Genomic basis of geographical adaptation to soil nitrogen in rice

Liu, Yongqiang; Wang, Hongru; Jiang, Zhimin; Wang, Wei; Xu, Ruineng; Wang, Qihui; Zhang, Zhihua; Li, Aifu; Liang, Yan; Ou, Shujun; Liu, Xiujie; Cao, Shuting; Tong, Hongning; Wang, Yonghong; Zhou, Feng; Liao, Hong; Hu, Bin; Chu, Chengcai

doi:10.1038/s41586-020-03091-w

Cited by 254 publications

(179 citation statements)

References 41 publications

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“…This raises an interesting question of whether these noncoding DNA regions have also contributed to the adaptations, divergence, and domestication of soybean, which is worth further investigation. Variations in noncoding regions have been reported as important resources for crop domestication in maize [ 33 ] and rice [ 34 ]. In maize, the increased apical dominance of the maize TEOSINTE BRANCHED 1 (tb1) mutant is due to a transposon insertion into the maize distal enhancer within the dOCR.…”

Section: Discussionmentioning

confidence: 99%

Genomic Features of Open Chromatin Regions (OCRs) in Wild Soybean and Their Effects on Gene Expressions

Huang

Zhang

Zhou

et al. 2021

Genes

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Transcription activation is tightly associated with the openness of chromatin, which allows direct contact between transcriptional regulators, such as transcription factors, and their targeted DNA for downstream gene activation. However, the annotation of open chromatin regions (OCRs) in the wild soybean (Glycine soja) genome is limited. We performed assay for transposase-accessible chromatin using sequencing (ATAC-seq) and successfully identified 22,333 OCRs in the leaf of W05 (a wild soybean accession). These OCRs were enriched in gene transcription start sites (TSS) and were positively correlated with downstream gene expression. Several known transcription factor (TF)-binding motifs were also enriched at the OCRs. A potential regulatory network was constructed using these transcription factors and the OCR-marked genes. Furthermore, by overlapping the OCR distribution with those of histone modifications from chromatin immunoprecipitation followed by sequencing (ChIP-seq), we found that the distribution of the activation histone mark, H3K4me3, but not that of the repressive H3K27me3 mark, was closely associated with OCRs for gene activation. Several putative enhancer-like distal OCRs were also found to overlap with LincRNA-encoding loci. Moreover, our data suggest that homologous OCRs could potentially influence homologous gene expression. Hence, the duplication of OCRs might be essential for plant genome architecture as well as for regulating gene expression.

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Section: Discussionmentioning

confidence: 99%

Genomic Features of Open Chromatin Regions (OCRs) in Wild Soybean and Their Effects on Gene Expressions

Huang

Zhang

Zhou

et al. 2021

Genes

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“…Recently, it has been reported that Os TCP19 can negatively regulate rice tillering by affecting the transcription of DLT , a downstream gene target of brassinosteroid (BR) signaling in rice (Liu et al, 2021). In addition, FC1, a TCP protein, acts downstream of the SL and BR signaling pathways and negatively affects tillering in rice (Takeda et al, 2003; Fang et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

MiR319‐targeted OsTCP21 and OsGAmyb regulate tillering and grain yield in rice

Wang

Yang

Guo

et al. 2021

JIPB

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Multiple genes and microRNAs (miRNAs) improve grain yield by promoting tillering. MiR319s are known to regulate several aspects of plant development; however, whether miR319s are essential for tillering regulation remains unclear. Here, we report that miR319 is highly expressed in the basal part of rice plant at different development stages. The miR319 knockdown line Short Tandem Target Mimic 319 (STTM319) showed higher tiller bud length in seedlings under low nitrogen (N) condition and higher tiller bud number under high N condition compared with the miR319a‐overexpression line. Through targets prediction, we identified OsTCP21 and OsGAmyb as downstream targets of miR319. Moreover, OsTCP21 and OsGAmyb overexpression lines and STTM319 had increased tiller bud length and biomass, whereas both were decreased in OsTCP21 and OsGAmyb knockout lines and OE319a. These data suggest that miR319 regulates rice tiller bud development and tillering through targeting OsTCP21 and OsGAmyb. Notably, the tiller number and grain yield increased in STTM319 and overexpression lines of OsTCP21 and OsGAmyb but decreased in OE319a and knockout lines of OsTCP21 and OsGAmyb. Taken together, our findings indicate that miR319s negatively affect tiller number and grain yield by targeting OsTCP21 and OsGAmyb, revealing a novel function for miR319 in rice.

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“…Its achievements are four‐fold: (1) it identifies metabolic predictors of salt tolerance; (2) it identifies candidate genes underlying metabolic aspects of salt tolerance; (3) it validates these candidates and carries out detailed evaluation of the underlying haplotypes; and (4) it proves that superior alleles can be bred into elite varieties and confer tolerance. Whilst similar progresses have been reported previously (Fernie & Gutierrez‐Marcos, 2019; Liu et al ., 2020; Liu et al ., 2021), it is very rare that work of this scope is described in a single article. As such, this article is an incredible resource.…”

Section: Figmentioning

confidence: 99%