Comprehensive study of rice YABBY gene family: evolution, expression and interacting proteins analysis

Zhang, Ting; Wu, Anqi; Hu, Xiaosong; Deng, Qiyu; Ma, Zhong‐Qi; Su, Li-Na

doi:10.7717/peerj.14783

Cited by 3 publications

(5 citation statements)

References 73 publications

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“…7 ( YAB1 ) affect both meristem, leaf, and floral development in rice (Toriba et al., 2007) and the NAC transcription factor, NAC111 , on chr. 10 (Y. Fang et al., 2008; T. Zhang et al., 2023).…”

Section: Resultsmentioning

confidence: 99%

Substitution mapping of yield‐related traits utilizing three Cybonnet rice × wild introgression libraries

Eizenga,

Edwards,

Jackson

et al. 2024

Crop Science

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Improving rice (Oryza sativa L.) yields is a major objective of breeding programs worldwide. The Oryza rufipogon species complex (ORSC), which includes the rice ancestral species O. rufipogon Griff. and O. nivara S. D. Sharma & Shastry, is an underutilized resource. Using three phenotypically and genotypically diverse ORSC accessions identified as OrA, OrB, and OrC, three Cybonnet × ORSC chromosome segment substitution line (CSSL) libraries were developed to make this genepool more accessible to breeders. The objective was to characterize these libraries for 20 yield‐related traits to discover genes not currently deployed for rice improvement. Cybonnet and 212 CSSLs from these libraries were evaluated for 2 years in field studies for six agronomic, six panicle architecture, and eight seed traits. Across the three libraries, 62 CSSLs were found to be significantly different from Cybonnet for one or more traits. Of these, 27 CSSLs were significantly different for seed size traits. To ascertain the chromosome region and underlying candidate gene(s) causing these differences, substitution mapping was performed with previously reported genotypes. Mapping with the CSSLs, which had delayed heading under long days, revealed five known genes associated with rice flowering time pathways. The OsMADS50, RFT1, HD3A, SE1, and GHD7 genes were mapped in the OrB and OrC derived CSSLs but only OsMADS50 mapped in the OrA derived CSSLs. Employing this approach for the other 19 traits revealed 28 total candidate genes. A total of 12 of these genes are currently not deployed for yield enhancement. The introgressed ORSC regions associated with these genes are potential sources of novel variation for rice improvement.

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Section: Resultsmentioning

confidence: 99%

Substitution mapping of yield‐related traits utilizing three Cybonnet rice × wild introgression libraries

Eizenga,

Edwards,

Jackson

et al. 2024

Crop Science

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“…As members of a TF family, YABBY genes have been investigated in many species; for example, six members have been found in A. thaliana [56,57], eight in rice [37,40], nine in tomato [58], thirteen in maize [59], twenty-one in wheat [38,39], seventeen in soybean [52], seven in grapevine (Vitis vinifera) [60], twelve in Gossypium arboreum [55], and ten in Juglans regia [61]. In this study, we identified 12 CqYAB genes in quinoa.…”

Section: Discussionmentioning

confidence: 99%

“…In addition, these genes are responsible for maintaining the proper activity of the meristem [31,36]. YABBYs were also found in rice, maize, and wheat [37][38][39][40] and found functioning in carpel specification and leaf midrib formation [41], the development of vasculature [42], the determination of the fate of abaxial cells in leaf development and architecture [43][44][45], lateral organ development and meristem maintenance in spikelet [46][47][48], seed shattering [49,50], and the regulation of gibberellin metabolism [51]. Recently, a few studies have shown that YABBY genes are involved in abiotic stress responses, such as salt and drought stresses [52,53], cadmium (Cd) stress [54], and cold and heat stresses [55].…”

Section: Introductionmentioning

confidence: 99%

Molecular Characterization and Expression Analysis of YABBY Genes in Chenopodium quinoa

Li,

Zhang,

et al. 2023

Genes

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Plant-specific YABBY transcription factors play an important role in lateral organ development and abiotic stress responses. However, the functions of the YABBY genes in quinoa remain elusive. In this study, twelve YABBY (CqYAB) genes were identified in the quinoa genome, and they were distributed on nine chromosomes. They were classified into FIL/YAB3, YAB2, YAB5, INO, and CRC clades. All CqYAB genes consist of six or seven exons, and their proteins contain both N-terminal C2C2 zinc finger motifs and C-terminal YABBY domains. Ninety-three cis-regulatory elements were revealed in CqYAB gene promoters, and they were divided into six groups, such as cis-elements involved in light response, hormone response, development, and stress response. Six CqYAB genes were significantly upregulated by salt stress, while one was downregulated. Nine CqYAB genes were upregulated under drought stress, whereas six CqYAB genes were downregulated under cadmium treatment. Tissue expression profiles showed that nine CqYAB genes were expressed in seedlings, leaves, and flowers, seven in seeds, and two specifically in flowers, but no CqYAB expression was detected in roots. Furthermore, CqYAB4 could rescue the ino mutant phenotype in Arabidopsis but not CqYAB10, a paralog of CqYAB4, indicative of functional conservation and divergence among these YABBY genes. Taken together, these results lay a foundation for further functional analysis of CqYAB genes in quinoa growth, development, and abiotic stress responses.

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“…In other eudicots and fleshy fruit species, nine YABBY genes have been identified both in tomato (Solanum lycopersicum) (Han et al 2015) and in pineapple (Ananas comosus) (Li et al 2019), seven in mango (Mangifera indica) (Xia et al 2022), six in pomegranate (Punica granatum) (Zhao et al 2020), and 59 in several cucurbit species (Yin et al 2022). Moreover, YABBY genes have also been studied in monocots species including the identification of eight genes in rice (Oryza sativa) (Toriba et al 2007;Zhang et al 2023), 21 in wheat (Triticum aestivum) (Buttar et al 2020), 13 in corn (Zea mays) (Strable et al 2017), and eight in foxtail millet (Setaria italica) (Jie et al 2022). Luo et al (2022) named the YABBY genes in F. 9 ananassa from YAB1 to YAB25 and performed transcriptional analyses of eight FaYABs in green and red fruits, showing differential expression levels between these two fruit stages in four genes (Luo et al 2022).…”

Section: Introductionmentioning

confidence: 99%

“…2007; Zhang et al . 2023), 21 in wheat ( Triticum aestivum ) (Buttar et al . 2020), 13 in corn ( Zea mays ) (Strable et al .…”

Section: Introductionmentioning

confidence: 99%

YABBY transcription factor family in the octoploid Fragaria × ananassa and five diploid Fragaria species

Jara‐Cornejo,

Zúñiga,

Rivera‐Mora

et al. 2024

Plant Biol J

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YABBY genes encode specific TFs of seed plants involved in development and formation of leaves, flowers, and fruit. In the present work, genome‐wide and expression analyses of the YABBY gene family were performed in six species of the Fragaria genus: Fragaria × ananassa, F. daltoniana, F. nilgerrensis, F. pentaphylla, F. viridis, and F. vesca. The chromosomal location, synteny pattern, gene structure, and phylogenetic analyses were carried out. By combining RNA‐seq data and RT‐qPCR analysis we explored specific expression of YABBYs in F. × ananassa and F. vesca. We also analysed the promoter regions of FaYABBYs and performed MeJA application to F. × ananassa fruit to observe effects on gene expression. We identified and characterized 25 YABBY genes in F. × ananassa and six in each of the other five species, which belong to FIL/YAB3 (YABBY1), YAB2 (YABBY2), YAB5 (YABBY5), CRC, and INO clades previously described. Division of the YABBY1 clade into YABBY1.1 and YABBY1.2 subclades is reported. We observed differential expression according to tissue, where some FaYABBYs are expressed mainly in leaves and flowers and to a minor extent during fruit development of F. × ananassa. Specifically, the FaINO genes contain jasmonate‐responsive cis‐acting elements in their promoters which may be functional since FaINOs are upregulated in F. × ananassa fruit under MeJA treatment. This study suggests that YABBY TFs play an important role in the development‐ and environment‐associated responses of the Fragaria genus.

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Comprehensive study of rice YABBY gene family: evolution, expression and interacting proteins analysis

Cited by 3 publications

References 73 publications

Substitution mapping of yield‐related traits utilizing three Cybonnet rice × wild introgression libraries

Substitution mapping of yield‐related traits utilizing three Cybonnet rice × wild introgression libraries

Molecular Characterization and Expression Analysis of YABBY Genes in Chenopodium quinoa

YABBY transcription factor family in the octoploid Fragaria × ananassa and five diploid Fragaria species

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