scholarly journals Epistasis and Quantitative Resistance to Pyricularia oryzae Revealed by GWAS in Advanced Rice Breeding Populations

Agriculture ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 622
Author(s):  
Juan E. Rosas ◽  
Maia Escobar ◽  
Sebastián Martínez ◽  
Pedro Blanco ◽  
Fernando Pérez ◽  
...  
Keyword(s):  
Genetic Background ◽  
Blast Resistance ◽  
Quantitative Resistance ◽  
Major Effect ◽  
Inbred Lines ◽  
Phenotypic Variance ◽  
Rice Breeding ◽  
Tropical Japonica ◽  
Breeding Populations ◽  
Multilocus Model

Rice blast caused by Pyricularia oryzae is a major rice disease worldwide. Despite the detailed knowledge on major resistance genes available to date, little is known about how these genes interact with quantitative blast resistance loci and with the genetic background. Knowledge on these interactions is crucial for assessing the usefulness of introgressed resistance loci in breeding germplasm. Our goal was to identify quantitative trait loci (QTL) for blast resistance in rice breeding populations and to describe how they interact among each other and with the genetic background. To that end, resistance to blast was mapped by genome-wide association study (GWAS) in two advanced rice breeding subpopulations, one made of 305 indica type inbred lines, and the other of 245 tropical japonica inbred lines. The interactions and main effects of blast resistance loci were assessed in a multilocus model. Well known, major effect blast resistance gene clusters were detected in both tropical japonica (Pii/Pi3/Pi5) and indica (Piz/Pi2/Pi9) subpopulations with the GWAS scan 1. When these major effect loci were included as fixed cofactors in subsequent GWAS scans 2 and 3, additional QTL and more complex genetic architectures were revealed. The multilocus model for the tropical japonica subpopulation showed that Pii/Pi3/Pi5 had significant interaction with two QTL in chromosome 1 and one QTL in chromosome 8, together explaining 64% of the phenotypic variance. In the indica subpopulation a significant interaction among the QTL in chromosomes 6 and 4 and the genetic background, together with Piz/Pi2/Pi9 and QTL in chromosomes 1, 4 and 7, explained 35% of the phenotypic variance. Our results suggest that epistatic interactions can play a major role modulating the response mediated by major effect blast resistance loci such as Pii/Pi3/Pi5. Furthermore, the additive and epistatic effects of multiple QTL bring additional layers of quantitative resistance with a magnitude comparable to that of major effect loci. These findings highlight the need of genetic background-specific validation of markers for molecular assisted blast resistance breeding and provide insights for developing quantitative resistance to blast disease in rice.

scholarly journals Epistasis and Quantitative Resistance to Pyricularia oryzae Revealed by GWAS in Advanced Rice Breeding Populations

2020 ◽  
Author(s):  
Juan Eduardo Rosas ◽  
Maia Escobar ◽  
Sebastián Martínez ◽  
Pedro Blanco ◽  
Fernando Pérez ◽  
...  
Keyword(s):  
Genetic Background ◽  
Blast Resistance ◽  
Quantitative Resistance ◽  
Major Effect ◽  
Inbred Lines ◽  
Phenotypic Variance ◽  
Rice Breeding ◽  
Tropical Japonica ◽  
Breeding Populations ◽  
Multilocus Model

Abstract Background: Rice blast caused by Pyricularia oryzae is a major rice disease worldwide. Despite the detailed knowledge on major resistance genes available to date, little is known about how these genes interact with quantitative blast resistance loci and with the genetic background. Knowledge on these interactions is crucial for assessing the usefulness of introgressed resistance loci in breeding germplasm. Our goal was to identify blast resistance loci in rice breeding populations and to describe how they interact among each other and with the genetic background. To that end, resistance to blast was mapped in two advanced rice breeding populations, one made of 305 indica type inbred lines, and the other of 245 tropical japonica inbred lines. The interactions and main effects of blast resistance loci were assessed in a multilocus model. Results: Well known, major effect blast resistance gene clusters were detected in both tropical japonica (Pii/Pi3/Pi5) and indica (Piz/Pi2/Pi9) populations with the GWAS scan 1. When these major effect loci were included as fixed cofactors in subsequent GWAS scans 2 and 3, additional QTL and more complex genetic architectures were revealed. The multilocus model for the tropical japonica population showed that Pii/Pi3/Pi5 had significant interaction with two QTL in chromosome 1 and one QTL in chromosome 8, together explaining 64% of the phenotypic variance. In the indica population a significant interaction among the QTL in chromosomes 6 and 4 and the genetic background, together with Piz/Pi2/Pi9 and QTL in chromosomes 1, 4 and 7, explained 35% of the phenotypic variance.Conclusions: Our results suggest that epistatic interactions can play a major role modulating the effect of major effect blast resistance loci such as Pii/Pi3/Pi5. Furthermore, the additive and epistatic effects of multiple QTL bring additional layers of quantitative resistance with a magnitude comparable to that of major effect loci. These findings highlight the need of genetic background-specific validation of markers for molecular assisted blast resistance breeding and provide insights for developing quantitative resistance to blast disease in rice.

scholarly journals Resistance in Rice Breeding Lines to the Blast Fungus in Nepal

1970 ◽  
Vol 6 ◽  
pp. 49-56 ◽  
Author(s):  
Bedanand Chaudhary ◽  
Sundar M Shrestha ◽  
Ram C Sharma
Keyword(s):  
Field Condition ◽  
Blast Resistance ◽  
Quantitative Resistance ◽  
Rice Breeding ◽  
Breeding Lines ◽  
Research Journal ◽  
Neck Blast ◽  
Upland Field ◽  
Major Resistance Genes ◽  
Greenhouse Assay

A total of 36 rice breeding lines including checks were evaluated for resistance to blast atRampur during 2000-2001. The experiments were conducted under both field condition andgreenhouse inoculated condition. Qualitative resistance in rice to blast was assessed based onlesion type, whereas quantitative resistance was assessed based on area under disease progresscurve (AUDPC) in the upland field condition. The number of sporulating lesions and the numberof leaves with at least one sporulating lesion per plant were considered as measures forevaluation of quantitative resistance in the greenhouse assay. The lesion type, neck blastpercentage and AUDPC data suggest that most of the rice lines possess higher level of resistanceto leaf and neck blast. The rice lines varied for the number of sporulating lesions and the numberof leaves with sporulating lesion per plant. Some lines were incompatible to virulent blastisolates, showing major resistance genes. NR 1558, NR 601-1-1-9, BW306-2 and CN 836-3-10were promising lines for quantitative resistance to both leaf and neck blast. Radha 12, Sabitri,Janaki possess higher level of quantitative resistance to blast, hence these could be promoted forcultivation in blast-prone environments. These genotypes could also be utilized as donor parentsfor breeding durable blast resistant varieties. The most virulent blast isolate could be used forevaluation of both qualitative and quantitative resistance to blast in early generation in thegreenhouse so that workload could be cut down in future works.Key words: Blast resistance; field condition; greenhouse assay; Pyricularia grisea; rice linesDOI: 10.3126/narj.v6i0.3344Nepal Agriculture Research Journal Vol.6 2005 pp.49-56

A set of near-isogenic lines for blast resistance genes with an Indica-type rainfed lowland elite rice (Oryza sativa L.) genetic background

2011 ◽  
Vol 123 (1) ◽  
pp. 19-27 ◽  
Author(s):  
Yohei Koide ◽  
Leodegario A. Ebron ◽  
Hiroshi Kato ◽  
Hiroshi Tsunematsu ◽  
Mary Jeanie Telebanco-Yanoria ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Resistance Genes ◽  
Genetic Background ◽  
Oryza Sativa L ◽  
Blast Resistance ◽  
Near Isogenic Lines ◽  
Isogenic Lines ◽  
Rainfed Lowland ◽  
Blast Resistance Genes

scholarly journals The impact of genetic background and cell lineage on the level and pattern of gene expression in position effect variegation

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Sidney H. Wang ◽  
Sarah C. R. Elgin
Keyword(s):  
Genetic Variants ◽  
Genetic Background ◽  
Position Effect ◽  
Cell Lineage ◽  
Inbred Lines ◽  
Position Effect Variegation ◽  
Fourth Chromosome ◽  
Heterochromatin Formation ◽  
Effect Variegation ◽  
The Impact

Abstract Background Chromatin-based transcriptional silencing is often described as a stochastic process, largely because of the mosaic expression observed in position effect variegation (PEV), where a euchromatic reporter gene is silenced in some cells as a consequence of juxtaposition with heterochromatin. High levels of variation in PEV phenotypes are commonly observed in reporter stocks. To ascertain whether background mutations are the major contributors to this variation, we asked how much of the variation is determined by genetic variants segregating in the population, examining both the level and pattern of expression using the fruit fly, Drosophila melanogaster, as the model. Results Using selective breeding of a fourth chromosome PEV reporter line, 39C-12, we isolated two inbred lines exhibiting contrasting degrees of variegation (A1: low expression, D1: high expression). Within each inbred population, remarkable similarity is observed in the degree of variegation: 90% of the variation between the two inbred lines in the degree of silencing can be explained by genotype. Further analyses suggest that this result reflects the combined effect of multiple independent trans-acting loci. While the initial observations are based on a PEV phenotype scored in the fly eye (hsp70-white reporter), similar degrees of silencing were observed using a beta-gal reporter scored across the whole fly. Further, the pattern of variegation becomes almost identical within each inbred line; significant pigment enrichment in the same quadrant of the eye was found for both A1 and D1 lines despite different degrees of expression. Conclusions The results indicate that background genetic variants play the major role in determining the variable degrees of PEV commonly observed in laboratory stocks. Interestingly, not only does the degree of variegation become consistent in inbred lines, the patterns of variegation also appear similar. Combining these observations with the spreading model for local heterochromatin formation, we propose an augmented stochastic model to describe PEV in which the genetic background drives the overall level of silencing, working with the cell lineage-specific regulatory environment to determine the on/off probability at the reporter locus in each cell. This model acknowledges cell type-specific events in the context of broader genetic impacts on heterochromatin formation.

scholarly journals Colour plasticity in response to social context and parasitic infection in a self-fertilizing fish

2019 ◽  
Vol 6 (7) ◽  
pp. 181418
Author(s):  
Rebecca Jane Pawluk ◽  
Carlos Garcia de Leaniz ◽  
Joanne Cable ◽  
Bernard Tiddeman ◽  
Sofia Consuegra
Keyword(s):  
Social Context ◽  
Individual Variation ◽  
Genetic Background ◽  
Social Dynamics ◽  
Parasitic Infection ◽  
Natural Populations ◽  
Data Interpretation ◽  
Inbred Lines ◽  
Body Coloration ◽  
Pathogen Avoidance

Many animal species rely on changes in body coloration to signal social dominance, mating readiness and health status to conspecifics, which can in turn influence reproductive success, social dynamics and pathogen avoidance in natural populations. Such colour changes are thought to be controlled by genetic and environmental conditions, but their relative importance is difficult to measure in natural populations, where individual genetic variability complicates data interpretation. Here, we studied shifts in melanin-related body coloration in response to social context and parasitic infection in two naturally inbred lines of a self-fertilizing fish to disentangle the relative roles of genetic background and individual variation. We found that social context and parasitic infection had a significant effect on body coloration that varied between genetic lines, suggesting the existence of genotype by environment interactions. In addition, individual variation was also important for some of the colour attributes. We suggest that the genetic background drives colour plasticity and that this can maintain phenotypic variation in inbred lines, an adaptive mechanism that may be particularly important when genetic diversity is low.

scholarly journals Fine mapping of a panicle blast resistance gene Pb-bd1 in Japonica landrace Bodao and its application in rice breeding

Rice ◽  
2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Nengyan Fang ◽  
Xiaorui Wei ◽  
Lingtong Shen ◽  
Yao Yu ◽  
Mengya Li ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Fine Mapping ◽  
Blast Resistance ◽  
Rice Breeding ◽  
Blast Resistance Gene ◽  
Panicle Blast

scholarly journals Coevolutionary Dynamics of Rice Blast Resistance Gene Pi-ta and Magnaporthe oryzae Avirulence Gene AVR-Pita 1

2016 ◽  
Vol 106 (7) ◽  
pp. 676-683 ◽  
Author(s):  
Yulin Jia ◽  
Erxun Zhou ◽  
Seonghee Lee ◽  
Tracy Bianco
Keyword(s):  
Magnaporthe Oryzae ◽  
Marker Assisted Selection ◽  
Defense Mechanism ◽  
Allelic Variation ◽  
Blast Resistance ◽  
Quantitative Resistance ◽  
Association Studies ◽  
The United States ◽  
Avirulence Gene ◽  
Genome Wide Association Studies

The Pi-ta gene in rice is effective in preventing infections by Magnaporthe oryzae strains that contain the corresponding avirulence gene, AVR-Pita1. Diverse haplotypes of AVR-Pita1 have been identified from isolates of M. oryzae from rice production areas in the United States and worldwide. DNA sequencing and mapping studies have revealed that AVR-Pita1 is highly unstable, while expression analysis and quantitative resistance loci mapping of the Pi-ta locus revealed complex evolutionary mechanisms of Pi-ta-mediated resistance. Among these studies, several Pi-ta transcripts were identified, most of which are probably derived from alternative splicing and exon skipping, which could produce functional resistance proteins that support a new concept of coevolution of Pi-ta and AVR-Pita1. User-friendly DNA markers for Pi-ta have been developed to support marker-assisted selection, and development of new rice varieties with the Pi-ta markers. Genome-wide association studies revealed a link between Pi-ta-mediated resistance and yield components suggesting that rice has evolved a complicated defense mechanism against the blast fungus. In this review, we detail the current understanding of Pi-ta allelic variation, its linkage with rice productivity, AVR-Pita allelic variation, and the coevolution of Pi-ta and AVR-Pita in Oryza species and M. oryzae populations, respectively. We also review the genetic and molecular basis of Pi-ta and AVR-Pita interaction, and its value in marker-assisted selection and engineering resistance.

scholarly journals Fine Mapping of a New Race-Specific Blast Resistance Gene, Pi-hk2, in Japonica Heikezijing from Taihu Region of China

2017 ◽  
Vol 107 (1) ◽  
pp. 84-91 ◽  
Author(s):  
Wanwan He ◽  
Nengyan Fang ◽  
Ruisen Wang ◽  
Yunyu Wu ◽  
Guoying Zeng ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Fine Mapping ◽  
Broad Spectrum ◽  
Blast Resistance ◽  
Recombinant Inbred Lines ◽  
Japonica Rice ◽  
Phenotypic Variance ◽  
Chromosome 11 ◽  
Essential Information ◽  
Broad Spectrum Resistance

Heikezijing, a japonica rice landrace from the Taihu region of China, exhibited broad-spectrum resistance to more than 300 isolates of the blast pathogen (Magnaporthe oryzae). In our previous research, we fine mapped a broad-spectrum resistance gene, Pi-hk1, in chromosome 11. In this research, 2010-9(G1), one of the predominant races of blast in the Taihu Lake region of China, was inoculated into 162 recombinant inbred lines (RIL) and two parents, Heikezijing and Suyunuo, for mapping the resistance-blast quantitative trait loci (QTL). Three QTL (Lsqtl4-1, Lsqtl9-1, and Lsqtl11-1) associated with lesion scores were detected on chromosomes 4, 9, and 11 and two QTL (Lnqtl1-1 and Lnqtl9-1) associated with average lesion numbers were detected on chromosomes 1 and 9. The QTL Lsqtl9-1 conferring race-specific resistance to 2010-9(G1) at seedling stages showed logarithm of the odds scores of 9.10 and phenotypic variance of 46.19% and might be a major QTL, named Pi-hk2. The line RIL84 with Pi-hk2 derived from a cross between Heikezijing and Suyunuo was selected as Pi-hk2 gene donor for developing fine mapping populations. According to the resistance evaluation of recombinants of three generations (BC1F2, BC1F3, and BC1F4), Pi-hk2 was finally mapped to a 143-kb region between ILP-19 and RM24048, and 18 candidate genes were predicted, including genes that encode pleiotropic drug resistance protein 4 (n = 2), WRKY74 (n = 1), cytochrome b5-like heme/steroid-binding domain containing protein (n = 1), protein kinase (n = 1), and ankyrin repeat family protein (n = 1). These results provide essential information for cloning of Pi-hk2 and its potential utility in breeding resistant rice cultivars by marker-assisted selection.

scholarly journals Genotyping-by-Sequencing-Based Genetic Analysis of African Rice Cultivars and Association Mapping of Blast Resistance Genes Against Magnaporthe oryzae Populations in Africa

2017 ◽  
Vol 107 (9) ◽  
pp. 1039-1046 ◽  
Author(s):  
Emmanuel M. Mgonja ◽  
Chan Ho Park ◽  
Houxiang Kang ◽  
Elias G. Balimponya ◽  
Stephen Opiyo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Association Mapping ◽  
Magnaporthe Oryzae ◽  
Rice Blast ◽  
Blast Resistance ◽  
Genotyping By Sequencing ◽  
Rice Breeding ◽  
Rice Cultivars ◽  
R Genes ◽  
African Rice

Understanding the genetic diversity of rice germplasm is important for the sustainable use of genetic materials in rice breeding and production. Africa is rich in rice genetic resources that can be utilized to boost rice productivity on the continent. A major constraint to rice production in Africa is rice blast, caused by the hemibiotrophic fungal pathogen Magnaporthe oryzae. In this report, we present the results of a genotyping-by-sequencing (GBS)-based diversity analysis of 190 African rice cultivars and an association mapping of blast resistance (R) genes and quantitative trait loci (QTLs). The 190 African cultivars were clustered into three groups based on the 184K single nucleotide polymorphisms generated by GBS. We inoculated the rice cultivars with six African M. oryzae isolates. Association mapping identified 25 genomic regions associated with blast resistance (RABRs) in the rice genome. Moreover, PCR analysis indicated that RABR_23 is associated with the Pi-ta gene on chromosome 12. Our study demonstrates that the combination of GBS-based genetic diversity population analysis and association mapping is effective in identifying rice blast R genes/QTLs that contribute to resistance against African populations of M. oryzae. The identified markers linked to the RABRs and 14 highly resistant cultivars in this study will be useful for rice breeding in Africa.

scholarly journals Some genetic tests on asymmetry of sternopleural chaeta number in Drosophila

1960 ◽  
Vol 1 (1) ◽  
pp. 151-172 ◽  
Author(s):  
E. C. R. Reeve
Keyword(s):  
Genetic Effect ◽  
Inbred Lines ◽  
Progeny Test ◽  
Published Data ◽  
Phenotypic Variance ◽  
Genetic Tests ◽  
Wild Stock ◽  
The Pacific ◽  
The Asymmetry ◽  
Change In Mean

1. Published data suggest that mean left-right asymmetry in number of sternopleural bristles of D. melanogaster declines when inbred lines are crossed, while the corresponding variance for sternite bristles remains unchanged. Some genetic tests were undertaken to analyse this difference in behaviour of the two characters.2. A progeny test on a wild stock showed that a small amount of genetic variance in sternopleural asymmetry was present, equivalent to about 2% of the total phenotypic variance.3. It was possible to increase and decrease the level of sternopleural asymmetry in two wild stocks by selection. These experiments gave an estimated heritability of some 2–3%, in close agreement with the progeny test. Change in asymmetry did not necessarily lead to a change in mean count.4. Homozygous lines, consisting of individual third chromosomes from the Renfrew wild stock made homozygous in an inbred line genetic background, were intercrossed, and the average indices for a number of characters of eight inter crosses involving eight lines were compared with their mid-parent averages. Thorax length was 2% greater and its variance 32% less in the crosses; total sternopleural count and its variance did not change significantly, but the asymmetry variance declined by 18%. In contrast, the corresponding asymmetry or independent variance for numbers of sternite bristles was 6% higher in the crosses, although the total sternite count and its variance did not change. These results fit in with previous work.5. Tests on a similar set of homozygous lines in which the third chromosomes came from the SP wild stock, and on some long inbred lines from the Pacific wild stock, gave discordant results. Of eight SP lines examined, four were homozygous for a gene polychaetoid, and four were homozygous for a genetic effect causing sockets without bristles to occur among the sternopleurals. Both types had much greater sternopleural variance and asymmetry than the Renfrew lines, and both indices declined sharply in intercrosses leaving these genetic effects heterozygous, but neither declined if they were left homozygous in the crosses. Similarly high sternopleural variances were found in the Pacific lines, but only the total variance declined in males and only the asymmetry variance declined in the females, when they were intercrossed. All the four Pacific lines tested appeared to be homozygous for a genetic effect which caused a variable number of dorso-central and scutellar bristles to be replaced by sockets without bristles, and an occasional extra scutellar bristle to appear. This effect was also probably responsible for the high sternopleural variances.6. Males of the Pacific inbred lines and intercrosses were compared when reared on the normal live medium and on a synthetic diet in reduced concentration, which reduced body-size by 23% (thorax area). The inbred lines were reduced more than the F1's in total sternopleural count and its variance, but the F1's were reduced more in sternopleural asymmetry, by the restricted diet.7. The problems of interpreting these experiments, in view of our ignorance of the biological functions and attributes of the sternopleural and sternite bristles, are discussed. It is concluded that we have no basis yet for deciding whether sternopleural bristle number is of adaptive significance, but this is considered improbable.8. The experimental evidence suggests that sternopleural asymmetry cannot be considered a measure of general developmental stability, particularly as the level of asymmetry can be reduced by selection well below that of typical wild stocks.9. The scaling problems arising when the mean asymmetry of lines with different mean counts are to be compared, are examined, and it is suggested that the ratio of asymmetry to total count does not eliminate scale effects.10. Developmental and anatomical differences between the sternopleural and sternite bristles suggest a possible reason why they behave differently when inbred lines are intercrossed.

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