Genome-wide identification and functional characterization of LEA genes during seed development process in linseed flax (Linum usitatissimum L.)

Li, Zhen; Chen, Hui; Liu, Caiyue; Zhang, Tianbao; Han, Lida; Li, Liang; Pei, Xinwu; Long, Yan

doi:10.1186/s12870-021-02972-0

Cited by 15 publications

(10 citation statements)

References 47 publications

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“…To examine the potential functions of RING finger genes during the seed development process in flax, a published flax RNA sequencing (RNA-seq) dataset (NCBI GEO accession: ) ( Li et al, 2021 ) was used to confirm the expression profiles of these genes. A total of 505 RING finger genes were expressed at four stages (days after pollination [DAP]5, DAP10, DAP20, and DAP30) during the seed development process in flax, determined based on the transcriptome data; the other 69 genes were not found and excluded from the analysis ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

“…The RNA-seq data (accession number and ) ( Li et al, 2021 ; Zhang & Deyholos, 2016 ) were downloaded from the NCBI GEO dataset ( Tables S5 and S6 ) and filtered to explore the expression patterns of RING finger genes in flax. These transcript data ( Li et al, 2021 ; Zhang & Deyholos, 2016 ) were obtained for seeds at four developmental stages (DAP5, DAP10, DAP20, and DAP30) and for the AR and BR of the shoot apex. The expression data represented log2 based Fragments per Kilobase of Exon per Million Fragments Mapped FPKM) values, and the heatmap of the expression profiles of flax RING finger genes was drawn using the heatmap.2 function in R.…”

Section: Methodsmentioning

confidence: 99%

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Genome-wide identification of RING finger genes in flax (Linum usitatissimum) and analyses of their evolution

Meng

Liu

Zhao

2021

PeerJ

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Background Flax (Linum usitatissimum) is an important crop for its seed oil and stem fiber. Really Interesting New Gene (RING) finger genes play essential roles in growth, development, and biotic and abiotic stress responses in plants. However, little is known about these genes in flax. Methods Here, we performed a systematic genome-wide analysis to identify RING finger genes in flax. Results We identified 587 RING domains in 574 proteins and classified them into RING-H2 (292), RING-HCa (181), RING-HCb (23), RING-v (53), RING-C2 (31), RING-D (2), RING-S/T (3), and RING-G (2). These proteins were further divided into 45 groups according to domain organization. These genes were located in 15 chromosomes and clustered into three clades according to their phylogenetic relationships. A total of 312 segmental duplicated gene pairs were inferred from 411 RING finger genes, indicating a major contribution of segmental duplications to the RING finger gene family expansion. The non-synonymous/synonymous substitution ratio of the segmentally duplicated gene pairs was less than 1, suggesting that the gene family was under negative selection since duplication. Further, most RING genes in flax were differentially expressed during seed development or in the shoot apex. This study provides useful information for further functional analysis of RING finger genes in flax and to develop gene-derived molecular markers in flax breeding.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Genome-wide identification of RING finger genes in flax (Linum usitatissimum) and analyses of their evolution

Meng

Liu

Zhao

2021

PeerJ

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“…Further, it has been suggested that comparative TTG2 quantity in antipodal cells to gametes regulates seed size, indicating the role of the maternal and paternal dose-dependent molecular framework. The late embryogenesis abundant (LEA) protein family named LuLEA is expressed at later stages of seed development [ 26 ]. LuLEA1 negatively regulates seed size and yield as its higher expression reduces seed size and fatty acid content in Arabidopsis.…”

Section: Genetic Factors Controlling Seed Sizementioning

confidence: 99%

Developing Genetic Engineering Techniques for Control of Seed Size and Yield

Alam

Batool

Huang

et al. 2022

IJMS

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Many signaling pathways regulate seed size through the development of endosperm and maternal tissues, which ultimately results in a range of variations in seed size or weight. Seed size can be determined through the development of zygotic tissues (endosperm and embryo) and maternal ovules. In addition, in some species such as rice, seed size is largely determined by husk growth. Transcription regulator factors are responsible for enhancing cell growth in the maternal ovule, resulting in seed growth. Phytohormones induce significant effects on entire features of growth and development of plants and also regulate seed size. Moreover, the vegetative parts are the major source of nutrients, including the majority of carbon and nitrogen-containing molecules for the reproductive part to control seed size. There is a need to increase the size of seeds without affecting the number of seeds in plants through conventional breeding programs to improve grain yield. In the past decades, many important genetic factors affecting seed size and yield have been identified and studied. These important factors constitute dynamic regulatory networks governing the seed size in response to environmental stimuli. In this review, we summarized recent advances regarding the molecular factors regulating seed size in Arabidopsis and other crops, followed by discussions on strategies to comprehend crops’ genetic and molecular aspects in balancing seed size and yield.

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“…Different groups of LEA proteins show a low similarity [43]. Motif analysis in A. thaliana [36], ax (Linum usitatissimum) [44] and wheat [45] indicated that the members of LEA gene subfamily contain speci cally conserved structures. In our study, the conserved motifs of PnoLEA proteins were different among subfamily groups (Fig.…”

Section: Molecular Characteristics Of Pnolea Genesmentioning

confidence: 99%

Genome-wide analysis on characterization of LEA gene family in responses to dehydration stress in recalcitrant Panax notoginseng seeds

Jia

Wang

et al. 2022

Preprint

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Background Late embryogenesis abundant (LEA) proteins play an important role in dehydration process of seed maturation. The seeds of Panax notoginseng (Burkill) F. H. Chen are typically characterized with the recalcitrance and are highly sensitive to dehydration. However, it is not very well known about the role of LEA proteins in response to dehydration stress in P. notoginseng seeds. A genome-wide analysis would be performed in the LEA gene family of recalcitrant P. notoginseng seeds to learn more about the function of LEA proteins in response to dehydration stress. Results In this study, 61 LEA genes were identified from the P. notoginseng genome, and they were renamed as PnoLEA. The PnoLEA genes were classified into seven subfamilies based on the phylogenetic relationships, gene structure and conserved domains. The PnoLEA genes family showed relatively few introns and was highly conserved. Unexpectedly, the LEA_6 subfamily were not found, and the LEA_2 subfamily contained 46 (75.4%) members. Within 19 pairs of fragment duplication events, among them 17 pairs were LEA_2 subfamily. The Ka/Ks ratios are between 0.06 and 0.58 in all the homologous genes pairs, indicating that these homologous genes have experienced a purifying selection. In addition, the expression of the PnoLEA genes was obviously induced under dehydration stress, but the germination rate of P. notoginseng seeds decreased as the dehydration time prolonged. Conclusions We found that the lack of the LEA_6 subfamily, the expansion of the LEA_2 subfamily and low transcriptional levels of most PnoLEA genes might be implicated in the recalcitrant formation of P. notoginseng seeds. LEA proteins are essential in the response to dehydration stress in recalcitrant seeds, but the protective effect of LEA protein is not efficient. These results could improve our understanding of the function of LEA proteins in the response of dehydration stress and their contributions to the formation of seed recalcitrance.

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Genome-wide identification and functional characterization of LEA genes during seed development process in linseed flax (Linum usitatissimum L.)

Cited by 15 publications

References 47 publications

Genome-wide identification of RING finger genes in flax (Linum usitatissimum) and analyses of their evolution

Genome-wide identification of RING finger genes in flax (Linum usitatissimum) and analyses of their evolution

Developing Genetic Engineering Techniques for Control of Seed Size and Yield

Genome-wide analysis on characterization of LEA gene family in responses to dehydration stress in recalcitrant Panax notoginseng seeds

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