Molecular mapping of a new source of Fusarium wilt resistance in tetraploid cotton (Gossypium hirsutum L.)

Fusarium wilt (FW) disease is an economically important disease of cotton worldwide and a major cause of crop losses in Australia and many other cotton-producing countries. Symptoms include wilting, vascular browning and death. Australian races of the causal agent Fusarium oxysporum f. sp. vasinfectum (Fov) are genetically distinct from those in other countries and are thought to have evolved from indigenous races. New sources of resistance for breeding are rare, as cotton cultivars with significant FW resistance against Fov isolates from other cotton-producing regions are usually susceptible to Australian Fov races. MCU-5, an Upland Indian cotton cultivar, has been identified as having improved resistance to Australian Fov and is being used to breed new commercial cultivars with higher resistance to FW. To investigate the genetic basis of the FW resistance in MCU-5, QTL analysis was performed on 244 F3 and 244 F4 families derived from an intraspecific cross between MCU-5 and Siokra 1-4, a cultivar highly sensitive to Australian Fov races. Resistance, as measured by leaf symptoms, vascular browning and survival, showed low to moderate heritability between generations. MCU-5 resistance to FW was found to be complex with three quantitative trait loci (QTL) identified in the F3, and eight in the F4, that explained between 9 and 41% of the phenotypic variation. The QTL were located on four linkage groups including chromosomes A6 (Chr 6), D4 (Chr 22) and D6 (Chr 25), with two QTL located in similar regions to previously identified FW resistance from the Sea Island cultivar Pima 3-79. The QTL identified in this study represent the first targets for marker-assisted selection of FW resistance in Australia.     

Identification and mapping of microsatellite markers linked to a root-knot nematode resistance gene (rkn1) in Acala NemX cotton (Gossypium hirsutum L.)

Host-plant resistance is the most economic and effective strategy for root-knot nematode (RKN) Meloidogyne incognita control in cotton (Gossypium hirsutum L.). Molecular markers linked to resistance are important for incorporating resistance genes into elite cultivars. To screen for microsatellite markers (SSR) closely linked to RKN resistance in G. hirsutum cv. Acala NemX, F₁, F₂, BC₁F₁, and F_2:7 recombinant inbred lines (RILs) from intraspecific crosses and an F₂ from an interspecific cross with G. barbadense cv. Pima S-7 were used. Screening of 284 SSR markers, which cover all the known identified chromosomes and most linkage groups of cotton, was performed by bulked segregant analysis, revealing informative SSRs. The informative SSRs were then mapped on the above populations. One co-dominant SSR marker CIR316 was identified tightly linked to a major resistance gene (designated as rkn1), producing amplified DNA fragments of approximately 221 bp (CIR316a) and 210 bp (CIR316c) in Acala NemX and susceptible Acala SJ-2, respectively. The linkage between CIR316a marker and resistance gene rkn1 in Acala NemX had an estimated distance of 2.1–3.3 cM depending on the population used. Additional markers, including BNL1231 with loose linkage to rkn1 (map distance 25.1–27.4 cM), BNL1066, and CIR003 allowed the rkn1 gene to be mapped to cotton linkage group A03. This is the first report in cotton with a closely linked major gene locus determining nematode resistance, and informative SSRs may be used for marker-assisted selection.     

Low resolution mapping around the flavivirus resistance locus (Flv) on mouse Chromosome 5

Although the phenomenon of innate resistance to flaviviruses in mice was recognized many years ago, it was only recently that the genetic locus (Flv) controlling this resistance was mapped to mouse Chromosome (Chr) 5. Here we report the fine mapping of the Flv locus, using 12 microsatellite markers which have recently been developed for mouse Chr 5. The new markers were genotyped in 325 backcross mice of both (C3H/HeJxC3H/ RV)F₁xC3H/HeJ and (BALB/cxC3H/RV)F₁xBALB/c backgrounds, relative to Flv. The composite genetic map that has been constructed identifies three novel microsatellite loci, D5Mit68, D5Mit159, and D5Mit242, tightly linked to the Flv locus. One of those loci, D5Mit159, showed no recombinations with Flv in any of the backcross mice analyzed, indicating tight linkage (<0.3 cM). The other two, D5Mit68 and D5Mit242, exhibited two and one recombinations with Flv (0.6 and 0.3 cM) respectively, defining the proximal and distal boundaries of a 0.9-cM segment around this locus. The proximal flanking marker, D5Mit68, maps to a segment on mouse Chr 5 homologous to human Chr 4. This, together with the previous data produced by our group, locates Flv to a region on mouse Chr 5 carrying segments that are conserved on either human Chr 4, 12, or 7, but present knowledge does not allow precise identification of the syntenic element.     

Mapping Fusarium wilt race 1 resistance genes in cotton by inheritance,QTL and sequencing composition

Knowledge of the inheritance of disease resistance and genomic regions housing resistance (R) genes is essential to prevent expanding pathogen threats such as Fusarium wilt [Fusarium oxysporum f.sp. vasinfectum (FOV) Atk. Sny & Hans] in cotton (Gossypium spp.). We conducted a comprehensive study combining conventional inheritance, genetic and quantitative trait loci (QTL) mapping, QTL marker-sequence composition, and genome sequencing to examine the distribution, structure and organization of disease R genes to race 1 of FOV in the cotton genome. Molecular markers were applied to F₂ and recombinant inbred line (RIL) interspecific mapping populations from the crosses Pima-S7 (G. barbadense L.) × ‘Acala NemX’ (G. hirsutum L.) and Upland TM-1 (G. hirsutum) × Pima 3-79 (G. barbadense), respectively. Three greenhouse tests and one field test were used to obtain sequential estimates of severity index (DSI) of leaves, and vascular stem and root staining (VRS). A single resistance gene model was observed for the F₂ population based on inheritance of phenotypes. However, additional inheritance analyses and QTL mapping indicated gene interactions and inheritance from nine cotton chromosomes, with major QTLs detected on five chromosomes [Fov1-C06, Fov1-C08, (Fov1-C11 ₁ and Fov1-C11 ₂₎ , Fov1-C16 and Fov1-C19 loci], explaining 8–31% of the DSI or VRS variation. The Fov1-C16 QTL locus identified in the F₂ and in the RIL populations had a significant role in conferring FOV race 1 resistance in different cotton backgrounds. Identified molecular markers may have important potential for breeding effective FOV race 1 resistance into elite cultivars by marker-assisted selection. Reconciliation between genetic and physical mapping of gene annotations from marker-DNA and new DNA sequences of BAC clones tagged with the resistance-associated QTLs revealed defenses genes induced upon pathogen infection and gene regions rich in disease-response elements, respectively. These offer candidate gene targets for Fusarium wilt resistance response in cotton and other host plants.     

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     

New slow-rusting leaf rust and stripe rust resistance genes <Emphasis Type="Italic">Lr67</Emphasis> and <Emphasis Type="Italic">Yr46</Emphasis> in wheat are pleiotropic or closely linked

The common wheat genotype ‘RL6077’ was believed to carry the gene Lr34/Yr18 that confers slow-rusting adult plant resistance (APR) to leaf rust and stripe rust but located to a different chromosome through inter-chromosomal reciprocal translocation. However, haplotyping using the cloned Lr34/Yr18 diagnostic marker and the complete sequencing of the gene indicated Lr34/Yr18 is absent in RL6077. We crossed RL6077 with the susceptible parent ‘Avocet’ and developed F₃, F₄ and F₆ populations from photoperiod-insensitive F₃ lines that were segregating for resistance to leaf rust and stripe rust. The populations were characterized for leaf rust resistance at two Mexican sites, Cd. Obregon during the 2008–2009 and 2009–2010 crop seasons, and El Batan during 2009, and for stripe rust resistance at Toluca, a third Mexican site, during 2009. The F₃ population was also evaluated for stripe rust resistance at Cobbitty, Australia, during 2009. Most lines had correlated responses to leaf rust and stripe rust, indicating that either the same gene, or closely linked genes, confers resistance to both diseases. Molecular mapping using microsatellites led to the identification of five markers (Xgwm165, Xgwm192, Xcfd71, Xbarc98 and Xcfd23) on chromosome 4DL that are associated with this gene(s), with the closest markers being located at 0.4 cM. In a parallel study in Canada using a Thatcher × RL6077 F₃ population, the same leaf rust resistance gene was designated as Lr67 and mapped to the same chromosomal region. The pleiotropic, or closely linked, gene derived from RL6077 that conferred stripe rust resistance in this study was designated as Yr46. The slow-rusting gene(s) Lr67/Yr46 can be utilized in combination with other slow-rusting genes to develop high levels of durable APR to leaf rust and stripe rust in wheat.     

Detection of a quantitative trait locus controlling carbon isotope discrimination and its contribution to stomatal conductance in japonica rice

Increasing leaf photosynthesis offers a possible way to improve yield potential in rice (Oryza sativa L.). Carbon isotope discrimination (Δ¹³C) has potential as an indirect selection criterion. In this study, we searched for quantitative trait loci (QTLs) controlling Δ¹³C, and assessed their association with leaf photosynthesis. Substitution mapping by using chromosome segment substitution lines (CSSLs), that carry segments from the indica cultivar Kasalath in the genetic background of the japonica cultivar Koshihikari, identified genomic regions affecting Δ¹³C on chromosomes (Chr.) 2, 3, 6, 7, and 12. One of the CSSLs, SL208, in which most regions on Chr. 3 were substituted with Kasalath segments, showed higher leaf stomatal conductance for CO₂ (g _s) and Δ¹³C than Koshihikari during the vegetative stage although leaf photosynthetic rate did not differ between them. These results suggest an association between Δ¹³C and g _s. To test this association, we performed a QTL analysis for Δ¹³C at vegetative and heading stages in an F₂ population derived from a cross between SL208 and Koshihikari. The results confirmed a QTL controlling Δ¹³C on the long arm of Chr. 3. By using a near-isogenic line specific to Hd6, we ruled out the possibility that variation in Δ¹³C was generated through the pleiotropic effect of heading date.     

Quantitative trait loci for resistance to spot blotch caused by Bipolarissorokiniana in wheat (T.aestivum L.) lines ‘Ning 8201’ and ‘Chirya 3’

Spot blotch caused by Bipolaris sorokiniana is a destructive disease of wheat in warm and humid wheat growing regions of the world. To identify quantitative trait loci (QTLs) for spot blotch resistance, two mapping populations were developed by making the crosses between common susceptible cultivar ‘Sonalika’ with the resistant breeding lines ‘Ning 8201’ and ‘Chirya 3’. Single seed descent derived F₆, F₇, F₈ lines of the first cross ‘Ning 8201’ × ‘Sonalika’ were evaluated for resistance to spot blotch in three blocks in each of the 3 years. After screening of 388 pairs of simple sequence repeat primers between the two parents, 119 polymorphic markers were used to genotype the mapping population. Four QTLs were identified on the chromosomes 2AS, 2BS, 5BL and 7DS and explained 62.9% of phenotypic variation in a simultaneous fit. The QTL on chromosome 2A was detected only in 1 year and explained 22.7% of phenotypic variation. In the second cross (‘Chirya 3’ × ‘Sonalika’), F₇ and F₈ population were evaluated in three blocks in each of the 2 years. In this population, five QTLs were identified on chromosomes 2BS, 2DS, 3BS, 7BS and 7DS. The QTLs identified in the ‘Chirya 3’ × ‘Sonalika’ population explained 43.4% of phenotypic variation in a simultaneous fit. The alleles for reduced disease severity in both the populations were derived from the respective resistant parent. The QTLs QSb.bhu-2B and QSb.bhu-7D from both populations were placed in the same deletion bins, 2BS1-0.53-0.75 and 7DS5-0.36-0.61, respectively. The closely linked markers Xgwm148 to the QTL on chromosome 2B and Xgwm111 to the QTL on chromosome 7D are potentially diagnostic markers for spot blotch resistance.     

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 the novel recessive gene pi55(t) conferring resistance to Magnaporthe oryzae

The elite rice cultivar Yuejingsimiao 2 (YJ2) is characterized by a high level of grain quality and yield, and resistance against Magnaporthe oryzae. YJ2 showed 100% resistance to four fungal populations collected from Guangdong, Sichuan, Liaoning, and Heilongjiang Provinces, which is a higher frequency than that shown by the well-known resistance (R) gene donor cultivars such as Sanhuangzhan 2 and 28zhan. Segregation analysis for resistance with F₂ and F₄ populations indicated the resistance of YJ2 was controlled by multiple genes that are dominant or recessive. The putative R genes of YJ2 were roughly tagged by SSR markers, located on chromosomes 2, 6, 8, and 12, in a bulked-segregant analysis using genome-wide selected SSR markers with F₄ lines that segregated into 3 resistant (R):1 susceptible (S) or 1R:3S. The recessive R gene on chromosome 8 was further mapped to an interval ≈1.9 cM/152 kb in length by linkage analysis with genomic position-ready markers in the mapping population derived from an F₄ line that segregated into 1R:3S. Given that no major R gene was mapped to this interval, the novel R gene was designated as pi55(t). Out of 26 candidate genes predicted in the region based on the reference genomic sequence of the cultivar Nipponbare, two genes that encode a leucine-rich repeat-containing protein and heavy-metal-associated domain-containing protein, respectively, were suggested as the most likely candidates for pi55(t).     

Genetics and molecular mapping of resistance to necrosis inducing race 5 of <Emphasis Type="Italic">Pyrenophora tritici-repentis</Emphasis> in tetraploid wheat

Race 5 of Pyrenophora tritici-repentis, causal agent of tan spot, induces two distinct symptoms, necrosis and chlorosis in susceptible tetraploid and hexaploid wheat, respectively. This study was conducted under controlled environmental conditions to determine the inheritance of resistance to P. tritici-repentis, race 5, in a tetraploid wheat population and to map the resistance genes. Additionally, the relationship between the resistance genes effective against necrosis inducing races 3 and 5 in tetraploid wheat was determined. A population of 98 recombinant-inbred lines (RIL) was developed from a cross between the resistant genotype Triticum turgidum # 283 (PI352519) and the susceptible durum cultivar Coulter. This RIL population was screened individually with race 3 and race 5 and molecular mapping of the resistance gene(s) in this population was conducted. Additionally, the F₂ and F_4:5 generations of this population were screened with race 5 to determine the genetic control of resistance. Plants were inoculated at the two-leaf stage and disease reaction was assessed based on 1 to 5 lesion-type rating scale eight days after inoculation. Segregation analysis of the F₂ generation and of the F_4:5 and F_6:7 families indicated that a single recessive gene controlled resistance to necrosis induced by race 5. Analysis of the mapping data of the T. turgidum # 283/Coulter RIL population indicate that a major gene, designated tsn5, controlling resistance to race 5 is located on the long arm of chromosome 3B. The tsn5 gene is 8.3 cM proximal to the gene tsn2 that controls resistance to necrosis induced by race 3.     

Molecular markers for wheat leaf rust resistance gene Lr41

Leaf rust, caused by Puccinia triticina Eriks., is an important foliar disease of common wheat (Triticum aestivum L.) worldwide. Pyramiding several major rust-resistance genes into one adapted cultivar is one strategy for obtaining more durable resistance. Molecular markers linked to these genes are essential tools for gene pyramiding. The rust-resistance gene Lr41 from T. tauschii has been introgressed into chromosome 2D of several wheat cultivars that are currently under commercial production. To discover molecular markers closely linked to Lr41, a set of near-isogenic lines (NILs) of the hard winter wheat cultivar Century were developed through backcrossing. A population of 95 BC₃F_2:6 NILs were evaluated for leaf rust resistance at both seedling and adult plant stages and analyzed with simple sequence repeat (SSR) markers using bulked segregant analysis. Four markers closely linked to Lr41 were identified on chromosome 2DS; the closest marker, Xbarc124, was about 1 cM from Lr41. Physical mapping using Chinese Spring nullitetrasomic and ditelosomic genetic stocks confirmed that markers linked to Lr41 were on chromosome arm 2DS. Marker analysis in a diverse set of wheat germplasm indicated that primers BARC124, GWM210, and GDM35 amplified polymorphic bands between most resistant and susceptible accessions and can be used for marker-assisted selection in breeding programs.     

The genetics of resistance to five races of downy mildew (Plasmopara halstedii) in sunflower (Helianthus annuus L.)

 These studies were undertaken to determine whether downy mildew resistance genes in sunflower were independent as first reported, or linked as suggested by more recent hypotheses. The segregations for downy mildew reaction of 111 F₃ progenies from a cross between a susceptible line and a line with Pl2 were used to locate this gene on the sunflower consensus RFLP linkage map. It was shown that Pl2 was linked to the same RFLP markers on linkage group 1 as Pl1 and Pl6, mapped earlier, and at a very similar distance. The F₃ progenies showed exactly the same segregation patterns when tested with race 1 and race D. One hundred and fifty four progenies from a cross between a susceptible line and HA335, containing Pl6 (considered as giving resistance to all Plasmopara halstedii races), were tested with the five French downy mildew races, 1, A, B, C and D. Two progenies were observed to show segregation for races 1 and D, while appearing homozygous-resistant to races A , B and C. Tests on F₄ progenies confirmed this separation of resistances with fixation of susceptibility to races 1 and D and resistance to races A, B and C. It is concluded that the Pl6 gene is not a “strong” gene, giving resistance to all downy mildew races, but rather a cluster of genes, each providing resistance to one, or a few, downy mildew races. The genes giving resistance to races 1 and D, on one hand, and to races A, B and C, on the other hand, must be very closely linked, with about 0.6 cM between the two groups. Received: 23 December 1996 / Accepted: 18 April 1997     

A new SNP haplotype associated with blue disease resistance gene in cotton (Gossypium hirsutum L.)

Resistance to cotton blue disease (CBD) was evaluated in 364 F_2.3 families of three populations derived from resistant variety ‘Delta Opal’. The CBD resistance in ‘Delta Opal’ was controlled by one single dominant gene designated Cbd. Two simple sequence repeat (SSR) markers were identified as linked to Cbd by bulked segregant analysis. Cbd resides at the telomere region of chromosome 10. SSR marker DC20027 was 0.75 cM away from Cbd. DC20027 marker fragments amplified from 3 diploid species and 13 cotton varieties whose CBD resistance was known were cloned and sequenced. One single nucleotide polymorphism (SNP) was identified at the 136th position by sequence alignment analysis. Screening SNP markers previously mapped on chromosome 10 identified an additional 3 SNP markers that were associated with Cbd. A strong association between a haplotype based on four SNP markers and Cbd was developed. This demonstrates one of the first examples in cotton where SNP markers were used to effectively tag a trait enabling marker-assisted selection for high levels of CBD resistance in breeding programs.     

Chromosomal location and molecular mapping of a tan spot resistance gene in the winter wheat cultivar Red Chief

The winter wheat cultivar Red Chief has been identified as the wheat cultivar most resistant toPyrenophora tritici-repentis (Ptr). This study was undertaken to determine the inheritance, chromosomal location and molecular mapping of a tan spot resistance gene in Red Chief. χ² analysis of the F₂ segregation data of the hybrids between 21 monosomic lines of the susceptible wheat cultivar Chinese Spring and the resistant cultivar Red Chief revealed that tan spot resistance in cv. Red Chief is controlled by a single recessive gene located on chromosome 3A. Linkage analysis using SSR markers in the Red Chief/Chinese Spring F2 population showed that thetsr4 gene is clustered in the region aroundXgwm2a, on the short arm of chromosome 3A. This marker has also been identified as the closest marker to thetsr3 locus on chromosome 3D in synthetic wheat lines. Validation analysis of this marker for thetsr3 andtsr4 genes using 28 resistant and 6 susceptible genotypes indicated that the 120 bp allele (thetsr3 gene) specific fragment was observed in 11 resistant genotypes, including the three synthetic lines XX41, XX45 and XX110, while the 130 bp allele was amplified only in cv. Red Chief and Dashen.Xgwm2a can be used to trace the presence of the target gene in successive backcross generations and pyramiding of thetsr3 &tsr4 genes into a commonly grown and adaptable cultivar.     

An interstitial telomere array proximal to the distal telomere of mouse chromosome 13

Lambda clones of mouse DNA from BALB/c and C57BL/10, each containing an array of telomere hexamers, were localized by FISH to a region close to the telomere of Chr 13. Amplification of mouse genomic DNA with primers flanking SSRs within the cloned DNA showed several alleles, which were used to type eight sets of RI strains. The two lambda clones contained allelic versions of the interstitial telomere array, Tel-rs4, which is 495 bp in C57BL/10 and which includes a variety of sequence changes from the consensus telomere hexamer. Comparison of the segregation of the amplification products of the SSRs with the segregation of other loci in an interspecies backcross (C57BL/6JEi × SPRET/Ei) F₁× SPRET/Ei shows recombination suppression, possibly associated with ribosomal DNA sequences present on distal Chr 13 in Mus spretus, when compared with recombination in an interstrain backcross, (C57BL/6J × DBA/J) F₁× C57BL/6J, and with the MIT F₂ intercross. Analysis of recombination in females using a second interstrain backcross, (ICR/Ha × C57BL/6Ha) F₁× C57BL/6Ha, also indicates recombination suppression when compared with recombination in males of the same strains, using backcross C57BL/6Ha × (ICR/Ha × C57BL/6Ha) F₁. Thus, more than one cause may contribute to recombination suppression in this region. The combined order of the loci typed was D13Mit37–D13Mit30–D13Mit148–(D13Rp1, 2, 3, 4, Tel-rs4)–D13Mit53–D13Mit196–D13Mit77–(D13Mit78, 35). Data from crosses where apparently normal frequencies of recombination occur suggest that the telomere array is about 6 map units proximal to the most distal loci on Chr 13. This distance is consistent with evidence from markers identified in two YAC clones obtained from the region. Received: 24 September 1996/Accepted: 20 January 1997     

Fine mapping the soybean aphid resistance gene Rag1 in soybean

The soybean aphid (Aphis glycines Matsumura) is an important soybean [Glycine max (L.) Merr.] pest in North America. The dominant aphid resistance gene Rag1 was previously mapped from the cultivar ‘Dowling’ to a 12 cM marker interval on soybean chromosome 7 (formerly linkage group M). The development of additional genetic markers mapping closer to Rag1 was needed to accurately position the gene to improve the effectiveness of marker-assisted selection (MAS) and to eventually clone it. The objectives of this study were to identify single nucleotide polymorphisms (SNPs) near Rag1 and to position these SNPs relative to Rag1. To generate a fine map of the Rag1 interval, 824 BC₄F₂ and 1,000 BC₄F₃ plants segregating for the gene were screened with markers flanking Rag1. Plants with recombination events close to the gene were tested with SNPs identified in previous studies along with new SNPs identified from the preliminary Williams 82 draft soybean genome shotgun sequence using direct re-sequencing and gene-scanning melt-curve analysis. Progeny of these recombinant plants were evaluated for aphid resistance. These efforts resulted in the mapping of Rag1 between the two SNP markers 46169.7 and 21A, which corresponds to a physical distance on the Williams 82 8× draft assembly (Glyma1.01) of 115 kilobase pair (kb). Several candidate genes for Rag1 are present within the 115-kb interval. The markers identified in this study that are closely linked to Rag1 will be a useful resource in MAS for this important aphid resistance gene.     

Identification and validation of RAPD and SCAR markers linked to the gene <Emphasis Type="Italic">Er3</Emphasis> conferring resistance to <Emphasis Type="Italic">Erysiphe pisi</Emphasis> DC in pea

Three genes, er1, er2 and Er3, conferring resistance to powdery mildew (Erysiphe pisi) in pea have been described so far. Because single gene-controlled resistance tends to be overcome by evolution of pathogen virulence, accumulation of several resistance genes into a single cultivar should enhance the durability of the resistance. Molecular markers linked to genes controlling resistance to E. pisi may facilitate gene pyramiding in pea breeding programs. Molecular markers linked to er1 and er2 are available. In the present study, molecular markers linked to Er3 have been obtained. A segregating F₂ population derived from the cross between a breeding line carrying the Er3 gene, and the susceptible cultivar ‘Messire’ was developed and genotyped. Bulk Segregant Analysis (BSA) was used to identify Random Amplified Polymorphic DNA (RAPD) markers linked to Er3. Four RAPD markers linked in coupling phase (OPW04_637, OPC04_640, OPF14_1103, and OPAH06_539) and two in repulsion phase (OPAB01_874 and OPAG05_1240), were identified. Two of these, flanking Er3, were converted to Sequence Characterized Amplified Region (SCAR) markers. The SCAR marker SCW4₆₃₇ co-segregated with the resistant gene, allowing the detection of all the resistant individuals. The SCAR marker SCAB1₈₇₄, in repulsion phase with Er3, was located at 2.8 cM from the gene and, in combination with SCW4₆₃₇, was capable to distinguish homozygous resistant individuals from heterozygous with a high efficiency. In addition, the validation for polymorphism in different genetic backgrounds and advanced breeding material confirmed the utility of both markers in marker-assisted selection.     

Genetic analysis of neonatal death with growth retardation in F1 male Dh/+ mice

Nearly all F₁ male mice with Dh/+ genotype between DDD female and DH–Dh/+ male die within a few days after birth; however, this is not observed in the reciprocal cross. The F₁ Dh/+ males usually exhibit growth retardation prior to death. To identify the putative genetic locus or loci in DDD genome that cause the abnormalities in the presence of the Dh, a linkage analysis was carried out in backcross progeny of a cross of (DDD female × DH–+/+ male) F₁ female × DH–Dh/+ male. Appearance of growth retardation was examined from the day of birth, and both growth-retarded and normally weaned Dh/+ males were genotyped for microsatellite marker loci spanning autosomes and the X Chromosome (Chr). Significant evidence for linkage was identified on the distal edge of the X Chr, near the microsatellite marker of DXMit135. Furthermore, among mice from DDD female × reciprocal F₁ Dh/+ male produced between DH–Dh/+ and progenitor strains (C57BL/6J, C3H/HeJ and BALB/cA), only the progeny from ♀DDD ×♂(♀DH–Dh/+×♂C3H/HeJ) F₁ Dh/+ male did not show any lethality and/or growth retardation. Thus, the lethality in F₁ Dh/+ males accompanied by growth retardation is caused by the interactions between the Dh gene, X Chr, and Y Chr. Based on the CAG repeat sequence length polymorphism among Mus musculus musculus Sry gene, C3H/HeJ was different from C57BL/6J, BALB/cA, and DH. These data suggest that there are at least two functional types of Y Chr in Mus musculus musculus. Received: 22 January 1999 / Accepted: 5 April 1999     

Mapping a resistance gene in wheat cultivar Yangfu 9311 to yellow mosaic virus, using microsatellite markers

Wheat yellow mosaic disease, which is caused by wheat yellow mosaic bymovirus (WYMV) and transmitted by soil-borne fungus, results in severe damage on wheat (Triticum aestivum L.) production in China. For development of resistant cultivars to reduce wheat yield losses due to wheat yellow mosaic disease, resistance test and genetic analysis indicated that a single dominant gene in wheat cultivar Yangfu 9311 contributed to the resistance. Bulk segregant analysis was used to identify microsatellite markers linked to the resistance gene in an F₂ population derived from the cross Yangfu 9311 (resistant) × Yangmai 10 (susceptible). Microsatellite markers Xwmc41, Xwmc181, Xpsp3039, and Xgwm349 were co-dominantly or dominantly linked with the gene responsible for WYMV resistance at a distance of 8.1–11.6 cM. Based on the wheat microsatellite consensus map and the results from amplification of the cultivar Chinese Spring nulli-tetrasomic stocks, the resistance gene to wheat yellow mosaic disease derived from Yangfu 9311, temporarily named as YmYF, was thus mapped on the long arm of chromosome 2D (2DL).