17m30710 at distances of 8.0 cM and 3.5 cM, respectively. These markers are the most closely linked ones known to date for this agronomically important Fw gene. Using the information obtained in this investigation, the development and mapping of microsatellite markers in the existing map of lentil could be substantially increased, thereby providing the possibility for the future localization of various loci of agronomic interest.     

A Genetic linkage map of Pinyon pine (Pinus edulis) based on amplified fragment length polymorphisms

 Amplified fragment length polymorphisms (AFLP) were used to rapidly generate a dense linkage map for pinyon pine (Pinus edulis). The map population consisted of 40 megagametophytes derived from one tree at Sunset Crater, Arizona. A total of 78 primer combinations, each with three to five selective nucleotides, amplified 542 polymorphic markers. Of these, 33 markers showed significant deviation from the expected Mendelian genotypic segregation ratio of 1 : 1, and 164 showed complete linkage with another marker. This resulted in 338 unique markers mapping to 25 linkage groups, each of which ranged from 2 to 22 markers, averaging 80 centiMorgans (cM) in size and covering 2,012 cM (2,200 cM with the inclusion of 25 cM for each of 7 unlinked markers). Pairwise linkage values gave a genome size estimate of 2,390 cM, suggesting comprehensive coverage of the genome. A search for subsets of primer combinations giving the best map coverage found 10 primer combinations which together marked 72% of the linkage map to within 10 cM; an additional 10 primer combinations increased this percentage to 85%. Our map represents an initial step towards the identification of quantitative trait loci associated with pest resistance and water stress in pinyons and will further allow us to examine introgression rates between P. edulis and P. californiarum. Received: 14 October 1997 / Accepted: 29 April 1998     

A composite map of expressed sequences and phenotypic traits of the sunflower (Helianthus annuus L.) genome

 A map of the sunflower genome, based on expressed sequences and consisting of 273 loci, was constructed. The map incorporates data from seven F₂ populations, for a total of 1115 individuals. Two hundred and fourty five loci corresponding to 170 anonymous cDNA markers and four loci for morphological markers were mapped. We also mapped 18 loci corresponding to previously described genes or to sequences obtained through homology cloning. The unit maps vary from 774 cM to 1060 cM, with an average value of 14 major linkage groups. The integrated map is arranged in 17 major linkage groups including 238 loci, plus four small segments with 2–5 marker loci; and covers 1573 cM with an overall average marker interval of 7 cM. Thirty five percent of the markers were dominant in nature and 30% showed inter-linkage group duplication without any indication of homoeologous linkage groups. Evidence is provided for the independence of two distinct fertility restoration genes, for the presence of two loosely linked branching loci, and for marker tightly linked to the Rf1 restoration locus. This map provides an efficient tool in breeding applications such as disease-resistance mapping, QTL analyses and marker-assisted selection. Received: 27 August 1998 / Accepted: 28 December 1998     

Genetic Linkage Maps of <Emphasis Type="Italic">Betula platyphylla</Emphasis> Suk Based on ISSR and AFLP Markers

Two separate genetic linkage maps for Chinese silver birch based on inter-simple sequence repeat (ISSR) and amplified fragment-length polymorphism (AFLP) were constructed by a pseudo-testcross mapping strategy. Eighty F₁ progenies were obtained from the cross between two parental trees with desirable traits (the paternal one selected from ‘Qinghai’ and the maternal one from ‘Wangqing’). A total of 46 ISSR primers and 31 AFLP primers were employed to generate 102 ISSR and 355 AFLP polymorphic markers in the F₁ progenies. About 5.7% of all the markers displayed high segregation distortion with a P value below 0.01 and such markers were not used for map constructions. The paternal map consisted of 137 loci, spread over 13 groups and spanned 694.2 cM at an average distance of 5.1 cM between the markers, while in the maternal map, 147 loci were distributed in 14 groups covering a map distance about 949.62 cM at an average distance of 6.5 cM. These initial maps can serve as the basis for developing a more detailed genetic map.     

Mapping of quantitative trait loci affecting Drechslera teres resistance in barley with molecular markers

 Resistance loci for seedling-stage resistance to net blotch disease (Drechslera teres) in barley were mapped with molecular markers in an F₂ population derived from a cross between the susceptible barley cultivar ‘Arena’ and the resistant Ethiopian landrace ‘Hor 9088’. Disease reactions were scored with first and second leaves of 2-week-old plants 7 and 9 days after inoculation with a single spore-derived isolate. For linkage analysis, 22 RFLP markers and 284 AFLP markers were used. The seven linkage groups covered 1153.3 cM with an average marker interval of 3.76 cM. The resistance was determined to be inherited in a quantitative manner. Altogether, 12 QTLs were mapped with positions depending on the leaf used for testing and the time period after infection. Heritability in the broad sense ranged between 0.21 and 0.37. Received: 26 May 1998 / Accepted: 9 June 1998     

An interspecific (Capsicum annuum ×C. chinese) F2 linkage map in pepper using RFLP and AFLP markers

We have constructed a molecular linkage map of pepper (Capsicum spp.) in an interspecific F₂ population of 107 plants with 150 RFLP and 430 AFLP markers. The resulting linkage map consists of 11 large (206–60.3 cM) and 5 small (32.6–10.3 cM) linkage groups covering 1,320 cM with an average map distance between framework markers of 7.5 cM. Most (80%) of the RFLP markers were pepper-derived clones, and these markers were evenly distributed across the genome. By using 30 primer combinations, we were able to generate 444 AFLP markers in the F₂ population. The majority of the AFLP markers clustered in each linkage group, although PstI/MseI markers were more evenly distributed than EcoRI/MseI markers within the linkage groups. Genes for the biosynthesis of carotenoids and capsaicinoids were mapped on our linkage map. This map will provide the basis of studying secondary metabolites in pepper. Received: 20 October 1999 / Accepted: 3 July 2000     

Allotetraploidy of Zoysia species with 2n=40 based on a RFLP genetic map

 A RFLP linkage map of Zoysia spp. (2n=40), a warm-season turfgrass, was constructed by using the self-pollinated progenies obtained from an interspecific hybrid. Out of 115 DNA clones tested, 100 (87.0%), including 55 genomic clones, 38 cDNA clones, and seven gene clones encoding photosynthetic enzymes showed allelic-RFLP banding patterns among the parental accessions. We found that 26 probes detected two or more loci segregating in the self-pollinated progenies independently. The RFLP linkage map of Zoysia spp. consists of 115 loci in 22 linkage groups ranging in size from 12.5 cM to 141.3 cM with a total map distance of 1506 cM. Six RFLP loci (5.4%) showed significant segregation distortion (P<0.01). Two loci out of six were mapped to linkage group II, and another two loci were mapped to group VII. In the RFLP linkage map of zoysiagrass, five pairs of linkage groups sharing a series of duplicated loci with approximately the same order were identified. Therefore, we conclude that Zoysia spp. with 2n=40 should be considered as allotetraploids, which might have evolved from progenitors with a basic chromosome number of ten (x=10). Received: 20 March 1998 / Accepted: 17 September 1998     

AFLP genetic maps of Eucalyptus globulus and E. tereticornis

 Amplified fragment length polymorphism (AFLP) analysis is a rapid and efficient technique for detecting large numbers of DNA markers in eucalypts. We have used AFLP markers in a two-way pseudo-testcross strategy to generate genetic maps of two clones of different Eucalyptus species (E. tereticornis and E. globulus). Of 606 polymorphic fragments scored, 487 segregated in a 1 : 1 ratio, corresponding to DNA polymorphisms heterozygous in one parent and null in the other. In the maternal E. tereticornis map, 268 markers were ordered in 14 linkage groups (919 cM); the paternal E. globulus map had 200 markers in 16 linkage groups (967 cM). Results from PGRI software were compared with MAPMAKER. The average density of markers was approximately 1 per 3.9 cM. Framework markers were ordered with an average confidence level of 90%, covering 80–100% of the estimated Eucalyptus genome size. In order to investigate the homologies between the E. tereticornis and the E. globulus genetic linkage maps, we included 19 markers segregating 3 : 1 in the analysis. Some homeologous linkage groups were recognized. The linkage data developed in these maps will be used to detect loci controlling commercially important traits. Received: 17 July 1997 / Accepted: 13 October 1997     

A genetic map of melon (Cucumis melo L.) based on amplified fragment length polymorphism (AFLP) markers

 Genetic maps facilitate the study of genome structure and evolution, and the identification of monogenic traits or Mendelian components of quantitative traits. We evaluated 228 RAPD, microsatellite and AFLP markers for linkage analysis in melon (Cucumis melo L.) varieties MR-1 (resistant to Fusarium wilt, powdery and downy mildews) and Ananas Yokneum (AY; susceptible to these diseases) and constructed a detailed genetic map. The mapping population consisted of 66 backcross progenies derived from AY×(MR-1×AY). Despite a relatively low level of polymorphism in the species, AFLP markers were found to be more efficient in mapping the melon genome than RAPD or microsatellite markers. The map contains 197 AFLPs, six RAPDs and one microsatellite marker assigned to 14 major and six minor linkage groups, and covers 1942 cM with the average distance between adjacent markers of approximately 10 cM. The maximum distance allowed between markers is 27.5 cM. About 11% of the intervals (20 out of 173) are over 20 cM (but less than 27.5 cM). The map has immediate utility for identifying markers linked to disease resistance genes that are suitable for marker-assisted breeding. The use of microsatellite markers for integration with other maps is also discussed. Received: 12 March 1997 / Accepted: 20 May 1997     

A linkage map of the chickpea (Cicer arietinum L.) genome based on recombinant inbred lines from a C. arietinum×C. reticulatum cross: localization of resistance genes for fusarium wilt races 4 and 5

An integrated molecular marker map of the chickpea genome was established using 130 recombinant inbred lines from a wide cross between a cultivar resistant to fusarium wilt caused by Fusarium oxysporum Schlecht. emend. Snyd. &. Hans f. sp. ciceri (Padwick) Snyd & Hans, and an accession of Cicer reticulatum (PI 489777), the wild progenitor of chickpea. A total of 354 markers were mapped on the RILs including 118 STMSs, 96 DAFs, 70 AFLPs, 37 ISSRs, 17 RAPDs, eight isozymes, three cDNAs, two SCARs and three loci that confer resistance against different races of fusarium wilt. At a LOD-score of 4.0, 303 markers cover 2077.9 cM in eight large and eight small linkage groups at an average distance of 6.8 cM between markers. Fifty one markers (14.4%) were unlinked. A clustering of markers in central regions of linkage groups was observed. Markers of the same class, except for ISSR and RAPD markers, tended to generate subclusters. Also, genes for resistance to races 4 and 5 of fusarium wilt map to the same linkage group that includes an STMS and a SCAR marker previously shown to be linked to fusarium wilt race 1, indicating a clustering of several fusarium-wilt resistance genes around this locus. Significant deviation from the expected 1 : 1 segregation ratio was observed for 136 markers (38.4%, P<0.05). Segregation was biased towards the wild progenitor in 68% of the cases. Segregation distortion was similar for all marker types except for ISSRs that showed only 28.5% aberrant segregation. The map is the most extended genetic map of chickpea currently available. It may serve as a basis for marker-assisted selection and map-based cloning of fusarium wilt resistance genes and other agronomically important genes in future. Received: 17 November 1999 / Accepted: 4 June 2000     

QTL mapping ofFusarium moniliforme ear rot resistance in maize. 1. Map construction with microsatellite and AFLP markers

To map the QTLsof Fusarium moniliforme ear rot resistance inZea mays L., a total of 230 F₂ individuals, derived from a single cross between inbred maize lines R15 (resistant) and Ye478 (susceptible), were genotyped for genetic map construction using simple sequence repeat (SSR) markers and amplified fragment length polymorphism (AFLP) markers. We used 778 pairs of SSR primers and 63 combinations of AFLP primers to detect the polymorphisms between parents, R15 and Ye478. From the polymorphic 30 AFLP primer combinations and 159 SSR primers, we scored 260 loci in the F₂ population, among which 8 SSR and 13 AFLP loci could not be assigned to any of the linkage groups. An integrated molecular genetic linkage map was constructed by the remaining 151 SSR and 88 AFLP markers, which distributed throughout the 10 linkage groups of maize and spanned the genome of about 3463.5 cM with an average of 14.5 cM between two markers. On 4 chromosomes, we detected 5 putative segregation distortion regions (SDR_s), including 2 new ones (SDR₂ and SDR₇). The other 3 SDR_s were located near the regions where gametophyte genes were mapped, indicating that segregation distortion could be partially caused by gametophytic factors.     

Linkage relationships among molecular markers and storage root traits of carrot (Daucus carota L. ssp. sativus)

 A 109-point linkage map consisting of three phenotypic loci (P ₁, Y ₂, and Rs), six restriction fragment length polymorphisms (RFLPs), two random amplified polymorphic DNAs (RAPDs), 96 amplified fragment length polymorphisms (AFLPs), and two selective amplification of microsatellite polymorphic loci (SAMPL) was constructed for carrot (Daucus carota L. ssp. sativus; 2n=2x=18). The incidence of polymorphism was 36% for RFLP probes, 20% for RAPD primers, and 42% for AFLP primers. The overall incidence of disturbed segregation was 18%. Linkage relationships at a LOD score of 4.0 and θ=0.25 indicated 11 linkage groups. The total map length was 534.4 cM and the map was clearly unsaturated with markers spaced at 4.9 cM. AFLP P6B15 was 1.7 cM from P ₁, AFLP P1B34 was 2.2 cM from Y ₂, and AFLP P3B30XA was 8.1 cM from Rs. Received: 2 September 1998 / Accepted: 28 November 1998     

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.     

A genetic linkage map of cowpea (Vigna unguiculata) developed from a cross between two inbred, domesticated lines

 We have constructed a genetic linkage map within the cultivated gene pool of cowpea (2n=2x=22) from an F₈ recombinant inbred population (94 individuals) derived from a cross between the inbreds IT84S-2049 and 524B. These breeding lines, developed in Nigeria and California, show contrasting reactions against several pests and diseases and differ in several morphological traits. Parental lines were screened with 332 random RAPD decamers, 74 RFLP probes (bean, cowpea and mung bean genomic DNA clones), and 17 AFLP primer combinations. RAPD primers were twice as efficient as AFLP primers and RFLP probes in detecting polymorphisms in this cross. The map consists of 181 loci, comprising 133 RAPDs, 19 RFLPs, 25 AFLPs, three morphological/classical markers, and a biochemical marker (dehydrin). These markers identified 12 linkage groups spanning 972 cM with an average distance of 6.4 cM between markers. Linkage groups ranged from 3 to 257 cM in length and included from 2 to 41 markers, respectively. A gene for earliness was mapped on linkage group 2. Seed weight showed a significant association with a RAPD marker on linkage group 5. This map should facilitate the identification of markers that “tag” genes for pest and disease resistance and other traits in the cultivated gene pool of cowpea. Received: 16 September 1996 / Accepted: 25 April 1997     

Genetic mapping in pea. 1. RAPD-based genetic linkage map of Pisum sativum

 A genetic linkage map of Pisum sativum L. was constructed based primarily on RAPD markers that were carefully selected for their reproducibility and scored in a population of 139 recombinant inbred lines (RILs). The mapping population was derived from a cross between a protein-rich dry-seed cultivar ‘Térèse’ and an increased branching mutant (K586) obtained from the pea cultivar ‘Torsdag’. The map currently comprises nine linkage groups with two groups comprising only 6 markers (n=7 in pea) and covers 1139 cM. This RAPD-based map has been aligned with the map based on the (JI281×JI399) RILs population that currently includes 355 markers in seven linkage groups covering 1881 cM. The difference in map lengths is discussed. For this alignment 7 RFLPs, 23 RAPD markers, the morphological marker le and the PCR marker corresponding to the gene Uni were used as common markers and scored in both populations. Received: 13 March 1998 / Accepted: 29 April 1998     

Genetic linkage map in sour cherry using RFLP markers

 Restriction fragment length polymorphism (RFLP) linkage maps of two tetraploid sour cherry (Prunus cerasus L., 2n=4x=32) cultivars, Rheinische Schattenmorelle (RS) and Erdi Botermo (EB), were constructed from 86 progeny from the cross RS×EB. The RS linkage map consists of 126 single-dose restriction fragment (SDRF, Wu et al. 1992) markers assigned to 19 linkage groups covering 461.6 cM. The EB linkage map has 95 SDRF markers assigned to 16 linkage groups covering 279.2 cM. Fifty three markers mapped in both parents were used as bridges between both maps and 13 sets of homologous linkage groups were identified. Homoeologous relationships among the sour cherry linkage groups could not be determined because only 15 probes identified duplicate loci. Fifty nine of the markers on the linkage maps were detected with probes used in other Prunus genetic linkage maps. Four of the sour cherry linkage groups may be homologous with four of the eight genetic linkage groups identified in peach and almond. Twenty one fragments expected to segregate in a 1 : 1 ratio segregated in a 2 : 1 ratio. Three of these fragments were used in the final map construction because they all mapped to the same linkage group. Six fragments exhibited segregation consistent with the expectations of intergenomic pairing and/or recombination. Received: 1 April 1998 / Accepted: 9 June 1998     

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     

Use of locus-specific AFLP markers to construct a high-density molecular map in barley

 By using 25 primer combinations, 563 AFLP markers segregating in a recombinant inbred population (103 lines, F₉) derived from L94/Vada were generated. The 38 AFLP markers in common to the existing AFLP/RFLP combined Proctor/Nudinka map, one STS marker, and four phenotypic markers with known map positions, were used to assign present AFLP linkage groups to barley chromosomes. The constructed high-density molecular map contains 561 AFLP markers, three morphological markers, one disease resistance gene and one STS marker, and covers a 1062-cM genetic distance, corresponding to an average of one marker per 1.9 cM. However, extremely uneven distributions of AFLP markers and strong clustering of markers around the centromere were identified in the present AFLP map. Around the centromeric region, 289 markers cover a genetic distance of 155 cM, corresponding to one marker per 0.5 cM; on the distal parts, 906 cM were covered by 277 markers, corresponding to one marker per 3.3 cM. Three gaps larger than 20 cM still exist on chromosomes 1, 3 and 5. A skeletal map with a uniform distribution of markers can be extracted from the high-density map, and can be applied to detect and map loci underlying quantitative traits. However, the application of this map is restricted to barley species since hardly any marker in common to a closely related Triticum species could be identified. Received: 16 June 1997 / Accepted: 9 October 1997