Differentially Regulated Orthologs in Sorghum and the Subgenomes of Maize

Zhang, Yang; Ngu, Daniel W.; Carvalho, Daclé Vilma; Liang, Zhikai; Qiu, Yumou; Roston, Rebecca; Schnable, James C.

doi:10.1105/tpc.17.00354

Cited by 68 publications

(47 citation statements)

References 78 publications

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“…ZCN12 expression also tightly correlated with that of ZCN8 (r = 0.76, Fig 2B and S6B Fig), suggesting common regulatory mechanisms. This was in contrast to the ZCN7 expression that displayed low heritability (narrow sense h 2 = 0.11, S1 Table) and a weaker correlation with flowering time (r = -0.31, S6C Fig) than ZCN8, despite synteny [30] and shared biochemical functions [31]. ZCN7 and ZCN8 expressions were also weakly correlated (S6C Fig).…”

Section: Zcn12 Is a Novel Regulator Of Maize Flowering And It Is Co-ementioning

confidence: 87%

“…Besides confirming the role of ZCN8 in flowering time regulation we also uncover the role of ZCN12 in this process. Interestingly ZCN12 is more distantly related to ZCN8 than ZCN7 [12] and located in a region which is not syntenic to ZCN8 [30], yet it underwent a similar regulatory trajectory to ZCN8 as shown by the strong co-variation across different lines and experiments.…”

Section: Zcn12 and Zcn8 Are Co-regulated By Trans-acting Factors To Cmentioning

confidence: 96%

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Maize adaptation across temperate climates was obtained via expression of two florigen genes

et al. 2020

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Expansion of the maize growing area was central for food security in temperate regions. In addition to the suppression of the short-day requirement for floral induction, it required breeding for a large range of flowering time that compensates the effect of South-North gradients of temperatures. Here we show the role of a novel florigen gene, ZCN12, in the latter adaptation in cooperation with ZCN8. Strong eQTLs of ZCN8 and ZCN12, measured in 327 maize lines, accounted for most of the genetic variance of flowering time in platform and field experiments. ZCN12 had a strong effect on flowering time of transgenic Arabidopsis thaliana plants; a path analysis showed that it directly affected maize flowering time together with ZCN8. The allelic composition at ZCN QTLs showed clear signs of selection by breeders. This suggests that florigens played a central role in ensuring a large range of flowering time, necessary for adaptation to temperate areas.

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Section: Zcn12 Is a Novel Regulator Of Maize Flowering And It Is Co-ementioning

confidence: 87%

Section: Zcn12 and Zcn8 Are Co-regulated By Trans-acting Factors To Cmentioning

confidence: 96%

Maize adaptation across temperate climates was obtained via expression of two florigen genes

et al. 2020

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“…officinalis loci corresponded to a single locus in Nipponbare, loci with the most stable mapping was used. Establishment of orthologous gene pairs for subsequent genome-wide comparison of gene expression and cis-element analysis were guided by established computational logic 5 , 53 .…”

Section: Methodsmentioning

confidence: 99%

Potential of Oryza officinalis to augment the cold tolerance genetic mechanisms of Oryza sativa by network complementation

Kitazumi

Pabuayon

Ohyanagi

et al. 2018

Sci Rep

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Oryza officinalis is an accessible alien donor for genetic improvement of rice. Comparison across a representative panel of Oryza species showed that the wild O. officinalis and cultivated O. sativa ssp. japonica have similar cold tolerance potentials. The possibility that either distinct or similar genetic mechanisms are involved in the low temperature responses of each species was addressed by comparing their transcriptional networks. General similarities were supported by shared transcriptomic signatures indicative of equivalent metabolic, hormonal, and defense status. However, O. officinalis has maintained an elaborate cold-responsive brassinosteroid-regulated BES1-network that appeared to have been fragmented in O. sativa. BES1-network is potentially important for integrating growth-related responses with physiological adjustments and defenses through the protection of photosynthetic machinery and maintenance of stomatal aperture, oxidative defenses, and osmotic adjustment. Equivalent physiological processes are functional in O. sativa but their genetic mechanisms are under the direct control of ABA-dependent, DREB-dependent and/or oxidative-mediated networks uncoupled to BES1. While O. officinalis and O. sativa represent long periods of speciation and domestication, their comparable cold tolerance potentials involve equivalent physiological processes but distinct genetic networks. BES1-network represents a novel attribute of O. officinalis with potential applications in diversifying or complementing other mechanisms in the cultivated germplasm.

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“…The protein sequences of the m 6 A functional factors were used for a BLAST search in the sorghum genome, with a threshold of E value ≤ 10 −5 . The best BLAST hits in sorghum were also verified by the gene orthology between maize and sorghum (Zhang et al, 2017).…”

Section: Expression Of Sorghum M 6 a Functional Factorsmentioning

confidence: 99%

Profiling Alternative 3′ Untranslated Regions in Sorghum using RNA-seq Data

2020

Front. Genet.

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Sorghum is an important crop widely used for food, feed, and fuel. Transcriptomewide studies of 3 untranslated regions (3 UTR) using regular RNA-seq remain scarce in sorghum, while transcriptomes have been characterized extensively using Illumina short-read sequencing platforms for many sorghum varieties under various conditions or developmental contexts. 3 UTR is a critical regulatory component of genes, controlling the translation, transport, and stability of messenger RNAs. In the present study, we profiled the alternative 3 UTRs at the transcriptome level in three genetically related but phenotypically contrasting lines of sorghum: Rio, BTx406, and R9188. A total of 1,197 transcripts with alternative 3 UTRs were detected using RNA-seq data. Their categorization identified 612 high-confidence alternative 3 UTRs. Importantly, the highconfidence alternative 3 UTR genes significantly overlapped with the genesets that are associated with RNA N 6-methyladenosine (m 6 A) modification, suggesting a clear indication between alternative 3 UTR and m 6 A methylation in sorghum. Moreover, taking advantage of sorghum genetics, we provided evidence of genotype specificity of alternative 3 UTR usage. In summary, our work exemplifies a transcriptome-wide profiling of alternative 3 UTRs using regular RNA-seq data in non-model crops and gains insights into alternative 3 UTRs and their genotype specificity.

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Differentially Regulated Orthologs in Sorghum and the Subgenomes of Maize

Cited by 68 publications

References 78 publications

Maize adaptation across temperate climates was obtained via expression of two florigen genes

Maize adaptation across temperate climates was obtained via expression of two florigen genes

Potential of Oryza officinalis to augment the cold tolerance genetic mechanisms of Oryza sativa by network complementation

Profiling Alternative 3′ Untranslated Regions in Sorghum using RNA-seq Data

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