Natural variation of the BRD2 allele affects plant height and grain size in rice

Huang, Junhua; Chen, Zhiming; Lin, Jiajia; Chen, Jinwen; Wei, Menghao; Liu, Liang; Yu, Feng; Zhang, Zesen; Chen, Fangyu; Jiang, Liangrong; Zheng, Jingsheng; Wang, Tiansheng; Chen, Huiqing; Xie, Wangyou; Huang, Senhao; Wang, Houcong; Huang, Yuxin; Huang, Rongyu

doi:10.1007/s00425-022-03939-7

Cited by 11 publications

(6 citation statements)

References 35 publications

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“…Such variations might be due to alterations in other epigenetics marks, altered chromatin state or due to mis-regulation of regulatory modules. We observed several auxin, brassinosteroid signaling pathway genes such as TUD1,OsDWARF/BRD1, BRD2, OsGSK3 which were well documented as important players in grain size (Hu et al, 2013a; Gao et al, 2019; Qin et al, 2018; Huang et al, 2022), were mis-expressed in clsy3-kd lines. Grain development related MAPK pathway genes (Liu et al, 2021; Xu et al, 2018) and transcription factors (TF) such as OsMADS6, OsMADS29 , OsWRKY53 which were known for starch synthesis, proper cellularization, cell size regulation and programmed cell death also mis-regulated in clsy3-kd lines (Yin and Xue, 2012; Nayar et al, 2013, 2014; Zhang et al, 2010; Tang et al, 2022).…”

Section: Discussionmentioning

confidence: 86%

Upstream regulator of genomic imprinting in rice endosperm is a small RNA-associated chromatin remodeler

Pal,

Sundar G,

et al. 2023

Preprint

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Genomic imprinting is observed in endosperm, a placenta-like seed tissue, where transposable elements (TEs) and repeat-derived small(s)RNAs mediate epigenetic changes in plants. In imprinting, uniparental gene expression arises due to parent-specific epigenetic marks on one allele but not on the other. The importance of sRNAs and their regulation in endosperm development or in imprinting is poorly understood in crops. Here we show that a previously uncharacterized CLASSY (CLSY)-family chromatin remodeler named OsCLSY3 is essential for rice endosperm development and imprinting, acting as an upstream player in sRNA pathway. Comparative transcriptome and genetic analysis indicated its endosperm-preferred expression and its paternally imprinted nature. These important features were modulated by RNA-directed DNA methylation (RdDM) of tandemly arranged TEs in its promoter. Upon perturbation of OsCLSY3 in transgenic lines we observed defects in endosperm development and loss of around 70% of all sRNAs. Interestingly, well-conserved endosperm-specific sRNAs (siren) that are vital for reproductive fitness in angiosperms were dependent on OsCLSY3. We also observed many imprinted genes and seed development-associated genes under the control of CLSY3-dependent RdDM. These results support an essential role of OsCLSY3 in rice endosperm development and imprinting, and propose similar regulatory strategies involving CLSY3 homologs among other cereals.

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Section: Discussionmentioning

confidence: 86%

Upstream regulator of genomic imprinting in rice endosperm is a small RNA-associated chromatin remodeler

Pal,

Sundar G,

et al. 2023

Preprint

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“…The plant stops growing when the main stem reaches its physiological height, as auxin is synthesized in the apical stem tip, inflorescence meristem replaces the function of the apical meristem, and the plant transitions from vegetative growth to reproductive growth [24,25]. Dwarf breeding is an important strategy for breeding wheat, rice, maize, and other crops [26][27][28][29]. Since the 1960s, breeders have triggered the first Green Revolution through the selection and breeding of semi-dwarf varieties that have greatly improved crop resistance and biological yields [30][31][32].…”

Section: Discussionmentioning

confidence: 99%

Transcriptome and Metabolome Reveal Key Genes from the Plant Hormone Signal Transduction Pathway Regulating Plant Height and Leaf Size in Capsicum baccatum

Xing,

Li,

et al. 2024

Cells

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Plant structure-related agronomic traits like plant height and leaf size are critical for growth, development, and crop yield. Defining the types of genes involved in regulating plant structure size is essential for the molecular-assisted breeding of peppers. This research conducted comparative transcriptome analyses using Capsicum baccatum germplasm HNUCB0112 and HNUCB0222 and their F2 generation as materials. A total of 6574 differentially expressed genes (DEGs) were detected, which contain 379 differentially expressed transcription factors, mainly including transcription factor families such as TCP, WRKY, AUX/IAA, and MYB. Seven classes of DEGs were annotated in the plant hormone signal transduction pathway, including indole acetic acid (IAA), gibberellin (GA), cytokinin (CK), abscisic acid (ABA), jasmonic acid (JA), ethylene (ET), and salicylic acid (SA). The 26 modules were obtained by WGCNA analysis, and the MEpink module was positively correlated with plant height and leaf size, and hub genes associated with plant height and leaf size were anticipated. Differential genes were verified by qRT-PCR, which was consistent with the RNA-Seq results, demonstrating the accuracy of the sequencing results. These results enhance our understanding of the developmental regulatory networks governing pepper key traits like plant height and leaf size and offer new information for future research on the pepper plant architecture system.

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“…Although weak correlations between PH and GL are documented in rice (Sabesan et al, 2009;Lakshmi et al, 2014), some genes for PH have pleiotropic effects influencing GL in rice. Huang and colleagues reported that the rice m u t a n t Z P D M 1 w i t h a n e w a l l e l e o f B R D 2 (BRASSINOSTEROID DEFICIENT DWARF 2) tended to result in the phenotype of reduced PH and smaller grain size (Huang et al, 2022). On the other hand, a novel rice germplasm with increased grain size but decreased height was developed, confirming the weak correlation between PH and GL or size.…”

Section: Introductionmentioning

confidence: 93%

Detecting and pyramiding target QTL for plant- and grain-related traits via chromosomal segment substitution line of rice

Mao

Xia

et al. 2022

Front. Plant Sci.

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IntroductionPlant height and grain length are important agronomic traits in rice, exhibiting a strong effect on plant architecture and grain quality of rice varieties.MethodsMethods: A novel rice chromosomal segment substitution line (CSSL), i.e., CSSL-Z1357, with significantly increased plant height (PH) and grain length (GL) was identified from CSSLs constructed by using Nipponbare as a receptor and a restorer line Xihui 18 as a donor. Seven agronomic traits of PH, PL, GL, GW, GPP, SPP, and TGW were phenotyped, and REML implemented in HPMIXED of SAS were used to detect the QTL for these traits. Secondary CSSLs were screened out via marker-assisted selection (MAS) to estimate the additive and epistatic effects of detected QTLs, evaluating the potential utilization of pyramiding the target QTLs for yield and quality improvement of rice varieties.Results and DiscussionResults and Discussion: CSSL-Z1357 carried nine segments from Xihui 18 with an average segment length of 4.13 Mb. The results show that the long grain of CSSL-Z1357 was caused by the increased number of surface cells and the length of the inner glume. Thirteen quantitative trait loci were identified via the F2 population of Nipponbare/CSSL-Z1357, including three each for GL (qGL-3, qGL-6, and qGL-7) and PH (qPH-1, qPH-7, and qPH-12I), among which qGL-3 increased GL by 0.23 mm with synergistic allele from CSSL-Z1357. Additionally, three single (S1 to S3), two double (D1, D2), and one triple segment (T1) substitution lines were developed in F3 via MAS. Results show that pyramiding the segments from Chr.3 (qGL-3 and qPH-3), Chr.6 (qGL-6 and qPH-6), and Chr.7 (Null and qPH-7) tended to result in better phenotype of increased GL and PH and decreased grain width, providing a potential basis for enhancing grain yield and quality in rice breeding.

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Natural variation of the BRD2 allele affects plant height and grain size in rice

Cited by 11 publications

References 35 publications

Upstream regulator of genomic imprinting in rice endosperm is a small RNA-associated chromatin remodeler

Upstream regulator of genomic imprinting in rice endosperm is a small RNA-associated chromatin remodeler

Transcriptome and Metabolome Reveal Key Genes from the Plant Hormone Signal Transduction Pathway Regulating Plant Height and Leaf Size in Capsicum baccatum

Detecting and pyramiding target QTL for plant- and grain-related traits via chromosomal segment substitution line of rice

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