Mining candidate genes for maize plant height based on GWAS, Meta-QTL, and WGCNA

Fu Qian¹Zhanqin Zhang²Shubin Chen²Zhiqin Sang^2*Weihua Li^1*

• ¹College of Agriculture, Shihezi University, Shihezi, China
• ²Institute of Crop Research, Xinjiang Academy of Agricultural and Reclamation Sciences (XAARS), Shihezi, Xinjiang Uyghur Region, China

In maize, plant height (PH) is one of the most important agronomic traits that directly influences planting density and yield. Therefore, identifying candidate genes related to PH will help manipulate maize yield indirectly. The present research carried out a genome-wide association study (GWAS) of PH using a natural population of 580 maize inbred lines. A total of 31 significant single-nucleotide polymorphisms (SNPs) were detected, and five co-located SNPs were simultaneously detected in two or more environments. Subsequent gene function annotation and prediction identified four candidate genes related to PH. Further, after collecting the published transcriptome data of maize B73, tissue-specific gene co-expression modules related to PH were generated using weighted gene co-expression network analysis (WGCNA), and use reported PH genes as hub genes to mine 31 candidate genes within the modules. Meanwhile, a meta-analysis of the already reported PH-related quantitative trait loci (QTLs) identified 18 Meta-QTLs (MQTLs) associated PH, of which nine MQTLs detected 10 PH-related candidate genes. Two significant SNPs detected based on GWAS were located within these MQTLs intervals, and one significant SNP was found close to a specific MQTL (229kb). Finally, the integrated analysis of the results based on the different approaches screened three candidate genes: Zm00001d031796 encoding AP2-EREBP transcription factor 172, Zm00001d009918 encoding Phytochrome A-associated F-box protein, and Zm00001d042454 encoding plastid specific ribosomal protein 4. The research results provide reference for analyzing the genetic basis and molecular mechanism of maize PH.