OsbZIP47 Is an Integrator for Meristem Regulators During Rice Plant Growth and Development

Prakash, Sandhan; Rai, Rashmi; Zamzam, Mohammed M.; Ahmad, Owais; Peesapati, Raghavaram; Vijayraghavan, Usha

doi:10.3389/fpls.2022.865928

Cited by 6 publications

(4 citation statements)

References 111 publications

(169 reference statements)

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“…Likewise, members of the NAC family proteins regulate NAM (no apical meristem), regulate drought stress response in rice ( Jeong et al, 2010 ), salt stress in garlic ( Wang et al, 2022 ), heat stress and grain filling in rice ( Ren et al, 2021 ), floral organ identity and lateral organ separation in Medicago truncatula ( Cheng et al, 2012 ), pattern formation in embryo and flowers in Petunia ( Souer et al, 1996 ), among others. Mutation in the NAM domain resulted in changes in shoot apical meristem (SAM) development in rice ( Prakash et al, 2022 ) or failure to develop SAM in Petunia embryos ( Souer et al, 1996 ). In the same way, mutant plants lacking the NAM showed abnormal organ differentiation in rice embryos ( Nagato et al, 1989 ).…”

Section: Discussionmentioning

confidence: 99%

Genome-wide association study (GWAS) with high-throughput SNP chip DNA markers identified novel genetic factors for mesocotyl elongation and seedling emergence in rice (Oryza sativa L.) using multiple GAPIT models

Kabange,

Alibu,

Kwon

et al. 2023

Front. Genet.

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This study employed a joint strategy high-density SNP Chip DNA markers and multiple Genome Association and Prediction Integrated Tool (GAPIT) models [(Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK), Fixed and random model Circulating Probability Uniform (FarmCPU), General Linear Model (GLM), and Settlement of Mixed Linear Model (MLM) Under Progressively Exclusive Relationship (SUPER)], to investigate novel genetic factors controlling mesocotyl elongation and seedling emergence for direct-seeded rice. Genotype data (230,526 SNP Chip DNA makers) of 117 doubled haploid lines (derived from a cross between 93–11 (Oryza sativa L. ssp. indica) and Milyang352 (O. sativa L. ssp. japonica) were used to perform a Genome-Wide Association Study (GWAS). Results revealed the association between five (5) topmost significant SNP markers, of which number two [AX-155741269, Chr2: 15422406 bp, and AX-155200917, Chr7: 23814085 bp, explaining 37.5% and 13.8% of the phenotypic variance explained (PVE)] are linked to the mesocotyl elongation loci, while three (AX-282097034 and AX-283652873, Chr9: 9882817 bp and 1023383 bp, PVE 64.5%, and 20.2%, respectively, and AX-154356231, Chr1: 17413989 bp, PVE 21.1%) are tightly linked to the loci controlling seedling emergence. The qMEL2-1 and qSEM9-1 are identified as major QTLs explaining 37.5% and 64.5% of the PVE for mesocotyl elongation and seedling emergence, respectively. The AX-282097034 (Chr9: 9882817 bp) was co-detected by four GAPIT models (BLINK, FarmCPU, SUPER, and GLM), while AX-155741269 was co-detected by BLINK and SUPER. Furthermore, a high estimated heritability (Mesocotyl elongation: h2 = 0.955; seedling emergence: h2 = 0.863; shoot length: h2 = 0.707) was observed. Genes harbored by qMEL2-1 and qSEM9-1 have interesting annotated molecular functions that could be investigated through functional studies to uncover their roles during mesocotyl elongation and seedling emergence events in rice. Furthermore, the presence of genes encoding transcription factors, growth- and stress response, or signaling-related genes would suggest that mesocotyl elongation and seedling emergence from deep direct-seeded rice might involve an active signaling cascade and transport of molecules, which could be elucidated through functional analysis. Likewise, genomic selection analysis suggested markers useful for downstream marker-assisted selection (MAS).

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Section: Discussionmentioning

confidence: 99%

Genome-wide association study (GWAS) with high-throughput SNP chip DNA markers identified novel genetic factors for mesocotyl elongation and seedling emergence in rice (Oryza sativa L.) using multiple GAPIT models

Kabange,

Alibu,

Kwon

et al. 2023

Front. Genet.

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“…These loci have been reported to be related to tillering and growth ability in rice. These results suggested the high efficiency of using genetically close model species genes to develop primers for non-model plant species plant growth, development, and tillering traits [68][69][70]. In our previous research, we also screened a large number of genes related to the growth and development of P. juncea, including CKX, IPT, and YUCCA genes.…”

Section: Association Analysis Of P Junceamentioning

confidence: 96%

Association Analysis of Tiller-Related Traits with EST-SSR Markers in Psathyrostachys juncea

Li,

Wang,

Yun

et al. 2023

Genes

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Psathyrostachys juncea is a long-lived perennial Gramineae grass with dense basal tillers and soft leaves. It is used widely in cold and dry areas of Eurasia and North America to establish grazing pasture and is even used as an ideal plant for revegetation and ecological restoration. Plant architecture, especially tillering traits, is critical for bunch grasses in breeding programs, and these traits in plants are mostly quantitative traits. In this study, the genetic diversity, population structure, and linkage disequilibrium of 480 individual lines were analyzed using 127 pairs of the EST-SSR marker, and a significant association between ten plant-architecture-related traits of P. juncea and molecular markers was found. The results of the genetic diversity analysis showed that the number of observed alleles was 1.957, the number of effective alleles was 1.682, Shannon’s information index was 0.554, observed heterozygosity was 0.353, expected heterozygosity was 0.379, and the polymorphism information content was 0.300. A total of 480 individual lines were clustered into five groups based on population genetic structure, principal coordinate analysis, and unweighted pair group method with arithmetic mean analysis (UPGMA). The linkage disequilibrium coefficient (r2) was between 0.00 and 0.68, with an average of 0.04, which indicated a relatively low level of linkage disequilibrium among loci. The results of the association analysis revealed 55 significant marker–trait associations (MTA). Moreover, nine SSR markers were associated with multiple traits. This study provides tools with promising applications in the molecular selection and breeding of P. juncea germplasm.

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“…What is more, mutants of LOC_Os01g59760 (OsbZIP09), encoding a bZIP transcription factor, exhibited longer seeds compared with the wild type [64]. It has been reported that LOC_Os09g34880 (OsbZIP76), LOC_Os06g50600 (OsbZIP55), and LOC_Os06g15480 (OsbZIP47) function as regulators of grain size [65][66][67]. Furthermore, LOC_Os01g59780 encodes a protein that contains an AP2 domain.…”

Section: Candidate Gene Analysis Of the Five Qtlsmentioning

confidence: 99%

Fine Mapping of Five Grain Size QTLs Which Affect Grain Yield and Quality in Rice

Zhou,

Yang,

Liu

et al. 2024

IJMS

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Grain size is a quantitative trait with a complex genetic mechanism, characterized by the combination of grain length (GL), grain width (GW), length to width ration (LWR), and grain thickness (GT). In this study, we conducted quantitative trait loci (QTL) analysis to investigate the genetic basis of grain size using BC1F2 and BC1F2:3 populations derived from two indica lines, Guangzhan 63-4S (GZ63-4S) and TGMS29 (core germplasm number W240). A total of twenty-four QTLs for grain size were identified, among which, three QTLs (qGW1, qGW7, and qGW12) controlling GL and two QTLs (qGW5 and qGL9) controlling GW were validated and subsequently fine mapped to regions ranging from 128 kb to 624 kb. Scanning electron microscopic (SEM) analysis and expression analysis revealed that qGW7 influences cell expansion, while qGL9 affects cell division. Conversely, qGW1, qGW5, and qGW12 promoted both cell division and expansion. Furthermore, negative correlations were observed between grain yield and quality for both qGW7 and qGW12. Nevertheless, qGW5 exhibited the potential to enhance quality without compromising yield. Importantly, we identified two promising QTLs, qGW1 and qGL9, which simultaneously improved both grain yield and quality. In summary, our results laid the foundation for cloning these five QTLs and provided valuable resources for breeding rice varieties with high yield and superior quality.

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OsbZIP47 Is an Integrator for Meristem Regulators During Rice Plant Growth and Development

Cited by 6 publications

References 111 publications

Genome-wide association study (GWAS) with high-throughput SNP chip DNA markers identified novel genetic factors for mesocotyl elongation and seedling emergence in rice (Oryza sativa L.) using multiple GAPIT models

Genome-wide association study (GWAS) with high-throughput SNP chip DNA markers identified novel genetic factors for mesocotyl elongation and seedling emergence in rice (Oryza sativa L.) using multiple GAPIT models

Association Analysis of Tiller-Related Traits with EST-SSR Markers in Psathyrostachys juncea

Fine Mapping of Five Grain Size QTLs Which Affect Grain Yield and Quality in Rice

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