Estimation of the position and effect of a lethal factor locus on a molecular marker linkage map

In the mapping of DNA markers the distortion of segregation of marker genotypes is often observed, which may be caused by a lethal factor acting in filial generations derived from distant crosses. A method is presented for estimating the recombination values between a lethal factor locus and neighboring molecular markers, and the relative viability or fertilization ability of gametes or zygotes affected by the lethal factor in an F₂ population using the maximum likelihood method and the expectation conditional maximization (ECM) algorithm. Three selection models of gamete or zygote were considered, and the most likely one was determined by goodness of fit of the observed frequency of the phenotypes to the expected ones under the models. The method was applied to segregation data of molecular markers of an F₂ population consisting of 144 individuals derived from a cross between an Indica and a Japonica rice variety. The presence of a lethal factor locus (L) located on chromosome III that caused partial gametic selection in both the male and female sides was suggested. The locus L was tightly linked to RFLP marker number 23 of the RFLP linkage map of Saito et al. (1991a), and the fertilization chance of a male or female gamete possessing the lethal factor was, on average, 41.5% of that of the normal gamete.     

Genetic mapping of a major gene affecting onion bulb fructan content

The non-structural dry matter content of onion bulbs consists principally of fructose, glucose, sucrose and fructans. The objective of this study was to understand the genetic basis for the wide variation observed in the relative amounts of these carbohydrates. Bulb carbohydrate composition was evaluated in progeny from crosses between high dry matter storage onion varieties and sweet, low dry matter varieties. When samples were analysed on a dry weight basis, reducing sugar and fructan content exhibited high negative correlations and bimodal segregation suggestive of the action of a major gene. A polymorphic SSR marker, ACM235, was identified which exhibited strong disequilibrium with bulb fructan content in F_2:3 families from the ‘W202A’ × ‘Texas Grano 438’ mapping population evaluated in two environments. This marker was mapped to chromosome 8 in the interspecific population ‘Allium cepa × A. roylei’. Mapping in the ‘Colossal Grano PVP’ × ‘Early Longkeeper P12’ F₂ population showed that a dominant major gene conditioning high-fructan content lay in the same genomic region. QTL analysis of total bulb fructan content in the intraspecific mapping population ‘BYG15-23’ × ‘AC43’ using a complete molecular marker map revealed only one significant QTL in the same chromosomal region. This locus, provisionally named Frc, may account for the major phenotypic differences in bulb carbohydrate content between storage and sweet onion varieties.     

Potential of doubled-haploid lines and localization of quantitative trait loci (QTL) for partial resistance to bacterial leaf streak (Xanthomonas campestris pv. hordei) in barley

 Genetic variability for partial resistance to bacterial leaf streak in barley, caused by Xanthomonas campestris pv. hordei, was investigated in 119 doubled-haploid lines (DH) developed by the Hordeum bulbosum method from the F₁ progeny of the cross between two cultivars, ‘Morex’ (resistant) and ‘Steptoe’ (susceptible). Two experiments were undertaken in a randomized complete block design with three replicates, in a controlled growth chamber. Twenty seeds per replicate were planted in plastic containers (60×40×8 cm) containing moistened vermiculite. At the two-leaf stage seedlings were inoculated with an Iranian strain of the pathogen. Genetic variability was observed among the 119 DH lines for partial resistance to the disease. Some DH lines were significantly more resistant than ‘Morex’ (resistant parent) to bacterial leaf streak. Genetic gain in percentage of resistant parent for 5% of the selected DH lines was significant (47.70% and 33.72% in the first and the second experiment, respectively). A QTL analysis of bacterial leaf streak resistance showed that three QTLs were detected on chromosomes 3 and 7. Multilocus allelic effects of the three QTLs account for almost 54% of the mean difference between the parents and nearly 30% of the phenotypic variation of the trait in the mean experiment. The resistance locus on chromosome 3, near ABG377, apprears to be a major gene. Received: 15 July 1997 / Accepted: 4 August 1997     

Identification and mapping of RAPD and RFLP markers linked to a fertility restorer gene for a new source of cytoplasmic male sterility in Beta vulgaris ssp. maritima

 The present study shows that the recently described mitochondrial H haplotype is associated with cytoplasmic male-sterility (CMS). This new source of CMS appears to be different from the mitotype E-associated CMS most frequently found in natural populations. A mitotype H progeny with a sexual phenotype segregation was used to identify a gene restoring male fertility (R1H ). Using bulk segregant analysis (BSA), nine RAPD markers linked to this restorer locus were detected and mapped. The comparison with other Beta genetic maps shows that the closest RAPD marker, distant from R1H by 5.2 cM, belongs to the same linkage group as the monogermy locus. In order to determine the position of R1H more precisely, four RFLP loci within this linkage group were mapped in the segregating progeny. It thus became possible to construct a linkage map of the region containing the RFLP, RAPD and R1H loci. The closest RFLP marker was located 1.7 cM away from R1H. However, a nuclear gene restoring the ‘Owen’ CMS which is currently used in sugar beet breeding is reportedly linked to the monogermy locus, raising the question of a possible identity between the new CMS system and the ‘Owen’ CMS. Received: 15 September 1997 / Accepted: 1 December 1997     

Fine mapping of the region on wheat chromosome 7D controlling grain weight

We report the fine mapping of the previously described quantitative trait loci (QTL) for grain weight QTgw.ipk-7D associated with microsatellite marker Xgwm1002-7D by using introgression lines (ILs) carrying introgressions of the synthetic wheat W-7984 in the genetic background of the German winter wheat variety ‘Prinz’. The BC₄F₃ ILs had a 10% increased thousand grain weight compared to the control group and the recurrent parent ‘Prinz’, and 84.7% of the phenotypic variance could be explained by the segregation of marker Xgwm1002-7D, suggesting the presence of a gene modulating grain weight, which was preliminarily designated gw1. It was possible to delimit the QTL QTgw.ipk-7D to the interval Xgwm295–Xgwm1002, which is located in the most telomeric bin 7DS4-0.61-1.00 in the physical map of wheat chromosome arm 7DS. Furthermore, our data suggest the presence of a novel plant height-reducing locus Rht on chromosome arm 7DS of ‘Prinz’. Larger grain and increased plant height may reflect the pleiotropic action of one gene or may be caused by two linked genes. In general, our data support the concept of using nearly isogenic ILs for validating and dissecting QTLs into single Mendelian genes and open the gateway for map-based cloning of a grain-weight QTL in wheat.     

A consensus map of rye integrating mapping data from five mapping populations

A consensus map of rye (Secale cereale L.) was constructed using JoinMap 2.0 based on mapping data from five different mapping populations, including ‘UC90’ × ‘E-line’, ‘P87’ × ‘P105’, ‘I_0.1-line’ × ‘I_0.1-line’, ‘E-line’ × ‘R-line’, and ‘Ds2’ × ‘RxL10’. The integration of the five mapping populations resulted in a 779-cM map containing 501 markers with the number of markers per chromosome ranging from 57 on 1R to 86 on 4R. The linkage sizes ranged from 71.5 cM on 2R to 148.7 cM on 4R. A comparison of the individual maps to the consensus map revealed that the linear locus order was generally in good agreement between the various populations, but the 4R orientations were not consistent among the five individual maps. The 4R short arm and long arm assignments were switched between the two population maps involving the ‘E-line’ parent and the other three individual maps. Map comparisons also indicated that marker order variations exist among the five individual maps. However, the chromosome 5R showed very little marker order variation among the five maps. The consensus map not only integrated the linkage data from different maps, but also greatly increased the map resolution, thus, facilitating molecular breeding activities involving rye and triticale.     

Genetic analysis of the dwarfing gene (Rht8) in wheat. Part I. Molecular mapping of Rht8 on the short arm of chromosome 2D of bread wheat (Triticum aestivum L.)

 Two sets of single chromosome recombinant lines comparing 2D chromosomes from the wheat varieties ‘Ciano 67’ and ‘Mara’ with the common 2D chromosome of ‘Cappelle-Desprez’ in a ‘Cappelle-Desprez’ background were used to detect a diagnostic wheat microsatellite marker for the dwarfing gene Rht8. The genetic linkage maps place the wheat microsatellite marker WMS 261 0.6 cM distal to Rht8 on the short arm of chromosome 2D. By PCR analysis the WMS 261 alleles of ‘Mara’, ‘Cappelle-Desprez’ and ‘Ciano 67’ could be distinguished by different fragment sizes of 192 bp, 174 bp and 165 bp, respectively. A screen of over 100 international varieties of wheat showed that the three allelic variants were all widespread. It also demonstrated that a limited number of varieties carried novel WMS 261 variants of over 200 bp. Following classification of the individual recombinant lines for allelic variants at the WMS 261 locus it was possible to attribute a 7- to 8-cm reduction in plant height with the WMS 261-192-bp allele compared to the WMS 261-174-bp allele in the set of recombinant lines comparing 2D chromosomes of ‘Mara’ and ‘Cappelle-Desprez’. A height reduction of around 3 cm was detected between the WMS 261-174-bp allele and the WMS 261-165-bp allele in the recombinant lines comparing 2D chromosomes of ‘Cappelle-Desprez’ and ‘Ciano 67’. Received: 17 October 1997 / Accepted: 12 November 1997     

Mapping QTLs for pre-harvest sprouting tolerance on chromosome 2D in a synthetic hexaploid wheat×common wheat cross

Based on segregation distortion of simple sequence repeat (SSR) molecular markers, we detected a significant quantitative trait loci (QTL) for pre-harvest sprouting (PHS) tolerance on the short arm of chromosome 2D (2DS) in the extremely susceptible population of F₂ progeny generated from the cross of PHS tolerant synthetic hexaploid wheat cultivar ‘RSP’ and PHS susceptible bread wheat cultivar ‘88–1643’. To identify the QTL of PHS tolerance, we constructed two SSR-based genetic maps of 2DS in 2004 and 2005. One putative QTL associated with PHS tolerance, designatedQphs.sau-2D, was identified within the marker intervalsXgwm261-Xgwm484 in 2004 and in the next year, nearly in the same position, between markerswmc112 andXgwm484. Confidence intervals based on the LOD-drop-off method ranged from 9 cM to 15.4 cM and almost completely overlapped with marker intervalXgwm261-Xgwm484. Flanking markers near this QTL could be assigned to the C-2DS1-0.33 chromosome bin, suggesting that the gene(s) controlling PHS tolerance is located in that chromosome region. The phenotypic variation explained by this QTL was about 25.73–27.50%. Genotyping of 48 F₆ PHS tolerant plants derived from the cross between PHS tolerant wheat cultivar ‘RSP’ and PHS susceptible bread wheat cultivar ‘MY11’ showed that the allele ofQphs.sau-2D found in the ‘RSP’ genome may prove useful for the improvement of PHS tolerance.     

Chromosome landing at the Mla locus in barley (Hordeum vulgare L.) by means of high-resolution mapping with AFLP markers

 The complex Mla locus of barley determines resistance to the powdery mildew pathogen Erysiphe graminis f. sp. hordei. With a view towards gene isolation, a population consisting of 950 F₂ individuals derived from a cross between the near-isogenic lines ‘P01’ (Mla1) and ‘P10’ (Mla12) was used to construct a high-resolution map of the Mla region. A fluorescence-based AFLP technique and bulked segregant analysis were applied to screen for polymorphic, tightly linked AFLP markers. Three AFLP markers were selected as suitable for a chromosome-landing strategy. One of these AFLP markers and a closely linked RFLP marker were converted into sequence-specific PCR markers. PCR-based screening of approximately 70 000 yeast artificial chromosome (YAC) clones revealed three identical YACs harbouring the Mla locus. Terminal insert sequences were obtained using inverse PCR. The derived STS marker from the right YAC end-clone was mapped distal to the Mla locus. Received: 17 July 1998 / Accepted: 9 August 1998     

Functional gene markers for polyphenol oxidase locus in bread wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.)

Higher polyphenol oxidase (PPO) activity in wheat kernels and flour has been implicated in the time dependent darkening of various end-products. Previous study conducted on a bread wheat (Triticum aestivum L.) doubled haploid (DH) mapping population derived from Chara (medium-high PPO) and WW2449 (low PPO) identified a major QTL for PPO activity located on the long arm of chromosome 2A. Physical mapping of SSR markers accounting for up to 84% of phenotypic variation for PPO activities suggests that the candidate PPO locus is localised in the deletion bin delimited by 2AL 0.77–0.85. In order to develop functional gene markers, nine wheat ESTs mapped to this deletion bin and partial PPO reference genes were explored for their sequence identities and linkage with PPO locus in a mapping population. In the present study, two markers: one SNP and one CAPS based upon BQ161439 sequence variation between the parents were identified which exhibited a tight linkage (0–0.6 cM) with the PPO loci designated as XTc1 and XPPO- _LDOPA. We also mapped the reference PPO gene (GenBank AY526268) characterised from developing kernels of wheat, on the long arm of chromosome 2A which exhibited a complete linkage with XPPO- _L DOPA locus. Results suggest that PPO variation displayed in the DH population from Chara/WW2449 is due to the same reference PPO gene. Allelic homoplasy of tightly linked markers, indicated that these markers are ‘diagnostic’ for the selection of low PPO gene in a range of germplasm being used in different Australian breeding programs. Identification and validation of ‘functional gene markers’ would facilitate in enhancing the selection efficiency for low PPO activity in wheat breeding programs.     

Localization of the rice stripe disease resistance gene, Stv-bi, by graphical genotyping and linkage analyses with molecular markers

 We used graphical genotyping and linkage analyses with molecular markers to determine the chromosomal location of the rice stripe disease resistance gene, Stv-b ⁱ . The stripe resistance gene from the indica rice (Oryza sativa) cv ‘Modan’ was introgressed into several Japanese rice varieties. We found 4 RFLP markers in ‘Modan’, five susceptible parental rice varieties (‘Norin No. 8’, ‘Sachihikari’, ‘Kanto No. 98’, ‘Hokuriku No.103’ and ‘Koganebare’) and four resistant progeny varieties (‘St. No. 1’, ‘Aichi No. 6’, ‘Aoisora’ and ‘Asanohikari’). Graphical genotyping of the resistant progeny revealed a chromosomal segment ascribable to ‘Modan’ and associated with stripe resistance. The chromosomal segment from ‘Modan’ was located at 35.85 cM on chromosome 11. Linkage analysis using 120 F₂ individuals from a cross between ‘Koshihikari’ (susceptible) and ‘Asanohikari’ (resistant) revealed another 8 RFLP markers in the same chromosome. We performed a bioassay for rice stripe resistance in F₃ lines of the F₂ individuals using infective small brown planthoppers and identified an 1.8-cM segment harboring the rice stripe disease resistance gene, Stv-b ⁱ , between XNpb220 and XNpb257/ XNpb254. Furthermore, Stv-b ⁱ was linked by 0.0 cM to a RFLP marker, ST10, which was developed on the basis of the results of RAPD analysis. These DNA markers near the Stv-b ⁱ locus may be useful in marker-assisted selection and map-based cloning of the Stv-b ⁱ gene. Received: 26 September 1997 / Accepted: 4 November 1997     

Using a limited mapping strategy to identify major QTLs for resistance to grapevine powdery mildew (<Emphasis Type="Italic">Erysiphe necator</Emphasis>) and their use in marker-assisted breeding

A limited genetic mapping strategy based on simple sequence repeat (SSR) marker data was used with five grape populations segregating for powdery mildew (Erysiphe necator) resistance in an effort to develop genetic markers from multiple sources and enable the pyramiding of resistance loci. Three populations derived their resistance from Muscadinia rotundifolia ‘Magnolia’. The first population (06708) had 97 progeny and was screened with 137 SSR markers from seven chromosomes (4, 7, 9, 12, 13, 15, and 18) that have been reported to be associated with powdery or downy mildew resistance. A genetic map was constructed using the pseudo-testcross strategy and QTL analysis was carried out. Only markers from chromosome 13 and 18 were mapped in the second (04327) and third (06712) populations, which had 47 and 80 progeny, respectively. Significant QTLs for powdery mildew resistance with overlapping genomic regions were identified for different tissue types (leaf, stem, rachis, and berry) on chromosome 18, which distinguishes the resistance in ‘Magnolia’ from that present in other accessions of M. rotundifolia and controlled by the Run1 gene on chromosome 12. The ‘Magnolia’ resistance locus was termed as Run2.1. Powdery mildew resistance was also mapped in a fourth population (08391), which had 255 progeny and resistance from M. rotundifolia ‘Trayshed’. A locus accounting for 50% of the phenotypic variation mapped to chromosome 18 and was named Run2.2. This locus overlapped the region found in the ‘Magnolia’-based populations, but the allele sizes of the flanking markers were different. ‘Trayshed’ and ‘Magnolia’ shared at least one allele for 68% of the tested markers, but alleles of the other 32% of the markers were not shared indicating that the two M. rotundifolia selections were very different. The last population, 08306 with 42 progeny, derived its resistance from a selection Vitis romanetii C166-043. Genetic mapping discovered a major powdery mildew resistance locus termed Ren4 on chromosome 18, which explained 70% of the phenotypic variation in the same region of chromosome 18 found in the two M. rotundifolia resistant accessions. The mapping results indicate that powdery mildew resistance genes from different backgrounds reside on chromosome 18, and that genetic markers can be used as a powerful tool to pyramid these loci and other powdery mildew resistance loci into a single line.     

Molecular mapping of a resistance-specific PCR-based marker linked to a gall midge resistance gene (Gm4t) in rice

 A PCR-based marker (E20₅₇₀) linked to the gene Gm4t, which confers resistance to a dipteran pest gall midge (Orseolia oryzae), has been mapped using the restriction fragment length polymorphism (RFLP) technique in rice. Gm4t is a dominant resistance gene. We initially failed to detect useful polymorphism for this marker in a F₃ mapping population derived from a cross between two indica parents, ‘Abhaya’בShyamala’, with as many as 35 restriction enzymes. ‘Abhaya’ carries the resistance gene Gm4t and ‘Shyamala’ is susceptible to gall midge. Subsequently, E20₅₇₀ was mapped using another mapping population represented by a F₂ progeny from a cross between ‘Nipponbare’, a japonica variety, and ‘Kasalath’, an indica variety, in which the gene Gm4t was not known to be present. Gm4t mapped onto chromosome 8 between markers R1813 and S1633B. Our method, thus, presents an alternative way of mapping genes which otherwise would be difficult to map because of a lack of polymorphism between closely related parents differing in desired agronomic traits. Received: 1 April 1997 / Accepted: 13 May 1997     

Molecular mapping of leaf rust resistance gene <Emphasis Type="Italic">Rph14</Emphasis> in <Emphasis Type="Italic">Hordeum vulgare</Emphasis>

An incompletely dominant gene conferring resistance to Puccinia hordei, Rph14, identified previously in an accession of Hordeum vulgare, confers resistance to all known pathotypes of P. hordei in Australia. Knowledge of the chromosomal location of Rph14 and the identification of DNA markers closely linked to it will facilitate combining it with other important leaf rust resistance genes to achieve long lasting resistance. The inheritance of Rph14 was confirmed using 146 and 106 F₃ lines derived from the crosses ‘Baudin’/‘PI 584760’ (Rph14) and ‘Ricardo’/‘PI 584760’ (Rph14), respectively. Bulk segregant analysis on DNA from the parental genotypes and resistant and susceptible DNA bulks using DArT markers located Rph14 to the short arm of chromosome 2H. DArT marker bPb-1664 was identified as having the closest genetic association with Rph14. PCR based marker analysis identified a single SSR marker, Bmag692, linked closely to Rph14 at a map distance of 2.1 and 3.8 cm in the ‘Baudin’/‘PI 584760’and ‘Ricardo’/‘PI 584760’ populations, respectively.     

An intervarietal molecular marker map in Triticum aestivum L. Em. Thell. and comparison with a map from a wide cross

 An intervarietal molecular marker map covering most of the nuclear genome was developed in Triticum aestivum. One hundred and six androgenetic-derived doubled haploid lines obtained from the F₁ between monosomics of ‘Chinese Spring’ and ‘Courtot’ were analysed for genetic mapping. The map covered 18 of the 21 chromosomes with an identical distribution of markers in the A and B genome, and only small segments of the D genome. Distorted markers were mapped using Bailey’s 2-point method and revealed skewed regions on 1A, 1DS, 2A, 2B, 4AS and 6B. Comparison with a wide cross [‘Opata’×Synthetic hexaploid (T. tauschii/‘Altar 84’)] showed colinearity for markers on homologous chromosomes, but revealed a large proportion (25%) of markers mapped on non-homoeologous chromosomes, i. e. heterologous markers. The origin of the material and distortion segregation are discussed with particular emphasis on investigations of D-genome markers. Received: 2 May 1996 / Accepted: 2 August 1996     

A genome-wide analysis of wide compatibility in rice and the precise location of the S5 locus in the molecular map

 The discovery of wide-compatibility varieties (WCVs) that are able to produce normal fertility hybrids when crossed both to indica and japonica rice has enabled the fertility barrier between indica and japonica subspecies to be broken and provided the possibility of developing inter-subspecific hybrids in rice breeding programs. However, a considerable variation in the fertility level of hybrids from the same WCV crossed to different varieties has often been observed. One hypothesis for this variable fertility is that additional genes are involved in hybrid fertility besides the wide-compatibility gene (WCG). To assess such a possibility, we performed a genome-wide analysis by assaying a large population from a three-way cross ‘02428’/‘Nanjing 11’//‘Balilla’ using a total of 171 RFLP probes detecting 191 polymorphic loci distributed throughout the entire rice linkage map. Our analysis recovered 3 loci conferring significant effects on hybrid fertility. The major locus on chromosome 6 coincided in chromosomal location with the previously identified S ₅ locus, and the 2 minor loci that mapped to chromosomes 2 and 12, respectively, were apparently distinct from all previously reported hybrid sterility genes. Interaction between the indica and japonica alleles at each of the loci caused a reduction in hybrid fertility. The joint effect of the 2 minor loci could lead to partial sterility even in the presence of the WCG. The location of the S ₅ locus on the molecular marker linkage map was determined to be approximately 1.0 cM from the RFLP locus R2349. This tight linkage will be useful for marker-aided transfer of the WCG in hybrid rice breeding and for map-based cloning. Received: 5 February 1997 / Accepted: 4 April 1997     

Aligning male and female linkage maps of apple (Malus pumila Mill.) using multi-allelic markers

 Linkage maps for the apple cultivars ‘Prima’ and ‘Fiesta’ were constructed using RFLP, RAPD, isozyme, AFLP, SCAR and microsatellite markers in a ‘Prima’בFiesta’ progeny of 152 individuals. Seventeen linkage groups, putatively corresponding to the seventeen haploid apple chromosomes, were obtained for each parent. These maps were aligned using 67 multi-allelic markers that were heterozygous in both parents. A large number of duplicate RFLP loci was observed and, in several instances, linked RFLP markers in one linkage group showed corresponding linkage in another linkage group. Distorted segregation was observed mainly in two regions of the genome, especially in the male parent alleles. Map positions were provided for resistance genes to scab and rosy leaf curling aphid (Vf and Sd ₁, respectively) for the fruit acidity gene Ma and for the self-incompatibility locus S. The high marker density and large number of mapped codominant RFLPs and some microsatellite markers make this map an ideal reference map for use in other progenies also and a valuable tool for the mapping of quantitative trait loci. Received: 17 November 1997 / Accepted: 9 December 1997     

Identification of quantitative trait loci contributing to Fusarium wilt resistance on an AFLP linkage map of flax (Linum usitatissimum)

 An AFLP genetic linkage map of flax (Linum usitatissimum) was used to identify two quantitative trait loci (QTLs) on independent linkage groups with a major effect on resistance to Fusarium wilt, a serious disease caused by the soil pathogen Fusarium oxysporum (lini). The linkage map was constructed using a mapping population from doubled-haploid (DH) lines. The DH lines were derived from the haploid component of F₂ haploid-diploid twin seed originating from a cross between a polyembryonic, low-linolenic-acid genotype (CRZY8/RA91) and the Australian cultivar ‘Glenelg’. The AFLP technique was employed to generate 213 marker loci covering approximately 1400 cM of the flax genome (n=15) with an average spacing of 10 cM and comprising 18 linkage groups. Sixty AFLP markers (28%) deviated significantly (P<0.05) from the expected segregation ratio. The map incorporated RFLP markers tightly linked to flax rust (Melamspora lini) resistance genes and markers detected by disease resistance gene-like sequences. The study illustrates the potential of the AFLP technique as a robust and rapid method to generate moderately saturated linkage maps, thereby allowing the molecular analysis of traits, such as resistance to Fusarium wilt, that show oligogenic patterns of inheritance. Received: 8 December 1997 / Accepted: 7 April 1998     

Resistance to <Emphasis Type="Italic">Erysiphe necator</Emphasis> in the grapevine ‘Kishmish vatkana’ is controlled by a single locus through restriction of hyphal growth

Vitis vinifera ‘Kishmish vatkana’, a cultivated grapevine from Central Asia, does not produce visible symptoms in response to natural or artificial inoculation with the fungus Erysiphe necator Schwein., the casual agent of powdery mildew. ‘Kishmish vatkana’ allowed pathogen entry into epidermal cells at a rate comparable to that in the susceptible control Vitis vinifera ‘Nimrang’, but was able to limit subsequent hyphal proliferation. Density of conidiophores was significantly lower in ‘Kishmish vatkana’ (33.6 ± 8.7 conidiophores mm⁻²) than in ‘Nimrang’ (310.5 ± 24.0 conidiophores mm⁻²) by 120 h after inoculation. A progeny of 310 plants from a ‘Nimrang’ × ‘Kishmish vatkana’ cross were scored for the presence or absence of visible conidiophores throughout two successive seasons. Phenotypic segregation revealed the presence of a single dominant allele termed Resistance to Erysiphe necator 1 (REN1), which was heterozygous in ‘Kishmish vatkana’. A bulked segregant analysis was carried out using 195 microsatellite markers uniformly distributed across the entire genome. For each marker, association with the resistance trait was inferred by measuring in the bulks the ratio of peak intensities of the two alleles inherited from ‘Kishmish vatkana’. The phenotypic locus was assigned to linkage group 13, a genomic region in which no disease resistance had been reported previously. The REN1 position was restricted to a 7.4 cM interval by analyzing the 310 offspring for the segregation of markers that surrounded the target region. The closest markers, VMC9H4-2, VMCNG4E10-1 and UDV-020, were located 0.9 cM away from the REN1 locus. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Identification and linkage mapping of complementary recessive genes causing hybrid breakdown in an intraspecific rice cross

One outcome of hybrid breakdown is poor growth, which we observed as a reduction in the number of panicles per plant and in culm length in an F₂ population derived from a cross between the genetically divergent rice (Oryza sativa L.) cultivars ‘Sasanishiki’ (japonica) and ‘Habataki’ (indica). Quantitative trait locus (QTL) analysis of the two traits and two-way ANOVA of the detected QTLs suggested that the poor growth was due mainly to an epistatic interaction between genes at QTLs located on chromosomes 2 and 11. The poor growth was likely to result when a plant was homozygous for the ‘Habataki’ allele at the QTL on chromosome 2 and homozygous for the ‘Sasanishiki’ allele at the QTL on chromosome 11. The results suggest that the poor growth found in the F₂ population was due to hybrid breakdown of a set of complementary genes. To test this hypothesis and determine the precise chromosomal location of the genes causing the hybrid breakdown, we performed genetic analyses using a chromosome segment substitution line, in which a part of chromosome 2 from ‘Habataki’ was substituted into the genetic background of ‘Sasanishiki’. The segregation patterns of poor growth in plants suggested that both of the genes underlying the hybrid breakdown were recessive. The gene on chromosome 2, designated hybrid breakdown 2 (hbd2), was mapped between simple sequence repeat markers RM3515 and RM3730. The gene on chromosome 11, hbd3, was mapped between RM5824 and RM1341. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.