Soybean DICER-LIKE2 Regulates Seed Coat Color via Production of Primary 22-Nucleotide Small Interfering RNAs from Long Inverted Repeats

Jia, Jinbu; Ji, Ronghuan; Li, Zhuowen; Yu, Yiming; Nakano, Mayumi; Long, Yanping; Li, Feng; Qin, Chao; Lu, Dongdong; Zhan, Junpeng; Xia, Rui; Meyers, Blake C.; Liu, Bin; Zhai, Jixian

doi:10.1105/tpc.20.00562

Cited by 43 publications

(45 citation statements)

References 66 publications

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“…There is potential for similar outcomes in the many other species carrying EPRVs including bitter orange, rice, lucky bamboo, Dahlia, pineapple, grapes, poplar and fig 10 . In sugar beet 15 and soybean 16 the EPRV are associated with 22nt sRNAs as in Solanum. This sRNA-based mechanism involving EPRVs could modify gene expression in hybrid populations of many species and increase the range of traits available for selection in natural evolution or breeding for agriculture.…”

Section: Discussionmentioning

confidence: 99%

Endogenous virus sRNA regulates gene expression following genome shock in tomato hybrids

López-Gomollón

Mueller

Baulcombe

2021

Preprint

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Hybridization and environmental stress trigger genome shock that perturbs patterns of gene expression leading to phenotypic changes. In extreme examples it is associated to transposon mobilization and genome rearrangement. Here we discover a novel alternative mechanism in interspecific Solanum hybrids in which changes to gene expression were associated with DCL2-mediated small (s)RNAs derived from endogenous (para)retroviruses (EPRVs). Correspondingly, the altered patterns of gene expression overlapped with the effects of dcl2 mutation and the changes to sRNA profiles involved 22nt species produced in the DCL2 biogenesis pathway. These findings implicate hybridization-induced genome shock leading to EPRV activation and sRNA silencing as causing changes in gene expression. Such hybridization-induced variation in gene expression could increase the range of traits available for selection in natural evolution or in breeding for agriculture.

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Section: Discussionmentioning

confidence: 99%

Endogenous virus sRNA regulates gene expression following genome shock in tomato hybrids

López-Gomollón

Mueller

Baulcombe

2021

Preprint

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“…To establish the role of the DCL2-dependent 22-nucleotide siRNA (derived from long inverted repeats) regulating chalcone synthase ( CHS ) genes attributing seed coat colour in soybean, a study conducted by Jia et al (2020) [ 176 ] revealed that CRISPR/Cas9-driven loss-of-function mutants of DCL2 ( GmDCL2a and GmDCL2b ) caused changes in seed coat colour from yellow to brown in Gmdcl2a/2b mutants in soybean. Thus, this study confirmed that DCL2 controls soybean seed coat colour via generating siRNA from long inverted repeats [ 176 ].…”

Section: Regulatory Role Of Ncrnas For Shaping Developmental Processes In Legume Speciesmentioning

confidence: 99%

Non-Coding RNAs in Legumes: Their Emerging Roles in Regulating Biotic/Abiotic Stress Responses and Plant Growth and Development

Jha

Nayyar

Mantri

et al. 2021

Cells

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Noncoding RNAs, including microRNAs (miRNAs), small interference RNAs (siRNAs), circular RNA (circRNA), and long noncoding RNAs (lncRNAs), control gene expression at the transcription, post-transcription, and translation levels. Apart from protein-coding genes, accumulating evidence supports ncRNAs playing a critical role in shaping plant growth and development and biotic and abiotic stress responses in various species, including legume crops. Noncoding RNAs (ncRNAs) interact with DNA, RNA, and proteins, modulating their target genes. However, the regulatory mechanisms controlling these cellular processes are not well understood. Here, we discuss the features of various ncRNAs, including their emerging role in contributing to biotic/abiotic stress response and plant growth and development, in addition to the molecular mechanisms involved, focusing on legume crops. Unravelling the underlying molecular mechanisms and functional implications of ncRNAs will enhance our understanding of the coordinated regulation of plant defences against various biotic and abiotic stresses and for key growth and development processes to better design various legume crops for global food security.

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“…Soybeans are available in a range of colors from yellow, green, brown, and black, to mottled [ 7 ]. Physiological and genetic studies indicate that the color variation is due to the difference in the accumulation of pigment-stimulating metabolites [ 8 , 9 , 10 , 11 ].…”

Section: Introductionmentioning

confidence: 99%

Protein, Amino Acid, Oil, Fatty Acid, Sugar, Anthocyanin, Isoflavone, Lutein, and Antioxidant Variations in Colored Seed-Coated Soybeans

Dhungana

Seo

Kang

et al. 2021

Plants

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Different physiological and genetic studies show that the variations in the accumulation of pigment-stimulating metabolites result in color differences in soybean seed coats. The objective of this study was to analyze the nutrient contents and antioxidant potential in black, brown, and green seed-coated soybeans. Significant variations in protein (38.9–43.3%), oil (13.9–20.4%), total sugar (63.5–97.0 mg/g seed), total anthocyanin (3826.0–21,856.0 μg/g seed coat), total isoflavone (709.5–3394.3 μg/g seed), lutein (1.9–14.8 μg/g), total polyphenol (123.0–385.8 mg gallic acid/100 g seed), total flavonoid (22.1–208.5 mg catechin/100 g seed), 2,2′-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid (ABTS; 275.0–818.8 mg Trolox/100 g seed), and 2,2-diphenyl-1-picrylhydrazyl (DPPH; 96.3–579.7 mg Trolox/100 g seed) were found among the soybean genotypes. Ilpumgeomjeong2 contained the lowest protein but the highest oil and total sugar. The lowest oil-containing Wonheug had the highest protein content. Socheong2 was rich in all four variables of antioxidants. Anthocyanins were detected only in black soybeans but not in brown and green soybeans. The variation in isoflavone content was up to 5-fold among the soybean genotypes. This study could be a valuable resource for the selection and improvement of soybean because an understanding of the nutrient content and antioxidant potentials is useful to develop effective strategies for improving the economic traits; for example, the major emphasis of soybean breeding for fatty acids is to enhance the oleic and linoleic acid contents and to decrease linolenic acid content.

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Soybean DICER-LIKE2 Regulates Seed Coat Color via Production of Primary 22-Nucleotide Small Interfering RNAs from Long Inverted Repeats

Abstract: Soybean DCL2 favors long inverted repeat-derived double-stranded RNA as its substrate, and generates primary 22-nt siRNAs to regulate seed coat color and silence transposable elements.

Cited by 43 publications

References 66 publications

Endogenous virus sRNA regulates gene expression following genome shock in tomato hybrids

Endogenous virus sRNA regulates gene expression following genome shock in tomato hybrids

Non-Coding RNAs in Legumes: Their Emerging Roles in Regulating Biotic/Abiotic Stress Responses and Plant Growth and Development

Protein, Amino Acid, Oil, Fatty Acid, Sugar, Anthocyanin, Isoflavone, Lutein, and Antioxidant Variations in Colored Seed-Coated Soybeans

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