Detecting major QTL associated with resistance to bacterial blight using a set of rice reciprocal introgression lines with high density SNP markers

Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is a worldwide rice disease. QTL providing BB resistance were identified using a set of introgression lines (ILs) derived from a cross between Teqing and Lemont, and 3924 evenly distributed SNP markers developed from the two parents. After inoculating three Xoo pathotypes, CII, CIV and CV, seven major BB resistance‐associated QTL were detected. The alleles at all loci with improved BB resistance were from the Teqing background. Four QTL resistance to CII and CIV were identified in the reciprocal backgrounds across 2 years. Six QTL conferring resistance to CV identified in Teqing background were not detected in Lemont background, indicating that genetic background had a strong effect on the BB resistance‐associated QTL. Based on the interactions of 27 significant digenic QTL pairs among the seven main‐effect QTL, the QTL were divided into three strain‐specific groups. Genotype analyses of resistant ILs suggest that rice lines with a high level of resistance to BB can be achieved by pyramiding R gene(s) and QTL that interact with R gene(s).     

Pyramiding of Xa7 and Xa21 for the improvement of disease resistance to bacterial blight in hybrid rice

‘Minghui 63’ is a restorer line widely used in hybrid rice production in China for the last two decades. This line and its derived hybrids, including ‘Shanyou 63’, are susceptible to bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo). To improve the bacterial blight resistance of hybrid rice, two resistance genes Xa21 and Xa7, have been introgressed into ‘Minghui 63’ by marker‐assisted selection and conventional backcrossing, respectively. The single resistance gene‐introgressed lines, Minghui 63 (Xa21) and Minghui 63 (Xa7) had higher levels of resistance to bacterial blight than their derived hybrids, Shanyou 63 (Xa21) or Shanyou 63 (Xa7). Both Xa21 and Xa7 showed incomplete dominance in the heterozygous background of rice hybrids by infection with GX325 and KS‐1‐21. The improved restorer lines, with the homozygous genotypes, Xa21Xa21 or Xa7Xa7, were more resistant than their hybrids with the heterozygous genotypes Xa21xa21 or Xa7xa7. To further enhance the bacterial blight resistance of ‘Minghui 63’ and its hybrids, Xa21 and Xa7 were pyramided into the same background using molecular marker‐aided selection. The restorer lines developed with the resistance genes Xa21 and Xa7, and their derived hybrids were evaluated for resistance after inoculation with 10 isolates of pathogens from China, Japan and the Philippines, and showed a higher level of resistance to BB than the restorer lines and derived hybrids having only one of the resistance genes. The pyramided double resistance lines and their derived hybrids have the same high level of resistance to BB. These results clearly indicate that pyramiding of dominant genes is a useful approach for improving BB resistance in hybrid rice.     

水稻抗白叶枯病新基因Xa32（t）的鉴定和初步定位

通过多菌系接种鉴定及抗谱分析,并与目前国际上已知抗白叶枯病基因比较,证明在水稻抗源C4064中含有一个新的抗白叶枯病基因,暂命名为Xa32(t)。应用分离集团分析法(BSA),借助SSR和EST等分子标记,对该基因进行了分子标记定位。通过对F₂分离群体及F₃家系单株进行遗传连锁性检测,发现6个位于水稻第11染色体长臂末端的分子标记RM27256、RM27274、RM2064、ZCK24、RM6293和RM5926与Xa32(t)基因连锁。它们与Xa32(t)基因间的遗传距离分别为2.1、1.0、1.0、0.5、1.5和2.6 cM。其中标记RM6293和RM5926位于染色体近端粒一侧,其他4个标记RM27256、RM27274、RM2064和ZCK24位于基因的另一侧。将Xa32(t)定位在水稻第11染色体长臂末端2.0 cM范围内。     

水稻抗白叶枯病新基因Xa32（t）的鉴定和初步定位

通过多菌系接种鉴定及抗谱分析,并与目前国际上已知抗白叶枯病基因比较,证明在水稻抗源C4064中含有一个新的抗白叶枯病基因,暂命名为Xa32(t)。应用分离集团分析法(BSA),借助SSR和EST等分子标记,对该基因进行了分子标记定位。通过对F₂分离群体及F₃家系单株进行遗传连锁性检测,发现6个位于水稻第11染色体长臂末端的分子标记RM27256、RM27274、RM2064、ZCK24、RM6293和RM5926与Xa32(t)基因连锁。它们与Xa32(t)基因间的遗传距离分别为2.1、1.0、1.0、0.5、1.5和2.6 cM。其中标记RM6293和RM5926位于染色体近端粒一侧,其他4个标记RM27256、RM27274、RM2064和ZCK24位于基因的另一侧。将Xa32(t)定位在水稻第11染色体长臂末端2.0 cM范围内。     

Elucidation of meiotic nuclear restitution mechanisms in potato through analysis of microtubular cytoskeleton

DNAs of 693 isolates of bacterial blight pathogen of rice, Xanthomonas oryzae pv. oryzae (Xoo), were characterized using PCR-based primers p^JEL1 and p^JEL2. The pathogen populations were grouped into 97 haplotypes based on DNA-banding patterns. An un-weighted pair-group method using arithmetic averages (UPGMA) indicated a high level of diversity in the pathogen isolates (51 lineages of Xoo at a 70% similarity level). Among these, lineages 5, 7, 27, and 29 are widely distributed and others are localized in the northern region of India. The isolates represent lineage-27, were prevalent in the entire disease-prone area in the region except at Ferozepur. Pathotyping data of the representative isolates of each lineage also indicate 17 different reaction patterns on a set of isogenic lines. Resistance genes xa8 and Xa21 were the most effective followed by xa5, and Xa7 against Xoo isolates prevalent in northern India. Different genes in combinations (xa5+xa13, xa5+Xa21, xa13+Xa21, and xa5+xa13+Xa21) in IR24 genetic background provided better protection against all the pathogen isolates tested in this study than did the component genes. This revised version was published online in July 2006 with corrections to the Cover Date.     

Multiplex PCR genotyping for five bacterial blight resistance genes applied to marker‐assisted selection in rice (Oryza sativa)

Bacterial blight (BB) is the most economically damaging disease of rice in Asia and other parts of the world. In this study, a multiplex PCR genotyping method was developed to simultaneously identify genotypes of five BB resistance genes, Xa4, xa5, Xa7, xa13 and Xa21. The resistance R alleles were amplified using five functional markers (FMs) to generate amplicons of 217, 103, 179, 381 and 595 bp in IRBB66. Amplicons of 198, 107, 87, 391 and 467 bp corresponded to susceptible alleles in Taiwanese japonica rice cultivars. In backcross breeding programmes, the multiplex PCR assay was integrated into selection from a population using BB resistance donor IRBB66 crossed to rice cultivar ‘Tainung82’. Two plants with homozygosity for Xa4, xa5, Xa7, xa13 and Xa21 were selected from 1100 BC₂F₂ plants. In addition, the five BB resistance genes were also accurately identified in F₂ populations. This multiplex PCR method provides a rapid and efficient method for detecting various BB resistance genes, which will assist in pyramiding genes to improve durability of BB resistance in Taiwanese elite rice cultivars.     

Introgression of bacterial blight resistance genes Xa7, Xa21, Xa22 and Xa23 into hybrid rice restorer lines by molecular marker-assisted selection

Four bacterial blight (BB) resistance genes, Xa7, Xa21, Xa22 and Xa23, were introgressed into an elite hybrid rice restorer line Huahui 1035, by marker-assisted selection (MAS). Ten promising BB resistant lines identified by MAS approach in Huahui 1035 restorer background and their respective F₁ hybrids with a cytoplasmic male sterile line i.e. Jinke 1A, three BB resistant gene donors and their recurrent parent were evaluated for BB resistance by inoculating them with eleven representative races of Xanthomonas oryzae pv. oryzae (Xoo) in China. Further, the ten marker assisted selection of BB (MAS-BB) resistant restorer lines and their F₁ hybrids were also characterized for agro-morphological traits and grain yield. Results revealed that restorer lines with Xa23 introgression i.e. HBQ809 and HBQ810 were found to be resistant to all eleven Chinese representative Xoo races, showing broad spectrum resistance to BB. However, the lines possessing Xa7 or Xa7+Xa21 were resistant to ten out of eleven Xoo races. While restorer lines with Xa21 were resistant to nine out of eleven Xoo races. Interestingly, the F₁ hybrids with Xa23, Xa7 or Xa7+Xa21 were resistant to two severe epidemic Xoo races of China. Restorer lines i.e. HBQ807 and HBQ808 possessing Xa22 were only resistant to six or five out of inoculated eleven Xoo races. Lesion length comparisons between restorer lines and their F₁ hybrids for the above four BB resistance genes showed them to be dominant in heterozygote genotype. Three promising high yielding F₁ hybrids with BB resistance were identified for immediate exploitation for hybrid rice production in China.     

Expression levels of three bacterial blight resistance genes against K3a race of Korea by molecular and phenotype analysis in japonica rice (O. sativa L.)

Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo) is a destructive disease of rice in the major rice growing countries of Asia. In 2003, a serious bacterial blight epidemic occurred in the southwestern coastal areas in Korea, causing significant yield loss due to the emergence of a new race, K3a. IR24 near-isogenic lines containing Xa4, xa5, Xa7 and Xa21 genes conferred different degrees of resistance to the most virulent K3a isolate, HB01009 in an inoculation experiment in the greenhouse. Expression levels of the resistance genes, Xa4, xa5 and Xa21 were studied in two F2 populations derived from the crosses between elite japonica cultivars and an advanced backcross breeding line possessing Xa4, xa5 and Xa21 genes. F₂ progenies segregated for K3a resistance (R) and susceptible (S) phenotypes in a ratio of 3(R):1(S) indicated that K3a resistance was controlled by a major dominant gene. Three PCR markers tightly linked to the resistance genes Xa4, xa5 and Xa21 confirmed the presence of the genes and their interaction with each gene. This study demonstrated that the Xa21 gene dominantly contributed to K3a resistance. However, the Xa4 gene also contributed to the full expression of resistance. The level of expression of strong resistance to K3a race was attributed to the presence of Xa21 and Xa4 genes irrespective of the presence of xa5 gene. Our results suggest that the R-gene combinations of Xa4+Xa21 could be a useful and effective strategy toward improving resistance to K3a race of Korean japonica cultivars.     

Development of broad‐spectrum bacterial blight resistance into thermo‐sensitive genic male sterile lines

Two‐line hybrid rice technology is an effective way to increase rice production and improve rice quality. In this study, three bacterial blight (BB) resistance genes, Xa7, Xa21 and Xa23, were introgressed separately into C815S, a popular thermo‐sensitive genic male sterile (TGMS) line to develop five BB‐resistant lines (Hua1005S, Hua1002S, Hua1009S, Hua1006S and Hua1001S) to be resistant against seven races of Xanthomonas oryzae pv. oryzae (Xoo). The two‐line hybrids with heterozygous Xa23 were resistant against seven Xoo strains. But, the hybrids with heterozygous loci for both Xa7 and Xa21 were only resistant against three Xoo strains and were moderately susceptible to the other four strains indicating the role of modifiers influencing the poor expression of dominant BB resistance genes under heterozygous state. Among them, Hua1006S was found to be a promising TGMS line with its higher degree of disease resistance level on account of broad‐spectrum resistance gene Xa23 besides possessing better plant type and rice grain quality features.     

Pyramiding of two bacterial blight resistance and a semidwarfing gene in Type 3 Basmati using marker-assisted selection

A traditional Type 3 Basmati rice cultivar grown in India is tall and lodges even under low nitrogen fertilizer dose. In addition to lodging, it is highly susceptible to several diseases and pests including bacterial blight (BB). BB resistance genes (Xa21 and xa13) and a semidwarfing gene (sd-1) were pyramided in Type 3 Basmati from a rice cultivar PR106-P2 using marker-assisted selection (MAS). Foreground selection for BB resistance genes, Xa21 and xa13 and reduced plant height gene, sd-1 was carried on the basis of linked molecular markers pTA248, RG136 and ‘h’, respectively. The BC₂F₃ progenies with both the BB resistance genes were highly resistant with lower lesion length than either of the genes individually. Background profiling of the selected 16 BC₂F₃ progenies was done using 95 anchored SSR and 12 ISSR markers. Among the selected 16 BC₂F₃ progenies, 38-5-2 and 38-5-36 closely clustered along with the recipient parent Type 3 Basmati showing above 85% genetic similarity with the same. Further selection was continued till F₅ generation for higher recovery for Type 3 Basmati characteristics. The desirable alleles of intermediate amylose content (wx) and aroma (fgr) loci of Type 3 Basmati were also tracked using the linked SSR markers. The BC₂F₅ pyramid lines T3-4, T3-5, T3-6 and T3-7 homozygous for the three target genes Xa21, xa13 and sd-1 from the donor parent with wx and fgr alleles of Type 3 Basmati had excellent cooking quality and strong aroma.     

Genotypic response of faba bean to water stress

Forty resistant rice cultivars were studied for theinheritance of resistance to bacterial blight usingPhilippine races of Xanthomonas oryzae pv.oryzae (Xoo). Results showed that all thevarieties have at least two recessive genes forresistance. One of these genes governs resistance torace 1 (PXO61) while the other gene confers resistanceto race 6 (PXO99). In addition to the recessivegenes, nine of the varieties possess another dominantgene which also confers resistance to race 1.Allelism tests revealed that the recessive genesgoverning resistance to race 1 in 39 varieties areallelic to xa5 while the dominant genes in thenine varieties are allelic to Xa4. Therecessive gene conferring resistance to race 1 incultivar Sada Diga is inherited independently of xa5. Similarly, the recessive genes governingresistance to race 6 in all the varieties arenon-allelic to xa13. The allelic relationshipsof these genes with xa-24(t), a new recessivegene identified in cultivar DV86 which conveysresistance to race 6 are now being investigated.     

Improving bacterial blight resistance of'6078', an elite restorer line of hybrid rice, by molecular marker-assisted selection

Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (X00), is one of the most devastating diseases of rice world‐wide; it is also a serious problem of hybrid rice production in China. In this study, a molecular marker‐assisted introgression of Xa21, a gene highly resistant to a broad spectrum of Xoo strains, from ‘IRBB21’ was performed to improve the BB resistance of‘6078′, a new restorer line with high yielding potential. The entire process took one generation of crossing followed by three generations of backcrossing and one generation of selfing. The presence of Xa21 in each generation was determined by both polymerase chain reaction (PCR) and pathogen inoculation. Recombinations between Xa21 and flanking markers were identified by PCR analysis. Background selection was conducted in BC₁F₁ and BC₂F₁ using amplified fragment length polymorphism (AFLP) markers detecting a total of 129 polymorphic bands between‘6078’ and ‘IRBB21′. The individual selected in BC₃F₂, or‘6078′(Xa21), carried a fragment of less than 3.8 cM from the donor line in the Xa21 region on chromosome 11, and about 98.8% of the genetic background from the recurrent parent. The results showed that‘6078′(Xa21) had the same level and spectrum of BB resistance as the donor parent ‘IRBB21′, while maintaining the agronomic performance and combining ability of the original 6078. A significant increase in BB resistance was also achieved in the hybrid using 6078(Xa21) as the restorer line.     

The host background of rice influences the resistance expression of a three genes pyramid (xa5 + xa13 + Xa21) to bacterial blight (Xanthomonas oryzae pv. oryzae) pathotypes of Indian mainland and Bay islands

Bacterial blight (BB) is a major disease of rice for which host resistance is the only effective solution. The three genes pyramid xa5 + xa13 + Xa21 is recently the most utilized combination for developing resistant varieties through marker‐assisted breeding. Our study was carried out to elicit the detailed response of twenty lines possessing these three genes in five genetic backgrounds to twelve diverse BB pathotypes in India. The lines developed from ADT 47 variety showed incomplete resistance to most of the pathotypes, whereas susceptibility varied from 8.3% to 16.6% in ADT 43 and IR24, respectively. However, in IMP ASD16/60 and Improved Samba Mahsuri, complete resistance against all pathotypes was observed. The overall results confirmed that genetic background plays crucial role for the effective expression of xa5 + xa13 + Xa21 combination. Molecular studies did not reveal correlation between origin of pathotypes and their virulence potential. It is suggested to deploy Improved Samba Mahsuri, IMP ASD 16/60 and AD1306 varieties in the bacterial blight prone areas or use them as donors for realizing wider and durable resistance.     

Linkage analysis of rice bacterial blight resistance gene xa20 in XM6, a mutant line from IR24

Bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is an important disease constraining rice (Oryza sativa L.) production worldwide. The XM6 line was induced by N-methyl-N-nitrosourea from IR24, an Indica cultivar that is susceptible to Philippine and Japanese Xoo races. XM6 was confirmed to carry a recessive gene named xa20, resistant to six Philippine and five Japanese Xoo races. The chromosomal gene location was found using 10 plants with the shortest lesion length in an F₂ population consisting of 298 plants from a susceptible Japonica variety Koshihikari × XM6. Analysis using PCR-based DNA markers covering the whole rice genome indicated the gene as located on the distal region of the long arm of chromosome 3. The IKC3 line carries IR24 genetic background with Koshihikari fragment on chromosome 3 where a resistance gene was thought to be located. The F₂ population from IKC3 × XM6 clearly showed a bimodal distribution separating resistant and susceptible plants. Further linkage analysis conducted using this F₂ population revealed that xa20 is located within the 0.8 cM region flanked by DNA markers KIC3-33.88 (33.0 Mb) and KIC3-34.06 (33.2 Mb). This study yields important findings for resistance breeding and for the genetic mechanism of Xoo resistance.     

Integrating marker assisted background analysis with foreground selection for identification of superior bacterial blight resistant recombinants in Basmati rice

Basmati rice is highly susceptible to bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae. Transfer of BB resistance genes from non‐Basmati sources to Basmati through cross‐hybridization requires strict monitoring for recovery of the desirable Basmati quality traits in the recombinants, which show complex inheritance pattern. We integrated background analysis using mapped microsatellite markers with foreground selection to identify superior lines that combine useful genes from a non‐Basmati BB resistance donor line IRBB55 with grain and cooking quality characteristics of the popular Basmati rice variety ‘Pusa Basmati 1’ (PB 1) employing backcross pedigree strategy. Foreground selection using linked markers ensured presence of two genes, xa13 and Xa21 for BB resistance from IRBB55, and the recurrent parent PB 1 allele for the waxy locus giving intermediate amylose content and maintainer allele at fertility restorer locus in the BC₁F₅ recombinants. Background analysis enabled selection of recombinants with recurrent parent genome to the extent of 86.3% along with the quality traits. The extent of introgression of non‐Basmati donor chromosome segments in the superior selections was estimated to be < 7.8 Mb and < 6.7 Mb in the xa13 and Xa21 linked genomic regions, respectively. Association mapping identified three quantitative trait loci, one each for 1000‐grain weight, fertile grains/panicle and cooked kernel length. The backcross‐pedigree breeding strategy facilitated recovery of additional desirable characteristics from the donor in some of the selections. The elite selection Pusa 1460‐01‐32‐6‐7‐67 with maximum genomic background and quality characteristics of the recurrent Basmati parent gave resistance reaction against BB, similar to that of the non‐Basmati resistant check variety and recorded an yield advantage of 11.9% over the best check in the multiplication agronomic trial in the Basmati growing region of India. This line, which has been released as a new variety in the name of ‘Improved Pusa Basmati 1’ for commercial cultivation in India, is an example of successful application of marker assisted selection to variety development.     

Introgression of Xa4, Xa7 and Xa21 for resistance to bacterial blight in thermosensitive genetic male sterile rice (Oryza sativa L.) for the development of two-line hybrids

Bacterial blight (BB) of rice caused by X. oryzae pv. oryzae is a major production constraint in commercial hybrid rice production in the Philippines because most of the parental lines used in hybrid production do not carry resistance genes against the pathogen. In this study, three bacterial blight resistance genes, Xa4, Xa7 and Xa21, were introgressed to a temperature-sensitive genetic male sterile (TGMS1) line. A three-way cross of AR32-19-3-3/TGMS1//IRBB4/7 (PR36944) was made to produce 1,364 F₂ plants carrying various combinations of Xa4, Xa7 and Xa21. Individual plants were characterized for reaction to bacterial blight PXO61 (race 1), PXO86 (race 2), PXO99 (race 6) and pollen sterility. Of 144 F₂ plants demonstrating resistance against PXO61, PXO86 and PXO99, 22 exhibited highly resistant phenotypes with mean lesion lengths ranging from 0.37–2.97 cm. Analysis of disease reaction identified 20 potential TGMS F₂ plants containing Xa4, Xa7 and Xa21 while 78 plants with Xa4 + Xa7. Phenotypic and polymerase chain reaction (PCR) analyses confirmed PR36944-450, PR36944-473 and PR36944-700 as homozygous for Xa7 and Xa21 and highly resistant to all three Xoo races. Fertility of PR36944-450 and PR36944-700 was restored at permissive temperature in a growth chamber. BB-resistant TGMS lines should facilitate breeding two-line hybrids in the tropics.     

水稻抗白叶枯病基因的聚合育种

白叶枯病是严重危害水稻生产的重要病害之一,利用聚合多个抗性基因的水稻品种是控制该病害的有效途径。本研究以携带Xa4、xa5、xa13、Xa214个抗白叶枯病基因的IRBB60与8个水稻新品系,组配8个杂交组合.应用分子标记辅助选择技术从F2和F3群体中共获得216个携带4个抗白叶枯病基因的纯合体。用华南地区的5个白叶枯病病原菌小种进行田间接种的试验表明,4个抗性基因聚合系的抗性水平高于只带1个抗性基因的近等基因系。这些聚合系可用作华南地区高抗白叶枯病水稻品种育种的亲本材料。     

云南3种野生稻中抗白叶枯病基因的鉴定

白叶枯病是水稻生产上最重要的细菌性病害之一,培育抗病新品种是防治白叶枯病最经济有效的途径。然而,栽培稻来源的抗病基因数量有限,并且部分抗病基因的抗病谱窄。因此,从野生稻中发掘抗病基因,将有利于培育抗病谱广且抗病能力强的水稻新品种。本研究通过抗性鉴定和PCR分析,检测云南野生稻中的抗白叶枯病基因。结果表明,云南野生稻对2个代表性白叶枯病菌Y8和PXO99具有不同程度的抗性,疣粒野生稻甚至达到免疫的程度。功能标记检测结果显示,3种野生稻中均不含xa5、xa13和Xa21抗病基因,元江普通野生稻含Xa23和Xa3/Xa26基因或其同源基因,景洪普通野生稻中含Xa1、Xa3/Xa26和Xa27基因或同源基因,药用野生稻含Xa3/Xa26基因或同源基因,而疣粒野生稻含有Xa27抗性基因。本研究结果为进一步发掘和克隆云南野生稻中的抗白叶枯病新基因提供了理论参考。     

Pyramiding of four resistance genes of bacterial blight in Tapaswini, an elite rice cultivar, through marker-assisted selection

Breeding for resistance against Bacterial blight (BB), a destructive disease in rice, is a major challenge because of the rich diversity of the pathogen, Xanthomonas oryzae pv. oryzae. Three resistance genes i.e. xa5, xa13 and Xa21 were transferred from IRBB 60 through marker-assisted backcross breeding to supplement the Xa4 gene present in Tapaswini, an elite cultivar having a wide coverage. The precise transfer was aided through effective foreground selection using STS markers RG 556, RG 136 and pTA248 linked to the three target genes, respectively. In the screening assays, the gene pyramids having four genes exhibited higher level of resistance against the disease. Background selection based on morphological and grain quality traits and SSR markers led to the recovery of 85–96 % of the recurrent parent genome in the gene pyramids. Multi location evaluation conducted over a two year period at several hotspot locations of bacterial blight in India has resulted in identification and release of CRMAS 2622-7-6 (IT-6), a promising gene pyramid as improved Tapaswini. The high levels of resistance exhibited in the improved genotype without any yield penalty and its similarity to the recurrent parent provides a successful demonstration of the potential of MAS in pyramiding genes as well as the recovery of the parental genome with high accuracy.     

A new rice gall midge resistance gene in the breeding line CR57-MR1523, mapping with flanking markers and development of NILs

Gall midge is the third most destructive insect pests of rice after stem borers and planthoppers. Host plant resistance has been recognized as the most effective and economic, means for gall midge management. With the characterization of a new gall midge biotype (GMB) 4M, unique feature of gall midge resistance in the breeding line CR57-MR1523 was highlighted. Multi-location evaluation of F₃ families derived from the cross TN1 × CR57-MR1523 against different gall midge biotypes helped to identify a new dominant gene conferring resistance against GMB4. This gene has been designated as Gm11t. Though CR57-MR1523 has been extensively used in breeding gall midge resistant rice varieties like Suraksha, neither the genetics of resistance nor chromosomal location of the resistance gene(s) is known. In the present study we have tagged and mapped the new gall midge resistance gene, Gm11t, on chromosome 12, using SSR markers. To map the gene locus, 466 F₁₀ generation Recurrent Inbred Lines (RILs), from the cross of TN1 × CR57-MR1523 were used. Of the 471 SSR markers spread across the rice genome, 56 markers showed polymorphism and were used to screen a subset of the mapping population consisting of 10 resistant (R) and 10 susceptible (S) F₁₀ RILs. Six SSR markers, RM28706, RM235, RM17, RM28784, RM28574 and RM28564 on chromosome 12 were initially found to be associated with resistance and susceptibility. Based on the linkage analysis in selected 158 RILs, we were able to map the locus between two flanking SSR markers, RM28574 and RM28706, on chromosome 12 within 4.4 and 3.8 cM, respectively. Further, two NILs with 99% genetic similarity, were identified from the RILs which differed in gall midge resistance. The tightly linked flanking SSR markers will facilitate marker-assisted gene pyramiding and map-based cloning of the resistant gene. NILs would be valuable materials for functional analysis of the identified candidate gene.