Progress in soybean functional genomics over the past decade

Abstract

Summary 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.

Integrated Bioinformatics Analyses of PIN1, CKX, and Yield-Related Genes Reveals the Molecular Mechanisms for the Difference of Seed Number Per Pod Between Soybean and Cowpea

“…In this study, all the known yield-related soybean genes in Zhang et al (2021) , along with the above known and candidate SNPP genes, were used to construct a comprehensive network for the two legumes. The results are shown in Figure 6 and Supplementary Table 9 .…”

Selection and Evaluation of Candidate Reference Genes for Quantitative Real-Time PCR in Aboveground Tissues and Drought Conditions in Rhododendron Delavayi

“…To screen and select a number of candidate genes for functional validation in R. delavayi via gene overexpression, virus-induced gene silencing (VIGS) and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) (CRSIPR/Cas) technology ( Zhang et al, 2022 ) from our transcriptomics dataset were carried out , and our research group attempted to validate the expression profile of RNA-sequencing (RNA-seq) data by qRT-PCR; however, the challenge of the reference gene was eminent; hence, we decided to screen 11 known reference genes reported in other crops ( Fan et al, 2013 ; Gao et al, 2017 ; Yang et al, 2019 ; Jin et al, 2019 ). First, we blasted the eleven known reference genes with the draft genome of R. delavayi and designed primer pairs for each of the genes ( Table 2 ).…”

Transcriptomic and Metabolomic Analysis of Seedling-Stage Soybean Responses to PEG-Simulated Drought Stress

“…In recent years, a large number of germplasm resources have been developed owing to advancements in breeding technology. To adjust to market demand, support sustainable agricultural development, and respond to future environmental changes, soybean breeding must be hastened [ 4 ]. Abiotic and biotic stresses (such as pests and diseases, high temperatures, drought, salt, flooding, and cold) are common in soybean production because of various environmental conditions.…”