Scientia Agricultura Sinica ›› 2017, Vol. 50 ›› Issue (24): 4671-4678.doi: 10.3864/j.issn.0578-1752.2017.24.001

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS •     Next Articles

Genome-Wide Association Analysis of Maize Stalk Anti-Thrust

MA QingMei1,3, PEI YuHe2,3, CHEN DongBin 1,3,SONG XiYun2,3   

  1. 1College of Life Science, Qingdao Agricultural University, Qingdao 266109, Shandong; 2College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao 266109, Shandong; 3Qingdao Key Laboratory of Major Crops, Germplasm Innovation and Application in Qingdao, Qingdao 266109, Shandong
  • Received:2017-05-10 Online:2017-12-16 Published:2017-12-16

Abstract: 【Objective】SNP loci related to stalk anti-thrust were detected by association analysis between genotype and phenotype data, so that various candidate genes related to stalk anti-thrust were explored.【Method】At present, genome-wide association analysis is widely used in the study of various traits in plants. In this study, 292 maize inbred lines were used as experimental materials, the determination of stalk anti-thrust was carried out in Heze, Zaozhuang, Qingzhou, Jiaozhou in 2015 and 2016. Besides, the plant height, ear height, tassel length and male spike length were measured. On the other hand, the DNA samples of the materials were extracted and then sent to Pioneer seed Products Ltd for genotyping by using MaizeSNP50 gene chip. The chip includes 55126 single nucleotide polymorphism (SNP) markers, after removing the markers whose heterozygous ratio was greater than 10%, loss rate was more than 20% and minimum allele frequency was less than 0.05, there were 25331 SNPs left. Combined with the use of farmCPU, genome-wide association analysis was carried out for analyzing stalk anti-thrust phenotype data, the SNP loci which were significantly related to thrust resistance of stem were detected. According to the physical location of the SNP, the region of the marker was located and then the corresponding candidate genes were obtained. Using SPSS statistics 20 data analysis software, the correlation analysis of plant height, ear height, tassel length and male spike length was carried out to determine the correlation between stem thrust resistance and the 4 traits. In addition, stalk anti-thrust was found to have a significant or extremely significant correlation with plant height, ear height, tassel length and male spike length, but the correlation in each environment was instable, which means that the environment might have a certain impact on the correlation.【Result】A total of 16 SNPs were found to be significantly correlated with stalk anti-thrust, which were located on chromosome box 3.06, 5.02, 4.08, 6.04 and 9.03. SNP loci detected in multiple environments were found to be located on the same chromosome box, for example, SNP loci PZE_108026930, SYN19532, PZE_108048987 and PZE_108050769 which were all found to be located on chromosome 8.03 were detected in Zaozhuang in 2015 and 2016. Moreover, PZE_103111295 and PZE_103125327 found to be located on chromosome 3.06 were detected in Qingzhou in 2015 and Zaozhuang in 2016. A total of 5 candidate genes GRMZM2G504401, GRMZM2G062974, GRMZM2G053767, GRMZM2G348551 and GRMZM2G024260 which encode basic endochitinase A, bZIP transcription factor superfamily protein, 40S ribosomal protein S4-like protein isoform X1, soluble starch synthase 2-3, adenine nucleotide alpha hydrolase-like superfamily protein were also obtained, respectively. 【Conclusion】GRMZM2G062974 is involved in the expression regulation of plants under stress and responds to a variety of abiotic stresses. GRMZM2G348551 participates in the pathway of glucose metabolism and regulates the synthesis of amylopectin, which is involved in the formation of cell walls. GRMZM2G504401 is induced by biotic or abiotic stresses in plant. Lodging is affected by its own or a variety of stresses, and the functions of these genes are compatible with lodging resistance, so future studies should focus on the function of these genes.

Key words: maize, stalk anti-thrust, genome-wide association analysis, candidate gene

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