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Ren J, Li W, Guo Z, Ma Z, Wan D, Lu S, Guo L, Gou H, Chen B, Mao J. Whole-genome resequencing and transcriptome analyses of four generation mutants to reveal spur-type and skin-color related genes in apple (Malus domestica Borkh. Cv. Red delicious). BMC PLANT BIOLOGY 2023; 23:607. [PMID: 38030998 PMCID: PMC10688089 DOI: 10.1186/s12870-023-04631-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 11/24/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND Bud sport is a kind of somatic mutation that usually occurred in apple. 'Red Delicious' is considered to be a special plant material of bud sport, whereas the genetic basis of plant mutants is still unknown. In this study, we used whole-genome resequencing and transcriptome sequencing to identify genes related to spur-type and skin-color in the 'Red Delicious' (G0) and its four generation mutants including 'Starking Red' (G1), 'Starkrimson' (G2), 'Campbell Redchief' (G3) and 'Vallee Spur' (G4). RESULTS The number of single nucleotide polymorphisms (SNPs), insertions and deletions (InDels) and structural variations (SVs) were decreased in four generation mutants compared to G0, and the number of unique SNPs and InDels were over 9-fold and 4-fold higher in G1 versus (vs.) G2 and G2 vs. G3, respectively. Chromosomes 2, 5, 11 and 15 carried the most SNPs, InDels and SVs, while chromosomes 1 and 6 carried the least. Meanwhile, we identified 4,356 variation genes by whole-genome resequencing and transcriptome, and obtained 13 and 16 differentially expressed genes (DEGs) related to spur-type and skin-color by gene expression levels. Among them, DELLA and 4CL7 were the potential genes that regulate the difference of spur-type and skin-color characters, respectively. CONCLUSIONS Our study identified potential genes associated with spur-type and skin-color differences in 'Red Delicious' and its four generation mutants, which provides a theoretical foundation for the mechanism of the apple bud sport.
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Affiliation(s)
- Jiaxuan Ren
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Wenfang Li
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Zhigang Guo
- Tianshui Normal University, Tianshui, 741001, PR China
| | - Zonghuan Ma
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Dongshi Wan
- College of Ecology, Lanzhou University, Lanzhou, 730000, PR China
| | - Shixiong Lu
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Lili Guo
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Huimin Gou
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Baihong Chen
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China.
| | - Juan Mao
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China.
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Yang F, Yuan Y, Liu Q, Zhang X, Gai S, Jin Y, Cheng K. Artificial humic acid promotes growth of maize seedling under alkali conditions. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 327:121588. [PMID: 37028787 DOI: 10.1016/j.envpol.2023.121588] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/02/2023] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
Salinization of cropland is one of the major abiotic stresses affecting global agricultural sustainability, posing a serious threat to agricultural productivity and food security. Application of artificial humic acid (A-HA) as plant biostimulants has been increasingly attracting farmers and researchers. However, its regulation of seed germination and growth under alkali stress has rarely received attention. The purpose of this study was to investigate the response of maize (Zea mays L.) seed germination and seedling growth after the addition of A-HA. The effects of A-HA on seed germination, seedling growth, chlorophyll contents and osmoregulation substance under black and saline soil conditions were studied by soaking maize in solutions with and without various concentrations of A-HA. Artificial humic acid treatments significantly increased the seed germination index and dry weight of seedlings. The effects of maize root in absence and presence of A-HA under alkali stress were also evaluated using transcriptome sequencing. GO and KEGG analyzes were performed on differentially expressed genes, and the reliability of transcriptome data was verified by qPCR analysis. Results showed that A-HA significantly activated phenylpropanoid biosynthesis, oxidative phosphorylation pathways and plant hormone signal transduction. Moreover, Transcription factor analysis revealed that A-HA induced the expression of several transcription factors under alkali stress which had a regulatory effect on the alleviation of alkali damage in the root system. Overall, our results suggested that soaking seeds with A-HA can alleviate alkali accumulation and toxicity in maize, constituting a simple and effective strategy to mitigate saline toxicity. These results will provide new insights for the application of A-HA in management to reduce alkali-caused crop loss.
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Affiliation(s)
- Fan Yang
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin, 150030, China; Joint Laboratory of Northeast Agricultural University and Max Planck Institute of Colloids and Interfaces (NEAU-MPICI), Harbin, 150030, China.
| | - Yue Yuan
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin, 150030, China; Joint Laboratory of Northeast Agricultural University and Max Planck Institute of Colloids and Interfaces (NEAU-MPICI), Harbin, 150030, China
| | - Qingyu Liu
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin, 150030, China; Joint Laboratory of Northeast Agricultural University and Max Planck Institute of Colloids and Interfaces (NEAU-MPICI), Harbin, 150030, China
| | - Xi Zhang
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin, 150030, China; Joint Laboratory of Northeast Agricultural University and Max Planck Institute of Colloids and Interfaces (NEAU-MPICI), Harbin, 150030, China
| | - Shuang Gai
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin, 150030, China; Joint Laboratory of Northeast Agricultural University and Max Planck Institute of Colloids and Interfaces (NEAU-MPICI), Harbin, 150030, China
| | - Yongxu Jin
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin, 150030, China; Joint Laboratory of Northeast Agricultural University and Max Planck Institute of Colloids and Interfaces (NEAU-MPICI), Harbin, 150030, China
| | - Kui Cheng
- Joint Laboratory of Northeast Agricultural University and Max Planck Institute of Colloids and Interfaces (NEAU-MPICI), Harbin, 150030, China; College of Engineering, Northeast Agricultural University, Harbin, 150030, China
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Thingnam SS, Lourembam DS, Tongbram PS, Lokya V, Tiwari S, Khan MK, Pandey A, Hamurcu M, Thangjam R. A Perspective Review on Understanding Drought Stress Tolerance in Wild Banana Genetic Resources of Northeast India. Genes (Basel) 2023; 14:genes14020370. [PMID: 36833297 PMCID: PMC9957078 DOI: 10.3390/genes14020370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/22/2023] [Accepted: 01/25/2023] [Indexed: 02/04/2023] Open
Abstract
The enormous perennial monocotyledonous herb banana (Musa spp.), which includes dessert and cooking varieties, is found in more than 120 countries and is a member of the order Zingiberales and family Musaceae. The production of bananas requires a certain amount of precipitation throughout the year, and its scarcity reduces productivity in rain-fed banana-growing areas due to drought stress. To increase the tolerance of banana crops to drought stress, it is necessary to explore crop wild relatives (CWRs) of banana. Although molecular genetic pathways involved in drought stress tolerance of cultivated banana have been uncovered and understood with the introduction of high-throughput DNA sequencing technology, next-generation sequencing (NGS) techniques, and numerous "omics" tools, unfortunately, such approaches have not been thoroughly implemented to utilize the huge potential of wild genetic resources of banana. In India, the northeastern region has been reported to have the highest diversity and distribution of Musaceae, with more than 30 taxa, 19 of which are unique to the area, accounting for around 81% of all wild species. As a result, the area is regarded as one of the main locations of origin for the Musaceae family. The understanding of the response of the banana genotypes of northeastern India belonging to different genome groups to water deficit stress at the molecular level will be useful for developing and improving drought tolerance in commercial banana cultivars not only in India but also worldwide. Hence, in the present review, we discuss the studies conducted to observe the effect of drought stress on different banana species. Moreover, the article highlights the tools and techniques that have been used or that can be used for exploring and understanding the molecular basis of differentially regulated genes and their networks in different drought stress-tolerant banana genotypes of northeast India, especially wild types, for unraveling their potential novel traits and genes.
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Affiliation(s)
| | | | - Punshi Singh Tongbram
- Department of Biotechnology, School of Life Sciences, Mizoram University, Aizawl 796004, India
| | - Vadthya Lokya
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali 140306, India
| | - Siddharth Tiwari
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali 140306, India
| | - Mohd. Kamran Khan
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya 42079, Turkey
| | - Anamika Pandey
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya 42079, Turkey
| | - Mehmet Hamurcu
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya 42079, Turkey
| | - Robert Thangjam
- Department of Biotechnology, School of Life Sciences, Mizoram University, Aizawl 796004, India
- Department of Life Sciences, School of Life Sciences, Manipur University, Imphal 795003, India
- Correspondence:
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Ferreira TMM, Ferreira Filho JA, Leão AP, de Sousa CAF, Souza MTJ. Structural and functional analysis of stress-inducible genes and their promoters selected from young oil palm ( Elaeis guineensis) under salt stress. BMC Genomics 2022; 23:735. [PMCID: PMC9620643 DOI: 10.1186/s12864-022-08926-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/04/2022] [Indexed: 11/10/2022] Open
Abstract
Background Soil salinity is a problem in more than 100 countries across all continents. It is one of the abiotic stress that threatens agriculture the most, negatively affecting crops and reducing productivity. Transcriptomics is a technology applied to characterize the transcriptome in a cell, tissue, or organism at a given time via RNA-Seq, also known as full-transcriptome shotgun sequencing. This technology allows the identification of most genes expressed at a particular stage, and different isoforms are separated and transcript expression levels measured. Once determined by this technology, the expression profile of a gene must undergo validation by another, such as quantitative real-time PCR (qRT-PCR). This study aimed to select, annotate, and validate stress-inducible genes—and their promoters—differentially expressed in the leaves of oil palm (Elaeis guineensis) plants under saline stress. Results The transcriptome analysis led to the selection of 14 genes that underwent structural and functional annotation, besides having their expression validated using the qRT-PCR technique. When compared, the RNA-Seq and qRT-PCR profiles of those genes resulted in some inconsistencies. The structural and functional annotation analysis of proteins coded by the selected genes showed that some of them are orthologs of genes reported as conferring resistance to salinity in other species. There were those coding for proteins related to the transport of salt into and out of cells, transcriptional regulatory activity, and opening and closing of stomata. The annotation analysis performed on the promoter sequence revealed 22 distinct types of cis-acting elements, and 14 of them are known to be involved in abiotic stress. Conclusion This study has helped validate the process of an accurate selection of genes responsive to salt stress with a specific and predefined expression profile and their promoter sequence. Its results also can be used in molecular-genetics-assisted breeding programs. In addition, using the identified genes is a window of opportunity for strategies trying to relieve the damages arising from the salt stress in many glycophyte crops with economic importance.
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Affiliation(s)
- Thalita Massaro Malheiros Ferreira
- grid.411269.90000 0000 8816 9513Graduate Program of Plant Biotechnology, Federal University of Lavras, 37200-000 Lavras, MG CP 3037, Brazil
| | - Jaire Alves Ferreira Filho
- grid.460200.00000 0004 0541 873XBrazilian Agricultural Research Corporation, Embrapa Agroenergy, 70770-901 Brasília, DF Brazil
| | - André Pereira Leão
- grid.460200.00000 0004 0541 873XBrazilian Agricultural Research Corporation, Embrapa Agroenergy, 70770-901 Brasília, DF Brazil
| | | | - Manoel Teixeira Jr. Souza
- grid.411269.90000 0000 8816 9513Graduate Program of Plant Biotechnology, Federal University of Lavras, 37200-000 Lavras, MG CP 3037, Brazil ,grid.460200.00000 0004 0541 873XBrazilian Agricultural Research Corporation, Embrapa Agroenergy, 70770-901 Brasília, DF Brazil
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