Maize root system plays a crucial role in the development of the aboveground plant and determines the yield through the uptake of water and nutrients in the field.  However, the genetic architecture of the maize root system is largely unknown mainly due to its complexity and the interactions between genotype and environment.  Using a high-throughput semi-automatic hydroponic platform with stable conditions, we comprehensively characterized the root system in a core population of 518 diverse inbred lines of maize.  Population structure analysis revealed that the panel has stratification and a linkage disequilibrium decay distance of less than 50 kb.  Based on genotyping with the high-density 600 K SNPs, we conducted a genome wide association analysis (GWAS) and identified nine SNPs and seven candidate genes significantly associated with 24 traits.  One candidate gene, GRMZM2G400533, is located at the upstream 5 kb region from the leading SNP (AX-91771718) and was significantly associated with primary root length and preferentially expressed in the primary root and crown root.  Expression of GRMZM2G400533 increased as the primary root developed but was negatively correlated with primary root elongation.  An analysis of candidate gene GRMZM2G400533 identified three functional variants and eight allelic haplotypes.  This study will broaden our understanding of maize root development and provide a theoretical basis for maize improvement through optimization of the root system.

The efficient genome editing tool (the CRISPR/Cas12a system) has been used in research on plant functionional genomics and improvement of agronomic traits.  In this study, CRISPR/Cas12a system was optimized by using the endogenous pGhαGloA promoter in cotton.  Using this system, crRNAs was driven by the Pol II pGhaGloA promoter to construct the pGhRBE3-pGhαGloA-GhPGF vector and carry out genetic transformation.  The vector could work efficiently in all positive transgenic plants and the editing efficiency at the crRNA1 target site was up to 93.37%, and the editing efficiency of the crRNA2 target was up to 88.24%, which is significantly higher in editing efficiency of the pGhRBE3 system with Pol III promoter-Ubi 6.7 promoter, this result indicates that the Pol II promoter is more suitable for expressing multiple sgRNA or crRNA than the pol III promoter in cotton.  The vector mainly generated the editing type of fragment deletion and the deletion size was in the range of 3-12 bp with the editing sites spanning at the 14th to 29th bases downstream of the protospacer adjacent motif (PAM).  All the targeted mutation loci were stably inherited from T₀ to T₂ generation and three transgene-free lines with target site mutations of GhPGF gene were obtained and these glandless and gossypol-free/(low contents) cotton germplasm will play key role for healthy cottonseeds oil/cake production.  Therefore, the CRISPR/Cas12a system driven by the pGhαGloA promoter can efficiently edit target genes in cotton, which provides a powerful tool for cotton functionional genomics and genetic improvement.