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Zhai R, Huang A, Mo R, Zou C, Wei X, Yang M, Tan H, Huang K, Qin J. SNP-based bulk segregant analysis revealed disease resistance QTLs associated with northern corn leaf blight in maize. Front Genet 2022; 13:1038948. [PMID: 36506330 PMCID: PMC9732028 DOI: 10.3389/fgene.2022.1038948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/31/2022] [Indexed: 11/27/2022] Open
Abstract
Maize (Zea mays L.) is the most important food security crop worldwide. Northern corn leaf blight (NCLB), caused by Exserohilum turcicum, severely reduces production causing millions of dollars in losses worldwide. Therefore, this study aimed to identify significant QTLs associated with NCLB by utilizing next-generation sequencing-based bulked-segregant analysis (BSA). Parental lines GML71 (resistant) and Gui A10341 (susceptible) were used to develop segregating population F2. Two bulks with 30 plants each were further selected from the segregating population for sequencing along with the parental lines. High throughput sequencing data was used for BSA. We identified 10 QTLs on Chr 1, Chr 2, Chr 3, and Chr 5 with 265 non-synonymous SNPs. Moreover, based on annotation information, we identified 27 candidate genes in the QTL regions. The candidate genes associated with disease resistance include AATP1, At4g24790, STICHEL-like 2, BI O 3-BIO1, ZAR1, SECA2, ABCG25, LECRK54, MKK7, MKK9, RLK902, and DEAD-box ATP-dependent RNA helicase. The annotation information suggested their involvement in disease resistance-related pathways, including protein phosphorylation, cytoplasmic vesicle, protein serine/threonine kinase activity, and ATP binding pathways. Our study provides a substantial addition to the available information regarding QTLs associated with NCLB, and further functional verification of identified candidate genes can broaden the scope of understanding the NCLB resistance mechanism in maize.
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Affiliation(s)
- Ruining Zhai
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Aihua Huang
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Runxiu Mo
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Chenglin Zou
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Xinxing Wei
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Meng Yang
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Hua Tan
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Kaijian Huang
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China,*Correspondence: Kaijian Huang, ; Jie Qin,
| | - Jie Qin
- Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China,*Correspondence: Kaijian Huang, ; Jie Qin,
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Quade A, Ash GJ, Park RF, Stodart B. Resistance in Maize ( Zea mays) to Isolates of Puccinia sorghi from Eastern Australia. PHYTOPATHOLOGY 2021; 111:1751-1757. [PMID: 33620235 DOI: 10.1094/phyto-11-20-0524-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The causal agent of maize common rust (CR), Puccinia sorghi, has increased in incidence and severity in Australia in recent years, prompting the assessment of sources of resistance and a preliminary survey of the diversity of P. sorghi populations. The maize commercial hybrids tested carried no resistance to 14 isolates of P. sorghi and had infection types comparable with that of a susceptible check. The resistance gene Rp1_D that remained effective in the United States for 35 years was ineffective against 7 of the 14 isolates. Maize lines carrying known "resistance to Puccinia" (Rp) genes were inoculated with the five isolates considered most diverse based on year of collection (2018 or 2019), location (Queensland or Victoria), and host from which they were isolated (maize or sweet corn). Lines carrying the resistance genes RpG, Rp5, Rp1_E, Rp1_I, Rp1_L, RpGDJ, RpGJF, and Rp5GCJ were resistant to all five isolates and to isolates collected in many agroecological regions. These lines were recommended as donors of effective resistance for maize breeding programs in Australia. Lines carrying no known resistance or resistance genes Rp8_A, Rp8_B, Rp1_J, Rp1_M, Rp7, and Rpp9 (conferring resistance to P. polysora) were susceptible to all five isolates. Differential lines carrying resistance genes Rp1_B, Rp1_C, Rp1_D, Rp1_F, Rp1_K, Rp3_D, or Rp4_A were either resistant or susceptible depending upon the isolate used, showing that the isolates varied in virulence for these genes. Urediniospore production was reduced on adult compared with juvenile plants, presumably due to changes in plant physiology associated with age or the presence of adult plant resistance.
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Affiliation(s)
- Aurelie Quade
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, QLD 4350, Australia
| | - Gavin J Ash
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, QLD 4350, Australia
- Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), School of Agricultural and Wine Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Robert F Park
- Plant Breeding Institute, University of Sydney, Cobbitty, NSW 2570, Australia
| | - Benjamin Stodart
- Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), School of Agricultural and Wine Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
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Kim S, Van den Broeck L, Karre S, Choi H, Christensen SA, Wang G, Jo Y, Cho WK, Balint‐Kurti P. Analysis of the transcriptomic, metabolomic, and gene regulatory responses to Puccinia sorghi in maize. MOLECULAR PLANT PATHOLOGY 2021; 22:465-479. [PMID: 33641256 PMCID: PMC7938627 DOI: 10.1111/mpp.13040] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/22/2020] [Accepted: 01/25/2021] [Indexed: 05/22/2023]
Abstract
Common rust, caused by Puccinia sorghi, is a widespread and destructive disease of maize. The Rp1-D gene confers resistance to the P. sorghi IN2 isolate, mediating a hypersensitive cell death response (HR). To identify differentially expressed genes (DEGs) and metabolites associated with the compatible (susceptible) interaction and with Rp1-D-mediated resistance in maize, we performed transcriptomics and targeted metabolome analyses of P. sorghi IN2-infected leaves from the near-isogenic lines H95 and H95:Rp1-D, which differed for the presence of Rp1-D. We observed up-regulation of genes involved in the defence response and secondary metabolism, including the phenylpropanoid, flavonoid, and terpenoid pathways. Metabolome analyses confirmed that intermediates from several transcriptionally up-regulated pathways accumulated during the defence response. We identified a common response in H95:Rp1-D and H95 with an additional H95:Rp1-D-specific resistance response observed at early time points at both transcriptional and metabolic levels. To better understand the mechanisms underlying Rp1-D-mediated resistance, we inferred gene regulatory networks occurring in response to P. sorghi infection. A number of transcription factors including WRKY53, BHLH124, NKD1, BZIP84, and MYB100 were identified as potentially important signalling hubs in the resistance-specific response. Overall, this study provides a novel and multifaceted understanding of the maize susceptible and resistance-specific responses to P. sorghi.
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Affiliation(s)
- Saet‐Byul Kim
- Department of Entomology and Plant PathologyNC State UniversityRaleighNorth CarolinaUSA
| | - Lisa Van den Broeck
- Department of Plant and Microbial BiologyNC State UniversityRaleighNorth CarolinaUSA
| | - Shailesh Karre
- Department of Entomology and Plant PathologyNC State UniversityRaleighNorth CarolinaUSA
| | - Hoseong Choi
- Research Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulRepublic of Korea
| | - Shawn A. Christensen
- Chemistry Research UnitDepartment of Agriculture–Agricultural Research Service (USDA‐ARS)Center for Medical, Agricultural, and Veterinary EntomologyGainesvilleFloridaUSA
| | - Guan‐Feng Wang
- Department of Entomology and Plant PathologyNC State UniversityRaleighNorth CarolinaUSA
- The Key Laboratory of Plant Development and Environmental Adaptation BiologyMinistry of EducationSchool of Life SciencesShandong UniversityQingdaoChina
| | - Yeonhwa Jo
- Research Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulRepublic of Korea
| | - Won Kyong Cho
- Research Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulRepublic of Korea
| | - Peter Balint‐Kurti
- Department of Entomology and Plant PathologyNC State UniversityRaleighNorth CarolinaUSA
- Plant Science Research Unit USDA‐ARSRaleighNorth CarolinaUSA
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Sserumaga JP, Makumbi D, Assanga SO, Mageto EK, Njeri SG, Jumbo BM, Bruce AY. Identification and diversity of tropical maize inbred lines with resistance to common rust ( Puccinia sorghi Schwein). CROP SCIENCE 2020; 60:2971-2989. [PMID: 33536660 PMCID: PMC7839556 DOI: 10.1002/csc2.20345] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 09/14/2020] [Indexed: 05/20/2023]
Abstract
Common rust (CR) caused by Puccinia sorghi Schwein is one of the major foliar diseases of maize (Zea mays L.) in Eastern and Southern Africa. This study was conducted to (i) evaluate the response of elite tropical adapted maize inbred lines to Puccinia sorghi and identify resistant lines (ii) examine associations between CR disease parameters and agronomic traits, and (iii) assess the genetic diversity of the inbred lines. Fifty inbred lines were evaluated in field trials for three seasons (2017-2019) in Uganda under artificial inoculation. Disease severity was rated on a 1-9 scale at 21 (Rust 1), 28 (Rust 2), and 35 (Rust 3) days after inoculation. Area under disease progress curve (AUDPC) was calculated. The genetic diversity of the lines was assessed using 44,975 single nucleotide polymorphism markers. Combined ANOVA across seasons showed significant (P < .001) line mean squares for the three rust scores and AUDPC. Heritability was high for Rust 2 (0.90), Rust 3 (0.83), and AUDPC (0.93). Of the 50 lines, 12 were highly resistant to CR. Inbred lines CKL1522, CKL05010, and CKL05017 had significantly lower Rust 3 scores and AUDPC compared to the resistant check CML444 and are potential donors of CR resistance alleles. The genetic correlations between CR disease resistance parameters were positive and strong. A neighbor-joining (NJ) tree and STRUCTURE suggested the presence of three major groups among the lines, with lines highly resistant to CR spread across the three groups. The genetic diversity among the highly resistant lines can be exploited by recycling genetically distant lines to develop new multiple disease resistant inbred lines for hybrid development and deployment.
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Affiliation(s)
- Julius Pyton Sserumaga
- National Agricultural Research Organization (NARO)National Livestock Resources Research Institute (NaLIRRI)P.O. Box 5704KampalaUganda
| | - Dan Makumbi
- International Maize and Wheat Improvement Center (CIMMYT)P.O. Box 1041‐00621NairobiKenya
| | - Silvano O. Assanga
- International Maize and Wheat Improvement Center (CIMMYT)P.O. Box 1041‐00621NairobiKenya
- Bayer Crop Science1506 Hwy 69 Suite 100WacoNE68460USA
| | - Edna K. Mageto
- International Maize and Wheat Improvement Center (CIMMYT)P.O. Box 1041‐00621NairobiKenya
- AgReliant Genetics LLC1249 South AvenueBooneIA50036USA
| | - Susan G. Njeri
- International Maize and Wheat Improvement Center (CIMMYT)P.O. Box 1041‐00621NairobiKenya
- Crop Science DivisionBayer East Africa Ltd.P.O. Box 30321‐00100NairobiKenya
| | - Bright M. Jumbo
- International Maize and Wheat Improvement Center (CIMMYT)P.O. Box 1041‐00621NairobiKenya
| | - Anani Y. Bruce
- International Maize and Wheat Improvement Center (CIMMYT)P.O. Box 1041‐00621NairobiKenya
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Characterization and comparative analysis of the genome of Puccinia sorghi Schwein, the causal agent of maize common rust. Fungal Genet Biol 2016; 112:31-39. [PMID: 27746189 DOI: 10.1016/j.fgb.2016.10.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 08/17/2016] [Accepted: 10/03/2016] [Indexed: 01/25/2023]
Abstract
Rust fungi are one of the most devastating pathogens of crop plants. The biotrophic fungus Puccinia sorghi Schwein (Ps) is responsible for maize common rust, an endemic disease of maize (Zea mays L.) in Argentina that causes significant yield losses in corn production. In spite of this, the Ps genomic sequence was not available. We used Illumina sequencing to rapidly produce the 99.6Mbdraft genome sequence of Ps race RO10H11247, derived from a single-uredinial isolate from infected maize leaves collected in the Argentine Corn Belt Region during 2010. High quality reads were obtained from 200bppaired-end and 5000bpmate-paired libraries and assembled in 15,722 scaffolds. A pipeline which combined an ab initio program with homology-based models and homology to in planta enriched ESTs from four cereal pathogenic fungus (the three sequenced wheat rusts and Ustilago maydis) was used to identify 21,087 putative coding sequences, of which 1599 might be part of the Ps RO10H11247 secretome. Among the 458 highly conserved protein families from the euKaryotic Orthologous Groups (KOG) that occur in a wide range of eukaryotic organisms, 97.5% have at least one member with high homology in the Ps assembly (TBlastN, E-value⩽e-10) covering more than 50% of the length of the KOG protein. Comparative studies with the three sequenced wheat rust fungus, and microsynteny analysis involving Puccinia striiformis f. sp. tritici (Pst, wheat stripe rust fungus), support the quality achieved. The results presented here show the effectiveness of the Illumina strategy for sequencing dikaryotic genomes of non-model organisms and provides reliable DNA sequence information for genomic studies, including pathogenic mechanisms of this maize fungus and molecular marker design.
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