An advanced systems biology framework of feature engineering for cold tolerance genes discovery from integrated omics and non-omics data in soybean

Kao, Pei-Hsiu; Baiya, Supaporn; Lai, Zheng-Yuan; Huang, Chih-Min; Jhan, Li-Hsin; Lin, Chian-Jiun; Lai, Ya-Syuan; Kao, Chung-Feng

doi:10.3389/fpls.2022.1019709

Cited by 6 publications

(5 citation statements)

References 74 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These CT genes outperformed the remaining genes, the random genes, and the other candidate genes recognized by other methods in an independent RNA-seq database. This proposes that the CT genes recognized from our projected systematic framework can efficiently differentiate cold-resistant and cold-sensitive lines (Kao et al, 2022). These studies indicated the role of potential genes in soybean response to cold stress; however, the data on this aspect is still insufficient to unfold the genetic mechanisms of cold tolerance and to accelerate the breeding programs.…”

Section: Gszfp1mentioning

confidence: 96%

“…The regulatory mechanism of omega-3 fatty acid desaturase in soybean affects the specific isoforms in plastid and endosperm to maintain the level of linoleic acid under low-temperature stress (Román et al, 2012). Kao et al (2022) proposed an advanced systems biology framework of feature engineering to identify the genes from omics and non-omics soybean data. A total of 44, 143, and 45 cold tolerant genes (CT genes) were recognized in short-, mid-, and long-term cruel treatment, correspondingly, from the corresponding gene pool.…”

Section: Gszfp1mentioning

confidence: 99%

See 1 more Smart Citation

Deciphering the myth of cold tolerance in soybean: An overview of molecular breeding applications

JIAN,

QIANG,

Guan YIJUN

et al. 2023

Not Bot Horti Agrobo

View full text Add to dashboard Cite

The soybean is a source of several dietary components, including milk, protein, and oil. Cold stress has significantly curtailed soybean growth and yield in large areas and caused a high risk to global food security. The main objective of soybean breeders is to improve soybean resistance to cold stress. Conventional breeding approaches have made significant progress in developing cold tolerance in soybean; however, the high cost and complex genetic mechanism of cold tolerance hindered the large scale of these techniques. Molecular tools like quantitative trait loci (QTL), genome-wide association studies (GWAS), transcription factors (TFs), genetic engineering, and transcriptome have been used to identify cold tolerant genes/QTL and to develop soybean cultivars tolerant to cold stress. Clustered, regularly interspaced short palindromic repeats (CRISPR/Cas9) is used to increase the abiotic stress tolerance in soybean; however, its use to edit the cold tolerance genes in soybean is limited. Mapping of QTL has accelerated the master-assisted selection (MAS) in soybean. This review presents a detailed overview of molecular techniques and their use in developing cold-tolerant soybean cultivars. Using CRISPR/Cas9 would increase the speed of molecular breeding for cold tolerance in soybean. This information will assist soybean researchers in uncovering the basis of cold stress tolerance in soybean and adopting the most suitable way to breed the cold tolerant cultivars which can thrive under the extreme pressure of cold stress.

show abstract

Section: Gszfp1mentioning

confidence: 96%

Section: Gszfp1mentioning

confidence: 99%

Deciphering the myth of cold tolerance in soybean: An overview of molecular breeding applications

JIAN,

QIANG,

Guan YIJUN

et al. 2023

Not Bot Horti Agrobo

View full text Add to dashboard Cite

show abstract

“…Several studies conducted on soybeans have shown that Circular (circRNA)- and MicroRNA (miRNA)-based gene regulation were also involved in coordinating soybean responses to cold stress in post-transcriptional regulation [ 6 , 73 , 74 , 75 , 76 , 77 , 78 ]. In cold-treated soybean plants, miR166u, miR171p, miR2111f, and miR169c may regulate different targets in mature nodules through mRNA degradation [ 6 ].…”

Section: Soybean Cold Responsive Regulators and Associated Cold Regul...mentioning

confidence: 99%

“…A study by Xu et al [ 74 ] showed that CO 2 tends to compensate for low-temperature stress fully or partially without other abiotic stress. Utilizing the omics and non-omics data, an advanced framework in molecular biology was constructed for detecting cold tolerance genes [ 77 ]. Pathway enrichment and crosstalk network research from the aspects of module analysis underlying cold tolerance provides a new way to identify cold-responsive genes and uncover the molecular mechanism of soybean cold-tolerance.…”

Section: Soybean Cold Responsive Regulators and Associated Cold Regul...mentioning

confidence: 99%

Progress and Prospects of the Molecular Basis of Soybean Cold Tolerance

Tsegaw

Zegeye

Jiang

et al. 2023

Plants

View full text Add to dashboard Cite

Cold stress is a major factor influencing the geographical distribution of soybean growth and causes immense losses in productivity. Understanding the molecular mechanisms that the soybean has undergone to survive cold temperatures will have immense value in improving soybean cold tolerance. This review focuses on the molecular mechanisms involved in soybean response to cold. We summarized the recent studies on soybean cold-tolerant quantitative trait loci (QTLs), transcription factors, associated cold-regulated (COR) genes, and the regulatory pathways in response to cold stress. Cold-tolerant QTLs were found to be overlapped with the genomic region of maturity loci of E1, E3, E4, pubescence color locus of T, stem growth habit gene locus of Dt1, and leaf shape locus of Ln, indicating that pleiotropic loci may control multiple traits, including cold tolerance. The C-repeat responsive element binding factors (CBFs) are evolutionarily conserved across species. The expression of most GmDREB1s was upregulated by cold stress and overexpression of GmDREB1B;1 in soybean protoplast, and transgenic Arabidopsis plants can increase the expression of genes with the DRE core motif in their promoter regions under cold stress. Other soybean cold-responsive regulators, such as GmMYBJ1, GmNEK1, GmZF1, GmbZIP, GmTCF1a, SCOF-1 and so on, enhance cold tolerance by regulating the expression of COR genes in transgenic Arabidopsis. CBF-dependent and CBF-independent pathways are cross-talking and work together to activate cold stress gene expression. Even though it requires further dissection for precise understanding, the function of soybean cold-responsive transcription factors and associated COR genes studied in Arabidopsis shed light on the molecular mechanism of cold responses in soybeans and other crops. Furthermore, the findings may also provide practical applications for breeding cold-tolerant soybean varieties in high-latitude and high-altitude regions.

show abstract

“…However, the success of early soybean sowing depends on high seed vigor, a high germination rate at low temperature, and rapid germination (Hu G et Therefore, obtaining soybean germplasms with high germination ability and low-temperature tolerance, as well as understanding the genetic structure underlying soybean low-temperature tolerance and identifying excellent gene allele variations, has practical importance for breeding. Plant cold tolerance is a complex quantitative trait controlled by genes, environmental factors and their interactions (Kao PH et al 2022). Cold tolerance in soybean plants has been extensively studied through molecular and QTL (quantitative trait loci) analyses.…”

Section: Introductionmentioning

confidence: 99%

Cold Tolerance SNPs and Candidate Gene Mining in the Soybean Germination Stage Based on Genome-Wide Association Analysis

Chen,

Liu,

Han

et al. 2024

Preprint

View full text Add to dashboard Cite

Low temperature is a key factor affecting the geographical distribution, growth, development, and yield of soybeans. Exposing soybean seeds to low-temperature stress during the germination stage can lead to a substantial reduction in productivity. At present, there is limited information on the genetic mechanisms associated with cold tolerance during the soybean germination stage. In this study, we assessed the germination phenotype of a population of 260 soybean accessions under low-temperature stress (3°C). Using a mixed linear model, we performed a genome-wide association analysis (GWAS) of 30,799 single nucleotide polymorphism (SNP) markers and identified a total of 71 SNPs associated with cold tolerance. SNP (BARC_2.01 Chr18_53718636_A_G) was associated with two traits: (1) the ratio of germination potential under low-temperature stress to germination potential under normal conditions (CT-GP) and (2) the germination potential at 3°C. Within the linked genetic region of this marker, there were six genes, including Glyma.18g250900 and Glyma.18g251400, which exhibited differential expression levels in two groups of materials with different cold tolerances. These two genes had 4 and 3 haplotypes, respectively. Soybean germplasms harboring Glyma.18g250900-Hap3, Glyma.18g251400-Hap2, and Glyma.18g251400-Hap3 exhibited strong cold tolerance during the germination stage. Glyma.18g250900 and Glyma.18g251400 were predicted to be potential candidate genes involved in the response of soybean germination to low-temperature stress. The SNPs and candidate genes identified in this study have important implications for marker-assisted selection and gene editing in cold-tolerant soybean breeding and provide a valuable reference for understanding the underlying genetic mechanisms of cold tolerance in soybean germination.

show abstract

An advanced systems biology framework of feature engineering for cold tolerance genes discovery from integrated omics and non-omics data in soybean

Cited by 6 publications

References 74 publications

Deciphering the myth of cold tolerance in soybean: An overview of molecular breeding applications

Deciphering the myth of cold tolerance in soybean: An overview of molecular breeding applications

Progress and Prospects of the Molecular Basis of Soybean Cold Tolerance

Cold Tolerance SNPs and Candidate Gene Mining in the Soybean Germination Stage Based on Genome-Wide Association Analysis

Contact Info

Product

Resources

About