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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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Yu T, Zhang J, Cao J, Li S, Cai Q, Li X, Li S, Li Y, He C, Ma X. Identification of Multiple Genetic Loci Related to Low-Temperature Tolerance during Germination in Maize ( Zea maize L.) through a Genome-Wide Association Study. Curr Issues Mol Biol 2023; 45:9634-9655. [PMID: 38132448 PMCID: PMC10742315 DOI: 10.3390/cimb45120602] [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: 10/25/2023] [Revised: 11/13/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Low-temperature stress during the germination stage is an important abiotic stress that affects the growth and development of northern spring maize and seriously restricts maize yield and quality. Although some quantitative trait locis (QTLs) related to low-temperature tolerance in maize have been detected, only a few can be commonly detected, and the QTL intervals are large, indicating that low-temperature tolerance is a complex trait that requires more in-depth research. In this study, 296 excellent inbred lines from domestic and foreign origins (America and Europe) were used as the study materials, and a low-coverage resequencing method was employed for genome sequencing. Five phenotypic traits related to low-temperature tolerance were used to assess the genetic diversity of maize through a genome-wide association study (GWAS). A total of 14 SNPs significantly associated with low-temperature tolerance were detected (-log10(P) > 4), and an SNP consistently linked to low-temperature tolerance in the field and indoors during germination was utilized as a marker. This SNP, 14,070, was located on chromosome 5 at position 2,205,723, which explained 4.84-9.68% of the phenotypic variation. The aim of this study was to enrich the genetic theory of low-temperature tolerance in maize and provide support for the innovation of low-temperature tolerance resources and the breeding of new varieties.
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Affiliation(s)
- Tao Yu
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.C.); (Q.C.); (X.L.); (X.M.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
- Key Laboratory of Germplasm Resources Creation and Utilization of Maize, Harbin 150086, China
| | - Jianguo Zhang
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.C.); (Q.C.); (X.L.); (X.M.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
- Key Laboratory of Germplasm Resources Creation and Utilization of Maize, Harbin 150086, China
| | - Jingsheng Cao
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.C.); (Q.C.); (X.L.); (X.M.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
- Key Laboratory of Germplasm Resources Creation and Utilization of Maize, Harbin 150086, China
| | - Shujun Li
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.C.); (Q.C.); (X.L.); (X.M.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
- Key Laboratory of Germplasm Resources Creation and Utilization of Maize, Harbin 150086, China
| | - Quan Cai
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.C.); (Q.C.); (X.L.); (X.M.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
- Key Laboratory of Germplasm Resources Creation and Utilization of Maize, Harbin 150086, China
| | - Xin Li
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.C.); (Q.C.); (X.L.); (X.M.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
| | - Sinan Li
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.C.); (Q.C.); (X.L.); (X.M.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
| | - Yunlong Li
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.C.); (Q.C.); (X.L.); (X.M.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
| | - Changan He
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
- Keshan Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihaer 161000, China
| | - Xuena Ma
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.C.); (Q.C.); (X.L.); (X.M.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
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Zhang J, Liang Y, Zhang S, Xu Q, Di H, Zhang L, Dong L, Hu X, Zeng X, Liu X, Wang Z, Zhou Y. Global Landscape of Alternative Splicing in Maize Response to Low Temperature. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:15715-15725. [PMID: 36479939 DOI: 10.1021/acs.jafc.2c05969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Maize (Zea mays L.) is an important food crop planted across the world, and low-temperature stress can affect maize germination. Alternative splicing (AS) is widely present in plants under abiotic stress; however, the response of AS to low-temperature stress in maize remains unclear. In this study, a genome-wide analysis of AS during maize response to low temperatures was performed. AS events were distributed on each chromosome, approximately 2.05-2.09 AS events per gene. Seven genes only had AS in low-temperature-resistant inbred lines. A total of 278 KEGGs and 46 GOs were enriched based on overlapping AS genes, which were associated with hormone and oxidoreductase activity. The mutant was used to verify the function of AS gene ZmWRKY48, and the RGR, RSL, RRL, and RRSA of the mutant decreased by 15.16%-19.87% compared with the normal line. These results contribute to subsequent analysis of the regulatory mechanism of maize in response to low-temperature stress.
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Affiliation(s)
- Jiayue Zhang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Yuhang Liang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Simeng Zhang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Qingyu Xu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Hong Di
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Lin Zhang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Ling Dong
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Xinge Hu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Xing Zeng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Xianjun Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Zhenhua Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Yu Zhou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
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Shen F, Hu C, Huang X, Wu R, Luo S, Xu C, Zhang H, Wang X, Zhao J. Characterization of the genetic and regulatory networks associated with sugar and acid metabolism in apples via an integrated strategy. FRONTIERS IN PLANT SCIENCE 2022; 13:1066592. [PMID: 36466245 PMCID: PMC9712955 DOI: 10.3389/fpls.2022.1066592] [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: 10/11/2022] [Accepted: 10/26/2022] [Indexed: 06/17/2023]
Abstract
Although sugars and acids have a substantial influence on the taste of apple fruits, the genetic and regulatory networks underlying their metabolism in fruit remain insufficiently determined. To fully decipher the genetic basis of the accumulation of sugars and acids in apple fruits, we adopted an integrated strategy that included time-course RNA-seq, QTL mapping, and whole-genome sequencing to examine two typical cultivars ('HanFu' and 'Huahong') characterized by distinctive flavors. Whole-genome sequencing revealed substantial genetic variation between the two cultivars, thereby providing an indication of the genetic basis of the distinct phenotypes. Constructed co-expression networks yielded information regarding the intra-relationships among the accumulation of different types of metabolites, and also revealed key regulatory nodes associated with the accumulation of sugars and acids, including the genes MdEF2, MdPILS5, and MdGUN8. Additionally, on the basis of QTL mapping using a high-density genetic map, we identified a series of QTLs and functional genes underlying vital traits, including sugar and acid contents. Collectively, our methodology and observations will provide an important reference for further studies focusing on the flavor of apples.
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Affiliation(s)
- Fei Shen
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Chenyang Hu
- College of Life Science, Shanxi Key Lab of Chinese Jujube, Yan’an University, Yan’an, Shanxi, China
| | - Xin Huang
- College of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, Hebei, China
| | - Ruigang Wu
- College of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, Hebei, China
| | - Shuzhen Luo
- College of Life Science, Shanxi Key Lab of Chinese Jujube, Yan’an University, Yan’an, Shanxi, China
| | - Chengnan Xu
- College of Life Science, Shanxi Key Lab of Chinese Jujube, Yan’an University, Yan’an, Shanxi, China
| | - Hong Zhang
- College of Life Science, Shanxi Key Lab of Chinese Jujube, Yan’an University, Yan’an, Shanxi, China
| | - Xuan Wang
- Hebei Normal University of Science & Technology, Qinhuangdao, Hebei, China
| | - Jirong Zhao
- College of Life Science, Shanxi Key Lab of Chinese Jujube, Yan’an University, Yan’an, Shanxi, China
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