Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean.

Understanding soybean (Glycine max) domestication and improvement at a genetic level is important to inform future efforts to further improve a crop that provides the world's main source of oilseed. We detect 230 selective sweeps and 162 selected copy number variants by analysis of 302 resequenced wild, landrace and improved soybean accessions at >11× depth. A genome-wide association study using these new sequences reveals associations between 10 selected regions and 9 domestication or improvement traits, and identifies 13 previously uncharacterized loci for agronomic traits including oil content, plant height and pubescence form. Combined with previous quantitative trait loci (QTL) information, we find that, of the 230 selected regions, 96 correlate with reported oil QTLs and 21 contain fatty acid biosynthesis genes. Moreover, we observe that some traits and loci are associated with geographical regions, which shows that soybean populations are structured geographically. This study provides resources for genomics-enabled improvements in soybean breeding.

A genomic perspective on the important genetic mechanisms of upland adaptation of rice.

BACKGROUND: Cultivated rice consists of two important ecotypes, upland and irrigated, that have respectively adapted to either dry land or irrigated cultivation. Upland rice, widely adopted in rainfed upland areas in virtue of its little water requirement, contains abundant untapped genetic resources, such as genes for drought adaptation. With water shortage exacerbated and population expanding, the need for breeding crop varieties with drought adaptation becomes more and more urgent. However, a previous oversight in upland rice research reveals little information regarding its genetic mechanisms for upland adaption, greatly hindering progress in harnessing its genetic resources for breeding and cultivation. RESULTS: In this study, we selected 84 upland and 82 irrigated accessions from all over the world, phenotyped them under both irrigated and dry land environments, and investigated the phylogenetic relations and population structure of the upland ecotype using whole genome variation data. Further comparative analysis yields a list of differentiated genes that may account for the phenotypic and physiological differences between upland and irrigated rice. CONCLUSIONS: This study represents the first genomic investigation in a large sample of upland rice, providing valuable gene list for understanding upland rice adaptation, especially drought-related adaptation, and its subsequent utilization in modern agriculture.

Heterotrimeric G proteins regulate nitrogen-use efficiency in rice.

The drive toward more sustainable agriculture has raised the profile of crop plant nutrient-use efficiency. Here we show that a major rice nitrogen-use efficiency quantitative trait locus (qNGR9) is synonymous with the previously identified gene DEP1 (DENSE AND ERECT PANICLES 1). The different DEP1 alleles confer different nitrogen responses, and genetic diversity analysis suggests that DEP1 has been subjected to artificial selection during Oryza sativa spp. japonica rice domestication. The plants carrying the dominant dep1-1 allele exhibit nitrogen-insensitive vegetative growth coupled with increased nitrogen uptake and assimilation, resulting in improved harvest index and grain yield at moderate levels of nitrogen fertilization. The DEP1 protein interacts in vivo with both the Gα (RGA1) and Gß (RGB1) subunits, and reduced RGA1 or enhanced RGB1 activity inhibits nitrogen responses. We conclude that the plant G protein complex regulates nitrogen signaling and modulation of heterotrimeric G protein activity provides a strategy for environmentally sustainable increases in rice grain yield.

Evolution of neurotransmitter gamma-aminobutyric acid, glutamate and their receptors.

Gamma-aminobutyric acid (GABA) and glutamate are two important amino acid neurotransmitters widely present in the nervous systems of mammals, insects, round worm, and platyhelminths, while their receptors are quite diversified across different animal phyla. However, the evolutionary mechanisms between the two conserved neurotransmitters and their diversified receptors remain elusive, and antagonistic interactions between GABA and glutamate signal transduction systems, in particular, have begun to attract significant attention. In this review, we summarize the extant results on the origin and evolution of GABA and glutamate, as well as their receptors, and analyze possible evolutionary processes and phylogenetic relationships of various GABAs and glutamate receptors. We further discuss the evolutionary history of Excitatory/Neutral Amino Acid Transporter (EAAT), a transport protein, which plays an important role in the GABA-glutamate "yin and yang" balanced regulation. Finally, based on current advances, we propose several potential directions of future research.