Genome-wide Association Studies and Genes for Seed Germination Chromosome under Low-Temperature Stress in Maize (Zea mays L) Cropping System

Xiaofen Li^{1, 2}, Rongzhen Wang^{1, 2}, Kaiyuan Cui^{1, 2}, Hafeeze Noor^{1, 2}, Pengcheng Ding^{1, 2,} and Fida Noor¹

¹College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China

²Key Laboratory of Functional Agriculture in the Loess Plateau, Ministry of Agriculture and Rural Affairs, Taigu, 030801, Shanxi, China

Cite this paper:
Xiaofen Li, Rongzhen Wang, Kaiyuan Cui, Hafeeze Noor, Pengcheng Ding and Fida Noor. Genome-wide Association Studies and Genes for Seed Germination Chromosome under Low-Temperature Stress in Maize (Zea mays L) Cropping System. Journal of Food and Nutrition Research. 2023; 11(3):193-204. doi: 10.12691/jfnr-11-3-4

Abstract

Low-temperature stress delays seed germination in maize. Different maize inbred lines display various low-temperature resistance, but the dynamic changes in seed germination under low-temperature stress in maize remain unknown, especially at the transcriptome level. Maize (Zea mays L.). 18 evaluation indexes of low temperature tolerance germination of 238 maize inbred lines were statistically analyzed, of which 12 evaluation indexes of low temperature tolerance had large coefficient of variation. The results of cluster analysis relative decrease of root length is similar to those of comprehensive evaluation cluster analysis of 12 low temperature tolerance indexes. The relative K + Q model was used to set the threshold - log10P = 4.61 to score the GWAS of evaluation indexes of low temperature tolerance. A total of 47 SNP loci significantly associated with low temperature tolerance were detected, of which the SNP loci significantly associated with chromosome 8 were the most, and the interpretation range of phenotypic contribution rate was 10.88% - 16.31%. It can be used as a candidate interval for subsequent screening and analysis. GWAS analysis showed that there were at least 2 evaluation indexes of low temperature tolerance, and a total of 6 SNPs were detected, of which 1 was on chromosome 5 and the other 5 were on chromosome 3. The consistent loci on chromosome 3 were located between PZE-103174386 (220,933,020) and PZE-103174950 (221,386,301).

Keywords:
seed germination seedling growth low-temperature stress maize peroxidase activity

This work is licensed under a Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

Figures

References:

[1]	Walbot, V., 10 Reasons to be Tantalized by the B73 Maize Genome. PLoS Genet. 2009, 5, e1000723.
[2]	June, C., Page, S.E.E.L.; Pasternak, S., Liang, C., Zhang, J., Fulton, L., Graves, T.A., Minx, P., Reily, A.D., Courtney, L., et al. The Maize Genome: Complexity, Diversity, and Dynamics. Science 2009, 1912, 1112-1115.
[3]	Tenaillon, M.I., Charcosset, A. A European perspective on maize history. Comptes Rendus-Biol. 2011, 334, 221-228.
[4]	Zeng, R., Li, Z., Shi, Y., Fu, D., Yin, P., Cheng, J., Jiang, C., Yang, S. Natural variation in a type—A response regulator confers maize chilling tolerance. Nat Commun. 2021, 12, 4713.
[5]	Santis D. A., Landi P., Genchi G. Changes of mitochondrial properties in maize seedlings associated with selection for germination at low temperature. fatty acid composition, cytochrome c oxidase and adenine nucleotide translocase activities. Plant Physiology., 1999, 119: 743-754.
[6]	Prasad T. K. Mechanisms of chilling-induced oxidative stress injury and tolerance in developing maize seedlings: changes in antioxidant system, oxidation of proteins and lipids, and protease activities. The plant journal., 1996, 10(6): 1017-1026.
[7]	Bewley J. D., Seed germination and dormancy. Plant Cell., 1997, 9: 1055-1066.
[8]	Han C., Yang P. Studies on the molecular mechanisms of seed germination. Proteomics., 2015, 15: 1671-1679.
[9]	Noblet A., Leymarie J., Bailly C. Chilling temperature remodels phospholipidome of Zea Mays seeds during imbibition. Scientific Reports., 2017, 7: 1-12.
[10]	Zheng H., Yang Z., Wang W., Guo S., Li Z., Liu K., Sui N. Transcriptome analysis of maize inbred lines differing in drought tolerance provides novel insights into the molecular mechanisms of drought responses in roots. Plant Physiology and Biochemistry., 2020, 149: 11-26.
[11]	Bhaskara G. B., Nguyen T. T., Verslues P. E. Unique drought resistance functions of the highly ABA-induced clade a protein phosphatase 2Cs. Plant Physiology., 2012, 160: 379-395.
[12]	Farooq M., Aziz T., Wahid A., Lee D. J., Siddique K. H. M. Chilling tolerance in maize: agronomic and physiological approaches. Crop and Pasture Science., 2009, 60: 501-516.
[13]	Gareau J. R., Lima C. D. The SUMO pathway: emerging mechanisms that shape specificity, conjugation and recognition. Nature Reviews Molecular Cell Biology., 2010, 11: 861-871.
[14]	Gilmour S. J., Fowler S. G., Thomashow M. F. Arabidopsis transcriptional activators CBF1, CBF2, and CBF3 have matching functional activities sarah. Plant Molecular Biology., 2004, 54: 767-781.
[15]	Gong Z., Dong C. H., Lee H., Zhu J., Xiong L., Gong D., Stevenson B., Zhu J. K. A DEAD box RNA helicase is essential for mRNA export and important for development and stress responses in Arabidopsis. Plant Cell., 2005, 17(1): 256-267.
[16]	Grant J. J., Yun B. W., Loake G. J. Oxidative burst and cognate redox signalling reported by luciferase imaging: identification of a signal network that functions independently of ethylene, SA and Me-JA but is dependent on MAPKK activity. Plant Journal., 2000, 24(5): 569-582.
[17]	Nagel K. A., Kastenholz B., Jahnke S., Van Dusschoten D., Aach T., Mühlich M., Truhn D., Scharr H., Terjung S., Walter A., Schurr U. Temperature responses of roots: impact on growth, root system architecture and implications for phenotyping. Functional Plant Biology., 2009, 36: 947-959.
[18]	Hu G., Li Z., Lu Y., Li C., Gong S., Yan S., Li G., Wang M., Ren H., Guan H., Zhang Z., Qin D., Chai M., Yu J., Li Y., Yang D., Wang T., Zhang Z. Genome-wide association study identified multiple genetic loci on chilling resistance during germination in maize. Scientific Reports. 2017, 7: 1-11.
[19]	Chu M., Chen P., Meng S., Xu P., Lan W. The Arabidopsis phosphatase PP2C49 negatively regulates salt tolerance through inhibition of AtHKT1;1. Journal of Integrative Plant Biology., 2021, 63: 528-542.
[20]	Nägele T., Heyer A. G. Approximating subcellular organisation of carbohydrate metabolism during cold acclimation in different natural accessions of Arabidopsis thaliana. New Phytologist., 2013, 198: 777-787.
[21]	Strigens A., Freitag N. M., Gilbert X., Grieder C., Riedelsheimer C., Schrag T. A., Messmer R., Melchinger A. E. Association mapping for chilling tolerance in elite flint and dent maize inbred lines evaluated in growth chamber and field experiments. Plant, Cell and Environment., 2013, 36: 1871-1887.
[22]	D., Mittler R., Breusegem F. Transcriptomic footprints disclose specificity of reactive oxygen species signaling in Arabidopsis. Plant Physiology., 2006, 141: 436-445.