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Dai W, Li Q, Liu T, Long P, He Y, Sang M, Zou C, Chen Z, Yuan G, Ma L, Pan G, Shen Y. Combining genome-wide association study and linkage mapping in the genetic dissection of amylose content in maize (Zea mays L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:159. [PMID: 38872054 DOI: 10.1007/s00122-024-04666-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 05/28/2024] [Indexed: 06/15/2024]
Abstract
KEY MESSAGE Integrated linkage and association analysis revealed genetic basis across multiple environments. The genes Zm00001d003102 and Zm00001d015905 were further verified to influence amylose content using gene-based association study. Maize kernel amylose is an important source of human food and industrial raw material. However, the genetic basis underlying maize amylose content is still obscure. Herein, we used an intermated B73 × Mo17 (IBM) Syn10 doubled haploid population composed of 222 lines and a germplasm set including 305 inbred lines to uncover the genetic control for amylose content under four environments. Linkage mapping detected 16 unique QTL, among which four were individually repeatedly identified across multiple environments. Genome-wide association study revealed 17 significant (P = 2.24E-06) single-nucleotide polymorphisms, of which two (SYN19568 and PZE-105090500) were located in the intervals of the mapped QTL (qAC2 and qAC5-3), respectively. According to the two population co-localized loci, 20 genes were confirmed as the candidate genes for amylose content. Gene-based association analysis indicated that the variants in Zm00001d003102 (Beta-16-galactosyltransferase GALT29A) and Zm00001d015905 (Sugar transporter 4a) affected amylose content across multi-environment. Tissue expression analysis showed that the two genes were specifically highly expressed in the ear and stem, respectively, suggesting that they might participate in sugar transport from source to sink organs. Our study provides valuable genetic information for breeding maize varieties with high amylose.
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Affiliation(s)
- Wei Dai
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qinglin Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tao Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ping Long
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yao He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mengxiang Sang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chaoying Zou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhong Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangsheng Yuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Langlang Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangtang Pan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yaou Shen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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2
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Luo B, Zhang H, Han Z, Zhang X, Guo J, Zhang S, Luo X, Zhao J, Wang W, Yang G, Zhang C, Li J, Ma J, Zheng H, Tang Z, Lan Y, Ma P, Nie Z, Li Y, Liu D, Wu L, Gao D, Gao S, Su S, Guo J, Gao S. Exploring the phosphorus-starch content balance mechanisms in maize grains using GWAS population and transcriptome data. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:158. [PMID: 38864891 DOI: 10.1007/s00122-024-04667-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/01/2024] [Indexed: 06/13/2024]
Abstract
Examining the connection between P and starch-related signals can help elucidate the balance between nutrients and yield. This study utilized 307 diverse maize inbred lines to conduct multi-year and multi-plot trials, aiming to explore the relationship among P content, starch content, and 100-kernel weight (HKW) of mature grains. A significant negative correlation was found between P content and both starch content and HKW, while starch content showed a positive correlation with HKW. The starch granules in grains with high-P and low-starch content (HPLS) were significantly smaller compared to grains with low-P high-starch content (LPHS). Additionally, mian04185-4 (HPLS) exhibited irregular and loosely packed starch granules. A significant decrease in ZmPHOs genes expression was detected in the HPLS line ZNC442 as compared to the LPHS line SCML0849, while no expression difference was observed in AGPase encoding genes between these two lines. The down-regulated genes in ZNC442 grains were enriched in nucleotide sugar and fatty acid anabolic pathways, while up-regulated genes were enriched in the ABC transporters pathway. An accelerated breakdown of fat as the P content increased was also observed. This implied that HPLS was resulted from elevated lipid decomposition and inadequate carbon sources. The GWAS analysis identified 514 significantly associated genes, out of which 248 were differentially expressed. Zm00001d052392 was found to be significantly associated with P content/HKW, exhibiting high expression in SCML0849 but almost no expression in ZNC442. Overall, these findings suggested new approaches for achieving a P-yield balance through the manipulation of lipid metabolic pathways in grains.
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Affiliation(s)
- Bowen Luo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, Sichuan, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Haiying Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Zheng Han
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Xiao Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Jianyong Guo
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Shuhao Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Xianfu Luo
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Jin Zhao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Wei Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Guohui Yang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Chong Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Jing Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Junchi Ma
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Hao Zheng
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zirui Tang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yuzhou Lan
- Department of Plant Breeding, The Swedish University of Agricultural Sciences, P.O. Box 190, 23422, Lomma, Sweden
| | - Peng Ma
- Mianyang Academy of Agricultural Sciences, Mianyang, 621023, Sichuan, China
- Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Province, Mianyang, China
| | - Zhi Nie
- Sichuan Academy of Agricultural Sciences, Biotechnology and Nuclear Technology Research Institute, Chengdu, China
| | - Yunjian Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Dan Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Ling Wu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Duojiang Gao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Shiqiang Gao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Shunzong Su
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jia Guo
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Shibin Gao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, Sichuan, China.
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China.
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Wu Z, Wang T, Chen J, Zhang Y, Lv G. Sweet corn association panel and genome-wide association analysis reveal loci for chilling-tolerant germination. Sci Rep 2024; 14:10791. [PMID: 38734751 PMCID: PMC11088700 DOI: 10.1038/s41598-024-61797-7] [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: 01/07/2024] [Accepted: 05/09/2024] [Indexed: 05/13/2024] Open
Abstract
Sweet corn is highly susceptible to the deleterious effects of low temperatures during the initial stages of growth and development. Employing a 56K chip, high-throughput single-nucleotide polymorphism (SNP) sequencing was conducted on 100 sweet corn inbred lines. Subsequently, six germination indicators-germination rate, germination index, germination time, relative germination rate, relative germination index, and relative germination time-were utilized for genome-wide association analysis. Candidate genes were identified via comparative analysis of homologous genes in Arabidopsis and rice, and their functions were validated using quantitative real-time polymerase chain reaction (qRT-PCR). The results revealed 35,430 high-quality SNPs, 16 of which were significantly correlated. Within 50 kb upstream and downstream of the identified SNPs, 46 associated genes were identified, of which six were confirmed as candidate genes. Their expression patterns indicated that Zm11ΒHSDL5 and Zm2OGO likely play negative and positive regulatory roles, respectively, in the low-temperature germination of sweet corn. Thus, we determined that these two genes are responsible for regulating the low-temperature germination of sweet corn. This study contributes valuable theoretical support for improving sweet corn breeding and may aid in the creation of specific germplasm resources geared toward enhancing low-temperature tolerance in sweet corn.
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Affiliation(s)
- Zhenxing Wu
- Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Dongyang, 322100, China
| | - Tingzhen Wang
- Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Dongyang, 322100, China
| | - Jianjian Chen
- Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Dongyang, 322100, China
| | - Yun Zhang
- Horticultural Research Institute, Jilin City Academy of Agricultural Sciences, Jilin, 132000, China
| | - Guihua Lv
- Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Dongyang, 322100, China.
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Zhao B, Li K, Wang M, Liu Z, Yin P, Wang W, Li Z, Li X, Zhang L, Han Y, Li J, Yang X. Genetic basis of maize stalk strength decoded via linkage and association mapping. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1558-1573. [PMID: 38113320 DOI: 10.1111/tpj.16583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 11/20/2023] [Accepted: 11/26/2023] [Indexed: 12/21/2023]
Abstract
Stalk lodging is a severe problem that limits maize production worldwide, although little attention has been given to its genetic basis. Here we measured rind penetrometer resistance (RPR), an effective index for stalk lodging, in a multi-parent population of 1948 recombinant inbred lines (RILs) and an association population of 508 inbred lines (AMP508). Linkage and association mapping identified 53 and 29 single quantitative trait loci (QTLs) and 50 and 19 pairs of epistatic interactions for RPR in the multi-parent population and AMP508 population, respectively. Phenotypic variation explained by all identified epistatic QTLs (up to ~5%) was much less than that explained by all single additive QTLs (up to ~33% in the multi-parent population and ~ 60% in the AMP508 population). Among all detected QTLs, only eight single QTLs explained >10% of phenotypic variation in single RIL populations. Alleles that increased RPR were enriched in tropical/subtropical (TST) groups from the AMP508 population. Based on genome-wide association studies in both populations, we identified 137 candidate genes affecting RPR, which were assigned to multiple biological processes, such as the biosynthesis of cell wall components. Sixty-six candidate genes were cross-validated by multiple methods or populations. Most importantly, 23 candidate genes were upregulated or downregulated in high-RPR lines relative to low-RPR lines, supporting the associations between candidate genes and RPR. These findings reveal the complex nature of the genetic basis underlying RPR and provide loci or candidate genes for developing elite varieties that are resistant to stalk lodging via molecular breeding.
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Affiliation(s)
- Binghao Zhao
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Kun Li
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Min Wang
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Zhiyuan Liu
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Pengfei Yin
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Weidong Wang
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Zhigang Li
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Xiaowei Li
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Lili Zhang
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Yingjia Han
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Jiansheng Li
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Xiaohong Yang
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
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Cao S, Liu B, Wang D, Rasheed A, Xie L, Xia X, He Z. Orchestrating seed storage protein and starch accumulation toward overcoming yield-quality trade-off in cereal crops. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:468-483. [PMID: 38409921 DOI: 10.1111/jipb.13633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/22/2024] [Accepted: 02/07/2024] [Indexed: 02/28/2024]
Abstract
Achieving high yield and good quality in crops is essential for human food security and health. However, there is usually disharmony between yield and quality. Seed storage protein (SSP) and starch, the predominant components in cereal grains, determine yield and quality, and their coupled synthesis causes a yield-quality trade-off. Therefore, dissection of the underlying regulatory mechanism facilitates simultaneous improvement of yield and quality. Here, we summarize current findings about the synergistic molecular machinery underpinning SSP and starch synthesis in the leading staple cereal crops, including maize, rice and wheat. We further evaluate the functional conservation and differentiation of key regulators and specify feasible research approaches to identify additional regulators and expand insights. We also present major strategies to leverage resultant information for simultaneous improvement of yield and quality by molecular breeding. Finally, future perspectives on major challenges are proposed.
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Affiliation(s)
- Shuanghe Cao
- State Key Laboratory of Crop Gene Resources and Breeding/National Wheat Improvement Center, Institute of Crop Sciences, Beijing, 100081, China
| | - Bingyan Liu
- State Key Laboratory of Crop Gene Resources and Breeding/National Wheat Improvement Center, Institute of Crop Sciences, Beijing, 100081, China
| | - Daowen Wang
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Awais Rasheed
- State Key Laboratory of Crop Gene Resources and Breeding/National Wheat Improvement Center, Institute of Crop Sciences, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lina Xie
- State Key Laboratory of Crop Gene Resources and Breeding/National Wheat Improvement Center, Institute of Crop Sciences, Beijing, 100081, China
| | - Xianchun Xia
- State Key Laboratory of Crop Gene Resources and Breeding/National Wheat Improvement Center, Institute of Crop Sciences, Beijing, 100081, China
| | - Zhonghu He
- State Key Laboratory of Crop Gene Resources and Breeding/National Wheat Improvement Center, Institute of Crop Sciences, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Ndlovu N, Kachapur RM, Beyene Y, Das B, Ogugo V, Makumbi D, Spillane C, McKeown PC, Prasanna BM, Gowda M. Linkage mapping and genomic prediction of grain quality traits in tropical maize ( Zea mays L.). Front Genet 2024; 15:1353289. [PMID: 38456017 PMCID: PMC10918846 DOI: 10.3389/fgene.2024.1353289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 02/07/2024] [Indexed: 03/09/2024] Open
Abstract
The suboptimal productivity of maize systems in sub-Saharan Africa (SSA) is a pressing issue, with far-reaching implications for food security, nutrition, and livelihood sustainability within the affected smallholder farming communities. Dissecting the genetic basis of grain protein, starch and oil content can increase our understanding of the governing genetic systems, improve the efficacy of future breeding schemes and optimize the end-use quality of tropical maize. Here, four bi-parental maize populations were evaluated in field trials in Kenya and genotyped with mid-density single nucleotide polymorphism (SNP) markers. Genotypic (G), environmental (E) and G×E variations were found to be significant for all grain quality traits. Broad sense heritabilities exhibited substantial variation (0.18-0.68). Linkage mapping identified multiple quantitative trait loci (QTLs) for the studied grain quality traits: 13, 7, 33, 8 and 2 QTLs for oil content, protein content, starch content, grain texture and kernel weight, respectively. The co-localization of QTLs identified in our research suggests the presence of shared genetic factors or pleiotropic effects, implying that specific genomic regions influence the expression of multiple grain quality traits simultaneously. Genomic prediction accuracies were moderate to high for the studied traits. Our findings highlight the polygenic nature of grain quality traits and demonstrate the potential of genomic selection to enhance genetic gains in maize breeding. Furthermore, the identified genomic regions and single nucleotide polymorphism markers can serve as the groundwork for investigating candidate genes that regulate grain quality traits in tropical maize. This, in turn, can facilitate the implementation of marker-assisted selection (MAS) in breeding programs focused on improving grain nutrient levels.
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Affiliation(s)
- Noel Ndlovu
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, Galway, Ireland
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Rajashekar M. Kachapur
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
- University of Agricultural Sciences, Dharwad, Karnataka, India
| | - Yoseph Beyene
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Biswanath Das
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Veronica Ogugo
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Dan Makumbi
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Charles Spillane
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, Galway, Ireland
| | - Peter C. McKeown
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, Galway, Ireland
| | | | - Manje Gowda
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
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Zeng Z, Zhang W, Shi Y, Wei H, Zhou C, Huang X, Chen Z, Xiang T, Wang L, Han N, Bian H. Coordinated Transcriptome and Metabolome Analyses of a Barley hvhggt Mutant Reveal a Critical Role of Tocotrienols in Endosperm Starch Accumulation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:1146-1161. [PMID: 38181192 DOI: 10.1021/acs.jafc.3c06301] [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: 01/07/2024]
Abstract
Tocotrienols and tocopherols (vitamin E) are potent antioxidants that are synthesized in green plants. Unlike ubiquitous tocopherols, tocotrienols predominantly accumulate in the endosperm of monocot grains, catalyzed by homogentiate geranylgeranyl transferase (HGGT). Previously, we generated a tocotrienol-deficient hvhggt mutant with shrunken barley grains. However, the relationship between tocotrienols and grain development remains unclear. Here, we found that the hvhggt lines displayed hollow endosperms with defective transfer cells and reduced aleurone layers. The carbohydrate and starch contents of the hvhggt endosperm decreased by approximately 20 and 23%, respectively. Weighted gene coexpression network analyses identified a critical gene module containing HvHGGT, which was strongly associated with the hvhggt mutation and enriched with gene functions in starch and sucrose metabolism. Metabolome measurements revealed an elevated soluble sugar content in the hvhggt endosperm, which was significantly associated with the identified gene modules. The hvhggt endosperm had significantly higher NAD(H) and NADP(H) contents and lower levels of ADPGlc (regulated by redox balance) than the wild-type, consistent with the absence of tocotrienols. Interestingly, exogenous α-tocotrienol spraying on developing hvhggt spikes partially rescued starch accumulation and endosperm defects. Our study supports a potential novel function of tocotrienols in grain starch accumulation and endosperm development in monocot crops.
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Affiliation(s)
- Zhanghui Zeng
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, Zhejiang, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou 311121, China
| | - Wenqian Zhang
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yaqi Shi
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Haonan Wei
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Chun Zhou
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Xiaoping Huang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, Zhejiang, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou 311121, China
| | - Zhehao Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, Zhejiang, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou 311121, China
| | - Taihe Xiang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, Zhejiang, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou 311121, China
| | - Lilin Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, Zhejiang, China
| | - Ning Han
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Hongwu Bian
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
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Duan H, Li J, Sun L, Xiong X, Xu S, Sun Y, Ju X, Xue Z, Gao J, Wang Y, Xie H, Ding D, Zhang X, Tang J. Identification of novel loci associated with starch content in maize kernels by a genome-wide association study using an enlarged SNP panel. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:91. [PMID: 38099287 PMCID: PMC10716104 DOI: 10.1007/s11032-023-01437-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 11/24/2023] [Indexed: 12/17/2023]
Abstract
Starch is a major component of cereals, comprising over 70% of dry weight. It serves as a primary carbon source for humans and animals. In addition, starch is an indispensable industrial raw material. While maize (Zea mays) is a key crop and the primary source of starch, the genetic basis for starch content in maize kernels remains poorly understood. In this study, using an enlarged panel, we conducted a genome-wide association study (GWAS) based on best linear unbiased prediction (BLUP) value for starch content of 261 inbred lines across three environments. Compared with previous study, we identified 14 additional significant quantitative trait loci (QTL), encompassed a total of 42 genes, and indicated that increased marker density contributes to improved statistical power. By integrating gene expression profiling, Gene Ontology (GO) enrichment and haplotype analysis, several potential target genes that may play a role in regulating starch content in maize kernels have been identified. Notably, we found that ZmAPC4, associated with the significant SNP chr4.S_175584318, which encodes a WD40 repeat-like superfamily protein and is highly expressed in maize endosperm, might be a crucial regulator of maize kernel starch synthesis. Out of the 261 inbred lines analyzed, they were categorized into four haplotypes. Remarkably, it was observed that the inbred lines harboring hap4 demonstrated the highest starch content compared to the other haplotypes. Additionally, as a significant achievement, we have developed molecular markers that effectively differentiate maize inbred lines based on their starch content. Overall, our study provides valuable insights into the genetic basis of starch content and the molecular markers can be useful in breeding programs aimed at developing maize varieties with high starch content, thereby improving breeding efficiency. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01437-6.
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Affiliation(s)
- Haiyang Duan
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Jianxin Li
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Li Sun
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xuehang Xiong
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Shuhao Xu
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Yan Sun
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xiaolong Ju
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Zhengjie Xue
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Jionghao Gao
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Yan Wang
- Zhucheng Mingjue Tender Company Limited, Weifang, China
| | - Huiling Xie
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
- Department of Agronomy, Henan Agricultural University, Agricultural Road No. 63, Zhengzhou, 450002 China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
- The Shennong Laboratory, Zhengzhou, China
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9
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Medison RG, Jiang J, Medison MB, Tan LT, Kayange CD, Sun Z, Zhou Y. Evaluating the potential of Bacillus licheniformis YZCUO202005 isolated from lichens in maize growth promotion and biocontrol. Heliyon 2023; 9:e20204. [PMID: 37767471 PMCID: PMC10520788 DOI: 10.1016/j.heliyon.2023.e20204] [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: 12/25/2022] [Revised: 09/08/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Lichens exist in an organismal organization of mycobiont, photobiont, and non-photoautotrophic bacteria. These organisms contribute to the growth of lichens even in poor nutrition substrates. However, studies on the isolation and application of non-photoautotrophic bacteria in plant growth and biocontrol are scanty. Therefore, a study was conducted to isolate and evaluate the potential of non-photoautotrophic bacteria from lichen tissues in maize plant growth promotion and biocontrol of plant pathogens (fungi and bacteria). Five bacterial strains were isolated and tested for their ability to produce indole-3-Acetic Acid (IAA). One bacterium named YZCUO202005 produced IAA, siderophores and biofilms, solubilized phosphate and potassium and exhibited extracellular enzymes (cellulases, proteases, amylase, and β -1,3-Glucanase). Based on the 16S rRNA sequence analysis results, YZCUO202005 was identified as Bacillus licheniformis. The strain inhibited the growth of five pathogenic fungi with an inhibition percent of between 58.7% and 71.7% and two pathogenic bacteria. Under greenhouse conditions, YZCUO202005 was tested for its abilities to enhance maize seed germination, and vegetative growth. Compared with the control treatment, the strain significantly enhanced the growth of stem length (i.e. 18 ± 0.64 cm, 78 ± 0.92 cm), leaf length (i.e. 10 ± 0.36 cm, 57 ± 1.42 cm), leaf chlorophyll levels (i.e., 13 ± 0.40, 40 ± 0.43 SPAD), and root length (i.e, 9.8 ± 2.25 cm, 22.5 ± 6.59 cm). Our results demonstrated that B. licheniformis YZCUO202005 from lichens has the potential to promote plant growth and reduce fungal and bacterial pathogens' growth. Furthermore, the results suggest that lichens are naturally rich sources of plant growth promotion and biocontrol agents that would be used in agriculture.
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Affiliation(s)
- Rudoviko Galileya Medison
- Department of Plant Protection, College of Agriculture, Yangtze University, 266 Jingmi Road, Jingzhou City, Hubei Province, 434025, China
| | - Jianwei Jiang
- Department of Plant Protection, College of Agriculture, Yangtze University, 266 Jingmi Road, Jingzhou City, Hubei Province, 434025, China
| | - Milca Banda Medison
- Department of Plant Protection, College of Agriculture, Yangtze University, 266 Jingmi Road, Jingzhou City, Hubei Province, 434025, China
| | - Li-Tao Tan
- Department of Plant Protection, College of Agriculture, Yangtze University, 266 Jingmi Road, Jingzhou City, Hubei Province, 434025, China
| | - Chicco D.M. Kayange
- Department of Land Resources Conservation, Mulanje District Agriculture Office, P.O. Box 49, Mulanje, Malawi
| | - Zhengxiang Sun
- Department of Plant Protection, College of Agriculture, Yangtze University, 266 Jingmi Road, Jingzhou City, Hubei Province, 434025, China
| | - Yi Zhou
- Department of Plant Protection, College of Agriculture, Yangtze University, 266 Jingmi Road, Jingzhou City, Hubei Province, 434025, China
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10
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Liang XG, Gao Z, Fu XX, Chen XM, Shen S, Zhou SL. Coordination of carbon assimilation, allocation, and utilization for systemic improvement of cereal yield. FRONTIERS IN PLANT SCIENCE 2023; 14:1206829. [PMID: 37731984 PMCID: PMC10508850 DOI: 10.3389/fpls.2023.1206829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 08/14/2023] [Indexed: 09/22/2023]
Abstract
The growth of yield outputs is dwindling after the first green revolution, which cannot meet the demand for the projected population increase by the mid-century, especially with the constant threat from extreme climates. Cereal yield requires carbon (C) assimilation in the source for subsequent allocation and utilization in the sink. However, whether the source or sink limits yield improvement, a crucial question for strategic orientation in future breeding and cultivation, is still under debate. To narrow the knowledge gap and capture the progress, we focus on maize, rice, and wheat by briefly reviewing recent advances in yield improvement by modulation of i) leaf photosynthesis; ii) primary C allocation, phloem loading, and unloading; iii) C utilization and grain storage; and iv) systemic sugar signals (e.g., trehalose 6-phosphate). We highlight strategies for optimizing C allocation and utilization to coordinate the source-sink relationships and promote yields. Finally, based on the understanding of these physiological mechanisms, we envisage a future scenery of "smart crop" consisting of flexible coordination of plant C economy, with the goal of yield improvement and resilience in the field population of cereals crops.
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Affiliation(s)
- Xiao-Gui Liang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education and Jiangxi Province/The Laboratory for Phytochemistry and Botanical Pesticides, College of Agriculture, Jiangxi Agricultural University, Nanchang, China
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, China
| | - Zhen Gao
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, China
| | - Xiao-Xiang Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education and Jiangxi Province/The Laboratory for Phytochemistry and Botanical Pesticides, College of Agriculture, Jiangxi Agricultural University, Nanchang, China
| | - Xian-Min Chen
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Si Shen
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Shun-Li Zhou
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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11
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Viana JMS, Souza CAS. Efficiency of mapping epistatic quantitative trait loci. Heredity (Edinb) 2023:10.1038/s41437-023-00618-5. [PMID: 37157025 DOI: 10.1038/s41437-023-00618-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 04/21/2023] [Accepted: 04/22/2023] [Indexed: 05/10/2023] Open
Abstract
Most theoretical studies on epistatic QTL mapping have shown that this procedure is powerful, efficient to control the false positive rate (FPR), and precise to localize QTLs. The objective of this simulation-based study was to show that mapping epistatic QTLs is not an almost-perfect process. We simulated 50 samples of 400 F2 plants/recombinant inbred lines, genotyped for 975 SNPs distributed in 10 chromosomes of 100 cM. The plants were phenotyped for grain yield, assuming 10 epistatic QTLs and 90 minor genes. Adopting basic procedures of r/qtl package, we maximized the power of detection for QTLs (56-74%, on average) but associated with a very high FPR (65%) and a low detection power for the epistatic pairs (7%). Increasing the average detection power for epistatic pairs (14%) highly increased the related FPR. Adopting a procedure to find the best balance between power and FPR, there was a significant decrease in the power of QTL detection (17-31%, on average), associated with a low average detection power for epistatic pairs (8%) and an average FPR of 31% for QTLs and 16% for epistatic pairs. The main reasons for these negative results are a simplified specification of the coefficients of epistatic effects, as theoretically proved, and the effects of minor genes since 2/3 of the FPR for QTLs were due to them. We hope that this study, including the partial derivation of the coefficients of epistatic effects, motivates investigations on how to increase the power of detection for epistatic pairs, effectively controlling the FPR.
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12
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Zhao M, Zhang J, Yang C, Cui Z, Chen L. Identification of QTLs and Putative Candidate Genes for Plant Architecture of Lotus Revealed by Regional Association Mapping. PLANTS (BASEL, SWITZERLAND) 2023; 12:1221. [PMID: 36986910 PMCID: PMC10051333 DOI: 10.3390/plants12061221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/26/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
The lotus (Nelumbo Adans.) is one of the most economically relevant ornamental aquatic plants. Plant architecture (PA) is an important trait for lotus classification, cultivation, breeding, and applications. However, the underlying genetic and molecular basis controlling PA remains poorly understood. In this study, an association study for PA-related traits was performed with 93 genome-wide microsatellite markers (simple sequence repeat, SSR) and 51 insertion-deletion (InDel) markers derived from the candidate regions using a panel of 293 lotus accessions. Phenotypic data analysis of the five PA-related traits revealed a wide normal distribution and high heritability from 2013 to 2016, which indicated that lotus PA-related traits are highly polygenic traits. The population structure (Q-matrix) and the relative kinships (K-matrix) of the association panels were analyzed using 93 SSR markers. The mixed linear model (MLM) taking Q-matrix and K-matrix into account was used to estimate the association between markers and the traits. A total of 26 markers and 65 marker-trait associations were identified by considering associations with p < 0.001 and Q < 0.05. Based on the significant markers, two QTLs on Chromosome 1 were identified, and two candidate genes were preliminarily determined. The results of our study provided useful information for the lotus breeding aiming at different PA phenotypes using a molecular-assisted selection (MAS) method and also laid the foundation for the illustration of the molecular mechanism underlying the major QTL and key markers associated with lotus PA.
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Affiliation(s)
- Mei Zhao
- College of Landscape and Forestry, Qingdao Agricultural University, Qingdao 266109, China
| | - Jibin Zhang
- College of Landscape and Forestry, Qingdao Agricultural University, Qingdao 266109, China
| | - Chuxuan Yang
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Zhenhua Cui
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Longqing Chen
- Southwest Landscape Architecture Engineering Research Center (National Forestry and Grassland Administration), Southwest Forestry University, Kunming 650224, China
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13
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Wan W, Wu Y, Hu D, Ye F, Wu X, Qi X, Liang H, Zhou H, Xue J, Xu S, Zhang X. Genome-wide association analysis of kernel nutritional quality in two natural maize populations. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:18. [PMID: 37313300 PMCID: PMC10248675 DOI: 10.1007/s11032-023-01360-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 02/05/2023] [Indexed: 06/15/2023]
Abstract
As one of the three staple crops, nutritional traits in maize are important for human and animal nutrition. Grain quality-related traits are closely related to grain commercial value. Understanding the genetic basis of quality-related traits in maize would be helpful for breeding high-quality maize varieties. In this study, two association panels (AM122 and AM180) were subjected to genome-wide association analysis of grain quality-related traits, including protein content, oil content, starch content, and fiber content. In total, 98 SNPs (P < 1 × 10-4) were identified to be significantly associated with these four grain quality-related traits. By integrating two sets of public transcriptome data, 31 genes located in 200 kb regions flanking the associated SNP showed high expression during kernel development and were differentially expressed in two maize inbred lines, KA225 and KB035, with significantly different quality. These genes might regulate maize grain quality by participating in plant hormone processes, autophagy processes, and others. All these results could provide important reference information for breeding high‑quality maize varieties. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01360-w.
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Affiliation(s)
- Wenting Wan
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Ying Wu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Die Hu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Fan Ye
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Xiaopeng Wu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Xingyue Qi
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Hangyu Liang
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Haiyang Zhou
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Jiquan Xue
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Shutu Xu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Xinghua Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
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14
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Chen G, Xiao Y, Dai S, Dai Z, Wang X, Li B, Jaqueth JS, Li W, Lai Z, Ding J, Yan J. Genetic basis of resistance to southern corn leaf blight in the maize multi-parent population and diversity panel. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:506-520. [PMID: 36383026 PMCID: PMC9946143 DOI: 10.1111/pbi.13967] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
Southern corn leaf blight (SLB), caused by the necrotrophic pathogen Cochliobolus heterostrophus, is one of the maize foliar diseases and poses a great threat to corn production around the world. Identification of genetic variations underlying resistance to SLB is of paramount importance to maize yield and quality. Here, we used a random-open-parent association mapping population containing eight recombinant inbred line populations and one association mapping panel consisting of 513 diversity maize inbred lines with high-density genetic markers to dissect the genetic basis of SLB resistance. Overall, 109 quantitative trait loci (QTLs) with predominantly small or moderate additive effects, and little epistatic effects were identified. We found 35 (32.1%) novel loci in comparison with the reported QTLs. We revealed that resistant alleles were significantly enriched in tropical accessions and the frequency of about half of resistant alleles decreased during the adaptation process owing to the selection of agronomic traits. A large number of annotated genes located in the SLB-resistant QTLs were shown to be involved in plant defence pathways. Integrating genome-wide association study, transcriptomic profiling, resequencing and gene editing, we identified ZmFUT1 and MYBR92 as the putative genes responsible for the major QTLs for resistance to C. heterostrophus. Our results present a comprehensive insight into the genetic basis of SLB resistance and provide resistant loci or genes as direct targets for crop genetic improvement.
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Affiliation(s)
- Gengshen Chen
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
| | - Sha Dai
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Zhikang Dai
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Xiaoming Wang
- Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | | | | | - Wenqiang Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Zhibing Lai
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Junqiang Ding
- College of AgronomyHenan Agricultural UniversityZhengzhouChina
- The State Key Laboratory of Wheat and Maize Crop Science and Center for Crop Genome EngineeringHenan Agricultural UniversityZhengzhouChina
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
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15
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Guo X, Ge Z, Wang M, Zhao M, Pei Y, Song X. Genome-wide association study of quality traits and starch pasting properties of maize kernels. BMC Genomics 2023; 24:59. [PMID: 36732681 PMCID: PMC9893588 DOI: 10.1186/s12864-022-09031-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/21/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Starch are the main nutritional components of maize (Zea mays L.), and starch pasting properties are widely used as essential indicators for quality estimation. Based on the previous studies, various genes related to pasting properties have been identified in maize. However, the loci underlying variations in starch pasting properties in maize inbred lines remain to be identified. RESULTS To investigate the genetic architecture of these traits, the starch pasting properties were examined based on 292 maize inbred lines, which were genotyped with the MaizeSNP50 BeadChip composed of 55,126 evenly spaced, random SNPs. A genome-wide association study (GWAS) implemented in the software package FarmCPU was employed to identify genomic loci for the starch pasting properties. 48 SNPs were found to be associated with pasting properties. Moreover, 37 candidate genes were correlated with pasting properties. Among the candidate genes, GRMZM2G143646 and GRMZM2G166407 were associated with breakdown and final viscosity significantly, and both genes encode PPR (Pentatricopeptide repeat) protein. We used GWAS to explore candidate genes of maize starch pasting properties in this study. The identified candidate genes will be useful for further understanding of the genetic architecture of starch pasting properties in maize. CONCLUSION This study showed a complex regulation network about maize quality trait and starch pasting properties. It may provide some useful markers for marker assisted selection and a basis for cloning the genes behind these SNPs.
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Affiliation(s)
- Xinmei Guo
- grid.412608.90000 0000 9526 6338College of Agronomy, Qingdao Agricultural University, Qingdao, 266109 China
| | - Zhaopeng Ge
- grid.412608.90000 0000 9526 6338College of Agronomy, Qingdao Agricultural University, Qingdao, 266109 China
| | - Ming Wang
- grid.412608.90000 0000 9526 6338College of Agronomy, Qingdao Agricultural University, Qingdao, 266109 China
| | - Meiai Zhao
- grid.412608.90000 0000 9526 6338College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109 China
| | - Yuhe Pei
- grid.412608.90000 0000 9526 6338College of Agronomy, Qingdao Agricultural University, Qingdao, 266109 China
| | - Xiyun Song
- grid.412608.90000 0000 9526 6338College of Agronomy, Qingdao Agricultural University, Qingdao, 266109 China
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16
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Sa KJ, Park H, Jang SJ, Lee JK. Association Mapping of Amylose Content in Maize RIL Population Using SSR and SNP Markers. PLANTS (BASEL, SWITZERLAND) 2023; 12:239. [PMID: 36678952 PMCID: PMC9865990 DOI: 10.3390/plants12020239] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
The ratio of amylose to amylopectin in maize kernel starch is important for the appearance, structure, and quality of food products and processing. This study aimed to identify quantitative trait loci (QTLs) controlling amylose content in maize through association mapping with simple sequence repeat (SSR) and single-nucleotide polymorphism (SNP) markers. The average value of amylose content for an 80-recombinant-inbred-line (RIL) population was 8.8 ± 0.7%, ranging from 2.1 to 15.9%. We used two different analyses-Q + K and PCA + K mixed linear models (MLMs)-and found 38 (35 SNP and 3 SSR) and 32 (29 SNP and 3 SSR) marker-trait associations (MTAs) associated with amylose content. A total of 34 (31 SNP and 3 SSR) and 28 (25 SNP and 3 SSR) MTAs were confirmed in the Q + K and PCA + K MLMs, respectively. This study detected some candidate genes for amylose content, such as GRMZM2G118690-encoding BBR/BPC transcription factor, which is used for the control of seed development and is associated with the amylose content of rice. GRMZM5G830776-encoding SNARE-interacting protein (KEULE) and the uncharacterized marker PUT-163a-18172151-1376 were significant with higher R2 value in two difference methods. GRMZM2G092296 were also significantly associated with amylose content in this study. This study focused on amylose content using a RIL population derived from dent and waxy inbred lines using molecular markers. Future studies would be of benefit for investigating the physical linkage between starch synthesis genes using SNP and SSR markers, which would help to build a more detailed genetic map and provide new insights into gene regulation of agriculturally important traits.
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Affiliation(s)
- Kyu Jin Sa
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Hyeon Park
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
- Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - So Jung Jang
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
- Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Ju Kyong Lee
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
- Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon 24341, Republic of Korea
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17
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Ma Y, Yao L, Zhang L, Su A, Wang R, Song W, Li Z, Zhao J. Genome‐wide association analysis of chilling‐tolerant germination in a new maize association mapping panel. Food Energy Secur 2022. [DOI: 10.1002/fes3.445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Yun Ma
- Beijing Academy of Agriculture and Forestry Sciences Institute of Maize Beijing China
| | - Lan Yao
- Beijing Academy of Agriculture and Forestry Sciences Institute of Maize Beijing China
- College of Food Science and Biology Hebei University of Science and Technology Hebei China
| | - Liwei Zhang
- Beijing Academy of Agriculture and Forestry Sciences Institute of Maize Beijing China
| | - Aiguo Su
- Beijing Academy of Agriculture and Forestry Sciences Institute of Maize Beijing China
| | - Ronghuan Wang
- Beijing Academy of Agriculture and Forestry Sciences Institute of Maize Beijing China
| | - Wei Song
- Beijing Academy of Agriculture and Forestry Sciences Institute of Maize Beijing China
| | - Zhaowei Li
- College of Food Science and Biology Hebei University of Science and Technology Hebei China
| | - Jiuran Zhao
- Beijing Academy of Agriculture and Forestry Sciences Institute of Maize Beijing China
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18
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Mural RV, Sun G, Grzybowski M, Tross MC, Jin H, Smith C, Newton L, Andorf CM, Woodhouse MR, Thompson AM, Sigmon B, Schnable JC. Association mapping across a multitude of traits collected in diverse environments in maize. Gigascience 2022; 11:6673780. [PMID: 35997208 PMCID: PMC9396454 DOI: 10.1093/gigascience/giac080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/25/2022] [Indexed: 11/14/2022] Open
Abstract
Classical genetic studies have identified many cases of pleiotropy where mutations in individual genes alter many different phenotypes. Quantitative genetic studies of natural genetic variants frequently examine one or a few traits, limiting their potential to identify pleiotropic effects of natural genetic variants. Widely adopted community association panels have been employed by plant genetics communities to study the genetic basis of naturally occurring phenotypic variation in a wide range of traits. High-density genetic marker data-18M markers-from 2 partially overlapping maize association panels comprising 1,014 unique genotypes grown in field trials across at least 7 US states and scored for 162 distinct trait data sets enabled the identification of of 2,154 suggestive marker-trait associations and 697 confident associations in the maize genome using a resampling-based genome-wide association strategy. The precision of individual marker-trait associations was estimated to be 3 genes based on a reference set of genes with known phenotypes. Examples were observed of both genetic loci associated with variation in diverse traits (e.g., above-ground and below-ground traits), as well as individual loci associated with the same or similar traits across diverse environments. Many significant signals are located near genes whose functions were previously entirely unknown or estimated purely via functional data on homologs. This study demonstrates the potential of mining community association panel data using new higher-density genetic marker sets combined with resampling-based genome-wide association tests to develop testable hypotheses about gene functions, identify potential pleiotropic effects of natural genetic variants, and study genotype-by-environment interaction.
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Affiliation(s)
- Ravi V Mural
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.,Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Guangchao Sun
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.,Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Marcin Grzybowski
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.,Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Michael C Tross
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.,Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Hongyu Jin
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.,Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Christine Smith
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Linsey Newton
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Carson M Andorf
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50010, USA.,Department of Computer Science, Iowa State University, Ames, IA 50011, USA
| | | | - Addie M Thompson
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Brandi Sigmon
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - James C Schnable
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.,Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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19
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Xu X, Wang Z, Xu S, Xu M, He L, Zhang J, Luo Z, Xie X, Wu M, Yang J. Identifying loci controlling total starch content of leaf in Nicotiana tabacum through genome-wide association study. Funct Integr Genomics 2022; 22:537-552. [PMID: 35404023 DOI: 10.1007/s10142-022-00851-x] [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: 11/19/2021] [Revised: 03/07/2022] [Accepted: 03/22/2022] [Indexed: 11/04/2022]
Abstract
Starch is an important primary metabolite in plants, which can provide bioenergy for fuel ethanol production. There are many studies focusing on starch metabolism in Arabidopsis, maize, and rice, but few reports have been made on the starch content of tobacco leaves. Hence, to identify the marker-trait associations and isolate the candidate genes related to starch content of tobacco leaf, the genome-wide association study (GWAS) was performed using a multiparent advanced generation intercross (MAGIC) population consisting of 276 accessions genotyped by a 430 K SNP array. In this study, we detected the leaf starch content of tobacco plants cultivated in two places (Zhucheng and Chenzhou), which showed a wide variation of starch content in the population. A total of 28 and 45 significant single-nucleotide polymorphism (SNP) loci associated with leaf starch content were identified by single-locus and multi-locus GWAS models, respectively, and the phenotypic variance explained by these loci varied from 1.80 to - 14.73%. Furthermore, among these quantitative trait loci (QTLs), one SNP, AX-106011713 located on chromosome 19, was detected repeatedly in multiple models and two environments, which was selected for linkage disequilibrium (LD) analysis to obtain the target candidate region. Through gene annotation, haplotype, and gene expression analysis, two candidate genes encoding E3 ubiquitin-protein ligase (Ntab0823160) and fructose-bisphosphate aldolase (Ntab0375050) were obtained. Results showed that the variety carrying the beneficial alleles of the two candidate genes had higher gene expression level and leaf starch content, suggesting the potential role of candidate genes in enhancing the level of tobacco leaf starch content. Furthermore, silencing of Ntab0823160 in tobacco leaves reduced the content of total starch to 39.41-69.75% of that in the wide type plants. Taken together, our results provide useful resources for further investigation of the starch metabolic pathway and are also beneficial for the creation of eco-friendly cultivars with increased accumulation of leaf starch content.
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Affiliation(s)
- Xin Xu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Zhong Wang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Shixiao Xu
- Henan Agricultural University, Zhengzhou, 450002, China
| | - Min Xu
- Henan Tobacco Company of CNTC, Zhengzhou, 450018, China
| | - Lei He
- Henan Tobacco Company of CNTC, Zhengzhou, 450018, China
| | - Jianfeng Zhang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Zhaopeng Luo
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Xiaodong Xie
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Mingzhu Wu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Jun Yang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China.
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20
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Finegan C, Boehlein SK, Leach KA, Madrid G, Hannah LC, Koch KE, Tracy WF, Resende MFR. Genetic Perturbation of the Starch Biosynthesis in Maize Endosperm Reveals Sugar-Responsive Gene Networks. FRONTIERS IN PLANT SCIENCE 2022; 12:800326. [PMID: 35211133 PMCID: PMC8861272 DOI: 10.3389/fpls.2021.800326] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/27/2021] [Indexed: 05/28/2023]
Abstract
In maize, starch mutants have facilitated characterization of key genes involved in endosperm starch biosynthesis such as large subunit of AGPase Shrunken2 (Sh2) and isoamylase type DBE Sugary1 (Su1). While many starch biosynthesis enzymes have been characterized, the mechanisms of certain genes (including Sugary enhancer1) are yet undefined, and very little is understood about the regulation of starch biosynthesis. As a model, we utilize commercially important sweet corn mutations, sh2 and su1, to genetically perturb starch production in the endosperm. To characterize the transcriptomic response to starch mutations and identify potential regulators of this pathway, differential expression and coexpression network analysis was performed on near-isogenic lines (NILs) (wildtype, sh2, and su1) in six genetic backgrounds. Lines were grown in field conditions and kernels were sampled in consecutive developmental stages (blister stage at 14 days after pollination (DAP), milk stage at 21 DAP, and dent stage at 28 DAP). Kernels were dissected to separate embryo and pericarp from the endosperm tissue and 3' RNA-seq libraries were prepared. Mutation of the Su1 gene led to minimal changes in the endosperm transcriptome. Responses to loss of sh2 function include increased expression of sugar (SWEET) transporters and of genes for ABA signaling. Key regulators of starch biosynthesis and grain filling were identified. Notably, this includes Class II trehalose 6-phosphate synthases, Hexokinase1, and Apetala2 transcription factor-like (AP2/ERF) transcription factors. Additionally, our results provide insight into the mechanism of Sugary enhancer1, suggesting a potential role in regulating GA signaling via GRAS transcription factor Scarecrow-like1.
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Affiliation(s)
- Christina Finegan
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Susan K. Boehlein
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Kristen A. Leach
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Gabriela Madrid
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - L. Curtis Hannah
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Karen E. Koch
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - William F. Tracy
- Department of Agronomy, University of Wisconsin- Madison, Madison, WI, United States
| | - Marcio F. R. Resende
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
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21
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Zhang X, Wang M, Zhang C, Dai C, Guan H, Zhang R. Genetic dissection of QTLs for starch content in four maize DH populations. FRONTIERS IN PLANT SCIENCE 2022; 13:950664. [PMID: 36275573 PMCID: PMC9583244 DOI: 10.3389/fpls.2022.950664] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/30/2022] [Indexed: 05/17/2023]
Abstract
Starch is the principal carbohydrate source in maize kernels. Understanding the genetic basis of starch content (SC) benefits greatly in improving maize yield and optimizing end-use quality. Here, four double haploid (DH) populations were generated and were used to identify quantitative trait loci (QTLs) associated with SC. The phenotype of SC exhibited continuous and approximate normal distribution in each population. A total of 13 QTLs for SC in maize kernels was detected in a range of 3.65-16.18% of phenotypic variation explained (PVE). Among those, only some partly overlapped with QTLs previously known to be related to SC. Meanwhile, 12 genes involved in starch synthesis and metabolism located within QTLs were identified in this study. These QTLs will lay the foundation to explore candidate genes regulating SC in maize kernel and facilitate the application of molecular marker-assisted selection for a breeding program to cultivate maize varieties with a deal of grain quality.
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Affiliation(s)
- Xiaolei Zhang
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Min Wang
- Institute of Advanced Agricultural Technology, Qilu Normal University, Jinan, China
| | | | - Changjun Dai
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Haitao Guan
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Ruiying Zhang
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- *Correspondence: Ruiying Zhang
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22
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Paul MJ. What are the regulatory targets for intervention in assimilate partitioning to improve crop yield and resilience? JOURNAL OF PLANT PHYSIOLOGY 2021; 266:153537. [PMID: 34619557 DOI: 10.1016/j.jplph.2021.153537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
Sucrose utilisation for the synthesis of cellular components involved in growth and development and the accumulation of biomass determines diversity in the plant kingdom; sucrose utilisation and partitioning also underpin crop yields. As a complex process the use of sucrose for the partitioning of plant products for yield is decided by the interaction of several regulatory hubs and the integration of metabolism and development. Understanding the regulation of assimilate partitioning has been a grand challenge in plant and crop science. There are emerging examples of genes and processes that appear important for assimilate partitioning that underpin yield in crops and which are amenable to intervention. Enzymes of carbon metabolism were some of the first targets in attempts to modify assimilate partitioning at the beginning (source) and end (sink) of the whole plant assimilate partitioning process. Metabolic enzymes are subject to regulatory and homeostatic mechanisms, a key factor to consider in modifying assimilate partitioning. Trehalose 6-phosphate, as a sucrose signal, may represent a special case in its ability to regulate and coordinate source and sink processes. This review summarises recent progress in understanding the underlying regulators of assimilate partitioning and the current and potentially most promising routes to crop yield enhancement with a main focus on cereals. A framework for how source-sink may regulate whole plant assimilate partitioning involving a few key elements and the central importance of reproductive development is presented.
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Affiliation(s)
- Matthew J Paul
- Plant Science, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK.
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