玉米elm1 突变体使得光敏色素载色体合成受阻并导致光敏色素活性下降,从而使得突变体植株表现出对光的不敏感性.为研究玉米ELM1 基因序列的多态性及其与主要农艺性状之间的关联,本研究对玉米ELM1 基因在80 个自交系中进行了目标序列重测序,并与株高和穗位高2 个株型性状以及穗长、穗粗、轴粗、穗重、行粒数、穗行数和穗粒数7 个穗部性状进行关联分析.ELM1 基因在供试玉米自交系中共有85 个变异,包括73 个SNP 和12 个Indel.尽管该基因的编码区不含Indel,但15 个SNP 变异位点依然可以将编码区划分成7 种单倍型,并编码6 种ELM1 蛋白质.关联分析发现,玉米ELM1 基因中1 个非同义突变位点与穗位高存在显著关联,另有2 个非同义突变位点与行粒数存在显著关联.
With the deficiency of the synthesis for the phytochromechromophore in the maize elm1 mutant, the phytochrome activity might be reduced and the mutant plant might show characteristics of light insensitivity. In order to reveal the nucleotide polymorphisms in the maize ELM1 gene and their associations with important agronomic traits, the sequences of the maize ELM1 gene are captured in 80 inbred lines in the present study, and the associations between the sequence variations of this gene and 2 plant types (including plant height and ear height) and 7 ear traits (ear length, ear diameter, cob diameter, ear weight, kernels per row, rows per ear and kernels per ear) are determined. A total of 85 variants, including 73 SNPs and 12 indels, are detected from the full sequences of this gene in the tested inbred lines. Although in the coding regions, the indel is not included, with the SNPs of CDS sequences, the maize ELM1 gene can be classified into 7 haplotypes, which encode 6 different ELM1 proteins. There are significant differences among inbred lines for all 9 plant types and ear traits. According to the results of the association analysis, one nonsynonymous SNP is found to be associated with the ear height, while two other nonsynonymous SNPs are associated with the kernels per row.
[1] Yin Z, Zhang Z, Deng D, et al. Characterization of Rubisco activase genes in maize: An alpha-isoform gene functions alongside a beta-isoform gene[J]. Plant Physiology, 2014, 164(4): 2096-2106.
[2] 詹克慧, 李志勇, 侯佩, 等. 利用修饰光敏色素信号途径进行作物改良 的可行性[J]. 中国农业科学, 2012, 45(16): 3249-3255. Zhan Kehui, Li Zhiyong, Hou Pei, et al. A new strategy from crop improvement through modification of phytochrome signalling pathways[J]. Scientia Agricultura Sinica, 2012, 45(16): 3249-3255.
[3] QuailPH.Phytochromephotosensorysignallingnetworks[J].NatureReviews Molecular Cell Biology, 2002, 3(2): 85-93.
[4] Ballaré C L, Casal J J. Light signals perceived by crop and weed plants[J]. Field Crops Research, 2000, 67(2): 149-160.
[5] Wu F Q, Fan C M, Zhang X M, et al. The phytochrome gene family in soybean and a dominant negative effect of a soybean PHYA transgene on endogenous Arabidopsis PHYA[J]. Plant Cell Reports, 2013, 32(12): 1879-1890.
[6] Abdurakhmonov I Y, Buriev Z T, Logan-Young C J, et al. Duplication, divergence and persistence in the phytochrome photoreceptor gene family of cottons (Gossypium spp.)[J]. BMC Plant Biology, 2010, 10: 119.
[7] 何冰, 刘玲珑, 张文伟, 等. 植物叶色突变体[J]. 植物生理学通讯, 2006, 42(1): 1-9. He Bing, Liu Linglong, Zhang Wenwei, et al. Plant leaf color mutants[J]. Plant Physiology Communications, 2006, 42(1): 1-9.
[8] Sawers R J, Linley P J, Farmer P R, et al. Elongated mesocotyl1, a phytochrome-deficient mutant of maize[J]. Plant Physiology, 2002, 130 (1): 155-163.
[9] Markelz N H, Costich D E, Brutnell T P. Photomorphogenic responses in maize seedling development[J]. Plant Physiology, 2003, 133(4): 1578- 1591.
[10] Sawers R J, Linley P J, Gutierrez-Marcos J F, et al. The ELM1 (ZmHy2) gene of maize encodes a phytochromobilin synthase[J]. Plant Physiology, 2004, 136(1): 2771-2781.
[11] Larkin M A, Blackshields G, Brown N P, et al. Clustal W and Clustal X version 2.0[J]. Bioinformatics, 2007, 23(21): 2947-2948.
[12] Librado P, Rozas J. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data[J]. Bioinformatics, 2009, 25(11): 1451-1452.
[13] Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism[J]. Genetics, 1989, 123(3): 585-595.
[14] Fu Y X, Li W H. Statistical tests of neutrality of mutations[J]. Genetics, 1993, 133(3): 693-709.
[15] Bradbury P J, Zhang Z, Kroon D E, et al. TASSEL: Software for association mapping of complex traits in diverse samples[J]. Bioinformatics, 2007, 23 (19): 2633-2635.
[16] Remington D L, Thornsberry J M, Matsuoka Y, et al. Structure of linkage disequilibrium and phenotypic associations in the maize genome[J]. Proceedings of the National Academy of Sciences of the United States of America, 2001, 98(20): 11479-11484.
[17] Yan J, Warburton M, Crouch J. Association mapping for enhancing maize (L.) genetic improvement[J]. Crop Science, 2011, 51(2): 433-449.
[18] Xu S, Yang Z, Zhang E, et al. Nucleotide diversity of maize ZmBT1 gene and association with starch physicochemical properties[J]. PloS One, 2014, 9(8): e103627.
[19] Jiao Y, Zhao H, Ren L, et al. Genome- wide genetic changes during modern breeding of maize[J]. Nature Genetics, 2012, 44(7): 812-815.
[20] Ching A, Caldwell K S, Jung M, et al. SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines[J]. BMC Genetics, 2002, 3: 19.
[21] Childs K L, Miller F R, Cordonnier- Pratt M M, et al. The sorghum photoperiod sensitivity gene, Ma3, encodes a phytochrome B[J]. Plant Physiology, 1997, 113(2): 611-619.
[22] BoylanMT,QuailPH.Oatphytochromeisbiologicallyactivein transgenic tomatoes[J]. The Plant Cell, 1989, 1(8): 765-773.
[23] Thiele A, Herold M, Lenk I, et al. Heterologous expression of arabidopsis phytochrome B in transgenic potato influences photosynthetic performance and tuber development[J]. Plant Physiology, 1999, 120(1): 73-82.
