RNA-Seq based transcriptomic analysis revealed genes associated with seed-flooding tolerance in wild soybean (Glycine soja Sieb. &amp; Zucc.)

Sharmin, Ripa Akter; Bhuiyan, Mashiur Rahman; Lv, Wenhuan; Yu, Zheping; Chang, Fangguo; Kong, Jiejie; Bhat, Javaid Akhter; Zhao, Tuanjie

doi:10.1016/j.envexpbot.2019.103906

Cited by 44 publications

(39 citation statements)

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“…As in a previous study (Sharmin et al 2020), some cell wall-related genes such as GLYMA_08G249800 and GLYMA_18G272100 associated with COBRA-like protein were significantly up-and down-regulated in tolerant and susceptible cultivars, respectively. However, a higher number of the genes related to proline-rich cell wall protein, which were up-regulated in tolerant genotype (Sharmin et al 2020), were down-regulated in the present study. Sharmin et al (2020) reported that these cell wall-related genes had an important function in retaining the cell wall flexibility under flooding stress condition.…”

Section: Discussionsupporting

confidence: 75%

“…Lipoxygenase was reported to play roles in the adaption of radish to biotic and abiotic stresses (Wang et al 2019). Results with higher numbers of up-regulated expansin-coding genes were also found in a seed-flooding tolerant soybean (Sharmin et al 2020). The roles of expansin on germination, root length, and the number of lateral roots under abiotic stresses have been reported (Lü et al 2013;Marowa et al 2016).…”

Section: Discussionmentioning

confidence: 93%

“…RNA sequencing (RNA-Seq), a sequencing-based recently advanced techniques, can overcome the limitations of microarray techniques (Trapnell et al 2013). Several RNA-Seq studies have been conducted to investigate the gene expression in numerous tissues of soybean under biotic and abiotic stresses, such as drought (Vidal et al 2012), drought and flooding (Chen et al 2016), common cutworm attack (Du et al 2019), salt (Zeng et al 2019), and seed-flooding (Sharmin et al 2020). The objective of this study was to analyze the differentially expressed genes (DEGs) revealed by RNA-Seq in soybean leaf tissue of tolerant and susceptible cultivars under flooding stress.…”

Section: Introductionmentioning

confidence: 99%

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Analysis of differentially expressed genes in soybean leaf tissue of tolerant and susceptible cultivars under flooding stress revealed by RNA sequencing

Dhungana

Kim

Kang

et al. 2020

J. Crop Sci. Biotechnol.

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Flooding stress causes severe yield reduction in soybean worldwide. The development of stress-tolerant cultivars could be an effective measure to reduce the negative effects of flooding stress. Molecular information on the gene expression pattern of tolerant and susceptible genotypes under flooding stress could be valuable to improve the flooding tolerance in soybean. The objective of this study was to analyze the differentially expressed genes (DEGs) revealed by RNA sequencing in the soybean leaf tissues of tolerant ('Paldalkong' and 'Danbaekkong') and susceptible ('NTS1116') cultivars under flooding stress. Seedlings were grown in a well-watered condition up to the V1-V2 stage and flood-stressed by inundating ~ 10-cm water for 14 days. A total of 22,468 genes were differentially expressed in flood-stressed condition compared to the well-watered control condition, out of which 13,729, 13,405, and 13,160 were differentially expressed in 'Paldalkong', 'Danbaekkong', and 'NTS1116', respectively. A higher number of some of the flooding tolerance-related genes such as lipoxygenase, expansin, glutathione S-transferase, and sugar efflux transporter were up-regulated in the tolerant cultivars than in the susceptible cultivar. The number of some abscisic acid-related transcription factors of basic leucine zipper domain and myeloblastosis families was also higher in the tolerant cultivars than in the susceptible cultivar. The molecular information about the DEGs of tolerant and susceptible cultivars obtained in the present study could be valuable to improve the flooding tolerance in soybeans.

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Section: Discussionsupporting

confidence: 75%

Section: Discussionmentioning

confidence: 93%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Analysis of differentially expressed genes in soybean leaf tissue of tolerant and susceptible cultivars under flooding stress revealed by RNA sequencing

Dhungana

Kim

Kang

et al. 2020

J. Crop Sci. Biotechnol.

View full text Add to dashboard Cite

show abstract

“…A total of 49,824 unigenes were annotated against the five public databases, including NCBI Non-redundant protein sequences (Nr), Gene Ontology (GO), Clusters of Orthologous Groups (COG), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Swiss-Prot. The numbers of annotated unigenes in Nr, GO, COG, KEGG and Swiss-prot were 46,783,29,310,14,063,19,071 and 30, 697, respectively (Additional file 1: Table S3).…”

Section: Functional Annotation Of Unigenesmentioning

confidence: 99%

“…In the GO enrichment analysis, the DEGs were implemented using topGO R packages based on the Kolmogorov-Smirnov test. In order to further reduce the redundant GO terms, REVIGO analysis [45] was carried out according to semantic similarity and SimRel semantic similarity measure, with an allowed similarity of 0.7 (medium) [46], after which the results were graphically displayed. KOBAS software [47] was applied to test the statistical enrichment of differentially expressed genes in KEGG (http://www.genome.jp/kegg/) pathways.…”

Section: Deg Functional Annotation and Enrichment Analysismentioning

confidence: 99%

To bloom once or more times: the reblooming mechanisms of Iris germanica revealed by transcriptome profiling

et al. 2020

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Background: The reblooming bearded iris (Iris germanica) can bloom twice a year, in spring and autumn. The extended ornamental period makes it more popular and brings additional commercial values. However, little is known about the reblooming mechanisms, making the breeding programs time-consuming and labor-wasting. Therefore, a comparative transcriptome profiling was conducted on once-bloomers and rebloomers from the same F 1 generation on six development stages, and the candidate genes associated with reblooming were identified. Results: A total of 100,391 unigenes were generated, the mean length being 785 bp. In the three comparisons (the floral initiation stage of spring flowering in once-bloomers (OB-T1) vs the floral initiation stage of spring flowering in rebloomers (RB-T1); RB-T1 vs the floral initiation stage of autumn flowering in rebloomers (RB-T5); OB-T1 vs RB-T5), a total of 690, 3515 and 2941 differentially expressed genes (DEGs) were annotated against the public databases, respectively. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis focused on the photoperiod response, the temperature insensitivity and the growth speed, to remove the redundant DEGs and figure out the candidate key genes. As a result, the following four genes, PHYTOCHROME A (PHYA), GIGANTEA (GI), SHORT VEGETATIVE PERIOD (SVP) and AUXIN RESPONSE FACTOR (ARF), were considered to be involved in the second floral initiation of the rebloomers. Conclusion: This research provides valuable information for the discovery of the reblooming-related genes. The insights into the molecular mechanisms of reblooming may accelerate the breeding of bearded iris and other perennials.

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High‐throughput NGS‐based genotyping and phenotyping: Role in genomics‐assisted breeding for soybean improvement

Bhat

2021

Legume Science

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Soybean is an important food crop that provides edible protein and oil for human and animal nutrition. Conventional phenotypic‐based breeding approaches have made significant contribution in the last century by developing many improved soybean varieties. However, due to the longer time taken to develop a variety, low genetic gain per unit time, and adverse environmental influence of phenotypic‐based selection, conventional approaches are not sufficient to maintain pace with growing population and climate change. In this context, the recent method of genotypic selection, that is, genomics‐assisted breeding (GAB) is considered a promising approach to address the challenges in soybean breeding. However, to harness the true potential of GAB in soybean improvement, the great coverage and precision in the genotyping and phenotyping are required. Previously, a huge gap was observed between the discovery and practical use of quantitative trait loci (QTLs) in soybean improvement. It has been suggested that low marker density and manually collected phenotypes are the major reasons for this failure. Hence, high‐throughput genotyping (HTG) providing higher genome‐wide marker density, as well as accurate and precise phenotyping using high‐throughput digital phenotyping (HTP) platforms, can significantly increase the success of QTL and candidate gene identification in soybean. These approaches can greatly increase the practical utility of GAB in soybean and also offer a faster characterization of germplasm and breeding materials. This review provides the detailed information on how the recent innovations in genomics and phenomics can assists in improving the efficiency and potential of GAB in soybean improvement.

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RNA-Seq based transcriptomic analysis revealed genes associated with seed-flooding tolerance in wild soybean (Glycine soja Sieb. & Zucc.)

Cited by 44 publications

References 91 publications

Analysis of differentially expressed genes in soybean leaf tissue of tolerant and susceptible cultivars under flooding stress revealed by RNA sequencing

Analysis of differentially expressed genes in soybean leaf tissue of tolerant and susceptible cultivars under flooding stress revealed by RNA sequencing

To bloom once or more times: the reblooming mechanisms of Iris germanica revealed by transcriptome profiling

High‐throughput NGS‐based genotyping and phenotyping: Role in genomics‐assisted breeding for soybean improvement

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