A genetic linkage map of rhodesgrass based on an F1 pseudo-testcross population

The linkage relationships between 164 polymorphic amplified fragment length polymorphism (AFLP) and 25 restriction fragment length polymorphism (RFLP) fragments assayed in a pseudo‐testcross population generated from the mating of single genotypes from two divergent cultivars were used to construct female, ‘Katambora’ (‘Kat’) and male, ‘Tochirakukei’ (‘Toch’) parental genetic maps for rhodesgrass. The ‘Kat’ genetic map consists of 84 marker loci (72 AFLP and 12 RFLP markers) distributed on 14 linkage groups and spans a total length of 488.3 cM, with an average distance of 7.8 cM between adjacent markers. The ‘Toch’ genetic map consists of 61 marker loci (52 AFLP and nine RFLP) mapped on 12 linkage groups spanning a total length of 443.3 cM, with an average spacing of 9.0 cM between adjacent markers. About 23% of the markers remained unassigned. The level of segregation distortion observed in this cross was 11.1%. In both maps, linked duplicated RFLP loci were found. These linkage maps will serve as a starting point for linkage studies in rhodesgrass with potential application for marker‐assisted selection in breeding programmes.     

Construction of a high-density SSR marker-based linkage map of zoysiagrass (<Emphasis Type="Italic">Zoysia japonica</Emphasis> Steud.)

A consensus genetic linkage map with 447 SSR markers was constructed for zoysiagrass (Zoysia japonica Steud.), using 86 F₁ individuals from the cross ‘Muroran 2’ × ‘Tawarayama Kita 1’. The consensus map identified 22 linkage groups and had a total length of 2,009.9 cM, with an average map density of 4.8 cM. When compared with a previous AFLP-SSR linkage map, the SSR markers from each linkage group mapped to similar positions in both maps. Eight pairs of linkage groups from the AFLP-SSR map were joined into eight new groups in the current map. This zoysiagrass consensus map contained 35 SSR markers exhibiting high homology with rice genomic sequences from known chromosomal locations. This allowed synteny to be identified between Zoysiagrass linkage groups 2, 3, 9, 19 and rice chromosomes 3, 12, 2, 7 respectively. These results provide important comparative genomics information and the new map is now available for quantitative trait locus analysis, marker-assisted selection and breeding for important traits in zoysiagrass.     

Clustering of amplified fragment length polymorphism markers in a linkage map of rye

Amplified fragment length polymorphisms (AFLPs) are now widely used in DNA fingerprinting and genetic diversity studies, the construction of dense genetic maps and in fine mapping of agronomically important traits. The AFLP markers have been chosen as a source to extend and saturate a linkage map of rye, which has previously been generated by means of restriction fragment length polymorphism, random amplified polymorphic DNA, simple sequence repeat and isozyme markers. Gaps between linkage groups, which were known to be part of chromosome 2R, have been closed, thus allowing the determination of their correct order. Eighteen EcoRI‐MseI primer combinations were screened for polymorphism and yielded 148 polymorphic bands out of a total of 1180. The level of polymorphism among the different primer combinations varied from 5.7% to 33.3%. Eight primer combinations, which revealed most polymorphisms, were further analysed in all individuals of the F₂ mapping population. Seventy‐one out of 80 polymorphic loci could be integrated into the linkage map, thereby increasing the total number of markers to 182. However, 46% of the mapped AFLP markers constituted four major clusters located on chromosomes 2R, 5R and 7R, predominantly in proximity to the centromere. The integration of AFLP markers caused an increase of 215 cM, which resulted in a total map length of almost 1100 cM.     

The first genetic linkage map of crape myrtle (Lagerstroemia) based on amplification fragment length polymorphisms and simple sequence repeats markers

Lagerstroemia (crape myrtle) are famous ornamental plants with large pyramidal racemes, long flower duration and diverse colours. Genetic maps provide an important genomic resource of basic and applied significance. A genetic linkage map was developed by genotyping 192 F₁ progeny from a cross between L. caudata (female) and L. indica (‘Xiang Xue Yun’) (male) with a combination of amplification fragment length polymorphisms (AFLP) and simple sequence repeats (SSR) markers in a double pseudo‐testcross mapping strategy. A total of 330 polymorphic loci consisting of 284 AFLPs and 46 SSRs showing Mendelian segregation were generated from 383 AFLP primer combinations and 150 SSR primers. The data were analysed using JoinMap 4.0 (evaluation version) to construct the linkage map. The map consisted of 20 linkage groups of 173 loci (160 AFLPs and 13 SSRs) covering 1162.1 cM with a mean distance of 10.69 cM between adjacent markers. The 20 linkage groups contained 2–49 loci and ranged in length from 7.38 to 163.57 cM. This map will serve as a framework for mapping QTLs and provide reference information for future molecular breeding work.     

AFLP-based STS markers closely linked to a fertility restoration locus (Rfm1) for cytoplasmic male sterility in barley

The Rfm1 gene restores the fertility of the msm1 and msm² male‐sterile cytoplasms in barley. Rfm1 is located on the short arm of chromosome 6H. To develop molecular markers tightly linked to Rfm1 for use in sophisticated marker‐assisted selection and map‐based cloning, an amplified fragment‐length polymorphism (AFLP) marker system with isogenic lines and a segregating BC₁F₁ population was used. Nine hundred primer combinations were screened and a linkage map was constructed around the Rfm1 locus by using 25 recombinant plants selected from 214 BC₁F₁ plants. Three AFLP markers were identified, e34m2, e46m19 and e48m17, linked to the locus. The most closely linked markers were e34m2, at 1.0 cM distally and e46m19, at 1.1 cM proximally. The two AFLP markers were converted to dominant STS markers. These markers should accelerate programmes for breeding restorer lines and will be useful for map‐based cloning.     

Molecular mapping of a new gene for resistance to frogeye leaf spot of soya bean in 'Peking'

Amplified fragment length polymorphism (AFLP) and microsatellite (simple sequence repeat, SSR) techniques were used to map the _RGSp_eking gene, which is resistant to most isolates of Cercospora sojina in the soya bean cultivar ‘Peking’. The mapping was conducted using a defined F₂ population derived from the cross of ‘Peking’(resistant) בLee’(susceptible). Of 64 EcoRI and MseI primer combinations, 30 produced polymorphisms between the two parents. The F₂ population, consisting of 116 individuals, was screened with the 30 AFLP primer pairs and three mapped SSR markers to detect markers possibly linked to Rcs_Peking. One AFLP marker amplified by primer pair E‐AAC/M‐CTA and one SSR marker Satt244 were identified to be linked to Res_Peking. The gene was located within a 2.1‐cM interval between markers AACCTA178 and Satt244, 1.1 cM from Satt244 and 1.0 cM from AACCTA178. Since the SSR markers Satt244 and Satt431 have been mapped to molecular linkage group (LG) J of soya bean, the Res_Peking resistance gene was putatively located on the LG J. This will provide soya bean breeders an opportunity to use these markers for marker‐assisted selection for frogeye leaf spot resistance in soya bean.     

Mapping of a gene for leaf scald resistance in barley line 'B87/14' and validation of microsatellite and RFLP markers for marker-assisted selection

Seedlings of the barley line ‘B87/14’ were resistant to 22 out of 23 Australian isolates of Rhynchosporium secalis, the causal agent of leaf scald.‘B87/14’‐based populations were developed to determine the location of the resistance locus. Scald resistance segregated as a single dominant trait in BC₁F₂ and BC₁F₃ populations. Bulked segregant analysis identified amplified fragment length polymorphisms (AFLPs) with close linkage to the resistance locus. Fully mapped populations not segregating for scald resistance located these AFLP markers on chromosome 3H, possibly within the complex Rrs1 scald locus. Microsatellite and restriction fragment length polymorphism markers adjacent to the AFLP markers were identified and validated for their linkage to scald resistance in a second segregating population, with the closest marker 2.2 cM from the resistance locus. These markers can be used for selection of the Rrs.B87 scald‐resistance locus, and other genes at the chromosome 3H Rrs1 locus.     

黄瓜远缘群体分子遗传连锁图谱的构建和分析

以野生黄瓜品种和普通栽培黄瓜品种作亲本获得的142个F2群体为材料,采用AFLP,SRAP,SSR等分子标记进行遗传分析,构建了包含10个连锁群,有159个标记组成的黄瓜遗传连锁图谱,其中包括112个AFLP标记,39个SRAP标记和8个SSR标记。该遗传图谱覆盖基因组长度743.11 cM,平均图距4.67 cM。     

Detection of linkage disequilibrium QTLs controlling low-temperature growth and metabolite accumulations in an admixed breeding population of <Emphasis Type="BoldItalic">Leymus</Emphasis> wildryes

Low-temperature soluble carbohydrate accumulations are commonly associated with anthocyanin coloration, attenuated growth, and cold adaptation of cool-season grasses. A total of 647 AFLP markers were tested for associations with anthocyanin coloration, tiller formation, leaf formation, cumulative leaf length, percent soluble carbohydrate, and dry matter regrowth among replicated clones of an admixed Leymus wildrye breeding population evaluated in low-temperature growth chambers. The admixed breeding population was derived from a heterogeneous population of L. cinereus × L. triticoides F₁ hybrids, with two additional generations of open pollination. Two AFLP linkage maps, constructed from two full-sib mapping populations derived from the same F₁ hybrid population, were integrated to produce a framework consensus map used to examine the distribution of marker-trait associations in the admixed F₁OP₂ population. Thirty-seven linkage blocks, spanning 258 cM (13.6%) of the 1895 cM consensus map, contained 119 (50%) of the 237 markers showing at least one possible trait association (P < 0.05). Moreover, 28 (68%) of the 41 most significant marker-trait associations (P < 0.005) were located in 15 QTL linkage blocks spanning 112.9 cM (6%) of the linkage map. The coincidence of these 28 significant marker-trait associations, and many less significant associations, in 15 relatively small linkage blocks (0.6 cM to 21.3 cM) provides evidence of admixture linkage disequilibrium QTLs (ALD QTLs) in this heterogeneous breeding population. At least four of the remaining 13 putative marker-trait associations (P < 0.005) were located in genetic map regions lacking other informative markers. The complexity of marker-trait associations results from heterogeneity within and substantial divergence among the parental accessions.     

Genetic maps of RAPD, AFLP and ISSR markers in Ananas bracteatus and A. comosus using the pseudo-testcross strategy

Genetic maps of random amplified polymorphic DNA (RAPD), amplified fragment length polymorphisms (AFLP) and inter simple sequence repeats (ISSR) markers in pineapple (2n = 2x = 50) are reported for the first time. On the basis of a segregating population of 46 F1 individuals from a cross Ananas comosus x A. bracteatus, genetic maps of these two species were constructed using the two‐way pseudo‐testcross approach. The A. bracteatus map consists of 335 markers (60 RAPDs, 264 AFLPs and 11 ISSRs) assembled into 50 linkage groups, 26 of them with at least four markers. The A. comosus map consists of 157 markers (33 RAPDs, 115 AFLPs, eight ISSRs and the ‘piping’ trait locus) organized into 30 linkage groups, 18 of them with at least four markers. These maps cover, respectively, 57.2% of the A. bracteatus genome estimated as 3693 cM long, and 31.6% of the A. comosus genome calculated as 4146 cM. A rough estimate of 120 and 127 kbp/ cM on average was found for the relationship between physical and genetic distance for A. bracteatus and A. comosus, respectively.     

Integration of AFLP markers into an RFLP-based map of durum wheat

Amplified fragment length polymorphism (AFLP) is a powerful technique which can readily be applied to a wide range of species for mapping purposes. AFLPs were added to a linkage map of durum wheat constructed using restriction fragment length polymorphisms (RFLPs). The mapping population included 65 recombinant inbred lines derived from a cross between the durum wheat cultivar ‘Messapia’ and accession ‘MG4343’ of the wild Triticum turgidum ssp. dicoccoides (Körn.). Genomic DNA was digested with MseI (4‐cutter) and Sse83871 (8‐cutter). Using a silver‐staining protocol, 14 primer combinations revealed 421 clearly scorable amplicons including 100 polymorphisms. The presence of nine pairs of bands linked in repulsion phase with each pair generated by one primer combination suggested the presence of codominant alleles; sequence analysis of four band pairs confirmed their codominant nature. The integration of 80 AFLP loci extended the map in several telomeric regions, reduced the size of four large gaps present in the previous map, and eliminated one gap. The new map obtained after the inclusion of the 80 AFLP loci and eight additional RFLP loci spans 2063cM which represent a 52.6% increment compared with the previous map. Compared with the distribution of RFLPs, no significant clustering of AFLP markers was observed.     

Genetic linkage map of cassava (Manihot esculenta Crantz) based on AFLP and SSR markers

To generate a genetic linkage map of cassava ( Manihot esculenta Crantz), 58 F₁ progenies from a cross between Rayong 90 (female) and Rayong 5 (male) were examined in amplification fragment length polymorphism (AFLP) and simple sequence repeat (SSR) analyses. A total of 469 polymorphic markers consisting of 378 AFLPs generated from 76 primer combinations and 91 SSRs were identified. These markers were analyzed using the joinmap ^® 3.0 package program to construct a genetic linkage map. A total of 33 linkage groups of a common map were constructed from 119 AFLPs and 18 SSRs, spanning 1095 cM with an average of 7.99 cM between markers. The genetic linkage map generated in this study will be useful for genetic studies in cassava particularly for the identification of genetic markers linked to traits of interest, although the complex cassava genome suggests that maybe a long term objective.     

High-resolution mapping of the nud locus controlling the naked caryopsis in barley

The hulled or naked caryopsis character of barley is an important agronomic trait because of the direct link to its use. A single recessive gene, nud, located on the long arm of chromosome 7H, controls the naked caryopsis character. Previously, linked amplified fragment length polymorphism (AFLP) bands from bulked segregant analysis were screened, and the nud gene was mapped in a population of 151 F₂ plants. In the present study, the aim was to construct a high‐resolution map of the nud gene towards its positional cloning. Two AFLP bands were converted into sequence‐characterized amplified region (SCAR) markers (sKT5 and sKT9), and a previously reported SCAR marker sKT3 was improved for more reliable detection of polymorphism. A total of 2380 segregants derived from five cross‐combinations were analysed, and the nud gene was flanked by sKT3 and sKT9, at the 0.6‐cM proximal and the 0.06‐cM distal side, respectively. The SCAR markers developed in this study should be useful for marker‐assisted selection in naked barley breeding employing crosses between naked and hulled accessions.     

Amplified fragment length polymorphism- and simple sequence repeat-based molecular tagging and mapping of greenbug resistance gene Gb3 in wheat

The greenbug, Schizaphis graminum (Rondani), is the most economically damaging aphid pest of wheat in the southern Great Plains of the USA. In this study, the single, dominant greenbug resistance gene, Gb3, was molecularly tagged and genetically mapped using amplified fragment length polymorphism (AFLP) and simple sequence repeat(SSR) markers. Three AFLP loci were associated with the Gb3 locus in linkage analysis with 75 F_2:3 families from the cross between two near‐isogenic lines (NILs) for Gb3,‘TXGBE273’ and ‘TXGBE281′. Two of these loci, XMgcc Pagg and Xmagg Patg cosegregate with Gb3 in the population analysed. Further analysis indicated that XMgcc Pagg and Xmagg Patg are specific for the Gb3 locus in diverse genetic backgrounds. Two SSR markers, Xgwm111 and Xgwm428 previously mapped in wheat chromosome 7D, were shown to be linked with Gb3, 22.5 cM and 33.1 cM from Gb3, respectively, in an F₂ population of ‘Largo’בTAM 107’, suggesting that Gb3 is located in the long arm of chromosome 7D. The two AFLP markers cosegregating with Gb3 are valuable tools in developing molecular markers for marker‐assisted selection of greenbug resistance in wheat breeding.     

Identification of molecular markers linked to salt‐tolerant genes at germination stage of rice

An F_2 : 4 population derived from the cross between salt‐tolerant variety ‘Gharib’ (indica) and salt‐sensitive variety Sepidroud (indica) was used to determine the germination traits. The seeds were treated with 80 mm NaCl (salt stress), and 11 traits were determined as indicators for salt‐tolerant including germination rate, germination percentage, radicle length, plumule length, coleoptile length, plumule fresh and dry weight, radicle fresh and dry weight and coleoptile fresh and dry weight. A linkage map of 2475.7 cM with an average interval of 10.48 cM was constructed using 105 amplified fragment length polymorphism (AFLP) markers and 131 SSR markers. As many as that 17 quantitative trait loci (QTLs) were detected related to germination traits under salt stress condition; some of them are being reported for first time. Also, overlapping of QTLs related to salt tolerance was observed in this study. The identification of genomic regions associated with salt‐tolerant and its components under salt stress will be useful for marker‐based approaches to improve salt‐tolerant for farmers in salt‐prone rice environments.     

Molecular mapping of a dominant genic male sterility gene Ms in rapeseed (Brassica napus)

Rs1046AB is a genic male sterile two‐type line in rapeseed that has great potential for hybrid seed production. The sterility of this line is conditioned by the interaction of two genes, i.e. the dominant genic male sterility gene (Ms) and the suppressor gene (Rf). The present study was undertaken to identify DNA markers for the Ms locus in a BC₁ population developed from a cross between a male‐sterile plant in Rs1046AB and the fertile canola‐type cultivar ‘Samourai’. Bulked segregant analysis was performed using the amplified fragment length polymorphism (AFLP) methodology. From the survey of 480 AFLP primer combinations, five AFLP markers (P10M13₃₅₀, P13M8₄₀₀, P6M6₄₁₀, E7M1₂₃₀ and E3M15₁₀₀) tightly linked to the target gene were identified. Two of them, E3M15₁₀₀ and P6M6₄₁₀, located the closest, at either side of Ms at a distance of 3.7 and 5.9 cM, respectively. The Ms locus was subsequently mapped on linkage group LG10 in the map developed in this laboratory, adding two additional markers weakly linked to it. This suite of markers will be valuable in designing a marker‐assisted genic male sterility three‐line breeding programme.     

Sequence characterized amplified region markers tightly linked to the dwarf mosaic resistance gene <Emphasis Type="Italic">mdm1 (t)</Emphasis> in maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.)

Maize dwarf mosaic is one of the devastating and wide spread viral diseases in the world. The present investigation was carried out to develop DNA markers closely linked to the resistance gene mdm1 (t). Linkage between the markers and phenotypes was confirmed by analyzing an F₂ population obtained from a cross between a resistant parent ‘Huangzaosi’ and a susceptible parent ‘Mo17(478)’. Four AFLP markers were found in the maize dwarf mosaic resistant plants. By using (BSA) bulked segregant analysis, two of the four AFLP markers were transformed into Sequence-characterized amplified regions markers (SCARs), nominated Rsun-1 and Rsun-2. The two amplified fragment length polymorphism (AFLP) markers, RHC-1and RHC-2, from the amplification products of primer combination E-AGC/M-CAA and E-AGC/M-GAA, showed linkage with the mdm1 (t) gene in a genetic distance 1.6 and 2.0 cM, respectively. The results indicate that the new SCAR markers will be valuable to distinguish resistant plants from susceptible plants in plantlets growing in seedbeds. The markers developed in this study are suitable for marker-assisted selection for maize dwarf mosaic resistance.     

Development of AFLP and derived CAPS markers for root-knot nematode resistance in cotton

Resistance to root-knot nematode (Meloidogyne incognita) is determined by a single major gene rkn1 in Gossypium hirsutum Acala NemX cotton. Bulked segregant analysis (BSA) combined with amplified fragment length polymorphism (AFLP) was used to identify molecular markers linked to rkn1. DNA pools from homozygous susceptible (S) and resistant (R) bulks of an F_2:3 originating from the intraspecific cross NemX × SJ-2 were screened with 128 EcoR1/Mse1 primer combinations. Putative AFLP markers were then screened with 60 F_2:7 RIL plants and four AFLP markers were found linked to rkn1. The linkage of AFLP markers to rkn1 was also confirmed in a F₂ population. The closest AFLP marker was converted to a cleaved amplified polymorphic sequence (CAPS) marker (designated GHACC1) by aligning the sequences from both susceptible and resistant parents. GHACC1 linkage to rkn1 was confirmed in the F₂ (1R:3S), F_2:7 RIL (1R:1S) and the backcross population SJ-2 × F₁ (NemX × SJ-2) (1 heterozygous: 1 homozygous). The four AFLP markers, GHACC1 plus two SSR markers (CIR316 and BNL1231) linked to rkn1 from previous work were mapped to intervals of 2.6–14.2 cM from the rkn1 locus, and the genomic region around rkn1 was spanned to about 28.2 cM in the F_2:7 population. The PCR-based GHACC1 and CIR316 markers were tested on 21 nematode resistant and susceptible cotton breeding lines and cultivars. GHACC1 was suitable for nematode resistance screening within G.␣hirsutum, but not G. barbadense, whereas CIR316 was useful in both species, indicating their␣potential for utilization in marker-assisted selection.     

Construction of integrated linkage map of a recombinant inbred line population of white lupin (Lupinus albus L.)

We report the development of a Diversity Arrays Technology (DArT) marker panel and its utilisation in the development of an integrated genetic linkage map of white lupin (Lupinus albus L.) using an F₈ recombinant inbred line population derived from Kiev Mutant/{"type":"entrez-protein","attrs":{"text":"P27174","term_id":"14195583","term_text":"P27174"}}P27174. One hundred and thirty-six DArT markers were merged into the first genetic linkage map composed of 220 amplified fragment length polymorphisms (AFLPs) and 105 genic markers. The integrated map consists of 38 linkage groups of 441 markers and spans a total length of 2,169 cM, with an average interval size of 4.6 cM. The DArT markers exhibited good genome coverage and were associated with previously identified genic and AFLP markers linked with quantitative trait loci for anthracnose resistance, flowering time and alkaloid content. The improved genetic linkage map of white lupin will aid in the identification of markers for traits of interest and future syntenic studies.     

A genetic linkage map of Spinacia oleracea and localization of a sex determination locus

A genetic map of Spinach (Spinacia oleracea) was constructed in a classical back cross population using 101 AFLP and 9 microsatellite markers. The map was divided into seven linkage groups with a total length of 585 cM and an average distance between the markers of 5.18 cM. The linkage map was constructed with LOD 3.5, but was quite stable with seven linkage groups remaining until LOD 7.0. Gender segregated 1 male to 1 female in the mapping population and was mapped to a small area of one linkage group with a distance of 1.9 cM to a microsatellite marker termed SO4. This small chromosomal region co-segregating with sex determination in the species is in contrast to previous reports on a heterologous XY chromosome system in spinach. Microsatellite markers used as anchors in the map construction were isolated from sequences of known nuclear encoded genes in spinach. This enabled simultaneous positioning on the map of these genes: Rubisco activase (Rca), Photosytem 1 subunit V (PsaG), Protein Kinase (Pk), Nitrate reductase (Nir), ferrodoxin:thioredoxin reductase (Ftr), Ribosomal protein L1 (Rps22), Choline monooxygenase (Cmo), Pseudogene for BZIP protein (Bzip), Glycerol-3-phosphate acyltransferase (Act1) and stromal ascorbate peroxidase, thylakoid-bound ascorbate peroxidase (Apx2). Spinach has a small genome, which makes it suitable for basic genomic studies and many physiologically important genes have been cloned from the species. The present map anchored with user friendly microsatellite markers will be useful for future studies of physiology and genetics of the species as well as studies of the nature of gender determination.