Tetratricopeptide repeat protein SlREC2 positively regulates cold tolerance in tomato

Zhang, Ying; Peng, Yinxia; Liu, Juan; Yan, Jiarong; Zhu, Kangyou; Sun, Xin; Bu, Xin; Wang, Xiujie; Ahammed, Golam Jalal; Liu, Yufeng; Sun, Zenghui; Qi, Mingfang; Wang, Feng; Li, Tianlai

doi:10.1093/plphys/kiad085

Cited by 13 publications

(5 citation statements)

References 77 publications

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“…RPM1 is a famous resistance (R) gene that affects plant disease resistance and morphology, which could act on ABC to resist cellular oxidative stress and prevent the invasion of pathogens. Recent research has suggested that this gene cluster may play a role in regulating light responses in grapes (Zhang et al, 2023). Many selected loci related to SVs are enriched in different KEGG pathways, which could be related to coastal adaptation (Figure 5B).…”

Section: Resultsmentioning

confidence: 99%

Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape

Zhang,

Peng,

Xiao

et al. 2024

JIPB

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Structural variations (SVs) are a feature of plant genomes that has been largely unexplored despite their significant impact on plant phenotypic traits and local adaptation to abiotic and biotic stress. In this study, we employed woolly grape (Vitis retordii), a species native to the tropical and subtropical regions of East Asia with both coastal and inland habitats, as a valuable model for examining the impact of SVs on local adaptation. We assembled a haplotype‐resolved chromosomal reference genome for woolly grape, and conducted population genetic analyses based on whole‐genome sequencing (WGS) data from coastal and inland populations. The demographic analyses revealed recent bottlenecks in all populations and asymmetric gene flow from the inland to the coastal population. In total, 1,035 genes associated with plant adaptive regulation for salt stress, radiation, and environmental adaptation were detected underlying local selection by SVs and SNPs in the coastal population, of which 37.29% and 65.26% were detected by SVs and SNPs, respectively. Candidate genes such as FSD2, RGA1, and AAP8 associated with salt tolerance were found to be highly differentiated and selected during the process of local adaptation to coastal habitats in SV regions. Our study highlights the importance of SVs in local adaptation; candidate genes related to salt stress and climatic adaptation to tropical and subtropical environments are important genomic resources for future breeding programs of grapevine and its rootstocks.

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Section: Resultsmentioning

confidence: 99%

Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape

Zhang,

Peng,

Xiao

et al. 2024

JIPB

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“…3, Table 2). TraesCS3B03G0028100 encodes a tetratricopeptide repeat (TPR) protein, which is involved in a variety of processes, such as peroxisomal import, mitochondrial and chloroplastic import, synaptic vesicle fusion and cold tolerance of plant (Zhang et al 2023). TPRs are also reported to participate in plant immune regulation.…”

Section: Discussionmentioning

confidence: 99%

High density mapping of durable and broad-spectrum stripe rust resistance gene Yr30 in wheat

Wang,

Xiang,

et al. 2024

Preprint

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Stripe rust is a global fungal disease that is a serious threat to wheat. Durable resistance is the most effective method of control. Yr30, an adult plant resistance (APR) gene with broad-spectrum effectiveness, was located in the putatively pleiotropic locus or QTL that harbors genes Sr2, Lr27, Pm70, Sb3 and Pbc1. Although the locus has been widely deployed worldwide to achieve durable resistance for over a centenary little is known about the genetic relationship and causal genes because of the effects are small and inconstant in different genetic backgrounds and environments. In this study, we identified a residual heterozygous line (RHL), YM91, derived from Yaco"S"/Mingxian169 F5:6 RIL population, where Yr30 was present alone, resistance was identified as dominant and clearly distinguishable. Through selection of heterozygous plants in YM91, a large mapping population was developed. Yr30 was fine-mapped to a 0.52-cM interval between KASP markers AX-109525141 and YM3B-7 corresponding to a physical distance of 610 kb on chromosome 3BS. A candidate gene TraesCS3B03G0028100 encoding tetratricopeptide repeat protein was identified for Yr30 from 30 high-confidence genes within the interval based on the expression level and sequence variation in whole genome RNA-seq data of cultivars with or without Yr30. Six haplotypes (Hap1-6) were identified among 1,215 wheat accessions based on the 660K array and Yr30-haplotype Hap6 conferred equal or higher resistance than the other five haplotypes. These results will accelerate map-based cloning and molecular-assisted selection of Yr30, a likely source of durable resistance.

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“…The regulatory mechanisms of LT response are complex and dynamic processes ( Ding et al., 2019 ; Ding and Yang, 2022 ; Kidokoro et al., 2022 ), involving the perception of signals at the cytomembrane, transduction of the signal from the cytomembrane to the cell nucleus, and the activation of regulatory mechanisms in the cell nucleus. Correspondingly, multiple factors participate in the LT regulatory response, including, transcription factors PPR ( Xing et al., 2018 ), NAC ( Zhuo et al., 2018 ; Liu et al., 2020a ), GRAS ( Wang et al., 2021 ; Li et al., 2022a ), bZIP ( Li et al., 2022b ) and WRKY ( Liu et al., 2022b ; Sun et al., 2022a ; Zhang et al., 2022 ; Zhao et al., 2022 ), phytohormones ABA ( Zhu, 2016 ; Song et al., 2022 ; Zhang et al., 2023 ), JA ( Li et al., 2021 ; Sun et al., 2022b ) and GA ( Magome et al., 2004 ; Achard et al., 2008 ) and various metabolic pathways especially those producing compatible solutes. In this study, ten genes in the GWAS regions, possibly related to abiotic stress were identified ( Table S8 ).…”

Section: Discussionmentioning

confidence: 99%

GWAS reveals novel loci and identifies a pentatricopeptide repeat-containing protein (CsPPR) that improves low temperature germination in cucumber

Dong

Beckles

et al. 2023

Front. Plant Sci.

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Low temperatures (LTs) negatively affect the percentage and rate of cucumber (Cucumis sativus L.) seed germination, which has deleterious effects on yield. Here, a genome-wide association study (GWAS) was used to identify the genetic loci underlying low temperature germination (LTG) in 151 cucumber accessions that represented seven diverse ecotypes. Over two years, phenotypic data for LTG i.e., relative germination rate (RGR), relative germination energy (RGE), relative germination index (RGI) and relative radical length (RRL), were collected in two environments, and 17 of the 151 accessions were found to be highly cold tolerant using cluster analysis. A total of 1,522,847 significantly associated single-nucleotide polymorphism (SNP) were identified, and seven loci associated with LTG, on four chromosomes, were detected: gLTG1.1, gLTG1.2, gLTG1.3, gLTG4.1, gLTG5.1, gLTG5.2, and gLTG6.1 after resequencing of the accessions. Of the seven loci, three, i.e., gLTG1.2, gLTG4.1, and gLTG5.2, showed strong signals that were consistent over two years using the four germination indices, and are thus strong and stable for LTG. Eight candidate genes associated with abiotic stress were identified, and three of them were potentially causal to LTG: CsaV3_1G044080 (a pentatricopeptide repeat-containing protein) for gLTG1.2, CsaV3_4G013480 (a RING-type E3 ubiquitin transferase) for gLTG4.1, and CsaV3_5G029350 (a serine/threonine-protein kinase) for gLTG5.2. The function for CsPPR (CsaV3_1G044080) in regulating LTG was confirmed, as Arabidopsis lines ectopically expressing CsPPR showed higher germination and survival rates at 4°C compared to the wild-type, which preliminarily illustrates that CsPPR negatively regulates cucumber cold tolerance at the germination stage. This study will provide insights into cucumber LT-tolerance mechanisms and further promote cucumber breeding development.

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Tetratricopeptide repeat protein SlREC2 positively regulates cold tolerance in tomato

Cited by 13 publications

References 77 publications

Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape

Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape

High density mapping of durable and broad-spectrum stripe rust resistance gene Yr30 in wheat

GWAS reveals novel loci and identifies a pentatricopeptide repeat-containing protein (CsPPR) that improves low temperature germination in cucumber

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