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Soybean is a leguminous crop that provides oil and protein. Exploring the genomic signatures of soybean evolution is crucial for breeding varieties with improved adaptability to environmental extremes. We analyzed the genome sequences of 2,214 soybeans and proposed a soybean evolutionary route, i.e., the expansion of annual wild soybean (Glycine soja Sieb.Zucc.) from southern China and its domestication in central China, followed by the expansion and local breeding selection of its landraces (G. max (L.) Merr.). We observed that the genetic introgression in soybean landraces was mostly derived from sympatric rather than allopatric wild populations during the geographic expansion. Soybean expansion and breeding were accompanied by the positive selection of flowering time genes, including GmSPA3c. Our study sheds light on the evolutionary history of soybean and provides valuable genetic resources for its future breeding.

Single-cross maize hybrids display superior heterosis and are produced from crossing two parental inbred lines belonging to genetically different heterotic groups. Here we assembled 1,604 historically utilized maize inbred lines belonging to various female heterotic groups (FHGs) and male heterotic groups (MHGs), and conducted phenotyping and genomic sequencing analyses. We found that the FHGs and MHGs have undergone both convergent and divergent changes for different sets of agronomic traits. Using genome-wide selection scans and association analyses, we identified a large number of candidate genes that contributed to the improvement of agronomic traits of the FHGs and MHGs. Moreover, we observed increased genetic differentiation between the FHGs and MHGs across the breeding eras, and we found a positive correlation between increasing heterozygosity levels in the differentiated genes and heterosis in hybrids. Furthermore, we validated the function of two selected genes and a differentiated gene. This study provides insights into the genomic basis of modern hybrid maize breeding.

Rose is an important aromatic plant and produces flowers that are used in medicine and food. We herein present a haplotype-resolved genome for Rosa rugosacultivar Hanxiang. Analyses of allele-specific expression identified a potential mechanism underlying floral scent biosynthesis. Population genomic analyses involving 133 Rosa accessions elucidated evolutionary histories and a single R. rugosa domestication event. Pathways mediating the synthesis of scent-related metabolites were enriched according to the analyses of the transcriptomes, haplotype variations, and allelic imbalances during the flower development stages of Hanxiang and Guomeigui (R. rugosa accessions with diverse fragrances). The enzyme-encoding ASE genes RrHX1G119800 and RrHX1G204700 (primary amine oxidases) and RrHX2G284700 (L-tryptophan decarboxylase) in the phenylethylamine pathway were tentatively designated as core genes useful for improving 2-phenylethanol production in rose flowers. Our results provide molecular insights into the formation of R. rugosa floral fragrances and genome-level data that are useful for enhancing rose traits via genetic engineering.

Dasypyrum villosum L. is one of the most valuable gene resources in wheat improvement, especially for disease resistance. The mining of favorable genes from D. villosum is frustrated by the lack of genome sequence. Here, by generating a doubled haploid line 91C43

The clarification of genomic signatures left during evolutionary histories of crops is crucial for breeding varieties adapting to changing climate. Soybean, a leguminous crop, provides both plant oil and protein. Here, we analyzed genome sequences of 2,214 soybeans and proposed its evolutionary route, which includes four geographic paths, expansion of annual wild soybean (Glycine soja Sieb. & Zucc.) from Southern China, domestication in Central China, expansion of landrace (G. max (L.) Merr.), and local breeding. We observed that local adaptation of the wild and cultivated soybeans was largely independent, and that genetic introgression was mostly derived from sympatric rather than allopatric wild populations during the range expansion of soybean landraces. Range expansion and breeding processes were accompanied with positive selection of flowering-time genes including GmSPA3c as validated by knock-out mutants. Our study shed lights on the evolutionary history of soybean and provides valuable genetic resources for future breeding.TeaserThe expansion and selection history of soybean