Genetic diversity and relatedness of selected Iranian rice cultivars and disease resistance donors assayed by simple sequence repeats and candidate defense gene … (original) (raw)
Related papers
2003
Blast, Pyricularia grisea (Cooke) Sacc., is one of the most destructive diseases of rice worldwide and can result in significant reductions in yield. The use of resistant cultivars is the most economical and effective way of controlling rice blast. A variety of DNA markers, including plant defense-related candidate gene markers are available for genetic characterization and molecular analysis of rice. A set of 161 recombinant inbred lines, RILs, from a cross between Nemat, an improved and high yielding cultivar, and Anbarboo, a traditional and aromatic rice, was used to identify defense-related candidate gene, RFLP and SSR markers linked to components of resistance to blast, i.e. infection type, lesion density, the percent of diseased leaf area, and lesion size in rice. The RILs were tested using two single blast isolates in greenhouse, and field population of blast in blast nursery in International Rice Research Institute, Philippines, in 2000-2001. Of the 86 defense-related candidate gene, 153 RFLP, and SSR markers 26 defense-related candidate gene, 66 RFLP, and 85 SSR markers were polymorphic in two parental lines. Results showed that a defense gene, b8, a NBS-LRR originated from barley, closely linked to different components of resistance to blast. The defense genes of r5, r7, PrP2, and ERS from rice, maize, and Arabidopsis, respectively, have had minor effects on different components of resistance to blast. The RFLP markers, i.e. RZ536, RG351, RZ76, RZ397 on chromosomes 7, 11 and 12, and the SSR markers including RM224, RM179, and RM277 on chromosomes 11 and 12 were tightly linked to components of resistance to blast. The linked markers can now be used for resistance gene pyramiding and markerassisted selection in the breeding population. The results suggested the presence of race-specific resistance genes exhibiting strong differential pathogenhost interaction. We need to incorporate new sources of gene pool to make the genetic base broaden.
Theoretical and Applied Genetics, 2011
SHZ-2 is an indica rice cultivar that exhibits broad-spectrum resistance to rice blast; it is widely used as a resistance donor in breeding programs. To dissect the QTL responsible for broad-spectrum blast resistance, we crossed SHZ-2 to TXZ-13, a blast susceptible indica variety, to produce 244 BC 4 F 3 lines. These lines were evaluated for blast resistance in greenhouse and Weld conditions. Chromosomal introgressions from SHZ-2 into the TXZ-13 genome were identiWed using a single feature polymorphism microarray, SSR markers and gene-speciWc primers. Segregation analysis of the BC 4 F 3 population indicated that three regions on chromosomes 2, 6, and 9, designated as qBR2.1, qBR6.1, and qBR9.1, respectively, was associated with blast resistance and contributed 16.2, 14.9, and 22.3%, respectively, to the phenotypic variance of diseased leaf area (DLA). We further narrowed the three QTL regions using pairs of sister lines extracted from heterogeneous inbred families (HIF). Pairwise comparison of these lines enabled the determination of the relative contributions of individual QTL. The qBR9.1 conferred strong resistance, whereas qBR2.1 or qBR6.1 individually did not reduce disease under Weld conditions. However, when qBR2.1 and qBR6.1 were combined, they reduced disease by 19.5%, suggesting that small eVect QTLs contribute to reduction of epidemics. The qBR6.1 and qBR9.1 regions contain nucleotide-binding sites and leucine rich repeats (NBS-LRR) sequences, whereas the qBR2.1 did not. In the qBR6.1 region, the patterns of expression of adjacent NBS-LRR genes were consistent in backcross generations and correlated with blast resistance, supporting the hypothesis that multiple resistance genes within a QTL region can contribute to non-race-speciWc quantitative resistance. Communicated by M. Wissuwa.
Development and large-scale genotyping of single-nucleotide polymorphism (SNP) is required to use identified sequence variation in the alleles of different genes to determine their functional relevance to the candidate gene(s). In the present study, Illumina GoldenGate assay was used to validate and genotype SNPs in a set of six major rice blast resistance genes, viz. Pi-ta, Piz(t), Pi54, Pi9, Pi5(1) and Pib, distributed over five chromosomes, to understand their functional relevance and study the population structure in rice. All the selected SNPs loci (96) of six blast (Magnaporthe oryzae) resistance genes were genotyped successfully in 92 rice lines with an overall genotype call rate of 92.0 % and minimum GenTrain cutoff score of C0.448. The highest genotyped SNPs were found in japonica type (97.1 %) rice lines, followed by indica (92.12 %), indica basmati (91.84 %) and minimum in case of wild species (82.0 %). Among the genotyped loci, the highest score (98.68 %) was observed in case of Piz(t), followed by Pi-ta, Pi5(1), Pib, Pi54 and Pi9. Polymorphism was obtained in 87.5 % SNPs loci producing 7,728 genotype calls. Minor allele frequency ranged from 0.01 to 0.49 and has good differentiating power for distinguishing different rice accessions. Population structure analysis revealed that a set of genotypes from four rice subpopulations had ‘‘admix’’ ancestry ([26 %) with more than one genetic background of indica, japonica and wild types. SNPs markers were validated in a set of 92 rice lines and converted into CAPS markers which can be used in blast resistance breeding programme.
Genetics and Molecular Research, 2011
Among 120 simple sequence repeat (SSR) markers, 23 polymorphic markers were used to identify the segregation ratio in 320 individuals of an F 2 rice population derived from Pongsu Seribu 2, a resistant variety, and Mahsuri, a susceptible rice cultivar. For phenotypic study, the most virulent blast (Magnaporthe oryzae) pathotype, P7.2, was used in screening of F 2 population in order to understand the inheritance of blast resistance as well as linkage with SSR markers. Only 11 markers showed a good fit to the expected segregation ratio (1:2:1) for the single gene model (d.f. = 1.0, P < 0.05) in chi-square (χ 2) analyses. In the phenotypic data analysis, the F 2 population segregated in a 3:1 (R:S) ratio for resistant and susceptible plants, respectively. Therefore, resistance to blast pathotype P7.2 in Pongsu Seribu 2 is most likely controlled by a single nuclear gene. The plants from F 2 lines that showed resistance to blast pathotype P7.2 were linked to six alleles ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 10 (3): 1345-1355 (2011) S. Ashkani et al. of SSR markers, RM168 (116 bp), RM8225 (221 bp), RM1233 (175 bp), RM6836 (240 bp), RM5961 (129 bp), and RM413 (79 bp). These diagnostic markers could be used in marker assisted selection programs to develop a durable blast resistant variety.
Molecular tagging, allele mining and marker aided breeding for blast resistance in rice
BSN e-Bulletin, 2009
Breeding work utilizing both genotypic and phenotypic markers is the most effective way of achieving target. Molecular markers eg restriction fragment length polymorphism (RFLP), single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) tightly linked to target gene have been identified in different chromosomes to impose the genetic selection ie marker assisted selection (MAS). This paper summarize the progress and achievement made in breeding for blast resistance based on DNA markers which help in planning blast resistance gene tagging in Nepalese rice genotypes and developing blast resistant inbred line or near isogenic line (NIL). Blast fungus (Pyricularia oryzae Cav.) can infect plants at any growth stage from seedling to maturity and at any part eg leaf, node, internode, neck and seed. Qualitative resistance gene may occasionally be broken down due to numerous races of blast fungus both physiological and geographical races available in Nepal. Quantitative gene resistance and gene pyramiding are the best alternative for creating durable resistance system. At least 40 genes conferring resistance to blast isolates with multiple alleles have been described. Both dominant and recessive resistance alleles have been found in many rice landraces. Morphological and isozymic markers are limited in number. Therefore, highly polymorphic and easily detectable SSR markers are being used in breeding for blast resistance. Bulked segregant analysis (BSA) is the simple method for tagging resistance gene by SSR markers. Quantitative trait loci (QTLs) have also been mapped and most of them are linked to qualitative genes. SSR markers linked to the gene are being used to select plants possessing the desired trait and markers throughout the genome are being used to select plants that are genetically similar to recurrent parent. Using SSR markers it may be possible to select blast resistance genotypes at any stage of crop development from any small part of crop, to conduct many round of selection, to select without inoculums, without scoring, and without testing in hot spot or artificial inoculation. Molecular based blast resistance breeding work is initiated focusing on resistance gene tagging in Nepalese rice landraces and transferring resistance genes in cvs Jumli Marshi, Khumal-4 and Mansuli.
The present investigation was conducted at Rice Research and Training Center Sakha, Kafr El-Sheikh, Egypt during 2010, 2011 and 2012 seasons. Eight genotypes were chosen to study the inheritance of resistance to leaf blast disease which caused by Magnaporthe grisea, three genotypes from monogenic lines IRBLA-A, IRBL1-CL and IRBLTA2-PI (contain specific blast resistance genes; Pi-a, Pi-1 and Pi-ta-2, respectively) as well as five Egyptian varieties/ line namely; Giza177, Sakha101, Sakha105, Sakha104 and GZ6903. The Eight genotypes were evaluated against blast disease under both natural (field) and artificial (greenhouse) infection conditions using 5 virulent races. The results showed that Giza177, GZ6903, Sakha105 and IRBLTA2-PI were resistant under field and greenhouse conditions, except for Giza177 and GZ6903 both were infected by the race IA-77, and IRBLTA2-PI was infected by the race ID-15 under artificial inoculation. Moreover, Sakha104, Sakha101, IRBLA-A and IRBL1-CL showed susceptibility under field and greenhouse conditions. Line X tester design was used and comprised 15 F1 crosses. In F1 generation, thirteen resistant crosses were produced from resistant by resistant and resistant by susceptible parents. On the other hand, two susceptible crosses (IRBLA-A X Sakha104 and IRBLA-A X Sakha101) were produced by crossing susceptible X susceptible parents. In F2 generations, ten resistant crosses showed that; five crosses gave segregating ratio as 15 resistant (R) : 1 susceptible (S), and other five crosses gave segregating ratio as 3 R : 1 S. In addition, three resistant crosses showed no segregation for blast infection. The two susceptible crosses which produced from susceptible varieties showed no segregation. These results indicate that the parents (Giza177, Sakha105, GZ6903, IRBLA-A and IRBLTA2-PI) carry dominant genes for resistance and that resistance was completely dominant over susceptibility for blast disease. The blast resistance genes in those parents could be the same or allelic. The genes Pi-1and Pi-ta-2 were effective under Egyptian condition and can be used for improving blast resistance in breeding program. Estimation of general combining ability (GCA) and Specific combining ability (SCA) showed that GCA differed significantly from zero in most cases. High positive values of GCA effects would be interest in most traits under investigation. Seven out of the fifteen hybrid combinations showed highly significant negative SCA effects and ranged from (-1.622 to-10.200) for heading date. Also, three of the fifteen crosses (IRBLA-A X Sakha104, IRBL1-CL X Sakha105 and IRBLTA-PI X Sakha105) showed useful heterosis regarding better parent and mid parent for heading date. Key words: Inheritance, rice blast resistance genes, heterosis, combining ability, line X tester analysis.
Theoretical and Applied Genetics, 2004
An advanced backcross population consisting of 80 BC3F3 lines derived from rice vars. Vandana/Moroberekan was analysed for blast resistance and genotyped with 50 candidate genes and 23 simple sequence repeat (SSR) markers. Six candidate defence response genes [thaumatin, three nucleotide-binding site-leucine-rich repeat sequences from maize and two resistance gene analogue (RGA) markers] and one SSR marker (RM21) were significantly associated with partial blast resistance in rice (P=0.01). These markers accounted for phenotypic variation ranging from 9.6% to 29.4% and contributed to 76% of the total variation of percentage diseased leaf area (DLA) observed under natural infection. Four candidate genes (oxalate oxidase, 14-3-3 protein and two RGA markers) and four SSR markers (RM21, RM168, RM215 and RM250) were significantly associated with resistance to a single pathogen isolate, PO6-6. Among these, two markers were for DLA, five for lesion number and one for lesion size. These markers accounted for 9.1–28.7% of the phenotypic variation. A moderate correlation (r=0.48, P<0.01) was found between the level of partial resistance measured in the greenhouse and that measured under natural conditions. Analysis of BC3F4 progeny using genotypes of BC3F3 confirmed the phenotypic contribution of these markers. Cluster analysis of DNA profiles showed that the BC3 population was genetically similar (>85%) to the recurrent parent Vandana. Although no obvious relationship between DNA profiles and resistant phenotypes was observed, three lines (VM19, VM46 and VM76) in a cluster with high similarity to Vandana (89–96%) expressed a high level of partial blast resistance in the field. Analysis of disease progress in the field confirmed the performance of selected lines based on greenhouse and nursery analyses. The advanced backcross progeny with resistance phenotypes tagged by markers will be useful for accumulating blast resistance in upland rice.
Development of Dominant Rice Blast Resistance Gene Markers
Crop Science, 2003
genotypes can be easily identified (Huang et al., 1997; Hittalmani et al., 2000). A PCR-based Pi-ta gene marker Incorporation of resistance genes into existing rice (Oryza sativa is useful in marker-assisted selection breeding since it L.) cultivars is a powerful strategy and is commonly applied in breeding rice resistance to blast disease [caused by Pyricularia grisea Sacc. ϭ is the part of resistance gene, and is simple, rapid and P. oryzae Cavara (teleomorph: Magnaporthe grisea (Hebert) Barr)]. inexpensive and can be used for analyzing large numbers The rice blast resistance gene, Pi-ta, originally introgressed into japonof samples. The Pi-ta gene marker is important for rice ica from indica rice is important in breeding for rice blast resistance breeding program worldwide (Bryan et al., 2000; Hittalworldwide. In the southern USA, the rice cultivar Katy contains Pimani et al., 2000; Inukai et al., 1994). In the southern ta and is resistant to the predominant blast M. grisea races IB-49 and USA breeding programs, Katy, a japonica rice cultivar IC-17 and has been used as the blast resistant breeding parent. Three containing a tightly linked cluster of at least seven resispairs of DNA primers specific to the dominant indica Pi-ta gene were tance genes near the Pi-ta locus, has been used as a designed to amplify the Pi-ta DNA fragments by polymerase chain blast resistant parent (Chao et al., 1999; Moldenhauer reaction (PCR). PCR products amplified by these Pi-ta specific primet al., 1990). Resulting progenies, such as 'Drew' and ers were cloned and sequenced. Sequence analysis confirmed the presence of the dominant indica Pi-ta allele. These Pi-ta primers 'Kaybonnet', have been successfully released as U.S. were used to examine the presence of Pi-ta alleles in advanced Arkan-blast-resistant cultivars (Gravois et al., 1995; Moldensas rice breeding lines. The Pi-ta containing rice lines, as determined hauer et al., 1998). More breeding lines based on Katy, by PCR analysis, were resistant to both IB-49 and IC-17 in standard Drew, and Kaybonnet as parents are still in the early pathogenicity assays. In contrast, lines lacking the Pi-ta genes failed trials (K. Moldenhauer and J. Gibbons, per. commun.). to protect rice plants against both races IB-49 and IC-17. The presence The objectives of this research were to develop Pi-ta of Pi-ta markers correlated with the Pi-ta resistance spectrum. Thus, gene-specific primers to distinguish the dominant indica the Pi-ta gene markers provide a basis for stacking other blast resis-Pi-ta allele from the japonica pi-ta allele, to examine the tance genes into high yielding and good quality advanced breeding presence of Pi-ta in 10 advanced Arkansas rice breeding rice lines.
Identification and validation of rice blast resistance genes in Indian rice germplasm
Blast disease caused by Magnaporthe oryzae is a major constraint in rice production. Identification of new donors for blast resistance is a pre-requisite for effective utilization of diverse germplasm for marker assisted incorporation of blast resistance into improved varieties. Therefore, in the present study, a set of 100 diverse rice germplasm accessions were evaluated for 11 blast resistance genes namely Pikm, Pik, Pikh, Pi1, Pi5, Pi54, Pib, Piz5, Piz, Pi9 and Pish, both at genotypic and phenotypic level. Genotyping with gene based/ gene linked markers could identify six genotypes from the germplasm possessing as many as six resistance specific alleles. A total of 34 and 67 germplasm lines were found to possess resistance alleles for two genes, Pikm and Pik, respectively. Phenotypic validation using artificial inoculation in the germplasm was carried out with 4 diverse isolates under controlled conditions. The congruence between marker genotype and disease phenotype on a set of monogenic lines for blast resistance in the LTH background was used to compute Disease Resistance Index (DRI) in the germplasm. Cumulative DRI for each genotype was computed over all the marker loci. The genotypes Heibao, Kalinga-I, Vijetha, Anjali, Bhaubhog, Sada Kaijam, Kala Jeera had high cumulative resistance score. Allelic Cumulative Disease Resistance Index (ACDRI), a measure for comparing the effectiveness of markers was calculated and markers linked to Pikm, Pik, Piz5, Pi1 were found to possess higher accuracy and better correlation with expected patterns of resistance under artificial inoculation. Based on disease resistance index, 25 germplasm accessions were found carrying blast resistance specific alleles at different loci and were fully validated for disease phenotype, which are valuable in breeding for resistance, allele mining and functional genomics studies.