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Nebli S, Rebai A, Ayadi I. Screening clusters of charged residues in plants' mitochondrial proteins and biological significance. Mitochondrion 2024; 78:101938. [PMID: 39013535 DOI: 10.1016/j.mito.2024.101938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 07/09/2024] [Accepted: 07/12/2024] [Indexed: 07/18/2024]
Abstract
Protein function is dependent on charge interactions and charge biased regions, which are involved in a wide range of cellular and biochemical processes. We report the development of a new algorithm implemented in Python and its use to identify charge clusters CC (NegativeCC: NCC, PositiveCC: PCC and MixedCC: MCC) and compare their presence in mitochondrial proteins of plant groups. To characterize the resulting CC, statistical, structural and functional analyses were conducted. The screening of 105 399 protein sequences showed that 2.6 %, 0.48 % and 0.03 % of the proteins contain NCC, PCC and MCC, respectively. Mitochondrial proteins encoded by the nuclear genome of green algae have the biggest proportion of both PCC (1.6 %) and MCC (0.4 %) and mitochondrial proteins coded by the nuclear genome of other plants group have the highest portion of NCC (7.5 %). The mapping of the identified CC showed that they are mainly located in the terminal regions of the protein. Annotation showed that proteins with CC are classified as binding proteins, are included in the transmembrane transport processes, and are mainly located in the membrane. The CC scanning revealed the presence of 2373 and 784 sites and 192 and 149 motif profiles within NCC and PCC, respectively. The investigation of CC within pentatricopeptide repeat-containing proteins revealed that they are involved in correct and specific RNA editing. CC were proven to play a key role in providing insightful structural and functional information of complex protein assemblies which could be useful in biotechnological applications.
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Affiliation(s)
- Syrine Nebli
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, P. O. Box 1177, 3018 Sfax, Tunisia.
| | - Ahmed Rebai
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, P. O. Box 1177, 3018 Sfax, Tunisia.
| | - Imen Ayadi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, P. O. Box 1177, 3018 Sfax, Tunisia.
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Molitor C, Kurowski TJ, Fidalgo de Almeida PM, Kevei Z, Spindlow DJ, Chacko Kaitholil SR, Iheanyichi JU, Prasanna HC, Thompson AJ, Mohareb FR. A chromosome-level genome assembly of Solanum chilense, a tomato wild relative associated with resistance to salinity and drought. FRONTIERS IN PLANT SCIENCE 2024; 15:1342739. [PMID: 38525148 PMCID: PMC10957597 DOI: 10.3389/fpls.2024.1342739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/12/2024] [Indexed: 03/26/2024]
Abstract
Introduction Solanum chilense is a wild relative of tomato reported to exhibit resistance to biotic and abiotic stresses. There is potential to improve tomato cultivars via breeding with wild relatives, a process greatly accelerated by suitable genomic and genetic resources. Methods In this study we generated a high-quality, chromosome-level, de novo assembly for the S. chilense accession LA1972 using a hybrid assembly strategy with ~180 Gbp of Illumina short reads and ~50 Gbp long PacBio reads. Further scaffolding was performed using Bionano optical maps and 10x Chromium reads. Results The resulting sequences were arranged into 12 pseudomolecules using Hi-C sequencing. This resulted in a 901 Mbp assembly, with a completeness of 95%, as determined by Benchmarking with Universal Single-Copy Orthologs (BUSCO). Sequencing of RNA from multiple tissues resulting in ~219 Gbp of reads was used to annotate the genome assembly with an RNA-Seq guided gene prediction, and for a de novo transcriptome assembly. This chromosome-level, high-quality reference genome for S. chilense accession LA1972 will support future breeding efforts for more sustainable tomato production. Discussion Gene sequences related to drought and salt resistance were compared between S. chilense and S. lycopersicum to identify amino acid variations with high potential for functional impact. These variants were subsequently analysed in 84 resequenced tomato lines across 12 different related species to explore the variant distributions. We identified a set of 7 putative impactful amino acid variants some of which may also impact on fruit development for example the ethylene-responsive transcription factor WIN1 and ethylene-insensitive protein 2. These variants could be tested for their ability to confer functional phenotypes to cultivars that have lost these variants.
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Affiliation(s)
- Corentin Molitor
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom
| | - Tomasz J. Kurowski
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom
| | | | - Zoltan Kevei
- Soil, Agrifood and Biosciences, Cranfield University, Wharley End, United Kingdom
| | - Daniel J. Spindlow
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom
| | - Steffimol R. Chacko Kaitholil
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom
| | - Justice U. Iheanyichi
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom
| | - H. C. Prasanna
- Division of Vegetable Crops, ICAR-Indian Institute of Horticultural Research, Bangalore, India
| | - Andrew J. Thompson
- Soil, Agrifood and Biosciences, Cranfield University, Wharley End, United Kingdom
| | - Fady R. Mohareb
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom
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Feng X, Guan H, Wen Y, Zhou H, Xing X, Li Y, Zheng D, Wang Q, Zhang W, Xiong H, Hu Y, Jia L, Luo S, Zhang X, Guo W, Wu F, Xu J, Liu Y, Lu Y. Profiling the selected hotspots for ear traits in two maize-teosinte populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:74. [PMID: 38451289 DOI: 10.1007/s00122-024-04554-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 01/12/2024] [Indexed: 03/08/2024]
Abstract
KEY MESSAGE Eight selected hotspots related to ear traits were identified from two maize-teosinte populations. Throughout the history of maize cultivation, ear-related traits have been selected. However, little is known about the specific genes involved in shaping these traits from their origins in the wild progenitor, teosinte, to the characteristics observed in modern maize. In this study, five ear traits (kernel row number [KRN], ear length [EL], kernel number per row [KNR], cob diameter [CD], and ear diameter [ED]) were investigated, and eight quantitative trait loci (QTL) hotspots were identified in two maize-teosinte populations. Notably, our findings revealed a significant enrichment of genes showing a selection signature and expressed in the ear in qbdCD1.1, qbdCD5.1, qbpCD2.1, qbdED1.1, qbpEL1.1, qbpEL5.1, qbdKNR1.1, and qbdKNR10.1, suggesting that these eight QTL are selected hotspots involved in shaping the maize ear. By combining the results of the QTL analysis with data from previous genome-wide association study (GWAS) involving two natural panels, we identified eight candidate selected genes related to KRN, KNR, CD, and ED. Among these, considering their expression pattern and sequence variation, Zm00001d025111, encoding a WD40/YVTN protein, was proposed as a positive regulator of KNR. This study presents a framework for understanding the genomic distribution of selected loci crucial in determining ear-related traits.
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Affiliation(s)
- Xuanjun Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, 611130, Sichuan, China
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Huarui Guan
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Ying Wen
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Hanmei Zhou
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Xiaobin Xing
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Yinzhi Li
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Dan Zheng
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Qingjun Wang
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Weixiao Zhang
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Hao Xiong
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Yue Hu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Li Jia
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Shuang Luo
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Xuemei Zhang
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Wei Guo
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Fengkai Wu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Jie Xu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Yaxi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Yanli Lu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, 611130, Sichuan, China.
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China.
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Liang H, He Q, Zhang H, Zhi H, Tang S, Wang H, Meng Q, Jia G, Chang J, Diao X. Identification and haplotype analysis of SiCHLI: a gene for yellow-green seedling as morphological marker to accelerate foxtail millet (Setaria italica) hybrid breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:24. [PMID: 36739566 DOI: 10.1007/s00122-023-04309-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
We cloned and developed functional markers for the SiCHLI gene, which is responsible for the yellow-green color of leaves in foxtail millet, a frequently used marker trait in the hybrid breeding of foxtail millet by using bulked segregant analysis sequencing and haplotype analysis on the F2 and core-collected nature populations. The color of leaves has been widely used as a marker for the hybrid breeding of foxtail millet; however, few related gene have been cloned to date. Here, we used two F2 populations generated from crosses between the highly male-sterile material 125A with yellow-green leaves, and CG58 and S410, which have green leaves, to identify the genes underlying the yellow-green color of the leaves of foxtail millet. The leaves of 125A seedlings were yellow-green, but they became green at the heading stage. The content of chlorophyll a and chlorophyll b was lower, the number of thylakoid lamellae and grana was reduced, and the chloroplasts was more rounded in 125A than in S410 at the yellow-green leaf stage; however, no differences were observed between 125A and S410 in these traits and photosynthetic at the heading stage. Bulked segregant analysis and map-based cloning revealed that the SiCHLI gene is responsible for the leaf colors of 125A. A nonsynonymous mutation (C/T) in exon 3 causes yellow-green leaves in 125A at the seedling stage. Haplotype analysis of the SiCHLI gene in 596 core collected accessions revealed a new haplotype associated with high photosynthetic metabolic potential at the heading and mature stages, which could be used to enhance sterile lines with yellow-green leaves. We developed a functional marker that will facilitate the identification of foxtail millet accessions with the different types of yellow-green leaves. Generally, our study provides new genetic resources to guide the future marker-assisted or target-base editing in foxtail millet hybrid breeding.
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Affiliation(s)
- Hongkai Liang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Hui Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Hui Zhi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Hailong Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Qiang Meng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Jinhua Chang
- College of Agronomy, Agricultural University of Hebei, Baoding, 071001, China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China.
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Feng X, Jia L, Cai Y, Guan H, Zheng D, Zhang W, Xiong H, Zhou H, Wen Y, Hu Y, Zhang X, Wang Q, Wu F, Xu J, Lu Y. ABA-inducible DEEPER ROOTING 1 improves adaptation of maize to water deficiency. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2077-2088. [PMID: 35796628 PMCID: PMC9616520 DOI: 10.1111/pbi.13889] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/31/2022] [Accepted: 07/03/2022] [Indexed: 05/26/2023]
Abstract
Root architecture remodelling is critical for forage moisture in water-limited soil. DEEPER ROOTING 1 (DRO1) in Oryza, Arabidopsis, and Prunus has been reported to improve drought avoidance by promoting roots to grow downward and acquire water from deeper soil. In the present study, we found that ZmDRO1 responded more strongly to abscisic acid (ABA)/drought induction in Zea mays ssp. mexicana, an ancestral species of cultivated maize, than in B73. It was proposed that this is one of the reasons why Zea mays ssp. mexicana has a more noticeable change in the downward direction angle of the root and fewer biomass penalties under water-deficient conditions. Thus, a robust, synthetic ABA/drought-inducible promoter was used to control the expression of ZmDRO1B73 in Arabidopsis and cultivated maize for drought-resistant breeding. Interestingly, ABA-inducible ZmDRO1 promoted a larger downward root angle and improved grain yield by more than 40% under water-limited conditions. Collectively, these results revealed that different responses to ABA/drought induction of ZmDRO1 confer different drought avoidance abilities, and we demonstrated the application of ZmDRO1 via an ABA-inducible strategy to alter the root architecture of modern maize to improve drought adaptation in the field.
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Affiliation(s)
- Xuanjun Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
- Maize Research Institute, Sichuan Agricultural UniversityWenjingChina
| | - Li Jia
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
| | - Yunting Cai
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
| | - Huarui Guan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
| | - Dan Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
| | - Weixiao Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
| | - Hao Xiong
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
| | - Hanmei Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
| | - Ying Wen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
| | - Yue Hu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
| | - Xuemei Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
| | - Qingjun Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
| | - Fengkai Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
| | - Jie Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
| | - Yanli Lu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
- Maize Research Institute, Sichuan Agricultural UniversityWenjingChina
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Xiao Y, Yu Y, Xie L, Li K, Guo X, Li G, Liu J, Li G, Hu J. A genome-wide association study of folates in sweet corn kernels. FRONTIERS IN PLANT SCIENCE 2022; 13:1004455. [PMID: 36247547 PMCID: PMC9562826 DOI: 10.3389/fpls.2022.1004455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/02/2022] [Indexed: 06/10/2023]
Abstract
Folate is commonly synthesized in natural plants and is an essential water-soluble vitamin of great importance inhuman health. Although the key genes involved in folate biosynthesis and transformation pathways have been identified in plants, the genetic architecture of folate in sweet corn kernels remain largely unclear. In this study, an association panel of 295 inbred lines of sweet corn was constructed. Six folate derivatives were quantified in sweet corn kernels at 20 days after pollination and a total of 95 loci were identified for eight folate traits using a genome-wide association study. A peak GWAS signal revealed that natural variation in ZmFCL, encoding a 5-formyltetrahydrofolate cyclo-ligase, accounted for 30.12% of phenotypic variation in 5-FTHF content. Further analysis revealed that two adjacent SNPs on the second exon resulting in an AA-to-GG in the gene and an Asn-to-Gly change in the protein could be the causative variant influencing 5-FTHF content. Meanwhile, 5-FTHF content was negatively correlated with ZmFCL expression levels in the population. These results extend our knowledge regarding the genetic basis of folate and provide molecular markers for the optimization of folate levels in sweet corn kernels.
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Affiliation(s)
- Yingni Xiao
- Crops Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, China
| | - Yongtao Yu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, China
| | - Lihua Xie
- Crops Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, China
| | - Kun Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, China
| | - Xinbo Guo
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Guangyu Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, China
| | - Jianhua Liu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, China
| | - Gaoke Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, China
| | - Jianguang Hu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, China
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