Collection of classic articles on leguminous soybeans 20 10-2020.

Soybean, also known as glutinous rice, has been planted in China for more than 5000 years. Soybean originated in China, and was domesticated from wild soybeans distributed in the Huanghuai Valley (32-40 degrees north latitude). And then spread to all parts of the world, providing major vegetable oil and protein resources for human beings.

According to statistics, there are 60,000 soybean germplasm resources of different types in the world. There is no doubt that the research value of soybean is the highest among all leguminous crops. The following is a review of the classic research on soybeans in the past ten years.

Genome sequence of ancient polyploid soybean

The researchers sequenced the whole soybean genome by whole-genome shotgun method, and used 444 Williams 82 soybean family recombinant inbred lines to construct genetic map to assist assembly. The final genome size was 994Mb, ContigN50 was 189.4 Kb, and ScaffoldN50 was 47.8 Mb. Among them, 397 scaffolds were assembled and anchored to the level of 20 chromosomes. In the assembled genome, 49,965,438+0 SNP and 874 SSR were identified, and 46,430 protein coding genes were predicted, and the repetitive sequences accounted for 59% of the whole genome.

In addition, in the follow-up study, in addition to the evolutionary problems such as gene composition, DNA duplication identification and genome-wide replication events, the diversity of biosynthesis genes and gene transcription factors of soybean nitrogen-fixing bacteria and oils was also identified, and the acquisition of accurate sequences of soybean genome accelerated the cultivation of improved soybean varieties.

Re-sequencing the genomes of 3 1 wild and cultivated soybeans identified the genetic diversity and selection patterns.

The researchers resequenced the whole genome of 17 wild soybean and 14 cultivated soybean. Compared with the reference genome, * * * found more than 6.3 million SNPs and established a high-density molecular marker map. In addition, through the preliminary assembly of wild soybean and cultivated soybean, more than 654.38+0.8 million pav were identified in the two kinds of soybeans, and the genes gained and lost in cultivated soybean were obtained. This study also found that there is a high degree of gene linkage imbalance and a high proportion of single nucleotide substitution/synonymous substitution in soybean genome, which indicates that soybean molecular marker breeding may have more advantages than gene map cloning.

Compared with cultivated soybean, wild soybean has a higher level of genetic diversity, which indicates that artificial selection leads to narrow biodiversity of cultivated soybean, which may have a negative impact on sustainable planting. The analysis of wild soybean shows that with the deterioration of the living environment of wild soybean, the growth potential of wild soybean is weakening, and the preservation of wild germplasm resources is imminent.

This study provided comprehensive resequencing data for soybean genomics research for the first time, and laid a solid foundation for soybean population genetics research, molecular marker breeding and new gene discovery in the future.

Recombination of wild related species of soybean for genome-wide analysis of diversity and agronomic traits

Qiu of China Academy of Agricultural Sciences took the lead in selecting seven representative wild soybeans for de novo sequencing and independent assembly, and constructed the whole genome of wild soybeans, with Contig N50 of 7.7-26.6 Kb and Scaffold N50 of 16.3-62.7 Kb. Through the comparative analysis of gene sets, it was found that 48.6% of the genes existed in seven wild soybeans, and more than 565,438+0.4% of the genes only existed in individual samples (endemic genes), and the endemic genes were mainly enriched in biotic and abiotic stress-related pathways, which also reflected the wide adaptability of wild soybeans. In addition, 3.6-4.7Mb SNP and 0.50-0.77Mb InDel were identified.

Evolutionary analysis shows that the ancestors of wild soybean and cultivated soybean differentiated about 800 thousand years ago; Positive selection analysis showed that most selection genes in cultivated soybeans were related to drought resistance, while those in wild soybeans were very diverse. At the same time, a large number of genes and variations related to stress resistance, disease resistance, flowering period, oil yield and plant height were identified. For example, the difference of flowering time between wild soybean and cultivated soybean is related to the variation of flowering time regulation genes SNP and InDel.

This achievement is the first genome-wide research achievement of important crops, which provides new enlightenment for studying the genetic diversity and evolution of soybean, and lays a foundation for analyzing the establishment of important domestication traits and discovering excellent genes/markers.

Re-sequencing of 302 wild and cultivated soybean resources identified genes related to soybean domestication and improvement.

The Tian team of Institute of Genetic Development of China Academy of Sciences re-sequenced 302 representative soybean germplasm (>: 10x), and the analysis showed that the genetic polymorphism of soybean was obviously reduced in the process of domestication and improvement, and the strong selection signal of 12 1 was identified in the domestication stage, and the strong selection signal of 109 was identified in the variety improvement stage.

In addition to the analysis of SNP variation, CNV variation information that can explain more biological problems was also analyzed through in-depth selection and whole gene association. Selection analysis showed that CNV was also artificially selected in the domestication process, and * * * found 162 selection regions in farm varieties and domesticated varieties; Through correlation analysis, it is found that the CNV related to chromosome 18 overlaps with the interval Rhg 1 reported by predecessors. Interestingly, this interval is also selected among domesticated species. In addition, a CNV on chromosome 8, which is closely related to the color of bean navel, is located in the interval related to chalcone synthesis and is also a selection site in domesticated species. In this paper, the research purpose of identifying more genes related to soybean excellent traits was realized through CNV research.

Genome-wide association (GWAS) analysis was conducted on seed size, seed coat color, growth habit and oil content, and a series of significant association sites were found. The research shows that the oil-producing traits of soybean are more artificially selected, forming a complex network system to regulate oil metabolism.

Genome-wide association studies analyzed the genetic network behind the agronomic traits of soybean.

After resequencing 302 soybeans, Tian team of Institute of Genetic Development of China Academy of Sciences resequenced 809 soybeans (8.3 times), deeply analyzed the genetic regulatory network among 84 agronomic traits of soybeans, identified 245 significant linkage sites, and found that 95 of them had epistatic effects with other sites.

For example, for traits related to oil content, * * * identified 24 genes related to fatty acid metabolism and 2 1 gene related to lipid metabolism. In-depth analysis showed that these genes regulated the formation of many soybean oil characters through additive effects.

These linkage loci reveal the genetic basis of mutual coupling between different traits. According to linkage disequilibrium analysis, it is found that 1 15 linkage sites can be linked with each other and with the observed 5 1 trait, forming a complex multi-trait and multi-locus regulatory network, which well explains the coupling relationship between different traits. Twenty-three related loci were also found, including 16 newly identified loci, which played a key role in regulating the formation of different traits.

Recombination of soybean genome in China

The genome (gmax _ zh 13) of Chinese soybean variety "Huangzhong13" was assembled by the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, using single molecule real-time sequencing (SMRT), single molecule optical mapping (optical mapping) and quantum chromosome conformation capture technology (Hi-C), and finally 65438 was obtained. The overlap group N50 of this genome is 3.46 Mb, and the scaffold N50 is 5 1.87 Mb, which is one of the most continuous plant genomes at present.

Further analysis showed that there were a lot of genetic variations between Gmax_ZH 13 and Williams 82 genomes, including 1404 translocation event, 16 1 inversion event, 1233 inversion translocation event and 554 in Gmax_ZH65438.

In this study, a large number of transcriptome data were integrated to construct a complete gene * * * expression network of Gmax_ZH 13 gene annotation gene. Based on the * * expression relationship between the reported genes controlling the flowering time of soybean and the candidate genes in the newly located QTL or GWAS interval, the genes controlling this trait in the newly located interval were screened more accurately, and 26 genes that might control the flowering time of soybean were obtained. Some of these genes were verified by the correlation between genetic variation and phenotypic difference of natural population, which provided a new idea for mining important agronomic traits genes. The publication of Gmax_ZH 13 genome provides important resources for basic research of soybean and lays a foundation for cultivating excellent domestic soybean varieties.

Reference wild soybean genome

Wild soybean is rich in gene resources, which can be used to improve the stress resistance, seed protein and secondary metabolites content of cultivated soybean, and is a natural treasure house for soybean variety improvement. From 2065438 to March 2009, the joint research team of the Chinese University of Hong Kong and BGI assembled the chromosome level reference genome of wild soybean W05 by using the data generated by the third generation PacBio sequencing technology, Bionano Genomics double enzyme digestion optical map (OM) and Qualcomm quantitative chromosome conformation capture technology (Hi-C). The final genome size was 10 13.2Mb, the overlapping group N50 3.3Mb and the scaffold N50 50.7Mb. A total of 55,539 protein-coding genes were obtained, corresponding to 89,477 protein-coding transcripts. In addition, 288 miRNA, 1, 988 snRNA and 147 rRNA were found in the genome of W05.

Whole genomes of wild soybean and cultivated soybean

Tian/Liang Chengzhi, Institute of Genetics and Development, China Academy of Sciences, jointly published a genome-wide map of soybean graphic structure. This study is the first time to realize the genome construction based on graphic structure in plants, breaking through the traditional storage form of linear genomes, and will lead the research ideas and methods of the next generation of genomics, which is called "the milestone work of genomics" by critics.

In this study, 2898 natural soybean germplasm resources from major soybean producing countries in the world were deeply sequenced and analyzed, and 26 most representative soybean germplasm materials were screened out. The 26 accessions include 3 wild soybeans, 9 farm varieties and 14 modern cultivated varieties, some of which have cultivated hundreds of excellent new varieties as the backbone core parents, and some of which are the main cultivated varieties with the largest popularization area in the main soybean producing areas. In addition, using the latest assembly strategy, 26 genomes of soybean germplasm were assembled from scratch and annotated accurately. On this basis, combined with the published genomes of Huang Zhong 13, Williams 82 and W05, a high-quality genome based on graphic structure was constructed. After genome-wide analysis, a large number of large fragment structural variations were found.

In-depth analysis shows that some structural variations lead to the fusion of different genes, which provides important clues for the study of new genes. Some structural variations play an important role in the regulation of important agronomic traits, such as seed coat brightness, domestication of seed coat color, iron deficiency and chlorosis.

To sum up, after 10 years of efforts, soybeans originating in China have once again ushered in their own highlight moment! The release of these genetic variations provides an extremely important resource and platform for soybean research, which will undoubtedly promote the molecular design and breeding of soybean and help to realize the "green revolution" of soybean.