Abstract
Key message
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.
Abstract
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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Acknowledgments
The research was supported by the National Natural Science Foundation of China–CGIAR International Collaborative Program (31361140364), National Key Research and Development Program of China (2016YFD0101803), Agricultural Science and Technology Innovation Program (ASTIP) of Chinese Academy of Agricultural Sciences (CAAS), Fundamental Research Funds for Central Non-Profit of Institute of Crop Sciences, CAAS (1610092016124), Bill and Melinda Gates Foundation, and CGIAR Research Program MAIZE.
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Communicated by Benjamin Stich.
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122_2018_3108_MOESM1_ESM.docx
Manhattan plots on ten maize chromosomes for six yield-related traits under two P conditions tested in Gansu, 2015. a Significant SNPs under NP (normal-phosphorus) condition. b Significant SNPs under LP (low-phosphorus) condition. EL: ear length; RN: row number; GNPR: grain number per row; GN: grain number; HGW: hundred grain weight; GWPP: grain weight per plant (DOCX 1561 kb)
122_2018_3108_MOESM2_ESM.docx
Manhattan plots on ten maize chromosomes for seven traits tested under two P conditions in Guangdong. a Significant SNPs under normal-phosphorus (NP) condition in Guangdong. b Significant SNPs under low-phosphorus (LP) condition in Guangdong. FEW: fresh ear weight; LN: leaf number; PH: plant height. The numbers after the trait abbreviations indicate the number of days after planting (DOCX 1575 kb)
122_2018_3108_MOESM5_ESM.docx
Gene ontology classification of candidate genes under low-phosphorus condition. Input means the input genes detected by this study; background means the background genes of inbred line B73 (DOCX 303 kb)
122_2018_3108_MOESM6_ESM.docx
Venn diagram summarizing three types of gene expression. “2 Day vs. 8 Day” indicates differential expression between 2 days and 8 days (after initiation of low-phosphorus treatment); “31778 vs. CCM454” indicates differential expression between tolerant line CCM454 and sensitive line 31778; “Normal P vs. Low P” indicates differential expression between low-phosphorus (LP) and normal-phosphorus (NP) treatments (DOCX 161 kb)
122_2018_3108_MOESM7_ESM.docx
Prediction accuracy of five GS models for 11 tested traits under normal-phosphorus (NP) condition in 2014 and 2015 using genome-wide SNPs. a NP condition in 2014. b NP condition in 2015. PH: plant height; EL: ear length; RN: row number; GNPR: grain number per row; GN: grain number; HGW: hundred grain weight; DTT: days to tassel; DTA: days to anthesis; DTS: days to silk; ASI: anthesis-silking interval; GWPP: grain weight per plant (DOCX 655 kb)
122_2018_3108_MOESM8_ESM.docx
Prediction accuracy of five tested traits under normal-phosphorus (NP) and low-phosphorus (LP) conditions in 2014 and 2015 with 100-20,000 SNPs using GBLUP. a NP condition. b LP condition. PH: plant height; EL: ear length; RN: row number; DTT: days to tassel; GWPP: grain weight per plant (DOCX 523 kb)
122_2018_3108_MOESM9_ESM.docx
Prediction accuracy of BayesB and haplotype-based BayesB for 11 tested traits under low-phosphorus (LP) conditions in 2014 and 2015 using genome-wide SNPs. a LP condition in 2014. b LP condition in 2015. PH: plant height; EL: ear length; RN: row number; GNPR: grain number per row; GN: grain number; HGW: hundred grain weight; DTT: days to tassel; DTA: days to anthesis; DTS: days to silk; ASI: anthesis-silking interval; GWPP: grain weight per plant (DOCX 432 kb)
122_2018_3108_MOESM10_ESM.docx
Prediction accuracy of BayesB and haplotype-based BayesB for 11 tested traits under normal phosphorus (NP) in 2014 and 2015 using genome-wide SNPs. a NP condition in 2014. b NP condition in 2015. PH: plant height; EL: ear length; RN: row number; GNPR: grain number per row; GN: grain number; HGW: hundred grain weight; DTT: days to tassel; DTA: days to anthesis; DTS: days to silk; ASI: anthesis-silking interval; GWPP: grain weight per plant (DOCX 444 kb)
122_2018_3108_MOESM11_ESM.docx
Gene ontology classification of candidate genes related to LPTI. Input means the input genes detected by this study; background means the background genes of inbred line B7311 (DOCX 279 kb)
122_2018_3108_MOESM12_ESM.docx
Phenotype distribution of 11 tested traits under normal-phosphorus (NP) and low-phosphorus (LP) conditions (DOCX 628 kb)
122_2018_3108_MOESM13_ESM.xlsx
SLI, LPPI, NPPI, and the extremely tolerant and susceptible inbred lines in 410 inbred lines tested in Gansu (XLSX 35 kb)
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Xu, C., Zhang, H., Sun, J. et al. Genome-wide association study dissects yield components associated with low-phosphorus stress tolerance in maize. Theor Appl Genet 131, 1699–1714 (2018). https://doi.org/10.1007/s00122-018-3108-4
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DOI: https://doi.org/10.1007/s00122-018-3108-4