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Qu J, Liu G, Zheng H, Wang X, Zhang H, Gou X, Xu S, Xue J. Deciphering the Genetic Basis of Kernel Composition in a Maize Association Panel. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:20182-20193. [PMID: 39196892 DOI: 10.1021/acs.jafc.4c04683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2024]
Abstract
The primary objective in contemporary maize breeding is to pursue high quality alongside high yield. Deciphering the genetic basis of natural variation in starch, protein, oil, and fiber contents is essential for manipulating kernel composition, thereby enhancing the kernel quality and meeting growing demands. Here, we identified 12 to 88 statistically significant loci associated with kernel composition traits through a genome-wide association study (GWAS) using a panel of 212 diverse inbred lines. A regional association study pinpointed numerous causal candidate genes at these loci. Coexpression and protein-protein interaction network analyses of candidate genes revealed several causal genes directly or indirectly involved in the metabolic processes related to kernel composition traits. Subsequent mutant experiment revealed that nonsense mutations in ZmTIFY12 affect starch, protein, and fiber content, whereas nonsense mutations in ZmTT12 affect starch, protein, and oil content. These findings provide valuable guidance for improving kernel quality in maize breeding efforts.
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Affiliation(s)
- Jianzhou Qu
- College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
- The Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region, Yangling, Shaanxi 712100, China
- Maize Engineering & Technology Research Centre, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gengyu Liu
- College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Hongyun Zheng
- College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Xiaoyue Wang
- The Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region, Yangling, Shaanxi 712100, China
- Maize Engineering & Technology Research Centre, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hao Zhang
- The Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region, Yangling, Shaanxi 712100, China
- Maize Engineering & Technology Research Centre, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaonan Gou
- The Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region, Yangling, Shaanxi 712100, China
- Maize Engineering & Technology Research Centre, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shutu Xu
- The Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region, Yangling, Shaanxi 712100, China
- Maize Engineering & Technology Research Centre, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiquan Xue
- The Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region, Yangling, Shaanxi 712100, China
- Maize Engineering & Technology Research Centre, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
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Li T, Yang H, Zhang X, Zhu L, Zhang J, Wei N, Li R, Dong Y, Feng Z, Zhang X, Xue J, Xu S. Genetic architecture of ear traits based on association mapping and co-expression networks in maize inbred lines and hybrids. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:78. [PMID: 37928364 PMCID: PMC10624778 DOI: 10.1007/s11032-023-01426-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/23/2023] [Indexed: 11/07/2023]
Abstract
Ear traits are key contributors to grain yield in maize; therefore, exploring their genetic basis facilitates the improvement of grain yield. However, the underlying molecular mechanisms of ear traits remain obscure in both inbred lines and hybrids. Here, two association panels, respectively, comprising 203 inbred lines (IP) and 246 F1 hybrids (HP) were employed to identify candidate genes for six ear traits. The IP showed higher phenotypic variation and lower phenotypic mean than the HP for all traits, except ear tip-barrenness length. By conducting a genome-wide association study (GWAS) across multiple environments, 101 and 228 significant single-nucleotide polymorphisms (SNPs) associated with six ear traits were identified in the IP and HP, respectively. Of these significant SNPs identified in the HP, most showed complete-incomplete dominance and over-dominance effects for each ear trait. Combining a gene co-expression network with GWAS results, 186 and 440 candidate genes were predicted in the IP and HP, respectively, including known ear development genes ids1 and sid1. Of these, nine candidate genes were detected in both populations and expressed in maize ear and spikelet tissues. Furthermore, two key shared genes (GRMZM2G143330 and GRMZM2G171139) in both populations were found to be significantly associated with ear traits in the maize Goodman diversity panel with high-density variations. These findings advance our knowledge of the genetic architecture of ear traits between inbred lines and hybrids and provide a valuable resource for the genetic improvement of ear traits in maize. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01426-9.
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Affiliation(s)
- Ting Li
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Haoxiang Yang
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Xiaojun Zhang
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Liangjia Zhu
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Jun Zhang
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Ningning Wei
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Ranran Li
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Yuan Dong
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Zhiqian Feng
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Xinghua Zhang
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Jiquan Xue
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Shutu Xu
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
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Dong Z, Wang Y, Bao J, Li Y, Yin Z, Long Y, Wan X. The Genetic Structures and Molecular Mechanisms Underlying Ear Traits in Maize ( Zea mays L.). Cells 2023; 12:1900. [PMID: 37508564 PMCID: PMC10378120 DOI: 10.3390/cells12141900] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Maize (Zea mays L.) is one of the world's staple food crops. In order to feed the growing world population, improving maize yield is a top priority for breeding programs. Ear traits are important determinants of maize yield, and are mostly quantitatively inherited. To date, many studies relating to the genetic and molecular dissection of ear traits have been performed; therefore, we explored the genetic loci of the ear traits that were previously discovered in the genome-wide association study (GWAS) and quantitative trait locus (QTL) mapping studies, and refined 153 QTL and 85 quantitative trait nucleotide (QTN) clusters. Next, we shortlisted 19 common intervals (CIs) that can be detected simultaneously by both QTL mapping and GWAS, and 40 CIs that have pleiotropic effects on ear traits. Further, we predicted the best possible candidate genes from 71 QTL and 25 QTN clusters that could be valuable for maize yield improvement.
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Affiliation(s)
- Zhenying Dong
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; (Z.D.)
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Yanbo Wang
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; (Z.D.)
| | - Jianxi Bao
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; (Z.D.)
| | - Ya’nan Li
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; (Z.D.)
| | - Zechao Yin
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; (Z.D.)
| | - Yan Long
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; (Z.D.)
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Xiangyuan Wan
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; (Z.D.)
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
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Qu J, Zhong Y, Ding L, Liu X, Xu S, Guo D, Blennow A, Xue J. Biosynthesis, structure and functionality of starch granules in maize inbred lines with different kernel dehydration rate. Food Chem 2022; 368:130796. [PMID: 34418691 DOI: 10.1016/j.foodchem.2021.130796] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 08/04/2021] [Accepted: 08/04/2021] [Indexed: 11/25/2022]
Abstract
In this study, we report important relationships between kernel starch and kernel dehydration rate for eight maize inbred lines with different dehydration characteristics. High-throughput RNA sequencing data of starch biosynthesis-related genes showed that kernel moisture content and dehydration rate were both associated with differential expression of most starch biosynthetic genes. Especially, kernel moisture content was positively correlated with the increased expression of SBEI and SBEIIb, thereby potentially inducing biosynthesis of amylose with low molecular weight and amylopectin with low content of amylopectin chains with degree of polymerization (DP) 6-12 in inbred lines with fast kernel dehydration rate. We found a negative correlation between short amylopectin chains (DP 6-12) and the starch retrogradation rate. Hence, a low amount of amylopectin chains with DP 6-12 in the inbred lines with fast kernel dehydration rate was a plausible reason for their high short- and long-term retrogradation.
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Affiliation(s)
- Jianzhou Qu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China; Maize Engineering Technology Research Centre of Shaanxi Province, Yanglin 712100, Shaanxi, China
| | - Yuyue Zhong
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China; Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Denmark
| | - Li Ding
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Denmark
| | - Xingxun Liu
- Lab of Food Soft Matter Structure and Advanced Manufacturing, College of Food Science and Engineering/Collaborative Innovation Center for Modern Grain Circulation and Safety/Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics, Nanjing 210023, China
| | - Shutu Xu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China; Maize Engineering Technology Research Centre of Shaanxi Province, Yanglin 712100, Shaanxi, China
| | - Dongwei Guo
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China; Maize Engineering Technology Research Centre of Shaanxi Province, Yanglin 712100, Shaanxi, China
| | - Andreas Blennow
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Denmark.
| | - Jiquan Xue
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China; Maize Engineering Technology Research Centre of Shaanxi Province, Yanglin 712100, Shaanxi, China.
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Li T, Wang Y, Shi Y, Gou X, Yang B, Qu J, Zhang X, Xue J, Xu S. Transcriptome profiling provides insights into the molecular mechanisms of maize kernel and silk development. BMC Genom Data 2021; 22:28. [PMID: 34418952 PMCID: PMC8379809 DOI: 10.1186/s12863-021-00981-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 08/04/2021] [Indexed: 12/02/2022] Open
Abstract
Background Maize kernel filling, which is closely related to the process of double fertilization and is sensitive to a variety of environmental conditions, is an important component of maize yield determination. Silk is an important tissue of maize ears that can discriminate pollen and conduct pollination. Therefore, investigating the molecular mechanisms of kernel development and silk senescence will provide important information for improving the pollination rate to obtain high maize yields. Results In this study, transcript profiles were determined in an elite maize inbred line (KA105) to investigate the molecular mechanisms functioning in self-pollinated and unpollinated maize kernels and silks. A total of 5285 and 3225 differentially expressed transcripts (DETs) were identified between self-pollinated and unpollinated maize in a kernel group and a silk group, respectively. We found that a large number of genes involved in key steps in the biosynthesis of endosperm storage compounds were upregulated after pollination in kernels, and that abnormal development and senescence appeared in unpollinated kernels (KUP). We also identified several genes with functions in the maintenance of silk structure that were highly expressed in silk. Further investigation suggested that the expression of autophagy-related genes and senescence-related genes is prevalent in maize kernels and silks. In addition, pollination significantly altered the expression levels of senescence-related and autophagy-related genes in maize kernels and silks. Notably, we identified some specific genes and transcription factors (TFs) that are highly expressed in single tissues. Conclusions Our results provide novel insights into the potential regulatory mechanisms of self-pollinated and unpollinated maize kernels and silks. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-00981-4.
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Affiliation(s)
- Ting Li
- Key Laboratory of Biology and Genetic Improvement of Maize in the Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
| | - Yapeng Wang
- Key Laboratory of Biology and Genetic Improvement of Maize in the Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
| | - Yaqin Shi
- Key Laboratory of Biology and Genetic Improvement of Maize in the Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
| | - Xiaonan Gou
- Key Laboratory of Biology and Genetic Improvement of Maize in the Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
| | - Bingpeng Yang
- Key Laboratory of Biology and Genetic Improvement of Maize in the Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
| | - Jianzhou Qu
- Key Laboratory of Biology and Genetic Improvement of Maize in the Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
| | - Xinghua Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in the Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
| | - Jiquan Xue
- Key Laboratory of Biology and Genetic Improvement of Maize in the Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi Province, China.
| | - Shutu Xu
- Key Laboratory of Biology and Genetic Improvement of Maize in the Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi Province, China.
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