ZmbHLH124 identified in maize recombinant inbred lines contributes to drought tolerance in crops.

Due to climate change, drought has become a severe abiotic stress that affects the global production of all crops. Elucidation of the complex physiological mechanisms underlying drought tolerance in crops will support the cultivation of new drought-tolerant crop varieties. Here, two drought-tolerant lines, RIL70 and RIL73, and two drought-sensitive lines, RIL44 and RIL93, from recombinant inbred lines (RIL) generated from maize drought-tolerant line PH4CV and drought-sensitive line F9721, were selected for a comparative RNA-seq study. Through transcriptome analyses, we found that gene expression differences existed between drought-tolerant and -sensitive lines, but also differences between the drought-tolerant lines, RIL70 and RIL73. ZmbHLH124 in RIL73, named as ZmbHLH124T-ORG which origins from PH4CV and encodes a bHLH type transcription factor, was specifically up-regulated during drought stress. In addition, we identified a substitution in ZmbHLH124 that produced an early stop codon in sensitive lines (ZmbHLH124S-ORG ). Overexpression of ZmbHLH124T-ORG , but not ZmbHLH124S-ORG , in maize and rice enhanced plant drought tolerance and up-regulated the expression of drought-responsive genes. Moreover, we found that ZmbHLH124T-ORG could directly bind the cis-acting elements in ZmDREB2A promoter to enhance its expression. Taken together, this work identified a valuable genetic locus and provided a new strategy for breeding drought-tolerant crops.

Effective identification of soybean candidate genes involved in resistance to soybean cyst nematode via direct whole genome re-sequencing of two segregating mutants.

KEY MESSAGE: Three soybean candidate genes involved in resistance to soybean cyst nematode race 4 were identified via direct whole genome re-sequencing of two segregating mutants. The genes conferring resistance to soybean cyst nematode (SCN) race 4 (Hg type 1.2.3.5.7) in soybean (Glycine max L. Merr.) remains unknown. Next generation sequencing-based methods identify a wide range of targets, it is difficult to identify genes underlying traits. Use of the MutMap and QTL-seq methods to identify trait candidate genes needs backcrossing and is very time-consuming. Here we report a simple method to effectively identify candidate genes involved in resistance to SCN race 4. Two ethane methylsulfonate mutagenized mutants of soybean 'PI 437654', whose SCN race 4-infection phenotype altered, were selected. Six relevant whole genomes were re-sequenced, and then calling of genomic variants (SNPs and InDels) was conducted and compared to 'Williams 82'. The comparison eliminated many genomic variants from the mutant lines that overlapped two non-phenotypic but mutant progeny plants, wild-type PI 437654 and 'Zhonghuang 13'. Finally, only 27 mutations were found among 10 genes. Of these 10 genes, 3 genes, Glyma.09g054000, Glyma.16g065700 and Glyma.18g192200 were overlapped between two phenotypic mutant progeny plants. Therefore, the three genes may be the candidate genes involved in resistance of PI 437654 to soybean cyst nematode race 4. This method simplifies the effective identification of candidate genes.

Genetic architecture and molecular regulation of sorghum domestication.

Over time, wild crops have been domesticated by humans, and the knowledge gained from parallel selection and convergent domestication-related studies in cereals has contributed to current techniques used in molecular plant breeding. Sorghum (Sorghum bicolor (L.) Moench) is the world's fifth-most popular cereal crop and was one of the first crops cultivated by ancient farmers. In recent years, genetic and genomic studies have provided a better understanding of sorghum domestication and improvements. Here, we discuss the origin, diversification, and domestication processes of sorghum based on archeological discoveries and genomic analyses. This review also comprehensively summarized the genetic basis of key genes related to sorghum domestication and outlined their molecular mechanisms. It highlights that the absence of a domestication bottleneck in sorghum is the result of both evolution and human selection. Additionally, understanding beneficial alleles and their molecular interactions will allow us to quickly design new varieties by further de novo domestication.

Isolation and characterization of Aspergillus niger NBC001 underlying suppression against Heterodera glycines.

Heterodera glycines is the most pervasive soybean pests worldwide. Biocontrol provides a strategy to sustainably control nematodes. In this study, 22 fungal isolates were obtained and identified from cysts of Heterodera spp. Among them, Aspergillus niger NBC001 showed high nematicidal activity against H. glycines. The 2-fold dilution of NBC001 culture filtrate caused 89% mortality of second-stage juveniles and inhibited more than 98% of egg hatching in vitro. In both pot and field experiments, the numbers of H. glycines cysts in soybean seedlings dressed with the the 5-fold concentrated culture filtrate of NBC001 were significantly reduced by 43% and 28%, respectively. In addition, application of NBC001 remarkably reduced the penetration of nematodes into the roots. Histochemical and fluorometric staining analyses indicate that application of NBC001 stimulated hydrogen peroxide activity in the roots and triggered callose deposition in the leaves and roots. Transcription of the PR1a and EREBP genes in the salicylic acid and ethylene signaling pathways was upregulated in soybean plants treated with NBC001. However, the application of concentrated culture filtrate of NBC001 had no significant impacts on the soil microbial community based on next generation DNA sequencing technology. In summary, NBC001 may be a good biocontrol agent against H. glycines via stimulation of the immunity/defense of the plant host.