Rhizobial infection and root nodule formation in legumes require recognition of signal molecules produced by the bacteria and their hosts. Here, we show that rhizobial transfer RNA (tRNA)-derived small RNA fragments (tRFs) are signal molecules that modulate host nodulation. Three families of rhizobial tRFs were confirmed to regulate host genes associated with nodule initiation and development through hijacking the host RNA-interference machinery that involves ARGONAUTE 1. Silencing individual tRFs with the use of short tandem target mimics or by overexpressing their targets represses root hair curling and nodule formation, whereas repressing these targets with artificial microRNAs identical to the respective tRFs or mutating these targets with CRISPR-Cas9 promotes nodulation. Our findings thus uncover a bacterial small RNA-mediated mechanism for prokaryote-eukaryote interaction and may pave the way for enhancing nodulation efficiency in legumes.

https://science.sciencemag.org/content/sci/early/2019/07/24/science.aav8907.full.pdf

Rhizobial tRNA-derived small RNAs are signal molecules regulating plant nodulation

Domestication of Industrial Microbes.

Soybean (Glycine max) production is severely affected in unfavorable environments. Identification of the regulatory factors conferring stress tolerance would facilitate soybean breeding. In this study, through coexpression network analysis of salt-tolerant wild soybeans, together with molecular and genetic approaches, we revealed a previously unidentified function of a class B heat shock factor, HSFB2b, in soybean salt stress response. We showed that HSFB2b improves salt tolerance through the promotion of flavonoid accumulation by activating one subset of flavonoid biosynthesis-related genes and by inhibiting the repressor gene GmNAC2 to release another subset of genes in the flavonoid biosynthesis pathway. Moreover, four promoter haplotypes of HSFB2b were identified from wild and cultivated soybeans. Promoter haplotype II from salt-tolerant wild soybean Y20, with high promoter activity under salt stress, is probably selected for during domestication. Another promoter haplotype, III, from salt-tolerant wild soybean Y55, had the highest promoter activity under salt stress, had a low distribution frequency and may be subjected to the next wave of selection. Together, our results revealed the mechanism of HSFB2b in soybean salt stress tolerance. Its promoter variations were identified, and the haplotype with high activity may be adopted for breeding better soybean cultivars that are adapted to stress conditions.

https://nph.onlinelibrary.wiley.com/doi/epdf/10.1111/nph.16104

A class B heat shock factor selected for during soybean domestication contributes to salt tolerance by promoting flavonoid biosynthesis.

Evidence of introgression, the transfer of genetic material, between crops and their wild relatives through spontaneous hybridization and subsequent backcrossing has been documented; however, the evolutionary patterns and consequences of introgression and its influence on the processes of crop domestication and varietal diversification are poorly understood. We investigate the genomic landscape and evolution of putative crop-wild-relative introgression by analyzing the nuclear and chloroplast genomes from a panel of wild (Glycine soja) and domesticated (Glycine max) soybeans. Our data suggest that naturally occurring introgression between wild and domesticated soybeans was widespread and that introgressed variation in both wild and domesticated soybeans was selected against throughout the genomes and preferentially removed from the genomic regions underlying selective sweeps and domestication quantitative trait locus (QTL). In both taxa, putative introgression was preferentially retained in recombination-repressed pericentromeric regions that exhibit lower gene densities, reflecting potential roles of recombination in purging introgression. Despite extensive removal of introgressed variation by recurrent selection for domestication-related QTL and associated genomic regions, spontaneous interspecific hybridization during soybean domestication appear to have contributed to a rapid varietal diversification with high levels of genetic diversity and asymmetric evolution between the nuclear and chloroplast genomes. This work reveals the evolutionary forces, patterns, and consequences of putative genomic introgression between crops and their wild relatives, and the effects of introgression on the processes of crop domestication and varietal diversification. We envision that interspecific introgression serves as an important mechanism for counteracting the reduction of genetic diversity in domesticated crops, particularly the ones under single domestication.

/pdf/genomic-introgression-through-interspecific-hybridization-44nyaulx0i.pdf

Genomic introgression through interspecific hybridization counteracts genetic bottleneck during soybean domestication

Soybean is one of the most important oilseed and fodder crops. Benefiting from the efforts of soybean breeders and the development of breeding technology, large number of germplasm has been generated over the last 100 years. Nevertheless, soybean breeding needs to be accelerated to meet the needs of a growing world population, to promote sustainable agriculture and to address future environmental changes. The acceleration is highly reliant on the discoveries in gene functional studies. The release of the reference soybean genome in 2010 has significantly facilitated the advance in soybean functional genomics. Here, we review the research progress in soybean omics (genomics, transcriptomics, epigenomics and proteomics), germplasm development (germplasm resources and databases), gene discovery (genes that are responsible for important soybean traits including yield, flowering and maturity, seed quality, stress resistance, nodulation and domestication) and transformation technology during the past decade. At the end, we also briefly discuss current challenges and future directions.

Progress in soybean functional genomics over the past decade.

Many leguminous species have adapted their seed coat with a layer of powdery bloom that contains hazardous allergens and makes the seeds less visible, offering duel protection against potential predators
 1
 . Nevertheless, a shiny seed surface without bloom is desirable for human consumption and health, and is targeted for selection under domestication. Here we show that seed coat bloom in wild soybeans is mainly controlled by Bloom1 (B1), which encodes a transmembrane transporter-like protein for biosynthesis of the bloom in pod endocarp. The transition from the ‘bloom’ to ‘no-bloom’ phenotypes is associated with artificial selection of a nucleotide mutation that naturally occurred in the coding region of B1 during soybean domestication. Interestingly, this mutation not only ‘shined’ the seed surface, but also elevated seed oil content in domesticated soybeans. Such an elevation of oil content in seeds appears to be achieved through b1-modulated upregulation of oil biosynthesis in pods. This study shows pleiotropy as a mechanism underlying the domestication syndrome
 2
 , and may pave new strategies for development of soybean varieties with increased seed oil content and reduced seed dust. The seed coat of many leguminous species has a powdery bloom containing hazardous allergens. In wild soybeans, the bloom is controlled by the BLOOM1 gene, a mutation in which abolishes bloom and elevates seed oil content in domesticated strains.

Zhifang Zhang

Papers

Elevation of soybean seed oil content through selection for seed coat shininess

Progress in soybean functional genomics over the past decade.

A Pd1–Ps–P1 Feedback Loop Controls Pubescence Density in Soybean