Low Temperature Inhibits Root Growth by Reducing Auxin Accumulation via ARR1/12

Zhu, Jiang; Zhang, Kun-Xiao; Wang, Wenshu; Gong, Wenping; Liu, Wen‐Cheng; Hong-guo, Chen; Xu, Heng-Hao; Lu, Ying‐Tang

doi:10.1093/pcp/pcu217

Cited by 108 publications

(80 citation statements)

References 60 publications

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“…We identified in our sweep list the birch ortholog of Arabidopsis transcription factor ARR1, a key regulator of Arabidopsis root meristem size 66 that mediates the balance between cell division and differentiation by integrating auxin and cytokinin responses. ARR1 is involved in cold-induced inhibition of root growth and reduced auxin accumulation 67 , and it also controls Arabidopsis drought susceptibility 68 . This may explain the link to the geographic and temperature variables detected here.…”

Section: Candidate Gene Adaptation Correlates With Environmentmentioning

confidence: 99%

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Salojärvi¹,

Smolander²,

Nieminen³

et al. 2017

Nat Genet

235

253

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Forest ecosystems maintain a large share of Northern Hemisphere biodiversity. Boreal forests comprise roughly 30% of global forest area 1 and contain the highest tree density among climate zones 2 . Moreover, boreal regions are undergoing extensive climate change. Annual temperature increases exceeding 1.5 °C are projected to result in a warming of 4-11 °C by the end of this century, with little concomitant increase in precipitation 1 . At this pace, climate zones will shift northward at a greater speed than trees can migrate 3 . To understand how future populations of forest trees may respond to climate change, it is essential to uncover past and present signatures of molecular adaptation in their genomes. Silver birch, B. pendula, is a pioneer species in boreal forests of Eurasia. Flowering of the species can be artificially accelerated 4 , giving it an advantage over other tree species with published genome sequences (such as poplar 5 , spruce 6 , and pine 7 ) for the optimization of fiber and biomass production.Here we sequenced 150 birch individuals and assembled a B. pendula reference genome from a fourth-generation inbred line, resulting in a high-quality assembly of 435 Mb that was linked to chromosomes using a dense genetic map. We analyzed SNPs in the genomes of 80 birch individuals spanning most of the geographic range of B. pendula, as well as seven other members of Betulaceae. Population genomic analyses of these data provide insights into the deep-time evolution of the birch family and on recent natural selection acting on silver birch.Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightlylinked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.A full list of affiliations appears at the end of the paper.

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Section: Candidate Gene Adaptation Correlates With Environmentmentioning

confidence: 99%

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Salojärvi¹,

Smolander²,

Nieminen³

et al. 2017

Nat Genet

235

253

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“…CRF3 responds to auxin and is unresponsive to auxin in arf7, arf19, and arf7 arf19 mutant backgrounds ( Figure 1A; Supplemental Figure 8), suggesting that auxin may regulate CRF3 expression through ARF7 and ARF19. The previous studies showed that cold temperature inhibits root basipetal auxin transport and reduces auxin accumulation, limiting root growth in Arabidopsis (Shibasaki et al, 2009;Zhu et al, 2015), indicating that cold temperature inhibits auxin transport, biosynthesis, and response in the root. We speculate that the expression of CRF2 and CRF3 in response to cold may be an adaptation mechanism of plants under cold stress, enabling LR initiation and development to overcome the auxinmediated cold-induced inhibition of root growth, thus influencing changes in root system architecture in response to cold.…”

Section: Discussionmentioning

confidence: 96%

“…Cold stress inhibits root basipetal auxin transport by reducing the trafficking of the auxin efflux carrier PIN2 and inhibiting the lateral relocalization of PIN3 in Arabidopsis (Shibasaki et al, 2009). Cold reduces both root meristem size and cell number, repressing the division potential of meristematic cells by reducing auxin accumulation (Zhu et al, 2015). Thus, cold stress inhibits root growth partly by modulating auxin synthesis, transport, and response.…”

Section: Introductionmentioning

confidence: 99%

“…Although the role of type-C ARRs in cytokinin signaling is unclear, it has been proposed that ARR22 plays a positive role in the stress tolerance response (Kang et al, 2012). A subset of the Arabidopsis cytokinin TCS system is utilized for cold stress signaling and response (Jeon et al, 2010;Jeon and Kim, 2013;Zhu et al, 2015). ARR1 mediates the cold signal via AHP2, AHP3, or AHP5 from AHK2 and AHK3 to express a subset of type-A ARRs, regulating cold stress response and tolerance along with cytokinin (Jeon et al, 2010;Jeon and Kim, 2013).…”

Section: Introductionmentioning

confidence: 99%

“…ARR1 mediates the cold signal via AHP2, AHP3, or AHP5 from AHK2 and AHK3 to express a subset of type-A ARRs, regulating cold stress response and tolerance along with cytokinin (Jeon et al, 2010;Jeon and Kim, 2013). ARR1 and ARR12 are also involved in the inhibition of Arabidopsis root growth by low temperature (Zhu et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

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CYTOKININ RESPONSE FACTOR2 (CRF2) and CRF3 Regulate Lateral Root Development in Response to Cold Stress in Arabidopsis

et al. 2016

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ORCID IDs: 0000-0001-7997-1544 (C.C.); 0000-0003-1735-5564 (J.K.)Lateral roots (LRs) are a major determinant of the root system architecture in plants, and developmental plasticity of LR formation is critical for the survival of plants in changing environmental conditions. In Arabidopsis thaliana, genetic pathways have been identified that regulate LR branching in response to numerous environmental cues, including some nutrients, salt, and gravity. However, it is not known how genetic components are involved in the LR adaptation response to cold. Here, we demonstrate that CYTOKININ RESPONSE FACTOR2 (CRF2) and CRF3, encoding APETALA2 transcription factors, play an important role in regulating Arabidopsis LR initiation under cold stress. Analysis of LR developmental kinetics demonstrated that both CRF2 and CRF3 regulate LR initiation. crf2 and crf3 single mutants exhibited decreased LR initiation under cold stress compared with the wild type, and the crf2 crf3 double mutants showed additively decreased LR densities compared with the single mutants. Conversely, CRF2 or CRF3 overexpression caused increased LR densities. CRF2 was induced by cold via a subset of the cytokinin two-component signaling (TCS) pathway, whereas CRF3 was upregulated by cold via TCSindependent pathways. Our results suggest that CRF2 and CRF3 respond to cold via TCS-dependent and TCS-independent pathways and control LR initiation and development, contributing to LR adaptation to cold stress.

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Genome‐wide association analysis of chilling‐tolerant germination in a new maize association mapping panel

Yao

Zhang

et al. 2022

Food and Energy Security

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Maize is a crop that is highly susceptible to the negative effects of low temperature. Low temperature can delay seed germination and cause a decrease in seed vigor, which seriously affects seedling emergence and yield. In this study, 190 maize accessions (inbred lines) with strong germination potential at normal temperature (25℃) were selected from more than 500 accessions to construct a new association mapping panel to further investigate germination under chilling stress (5℃). We re-sequenced the genomes of the 190 diverse accessions and obtained 4,886,919 high quality SNPs. We then used this data to analyze population structure, perform principal components analysis, and construct a phylogenetic tree of the new maize panel. The relative germination rate (RGR) and relative germination index (RGI) are two traits that are signi cantly related to chilling-tolerant germination. Genome-wide association analysis showed that RGR and RGI shared a major QTL, and they also shared the top SNP.There were a total of 26 signi cant SNPs in common. These SNPs hit directly or indirectly within 37 candidate genes. Among these 37 gene candidates are homologs of eight genes previously reported to be related to both germination and low temperature stress, and another 12 genes related to low temperature stress or other abiotic stresses such as drought, salinity, oxidative, and high light stress. In addition, RGR and RGI had another 15 and 26 signi cant SNPs, respectively, which were associated with 17 and 92 candidate genes, respectively. Further qRT-PCR analysis using 26 chilling-tolerant and 22 chilling-sensitive accessions implied that Zm00001eb272370, Zm00001eb272390, and Zm00001eb272400 associated with the top SNP, may play different roles during cold-germination. Thus, our study not only established a new association mapping panel suitable for investigation of germination at low temperature, but also provided valuable genetic resources for future studies to improve chilling-tolerant maize varieties.

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Low Temperature Inhibits Root Growth by Reducing Auxin Accumulation via ARR1/12

Cited by 108 publications

References 60 publications

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

CYTOKININ RESPONSE FACTOR2 (CRF2) and CRF3 Regulate Lateral Root Development in Response to Cold Stress in Arabidopsis

Genome‐wide association analysis of chilling‐tolerant germination in a new maize association mapping panel

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