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Xu C, Zhang H, Sun J, Guo Z, Zou C, Li WX, Xie C, Huang C, Xu R, Liao H, Wang J, Xu X, Wang S, Xu Y. Genome-wide association study dissects yield components associated with low-phosphorus stress tolerance in maize. Theor Appl Genet 2018; 131:1699-1714. [PMID: 29754325 DOI: 10.1007/s00122-018-3108-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 05/07/2018] [Indexed: 05/28/2023]
Abstract
Phosphorus deficiency in soil is a worldwide constraint threatening maize production. Through a genome-wide association study, we identified molecular markers and associated candidate genes and molecular pathways for low-phosphorus stress tolerance. Phosphorus deficiency in soils will severely affect maize (Zea mays L.) growth and development, thus decreasing the final yield. Deciphering the genetic basis of yield-related traits can benefit our understanding of maize tolerance to low-phosphorus stress. However, considering that yield-related traits should be evaluated under field condition with large populations rather than under hydroponic condition at a single-plant level, searching for appropriate field experimental sites and target traits for low-phosphorus stress tolerance is still very challenging. In this study, a genome-wide association analysis using two natural populations was performed to detect candidate genes in response to low-phosphorus stress at two experimental sites representative of different climate and soil types. In total, 259 candidate genes were identified and these candidate genes are mainly involved in four major pathways: transcriptional regulation, reactive oxygen scavenging, hormone regulation, and remodeling of cell wall. Among these candidate genes, 98 showed differential expression by transcriptome data. Based on a haplotype analysis of grain number under phosphorus deficiency condition, the positive haplotypes with favorable alleles across five loci increased grain number by 42% than those without favorable alleles. For further verifying the feasibility of genomic selection for improving maize low-phosphorus tolerance, we also validated the predictive ability of five genomic selection methods and suggested that moderate-density SNPs were sufficient to make accurate predictions for low-phosphorus tolerance traits. All these results will facilitate elucidating genetic basis of maize tolerance to low-phosphorus stress and improving marker-assisted selection efficiency in breeding process.
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Affiliation(s)
- Cheng Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 South Zhongguancun Street, Beijing, 100081, China
| | - Hongwei Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 South Zhongguancun Street, Beijing, 100081, China
| | - Jianhao Sun
- Institute of Soil Fertilizer and Water-saving Agriculture, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Zifeng Guo
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 South Zhongguancun Street, Beijing, 100081, China
| | - Cheng Zou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 South Zhongguancun Street, Beijing, 100081, China
| | - Wen-Xue Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 South Zhongguancun Street, Beijing, 100081, China
| | - Chuanxiao Xie
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 South Zhongguancun Street, Beijing, 100081, China
| | - Changling Huang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 South Zhongguancun Street, Beijing, 100081, China
| | - Ruineng Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Root Biology Center, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Hong Liao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Root Biology Center, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Jinxiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Root Biology Center, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Xiaojie Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 South Zhongguancun Street, Beijing, 100081, China
| | - Shanhong Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 South Zhongguancun Street, Beijing, 100081, China
| | - Yunbi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 South Zhongguancun Street, Beijing, 100081, China.
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, CP 56130, Mexico.
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Li HL, Guo D, Peng SQ. Molecular characterization of the Jatropha curcas JcR1MYB1 gene encoding a putative R1-MYB transcription factor. Genet Mol Biol 2014; 37:549-55. [PMID: 25249778 PMCID: PMC4171771 DOI: 10.1590/s1415-47572014000400011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 05/16/2014] [Indexed: 11/22/2022] Open
Abstract
The cDNA encoding the R1-MYB transcription factor, designated as JcR1MYB1, was isolated from Jatropha curcas using rapid amplification of cDNA ends. JcR1MYB1 contains a 951 bp open reading frame that encodes 316 amino acids. The deduced JcR1MYB1 protein was predicted to possess the conserved, 56-amino acid-long DNA-binding domain, which consists of a single helix-turn-helix module and usually occurs in R1-MYBs. JcR1MYB1 is a member of the R1-MYB transcription factor subfamily. A subcellular localization study confirmed the nuclear localization of JcR1MYB1. Expression analysis showed that JcR1MYB1 transcripts accumulated in various examined tissues, with high expression levels in the root and low levels in the stem. JcR1MYB1 transcription was up-regulated by polyethylene glycol, NaCl, and cold treatments, as well as by abscisic acid, jasmonic acid, and ethylene treatment. Analysis of transgenic tobacco plants over-expressing JcR1MYB1 indicates an inportant function for this gene in salt stress.
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Affiliation(s)
- Hui-Liang Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops , Ministry of Agriculture , Institute of Tropical Bioscience and Biotechnology , Chinese Academy of Tropical Agricultural Sciences , Haikou , China
| | - Dong Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops , Ministry of Agriculture , Institute of Tropical Bioscience and Biotechnology , Chinese Academy of Tropical Agricultural Sciences , Haikou , China
| | - Shi-Qing Peng
- Key Laboratory of Biology and Genetic Resources of Tropical Crops , Ministry of Agriculture , Institute of Tropical Bioscience and Biotechnology , Chinese Academy of Tropical Agricultural Sciences , Haikou , China
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Chang JC, Liao YC, Yang CC, Wang AY. The purine-rich DNA-binding protein OsPurα participates in the regulation of the rice sucrose synthase 1 gene expression. Physiol Plant 2011; 143:219-234. [PMID: 21834856 DOI: 10.1111/j.1399-3054.2011.01501.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The rice sucrose synthase 1 (RSus1) gene is transcriptionally induced by sucrose, and a region within its promoter, at -1117 to -958 upstream of the transcription initiation site, was found to be essential for enhancing the sucrose-induced expression. Further dissection of this region revealed that a group of nuclear proteins interact with a 39-bp fragment named A-3-2 (-1045 to -1007). A protein that specifically and directly interacted with A-3-2 was isolated from the suspension-cultured cells of rice and was subsequently identified as a purine-rich DNA-binding protein. The amino acid sequence of this protein, OsPurα, exhibited 73% identity with the Arabidopsis Purα-1 protein, and its modeled structure resembled the structure of Pur-α in Drosophila. Recombinant OsPurα expressed and purified from Escherichia coli was demonstrated to have DNA-binding activity and to interact with A-3-2 specifically. Moreover, OsPurα was able to enhance sucrose-induced expression of the β-glucuronidase (GUS) reporter gene, which was transcriptionally fused to two copies of a DNA fragment containing A-3-2 and the cauliflower mosaic virus 35S minimal promoter, in vivo. The level of OsPurα bound to A-3-2 was higher in cells cultured in the presence of sucrose; however, the level of OsPurα mRNA in cells was not affected by sucrose. The results of this study demonstrate that OsPurα participates in the regulation of RSus1 expression in response to sucrose; nevertheless, it may require other partner proteins for full function.
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Affiliation(s)
- Jui-Che Chang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
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Guo P, Bai G, Carver B, Li R, Bernardo A, Baum M. Transcriptional analysis between two wheat near-isogenic lines contrasting in aluminum tolerance under aluminum stress. Mol Genet Genomics 2006; 277:1-12. [PMID: 17039377 DOI: 10.1007/s00438-006-0169-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Revised: 08/23/2006] [Accepted: 09/07/2006] [Indexed: 10/24/2022]
Abstract
To understand the mechanisms of aluminum (Al) tolerance in wheat (Triticum aestivum L.), suppression subtractive hybridization (SSH) libraries were constructed from Al-stressed roots of two near-isogenic lines (NILs). A total of 1,065 putative genes from the SSH libraries was printed in a cDNA array. Relative expression levels of those genes were compared between two NILs at seven time points of Al stress from 15 min to 7 days. Fifty-seven genes were differentially expressed for at least one time point of Al treatment. Among them, 28 genes including genes for aluminum-activated malate transporter-1, ent-kaurenoic acid oxidase-1, beta-glucosidase, lectin, histidine kinase, and phospoenolpyruvate carboxylase showed more abundant transcripts in Chisholm-T and therefore may facilitate Al tolerance. In addition, a set of genes related to senescence and starvation of nitrogen, iron, and sulfur, such as copper chaperone homolog, nitrogen regulatory gene-2, yellow stripe-1, and methylthioribose kinase, was highly expressed in Chisholm-S under Al stress. The results suggest that Al tolerance may be co-regulated by multiple genes with diverse functions, and those genes abundantly expressed in Chisholm-T may play important roles in enhancing Al tolerance. The down-regulated genes in Chisholm-S may repress root growth and restrict uptake of essential nutrient elements, and lead to root senescence.
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Affiliation(s)
- Peiguo Guo
- College of Life Science, Guangzhou University, Guangzhou, 510006, China
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Abstract
The past half decade has provided a wealth of information concerning the molecular and genetic control of floral organ and meristem identity in dicotyledonous plants. Comparatively little is understood about these processes in grass species in spite of the importance that these species play in human agriculture. The isolation of grass genes that are homologous to dicot floral homeotic genes in combination with recent advances in reverse genetic technology and improvements in cereal transformation opens the door for understanding molecular mechanisms of grass flower development. Such information will also focus attention on the evolutionary relationships between grass and dicot flowers and the degree to which the developmental pathways leading to reproductive organ development in divergent angiosperms have utilized conserved mechanisms.
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Affiliation(s)
- R J Schmidt
- Department of Biology, Center for Molecular Genetics, University of California, San Diego, CA 92093-0116, USA.
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