Molecular mapping of two semidwarf genes in an indica rice variety Aitaiyin3 (Oryza sativa L.)

Genetic analysis established that Aitaiyin3, a dwarf rice variety derived from a semidwarf cultivar Taiyin1, carries two recessive semidwarf genes. By using simple sequence repeat (SSR) markers, we mapped the two semidwarf genes, sd-1 and sd-t2 on chromosomes 1 and 4, respectively. Sd-t2 was thus named because the semidrawf gene sd-t has already been identified from Aitaiyin 2 whose origin could be traced back to Taiyin1. The result of the molecular mapping of sd-1 gene revealed it is linked to four SSR markers found on chromosome 1. These markers are: RM297, RM302, RM212, and OSR3 spaced at 4.7 cM, 0 cM, 0.8cM and 0 cM, respectively. Sd-t2 was found to be located on chromosome 4 using five SSR markers: two markers, SSR332 and RM1305 located proximal to sd-t2 are spaced 11.6 cM, 3.8 cM, respectively, while the three distally located primers, RM5633, RM307, and RM401 are separated by distances of 0.4 cM, 0.0 cM, and 0.4 cM, respectively. __________ Translated from Acta Genetica Sinica, 2005, 32 (2) [译自: 遗传学报, 2005,32(2)]     

Molecular mapping of two reverse photoperiod-sensitive genic male sterility genes (rpms1 and rpms2) in rice (Oryza sativa L.)

The reverse photoperiod-sensitive genic male sterility (PGMS) and thermo-sensitive genic male sterility (TGMS) lines have an opposite phenotype compared with normal PGMS and TGMS lines widely used by the two-line system in current hybrid rice seed production. Thus, the application of reverse PGMS and TGMS lines can compensate PGMS and TGMS lines in hybrid rice production. YiD1S is a reverse PGMS line, in which pollen fertility is mainly regulated by day-length, but also influenced by temperature. Genetic analysis indicated that male sterility of YiD1S was controlled by two recessive major genes. An F₂ population from a cross between YiD1S and 8528 was developed and used for molecular mapping of the two reverse PGMS genes which were first named rpms1 and rpms2. Both simple sequence repeat (SSR) markers and bulked segregant analysis (BSA) were used in this study. As a result, one reverse PGMS gene (rpms1) was mapped to the interval between SSR markers RM22980 (0.9 cM) and RM23017 (1.8 cM) on chromosome 8. Eight SSR markers, YDS818, RM22984, RM22986, RM22997, YDS816, RM23002, RM339 and YDS810 completely co-segregated with the rpms1 gene. Another reverse PGMS gene (rpms2) was mapped to the interval between SSR markers RM23898 (0.9 cM) and YDS926 (0.9 cM) on chromosome 9. The physical mapping information from publicly available resources shows that the rpms1 and rpms2 loci are located in a region of 998 and 68 kb, respectively. The analysis based on marker genotypes showed that the effect of rpms1 was slightly larger than that of rpms2 and that the two genes interacted in controlling male sterility. H. F. Peng, Z. F. Zhang and B. Wu contributed equally to this work.     

Construction of a comprehensive PCR-based marker linkage map and QTL mapping for fiber quality traits in upland cotton (Gossypium hirsutum L.)

To facilitate marker assisted selection, there is an urgent need to construct a saturated genetic map of upland cotton (Gossypium hirsutum L.). Four types of markers including SSR, SRAP, morphological marker, and intron targeted intron–exon splice junction (IT-ISJ) marker were used to construct a linkage map with 270 F_2:7 recombinant inbred lines derived from an upland cotton cross (T586 × Yumian 1). A total of 7,508 SSR, 740 IT-ISJ and 384 SRAP primer pairs/combinations were used to screen for polymorphism between the two mapping parents, and the average polymorphisms of three types of molecular markers represented 6.8, 6.6 and 7.0%, respectively. The polymorphic primer pairs/combinations and morphological markers were used to genotype 270 recombinant inbred lines, and a map including 604 loci (509 SSR, 58 IT-ISJ, 29 SRAP and 8 morphological loci) and 60 linkage groups was constructed. The map spanned 3,140.9 cM with an average interval of 5.2 cM between two markers, approximately accounting for 70.6% of the cotton genome. Fifty-four of 60 linkage groups were ordered into 26 chromosomes. Multiple QTL mapping was used to identify QTL for fiber quality traits in five environments, and thirteen QTL were detected. These QTL included four for fiber length (FL), two for fiber strength (FS), two for fiber fineness (FF), three for fiber length uniformity (FU), and two for fiber elongation (FE), respectively. Each QTL explained between 7.4 and 43.1% of phenotypic variance. Five out of thirteen QTL (FL1 and FU1 on chromosome 6, FL2, FU2 and FF1 on chromosome7) were detected in five environments, and they explained more than 20% of the phenotypic variance. Eleven QTL were distributed on A genome, while the other two on D genome.     

High-resolution mapping of <Emphasis Type="Italic">Rsn1</Emphasis>, a locus controlling sensitivity of rice to a necrosis-inducing phytotoxin from <Emphasis Type="Italic">Rhizoctonia solani</Emphasis> AG1-IA

Rhizoctonia solani is a necrotrophic fungal pathogen that causes disease on many crop-plant species. Anastomosis group 1-IA is the causal agent of sheath blight of rice (Oryza sativa L.), one of the most important rice diseases worldwide. R. solani AG1-IA produces a necrosis-inducing phytotoxin and rice cultivar’s sensitivity to the toxin correlates with disease susceptibility. Unlike genetic analyses of sheath blight resistance where resistance loci have been reported as quantitative trait loci, phytotoxin sensitivity is inherited as a Mendelian trait that permits high-resolution mapping of the sensitivity genes. An F₂ mapping population derived from parent cultivars ‘Cypress’ (toxin sensitive) and ‘Jasmine 85’ (toxin insensitive) was used to map Rsn1, the necrosis-inducing locus. Initial mapping based on 176 F₂ progeny and 69 simple sequence repeat (SSR) markers located Rsn1 on the long arm of chromosome 7, with tight linkage to SSR marker RM418. A high-resolution genetic map of the region was subsequently developed using a total of 1,043 F₂ progeny, and Rsn1 was mapped to a 0.7 cM interval flanked by markers NM590 and RM418. Analysis of the corresponding 29 Kb genomic sequences from reference cultivars ‘Nipponbare’ and ‘93-11’ revealed the presence of four putative genes within the interval. Two are expressed cytokinin-O-glucosyltransferases, which fit an apoptotic pathway model of toxin activity, and are individually being investigated further as potential candidates for Rsn1.     

Mapping of a wide compatibility locus in indica rice using SSR markers

Hybrid sterility between indica and japonica subspecies in rice is basically caused by partial abortion of gametes and hybrid fertility could be recovered by a single wide compatibility (WC) allele. In this study, a typical indica germplasm source of rice, UPRI 95-162, with strong wide compatibility in cross with japonica rice was studied for location of its WC locus. Bulked segregant analysis was performed and SSRs (simple sequence repeats) were conducted on a F₁ population derived from a three-way cross (UPRI 95-162/T8//Akihikari). The locus was located on chromosome 1 approximately 0.2 cM to SSR markers RM581 on one side and 1.5 cM to RM292 on another. This WC locus, tentatively designated as S-20 ⁿ (t), and its tight linkage markers, RM581 and RM292, would be very useful for efficient marker-assisted selection for breeding new WC varieties and for map-based cloning of the gene.     

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.     

Molecular tagging and mapping of the erect panicle gene in rice

Erect panicle (EP) is one of the more important traits of the proposed ideotype of high-yielding rice. Several rice cultivars with the EP phenotype, which has been reported to be controlled by a dominant gene, have been successfully developed and released for commercial production in North China. To analyze the inheritance of the EP trait, we generated segregating F₂ and BC₁F₁ populations by crossing an EP-type variety, Liaojing 5, and a curved-panicle-type variety, Fengjin. Our results confirmed that a dominant gene controls the EP trait. Simple-sequence repeat (SSR) and bulked segregant analyses of the F₂ population revealed that the EP gene is located on chromosome 9, between two newly developed SSR markers, RM5833-11 and RM5686-23, at a genetic distance of 1.5 and 0.9 cM, respectively. Markers closer to the EP gene were developed by amplified fragment length polymorphism (AFLP) analysis with 128 AFLP primer combinations. Three AFLP markers were found to be linked to the EP gene, and the nearest marker, E-TA/M-CTC₂₀₀, was mapped to the same location as SSR marker RM5686-23, 1.5 cM from the EP gene. A local map around the EP gene comprising nine SSR and one AFLP marker was constructed. These markers will be useful for marker-assisted selection (MAS) for the EP trait in rice breeding programs.     

Fine mapping of a grain weight quantitative trait locus on rice chromosome 8 using near-isogenic lines derived from a cross between Oryza sativa and Oryza rufipogon

A quantitative trait locus (QTL) for grain weight (GW) was detected near SSR marker RM210 on chromosome 8 in backcross populations derived from a cross between the Korean japonica cultivar Hwaseongbyeo and Oryza rufipogon (IRGC 105491). The O. rufipogon allele increased GW in the Hwaseongbyeo background despite the fact that O. rufipogon was the small-seeded parent. Using sister BC₃F₃ near-isogenic lines (NILs), gw8.1 was validated and mapped to a 6.1 cM region in the interval between RM42 and RM210 (P≤0.0001). Substitution mapping with eight BC₃F₄ sub-NILs further narrowed the interval containing gw8.1 to about 306.4 kb between markers RM23201.CNR151 and RM30000.CNR99. A yield trial using homozygous BC₃F₄ sister sub-NILs and the Hwaseongbyeo recurrent parent indicated that the NIL carrying an O. rufipogon chromosome segment across the entire gw8.1 target region out-yielded its sister NIL (containing Hwaseongbyeo chromosome in the RM42–RM210 interval) by 9% (P=0.029). The higher-yielding NIL produced 19.3% more grain than the Hwaseongbyeo recurrent parent (P=0.018). Analysis of a BC₃F₄ NIL indicated that the variation for GW is associated with variation in grain shape, specifically grain length. The locus, gw8.1 is of particular interest because of its independence from undesirable height and grain quality traits. SSR markers tightly linked to the GW QTL will facilitate cloning of the gene underlying this QTL as well as marker-assisted selection for variation in GW in an applied breeding program.     

Genetics and molecular mapping of genes for high-temperature resistance to stripe rust in wheat cultivar Xiaoyan 54

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most widespread and destructive wheat diseases worldwide. Growing resistant cultivars is the preferred means of control of the disease. The winter wheat cultivar Xiaoyan 54 has high-temperature resistance to stripe rust. To identify genes for stripe rust resistance, Xiaoyan 54 was crossed with Mingxian 169, a winter wheat genotype susceptible to all Chinese races of the pathogen. Seedlings and adult plants of the parents and F₁, F₂, F₃ and F₄ progeny were tested with Chinese race CYR32 under controlled greenhouse conditions and in the field. Xiaoyan 54 has two recessive resistance genes, designated as Yrxy1 and Yrxy2, conferring high-temperature resistance. Simple sequence repeat (SSR) primers were used to identify molecular markers flanking Yrxy2 using 181 plants from one segregating F₃ line. A total of nine markers, two of which flanked the locus at genetic distances of 4.0 and 6.4 cM on the long arm of chromosome 2A were identified. Resistance gene analog polymorphism (RGAP) and SSR techniques were used to identify molecular markers linked to Yrxy1. A linkage group of nine RGAP and two SSR markers was constructed for Yrxy1 using 177 plants of another segregating F₃ line. Two RGAP markers were closely linked to the locus with genetic distances of 2.3 and 3.5 cM. Amplification of a set of nulli-tetrasomic Chinese Spring lines with RGAP markers M8 and M9 and the two SSR markers located Yrxy1 on the short arm of chromosome 7A. The SSR markers Xbarc49 and Xwmc422 were 15.8 and 26.1 cM, respectively, from the gene. The closely linked molecular markers should be useful for incorporating the resistance genes into commercial cultivars and combining them with other genes for stripe rust resistance.     

Identification of simple sequence repeat markers for utilizing wide-compatibility genes in inter-subspecific hybrids in rice (Oryza sativa L.)

Although pronounced heterosis in inter-subspecific hybrids was known in rice for a long time, its utilization for hybrid rice breeding has been limited due to their hybrid sterility (HS). For the last two decades, however, a few inter-subspecific hybrids have been developed by incorporating wide-compatibility genes (WCG) that resolve HS, into parental lines of these inter-subspecific hybrids. For effective use of WCG, it is necessary to find convenient markers linked to WCG of practical importance. In this paper, initially a set of simple sequence repeat (SSR) markers in the vicinity of known WCG loci identified based on comparative linkage maps have been surveyed in a population derived from the three-way cross- IR36/Dular//Akihikari, where a known donor of WCG Dular was crossed to a representative indica and japonica cultivar. Of the five parental polymorphic markers, RM253 and RM276 were found to be closely linked to the WCG locus S5 at a distance of 3.0 and 2.8 cM, respectively. Later, loci for HS were examined in three F₂ populations derived from inter-subspecific crosses, with same set of SSR markers. The locus S8 was confirmed to have major influence on HS in the F₂ population derived from CHMRF-1/Taichung65 since two SSR markers in its vicinity, RM412 and RM141, co-segregated with HS at a map distance of 7.6 and 4.8 cM, respectively. In the F₂ population derived from the cross BPT5204/Taipei309, three SSR markers in the vicinity of S5, RM50, RM276 and RM136 co-segregated with HS at a map distance of 4.2, 3.2 and 7.8 cM, respectively. In the third F₂ population derived from Swarna/Taipei309, the SSR markers in the vicinity of S5, RM225, RM253, RM50, RM276 and RM136 were identified to co-segregate with HS at a map distance of 3.2, 2.6, 3.4, 2.6 and 6.6 cM, respectively. These results indicated a clear picture of WCG in Dular as well as the predominant role of HS alleles at S5 locus. The identified SSR markers are expected to be used for incorporation of WCG into parental lines in hybrid rice breeding to solve HS in inter-subspecific hybrids.S.P. Singh , R.M. Sundaram contributed equally     

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.     

Inheritance and molecular mapping of a downy mildew resistance gene, Pl 13 in cultivated sunflower (Helianthus annuus L.)

The inheritance of resistance to sunflower downy mildew (SDM) derived from HA-R5 conferring resistance to nine races of the pathogen has been determined and the new source has been designated as Pl ₁₃ . The F₂ individuals and F₃ families of the cross HA-R5 (resistant) × HA 821 (susceptible) were screened against the four predominant SDM races 300, 700, 730, and 770 in separate tests which indicated dominant control by a single locus or a cluster of tightly linked genes. Bulked segregant analysis (BSA) was carried out on 116 F₂ individuals with 500 SSR primer pairs that resulted in the identification of 10 SSR markers of linkage groups 1 (9 markers) and 10 (1 marker) of the genetic map (Tang et al. in Theor Appl Genet 105:1124–1136, 2002) that distinguished the bulks. Of these, the SSR marker ORS 1008 of linkage group 10 was tightly linked (0.9 cM) to the Pl ₁₃ gene. Genotyping the F₂ population and linkage analysis with 20 polymorphic primer pairs located on linkage group 10 failed to show linkage of the markers with downy mildew resistance and the ORS 1008 marker. Nevertheless, validation of polymorphic SSR markers of linkage group 1 along with six RFLP-based STS markers of linkage group 12 of the RFLP map of Jan et al. (Theor Appl Genet 96:15–22, 1998) corresponding to linkage group 1 of the SSR map, mapped seven SSR markers (ORS 965-1, ORS 965-2, ORS 959, ORS 371, ORS 716, and ORS 605) including ORS 1008 and one STS marker (STS10D6) to linkage group 1 covering a genetic distance of 65.0 cM. The Pl ₁₃ gene, as a different source with its location on linkage group 1, was flanked by ORS 1008 on one side at a distance of 0.9 cM and ORS 965-1 on another side at a distance of 5.8 cM. These closely linked markers to the Pl ₁₃ gene provide a valuable basis for marker-assisted selection in sunflower breeding programs.     

Identification of SSR markers for a broad-spectrum blast resistance gene Pi20(t) for marker-assisted breeding

The Pi20(t) gene was determined to confer a broad-spectrum resistance against diverse blast pathotypes (races) in China based on inoculation experiments utilizing 160 Chinese Magnaporthe oryzae (formerly Magnaporthe grisea) isolates, among which isolate 98095 can specifically differentiate the Pi20(t) gene present in cv. IR24. Two flanking and three co-segregating simple sequence repeat (SSR) markers for Pi20(t), located near the centromere region of chromosome 12, were identified using 526 extremely susceptible F₂ plants derived from a cross of Asominori, an extremely susceptible cultivar, with resistant cultivar IR24. The SSR OSR32 was mapped at a distance of 0.2 cM from Pi20(t), and the SSR RM28050 was mapped to the other side of Pi20(t) at a distance of 0.4 cM. The other three SSR markers, RM1337, RM5364 and RM7102, co-segregated with Pi20(t). RM1337 and RM5364 were found to be reliable markers of resistance conditioned by Pi20(t) in a wide range of elite rice germplasm in China. As such, they are useful tags in marker-assisted rice breeding programs aimed at incorporating Pi20(t) into advanced rice breeding lines and, ultimately, at obtaining a durable and broad spectrum of resistance to M. oryaze. Wei Li and Cailin Lei contributed equally to this work.     

Identification and mapping of molecular markers linked to the tuberculate fruit gene in the cucumber (Cucumis sativus L.)

Warty fruit is one of the highly valuable external quality traits related to the market values of cucumber. Genetic analysis has shown that a single dominant gene, Tu (Tuberculate fruit), determines the warty fruit trait in the cucumber plant. An F₂ population (247 individuals) from the cross of S06 × S52 was used for the mapping of the Tu/tu locus. By combining bulked segregant analysis with the sequence-related amplified polymorphism (SRAP) and simple sequence repeat (SSR) markers, 15 markers (9 SRAPs and 6 SSRs) linked to the Tu/tu locus were identified. Of nine SRAP markers, three closely linked to the Tu/tu locus were successfully converted into sequence characterized amplified region (SCAR) markers. The Tu/tu locus was mapped between the co-dominant SSR marker SSR16203 and the SCAR marker C_SC933, at a genetic distance of 1.4 and 5.9 cM, respectively. Then the linked SSR markers in the study were used as anchor loci to locate the Tu/tu locus on cucumber chromosome 5. Moreover, the validity analysis of the C_SC69 and C_SC24 markers was performed with 62 cucumber lines of diverse origins, showing that the two SCAR markers can be used for marker-assisted selection (MAS) of the warty fruit trait in cucumber breeding. The information provided in this study will facilitate the map-based cloning of the Tu/tu gene.     

The Pik m gene, conferring stable resistance to isolates of Magnaporthe oryzae , was finely mapped in a crossover-cold region on rice chromosome 11

The Pik ^m gene in rice confers a high and stable resistance to many isolates of Magnaporthe oryzae collected from southern China. This gene locus was roughly mapped to the long arm of rice chromosome 11 with restriction fragment length polymorphic (RFLP) markers in the previous study. To effectively utilize the resistance, a linkage analysis was performed in a mapping population consisting of 659 highly susceptible plants collected from four F₂ populations using the publicly available simple sequence repeat (SSR) markers. The result showed that the locus was linked to the six SSR markers and defined by RM254 and RM144 with ≈13.4 and ≈1.2 cM, respectively. To fine map this locus, additional 10 PCR-based markers were developed in a region flanked by RM254 and RM144 through bioinformatics analysis (BIA) using the reference sequence of cv. Nipponbare. The linkage analysis with these 10 markers showed that the locus was further delimited to a 0.3-cM region flanked by K34 and K10, in which three markers, K27, K28, and K33, completely co-segregated with the locus. To physically map the locus, the Pik ^m -linked markers were anchored to bacterial artificial chromosome clones of the reference cv. Nipponbare by BIA. A physical map spanning ≈278 kb in length was constructed by alignment of sequences of the clones anchored by BIA, in which only six candidate genes having the R gene conserved structure, protein kinase, were further identified in an 84-kb segment.     

Delimitation of the <Emphasis Type="Italic">fgr</Emphasis> gene for rice fragrance to a 28-kb DNA fragment

The fragrance gene plays an important role in high-quality rice varieties and has been widely used in breeding programs. Using a random sample of 370 individuals from an F₂ segregating population developed from a cross between a japonica rice variety 9407 with fragrant flavor and an indica variety IRBB60, the fgr locus was mapped on chromosome 8 between SSR markers, PSM465 and RM1109, with genetic distances of 0.3 cM and 0.1 cM to respective markers. These mapping efforts confirmed the previous mapping results. A large F₃ mapping population with 7300 individuals was then developed from F₂ plants, in which a small chromosomal region defined by the SSR markers, PSM465 and RM1109, was heterozygous. The analysis of recombinants in the fgr region anchored the gene locus to an interval of 28 kb flanked by the left marker NS9 and the right marker L06. Sequence analysis of this fragment predicted three open reading frames encoding putative 3-methylcrotonyl-CoA carboxylase, putative isoleucyl-tRNA synthetase, and betaine aldehyde dehydrogenase (BADH2). The latter was presumed to be the candidate gene for fragrance. This result will be very useful in molecular cloning of the fgr gene and marker-assisted transfer of the fgr gene in rice breeding programs. Published in Russian in Fiziologiya Rastenii, 2009, vol. 56, No. 4, pp. 587–595. This text was submitted by the authors in English.     

Inheritance and Mechanism of Resistance to Rice Stripe Disease in cv. Zhendao 88, a Chinese Rice Cultivar

Mechanisms of resistance to rice stripe disease in a Chinese rice cultivar (Oryza sativa L., cv. Zhendao 88) were determined, and molecular markers for the resistance gene were identified. Single tillers at the seedling stage were inoculated with Rice stripe virus (RSV) and its vector, the small brown planthopper (SBPH) Laodelphax striatellus Fallen, to test for non‐preference and antibiosis. The inheritance of resistance in the F₂ and F_{2 : 3} lines from the cross cvs Zhendao 88× Wuyujing No. 3 was also examined by single‐tiller inoculation. Cv. Zhendao 88 was highly resistant to RSV and weakly resistant to SBPH. The resistance gene was mapped by SSR and RAPD analyses to rice chromosome 11 within 4.7 cm of a SSR marker RM229 and a RAPD marker OPO11. Data and inheritance analysis indicated that rice stripe disease resistance in cv. Zhendao 88 was derived principally from resistance to RSV and controlled by a single dominant gene. Breeding for rice stripe resistance could be accelerated by using cv. Zhendao 88 as a resistant parent if the linked marker for virus resistance were used in a marker‐assisted progeny selection programme.     

Identification of SSR Markers for Salt-tolerance in Rice Variety CSR10 by Selective Genotyping

A population of 171 F3 genotypes derived from a cross between CSR10 (salt tolerant, indica) and Taraori Basmati (HBC19) was evaluated for various salt-tolerance attributes at vegetative stage using a hydroponic culture system. Substantial variation was observed in F₃ population for relative growth rate (range 0.065–0.187), Na-K ratio (0.023–0.376) and visual injury symptoms (score 1–9). The mean individual score of CSR10 × HBC19 F₃ plants ranged from 1.7 to 9.0 with mean value of 5.07. Seven of the F₃ plants showed transgressive segregation for salt tolerance. F₃ individuals at both extremes of the response distribution were selected and genotyped using 30 SSR markers displaying polymorphism between the two parental genotypes. As many as 18/30 SSR markers showed distorted segregation ratios among the 30 selected salt-tolerant and salt-sensitive CSR10 × HBC19 F3 plants. Linear regression analysis showed significant association of three markers (RM162 mapped on chromosome 6, and RM209 and RM287 on chromosome 11) with relative growth rate and two markers (RM212 on chromosome 1 and RM206 on chromosome 11) with Na-K ratio explaining 31.3% and 25.6% of phenotypic variation, respectively.     

SSRs for Marker-Assisted Selection for Blast Resistance in Rice (Oryza sativa L.)

Rice blast caused by the fungus Magnaporthe oryzae is one of the most devastating diseases of rice in nearly all rice growing areas of the world including Malaysia. To develop cultivars with resistance against different races of M. oryzae, availability of molecular markers along with marker-assisted selection strategies are essential. In this study, 11 polymorphic simple sequence repeat (SSR) markers with good fit of 1:2:1 ratio for single gene model in F₂ population derived from the cross of Pongsu seribu 2 (Resistant) and Mahsuri (Susceptible) rice cultivars were analysed in 296 F₃ families derived from individual F₂ plants to investigate association with Pi gene conferring resistance to M. oryzae pathotype. Parents and progeny were grouped into two phenotypic classes based on their blast reactions. Chi-square test for the segregation of resistance and susceptibility in F₃ generation fitted a ratio of approximately 3:1. Association of SSR markers with phenotypic trait in F₃ families was identified by statistical analysis. Four SSR markers (RM413, RM5961, RM1233 and RM8225) were significantly associated with blast resistance to pathotype 7.2 of M. oryzae in rice (p ≤ 0.01). These four markers accounted for about 20% of total phenotypic variation. So, these markers were confirmed as suitable markers for use in marker-assisted selection and confirmation of blast resistance genes to develop rice cultivars with durable blast resistance in Malaysian rice breeding programmes.     

Identification of QTL regions and SSR markers associated with resistance to reniform nematode in <Emphasis Type="Italic">Gossypium barbadense</Emphasis> L. accession GB713

The identification of molecular markers that are closely linked to gene(s) in Gossypium barbadense L. accession GB713 that confer a high level of resistance to reniform nematode (RN), Rotylenchulus reniformis Linford & Oliveira, would be very useful in cotton breeding programs. Our objectives were to determine the inheritance of RN resistance in the accession GB713, to identify SSR markers linked with RN resistance QTLs, and to map these linked markers to specific chromosomes. We grew and scored plants for RN reproduction in the P₁, P₂, F₁, F₂, BC₁P₁, and BC₁P₂ generations from the cross of GB713 × Acala Nem-X. The generation means analysis using the six generations indicated that one or more genes were involved in the RN resistance of GB713. The interspecific F₂ population of 300 plants was genotyped with SSR molecular markers that covered most of the chromosomes of Upland cotton (G. hirsutum L.). Results showed two QTLs on chromosome 21 and one QTL on chromosome 18. One QTL on chromosome 21 was at map position 168.6 (LOD 28.0) flanked by SSR markers, BNL 1551_162 and GH 132_199 at positions 154.2 and 177.3, respectively. A second QTL on chromosome 21 was at map position 182.7 (LOD 24.6) flanked by SSR markers BNL 4011_155 and BNL 3279_106 at positions 180.6 and 184.5, respectively. Our chromosome 21 map had 61 SSR markers covering 219 cM. One QTL with smaller genetic effects was localized to chromosome 18 at map position 39.6 (LOD 4.0) and flanked by SSR markers BNL 1721_178 and BNL 569_131 at positions 27.6 and 42.9, respectively. The two QTLs on chromosome 21 had significant additive and dominance effects, which were about equal for each QTL. The QTL on chromosome 18 showed larger additive than dominance effects. Following the precedent set by the naming of the G. longicalyx Hutchinson & Lee and G. aridum [(Rose & Standley) Skovsted] sources of resistance, we suggest the usage of Ren ^barb1 and Ren ^barb2 to designate these QTLs on chromosome 21 and Ren ^barb3 on chromosome 18.