Yanting Shen

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

Resequencing of 302 soybean accessions and GWAS provide a comprehensive resource for soybean geneticists and breeders.

Global dissection of alternative splicing in paleopolyploid soybean.

Through comprehensive analyses, this study reveals that a large number of genes are alternatively spliced in the soybean genome and that variations in gene structure, genomic environment, and gene transcriptional level may play important roles in regulating alternative splicing. Alternative splicing (AS) is common in higher eukaryotes and plays an important role in gene posttranscriptional regulation. It has been suggested that AS varies dramatically among species, tissues, and duplicated gene families of different sizes. However, the genomic forces that govern AS variation remain poorly understood. Here, through genome-wide identification of AS events in the soybean (Glycine max) genome using high-throughput RNA sequencing of 28 samples from different developmental stages, we found that more than 63% of multiexonic genes underwent AS. More AS events occurred in the younger developmental stages than in the older developmental stages for the same type of tissue, and the four main AS types, exon skipping, intron retention, alternative donor sites, and alternative acceptor sites, exhibited different characteristics. Global computational analysis demonstrated that the variations of AS frequency and AS types were significantly correlated with the changes of gene features and gene transcriptional level. Further investigation suggested that the decrease of AS within the genome-wide duplicated genes were due to the diminution of intron length, exon number, and transcriptional level. Altogether, our study revealed that a large number of genes were alternatively spliced in the soybean genome and that variations in gene structure and transcriptional level may play important roles in regulating AS.

Functional Evolution of Phosphatidylethanolamine Binding Proteins in Soybean and Arabidopsis

Functional analysis identifies amino acid substitutions causing PEBP functional evolution and shows the importance of coding sequence divergence in driving functional divergence of duplicated genes. Gene duplication provides resources for novel gene functions. Identification of the amino acids responsible for functional conservation and divergence of duplicated genes will strengthen our understanding of their evolutionary course. Here, we conducted a systemic functional investigation of phosphatidylethanolamine binding proteins (PEBPs) in soybean (Glycine max) and Arabidopsis thaliana. Our results demonstrated that after the ancestral duplication, the lineage of the common ancestor of the FLOWERING LOCUS T (FT) and TERMINAL FLOWER1 (TFL1) subfamilies functionally diverged from the MOTHER OF FT AND TFL1 (MFT) subfamily to activate flowering and repress flowering, respectively. They also underwent further specialization after subsequent duplications. Although the functional divergence increased with duplication age, we observed rapid functional divergence for a few pairs of young duplicates in soybean. Association analysis between amino acids and functional variations identified critical amino acid residues that led to functional differences in PEBP members. Using transgenic analysis, we validated a subset of these differences. We report clear experimental evidence for the functional evolution of the PEBPs in the MFT, FT, and TFL1 subfamilies, which predate the origin of angiosperms. Our results highlight the role of amino acid divergence in driving evolutionary novelty after duplication.

Genome-wide association studies dissect the genetic networks underlying agronomical traits in soybean

BackgroundSoybean (Glycine max [L.] Merr.) is one of the most important oil and protein crops. Ever-increasing soybean consumption necessitates the improvement of varieties for more efficient production. However, both correlations among different traits and genetic interactions among genes that affect a single trait pose a challenge to soybean breeding.ResultsTo understand the genetic networks underlying phenotypic correlations, we collected 809 soybean accessions worldwide and phenotyped them for two years at three locations for 84 agronomic traits. Genome-wide association studies identified 245 significant genetic loci, among which 95 genetically interacted with other loci. We determined that 14 oil synthesis-related genes are responsible for fatty acid accumulation in soybean and function in line with an additive model. Network analyses demonstrated that 51 traits could be linked through the linkage disequilibrium of 115 associated loci and these links reflect phenotypic correlations. We revealed that 23 loci, including the known Dt1, E2, E1, Ln, Dt2, Fan, and Fap loci, as well as 16 undefined associated loci, have pleiotropic effects on different traits.ConclusionsThis study provides insights into the genetic correlation among complex traits and will facilitate future soybean functional studies and breeding through molecular design.

Comprehensive analyses of microRNA gene evolution in paleopolyploid soybean genome.

miRNA genes are thought to undergo quick birth and death processes in genomes and the emergence of a MIRNA-like hairpin provides the base for functional miRNA gene formation. However, the factors affecting the formation of an active miRNA gene from a MIRNA-like hairpin within a genome remain unclear. We performed a genome-wide investigation of MIRNA-like hairpin accumulation, expression, structural changes and relationships with annotated genomic features in the paleopolyploid soybean genome. Our results showed that adjacent gene and transposable element content, rates of genetic recombination at location of emergence, along with its own gene structure divergence greatly affected miRNA gene evolution. Further investigation suggested that miRNA genes from different duplication sources followed distinct evolutionary trajectories and that the accumulation of MIRNA-like hairpins might be an important factor in causing long terminal repeat retrotransposons to lose activity during genome evolution.

Global investigation of the co-evolution of MIRNA genes and microRNA targets during soybean domestication

Although the selection of coding genes during plant domestication has been well studied, the evolution of MIRNA genes (MIRs) and the interaction between microRNAs (miRNAs) and their targets in this process are poorly understood. Here, we present a genome-wide survey of the selection of MIRs and miRNA targets during soybean domestication and improvement. Our results suggest that, overall, MIRs have higher evolutionary rates than miRNA targets. Nonetheless, they do demonstrate certain similar evolutionary patterns during soybean domestication: MIRs and miRNA targets with high expression and duplication status, and with greater numbers of partners, exhibit lower nucleotide divergence than their counterparts without these characteristics, suggesting that expression level, duplication status, and miRNA-target interaction are essential for evolution of MIRs and miRNA targets. Further investigation revealed that miRNA-target pairs that are subjected to strong purifying selection have greater similarities than those that exhibited genetic diversity. Moreover, mediated by domestication and improvement, the similarities of a large number of miRNA-target pairs in cultivated soybean populations were increased compared to those in wild soybeans, whereas a small number of miRNA-target pairs exhibited decreased similarity, which may be associated with the adoption of particular domestication traits. Taken together, our results shed light on the co-evolution of MIRs and miRNA targets during soybean domestication.

Cloning of Ln gene through combined approach of map-based cloning and association study in soybean.

Increasing yield is one of the most important goals in crop breeding. Soybean (Glycine max L. Merr.), one of the most economically important leguminous seed crops, provides the majority of plant proteins, and more than a quarter of the world’s food and animal feed (Graham and Vance, 2003). The yield of soybean is finally determined by the number of seeds per unit area, which affected by many characters, such as height, branching number, photosynthesis, seed size, seed number. The number of seeds per pod is taken for one of the critical components that related to yield (You et al., 1995), and it has long been considered in soybean production (Takahashi, 1934). Genetics studies indicated one major gene (termed as Ln) contributed to the variations of leaflet and seed number per pod (Domingo, 1945; Sawada, 1988). Ovate leaflet usually associated with non-4-seeded pod, and narrow leaflet linked with 4-seeded pod. It was suggested that the ovate leaflet and non-4-seeded pod were dominant over narrow leaflet and 4seeded pod (Domingo, 1945; Sawada, 1988; Jeong et al., 2011). The inconsistent results from different studies on the effects of narrow leaflet and 4-seeded pod on final yield indicated that it may related to the circumstance (Mandl and Buss, 1981; You et al., 1995; Dinkins et al., 2002). Additionally, it was suggested that the trait is associated with geographical origin (Chen and Nelson, 2004), which indicated that this trait might undergo domestication process and has been used for breeding to adapt particular environment. The seed was developed from ovule, thus the number of seeds per pod was mainly determined by the number of ovules per placenta. To check if the difference of seed numbers between Ln and ln was caused by the inherent ovules per ovary, we selected two typical cultivars to investigate the ovules under microscope. Han2296, a cultivar from Korea, has the characters of ovate leaflet (Fig. S1A), and a high ratio of 2-seed pod and 1-seed pod (account for w60% and w35% of the total pods respectively) (Fig. S1B and C). Whereas, Lvbaoshi, a cultivar from Shanxi Province, has the properties of narrow leaflet (Fig. S1A), and a high ratio of 4-seeded pod and 3-seed pod (account for w40% and w45% of the total pods respectively) (Fig. S1B and C). The investigation showed

Genome-wide expression analysis in a dwarf soybean mutant

Plant height is important for crop yield improvement. In this study, a dwarf mutant, Gmdwarf1 , was screened from a γ-ray-treated soybean population. Compared with the wild type, the mutant exhibited later germination, smaller and darker green leaves, and less-elongated shoots. Genome-wide transcriptome detection through RNA-seq analysis revealed that not only gibberellin-related genes but many other genes involved in hormone biosynthetic pathways were also significantly influenced in the mutant. We presumed that Gmdwarf1 might play essential roles in the plant hormone pathways. Future functional analysis of this dwarf mutant would help us to understand the underlying mechanisms and be beneficial for improving soybean yield.

De novo assembly of a Chinese soybean genome

Soybean was domesticated in China and has become one of the most important oilseed crops. Due to bottlenecks in their introduction and dissemination, soybeans from different geographic areas exhibit extensive genetic diversity. Asia is the largest soybean market; therefore, a high–quality soybean reference genome from this area is critical for soybean research and breeding. Here, we report the de novo assembly and sequence analysis of a Chinese soybean genome for “Zhonghuang 13” by a combination of SMRT, Hi–C and optical mapping data. The assembled genome size is 1.025 Gb with a contig N50 of 3.46 Mb and a scaffold N50 of 51.87 Mb. Comparisons between this genome and the previously reported reference genome (cv. Williams 82) uncovered more than 250,000 structure variations. A total of 52,051 protein coding genes and 36,429 transposable elements were annotated for this genome, and a gene co–expression network including 39,967 genes was also established. This high quality Chinese soybean genome and its sequence analysis will provide valuable information for soybean improvement in the future.

DNA methylation footprints during soybean domestication and improvement

BackgroundIn addition to genetic variation, epigenetic variation plays an important role in determining various biological processes. The importance of natural genetic variation to crop domestication and improvement has been widely investigated. However, the contribution of epigenetic variation in crop domestication at population level has rarely been explored.ResultsTo understand the impact of epigenetics on crop domestication, we investigate the variation of DNA methylation during soybean domestication and improvement by whole-genome bisulfite sequencing of 45 soybean accessions, including wild soybeans, landraces, and cultivars. Through methylomic analysis, we identify 5412 differentially methylated regions (DMRs). These DMRs exhibit characters distinct from those of genetically selected regions. In particular, they have significantly higher genetic diversity. Association analyses suggest only 22.54% of DMRs can be explained by local genetic variations. Intriguingly, genes in the DMRs that are not associated with any genetic variation are enriched in carbohydrate metabolism pathways.ConclusionsThis study provides a valuable map of DNA methylation across diverse accessions and dissects the relationship between DNA methylation variation and genetic variation during soybean domestication, thus expanding our understanding of soybean domestication and improvement.