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Oliveira-Garcia E, Budot BO, Manangkil J, Lana FD, Angira B, Famoso A, Jia Y. An Efficient Method for Screening Rice Breeding Lines Against Races of Magnaporthe oryzae. Plant Dis 2024:PDIS05230922RE. [PMID: 37807096 DOI: 10.1094/pdis-05-23-0922-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Rice blast, caused by Magnaporthe oryzae, is the most destructive rice disease worldwide. The disease symptoms are usually expressed on the leaf and panicle. The leaf disease intensity in controlled environmental conditions is frequently quantified using a 0 to 5 scale, where 0 represents the absence of symptoms, and 5 represents large eyespot lesions. However, this scale restricts the qualitative classification of the varieties into intermediate resistant and susceptible categories. Here, we develop a 0 to 6 scale for blast disease that allows proper assignment of rice breeding lines and varieties into six resistance levels (highly resistant, resistant, moderately resistant, moderately susceptible, susceptible, and highly susceptible). We evaluated 40 common rice varieties against four major blast races (IB1, IB17, IB49, and IE1-K). Varieties carrying the Pi-ta gene were either highly resistant, resistant, or moderately resistant to IB17. The IE1-K race was able to break Pi-ta-mediated resistance of the rice varieties. The Pi-z gene conferred resistance to the IB17 and IE1-K races. The varieties M201, Cheniere, and Frontier were highly susceptible (score 6; 100% disease) to the race IE1-K. Moreover, varieties that were resistant or susceptible to all four blast races also showed similar levels of resistance/susceptibility to blast disease in the field. Taken together, our data proved that the 0 to 6 blast scale can efficiently determine the resistance levels of rice varieties against major blast races. This robust method will assist rice breeding programs to incorporate durable resistance against major and emerging blast races.[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Ely Oliveira-Garcia
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, U.S.A
| | - Bernard Orense Budot
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, U.S.A
- University of the Philippines Los Baños, Los Baños, Philippines
| | - Jennifer Manangkil
- H. Rouse Caffey Rice Research Station, Louisiana State University Agricultural Center, LA 70578, U.S.A
| | - Felipe Dala Lana
- H. Rouse Caffey Rice Research Station, Louisiana State University Agricultural Center, LA 70578, U.S.A
| | - Brijesh Angira
- H. Rouse Caffey Rice Research Station, Louisiana State University Agricultural Center, LA 70578, U.S.A
| | - Adam Famoso
- H. Rouse Caffey Rice Research Station, Louisiana State University Agricultural Center, LA 70578, U.S.A
| | - Yulin Jia
- Dale Bumpers National Rice Research Center, USDA-ARS, Stuttgart, AR 72160, U.S.A
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Kumar A, Thomas J, Gill N, Dwiningsih Y, Ruiz C, Famoso A, Pereira A. Molecular mapping and characterization of QTLs for grain quality traits in a RIL population of US rice under high nighttime temperature stress. Sci Rep 2023; 13:4880. [PMID: 36966148 PMCID: PMC10039871 DOI: 10.1038/s41598-023-31399-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 03/10/2023] [Indexed: 03/27/2023] Open
Abstract
Elevated nighttime temperatures resulting from climate change significantly impact the rice crop worldwide. The rice (Oryza sativa L.) plant is highly sensitive to high nighttime temperature (HNT) during grain-filling (reproductive stage). HNT stress negatively affects grain quality traits and has a major impact on the value of the harvested rice crop. In addition, along with grain dimensions determining rice grain market classes, the grain appearance and quality traits determine the rice grain market value. During the last few years, there has been a major concern for rice growers and the rice industry over the prevalence of rice grains opacity and the reduction of grain dimensions affected by HNT stress. Hence, the improvement of heat-stress tolerance to maintain grain quality of the rice crop under HNT stress will bolster future rice value in the market. In this study, 185 F12-recombinant inbred lines (RILs) derived from two US rice cultivars, Cypress (HNT-tolerant) and LaGrue (HNT-sensitive) were screened for the grain quality traits grain length (GL), grain width (GW), and percent chalkiness (%chalk) under control and HNT stress conditions and evaluated to identify the genomic regions associated with the grain quality traits. In total, there were 15 QTLs identified; 6 QTLs represented under control condition explaining 3.33% to 8.27% of the phenotypic variation, with additive effects ranging from - 0.99 to 0.0267 on six chromosomes and 9 QTLs represented under HNT stress elucidating 6.39 to 51.53% of the phenotypic variation, with additive effects ranging from - 8.8 to 0.028 on nine chromosomes for GL, GW, and % chalk. These 15 QTLs were further characterized and scanned for natural genetic variation in a japonica diversity panel (JDP) to identify candidate genes for GL, GW, and %chalk. We found 6160 high impact single nucleotide polymorphisms (SNPs) characterized as such depending on their type, region, functional class, position, and proximity to the gene and/or gene features, and 149 differentially expressed genes (DEGs) in the 51 Mbp genomic region comprising of the 15 QTLs. Out of which, 11 potential candidate genes showed high impact SNP associations. Therefore, the analysis of the mapped QTLs and their genetic dissection in the US grown Japonica rice genotypes at genomic and transcriptomic levels provide deep insights into genetic variation beneficial to rice breeders and geneticists for understanding the mechanisms related to grain quality under heat stress in rice.
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Affiliation(s)
- Anuj Kumar
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Julie Thomas
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Navdeep Gill
- Department of Biological Sciences, Nova Southeastern University, Fort Lauderdale, FL, 33314, USA
| | - Yheni Dwiningsih
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Charles Ruiz
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Adam Famoso
- H. Rouse Caffey Rice Research Station, Louisiana State University Agricultural Center, Rayne, LA, 70578, USA
| | - Andy Pereira
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA.
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Ontoy JC, Shrestha B, Karki HS, Barphagha I, Angira B, Famoso A, Ham JH. Genetic Characterization of the Partial Disease Resistance of Rice to Bacterial Panicle Blight and Sheath Blight by Combined QTL Linkage and QTL-seq Analyses. Plants (Basel) 2023; 12:559. [PMID: 36771643 PMCID: PMC9920235 DOI: 10.3390/plants12030559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/09/2023] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Bacterial panicle blight (BPB) and sheath blight (SB) are major diseases of rice and few cultivars have shown a high level of resistance to these diseases. A recombinant inbred line (RIL) population developed from the U.S. cultivars Jupiter (moderately resistant) and Trenasse (susceptible) was investigated to identify loci associated with the partial disease resistance to BPB and SB. Disease phenotypes in BPB and SB, as well as the days-to-heading (DTH) trait, were evaluated in the field. DTH was correlated to BPB and SB diseases, while BPB was positively correlated to SB in the field trials with this RIL population. Genotyping was performed using Kompetitive Allele Specific PCR (KASP) assays and whole-genome sequence (WGS) analyses. Quantitative trait locus (QTL) mapping and bulk segregant analysis using a set of WGS data (QTL-seq) detected a major QTL on the upper arm of chromosome 3 for BPB, SB, and DTH traits within the 1.0-1.9 Mb position. Additional QTLs associated with BPB and SB were also identified from other chromosomes by the QTL-seq analysis. The QTLs identified in this study contain at least nine candidate genes that are predicted to have biological functions in defense or flowering. These findings provide an insight into the complex nature of the quantitative resistance to BPB and SB, which may also be closely linked to the flowering trait.
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Affiliation(s)
- John Christian Ontoy
- Department of Plant Pathology and Crop Physiology, LSU AgCenter, Baton Rouge, LA 70803, USA
- Department of Plant Pathology and Crop Physiology, College of Agriculture, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Bishnu Shrestha
- Department of Plant Pathology and Crop Physiology, LSU AgCenter, Baton Rouge, LA 70803, USA
- Department of Plant Pathology and Crop Physiology, College of Agriculture, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Hari Sharan Karki
- Department of Plant Pathology and Crop Physiology, LSU AgCenter, Baton Rouge, LA 70803, USA
- Department of Plant Pathology and Crop Physiology, College of Agriculture, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Inderjit Barphagha
- Department of Plant Pathology and Crop Physiology, LSU AgCenter, Baton Rouge, LA 70803, USA
| | - Brijesh Angira
- H. Rouse Caffey Rice Research Station, LSU AgCenter, Rayne, LA 70578, USA
| | - Adam Famoso
- H. Rouse Caffey Rice Research Station, LSU AgCenter, Rayne, LA 70578, USA
| | - Jong Hyun Ham
- Department of Plant Pathology and Crop Physiology, LSU AgCenter, Baton Rouge, LA 70803, USA
- Department of Plant Pathology and Crop Physiology, College of Agriculture, Louisiana State University, Baton Rouge, LA 70803, USA
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Morales KY, Singh N, Perez FA, Ignacio JC, Thapa R, Arbelaez JD, Tabien RE, Famoso A, Wang DR, Septiningsih EM, Shi Y, Kretzschmar T, McCouch SR, Thomson MJ. An improved 7K SNP array, the C7AIR, provides a wealth of validated SNP markers for rice breeding and genetics studies. PLoS One 2020; 15:e0232479. [PMID: 32407369 PMCID: PMC7224494 DOI: 10.1371/journal.pone.0232479] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 04/15/2020] [Indexed: 11/25/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are highly abundant, amendable to high-throughput genotyping, and useful for a number of breeding and genetics applications in crops. SNP frequencies vary depending on the species and populations under study, and therefore target SNPs need to be carefully selected to be informative for each application. While multiple SNP genotyping systems are available for rice (Oryza sativa L. and its relatives), they vary in their informativeness, cost, marker density, speed, flexibility, and data quality. In this study, we report the development and performance of the Cornell-IR LD Rice Array (C7AIR), a second-generation SNP array containing 7,098 markers that improves upon the previously released C6AIR. The C7AIR is designed to detect genome-wide polymorphisms within and between subpopulations of O. sativa, as well as O. glaberrima, O. rufipogon and O. nivara. The C7AIR combines top-performing SNPs from several previous rice arrays, including 4,007 SNPs from the C6AIR, 2,056 SNPs from the High Density Rice Array (HDRA), 910 SNPs from the 384-SNP GoldenGate sets, 189 SNPs from the 44K array selected to add information content for elite U.S. tropical japonica rice varieties, and 8 trait-specific SNPs. To demonstrate its utility, we carried out a genome-wide association analysis for plant height, employing the C7AIR across a diversity panel of 189 rice accessions and identified 20 QTLs contributing to plant height. The C7AIR SNP chip has so far been used for genotyping >10,000 rice samples. It successfully differentiates the five subpopulations of Oryza sativa, identifies introgressions from wild and exotic relatives, and is useful for quantitative trait loci (QTL) and association mapping in diverse materials. Moreover, data from the C7AIR provides valuable information that can be used to select informative and reliable SNP markers for conversion to lower-cost genotyping platforms for genomic selection and other downstream applications in breeding.
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Affiliation(s)
- Karina Y. Morales
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Namrata Singh
- Plant Breeding and Genetics Section, School of Integrative Plant Sciences, Cornell University, Ithaca, New York, United States of America
| | - Francisco Agosto Perez
- Plant Breeding and Genetics Section, School of Integrative Plant Sciences, Cornell University, Ithaca, New York, United States of America
| | - John Carlos Ignacio
- Rice Breeeding Platform, International Rice Research Institute, Los Baños, Philippines
| | - Ranjita Thapa
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Juan D. Arbelaez
- Rice Breeeding Platform, International Rice Research Institute, Los Baños, Philippines
| | - Rodante E. Tabien
- Texas A&M AgriLife Research Center, Beaumont, TX, United States of America
| | - Adam Famoso
- Louisiana State University Ag Center, H. Rouse Caffey Rice Research Station, Rayne, LA, United States of America
| | - Diane R. Wang
- Plant Breeding and Genetics Section, School of Integrative Plant Sciences, Cornell University, Ithaca, New York, United States of America
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Yuxin Shi
- Plant Breeding and Genetics Section, School of Integrative Plant Sciences, Cornell University, Ithaca, New York, United States of America
| | - Tobias Kretzschmar
- Rice Breeeding Platform, International Rice Research Institute, Los Baños, Philippines
| | - Susan R. McCouch
- Plant Breeding and Genetics Section, School of Integrative Plant Sciences, Cornell University, Ithaca, New York, United States of America
- * E-mail: (MJT); (SRM)
| | - Michael J. Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, United States of America
- * E-mail: (MJT); (SRM)
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