Mapping of a broad-spectrum brown planthopper resistance gene, <Emphasis Type="Italic">Bph3</Emphasis>, on rice chromosome 6

The brown planthopper (BPH) is one of the most destructive insect pests of rice in Thailand. We performed a cluster analysis that revealed the existence of four groups corresponding to the variation of virulence against BPH resistance genes in 45 BPH populations collected in Thailand. Rice cultivars Rathu Heenati and PTB33, which carry Bph3, showed a broad-spectrum resistance against all BPH populations used in this study. The resistant gene Bph3 has been extensively studied and used in rice breeding programs against BPH; however, the chromosomal location of Bph3 in the rice genome has not yet been determined. In this study, a simple sequence repeat (SSR) analysis was performed to identify and localize the Bph3 gene derived from cvs. Rathu Heenati and PTB33. For mapping of the Bph3 locus, we developed two backcross populations, BC₁F₂ and BC₃F₂, from crosses of PTB33 × RD6 and Rathu Heenati × KDML105, respectively, and evaluated these for BPH resistance. Thirty-six polymorphic SSR markers on chromosomes 4, 6 and 10 were used to survey 15 resistant (R) and 15 susceptible (S) individuals from the backcross populations. One SSR marker, RM190, on chromosome 6 was associated with resistance and susceptibility in both backcross populations. Additional SSR markers surrounding the RM190 locus were also examined to define the location of Bph3. Based on the linkage analysis of 208 BC₁F₂ and 333 BC₃F₂ individuals, we were able to map the Bph3 locus between two flanking SSR markers, RM589 and RM588, on the short arm of chromosome 6 within 0.9 and 1.4 cM, respectively. This study confirms both the location of Bph3 and the allelic relationship between Bph3 and bph4 on chromosome 6 that have been previously reported. The tightly linked SSR markers will facilitate marker-assisted gene pyramiding and provide the basis for map-based cloning of the resistant gene.     

Inheritance and gene mapping of spotted to non-spotted trait gene <Emphasis Type="Italic">CmSp-1</Emphasis> in melon (<Emphasis Type="Italic">Cucumis melo</Emphasis> L<Emphasis Type="Italic">.</Emphasis> var. <Emphasis Type="Italic">chinensis</Emphasis> Pangalo)

Melon (Cucumis melo L.) is one of the most popular and highly nutritious vegetable species within Cucurbitaceae. Because appearance is used as an important indicator of quality, the spotted to non-spotted trait associated with this product somewhat influences the buying habits of consumers. We tested a six-generation family to determine the inheritance and genetic basis of this trait. Genetic groups F₁, F₂, BC₁P₁, and BC₁P₂ were from a cross between “IM16559” (non-spotted) and “IM16553” (spotted). Our genetic analysis showed that the spotted to non-spotted trait was controlled by a single dominant gene that we named CmSp-1. Whole-genome resequencing-bulked segregant analysis (WG-BSA) demonstrated that this gene was located on the end of chromosome 2, in the intersections of 22,160,000 to 22,180,000 bp and 22,260,000 to 26,180,000 bp, an interval distance of 3.94 Mb. Insertion-deletion (InDel) markers designed based on WG-BSA data were used to map this gene. Using 13 InDel markers, we produced a genetic map indicating that CmSp-1 was tightly linked to markers I734-2 and I757, with genetic distances of 1.8 and 0.4 cM and an interval distance of 280.872 kb. The closest marker was I757. Testing of 107 different melon genotypes presented an accuracy of 84.11% in predicting the phenotype. By being able to locate CmSp-1 in melon, we can now use the findings to identify potential targets for further marker-assisted breeding and cloning projects.     

Genetics and fine mapping of a yellow-green leaf gene (<Emphasis Type="Italic">ygl</Emphasis>-<Emphasis Type="Italic">1</Emphasis>) in cabbage (<Emphasis Type="Italic">Brassica oleracea</Emphasis> var. <Emphasis Type="Italic">capitata</Emphasis> L.)

Cabbage (Brassica oleracea var. capitata L.) is one of the most popular cultivated vegetables worldwide. Cabbage has rich phenotypic diversity, including plant height, head shape, head color, leaf shape and leaf color. Leaf color plays an important role in cabbage growth and development. At present, there are few reports on fine mapping of leaf color mutants in B. oleracea. In this study, a naturally occurring yellow-green leaf cabbage mutant (YL-1), derived from the self-pollinated progenies of the hybrid ‘Hosom’, was used for inheritance analysis and gene mapping. Segregation populations including F₂ and BC₁ were generated from the cross of two inbred lines, YL-1 and 01–20. Genetic analysis with the F₂ and BC₁ populations demonstrated that the yellow-green leaf color was controlled by a single recessive nuclear gene, ygl-1. Insertion–deletion (InDel) markers, designed based on the parental re-sequencing data, were used for the preliminary mapping with BSA (bulked segregant analysis) method. A genetic map constructed with 15 InDels indicated that ygl-1 was located on chromosome C01. The ygl-1 gene is flanked by InDel markers ID2 and M8, with genetic distances of 0.4 cM and 0.35 cM, respectively. The interval distance between two markers is 167 kb. Thus, it enables us to locate the ygl-1 gene for the first time in B. oleracea. This study lays the foundation for candidate gene prediction and ygl-1gene cloning.     

Fine mapping of <Emphasis Type="Italic">Sta1</Emphasis>, a quantitative trait locus determining stele transversal area,on rice chromosome 9

The stele (root vascular cylinder) in plants plays an important role in the transport of water and nutrients from the root to the shoot. A quantitative trait locus (QTL) on rice chromosome 9 that controls stele transversal area (STA) was previously detected in an F₃ mapping population derived from a cross between the lowland cultivar ‘IR64’, with a small STA, and the upland cultivar ‘Kinandang Patong’, with a large STA. To identify the gene(s) underlying this QTL, we undertook fine mapping of the locus. We screened eight plants from BC₂F₃ lines in which recombination occurred near the QTL. Progeny testing of BC₂F₄ plants was used to determine the genotype classes for the QTL in each BC₂F₃ line. Accordingly, the STA QTL Sta1 (Stele Transversal Area 1) was mapped between the InDel markers ID07_12 and ID07_14. A candidate genomic region for Sta1 was defined more precisely between markers RM566 and RM24334, which delimit a 359-kb interval in the reference cultivar ‘Nipponbare’. A line homozygous for the ‘Kinandang Patong’ allele of Sta1 had an STA approximately 28.4% larger than that of ‘IR64’. However, Sta1 did not influence maximum or total root length, suggesting that this QTL specifically controls STA.     

Identification of flanking SSR markers for a major rice gall midge resistance gene <Emphasis Type="Italic">Gm1</Emphasis> and their validation

Host-plant resistance is the preferred strategy for management of Asian rice gall midge (Orseolia oryzae), a serious pest in many rice-growing countries. The deployment of molecular markers linked to gall midge resistance genes in breeding programmes can accelerate the development of resistant cultivars. In the present study, we have tagged and mapped a dominant gall midge resistance gene, Gm1, from the Oryza sativa cv. W1263 on chromosome 9, using SSR markers. A progeny-tested F₂ mapping population derived from the cross W1263/TN1 was used for analysis. To map the gene locus, initially a subset of the F₂ mapping population consisting of 20 homozygous resistant and susceptible lines each was screened with 63 parental polymorphic SSR markers. The SSR markers RM316, RM444 and RM219, located on chromosome 9, are linked to Gm1 at genetic distances of 8.0, 4.9 and 5.9 cM, respectively, and flank the gene locus. Further, gene/marker order was also determined. The utility of the co-segregating SSR markers was tested in a backcross population derived from the cross Swarna/W1263//Swarna, and allelic profiles of these markers were analysed in a set of donor rice genotypes possessing Gm1 and in a few gall midge-susceptible, elite rice varieties.     

Fine genetic mapping and physical delimitation of the lesion mimic gene <Emphasis Type="Italic">spotted leaf 5</Emphasis> (<Emphasis Type="Italic">spl5</Emphasis>) in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

Spotted leaf 5 (spl5), a lesion mimic mutant, was first identified in rice (Oryza sativa L.) japonica cv. Norin8 in 1978. This mutant exhibits spontaneous disease-like lesions in the absence of any pathogens and resistance to rice blast and bacterial blight; however, the target gene has not yet been isolated. In the present study, we employed a map-based cloning strategy to finely map the spl5 gene. In an initial mapping with 100 F₂ individuals (spl5/spl5) derived from a cross between the spl5 mutant and indica cv. 93-11, the spl5 gene was located in a 3.3-cM region on chromosome 7 using six simple sequence repeat (SSR) markers. In a high-resolution genetic mapping, two F₂ populations with 3,149 individuals (spl5/spl5) were derived from two crosses between spl5 mutant and two indica cvs. 93-11 and Zhefu802 and six sequence-tagged site (STS) markers were newly developed. Finally, the spl5 gene was mapped to a region of 0.048 cM between two markers SSR7 and RM7121. One BAC/PAC contig map covering these markers’ loci and the spl5 gene was constructed through Pairwise BLAST analysis. Our bioinformatics analysis shows that the spl5 gene is located in the 80-kb region between two markers SSR7 and RM7121 with a high average ratio of physical to genetic distance (1.67 Mb/cM) and eighteen candidate genes. The analysis of these candidate genes indicates that the spl5 gene represents a novel class of regulators controlling cell death and resistance response in plants.     

Marker-assisted breeding of a photoperiod-sensitive male sterile <Emphasis Type="Italic">japonica</Emphasis> rice with high cross-compatibility with <Emphasis Type="Italic">indica</Emphasis> rice

The incomplete fertility of japonica × indica rice hybrids has inhibited breeders’ access to the substantial heterotic potential of these hybrids. As hybrid sterility is caused by an allelic interaction at a small number of loci, it is possible to overcome it by simple introgression at the major sterility loci. Here we report the use of marker-assisted backcrossing to transfer into the elite japonica cv. Zhendao88 a photoperiod-sensitive male sterility gene from cv. Lunhui422S (indica) and the yellow leaf gene from line Yellow249 (indica). The microsatellite markers RM276, RM455, RM141 and RM185 were used to tag the fertility genes S5, S8, S7 and S9, respectively. Line 509S is a true-breeding photoperiod-sensitive male sterile plant, which morphologically closely resembles the japonica type. Genotypic analysis showed that the genome of line 509S comprises about 92% japonica DNA. Nevertheless, hybrids between line 509S and japonica varieties suffer from a level of hybrid sterility, although the line is highly cross-compatible with indica types, with the resulting hybrids expressing a significant degree of heterosis. Together, these results suggest that segment substitution on fertility loci based on known information and marker-assisted selection are an effective approach for utilizing the heterosis of rice inter-subspecies.     

Inheritance and mapping of powdery mildew resistance gene <Emphasis Type="Italic">Pm43</Emphasis> introgressed from <Emphasis Type="Italic">Thinopyrum</Emphasis><Emphasis Type="Italic">intermedium</Emphasis> into wheat

Powdery mildew resistance from Thinopyrum intermedium was introgressed into common wheat (Triticum aestivum L.). Genetic analysis of the F₁, F₂, F₃ and BC₁ populations from powdery mildew resistant line CH5025 revealed that resistance was controlled by a single dominant allele. The gene responsible for powdery mildew resistance was mapped by the linkage analysis of a segregating F₂ population. The resistance gene was linked to five co-dominant genomic SSR markers (Xcfd233, Xwmc41, Xbarc11, Xgwm539 and Xwmc175) and their most likely order was Xcfd233–Xwmc41–Pm43–Xbarc11–Xgwm539–Xwmc175 at 2.6, 2.3, 4.2, 3.5 and 7.0 cM, respectively. Using the Chinese Spring nullisomic-tetrasomic and ditelosomic lines, the polymorphic markers and the resistance gene were assigned to chromosome 2DL. As no powdery mildew resistance gene was previously assigned to chromosome 2DL, this new resistance gene was designated Pm43. Pm43, together with the identified closely linked markers, could be useful in marker-assisted selection for pyramiding powdery mildew resistance genes. Runli He and Zhijian Chang contributed equally to this work.     

High-resolution mapping and gene prediction of <Emphasis Type="Italic">Xanthomonas Oryzae</Emphasis> pv. <Emphasis Type="Italic">Oryzae</Emphasis> resistance gene <Emphasis Type="Italic">Xa7</Emphasis>

Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a devastating disease in rice worldwide. The resistance gene Xa7, which provides dominant resistance against the pathogen with avirulence (Avr) gene AvrXa7, has proved to be durably resistant to BB. A set of SSR markers were selected from the “gramene” database based on the Xa7 gene initial mapping region on chromosome 6. These markers were used to construct a high-resolution genetic map of the chromosomal region surrounding the Xa7 gene. An F₂ mapping population with 721 highly susceptible individuals derived from a cross between the near isogenic lines (NILs) IRBB7 and IR24 were constructed to localize the Xa7 gene. In a primary analysis with eleven polymorphic SSR markers, Xa7 was located in approximately the 0.28-cM region. To walk closer to the target gene, recombinant F₂ individuals were tested using newly developed STMS (sequence tagged microsatellite) markers. Finally, the Xa7 gene was mapped to a 0.21-cM interval between the markers GDSSR02 and RM20593. The Xa7-linked markers were landed on the reference sequence of cv. Nipponbare through bioinformatics analysis. A contig map corresponding to the Xa7 gene was constructed. The target gene was assumed to span an interval of approximately 118.5-kb which contained a total of fourteen genes released by the TIGR Genome Annotation Version 5.0. Candidate-gene analysis of Xa7 revealed that the fourteen genes encode novel domains that have no amino acid sequence similar to other cloned Xa(xa) genes. Shen Chen and Zhanghui Huang are contributed equally to this work.     

Fine Mapping of <Emphasis Type="Italic">qHD8-1</Emphasis>, a QTL Controlling the Heading Date,to a 26-kb DNA Fragment in Rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

Heading date is one of the importance agronomic traits. A library consisting of 1,123 single segment substitution lines (SSSLs) in the same genetic background of an elite rice variety Huajingxian 74 (HJX74) was evaluated for heading date (HD). From this library, the SSSL W06-26-35-1-5-2 with the substituted interval of PSM152–PSM154–PSM155–RM25–RM547–RM72–RM404 was found having a gene, which performed stable and late heading in the different environments of Shandong and Hainan provinces. To map the gene governing heading date, the SSSL W06-26-35-1-5-2 was crossed with the recipient HJX74 to develop an F₂ segregating population. The distribution of late and early heading plants in this population fitted a segregation ratio of 3:1, indicating the late heading was controlled by a dominant gene. The gene locus for heading date was tentatively designated as qHD8-1. Using a random sample of 460 individuals from the F₂ population, the qHD8-1 was narrowed down to a region flanking by two SSR markers PSM155 and RM547. For fine mapping of qHD8-1, a large F_2:3 segregating population of 3,000 individuals were developed from F₂ plants heterozygous in the PSM155–RM547 region. Recombinants analysis further mapped qHD8-1 to an interval of region 26 kb with markers RM22492 and P23 bounded on the left and right sides, respectively. Sequence analysis of this 26-kb fragment revealed that it contains five putative open reading frames, which were regarded as candidates of qHD8-1. These results will be useful in cloning of the qHD8-1 gene.     

Fine mapping of the rice thermo-sensitive genic male-sterile gene <Emphasis Type="Italic">tms5</Emphasis>

AnnongS-1, a thermo-sensitive genic male-sterile (TGMS) rice line, has a new TGMS gene. Genetic analysis indicated that the sterility of AnnongS-1 was controlled by a single resessive gene named tms5. In our previous studies based on an F₂ population from the cross between AnnongS-1 and Nanjing11, tms5 was mapped on chromosome 2. Recently, a RIL (recombinant inbred line) population from the same cross was developed and used for the fine mapping of the tms5 gene. Molecular marker techniques combined with BSA (bulked segregant analysis) were used. As a result, two AFLP markers (AF10, AF8), one RAPD marker (RA4), one STS marker (C365-1), one CAPs marker (G227-1) and four SSR markers (RM279, RM492, RM327, RM324) were found to be closely linked to tms5 gene. The DNA sequences of the RFLP marker of C365 and G227 were found in GenBank, and on the basis of these sequences, many primers were designed to amplify the two parents and their RIL population plants. Finally, the tms5 gene was mapped between STS marker C365-1 and CAPs marker G227-1 at a distance of 1.04 cM from C365-1 and 2.08 cM from G227-1.Communicated by H.F. LinskensY.G. Wang and Q.H. Xing contributed equally to this contribution.     

Map-based cloning of the dominant genic male sterile <Emphasis Type="Italic">Ms</Emphasis>-<Emphasis Type="Italic">cd1</Emphasis> gene in cabbage (<Emphasis Type="Italic">Brassica oleracea</Emphasis>)

Key message

Using map-based cloning, we delimited the Ms - cd1 gene responsible for the male sterile phenotype in B. oleracea to an approximately 39-kb fragment. Expression analysis suggests that a new predicted gene, a homolog of the Arabidopsis SIED1 gene, is a potential candidate gene.

Abstract

A dominant genic male sterile (DGMS) mutant 79-399-3 in Brassica oleracea (B. oleracea) is controlled by a single gene named Ms-cd1, which was genetically mapped on chromosome C09. The derived DGMS lines of 79-399-3 have been successfully applied in hybrid cabbage breeding and commercial hybrid seed production of several B. oleracea cultivars in China. However, the Ms-cd1 gene responsible for the DGMS has not been identified, and the molecular basis of the DGMS is unclear, which then limits its widespread application in hybrid cabbage seed production. In the present study, a large BC₉ population with 12,269 individuals was developed for map-based cloning of the Ms-cd1 gene, and Ms-cd1 was mapped to a 39.4-kb DNA fragment between two InDel markers, InDel14 and InDel24. Four genes were identified in this region, including two annotated genes based on the available B. oleracea annotation database and two new predicted open reading frames (ORFs). Finally, a newly predicted ORF designated Bol357N3 was identified as the candidate of the Ms-cd1 gene. These results will be useful to reveal the molecular mechanism of the DGMS and develop more practical DGMS lines with stable male sterility for hybrid seed production in cabbage.

     

Fine mapping of <Emphasis Type="Italic">Pa-6</Emphasis> gene for purple apiculus in rice

Purple apiculus is one of the important agronomic traits of rice. Single-segment substitution line (SSSL) W23-07-6-02-14 in the genetic background of an elite rice variety Huajingxian74 (HJX74) with the substituted interval of RM225-RM217-RM253 on the chromosome 6 was found to have purple apiculus (Pa). To map the gene governing Pa, W23-07-6-02-14 was crossed with the recipient HJX74 to develop an F₂ secondary segregation population. The ratio of purple apiculus to green apiculus showed a good fit to 3:1 ratio, indicating that Pa was controlled by a major dominant gene. The gene locus for Pa was tentatively designated as Pa-6. Using 430 individuals from the F₂ segregation population, the Pa-6 locus was mapped between two SSR markers RM19556 and RM19561 with genetic distances of 0.2 and 0.3 cM, respectively. For fine mapping of the Pa-6 gene, a large F_2:3 segregation population of 3890 individuals was developed from F₂ heterzygous plants in the RM19556-RM19561 region. Recombinant analyses further mapped the Pa-6 gene locus to an interval of 41.7-kb bounded L02 and RM19561. Sequence analysis of this 41.7-kb region revealed that it contains eleven open reading frames (ORFs), of which, ORF5 is classified as the one that is associated with the C (chromogen for anthocyanin) gene, it was presumed to be the candidate gene for Pa. This result provided a foundation of map-based cloning and function analysis of the Pa-6 gene.     

Identification and fine mapping of <Emphasis Type="Italic">Pi39</Emphasis>(t), a major gene conferring the broad-spectrum resistance to <Emphasis Type="Italic">Magnaporthe oryzae</Emphasis>

Blast, caused by the ascomycete fungus Magnaporthe oryzae, is one of the most devastating diseases of rice worldwide. The Chinese native cultivar (cv.) Q15 expresses the broad-spectrum resistance to most of the isolates collected from China. To effectively utilize the resistance, three rounds of linkage analysis were performed in an F₂ population derived from a cross of Q15 and a susceptible cv. Tsuyuake, which segregated into 3:1 (resistant/susceptible) ratio. The first round of linkage analysis employing simple sequence repeat (SSR) markers was carried out in the F₂ population through bulked-segregant assay. A total of 180 SSR markers selected from each chromosome equally were surveyed. The results revealed that only two polymorphic markers, RM247 and RM463, located on chromosome 12, were linked to the resistance (R) gene. To further define the chromosomal location of the R gene locus, the second round of linkage analysis was performed using additional five SSR markers, which located in the region anchored by markers RM247 and RM463. The locus was further mapped to a 0.27 cM region bounded by markers RM27933 and RM27940 in the pericentromeric region towards the short arm. For fine mapping of the R locus, seven new markers were developed in the smaller region for the third round of linkage analysis, based on the reference sequences. The R locus was further mapped to a 0.18 cM region flanked by marker clusters 39M11 and 39M22, which is closest to, but away from the Pita/Pita ² locus by 0.09 cM. To physically map the locus, all the linked markers were landed on the respective bacterial artificial chromosome clones of the reference cv. Nipponbare. Sequence information of these clones was used to construct a physical map of the locus, in silico, by bioinformatics analysis. The locus was physically defined to an interval of ≈37 kb. To further characterize the R gene, five R genes mapped near the locus, as well as 10 main R genes those might be exploited in the resistance breeding programs, were selected for differential tests with 475 Chinese isolates. The R gene carrier Q15 conveys resistances distinct from those conditioned by the carriers of the 15 R genes. Together, this valuable R gene was, therefore, designated as Pi39(t). The sequence information of the R gene locus could be used for further marker-based selection and cloning. Xinqiong Liu and Qinzhong Yang contributed equally to this work.     

Exploiting co-linearity among grass species to map the <Emphasis Type="Italic">Aegilops ventricosa-</Emphasis>derived <Emphasis Type="Italic">Pch1</Emphasis> eyespot resistance in wheat and establish its relationship to <Emphasis Type="Italic">Pch2</Emphasis>

Introgressions into wheat from related species have been widely used as a source of agronomically beneficial traits. One such example is the introduction of the potent eyespot resistance gene Pch1 from the wild relative Aegilops ventricosa onto chromosome 7DL of wheat. In common with genes carried on many other such introgressions, the use of Pch1 in commercial wheat varieties has been hindered by linkage drag with yield-limiting traits. Attempts to break this linkage have been frustrated by a lack of co-dominant PCR markers suitable for identifying heterozygotes in F₂ populations. We developed conserved orthologous sequence (COS) markers, utilising the Brachypodium distachyon (Brachypodium) genome sequence, to provide co-dominant markers in the Pch1 region. These were supplemented with previously developed sequence-tagged site (STS) markers and simple sequence repeat (SSR) markers. Markers were applied to a panel of varieties and to a BC₆ F₂ population, segregating between wheat and Ae. ventricosa over the distal portion of 7DL, to identify recombinants in the region of Pch1. By exploiting co-linearity between wheat chromosome 7D, Brachypodium chromosome 1, rice chromosome 6 and sorghum chromosome 10, Pch1 was located to an interval between the flanking markers Xwg7S and Xcos7-9. Furthermore candidate gene regions were identified in Brachypodium (364 Kb), rice (178 Kb) and sorghum (315 Kb) as a prelude to the map-based cloning of the gene. In addition, using homoeologue transferable markers, we obtained evidence that the eyespot resistances Pch1 and Pch2 on chromosomes 7D and 7A, respectively, are potentially homoeoloci. It is anticipated that the COS marker methodology could be used for the identification of recombinants in other introgressions into wheat from wild relatives. This would assist the mapping of genes of interest and the breaking of deleterious linkages to enable greater use of these introgressions in commercial varieties.     

Fine mapping of <Emphasis Type="Italic">qSTV11</Emphasis><Superscript><Emphasis Type="Italic">KAS</Emphasis></Superscript>, a major QTL for rice stripe disease resistance

Rice stripe disease, caused by rice stripe virus (RSV), is one of the most serious diseases in temperate rice-growing areas. In the present study, we performed quantitative trait locus (QTL) analysis for RSV resistance using 98 backcross inbred lines derived from the cross between the highly resistant variety, Kasalath, and the highly susceptible variety, Nipponbare. Under artificial inoculation in the greenhouse, two QTLs for RSV resistance, designated qSTV7 and qSTV11 ^KAS , were detected on chromosomes 7 and 11 respectively, whereas only one QTL was detected in the same location of chromosome 11 under natural inoculation in the field. The stability of qSTV11 ^KAS was validated using 39 established chromosome segment substitution lines. Fine mapping of qSTV11 ^KAS was carried out using 372 BC₃F_2:3 recombinants and 399 BC₃F_3:4 lines selected from 7,018 BC₃F₂ plants of the cross SL-234/Koshihikari. The qSTV11 ^KAS was localized to a 39.2 kb region containing seven annotated genes. The most likely candidate gene, LOC_Os11g30910, is predicted to encode a sulfotransferase domain-containing protein. The predicted protein encoded by the Kasalath allele differs from Nipponbare by a single amino acid substitution and the deletion of two amino acids within the sulfotransferase domain. Marker-resistance association analysis revealed that the markers L104-155 bp and R48-194 bp were highly correlated with RSV resistance in the 148 landrace varieties. These results provide a basis for the cloning of qSTV11 ^KAS , and the markers may be used for molecular breeding of RSV resistant rice varieties.     

Fine mapping of a male sterility gene <Emphasis Type="Italic">MS-cd1</Emphasis> in <Emphasis Type="Italic">Brassica oleracea</Emphasis>

A dominant male sterility (DGMS) line 79-399-3, developed from a spontaneous mutation in Brassica oleracea var. capitata, has been widely used in production of hybrid cultivars in China. In this line, male sterility is controlled by a dominant gene Ms-cd1. In the present study, fine mapping of Ms-cd1 was conducted by screening a segregating population Ms79-07 with 2,028 individuals developed by four times backcrossing using a male sterile Brassica oleracea var. italica line harboring Ms-cd1 as donor and Brassica oleracea var. alboglabra as the recipient. Bulked segregation analysis (BSA) was performed for the BC₄ population Ms79-07 using 26,417 SRAP primer SRAPs and 1,300 SSRs regarding of male sterility and fertility. A high-resolution map surrounding Ms-cd1 was constructed with 14 SRAPs and one SSR. The SSR marker 8C0909 was closely linked to the MS-cd1 gene with a distance of 2.06 cM. Fourteen SRAPs closely linked to the target gene were identified; the closest ones on each side were 0.18 cM and 2.16 cM from Ms-cd1. Three of these SRAPs were successfully converted to dominant SCAR markers with a distance to the Ms-cd1 gene of 0.18, 0.39 and 4.23 cM, respectively. BLAST analysis with these SCAR marker sequences identified a collinear genomic region about 600 kb in scaffold 000010 on chromosomeA10 in B. rapa and on chromosome 5 in A. thaliana. These results provide additional information for map-based cloning of the Ms-cd1 gene and will be helpful for marker-assisted selection (MAS).     

Glycoalkaloids and acclimation capacity of hybrids between <Emphasis Type="Italic">Solanum tuberosum</Emphasis> and the incongruent hardy species <Emphasis Type="Italic">Solanum commersonii</Emphasis>

F₁ and backcross hybrids between sexually incompatible species Solanum commersonii and Solanum tuberosum were characterized for glycoalkaloid content and capacity to cold acclimate. Glycoalkaloid (GA) analysis revealed that F₁ triploids and BC₁ pentaploids contained the glycoalkaloids of both parents. In BC₂ (near) tetraploids the situation was different, in that some hybrids produced the GAs of both parents, whereas others contained only the GAs of S. tuberosum. This suggested that the GAs from S. commersonii may be lost rapidly, and that they may have a simple genetic control. The total tuber GA content of BC₁ and BC₂ groups averaged quite acceptable levels (165.9 mg/kg in BC₁ and 192.8 mg/kg in BC₂), with six genotypes having a GA content <200 mg/kg fresh weight. The F₁ triploid hybrids expressed a capacity to cold acclimate similar to S. commersonii, whereas BC₁ and BC₂ genotypes generally displayed an acclimation capacity higher than the sensitive parent but lower than S. commersonii. However, one BC₁ and two BC₂ genotypes with an acclimation capacity as high as S. commersonii were identified. The polar lipid fatty acid composition in S. commersonii and its hybrid derivatives showed that, following acclimation, there was a significant increase in 18:3. Correlation analysis between the capacity to cold acclimate and the increase in 18:3 was significant, suggesting that the increase in 18:3 can be used as a biochemical marker for the assisted selection of cold-acclimating genotypes in segregating populations.Communicated by G. Wenzel     

Molecular mapping of rice blast resistance gene <Emphasis Type="Italic">Pi-1</Emphasis>(<Emphasis Type="Italic">t</Emphasis>) in the elite <Emphasis Type="Italic">indica</Emphasis> variety Samba mahsuri

Samba mahsuri (BPT 5204) is a cultivar of the medium slender grain indica variety of Oryza sativa grown across India for its high yield and quality. However, this cultivar is susceptible to several diseases and pests including rice blast. The analysis of near isogenic lines indicated the presence of a resistance gene, Pi-1(t) in the donor cultivar C101LAC which is highly resistant to the rice blast fungus Magnaporthe grisea (M. grisea). C101LAC was crossed with susceptible indica rice cultivar (BPT 5204) to generate the mapping population. A mendelian segregation ratio of 3:1 for resistant to susceptible F₂ plants using bulk segregation analysis confirmed the presence of a major gene pi-1(t) by simple sequence repeats marker RM224 to the highly virulent blast isolate DRR 001.     

Genetic analysis and molecular mapping of maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.) stalk rot resistant gene<Emphasis Type="Italic"> Rfg</Emphasis>1

One single pathogen Fusarium graminearum Schw. was inoculated to maize inbred lines 1,145 (Resistant) and Y331 (Susceptive), and their progenies of F₁, F₂ and BC₁F₁ populations. Field statistical data revealed that all of the F₁ individuals were resistant to the disease and that the ratio of resistant plants to susceptive plants was 3:1 in the F₂ population, and 1:1 in the BC₁F₁ population. The results revealed that a single dominant gene controls the resistance to F. graminearum Schw.. The resistant gene to F. graminearum Schw. was denominated as Rfg1 according to the standard principle of the nomenclature of the plant disease resistant genes. RAPD (randomly amplified polymorphic DNA) combined with BSA (bulked segregant analysis) analysis was carried out in the developed F₂ and BC₁F₁ populations, respectively. Three RAPD products screened from the RAPD analysis with 820 Operon 10-mer primers showed the linkage relation with the resistant gene Rfg1. The three RAPD amplification products (OPD-20₁₀₀₀, OPA-04₁₁₀₀ and OPY-04₉₀₀) were cloned and their copy numbers were determined. The results indicated that only OPY-04₉₀₀ was a single-copy sequence. Then, OPY-04₉₀₀ was used as a probe to map the Rfg1 gene with a RIL F₇ mapping population provided by Henry Nguyen, which was developed from the cross S3×Mo17. Rfg1 was primarily mapped on chromosome 6 between the two linked markers OPY-04₉₀₀ and umc21 (Bin 6.04–6.05). In order to confirm the primary mapping result, 25 SSR (simple sequence repeat) markers and six RFLP (restriction fragment length polymorphism) markers in the Rfg1 gene-encompassing region were selected, and their linkage relation with Rfg1 was analyzed in our F₂ population. Results indicated that SSR marker mmc0241 and RFLP marker bnl3.03 are flanking the Rfg1 gene with a genetic distance of 3.0 cM and 2.0 cM, respectively. This is the first time to name and to map a single resistant gene of maize stalk rot through a single pathogen inoculation and molecular marker analysis.Communicated by H.F. Linskens