Genome-wide Association Study on Plant Height of Wheat (Triticum aestivum) from Yellow and Huai Valley Wheat Region of China Under Different Nitrogen Environments
ZHANG Na1, ZHANG Xi-Lan2, ZHAO Ming-Hui3, QIAO Wen-Chen3, FU Xiao-Yi4, HE Ming-Qi4, SUN Li-Jing5, LI Hui5, JI Jun2,*
1 Jiangsu Xuhuai Regional Institute of Agricultural Sciences, Xuzhou 221131, China; 2 Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China; 3 Institute of Dry Farming Agriculture, Hebei Academy of Agricultural and Forestry Sciences, Hengshui 053000, China; 4 Shijiazhuang Academy of Agricultural and Forestry Sciences, Shijiazhuang 050041, China; 5 Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China
Abstract Plant height (PH) is an important agronomic trait of wheat (Triticum aestivum), which is closely related to high and stable yield. Nitrogen is an essential mineral nutrient for plant growth and development, critically affects PH and yield of wheat. The sensitivity to nitrogen varies among different cultivars. In order to explore genetic loci influencing PH and PH tolerance to low nitrogen stress, and to provide excellent genetic resources of dwarf and high nitrogen efficiency, in this study, 132 elite wheat varieties (lines) mainly from the north Yellow and Huai Valley Wheat Region of China in recent 30 years were selected to carry out genome-wide association study (GWAS). PH and tolerant index (TI) of PH to low nitrogen stress under 8 environments with different nitrogen fertilizer conditions were identified. The genetic data were acquired by Affymetrix Wheat 55K SNP chip. Finally, 13 SNPs distributed on 1B, 1D, 2A, 2B, 2D, 3B, 4D, 5A, 6B and 7D were identified to be significantly associated with PH in 3 or more environments, which could explain 9.6%~26.6% of the phenotypic variation. Among them 4 significant association SNPs on 1B (2), 3B and 7D could be identified in both low nitrogen environment (LN) and high nitrogen environment (HN). AX-108824683-7D was significantly associated with PH in 7 environments, accounting for 16.8%~26.6% of the phenotypic variation. This locus has not been reported in previous studies, suggesting that it is a new dwarf gene locus. 7 SNPs were identified to be significantly associated with tolerant index of PH to low nitrogen stress, among which AX-111004994-4B was stably identified in 2 environments, explained 12.4%~13.1% of the phenotypic variation. The results provide references for dwarfing and high nitrogen efficiency in wheat molecular breeding.
ZHANG Na,ZHANG Xi-Lan,ZHAO Ming-Hui, et al. Genome-wide Association Study on Plant Height of Wheat (Triticum aestivum) from Yellow and Huai Valley Wheat Region of China Under Different Nitrogen Environments[J]. 农业生物技术学报, 2021, 29(2): 207-215.
[1] 陈凯. 2018. 水稻氮高效利用和耐低氮优异基因挖掘与种质创新[D]. 博士后出站报告, 中国农业科学院, 导师:黎志康. pp8-9. (Chen K.2018. Mining of excellent genes for nitrogen use efficiency and nitrogen deficiency tolerance and creation of germplasm in rice[D]. Thesis for P.D., Chinese Academy of Agricultural Sciences, Supervisor: Li Z K, pp8-9.) [2] 贾继增, 丁寿涛, 李月华, 等. 1992. 中国小麦的主要矮秆基因及矮源的研究[J]. 中国农业科学, 25(1), 1-5. (Jia J Z, Ding S K, Li Y H, et al.1992. Studies of main dwarf genes and dwarf resources on Chinese wheat[J]. Scientia Agricultura Sinica, 25(1), 1-5.) [3] Buss W, Ford B A, Foo E, et al.2020. Overgrowth mutants determine the causal role of gibberellin GA2oxidasea13 in Rht12 dwarfism of wheat[J]. Journal of Experimental Botany, 71(22): 7171-7178. [4] Chen S, Gao R H, Wang H Y, et al.2015. Characterization of a novel reduced height gene (Rht23) regulating panicle morphology and plant architecture in bread wheat[J]. Euphytica, 203: 583-594. [5] Ellis M H, Rebetzke G J, Azanza F, et al.2005. Molecular mapping of gibberellin-responsive dwarfing genes in bread wheat[J]. Theoretical and Applied Genetics, 111(3): 423-430. [6] Gao F M, Ma D Y, Yin G H, et al.2017. Genetic progress in grain yield and physiological traits in Chinese wheat cultivars of Sothern Yellow and Huai Valley since 1950[J]. Crop Science, 57(2): 760-773. [7] Griffiths S, Simmonds J, Leverington M, et al.2012. Meta-QTL analysis of the genetic control of crop height in elite European winter wheat germplasm[J]. Molecular Breeding, 29(1): 159-171. [8] Huang X Q, Kempf H, Ganal M W, et al.2004. Advanced backcross QTL analysis in progenies derived from a cross between a German elite winter wheat variety and a synthetic wheat (Triticum aestivum L.)[J]. Theoretical and Applied Genetics, 109(5): 933-943. [9] Ju X T, Xing G X, Chen X P, et al.2009. Reducing environmental risk by improving N management in intensive Chinese agricultural systems[J]. Proceedings of the National Academy of Sciences of the USA, 106(9): 3041-3046. [10] Kang H Y, Lin L J, Song Z J, et al.2012. Identification, fine mapping and characterization of Rht-dp, a recessive wheat dwarfing (reduced height) gene derived from Triticum polonicum[J]. Genes & Genomics, 34: 509-515. [11] Kim H, Hwang H, Hong J W, et al.2012. A rice orthologue of the ABA receptor, OsPYL/RCAR5, is a positive regulator of the ABA signal transduction pathway in seed germination and early seedling growth[J]. Journal of Experimental Botany, 63(2): 1013-1024. [12] Li S, Tian Y, Wu K, et al.2018. Modulating plant growth-metabolism coordination for sustainable agriculture[J]. Nature, 560(7720): 595-600. [13] Liu Y X, Lin Y, Gao S, et al.2017. A genome-wide association study of 23 agronomic traits in Chinese wheat landraces[J]. The Plant Journal, 91: 861-873. [14] Lozada D N, Mason R E, Babar M A, et al.2017. Association mapping reveals loci associated with multiple traits that affect grain yield and adaptation in soft winter wheat[J]. Euphytica, 213(9): 222. [15] Lu Y, Xing L P, Xing S J, et al.2015.Characterization of a putative new semi-dominant reduced height gene, Rht_NM9, in wheat (Triticum aestivum L.)[J]. Journal of Genetics and Genomics, 42(12): 685-698. [16] Ma F, Xu Y, Ma Z, et al.2018. Genome-wide association and validation of key loci for yield-related traits in wheat founder parent Xiaoyan 6[J]. Molecular Breeding, 38(7): 91. [17] Mcintosh R A, Yamazaki Y Y, Dubcovsky J, et al.2013. Catalogue of gene symbols for wheat[C]. 12th International Wheat Genetics Symposium: Yokohama, Japan, 1:1-32. [18] Mo Y, Vanzetti L S, Hale I, et al.2018. Identification and characterization of Rht25, a locus on chromosome arm 6AS affecting wheat plant height, heading time, and spike development[J]. Theoretical and Applied Genetics, 131(10): 2021-2035. [19] Peng J R, Richards D E, Hartley N M, et al.1999. Green revolution genes encode mutant gibberellin response modulators[J]. Nature, 400(6741): 256-261. [20] Pritchard J K, Stephens M, Rosenberg N A, et al.2000. Association mapping in structured populations[J]. American Journal of Human Genetics, 67(1): 170-181. [21] Reinhardt D, Kuhlemeier C.2002. Plant architecture[J]. EMBO reports, 3(9): 846-851. [22] Röde M S, Huang X Q, Börner A.2008. Fine mapping of the region on wheat chromosome 7D controlling grain weight[J]. Functional & Integrative Genomics, 8(1): 79-86. [23] Sun C W, Zhang F Y, Yan X F, et al.2017. Genome-wide association study for 13 agronomic traits reveals distribution of superior alleles in bread wheat from the Yellow and Huai Valley of China[J]. Plant Biotechnology Journal, 15(8): 953-969. [24] Sun L, Yang W, Li Y, et al.2019. A wheat dominant dwarfing line with Rht12, which reduces stem cell length and affects gibberellic acid synthesis, is a 5AL terminal deletion line[J]. The Plant Journal 97(5): 887-900. [25] Tian X L, Wen W E, Xie L, et al.2017. Molecular mapping of reduced plant height gene Rht24 in bread wheat[J]. Frontiers in Plant Science, 8: 1379. [26] Wang Z, Wu X, Qian R, et al.2010. QTL mapping for developmental behavior of plant height in wheat (Triticum aestivum L.)[J]. Euphytica, 174(3): 447-458. [27] Worland A J, Korzun V, Röder M S, et al.1998. Genetic analysis of the dwarfing gene Rht8 in wheat. Part II. The distribution and adaptive significance of allelic variants at the Rht8 locus of wheat as revealed by microsatellite screening[J]. Theoretical and Applied Genetics, 96: 1110-1120. [28] Worland A, Law C, Shakoor A, et al.1980. The genetical analysis of an induced height mutant in wheat[J]. Heredity, 45: 61-71. [29] Würschum T, Langer S M, Longin C F H, et al.2017. A modern green revolution gene for reduced height in wheat[J]. The Plant Journal, 92(5) 892-903. [30] Xu T, Bian N F, Wen M X, et al.2017. Characterization of a common wheat (Triticum aestivum L.) high-tillering dwarf mutant[J]. Theoretical and Applied Genetics, 130(3): 483-494. [31] Yu J M, Pressoir G, Briggs W H, et al.2006. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness[J]. Nature Genetics, 38(2): 203-208. [32] Yu M, Mao S L, Chen G Y, et al.2014. QTLs for uppermost internode and spike length in two wheat RIL populations and their affect upon plant height at an individual QTL level[J]. Euphytica, 200(1): 95-108. [33] Zhang N, Fan X, Cui F, et al.2017. Characterization of the temporal and spatial expression of wheat (Triticum aestivum L.) plant height at the QTL level and their influence on yield-related traits[J]. Theoretical and Applied Genetics, 130(6): 1235-1252. [34] Zhang N, Zhang X L, Song L, et al.2020. Identification and validation of the superior alleles for wheat kernel traits detected by genome-wide association study under different nitrogen environments[J]. Euphytica, 216: 52.
