1
|
Sharma D, Kumari A, Sharma P, Singh A, Sharma A, Mir ZA, Kumar U, Jan S, Parthiban M, Mir RR, Bhati P, Pradhan AK, Yadav A, Mishra DC, Budhlakoti N, Yadav MC, Gaikwad KB, Singh AK, Singh GP, Kumar S. Meta-QTL analysis in wheat: progress, challenges and opportunities. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:247. [PMID: 37975911 DOI: 10.1007/s00122-023-04490-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 10/16/2023] [Indexed: 11/19/2023]
Abstract
Wheat, an important cereal crop globally, faces major challenges due to increasing global population and changing climates. The production and productivity are challenged by several biotic and abiotic stresses. There is also a pressing demand to enhance grain yield and quality/nutrition to ensure global food and nutritional security. To address these multifaceted concerns, researchers have conducted numerous meta-QTL (MQTL) studies in wheat, resulting in the identification of candidate genes that govern these complex quantitative traits. MQTL analysis has successfully unraveled the complex genetic architecture of polygenic quantitative traits in wheat. Candidate genes associated with stress adaptation have been pinpointed for abiotic and biotic traits, facilitating targeted breeding efforts to enhance stress tolerance. Furthermore, high-confidence candidate genes (CGs) and flanking markers to MQTLs will help in marker-assisted breeding programs aimed at enhancing stress tolerance, yield, quality and nutrition. Functional analysis of these CGs can enhance our understanding of intricate trait-related genetics. The discovery of orthologous MQTLs shared between wheat and other crops sheds light on common evolutionary pathways governing these traits. Breeders can leverage the most promising MQTLs and CGs associated with multiple traits to develop superior next-generation wheat cultivars with improved trait performance. This review provides a comprehensive overview of MQTL analysis in wheat, highlighting progress, challenges, validation methods and future opportunities in wheat genetics and breeding, contributing to global food security and sustainable agriculture.
Collapse
Affiliation(s)
- Divya Sharma
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Anita Kumari
- Department of Botany, University of Delhi, Delhi, India
| | - Priya Sharma
- Department of Botany, University of Delhi, Delhi, India
| | - Anupma Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Anshu Sharma
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Zahoor Ahmad Mir
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Uttam Kumar
- Borlaug Institute for South Asia (BISA), Ludhiana, India
| | - Sofora Jan
- Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Srinagar, Kashmir, India
| | - M Parthiban
- Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Srinagar, Kashmir, India
| | - Reyazul Rouf Mir
- Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Srinagar, Kashmir, India
| | - Pradeep Bhati
- Borlaug Institute for South Asia (BISA), Ludhiana, India
| | - Anjan Kumar Pradhan
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Aakash Yadav
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | | | - Neeraj Budhlakoti
- ICAR- Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mahesh C Yadav
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Kiran B Gaikwad
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Amit Kumar Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | | | - Sundeep Kumar
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India.
| |
Collapse
|
2
|
Zhu M, Ma J, Liu X, Guo Y, Qi X, Gong X, Zhu Y, Wang Y, Jiang M. High-resolution mapping reveals a Ht3-like locus against northern corn leaf blight. FRONTIERS IN PLANT SCIENCE 2022; 13:968924. [PMID: 36160951 PMCID: PMC9506542 DOI: 10.3389/fpls.2022.968924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
Northern corn leaf blight (NCLB), caused by the fungal pathogen Exserohilum turcicum, poses a grave threat to maize production worldwide. The resistance gene in A619Ht3, discovered decades ago, is an important genetic resource for NCLB control. By using a pair of near-isogenic lines (NILs) A619Ht3 and A619, together with the resistant and susceptible bulks derived from the cross of A619Ht3 and L3162 lines, we initially detected a Ht3-like (Ht3L) locus in bin 8.06 that was closely associated with NCLB resistance. We then performed five rounds of fine-mapping, which ultimately delimited the Ht3L locus to a 577-kb interval flanked by SNP markers KA002081 and KA002084. Plants homozygous for the Ht3L/Ht3L genotype exhibited an average reduction in diseased leaf area (DLA) by 16.5% compared to plants lacking Ht3L locus. The Ht3L locus showed extensive variation in genomic architecture among different maize lines and did not appear to contain any genes encoding canonical cell wall-associated kinases against NCLB. Moreover, the Ht3L locus was located ∼2.7 Mb away from the known Htn1 locus. We speculate that the Ht3L locus may contain a bona fide Ht3 gene or a novel NCLB resistance gene closely linked to Ht3. In practice, the Ht3L locus is a valuable resource for improving maize resistance to NCLB.
Collapse
Affiliation(s)
- Mang Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Jun Ma
- Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Xinfang Liu
- Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Yanling Guo
- Liaoning Dongya Agricultural Development Co., Ltd., Shenyang, China
| | - Xin Qi
- Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Xue Gong
- Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Yanbin Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
- Liaoning Dongya Agricultural Development Co., Ltd., Shenyang, China
| | - Yanbo Wang
- Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Min Jiang
- Liaoning Academy of Agricultural Sciences, Shenyang, China
| |
Collapse
|
3
|
Rashid Z, Kaur H, Babu V, Singh PK, Harlapur SI, Nair SK. Identification and Validation of Genomic Regions Associated With Charcoal Rot Resistance in Tropical Maize by Genome-Wide Association and Linkage Mapping. FRONTIERS IN PLANT SCIENCE 2021; 12:726767. [PMID: 34691105 PMCID: PMC8531636 DOI: 10.3389/fpls.2021.726767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 08/30/2021] [Indexed: 06/01/2023]
Abstract
Charcoal rot is a post-flowering stalk rot (PFSR) disease of maize caused by the fungal pathogen, Macrophomina phaseolina. It is a serious concern for smallholder maize cultivation, due to significant yield loss and plant lodging at harvest, and this disease is expected to surge with climate change effects like drought and high soil temperature. For identification and validation of genomic variants associated with charcoal rot resistance, a genome-wide association study (GWAS) was conducted on CIMMYT Asia association mapping panel comprising 396 tropical-adapted lines, especially to Asian environments. The panel was phenotyped for disease severity across two locations with high disease prevalence in India. A subset of 296,497 high-quality SNPs filtered from genotyping by sequencing was correcting for population structure and kinship matrices for single locus mixed linear model (MLM) of GWAS analysis. A total of 19 SNPs were identified to be associated with charcoal rot resistance with P-value ranging from 5.88 × 10-06 to 4.80 × 10-05. Haplotype regression analysis identified 21 significant haplotypes for the trait with Bonferroni corrected P ≤ 0.05. For validating the associated variants and identifying novel QTLs, QTL mapping was conducted using two F2:3 populations. Two QTLs with overlapping physical intervals, qMSR6 and qFMSR6 on chromosome 6, identified from two different mapping populations and contributed by two different resistant parents, were co-located with the SNPs and haplotypes identified at 103.51 Mb on chromosome 6. Similarly, several SNPs/haplotypes identified on chromosomes 3, 6 and 8 were also found to be physically co-located within QTL intervals detected in one of the two mapping populations. The study also noted that several SNPs/haplotypes for resistance to charcoal rot were located within physical intervals of previously reported QTLs for Gibberella stalk rot resistance, which opens up a new possibility for common disease resistance mechanisms for multiple stalk rots.
Collapse
Affiliation(s)
- Zerka Rashid
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Hyderabad, India
| | - Harleen Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Veerendra Babu
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Hyderabad, India
| | - Pradeep Kumar Singh
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Hyderabad, India
| | | | - Sudha K. Nair
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Hyderabad, India
| |
Collapse
|
4
|
Yang P, Scheuermann D, Kessel B, Koller T, Greenwood JR, Hurni S, Herren G, Zhou S, Marande W, Wicker T, Krattinger SG, Ouzunova M, Keller B. Alleles of a wall-associated kinase gene account for three of the major northern corn leaf blight resistance loci in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:526-535. [PMID: 33533097 DOI: 10.1111/tpj.15183] [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: 10/08/2020] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 06/12/2023]
Abstract
Northern corn leaf blight, caused by the fungal pathogen Setosphaeria turcica (anamorph Exserohilum turcicum), is one of the most devastating foliar diseases of maize (Zea mays). Four genes Ht1, Ht2, Ht3 and Htn1 represent the major sources of genetic resistance against the hemibiotrophic fungus S. turcica. Differential maize lines containing these genes also form the basis to classify S. turcica races. Here, we show that Ht2 and Ht3 are identical and allelic to the previously cloned Htn1 gene. Using a map-based cloning approach and Targeting Induced Local Lesions in Genomes (TILLING), we demonstrate that Ht2/Ht3 is an allele of the wall-associated receptor-like kinase gene ZmWAK-RLK1. The ZmWAK-RLK1 variants encoded by Htn1 and Ht2/Ht3 differ by multiple amino acid polymorphisms that particularly affect the putative extracellular domain. A diversity analysis in maize revealed the presence of dozens of ZmWAK-RLK1 alleles. Ht2, Ht3 and Htn1 have been described over decades as independent resistance loci with different race spectra and resistance responses. Our work demonstrates that these three genes are allelic, which has major implications for northern corn leaf blight resistance breeding and nomenclature of S. turcica pathotypes. We hypothesize that genetic background effects have confounded the classical description of these disease resistance genes in the past.
Collapse
Affiliation(s)
- Ping Yang
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, CH-8008, Switzerland
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | | | | | - Teresa Koller
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, CH-8008, Switzerland
| | - Julian R Greenwood
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, CH-8008, Switzerland
| | - Severine Hurni
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, CH-8008, Switzerland
| | - Gerhard Herren
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, CH-8008, Switzerland
| | - Shenghui Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - William Marande
- INRA-CNRGV, 24 Chemin de Borde Rouge - Auzeville, Castanet Tolosan Cedex, CS 52627, 31326, France
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, CH-8008, Switzerland
| | - Simon G Krattinger
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, CH-8008, Switzerland
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | | | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, CH-8008, Switzerland
| |
Collapse
|
5
|
Ranganatha HM, Lohithaswa HC, Pandravada A. Mapping and Validation of Major Quantitative Trait Loci for Resistance to Northern Corn Leaf Blight Along With the Determination of the Relationship Between Resistances to Multiple Foliar Pathogens of Maize ( Zea mays L.). Front Genet 2021; 11:548407. [PMID: 33584784 PMCID: PMC7878677 DOI: 10.3389/fgene.2020.548407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 12/14/2020] [Indexed: 11/13/2022] Open
Abstract
Among various foliar diseases affecting maize yields worldwide, northern corn leaf blight (NCLB) is economically important. The genetics of resistance was worked out to be quantitative in nature thereby suggesting the need for the detection of quantitative trait loci (QTL) to initiate effective marker-aided breeding strategies. From the cross CML153 (susceptible) × SKV50 (resistant), 344 F2 : 3 progenies were derived and screened for their reaction to NCLB during the rainy season of 2013 and 2014. The identification of QTL affecting resistance to NCLB was carried out using the genetic linkage map constructed with 194 polymorphic SNPs and the disease data recorded on F2 : 3 progeny families. Three QTL for NCLB resistance were detected on chromosomes 2, 5, and 8 with the QTL qNCLB-8-2 explaining the highest phenotypic variation of 16.34% followed by qNCLB-5 with 10.24%. QTL for resistance to sorghum downy mildew (SDM) and southern corn rust (SCR) were also identified from one season phenotypic data, and the co-location of QTL for resistance to three foliar diseases was investigated. QTL present in chromosome bins 8.03, 5.03, 5.04, and 3.04 for resistance to NCLB, SDM, and SCR were co-localized, indicating their usefulness for the pyramiding of quantitative resistance to multiple foliar pathogens. Marker-assisted selection was practiced in the crosses CM212 × SKV50, HKI162 × SKV50, and CML153 × SKV50 employing markers linked to major QTL on chromosomes 8, 2, and 10 for NCLB, SDM, and SCR resistance, respectively. The populations were advanced to F6 stage to derive multiple disease-resistant inbred lines. Out of the 125 lines developed, 77 lines were tested for their combining ability and 39 inbred lines exhibited high general combining ability with an acceptable level of resistance to major diseases.
Collapse
Affiliation(s)
- Hosahally Muddrangappa Ranganatha
- Department of Genetics and Plant Breeding, College of Agriculture - Mandya, University of Agricultural Sciences, Bengaluru, Bengaluru, India
| | - Hirenallur Chandappa Lohithaswa
- Department of Genetics and Plant Breeding, College of Agriculture - Mandya, University of Agricultural Sciences, Bengaluru, Bengaluru, India
| | | |
Collapse
|
6
|
Miedaner T, Boeven ALGC, Gaikpa DS, Kistner MB, Grote CP. Genomics-Assisted Breeding for Quantitative Disease Resistances in Small-Grain Cereals and Maize. Int J Mol Sci 2020; 21:E9717. [PMID: 33352763 PMCID: PMC7766114 DOI: 10.3390/ijms21249717] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 12/31/2022] Open
Abstract
Generating genomics-driven knowledge opens a way to accelerate the resistance breeding process by family or population mapping and genomic selection. Important prerequisites are large populations that are genomically analyzed by medium- to high-density marker arrays and extensive phenotyping across locations and years of the same populations. The latter is important to train a genomic model that is used to predict genomic estimated breeding values of phenotypically untested genotypes. After reviewing the specific features of quantitative resistances and the basic genomic techniques, the possibilities for genomics-assisted breeding are evaluated for six pathosystems with hemi-biotrophic fungi: Small-grain cereals/Fusarium head blight (FHB), wheat/Septoria tritici blotch (STB) and Septoria nodorum blotch (SNB), maize/Gibberella ear rot (GER) and Fusarium ear rot (FER), maize/Northern corn leaf blight (NCLB). Typically, all quantitative disease resistances are caused by hundreds of QTL scattered across the whole genome, but often available in hotspots as exemplified for NCLB resistance in maize. Because all crops are suffering from many diseases, multi-disease resistance (MDR) is an attractive aim that can be selected by specific MDR QTL. Finally, the integration of genomic data in the breeding process for introgression of genetic resources and for the improvement within elite materials is discussed.
Collapse
Affiliation(s)
- Thomas Miedaner
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70599 Stuttgart, Germany; (A.L.G.-C.B.); (D.S.G.); (M.B.K.); (C.P.G.)
| | - Ana Luisa Galiano-Carneiro Boeven
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70599 Stuttgart, Germany; (A.L.G.-C.B.); (D.S.G.); (M.B.K.); (C.P.G.)
- Kleinwanzlebener Saatzucht (KWS) SAAT SE & Co. KGaA, 37574 Einbeck, Germany
| | - David Sewodor Gaikpa
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70599 Stuttgart, Germany; (A.L.G.-C.B.); (D.S.G.); (M.B.K.); (C.P.G.)
| | - Maria Belén Kistner
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70599 Stuttgart, Germany; (A.L.G.-C.B.); (D.S.G.); (M.B.K.); (C.P.G.)
- Estación Experimental Pergamino, Instituto Nacional de Tecnología Agropecuaria (INTA), CC31, B2700WAA Pergamino, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, C1425FQB Buenos Aires, Argentina
| | - Cathérine Pauline Grote
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70599 Stuttgart, Germany; (A.L.G.-C.B.); (D.S.G.); (M.B.K.); (C.P.G.)
| |
Collapse
|
7
|
Rashid Z, Sofi M, Harlapur SI, Kachapur RM, Dar ZA, Singh PK, Zaidi PH, Vivek BS, Nair SK. Genome-wide association studies in tropical maize germplasm reveal novel and known genomic regions for resistance to Northern corn leaf blight. Sci Rep 2020; 10:21949. [PMID: 33319847 PMCID: PMC7738672 DOI: 10.1038/s41598-020-78928-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 11/26/2020] [Indexed: 02/08/2023] Open
Abstract
Northern Corn Leaf Blight (NCLB) caused by Setosphaeria turcica, is one of the most important diseases of maize world-wide, and one of the major reasons behind yield losses in maize crop in Asia. In the present investigation, a high-resolution genome wide association study (GWAS) was conducted for NCLB resistance in three association mapping panels, predominantly consisting of tropical lines adapted to different agro-ecologies. These panels were phenotyped for disease severity across three locations with high disease prevalence in India. High density SNPs from Genotyping-by-sequencing were used in GWAS, after controlling for population structure and kinship matrices, based on single locus mixed linear model (MLM). Twenty-two SNPs were identified, that revealed a significant association with NCLB in the three mapping panels. Haplotype regression analysis revealed association of 17 significant haplotypes at FDR ≤ 0.05, with two common haplotypes across three maize panels. Several of the significantly associated SNPs/haplotypes were found to be co-located in chromosomal bins previously reported for major genes like Ht2, Ht3 and Htn1 and QTL for NCLB resistance and multiple foliar disease resistance. Phenotypic variance explained by these significant SNPs/haplotypes ranged from low to moderate, suggesting a breeding strategy of combining multiple resistance alleles towards resistance for NCLB.
Collapse
Affiliation(s)
- Zerka Rashid
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Greater Hyderabad Telangana, 502324, India
| | - Mehrajuddin Sofi
- High Mountain Arid Agricultural Research Institute (HMAARI) Stakna, SKUAST-Kashmir, Leh, 194101, India
| | - Sharanappa I Harlapur
- University of Agricultural Sciences, Krishi Nagar, Dharwad, Karnataka, 580005, India
| | | | - Zahoor Ahmed Dar
- Sher-E-Kashmir University of Agriculture Sciences and Technology (SKUAST), Srinagar, Jammu and Kashmir, 190001, India
| | - Pradeep Kumar Singh
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Greater Hyderabad Telangana, 502324, India
| | - Pervez Haider Zaidi
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Greater Hyderabad Telangana, 502324, India
| | - Bindiganavile Sampath Vivek
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Greater Hyderabad Telangana, 502324, India
| | - Sudha Krishnan Nair
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Greater Hyderabad Telangana, 502324, India.
| |
Collapse
|
8
|
Maize Introgression Library Provides Evidence for the Involvement of liguleless1 in Resistance to Northern Leaf Blight. G3-GENES GENOMES GENETICS 2020; 10:3611-3622. [PMID: 32816917 PMCID: PMC7534436 DOI: 10.1534/g3.120.401500] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Plant disease resistance is largely governed by complex genetic architecture. In maize, few disease resistance loci have been characterized. Near-isogenic lines are a powerful genetic tool to dissect quantitative trait loci. We analyzed an introgression library of maize (Zea mays) near-isogenic lines, termed a nested near-isogenic line library for resistance to northern leaf blight caused by the fungal pathogen Setosphaeria turcica The population was comprised of 412 BC5F4 near-isogenic lines that originated from 18 diverse donor parents and a common recurrent parent, B73. Single nucleotide polymorphisms identified through genotyping by sequencing were used to define introgressions and for association analysis. Near-isogenic lines that conferred resistance and susceptibility to northern leaf blight were comprised of introgressions that overlapped known northern leaf blight quantitative trait loci. Genome-wide association analysis and stepwise regression further resolved five quantitative trait loci regions, and implicated several candidate genes, including Liguleless1, a key determinant of leaf architecture in cereals. Two independently-derived mutant alleles of liguleless1 inoculated with S. turcica showed enhanced susceptibility to northern leaf blight. In the maize nested association mapping population, leaf angle was positively correlated with resistance to northern leaf blight in five recombinant inbred line populations, and negatively correlated with northern leaf blight in four recombinant inbred line populations. This study demonstrates the power of an introgression library combined with high density marker coverage to resolve quantitative trait loci. Furthermore, the role of liguleless1 in leaf architecture and in resistance to northern leaf blight has important applications in crop improvement.
Collapse
|
9
|
Xia H, Gao W, Qu J, Dai L, Gao Y, Lu S, Zhang M, Wang P, Wang T. Genetic mapping of northern corn leaf blight-resistant quantitative trait loci in maize. Medicine (Baltimore) 2020; 99:e21326. [PMID: 32756117 PMCID: PMC7402768 DOI: 10.1097/md.0000000000021326] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Northern corn leaf blight (NCLB), a corn disease infected by Exserohilum turcicum, can cause loss of harvest and economy. Identification or evaluation of NCLB-resistant quantitative trait loci (QTL) and genes could improve maize breeds. This study aimed to identify novel QTLs for NCLB-resistance.Two maize strains (BB and BC) were utilized to generate B73 × B97 and B73 × CML322 and constructed the genetic linkage using high-throughput single nucleotide polymorphism (SNP) linkage map analysis of 170 (BB) and 163(BC) recombinant inbred line (RIL) genomic DNA samples. NCLB-resistant QTL was associated with phenotypic data from the field trial of 170 BB and 163 BC strains over two years using these 1100 SNPs to identify high-density NCLB-resistant QTLs.In BB, QTL of the NCLB resistance was on chromosome 1 and 3 (LOD scores between 2.74 and 5.44); in BC, QTL of NCLB resistance was on chromosome 1, 2, 4, 8, and 9 (LOD scores between 2.52 and 8.53). A number of genes or genetic information related to NCLB resistance in both BB and BC were identified with the maximum number of genes/NCLB resistance-related QTL on chromosome 3 for BB and on chromosome 1 for BC.This study successfully mapped and identified NCLB-resistant QTL and genes for these 2 different maize strains, which provides insightful information for future study of NCLB-resistance and selection of NCLB-resistant maize variants.
Collapse
Affiliation(s)
- Haifeng Xia
- Tonghua Academy of Agricultural Sciences, Tonghua
- College of Agronomy, Jilin Agricultural University, Changchun
| | - Wei Gao
- Tonghua Academy of Agricultural Sciences, Tonghua
| | - Jing Qu
- College of Agronomy, Jilin Agricultural University, Changchun
| | - Liqiang Dai
- College of Agronomy, Jilin Agricultural University, Changchun
| | - Yan Gao
- Tonghua Academy of Agricultural Sciences, Tonghua
| | - Shi Lu
- College of Agronomy, Jilin Agricultural University, Changchun
| | - Mo Zhang
- College of Agronomy, Jilin Agricultural University, Changchun
| | - Piwu Wang
- College of Agronomy, Jilin Agricultural University, Changchun
| | - Tianyu Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
10
|
Ismael A, Suontama M, Klápště J, Kennedy S, Graham N, Telfer E, Dungey H. Indication of Quantitative Multiple Disease Resistance to Foliar Pathogens in Pinus radiata D.Don in New Zealand. FRONTIERS IN PLANT SCIENCE 2020; 11:1044. [PMID: 32754186 PMCID: PMC7365928 DOI: 10.3389/fpls.2020.01044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/24/2020] [Indexed: 05/06/2023]
Abstract
Increasing resistance against foliar diseases is an important goal in the Pinus radiata D.Don breeding program in New Zealand, and screening for resistance has been in place for some time, since the late 1960s. The current study presents results of four progeny trials within the breeding program to investigate whether multiple disease resistance could be detected against three different needle diseases in P. radiata: Dothistroma needle blight (DNB) caused by Dothistroma septosporum, Cyclaneusma needle cast (CNC) caused by Cyclaneusma minus, and red needle cast (RNC) caused by Phytophthora pluvialis. Four progeny trials in the North Island of New Zealand were available to estimate heritabilities and between-trait genetic correlations. Two of the trials were assessed for DNB, involving 63 full-sib families. A third trial was assessed for CNC, involving 172 half-sib families, and a fourth trial was assessed for RNC, involving 170 half-sib families. Disease resistances had moderate estimates of heritability (0.28-0.48) in all trials. We investigated the potential for multiple disease resistance to the three foliar diseases by estimating genetic correlations between disease resistances using a spatial linear mixed model. The correlation between DNB and CNC resistance was favorable and strong (0.81), indicating that genotypes that are highly resistant to DNB also have a high resistance to CNC. These results suggest that selection based on resistance to DNB could allow for simultaneous indirect selection for resistance to CNC, usually only expressed at a later age. This would allow selections to be made earlier due to the earlier expression of DNB than CNC and reduce the number of expensive disease assessments being undertaken. Conversely, genetic correlation estimates for RNC with DNB and CNC were close to zero, and very imprecise. As such, later-age assessments for this disease would still be required.
Collapse
Affiliation(s)
| | - Mari Suontama
- Forest Genetics, Scion, Rotorua, New Zealand
- Tree Breeding, Skogforsk, Umeå, Sweden
| | | | | | | | | | | |
Collapse
|
11
|
Zhang X, Fernandes SB, Kaiser C, Adhikari P, Brown PJ, Mideros SX, Jamann TM. Conserved defense responses between maize and sorghum to Exserohilum turcicum. BMC PLANT BIOLOGY 2020; 20:67. [PMID: 32041528 PMCID: PMC7011368 DOI: 10.1186/s12870-020-2275-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/03/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Exserohilum turcicum is an important pathogen of both sorghum and maize, causing sorghum leaf blight and northern corn leaf blight. Because the same pathogen can infect and cause major losses for two of the most important grain crops, it is an ideal pathosystem to study plant-pathogen evolution and investigate shared resistance mechanisms between the two plant species. To identify sorghum genes involved in the E. turcicum response, we conducted a genome-wide association study (GWAS). RESULTS Using the sorghum conversion panel evaluated across three environments, we identified a total of 216 significant markers. Based on physical linkage with the significant markers, we detected a total of 113 unique candidate genes, some with known roles in plant defense. Also, we compared maize genes known to play a role in resistance to E. turcicum with the association mapping results and found evidence of genes conferring resistance in both crops, providing evidence of shared resistance between maize and sorghum. CONCLUSIONS Using a genetics approach, we identified shared genetic regions conferring resistance to E. turcicum in both maize and sorghum. We identified several promising candidate genes for resistance to leaf blight in sorghum, including genes related to R-gene mediated resistance. We present significant advancements in the understanding of host resistance to E. turcicum, which is crucial to reduce losses due to this important pathogen.
Collapse
Affiliation(s)
- Xiaoyue Zhang
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Samuel B Fernandes
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Christopher Kaiser
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Pragya Adhikari
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Patrick J Brown
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Santiago X Mideros
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Tiffany M Jamann
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| |
Collapse
|
12
|
Lopez-Zuniga LO, Wolters P, Davis S, Weldekidan T, Kolkman JM, Nelson R, Hooda KS, Rucker E, Thomason W, Wisser R, Balint-Kurti P. Using Maize Chromosome Segment Substitution Line Populations for the Identification of Loci Associated with Multiple Disease Resistance. G3 (BETHESDA, MD.) 2019; 9:189-201. [PMID: 30459178 PMCID: PMC6325898 DOI: 10.1534/g3.118.200866] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 11/15/2018] [Indexed: 11/24/2022]
Abstract
Southern Leaf Blight (SLB), Northern Leaf Blight (NLB), and Gray Leaf Spot (GLS) caused by Cochliobolus heterostrophus, Setosphaeria turcica, and Cercospora zeae-maydis respectively, are among the most important diseases of corn worldwide. Previously, moderately high and significantly positive genetic correlations between resistance levels to each of these diseases were identified in a panel of 253 diverse maize inbred lines. The goal of this study was to identify loci underlying disease resistance in some of the most multiple disease resistant (MDR) lines by the creation of chromosome segment substitution line (CSSL) populations in multiple disease susceptible (MDS) backgrounds. Four MDR lines (NC304, NC344, Ki3, NC262) were used as donor parents and two MDS lines (Oh7B, H100) were used as recurrent parents to produce eight BC3F4:5 CSSL populations comprising 1,611 lines in total. Each population was genotyped and assessed for each disease in replicated trials in two environments. Moderate to high heritabilities on an entry mean basis were observed (0.32 to 0.83). Several lines in each population were significantly more resistant than the MDS parental lines for each disease. Multiple quantitative trait loci (QTL) for disease resistance were detected for each disease in most of the populations. Seventeen QTL were associated with variation in resistance to more than one disease (SLB/NLB: 2; SLB/GLS: 7; NLB/GLS: 2 and 6 to all three diseases). For most populations and most disease combinations, significant correlations were observed between disease scores and also between marker effects for each disease. The number of lines that were resistant to more than one disease was significantly higher than would be expected by chance. Using the results from individual QTL analyses, a composite statistic based on Mahalanobis distance (Md) was used to identify joint marker associations with multiple diseases. Across all populations and diseases, 246 markers had significant Md values. However further analysis revealed that most of these associations were due to strong QTL effects on a single disease. Together, these findings reinforce our previous conclusions that loci associated with resistance to different diseases are clustered in the genome more often than would be expected by chance. Nevertheless true MDR loci which have significant effects on more than one disease are still much rarer than loci with single disease effects.
Collapse
Affiliation(s)
- Luis O Lopez-Zuniga
- Dept. of Crop Science, North Carolina State University, Box 7620, Raleigh, NC 27695
| | - Petra Wolters
- Dupont-Pioneer 7300 NW 62 Avenue P.O Box 1004 Johnston, IA, 50131-1004
| | - Scott Davis
- Dupont-Pioneer 7300 NW 62 Avenue P.O Box 1004 Johnston, IA, 50131-1004
| | | | - Judith M Kolkman
- Department of Plant Pathology and Plant-Microbe Biology Cornell University, Ithaca, NY 14853
| | - Rebecca Nelson
- Department of Plant Pathology and Plant-Microbe Biology Cornell University, Ithaca, NY 14853
| | - K S Hooda
- ICAR-Indian Institute of Maize Research, Indian Council of Agricultural Research, Pusa Campus, New Delhi 110 012, India
| | - Elizabeth Rucker
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061
| | - Wade Thomason
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061
| | - Randall Wisser
- Dept. of Plant and Soil Sciences, University of Delaware, Newark, DE 19716
| | - Peter Balint-Kurti
- Dept. of Entomology and Plant Pathology, North Carolina State University, Box 7616 Raleigh, NC 27695
- Plant Science Research Unit, USDA-ARS, Raleigh NC 27695-7616
| |
Collapse
|
13
|
Yang P, Praz C, Li B, Singla J, Robert CAM, Kessel B, Scheuermann D, Lüthi L, Ouzunova M, Erb M, Krattinger SG, Keller B. Fungal resistance mediated by maize wall-associated kinase ZmWAK-RLK1 correlates with reduced benzoxazinoid content. THE NEW PHYTOLOGIST 2019; 221:976-987. [PMID: 30178602 DOI: 10.1111/nph.15419] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 07/30/2018] [Indexed: 05/20/2023]
Abstract
Wall-associated kinases (WAKs) have recently been identified as major components of fungal and bacterial disease resistance in several cereal crop species. However, the molecular mechanisms of WAK-mediated resistance remain largely unknown. Here, we investigated the function of the maize gene ZmWAK-RLK1 (Htn1) that confers quantitative resistance to northern corn leaf blight (NCLB) caused by the hemibiotrophic fungal pathogen Exserohilum turcicum. ZmWAK-RLK1 was found to localize to the plasma membrane and its presence resulted in a modification of the infection process by reducing pathogen penetration into host tissues. A large-scale transcriptome analysis of near-isogenic lines (NILs) differing for ZmWAK-RLK1 revealed that several differentially expressed genes are involved in the biosynthesis of the secondary metabolites benzoxazinoids (BXs). The contents of several BXs including DIM2 BOA-Glc were significantly lower when ZmWAK-RLK1 is present. DIM2 BOA-Glc concentration was significantly elevated in ZmWAK-RLK1 mutants with compromised NCLB resistance. Maize mutants that were affected in overall BXs biosynthesis or content of DIM2 BOA-Glc showed increased NCLB resistance. We conclude that Htn1-mediated NCLB resistance is associated with a reduction of BX secondary metabolites. These findings suggest a link between WAK-mediated quantitative disease resistance and changes in biochemical fluxes starting with indole-3-glycerol phosphate.
Collapse
Affiliation(s)
- Ping Yang
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Coraline Praz
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
| | - Beibei Li
- Institute of Plant Sciences, University of Bern, CH-3013, Bern, Switzerland
| | - Jyoti Singla
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
| | | | | | | | - Linda Lüthi
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
| | | | - Matthias Erb
- Institute of Plant Sciences, University of Bern, CH-3013, Bern, Switzerland
| | - Simon G Krattinger
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
- King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
| |
Collapse
|
14
|
Jiménez-Galindo JC, Malvar RA, Butrón A, Caicedo M, Ordás B. Fine analysis of a genomic region involved in resistance to Mediterranean corn borer. BMC PLANT BIOLOGY 2018; 18:169. [PMID: 30111285 PMCID: PMC6094900 DOI: 10.1186/s12870-018-1385-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 08/01/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Sesamia nonagrioides Lefebvere (Mediterranean corn borer, MCB) is the main pest of maize in the Mediterranean area. QTL for MCB stalk tunneling and grain yield under high MCB infestation had been located at bin 8.03-8.05 (4-21 cM and 10-30 cM respectively) in a previous analysis of the EP42 x EP39 RILs mapping population. The objective of the present work was to study with higher resolution those QTL, and validating and estimating with higher precision their locations and effects. To achieve this objective, we developed a set of 38 heterogeneous inbred families (HIFs) which were near-homozygous in the genome, except in the region under study. The HIFs were evaluated in multiple environments under artificial infestation with MCB and genotyped with SNPs. RESULTS The QTL for grain yield under high infestation was confirmed with higher precision and improved reliability at 112.6-116.9 Mb. On the contrary, the location of the QTL for stalk tunneling was not validated probably due to the fixation of some genomic regions during the development of the HIFs. Our study confirmed that the co-localization of the QTL for stalk tunneling and grain yield in the previous study was due to linked genes, not to pleiotropic effects. So, the QTL for grain yield can be used for improving grain yield without undesirable effect on stalk tunneling. CONCLUSIONS The HIF analysis is useful for validating QTL and for conducting deeper studies in traits related to corn borer resistance.
Collapse
Affiliation(s)
- José Cruz Jiménez-Galindo
- Misión Biológica de Galicia, Spanish National Research Council (CSIC), Apartado 28, 36080 Pontevedra, Spain
- National Institute of Forestry, Agriculture and Livestock Research (INIFAP), Ave. Hidalgo 1213, Cd., 31500 Cuauhtémoc, Chihuahua, Mexico
| | - Rosa Ana Malvar
- Misión Biológica de Galicia, Spanish National Research Council (CSIC), Apartado 28, 36080 Pontevedra, Spain
| | - Ana Butrón
- Misión Biológica de Galicia, Spanish National Research Council (CSIC), Apartado 28, 36080 Pontevedra, Spain
| | - Marlon Caicedo
- Misión Biológica de Galicia, Spanish National Research Council (CSIC), Apartado 28, 36080 Pontevedra, Spain
- National Institute of Agricultural Research (INIAP), 170315 Quito, Ecuador
| | - Bernardo Ordás
- Misión Biológica de Galicia, Spanish National Research Council (CSIC), Apartado 28, 36080 Pontevedra, Spain
| |
Collapse
|
15
|
Du X, Liu S, Sun J, Zhang G, Jia Y, Pan Z, Xiang H, He S, Xia Q, Xiao S, Shi W, Quan Z, Liu J, Ma J, Pang B, Wang L, Sun G, Gong W, Jenkins JN, Lou X, Zhu J, Xu H. Dissection of complicate genetic architecture and breeding perspective of cottonseed traits by genome-wide association study. BMC Genomics 2018; 19:451. [PMID: 29895260 PMCID: PMC5998501 DOI: 10.1186/s12864-018-4837-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 05/29/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Cottonseed is one of the most important raw materials for plant protein, oil and alternative biofuel for diesel engines. Understanding the complex genetic basis of cottonseed traits is requisite for achieving efficient genetic improvement of the traits. However, it is not yet clear about their genetic architecture in genomic level. GWAS has been an effective way to explore genetic basis of quantitative traits in human and many crops. This study aims to dissect genetic mechanism seven cottonseed traits by a GWAS for genetic improvement. RESULTS A genome-wide association study (GWAS) based on a full gene model with gene effects as fixed and gene-environment interaction as random, was conducted for protein, oil and 5 fatty acids using 316 accessions and ~ 390 K SNPs. Totally, 124 significant quantitative trait SNPs (QTSs), consisting of 16, 21, 87 for protein, oil and fatty acids (palmitic, linoleic, oleic, myristic, stearic), respectively, were identified and the broad-sense heritability was estimated from 71.62 to 93.43%; no QTS-environment interaction was detected for the protein, the palmitic and the oleic contents; the protein content was predominantly controlled by epistatic effects accounting for 65.18% of the total variation, but the oil content and the fatty acids except the palmitic were mainly determined by gene main effects and no epistasis was detected for the myristic and the stearic. Prediction of superior pure line and hybrid revealed the potential of the QTSs in the improvement of cottonseed traits, and the hybrid could achieve higher or lower genetic values compared with pure lines. CONCLUSIONS This study revealed complex genetic architecture of seven cottonseed traits at whole genome-wide by mixed linear model approach; the identified genetic variants and estimated genetic component effects of gene, gene-gene and gene-environment interaction provide cotton geneticist or breeders new knowledge on the genetic mechanism of the traits and the potential molecular breeding design strategy.
Collapse
Affiliation(s)
- Xiongming Du
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences (ICR, CAAS), State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000 People’s Republic of China
| | - Shouye Liu
- Institute of crop science and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058 People’s Republic of China
| | - Junling Sun
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences (ICR, CAAS), State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000 People’s Republic of China
| | - Gengyun Zhang
- Shenzhen Huada Gene Research Institute, Shenzhen, 518031 People’s Republic of China
| | - Yinhua Jia
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences (ICR, CAAS), State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000 People’s Republic of China
| | - Zhaoe Pan
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences (ICR, CAAS), State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000 People’s Republic of China
| | - Haitao Xiang
- Shenzhen Huada Gene Research Institute, Shenzhen, 518031 People’s Republic of China
| | - Shoupu He
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences (ICR, CAAS), State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000 People’s Republic of China
| | - Qiuju Xia
- Shenzhen Huada Gene Research Institute, Shenzhen, 518031 People’s Republic of China
| | - Songhua Xiao
- Institute of industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 People’s Republic of China
| | - Weijun Shi
- Economic Crop Research Institute, Xinjiang Academy of Agricultural Science, Urumqi, 830002 People’s Republic of China
| | - Zhiwu Quan
- Shenzhen Huada Gene Research Institute, Shenzhen, 518031 People’s Republic of China
| | - Jianguang Liu
- Institute of industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 People’s Republic of China
| | - Jun Ma
- Economic Crop Research Institute, Xinjiang Academy of Agricultural Science, Urumqi, 830002 People’s Republic of China
| | - Baoyin Pang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences (ICR, CAAS), State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000 People’s Republic of China
| | - Liru Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences (ICR, CAAS), State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000 People’s Republic of China
| | - Gaofei Sun
- Department of Computer Science and Information Engineering, Anyang Institute of Technology, Anyang, 455000 People’s Republic of China
| | - Wenfang Gong
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences (ICR, CAAS), State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000 People’s Republic of China
| | | | - Xiangyang Lou
- Department of Pediatrics, Biostatistics Division Arkansas Children‘s Hospital Research Institute School of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72202 USA
| | - Jun Zhu
- Institute of crop science and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058 People’s Republic of China
| | - Haiming Xu
- Institute of crop science and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058 People’s Republic of China
| |
Collapse
|
16
|
Increased experimental conditions and marker densities identified more genetic loci associated with southern and northern leaf blight resistance in maize. Sci Rep 2018; 8:6848. [PMID: 29717181 PMCID: PMC5931595 DOI: 10.1038/s41598-018-25304-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/19/2018] [Indexed: 01/01/2023] Open
Abstract
Southern leaf blight (SLB) and northern leaf blight (NLB) are the two major foliar diseases limiting maize production worldwide. Upon previous study with the nested association mapping (NAM) population, which consist of 5,000 recombinant inbred lines from 25 parents crossed with B73, we expanded the phenotyping environments from the United States (US) to China, and increased the marker densities from 1106 to 7386 SNPs for linkage mapping, and from 1.6 to 28.5 million markers for association mapping. We identified 49 SLB and 48 NLB resistance-related unique QTLs in linkage mapping, and multiple loci in association mapping with candidate genes involved in known plant disease-resistance pathways. Furthermore, an independent natural population with 282 diversified inbred lines were sequenced for four candidate genes selected based on their biological functions. Three of them demonstrated significant associations with disease resistance. These findings provided valuable resources for further implementations to develop varieties with superior resistance for NLB and SLB.
Collapse
|
17
|
Mideros SX, Chung CL, Wiesner-Hanks T, Poland JA, Wu D, Fialko AA, Turgeon BG, Nelson RJ. Determinants of Virulence and In Vitro Development Colocalize on a Genetic Map of Setosphaeria turcica. PHYTOPATHOLOGY 2018; 108:254-263. [PMID: 28952420 DOI: 10.1094/phyto-01-17-0021-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Generating effective and stable strategies for resistance breeding requires an understanding of the genetics of host-pathogen interactions and the implications for pathogen dynamics and evolution. Setosphaeria turcica causes northern leaf blight (NLB), an important disease of maize for which major resistance genes have been deployed. Little is known about the evolutionary dynamics of avirulence (AVR) genes in S. turcica. To test the hypothesis that there is a genetic association between avirulence and in vitro development traits, we (i) created a genetic map of S. turcica, (ii) located candidate AVRHt1 and AVRHt2 regions, and (iii) identified genetic regions associated with several in vitro development traits. A cross was generated between a race 1 and a race 23N strain, and 221 progeny were isolated. Genotyping by sequencing was used to score 2,078 single-nucleotide polymorphism markers. A genetic map spanning 1,981 centimorgans was constructed, consisting of 21 linkage groups. Genetic mapping extended prior evidence for the location and identity of the AVRHt1 gene and identified a region of interest for AVRHt2. The genetic location of AVRHt2 colocalized with loci influencing radial growth and mycelial abundance. Our data suggest a trade-off between virulence on Ht1 and Ht2 and the pathogen's vegetative growth rate. In addition, in-depth analysis of the genotypic data suggests the presence of significant duplication in the genome of S. turcica.
Collapse
Affiliation(s)
- Santiago X Mideros
- First author: University of Illinois at Urbana-Champaign, Urbana 61801; second author: National Taiwan University, Taipei, 10617, Taiwan; and third, fourth, fifth, sixth, seventh, and eighth authors: School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Chia-Lin Chung
- First author: University of Illinois at Urbana-Champaign, Urbana 61801; second author: National Taiwan University, Taipei, 10617, Taiwan; and third, fourth, fifth, sixth, seventh, and eighth authors: School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Tyr Wiesner-Hanks
- First author: University of Illinois at Urbana-Champaign, Urbana 61801; second author: National Taiwan University, Taipei, 10617, Taiwan; and third, fourth, fifth, sixth, seventh, and eighth authors: School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Jesse A Poland
- First author: University of Illinois at Urbana-Champaign, Urbana 61801; second author: National Taiwan University, Taipei, 10617, Taiwan; and third, fourth, fifth, sixth, seventh, and eighth authors: School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Dongliang Wu
- First author: University of Illinois at Urbana-Champaign, Urbana 61801; second author: National Taiwan University, Taipei, 10617, Taiwan; and third, fourth, fifth, sixth, seventh, and eighth authors: School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Ariel A Fialko
- First author: University of Illinois at Urbana-Champaign, Urbana 61801; second author: National Taiwan University, Taipei, 10617, Taiwan; and third, fourth, fifth, sixth, seventh, and eighth authors: School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - B Gillian Turgeon
- First author: University of Illinois at Urbana-Champaign, Urbana 61801; second author: National Taiwan University, Taipei, 10617, Taiwan; and third, fourth, fifth, sixth, seventh, and eighth authors: School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Rebecca J Nelson
- First author: University of Illinois at Urbana-Champaign, Urbana 61801; second author: National Taiwan University, Taipei, 10617, Taiwan; and third, fourth, fifth, sixth, seventh, and eighth authors: School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| |
Collapse
|
18
|
Yang P, Herren G, Krattinger SG, Keller B. Large-scale Maize Seedling Infection with Exserohilum turcicum in the Greenhouse. Bio Protoc 2017; 7:e2567. [PMID: 34595250 DOI: 10.21769/bioprotoc.2567] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 09/11/2017] [Accepted: 09/12/2017] [Indexed: 11/02/2022] Open
Abstract
Northern corn leaf blight (NCLB) is a serious foliar disease of maize (Zea mays) worldwide and breeding for resistance is of primary importance for maize crop protection. Phenotyping for NCLB resistance is well established in the field, but such experiments depend on suitable environmental conditions and are seasonal. Here we describe a greenhouse seedling approach that is suitable for testing thousands of seedling plants in a single experiment with a duration of 37 days. Three scoring methods were used to quantify the disease severity: the area under the disease progress curve (AUDPC), the primary diseased leaf area of the inoculated leaves at 16 days post inoculation (PrimDLA at 16 dpi) and the incubation period (IP) that was determined as days from inoculation to symptom appearance. By testing a diverse panel of maize genotypes, a high correlation between the three different methods was observed (81.9% to 94.1%), indicating that each of scoring methods can be applied for disease quantification. Thus, the seedling assay developed served as a relatively simple and high-throughput method for phenotyping NCLB disease resistance under greenhouse condition.
Collapse
Affiliation(s)
- Ping Yang
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.,Centre of Crop Germplasm Resources, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Gerhard Herren
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Simon G Krattinger
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| |
Collapse
|
19
|
Zhang X, Yang Q, Rucker E, Thomason W, Balint-Kurti P. Fine mapping of a quantitative resistance gene for gray leaf spot of maize (Zea mays L.) derived from teosinte (Z. mays ssp. parviglumis). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1285-1295. [PMID: 28342108 DOI: 10.1007/s00122-017-2888-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 02/27/2017] [Indexed: 05/02/2023]
Abstract
In this study we mapped the QTL Qgls8 for gray leaf spot (GLS) resistance in maize to a ~130 kb region on chromosome 8 including five predicted genes. In previous work, using near isogenic line (NIL) populations in which segments of the teosinte (Zea mays ssp. parviglumis) genome had been introgressed into the background of the maize line B73, we had identified a QTL on chromosome 8, here called Qgls8, for gray leaf spot (GLS) resistance. We identified alternate teosinte alleles at this QTL, one conferring increased GLS resistance and one increased susceptibility relative to the B73 allele. Using segregating populations derived from NIL parents carrying these contrasting alleles, we were able to delimit the QTL region to a ~130 kb (based on the B73 genome) which encompassed five predicted genes.
Collapse
Affiliation(s)
- Xinye Zhang
- Maize Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, China
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Qin Yang
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Elizabeth Rucker
- Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Wade Thomason
- Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Peter Balint-Kurti
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA.
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS) Plant Science Research Unit, Raleigh, NC, USA.
| |
Collapse
|
20
|
Yang Q, Balint-Kurti P, Xu M. Quantitative Disease Resistance: Dissection and Adoption in Maize. MOLECULAR PLANT 2017; 10:402-413. [PMID: 28254471 DOI: 10.1016/j.molp.2017.02.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 02/16/2017] [Accepted: 02/16/2017] [Indexed: 06/06/2023]
Abstract
Maize is the world's most produced crop, providing food, feed, and biofuel. Maize production is constantly threatened by the presence of devastating pathogens worldwide. Characterization of the genetic components underlying disease resistance is a major research area in maize which is highly relevant for resistance breeding programs. Quantitative disease resistance (QDR) is the type of resistance most widely used by maize breeders. The past decade has witnessed significant progress in fine-mapping and cloning of genes controlling QDR. The molecular mechanisms underlying QDR remain poorly understood and exploited. In this review we discuss recent advances in maize QDR research and strategy for resistance breeding.
Collapse
Affiliation(s)
- Qin Yang
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Peter Balint-Kurti
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA; USDA-ARS Plant Sciences Research Unit, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA.
| | - Mingliang Xu
- National Maize Improvement Centre of China, China Agricultural University, Beijing 100193, People's Republic of China.
| |
Collapse
|
21
|
Lana UGDP, Prazeres de Souza IR, Noda RW, Pastina MM, Magalhaes JV, Guimaraes CT. Quantitative Trait Loci and Resistance Gene Analogs Associated with Maize White Spot Resistance. PLANT DISEASE 2017; 101:200-208. [PMID: 30682293 DOI: 10.1094/pdis-06-16-0899-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Maize white spot (MWS), caused by the bacterium Pantoea ananatis, is one of the most important maize foliar diseases in tropical and subtropical regions, causing significant yield losses. Despite its economic importance, genetic studies of MWS are scarce. The aim of this study was to map quantitative trait loci (QTL) associated with MWS resistance and to identify resistance gene analogs (RGA) underlying these QTL. QTL mapping was performed in a tropical maize F2:3 population, which was genotyped with simple-sequence repeat and RGA-tagged markers and phenotyped for the response to MWS in two Brazilian southeastern locations. Nine QTL explained approximately 70% of the phenotypic variance for MWS resistance at each location, with two of them consistently detected in both environments. Data mining using 112 resistance genes cloned from different plant species revealed 1,697 RGA distributed in clusters within the maize genome. The RGA Pto19, Pto20, Pto99, and Xa26.151.4 were genetically mapped within MWS resistance QTL on chromosomes 4 and 8 and were preferentially expressed in the resistant parental line at locations where their respective QTL occurred. The consistency of QTL mapping, in silico prediction, and gene expression analyses revealed RGA and genomic regions suitable for marker-assisted selection to improve MWS resistance.
Collapse
|
22
|
Jamann TM, Luo X, Morales L, Kolkman JM, Chung CL, Nelson RJ. A remorin gene is implicated in quantitative disease resistance in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:591-602. [PMID: 26849237 DOI: 10.1007/s00122-015-2650-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 12/08/2015] [Indexed: 05/02/2023]
Abstract
Quantitative disease resistance is used by plant breeders to improve host resistance. We demonstrate a role for a maize remorin ( ZmREM6.3 ) in quantitative resistance against northern leaf blight using high-resolution fine mapping, expression analysis, and mutants. This is the first evidence of a role for remorins in plant-fungal interactions. Quantitative disease resistance (QDR) is important for the development of crop cultivars and is particularly useful when loci also confer multiple disease resistance. Despite its widespread use, the underlying mechanisms of QDR remain largely unknown. In this study, we fine-mapped a known quantitative trait locus (QTL) conditioning disease resistance on chromosome 1 of maize. This locus confers resistance to three foliar diseases: northern leaf blight (NLB), caused by the fungus Setosphaeria turcica; Stewart's wilt, caused by the bacterium Pantoea stewartii; and common rust, caused by the fungus Puccinia sorghi. The Stewart's wilt QTL was confined to a 5.26-Mb interval, while the rust QTL was reduced to an overlapping 2.56-Mb region. We show tight linkage between the NLB QTL locus and the loci conferring resistance to Stewart's wilt and common rust. Pleiotropy cannot be excluded for the Stewart's wilt and the common rust QTL, as they were fine-mapped to overlapping regions. Four positional candidate genes within the 243-kb NLB interval were examined with expression and mutant analysis: a gene with homology to an F-box gene, a remorin gene (ZmREM6.3), a chaperonin gene, and an uncharacterized gene. The F-box gene and ZmREM6.3 were more highly expressed in the resistant line. Transposon tagging mutants were tested for the chaperonin and ZmREM6.3, and the remorin mutant was found to be more susceptible to NLB. The putative F-box is a strong candidate, but mutants were not available to test this gene. Multiple lines of evidence strongly suggest a role for ZmREM6.3 in quantitative disease resistance.
Collapse
Affiliation(s)
- Tiffany M Jamann
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA.
| | - Xingyu Luo
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Laura Morales
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Judith M Kolkman
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Chia-Lin Chung
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Rebecca J Nelson
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| |
Collapse
|
23
|
Ding J, Ali F, Chen G, Li H, Mahuku G, Yang N, Narro L, Magorokosho C, Makumbi D, Yan J. Genome-wide association mapping reveals novel sources of resistance to northern corn leaf blight in maize. BMC PLANT BIOLOGY 2015; 15:206. [PMID: 26289207 PMCID: PMC4546088 DOI: 10.1186/s12870-015-0589-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 08/13/2015] [Indexed: 05/02/2023]
Abstract
BACKGROUND Northern corn leaf blight (NCLB) caused by Exserohilum turcicum is a destructive disease in maize. Using host resistance to minimize the detrimental effects of NCLB on maize productivity is the most cost-effective and appealing disease management strategy. However, this requires the identification and use of stable resistance genes that are effective across different environments. RESULTS We evaluated a diverse maize population comprised of 999 inbred lines across different environments for resistance to NCLB. To identify genomic regions associated with NCLB resistance in maize, a genome-wide association analysis was conducted using 56,110 single-nucleotide polymorphism markers. Single-marker and haplotype-based associations, as well as Anderson-Darling tests, identified alleles significantly associated with NCLB resistance. The single-marker and haplotype-based association mappings identified twelve and ten loci (genes), respectively, that were significantly associated with resistance to NCLB. Additionally, by dividing the population into three subgroups and performing Anderson-Darling tests, eighty one genes were detected, and twelve of them were related to plant defense. Identical defense genes were identified using the three analyses. CONCLUSION An association panel including 999 diverse lines was evaluated for resistance to NCLB in multiple environments, and a large number of resistant lines were identified and can be used as reliable resistance resource in maize breeding program. Genome-wide association study reveals that NCLB resistance is a complex trait which is under the control of many minor genes with relatively low effects. Pyramiding these genes in the same background is likely to result in stable resistance to NCLB.
Collapse
Affiliation(s)
- Junqiang Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Farhan Ali
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Gengshen Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Huihui Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - George Mahuku
- Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico.
| | - Ning Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Luis Narro
- Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico.
| | - Cosmos Magorokosho
- Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico.
| | - Dan Makumbi
- Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico.
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
24
|
Hurni S, Scheuermann D, Krattinger SG, Kessel B, Wicker T, Herren G, Fitze MN, Breen J, Presterl T, Ouzunova M, Keller B. The maize disease resistance gene Htn1 against northern corn leaf blight encodes a wall-associated receptor-like kinase. Proc Natl Acad Sci U S A 2015; 112:8780-5. [PMID: 26124097 PMCID: PMC4507197 DOI: 10.1073/pnas.1502522112] [Citation(s) in RCA: 186] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Northern corn leaf blight (NCLB) caused by the hemibiotrophic fungus Exserohilum turcicum is an important foliar disease of maize that is mainly controlled by growing resistant maize cultivars. The Htn1 locus confers quantitative and partial NCLB resistance by delaying the onset of lesion formation. Htn1 represents an important source of genetic resistance that was originally introduced from a Mexican landrace into modern maize breeding lines in the 1970s. Using a high-resolution map-based cloning approach, we delimited Htn1 to a 131.7-kb physical interval on chromosome 8 that contained three candidate genes encoding two wall-associated receptor-like kinases (ZmWAK-RLK1 and ZmWAK-RLK2) and one wall-associated receptor-like protein (ZmWAK-RLP1). TILLING (targeting induced local lesions in genomes) mutants in ZmWAK-RLK1 were more susceptible to NCLB than wild-type plants, both in greenhouse experiments and in the field. ZmWAK-RLK1 contains a nonarginine-aspartate (non-RD) kinase domain, typically found in plant innate immune receptors. Sequence comparison showed that the extracellular domain of ZmWAK-RLK1 is highly diverse between different maize genotypes. Furthermore, an alternative splice variant resulting in a truncated protein was present at higher frequency in the susceptible parents of the mapping populations compared with in the resistant parents. Hence, the quantitative Htn1 disease resistance in maize is encoded by an unusual innate immune receptor with an extracellular wall-associated kinase domain. These results further highlight the importance of this protein family in resistance to adapted pathogens.
Collapse
Affiliation(s)
- Severine Hurni
- Institute of Plant Biology, University of Zurich, CH-8008 Zurich, Switzerland
| | | | - Simon G Krattinger
- Institute of Plant Biology, University of Zurich, CH-8008 Zurich, Switzerland
| | | | - Thomas Wicker
- Institute of Plant Biology, University of Zurich, CH-8008 Zurich, Switzerland
| | - Gerhard Herren
- Institute of Plant Biology, University of Zurich, CH-8008 Zurich, Switzerland
| | - Mirjam N Fitze
- Institute of Plant Biology, University of Zurich, CH-8008 Zurich, Switzerland
| | - James Breen
- Institute of Plant Biology, University of Zurich, CH-8008 Zurich, Switzerland
| | | | | | - Beat Keller
- Institute of Plant Biology, University of Zurich, CH-8008 Zurich, Switzerland;
| |
Collapse
|
25
|
Abstract
Multiple disease resistance has important implications for plant fitness, given the selection pressure that many pathogens exert directly on natural plant populations and indirectly via crop improvement programs. Evidence of a locus conditioning resistance to multiple pathogens was found in bin 1.06 of the maize genome with the allele from inbred line "Tx303" conditioning quantitative resistance to northern leaf blight (NLB) and qualitative resistance to Stewart's wilt. To dissect the genetic basis of resistance in this region and to refine candidate gene hypotheses, we mapped resistance to the two diseases. Both resistance phenotypes were localized to overlapping regions, with the Stewart's wilt interval refined to a 95.9-kb segment containing three genes and the NLB interval to a 3.60-Mb segment containing 117 genes. Regions of the introgression showed little to no recombination, suggesting structural differences between the inbred lines Tx303 and "B73," the parents of the fine-mapping population. We examined copy number variation across the region using next-generation sequencing data, and found large variation in read depth in Tx303 across the region relative to the reference genome of B73. In the fine-mapping region, association mapping for NLB implicated candidate genes, including a putative zinc finger and pan1. We tested mutant alleles and found that pan1 is a susceptibility gene for NLB and Stewart's wilt. Our data strongly suggest that structural variation plays an important role in resistance conditioned by this region, and pan1, a gene conditioning susceptibility for NLB, may underlie the QTL.
Collapse
|
26
|
Ali F, Pan Q, Chen G, Zahid KR, Yan J. Evidence of Multiple Disease Resistance (MDR) and implication of meta-analysis in marker assisted selection. PLoS One 2013; 8:e68150. [PMID: 23874526 PMCID: PMC3707948 DOI: 10.1371/journal.pone.0068150] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 05/26/2013] [Indexed: 11/30/2022] Open
Abstract
Meta-analysis was performed for three major foliar diseases with the aim to find out the total number of QTL responsible for these diseases and depict some real QTL for molecular breeding and marker assisted selection (MAS) in maize. Furthermore, we confirmed our results with some major known disease resistance genes and most well-known gene family of nucleotide binding site (NBS) encoding genes. Our analysis revealed that disease resistance QTL were randomly distributed in maize genome, but were clustered at different regions of the chromosomes. Totally 389 QTL were observed for these three major diseases in diverse maize germplasm, out of which 63 QTL were controlling more than one disease revealing the presence of multiple disease resistance (MDR). 44 real-QTLs were observed based on 4 QTL as standard in a specific region of genome. We also confirmed the Ht1 and Ht2 genes within the region of real QTL and 14 NBS-encoding genes. On chromosome 8 two NBS genes in one QTL were observed and on chromosome 3, several cluster and maximum MDR QTL were observed indicating that the apparent clustering could be due to genes exhibiting pleiotropic effect. Significant relationship was observed between the number of disease QTL and total genes per chromosome based on the reference genome B73. Therefore, we concluded that disease resistance genes are abundant in maize genome and these results can unleash the phenomenon of MDR. Furthermore, these results could be very handy to focus on hot spot on different chromosome for fine mapping of disease resistance genes and MAS.
Collapse
Affiliation(s)
- Farhan Ali
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Cereal Crops Research Institute (CCRI) Pirsabak Nowshera, Khyber Pakhtunkhwa, Pakistan
| | - Qingchun Pan
- National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Genshen Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Kashif Rafiq Zahid
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
27
|
Holliday JL, Jones SA, Simpson JA, Glen M, Edwards J, Robinson A, Burgman MA. A Novel Spore Collection Device for Sampling Exposure Pathways: A Case Study of Puccinia psidii. PLANT DISEASE 2013; 97:828-834. [PMID: 30722638 DOI: 10.1094/pdis-06-12-0565-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A device comprising a filter attached to a vacuum cleaner was purpose-built to sample rust spores from three potentially high-risk pathways in Australia: passengers, fresh flowers, and sea cargo. The proportion of spores recovered from eight surfaces comparable with those on each pathway (cotton, denim, roses, carnations, chrysanthemums, wood, plastic, and metal) was estimated in the laboratory. Spore recovery percentages were highest for denim clothing (61% Puccinia triticina Erikss. and 62% Uromycladium tepperianum) and lowest for carnations (4% P. triticina Erikss. and 5% U. tepperianum). Subsequently, the device was tested at several locations on the Central Coast of New South Wales, Australia, recently affected by a "myrtle rust" outbreak. Symptomatic and asymptomatic myrtle rust hosts, myrtle rust nonhosts, and inanimate objects (e.g., clothing and vehicles) were sampled in conjunction with the emergency response to the outbreak. A polymerase chain reaction (PCR) assay developed for P. psidii established the presence of myrtle rust, and visual inspections provided spore count estimations. All samples from symptomatic myrtle rust hosts produced positive PCR results and spore count estimations were generally much greater. Several samples from asymptomatic myrtle rust hosts, myrtle rust nonhosts, and inanimate objects also produced positive PCR results; however, there were discrepancies between PCR results and spore count estimations in some of these samples, all of which had <100 spores. This study highlights the utility of the device and analytical methodology, especially during the early stages of a disease outbreak when infection symptoms on plants and contamination on objects is not visible upon gross examination.
Collapse
Affiliation(s)
- J L Holliday
- Australian Centre of Excellence for Risk Analysis, School of Botany, University of Melbourne, Parkville, Victoria 3010, Australia
| | - S A Jones
- Australian Centre of Excellence for Risk Analysis, School of Botany, University of Melbourne, Parkville, Victoria 3010, Australia
| | - J A Simpson
- Department of Agriculture, Fisheries and Forestry, Canberra, ACT 2601, Australia
| | - M Glen
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - J Edwards
- Department of Primary Industries, Knoxfield, Victoria 3180, Australia
| | - A Robinson
- Australian Centre of Excellence for Risk Analysis, School of Botany, and Department of Mathematics and Statistics, University of Melbourne
| | - M A Burgman
- Australian Centre of Excellence for Risk Analysis, School of Botany, University of Melbourne
| |
Collapse
|
28
|
Ali F, Yan J. Disease resistance in maize and the role of molecular breeding in defending against global threat. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2012; 54:134-51. [PMID: 22333113 DOI: 10.1111/j.1744-7909.2012.01105.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Diseases are a potential threat to global food security but plants have evolved an extensive array of methodologies to cope with the invading pathogens. Non-host resistance and quantitative resistance are broad spectrum forms of resistance, and all kinds of resistances are controlled by extremely diverse genes called "R-genes". R-genes follow different mechanisms to defend plants and PAMP-induced defenses in susceptible host plants are referred to as basal resistance. Genetic and phenotypic diversity are vital in maize (Zea mays L.); as such, genome wide association study (GWAS) along with certain other methodologies can explore the maximum means of genetic diversity. Exploring the complete genetic architecture to manipulate maize genetically reduces the losses from hazardous diseases. Genomic studies can reveal the interaction between different genes and their pathways. By confirming the specific role of these genes and protein-protein interaction (proteomics) via advanced molecular and bioinformatics tools, we can shed a light on the most complicated and abstruse phenomena of resistance.
Collapse
Affiliation(s)
- Farhan Ali
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | | |
Collapse
|
29
|
Belcher AR, Zwonitzer JC, Santa Cruz J, Krakowsky MD, Chung CL, Nelson R, Arellano C, Balint-Kurti PJ. Analysis of quantitative disease resistance to southern leaf blight and of multiple disease resistance in maize, using near-isogenic lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:433-445. [PMID: 21997760 DOI: 10.1007/s00122-011-1718-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 09/27/2011] [Indexed: 05/31/2023]
Abstract
Maize inbred lines NC292 and NC330 were derived by repeated backcrossing of an elite source of southern leaf blight (SLB) resistance (NC250P) to the SLB-susceptible line B73, with selection for SLB resistance among and within backcross families at each generation. Consequently, while B73 is very SLB susceptible, its sister lines NC292 and NC330 are both SLB resistant. Previously, we identified the 12 introgressions from NC250P that differentiate NC292 and NC330 from B73. The goals of this study were to determine the effects of each introgression on resistance to SLB and to two other foliar fungal diseases of maize, northern leaf blight and gray leaf spot. This was achieved by generating and testing a set of near isogenic lines carry single or combinations of just two or three introgressions in a B73 background. Introgressions 3B, 6A, and 9B (bins 3.03-3.04, 6.01, and 9.02-9.03) all conferred significant levels of SLB resistance in the field. Introgression 6A was the only introgression that had a significant effect on juvenile plant resistance to SLB. Introgressions 6A and 9B conferred resistance to multiple diseases.
Collapse
Affiliation(s)
- Araby R Belcher
- Department of Plant Pathology, North Carolina State University, Raleigh, NC 27695-7616, USA
| | | | | | | | | | | | | | | |
Collapse
|
30
|
Berkman PJ, Lai K, Lorenc MT, Edwards D. Next-generation sequencing applications for wheat crop improvement. AMERICAN JOURNAL OF BOTANY 2012; 99:365-71. [PMID: 22268223 DOI: 10.3732/ajb.1100309] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Bread wheat (Triticum aestivum; Poaceae) is a crop plant of great importance. It provides nearly 20% of the world's daily food supply measured by calorie intake, similar to that provided by rice. The yield of wheat has doubled over the last 40 years due to a combination of advanced agronomic practice and improved germplasm through selective breeding. More recently, yield growth has been less dramatic, and a significant improvement in wheat production will be required if demand from the growing human population is to be met. Next-generation sequencing (NGS) technologies are revolutionizing biology and can be applied to address critical issues in plant biology. Technologies can produce draft sequences of genomes with a significant reduction to the cost and timeframe of traditional technologies. In addition, NGS technologies can be used to assess gene structure and expression, and importantly, to identify heritable genome variation underlying important agronomic traits. This review provides an overview of the wheat genome and NGS technologies, details some of the problems in applying NGS technology to wheat, and describes how NGS technologies are starting to impact wheat crop improvement.
Collapse
Affiliation(s)
- Paul J Berkman
- University of Queensland, School of Agriculture and Food Sciences and Australian Centre for Plant Functional Genomics, Brisbane, QLD 4072, Australia
| | | | | | | |
Collapse
|
31
|
Chung CL, Poland J, Kump K, Benson J, Longfellow J, Walsh E, Balint-Kurti P, Nelson R. Targeted discovery of quantitative trait loci for resistance to northern leaf blight and other diseases of maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:307-26. [PMID: 21526397 DOI: 10.1007/s00122-011-1585-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2010] [Accepted: 03/24/2011] [Indexed: 05/02/2023]
Abstract
To capture diverse alleles at a set of loci associated with disease resistance in maize, heterogeneous inbred family (HIF) analysis was applied for targeted QTL mapping and near-isogenic line (NIL) development. Tropical maize lines CML52 and DK888 were chosen as donors of alleles based on their known resistance to multiple diseases. Chromosomal regions ("bins"; n = 39) associated with multiple disease resistance (MDR) were targeted based on a consensus map of disease QTLs in maize. We generated HIFs segregating for the targeted loci but isogenic at ~97% of the genome. To test the hypothesis that CML52 and DK888 alleles at MDR hotspots condition broad-spectrum resistance, HIFs and derived NILs were tested for resistance to northern leaf blight (NLB), southern leaf blight (SLB), gray leaf spot (GLS), anthracnose leaf blight (ALB), anthracnose stalk rot (ASR), common rust, common smut, and Stewart's wilt. Four NLB QTLs, two ASR QTLs, and one Stewart's wilt QTL were identified. In parallel, a population of 196 recombinant inbred lines (RILs) derived from B73 × CML52 was evaluated for resistance to NLB, GLS, SLB, and ASR. The QTLs mapped (four for NLB, five for SLB, two for GLS, and two for ASR) mostly corresponded to those found using the NILs. Combining HIF- and RIL-based analyses, we discovered two disease QTLs at which CML52 alleles were favorable for more than one disease. A QTL in bin 1.06-1.07 conferred resistance to NLB and Stewart's wilt, and a QTL in 6.05 conferred resistance to NLB and ASR.
Collapse
Affiliation(s)
- Chia-Lin Chung
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY14853, USA
| | | | | | | | | | | | | | | |
Collapse
|
32
|
Poland JA, Bradbury PJ, Buckler ES, Nelson RJ. Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize. Proc Natl Acad Sci U S A 2011; 108:6893-8. [PMID: 21482771 PMCID: PMC3084105 DOI: 10.1073/pnas.1010894108] [Citation(s) in RCA: 220] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Quantitative resistance to plant pathogens, controlled by multiple loci of small effect, is important for food production, food security, and food safety but is poorly understood. To gain insights into the genetic architecture of quantitative resistance in maize, we evaluated a 5,000-inbred-line nested association mapping population for resistance to northern leaf blight, a maize disease of global economic importance. Twenty-nine quantitative trait loci were identified, and most had multiple alleles. The large variation in resistance phenotypes could be attributed to the accumulation of numerous loci of small additive effects. Genome-wide nested association mapping, using 1.6 million SNPs, identified multiple candidate genes related to plant defense, including receptor-like kinase genes similar to those involved in basal defense. These results are consistent with the hypothesis that quantitative disease resistance in plants is conditioned by a range of mechanisms and could have considerable mechanistic overlap with basal resistance.
Collapse
Affiliation(s)
- Jesse A. Poland
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853
| | - Peter J. Bradbury
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853
- US Department of Agriculture, Agricultural Research Service, Ithaca, NY 14853; and
| | - Edward S. Buckler
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853
- US Department of Agriculture, Agricultural Research Service, Ithaca, NY 14853; and
| | - Rebecca J. Nelson
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853
| |
Collapse
|
33
|
Multivariate analysis of maize disease resistances suggests a pleiotropic genetic basis and implicates a GST gene. Proc Natl Acad Sci U S A 2011; 108:7339-44. [PMID: 21490302 DOI: 10.1073/pnas.1011739108] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plants are attacked by pathogens representing diverse taxonomic groups, such that genes providing multiple disease resistance (MDR) are expected to be under positive selection pressure. To address the hypothesis that naturally occurring allelic variation conditions MDR, we extended the framework of structured association mapping to allow for the analysis of correlated complex traits and the identification of pleiotropic genes. The multivariate analytical approach used here is directly applicable to any species and set of traits exhibiting correlation. From our analysis of a diverse panel of maize inbred lines, we discovered high positive genetic correlations between resistances to three globally threatening fungal diseases. The maize panel studied exhibits rapidly decaying linkage disequilibrium that generally occurs within 1 or 2 kb, which is less than the average length of a maize gene. The positive correlations therefore suggested that functional allelic variation at specific genes for MDR exists in maize. Using a multivariate test statistic, a glutathione S-transferase (GST) gene was found to be associated with modest levels of resistance to all three diseases. Resequencing analysis pinpointed the association to a histidine (basic amino acid) for aspartic acid (acidic amino acid) substitution in the encoded protein domain that defines GST substrate specificity and biochemical activity. The known functions of GSTs suggested that variability in detoxification pathways underlie natural variation in maize MDR.
Collapse
|
34
|
Poland JA, Nelson RJ. In the eye of the beholder: the effect of rater variability and different rating scales on QTL mapping. PHYTOPATHOLOGY 2011; 101:290-8. [PMID: 20955083 DOI: 10.1094/phyto-03-10-0087] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The agronomic importance of developing durably resistant cultivars has led to substantial research in the field of quantitative disease resistance (QDR) and, in particular, mapping quantitative trait loci (QTL) for disease resistance. The assessment of QDR is typically conducted by visual estimation of disease severity, which raises concern over the accuracy and precision of visual estimates. Although previous studies have examined the factors affecting the accuracy and precision of visual disease assessment in relation to the true value of disease severity, the impact of this variability on the identification of disease resistance QTL has not been assessed. In this study, the effects of rater variability and rating scales on mapping QTL for northern leaf blight resistance in maize were evaluated in a recombinant inbred line population grown under field conditions. The population of 191 lines was evaluated by 22 different raters using a direct percentage estimate, a 0-to-9 ordinal rating scale, or both. It was found that more experienced raters had higher precision and that using a direct percentage estimation of diseased leaf area produced higher precision than using an ordinal scale. QTL mapping was then conducted using the disease estimates from each rater using stepwise general linear model selection (GLM) and inclusive composite interval mapping (ICIM). For GLM, the same QTL were largely found across raters, though some QTL were only identified by a subset of raters. The magnitudes of estimated allele effects at identified QTL varied drastically, sometimes by as much as threefold. ICIM produced highly consistent results across raters and for the different rating scales in identifying the location of QTL. We conclude that, despite variability between raters, the identification of QTL was largely consistent among raters, particularly when using ICIM. However, care should be taken in estimating QTL allele effects, because this was highly variable and rater dependent.
Collapse
Affiliation(s)
- Jesse A Poland
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | | |
Collapse
|