Genome-wide analysis of the auxin/indoleacetic acid (Aux/IAA) gene family in allotetraploid rapeseed (Brassica napus L.)

Li, Haitao; Wang, Bo; Zhang, Qinghua; Wang, Jing; King, Graham J.; Liu, Kede

doi:10.1186/s12870-017-1165-5

Cited by 43 publications

(46 citation statements)

References 61 publications

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“…Within this tree, a total of 25 sister pairs were found, consisting of 10 and 15 pairs in group A and B. This pattern of two major groups for Aux/IAA gene family members in the phylogenetic tree was similar to that reported for other plants including rice [22], Moso bamboo (Phyllostachys pubescens) [23], soybean [12] and Brassica napus [2], which suggested that the Aux/IAA genes have been widely conserved in different groups. Meanwhile, to gain a better understanding of the structural diversity of the BsIAAs, we also built a separate phylogenetic tree using the same method (Figure 4).…”

Section: Comparative Phylogenetic Analysis Of Bsiaasupporting

confidence: 81%

Identification and bioinformatic analysis of Aux/IAA family based on transcriptome data of Bletilla striata

Liu

Li³

et al. 2019

Bioengineered

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Auxin/Indole-3-Acetic Acid (Aux/IAA) genes are involved in auxin signaling pathway and play an important role in plant growth and development. However, many studies focus on Aux/IAA gene families and much less known in Bletilla striata. In this study, a total of 27 Aux/IAA genes (BsIAA1-27) were cloned from the transcriptome of Bletilla striata. Based on a phylogenetic analysis of the Aux/IAA protein sequences from B. striata, Arabidopsis thaliana and Dendrobium officinale, the Aux/IAA genes of B. striata (BsIAAs) were categorized into 2 subfamilies and 9 groups. While BsIAAs were more closer to those of D. officinale compared to A. thaliana. EST-SSR marker mining test showed that 4 markers could be stably amplified with obvious polymorphisms among 4 landraces. Our results suggested that BsIAAs were involved in the process of tuber development and provided insights into functional roles of Aux/IAA genes in B. striata and other plants.In this paper, we identified the 27 members of the Aux/IAA gene family which can be divided into 2 groups and 9 subfamilies. The similar branches of Aux/IAA proteins had the same or similar motifs, such as genes between BsIAA10 and BsIAA12, BsIAA11 and BsIAA13, BsIAA18 and BsIAA20, indicating that Aux/IAA proteins were conserved. Among them, BsIAAs were more closer to those of D. officinale compared to A. thaliana.

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Section: Comparative Phylogenetic Analysis Of Bsiaasupporting

confidence: 81%

Identification and bioinformatic analysis of Aux/IAA family based on transcriptome data of Bletilla striata

Liu

Li³

et al. 2019

Bioengineered

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“…Of these, two neighboring genes, BnaA03g36940D and BnaA03g36950D , were found to encode Aux/IAA proteins homologous to IAA2 (At3g23030) and IAA7 (At3g23050) in Arabidopsis thaliana , respectively (Fig. e) that had been established previously (Li et al ., ). In Arabidopsis , the Aux/IAA proteins act as repressors in the auxin signaling pathway and mutations of Aux/IAA genes usually generate auxin‐related growth defects, including aberrant leaf architecture and dwarfism (Reed, ; Overvoorde et al ., ).…”

Section: Resultsmentioning

confidence: 97%

An auxin signaling gene BnaA3.IAA7 contributes to improved plant architecture and yield heterosis in rapeseed

Song

et al. 2019

New Phytologist

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Summary Plant architecture is the key factor affecting overall yield in many crops. The genetic basis underlying plant architecture in rapeseed (Brassica napus), a key global oil crop, is elusive. We characterized an ethyl methanesulfonate (EMS)‐mutagenized rapeseed mutant, sca, which had multiple phenotypic alterations, including crinkled leaves, semi‐dwarf stature, narrow branch angles and upward‐standing siliques. We identified the underlying gene, which encodes an Aux/IAA protein (BnaA3.IAA7). A G‐to‐A mutation changed the glycine at the 84th position to glutamic acid (G84E), disrupting the conserved degron motif GWPPV and reducing the affinity between BnaA3.IAA7 and TIR1 (TRANSPORT INHIBITOR RESPONSE 1) in an auxin dosage‐dependent manner. This change repressed the degradation of BnaA3.IAA7 and therefore repressed auxin signaling at low levels of auxin that reduced the length of internodes. The G84E mutation reduced branch angles by enhancing the gravitropic response. The heterozygote +/sca closely resembled a proposed ideal plant architecture, displaying strong yield heterosis through single‐locus overdominance by improving multiple component traits. Our findings demonstrate that a weak gain‐of‐function mutation in BnaA3.IAA7 contributes to yield heterosis by improving plant architecture and would be valuable for breeding superior rapeseed hybrid cultivars and such a mutation may increase the yield in other Brassica crops.

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“…However, most of the duplicated ANN genes were retained after the whole-genome duplication (WGD) event in B. napus. WGD event of gene family appears to be a widespread phenomenon, such as the auxin response factor (ARF) 47 , Auxin/Indoleacetic acid (Aux/IAA) 48 , glutathione transferases (GST) 49 , BRI1-EMS-SUPPRESSOR1 (BES1) 50 , Heat stress transcription factors (Hsfs) 51,52 , GRAS 53 family genes in diploid and allopolyploid Brassicaceae and Calcium-dependent protein kinases (CPK) 54 , Jasmonate ZIM-domain (JAZ) 55 and Nuclear factor YB (NF-YB) 56 in diploid and allopolyploid Gossypium species (G. raimondii: DD genome; G. arboretum: AA genome; G. hirsutum: AADD genome). Among the 51 Brassica ANN genes, 35 were the typical ANN, which encoded proteins ranging from 315-325 amino acids (AA) and contained four annexin repeats.…”

Section: Resultsmentioning

confidence: 99%

Comprehensive analyses of the annexin (ANN) gene family in Brassica rapa, Brassica oleracea and Brassica napus reveals their roles in stress response

Liao

Xie

et al. 2020

Sci Rep

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Annexins (Ann) are a multigene, evolutionarily conserved family of calcium-dependent and phospholipid-binding proteins that play important roles in plant development and stress resistance. However, a systematic comprehensive analysis of ANN genes of Brassicaceae species (Brassica rapa, Brassica oleracea, and Brassica napus) has not yet been reported. In this study, we identified 13, 12, and 26 ANN genes in B. rapa, B. oleracea, and B. napus, respectively. About half of these genes were clustered on various chromosomes. Molecular evolutionary analysis showed that the ANN genes were highly conserved in Brassicaceae species. Transcriptome analysis showed that different group ANN members exhibited varied expression patterns in different tissues and under different (abiotic stress and hormones) treatments. Meanwhile, same group members from Arabidopsis thaliana, B. rapa, B. oleracea, and B. napus demonstrated conserved expression patterns in different tissues. The weighted gene coexpression network analysis (WGcnA) showed that BnaANN genes were induced by methyl jasmonate (MeJA) treatment and played important roles in jasmonate (JA) signaling and multiple stress response in B. napus.Annexins (ANN) are a multigene, evolutionarily conserved family of calcium (Ca 2+ )-dependent and phospholipid-binding proteins present in plants, animals, and microorganisms 1,2 . ANN contain the characteristic annexin repeat and they regulate membrane dynamics, mediate Ca 2+ sensing and signaling, link Ca 2+ dynamics to cytoskeletal responses, and mediate immune or stress responses and signaling during plant growth and development 1,3 . A typical ANN contains four annexin repeats at the C-terminal region and a highly variable N-terminal region. Each annexin repeat usually contains a characteristic type II motif for Ca 2+ binding 1,3 . The variable N-terminal region interacts with other proteins and is responsible for the functional diversity of ANN 4 .Recent studies have identified the ANN gene family in Arabidopsis thaliana (8 genes), Brassica rapa (13), Solanum lycopersicum (9), Solanum tuberosum (9), Oryza sativa (10), Triticum aestivum (25), Gossypium raimondii (14), Arachis hypogaea L. (8), Hordeum vulgare (11), Medicago truncatula (10), Populus trichocarpa (12), Vitis vinifera (14), Carica papaya (12), Glycine max (22), Cochliobolus sativus (11), Sorghum bicolor (10), Zea mays (12), Brachypodium distachyon (11), Selaginella mollendorffii (5), and Physcomitrella patens (7) via genome-wide analysis 2,5-11 .Studies have shown that ANN gene family plays a significant role in plant development and plant protection during both abiotic and biotic stresses 1,3,12,13 . In Arabidopsis, two ANN genes (AtANN1 and AtANN4) were regulated by abiotic stress, negatively regulated plant tolerance to drought, salinity, and heat stress, while AtANN8 was open Scientific RepoRtS | (2020) 10:4295 | https://doi.org/10.1038/s41598-020-59953-w www.nature.com/scientificreports www.nature.com/scientificreports/ positive regulated the plant abiotic tolerance [...

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Genome-wide analysis of the auxin/indoleacetic acid (Aux/IAA) gene family in allotetraploid rapeseed (Brassica napus L.)

Cited by 43 publications

References 61 publications

Identification and bioinformatic analysis of Aux/IAA family based on transcriptome data of Bletilla striata

Identification and bioinformatic analysis of Aux/IAA family based on transcriptome data of Bletilla striata

An auxin signaling gene BnaA3.IAA7 contributes to improved plant architecture and yield heterosis in rapeseed

Comprehensive analyses of the annexin (ANN) gene family in Brassica rapa, Brassica oleracea and Brassica napus reveals their roles in stress response

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