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Cui L, Sun M, Zhang L, Zhu H, Kong Q, Dong L, Liu X, Zeng X, Sun Y, Zhang H, Duan L, Li W, Zou C, Zhang Z, Cai W, Ming Y, Lübberstedt T, Liu H, Yang X, Li X. Quantitative trait locus analysis of gray leaf spot resistance in the maize IBM Syn10 DH population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:183. [PMID: 39002016 DOI: 10.1007/s00122-024-04694-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 07/04/2024] [Indexed: 07/15/2024]
Abstract
KEY MESSAGE The exploration and dissection of a set of QTLs and candidate genes for gray leaf spot disease resistance using two fully assembled parental genomes may help expedite maize resistance breeding. The fungal disease of maize known as gray leaf spot (GLS), caused by Cercospora zeae-maydis and Cercospora zeina, is a significant concern in China, Southern Africa, and the USA. Resistance to GLS is governed by multiple genes with an additive effect and is influenced by both genotype and environment. The most effective way to reduce the cost of production is to develop resistant hybrids. In this study, we utilized the IBM Syn 10 Doubled Haploid (IBM Syn10 DH) population to identify quantitative trait loci (QTLs) associated with resistance to gray leaf spot (GLS) in multiple locations. Analysis of seven distinct environments revealed a total of 58 QTLs, 49 of which formed 12 discrete clusters distributed across chromosomes 1, 2, 3, 4, 8 and 10. By comparing these findings with published research, we identified colocalized QTLs or GWAS loci within eleven clustering intervals. By integrating transcriptome data with genomic structural variations between parental individuals, we identified a total of 110 genes that exhibit both robust disparities in gene expression and structural alterations. Further analysis revealed 19 potential candidate genes encoding conserved resistance gene domains, including putative leucine-rich repeat receptors, NLP transcription factors, fucosyltransferases, and putative xyloglucan galactosyltransferases. Our results provide a valuable resource and linked loci for GLS marker resistance selection breeding in maize.
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Affiliation(s)
- Lina Cui
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
- Key Laboratory of Integrated Pest Management on Crops in Southwest China, Ministry of Agriculture, Chengdu, 610066, China
| | - Mingfei Sun
- State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Lin Zhang
- Department of Agronomy, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
| | - Hongjie Zhu
- State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Qianqian Kong
- School of Agriculture, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Ling Dong
- Department of Agronomy, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
| | - Xianjun Liu
- Department of Agronomy, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
| | - Xing Zeng
- Department of Agronomy, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
| | - Yanjie Sun
- Suihua Branch, Heilongjiang Academy of Agricultural Sciences, Suihua, 152052, China
| | - Haiyan Zhang
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
- Key Laboratory of Integrated Pest Management on Crops in Southwest China, Ministry of Agriculture, Chengdu, 610066, China
| | - Luyao Duan
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
- Key Laboratory of Integrated Pest Management on Crops in Southwest China, Ministry of Agriculture, Chengdu, 610066, China
| | - Wenyi Li
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
- Key Laboratory of Integrated Pest Management on Crops in Southwest China, Ministry of Agriculture, Chengdu, 610066, China
| | - Chengjia Zou
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
- Key Laboratory of Integrated Pest Management on Crops in Southwest China, Ministry of Agriculture, Chengdu, 610066, China
| | - Zhenyu Zhang
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
- Key Laboratory of Integrated Pest Management on Crops in Southwest China, Ministry of Agriculture, Chengdu, 610066, China
| | - WeiLi Cai
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
- Key Laboratory of Integrated Pest Management on Crops in Southwest China, Ministry of Agriculture, Chengdu, 610066, China
| | - Yulin Ming
- Liangshan Seed Management Station, Xichang, 615000, China
| | | | - Hongjun Liu
- State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Xuerong Yang
- State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
| | - Xiao Li
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China.
- Key Laboratory of Integrated Pest Management on Crops in Southwest China, Ministry of Agriculture, Chengdu, 610066, China.
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Shinder I, Hu R, Ji HJ, Chao KH, Pertea M. EASTR: Identifying and eliminating systematic alignment errors in multi-exon genes. Nat Commun 2023; 14:7223. [PMID: 37940654 PMCID: PMC10632439 DOI: 10.1038/s41467-023-43017-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 10/30/2023] [Indexed: 11/10/2023] Open
Abstract
Accurate alignment of transcribed RNA to reference genomes is a critical step in the analysis of gene expression, which in turn has broad applications in biomedical research and in the basic sciences. We reveal that widely used splice-aware aligners, such as STAR and HISAT2, can introduce erroneous spliced alignments between repeated sequences, leading to the inclusion of falsely spliced transcripts in RNA-seq experiments. In some cases, the 'phantom' introns resulting from these errors make their way into widely-used genome annotation databases. To address this issue, we present EASTR (Emending Alignments of Spliced Transcript Reads), a software tool that detects and removes falsely spliced alignments or transcripts from alignment and annotation files. EASTR improves the accuracy of spliced alignments across diverse species, including human, maize, and Arabidopsis thaliana, by detecting sequence similarity between intron-flanking regions. We demonstrate that applying EASTR before transcript assembly substantially reduces false positive introns, exons, and transcripts, improving the overall accuracy of assembled transcripts. Additionally, we show that EASTR's application to reference annotation databases can detect and correct likely cases of mis-annotated transcripts.
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Affiliation(s)
- Ida Shinder
- Cross Disciplinary Graduate Program in Biomedical Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA.
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
| | - Richard Hu
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Hyun Joo Ji
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Kuan-Hao Chao
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Mihaela Pertea
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA.
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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Zhang Y, Zhang Y, Ge X, Yuan Y, Jin Y, Wang Y, Zhao L, Han X, Hu W, Yang L, Gao C, Wei X, Li F, Yang Z. Genome-wide association analysis reveals a novel pathway mediated by a dual-TIR domain protein for pathogen resistance in cotton. Genome Biol 2023; 24:111. [PMID: 37165460 PMCID: PMC10170703 DOI: 10.1186/s13059-023-02950-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 04/24/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Verticillium wilt is one of the most devasting diseases for many plants, leading to global economic loss. Cotton is known to be vulnerable to its fungal pathogen, Verticillium dahliae, yet the related genetic mechanism remains unknown. RESULTS By genome-wide association studies of 419 accessions of the upland cotton, Gossypium hirsutum, we identify ten loci that are associated with resistance against Verticillium wilt. Among these loci, SHZDI1/SHZDP2/AYDP1 from chromosome A10 is located on a fragment introgressed from Gossypium arboreum. We characterize a large cluster of Toll/interleukin 1 (TIR) nucleotide-binding leucine-rich repeat receptors in this fragment. We then identify a dual-TIR domain gene from this cluster, GhRVD1, which triggers an effector-independent cell death and is induced by Verticillium dahliae. We confirm that GhRVD1 is one of the causal gene for SHZDI1. Allelic variation in the TIR domain attenuates GhRVD1-mediated resistance against Verticillium dahliae. Homodimerization between TIR1-TIR2 mediates rapid immune response, while disruption of its αD- and αE-helices interface eliminates the autoactivity and self-association of TIR1-TIR2. We further demonstrate that GhTIRP1 inhibits the autoactivity and self-association of TIR1-TIR2 by competing for binding to them, thereby preventing the resistance to Verticillium dahliae. CONCLUSIONS We propose the first working model for TIRP1 involved self-association and autoactivity of dual-TIR domain proteins that confer compromised pathogen resistance of dual-TIR domain proteins in plants. The findings reveal a novel mechanism on Verticillium dahliae resistance and provide genetic basis for breeding in future.
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Affiliation(s)
- Yihao Zhang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450000, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yaning Zhang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450000, China
| | - Xiaoyang Ge
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yuan Yuan
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yuying Jin
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Ye Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Lihong Zhao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiao Han
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wei Hu
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450000, China
| | - Lan Yang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Chenxu Gao
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450000, China
| | - Xi Wei
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Fuguang Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450000, China.
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China.
| | - Zhaoen Yang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450000, China.
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
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Xia X, Wei Q, Xiao C, Ye Y, Li Z, Marivingt-Mounir C, Chollet JF, Liu W, Wu H. Genomic survey of NPF and NRT2 transporter gene families in five inbred maize lines and their responses to pathogens infection. Genomics 2023; 115:110555. [PMID: 36596368 DOI: 10.1016/j.ygeno.2022.110555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 11/02/2022] [Accepted: 12/30/2022] [Indexed: 01/01/2023]
Abstract
Besides manipulating nitrate uptake and allocation, nitrate transporters (NRTs) are also known to play crucial roles in pathogen defense and stress response. By blasting with the model NRT genes of poplar and Arabidopsis, a total of 408 gene members were identified from 5 maize inbred lines in which the number of NRTs ranged from 72 to 88. Phylogenetic analysis showed that the NRT genes of maize were classified into NRT1/PTR (NPF), NRT2 and NRT3 subfamilies, respectively. Marked divergence of the duplication patterns of NRT genes were identified, which may be a new basis for classification and identification of maize varieties. In terms of biotic stress, NRT2.5A showed an enhanced expression during the pathogen infection of Colletotrichum graminicola, while NRT1c4C was down-regulated, suggesting that maize NRT transporters may have both positive and negative roles in the disease resistance response. This work will promote the further studies of NRT gene families in maize, as well as be beneficial for further understanding of their potential roles in plant-pathogen interactions.
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Affiliation(s)
- Xinyao Xia
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing 100193, China
| | - Qiuhe Wei
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing 100193, China
| | - Chunxia Xiao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing 100193, China
| | - Yiping Ye
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing 100193, China
| | - Zhiqiang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing 100193, China
| | - Cécile Marivingt-Mounir
- Institut de Chimie des Milieux et des Matériaux de Poitiers (IC2MP), Unité Mixte de Recherche CNRS 7285, Université de Poitiers, 4 rue Michel Brunet, TSA 51106, F-86073 Poitiers, Cedex 9, France
| | - Jean-François Chollet
- Institut de Chimie des Milieux et des Matériaux de Poitiers (IC2MP), Unité Mixte de Recherche CNRS 7285, Université de Poitiers, 4 rue Michel Brunet, TSA 51106, F-86073 Poitiers, Cedex 9, France
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing 100193, China.
| | - Hanxiang Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing 100193, China.
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He W, Zhu Y, Leng Y, Yang L, Zhang B, Yang J, Zhang X, Lan H, Tang H, Chen J, Gao S, Tan J, Kang J, Deng L, Li Y, He Y, Rong T, Cao M. Transcriptomic Analysis Reveals Candidate Genes Responding Maize Gray Leaf Spot Caused by Cercospora zeina. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112257. [PMID: 34834621 PMCID: PMC8625984 DOI: 10.3390/plants10112257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 05/27/2023]
Abstract
Gray leaf spot (GLS), caused by the fungal pathogen Cercospora zeina (C. zeina), is one of the most destructive soil-borne diseases in maize (Zea mays L.), and severely reduces maize production in Southwest China. However, the mechanism of resistance to GLS is not clear and few resistant alleles have been identified. Two maize inbred lines, which were shown to be resistant (R6) and susceptible (S8) to GLS, were injected by C. zeina spore suspensions. Transcriptome analysis was carried out with leaf tissue at 0, 6, 24, 144, and 240 h after inoculation. Compared with 0 h of inoculation, a total of 667 and 419 stable common differentially expressed genes (DEGs) were found in the resistant and susceptible lines across the four timepoints, respectively. The DEGs were usually enriched in 'response to stimulus' and 'response to stress' in GO term analysis, and 'plant-pathogen interaction', 'MAPK signaling pathways', and 'plant hormone signal transduction' pathways, which were related to maize's response to GLS, were enriched in KEGG analysis. Weighted-Genes Co-expression Network Analysis (WGCNA) identified two modules, while twenty hub genes identified from these indicated that plant hormone signaling, calcium signaling pathways, and transcription factors played a central role in GLS sensing and response. Combing DEGs and QTL mapping, five genes were identified as the consensus genes for the resistance of GLS. Two genes, were both putative Leucine-rich repeat protein kinase family proteins, specifically expressed in R6. In summary, our results can provide resources for gene mining and exploring the mechanism of resistance to GLS in maize.
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Affiliation(s)
- Wenzhu He
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.Z.); (H.L.); (S.G.); (T.R.)
| | - Yonghui Zhu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Yifeng Leng
- College of Agricultural Sciences, Xichang University, Xichang 615000, China;
| | - Lin Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Biao Zhang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Junpin Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Xiao Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.Z.); (H.L.); (S.G.); (T.R.)
| | - Hai Lan
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.Z.); (H.L.); (S.G.); (T.R.)
| | - Haitao Tang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Jie Chen
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Shibin Gao
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.Z.); (H.L.); (S.G.); (T.R.)
| | - Jun Tan
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Jiwei Kang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Luchang Deng
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Yan Li
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Yuanyuan He
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Tingzhao Rong
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.Z.); (H.L.); (S.G.); (T.R.)
| | - Moju Cao
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.Z.); (H.L.); (S.G.); (T.R.)
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Chen L, Liu L, Li Z, Zhang Y, Kang MS, Wang Y, Fan X. High-density mapping for gray leaf spot resistance using two related tropical maize recombinant inbred line populations. Mol Biol Rep 2021; 48:3379-3392. [PMID: 33890197 DOI: 10.1007/s11033-021-06350-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/08/2021] [Indexed: 01/18/2023]
Abstract
Gray leaf spot (GLS) caused by Cercospora zeae-maydis or Cercospora zeina is one of the devastating maize foliar diseases worldwide. Identification of GLS-resistant quantitative trait loci (QTL)/genes plays an urgent role in improving GLS resistance in maize breeding practice. Two groups of recombinant inbred line (RIL) populations derived from CML373 × Ye107 and Chang7-2 × Ye107 were generated and subjected to genotyping-by-sequencing (GBS). A total of 1,929,222,287 reads in CML373 × Ye107 (RIL-YCML) and 2,585,728,312 reads in Chang7-2 × Ye107 (RIL-YChang), with an average of 10,961,490 (RIL-YCML) and 13,609,096 (RIL-YChang) reads per individual, were got, which was roughly equal to 0.70-fold and 0.87-fold coverage of the maize B73 RefGen_V4 genome for each F7 individual, respectively. 6418 and 5139 SNP markers were extracted to construct two high-density genetic maps. Comparative analysis using these physically mapped marker loci demonstrated a satisfactory colinear relationship with the reference genome. 11 GLS-resistant QTL have been detected. The individual QTL accounted for 1.53-24.00% of the phenotypic variance explained (PVE). The new consensus QTL (qYCM-DS3-3/qYCM-LT3-1/qYCM-LT3-2) with the largest effect was located in chromosome bin 3.05, with an interval of 2.7 Mb, representing 13.08 to 24.00% of the PVE. Further gene annotation indicated that there were four candidate genes (GRMZM2G032384, GRMZM2G041415, GRMZM2G041544, and GRMZM2G035992) for qYCM-LT3-1, which may be related to GLS resistance. Combining RIL populations and GBS-based high-density genetic maps, a new larger effect QTL was delimited to a narrow genomic interval, which will provide a new resistance source for maize breeding programs.
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Affiliation(s)
- Long Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Ministry of Education Key Laboratory of Agriculture Biodiversity for Plant Disease Management, Yunnan Agricultural University, Kunming, 650201, China
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Li Liu
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Ziwei Li
- Yunnan Dehong Dai and Jingpo Nationality Institute of Agricultural Sciences, Mangshi, Yunnan, China
| | - Yudong Zhang
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Manjit S Kang
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Yunyue Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Ministry of Education Key Laboratory of Agriculture Biodiversity for Plant Disease Management, Yunnan Agricultural University, Kunming, 650201, China.
| | - Xingming Fan
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China.
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