Maize is moderately sensitive to salt stress; therefore, soil salinity is a serious threat to its production worldwide. Here, excellent salt-tolerant maize inbred line TL1317 and extremely salt-sensitive maize inbred line SL1303 were screened to understand the maize response to salt stress and its tolerance mechanisms. Relative water content, membrane stability index, stomatal conductance, chlorophyll content, maximum photochemical efficiency, photochemical efficiency, shoot and root fresh/dry weight, and proline and water soluble sugar content analyses were used to identify that the physiological effects of osmotic stress of salt stress were obvious and manifested at about 3 days after salt stress in maize. Moreover, the ion concentration of two maize inbred lines revealed that the salt-tolerant maize inbred line could maintain low Na+ concentration by accumulating Na+ in old leaves and gradually shedding them to exclude excessive Na+. Furthermore, the K+ uptake and retention abilities of roots were important in maintaining K+ homeostasis for salt tolerance in maize. RNA-seq and qPCR results revealed some Na+/H+ antiporter genes and Ca2+ transport genes were up-regulated faster and higher in TL1317 than those in SL1303. Some K+ transport genes were down-regulated in SL1303 but up-regulated in TL1317. RNA-seq results, along with the phenotype and physiological results, suggested that the salt-tolerant maize inbred line TL1317 possesses more rapidly and effectively responses to remove toxic Na+ ions and maintain K+ under salt stress than the salt-sensitive maize inbred line SL1303. This response should facilitate cell homoeostasis under salt stress and result in salt tolerance in TL1317.

Auxin response factors (ARFs), member of the plant-specific B3 DNA binding superfamily, target specifically to auxin response elements (AuxREs) in promoters of primary auxin-responsive genes and heterodimerize with Aux/IAA proteins in auxin signaling transduction cascade. In previous research, we have isolated and characterized maize Aux/IAA genes in whole-genome scale. Here, we report the comprehensive analysis of ARF genes in maize. A total of 36 ARF genes were identified and validated from the B73 maize genome through an iterative strategy. Thirty-six maize ARF genes are distributed in all maize chromosomes except chromosome 7. Maize ARF genes expansion is mainly due to recent segmental duplications. Maize ARF proteins share one B3 DNA binding domain which consists of seven-stranded β sheets and two short α helixes. Twelve maize ARFs with glutamine-rich middle regions could be as activators in modulating expression of auxin-responsive genes. Eleven maize ARF proteins are lack of homo- and heterodimerization domains. Putative cis-elements involved in phytohormones and light signaling responses, biotic and abiotic stress adaption locate in promoters of maize ARF genes. Expression patterns vary greatly between clades and sister pairs of maize ARF genes. The B3 DNA binding and auxin response factor domains of maize ARF proteins are primarily subjected to negative selection during selective sweep. The mixed selective forces drive the diversification and evolution of genomic regions outside of B3 and ARF domains. Additionally, the dicot-specific proliferation of ARF genes was detected. Comparative genomics analysis indicated that maize, sorghum and rice duplicate chromosomal blocks containing ARF homologs are highly syntenic. This study provides insights into the distribution, phylogeny and evolution of ARF gene family.

Rubisco activase (RCA) catalyzes the activation of Rubisco in vivo and plays a crucial role in photosynthesis. However, until now, little was known about the molecular genetics of RCA in soybean (Glycine max), one of the most important legume crops. Here, we cloned and characterized two genes encoding the longer α -isoform and the shorter β -isoform of soybean RCA (GmRCA α and GmRCA β, respectively). The two corresponding cDNAs are divergent in both the translated and 3 ′ untranslated regions. Analysis of genomic DNA sequences suggested that the corresponding mRNAs are transcripts of two different genes and not the products of a single alternatively splicing pre-mRNA. Two additional possible α -form RCA-encoding genes, GmRCA03 and GmRCA14, and one additional β -form RCA-encoding gene, GmRCA11, were also isolated. To examine the function and modulation of RCA genes in soybean, we determined the expression levels of GmRCA α and GmRCA β, Rubisco initial activity, photosynthetic rate, and seed yield in 184 soybean recombinant inbred lines. Correlation of gene expression levels with three other traits indicates that RCA genes could play an important role in regulating soybean photosynthetic capacity and seed yield. Expression quantitative trait loci mapping revealed four trans-expression quantitative trait loci for GmRCA α and GmRCA β. These results could provide a new approach for the modulation of RCA genes to improve photosynthetic rate and plant growth in soybean and other plants.