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Huang X, Hu X, Liu Q, Xie Z, Tan S, Qin X, Chen T, Wu W, Saud S, Nawaz T, El-Kahtany K, Fahad S, Yi K. Full-length agave transcriptome reveals candidate glycosyltransferase genes involved in hemicellulose biosynthesis. Int J Biol Macromol 2024; 274:133508. [PMID: 38944067 DOI: 10.1016/j.ijbiomac.2024.133508] [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: 01/27/2024] [Revised: 06/07/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Agave species are typical crassulacean acid metabolism (CAM) plants commonly cultivated to produce beverages, fibers, and medicines. To date, few studies have examined hemicellulose biosynthesis in Agave H11648, which is the primary cultivar used for fiber production. We conducted PacBio sequencing to obtain full-length transcriptome of five agave tissues: leaves, shoots, roots, flowers, and fruits. A total of 41,807 genes were generated, with a mean length of 2394 bp and an annotation rate of 97.12 % using public databases. We identified 42 glycosyltransferase genes related to hemicellulose biosynthesis, including mixed-linkage glucan (1), glucomannan (5), xyloglucan (16), and xylan (20). Their expression patterns were examined during leaf development and fungal infection, together with hemicellulose content. The results revealed four candidate glycosyltransferase genes involved in xyloglucan and xylan biosynthesis, including glucan synthase (CSLC), xylosyl transferase (XXT), xylan glucuronyltransferase (GUX), and xylan α-1,3-arabinosyltransferase (XAT). These genes can be potential targets for manipulating xyloglucan and xylan traits in agaves, and can also be used as candidate enzymatic tools for enzyme engineering. We have provided the first full-length transcriptome of agave, which will be a useful resource for gene identification and characterization in agave species. We also elucidated the hemicellulose biosynthesis machinery, which will benefit future studies on hemicellulose traits in agave.
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Affiliation(s)
- Xing Huang
- National Key Laboratory for Tropical Crop Breeding, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xiaoli Hu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingqing Liu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Zhouli Xie
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shibei Tan
- National Key Laboratory for Tropical Crop Breeding, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xu Qin
- Guangxi Subtropical Crops Research Institute, Nanning 530001, China
| | - Tao Chen
- Guangxi Subtropical Crops Research Institute, Nanning 530001, China
| | - Weihuai Wu
- National Key Laboratory for Tropical Crop Breeding, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Shah Saud
- College of Life Science, Linyi University, Linyi, Shandong 276000, China
| | - Taufiq Nawaz
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA
| | - Khaled El-Kahtany
- Geology and Geophysics Department, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | - Shah Fahad
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA; Department of Agronomy, Abdul Wali Khan University Mardan, Khyber Pakh-tunkhwa, 23200, Pakistan.
| | - Kexian Yi
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China; Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou 571101, China; Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou 571101, China.
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Wang W, Zheng Y, Qiu L, Yang D, Zhao Z, Gao Y, Meng R, Zhao H, Zhang S. Genome-wide identification of the SAUR gene family and screening for SmSAURs involved in root development in Salvia miltiorrhiza. PLANT CELL REPORTS 2024; 43:165. [PMID: 38861173 DOI: 10.1007/s00299-024-03260-5] [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: 04/24/2024] [Accepted: 06/05/2024] [Indexed: 06/12/2024]
Abstract
KEY MESSAGE SmSAUR4, SmSAUR18, SmSAUR28, SmSAUR37, and SmSAUR38 were probably involved in the auxin-mediated root development in Salvia miltiorrhiza. Salvia miltiorrhiza is a widely utilized medicinal plant in China. Its roots and rhizomes are the main medicinal portions and are closely related to the quality of this herb. Previous studies have revealed that auxin plays pivotal roles in S. miltiorrhiza root development. Whether small auxin-up RNA genes (SAURs), which are crucial early auxin response genes, are involved in auxin-mediated root development in S. miltiorrhiza is worthy of investigation. In this study, 55 SmSAUR genes in S. miltiorrhiza were identified, and their physical and chemical properties, gene structure, cis-acting elements, and evolutionary relationships were analyzed. The expression levels of SmSAUR genes in different organs of S. miltiorrhiza were detected using RNA-seq combined with qRT‒PCR. The root development of S. miltiorrhiza seedlings was altered by the application of indole-3-acetic acid (IAA), and Pearson correlation coefficient analysis was conducted to screen SmSAURs that potentially participate in this physiological process. The diameter of primary lateral roots was positively correlated with SmSAUR4. The secondary lateral root number was positively correlated with SmSAUR18 and negatively correlated with SmSAUR4. The root length showed a positive correlation with SmSAUR28 and SmSAUR37 and a negative correlation with SmSAUR38. The fresh root biomass exhibited a positive correlation with SmSAUR38 and a negative correlation with SmSAUR28. The aforementioned SmSAURs were likely involved in auxin-mediated root development in S. miltiorrhiza. Our study provides a comprehensive overview of SmSAURs and provides the groundwork for elucidating the molecular mechanism underlying root morphogenesis in this species.
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Affiliation(s)
- Wei Wang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Yuwei Zheng
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Lin Qiu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Dongfeng Yang
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China
| | - Ziyang Zhao
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Yuanyuan Gao
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Ru Meng
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Hongguang Zhao
- Shaanxi Tasly Plants Pharmaceutical Co., Ltd., Shangluo, 726000, Shaanxi, China
| | - Shuncang Zhang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
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Tian Z, Wu B, Liu J, Zhang L, Wu T, Wang Y, Han Z, Zhang X. Genetic variations in MdSAUR36 participate in the negative regulation of mesocarp cell division and fruit size in Malus species. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:1. [PMID: 38222974 PMCID: PMC10784262 DOI: 10.1007/s11032-024-01441-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 12/06/2023] [Indexed: 01/16/2024]
Abstract
Final fruit size of apple (Malus domestica) cultivars is related to both mesocarp cell division and cell expansion during fruit growth, but it is unclear whether the cell division and/or cell enlargement determine most of the differences in fruit size between Malus species. In this study, by using an interspecific hybrid population between Malus asiatica "Zisai Pearl" and Malus domestica cultivar "Red Fuji," we found that the mesocarp cell number was the main causal factor of diversity in fruit size between Malus species. Rapid increase in mesocarp cell number occurred prior to 28 days after anthesis (DAA), while cell size increased gradually after 28 DAA until fruit ripening. Six candidate genes related to auxin signaling or cell cycle were predicted by combining the RNA-seq data and previous QTL data for fruit weight. Two InDels and 10 SNPs in the promoter of a small auxin upregulated RNA gene MdSAUR36 in Zisai Pearl led to a lower promoter activity than that of Red Fuji. One non-synonymous SNP G/T at 379 bp downstream of the ATG codon of MdSAUR36, which was heterozygous in Zisai Pearl, exerted significant genotype effects on fruit weight, length, and width. Transgenic apple calli by over-expressing or RNAi MdSAUR36 confirmed that MdSAUR36 participated in the negative regulation of mesocarp cell division and thus apple fruit size. These results could provide new insights in the molecular mechanism of small fruit size in Malus accession and be potentially used in molecular assisted breeding via interspecific hybridization. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01441-4.
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Affiliation(s)
- Zhendong Tian
- College of Horticulture, China Agricultural University, Beijing, China
| | - Bei Wu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Jing Liu
- College of Horticultural Science & Technology, Hebei Normal University of Science & Technology, Qinhuangdao, China
| | - Libo Zhang
- Zhongbaolvdu Agricultural Research Centre, Beidaihe, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, China
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Lin D, Zhou X, Zhao H, Tao X, Yu S, Zhang X, Zang Y, Peng L, Yang L, Deng S, Li X, Mao X, Luan A, He J, Ma J. The Synergistic Mechanism of Photosynthesis and Antioxidant Metabolism between the Green and White Tissues of Ananas comosus var. bracteatus Chimeric Leaves. Int J Mol Sci 2023; 24:ijms24119238. [PMID: 37298190 DOI: 10.3390/ijms24119238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/30/2023] [Accepted: 05/03/2023] [Indexed: 06/12/2023] Open
Abstract
Ananas comosus var. bracteatus (Ac. bracteatus) is a typical leaf-chimeric ornamental plant. The chimeric leaves are composed of central green photosynthetic tissue (GT) and marginal albino tissue (AT). The mosaic existence of GT and AT makes the chimeric leaves an ideal material for the study of the synergistic mechanism of photosynthesis and antioxidant metabolism. The daily changes in net photosynthetic rate (NPR) and stomatal conductance (SCT) of the leaves indicated the typical crassulacean acid metabolism (CAM) characteristic of Ac. bracteatus. Both the GT and AT of chimeric leaves fixed CO2 during the night and released CO2 from malic acid for photosynthesis during the daytime. The malic acid content and NADPH-ME activity of the AT during the night was significantly higher than that of GT, which suggests that the AT may work as a CO2 pool to store CO2 during the night and supply CO2 for photosynthesis in the GT during the daytime. Furthermore, the soluble sugar content (SSC) in the AT was significantly lower than that of GT, while the starch content (SC) of the AT was apparently higher than that of GT, indicating that AT was inefficient in photosynthesis but may function as a photosynthate sink to help the GT maintain high photosynthesis activity. Additionally, the AT maintained peroxide balance by enhancing the non-enzymatic antioxidant system and antioxidant enzyme system to avoid antioxidant damage. The enzyme activities of reductive ascorbic acid (AsA) and the glutathione (GSH) cycle (except DHAR) and superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) were enhanced, apparently to make the AT grow normally. This study indicates that, although the AT of the chimeric leaves was inefficient at photosynthesis because of the lack of chlorophyll, it can cooperate with the GT by working as a CO2 supplier and photosynthate store to enhance the photosynthetic ability of GT to help chimeric plants grow well. Additionally, the AT can avoid peroxide damage caused by the lack of chlorophyll by enhancing the activity of the antioxidant system. The AT plays an active role in the normal growth of the chimeric leaves.
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Affiliation(s)
- Dongpu Lin
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu 611100, China
| | - Xuzixin Zhou
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu 611100, China
| | - Huan Zhao
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu 611100, China
| | - Xiaoguang Tao
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu 611100, China
| | - Sanmiao Yu
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu 611100, China
| | - Xiaopeng Zhang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu 611100, China
| | - Yaoqiang Zang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu 611100, China
| | - Lingli Peng
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu 611100, China
| | - Li Yang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu 611100, China
| | - Shuyue Deng
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu 611100, China
| | - Xiyan Li
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu 611100, China
| | - Xinjing Mao
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu 611100, China
| | - Aiping Luan
- Tropical Crop Genetic Resources Institute, Chinese Academy of Agricultural Science, Haikou 571101, China
| | - Junhu He
- Tropical Crop Genetic Resources Institute, Chinese Academy of Agricultural Science, Haikou 571101, China
| | - Jun Ma
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu 611100, China
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Tan S, Liang Y, Huang Y, Xi J, Huang X, Yang X, Yi K. Phylogeny and Expression Atlas of the NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER FAMILY in Agave. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11111434. [PMID: 35684207 PMCID: PMC9182991 DOI: 10.3390/plants11111434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/24/2022] [Accepted: 05/26/2022] [Indexed: 05/08/2023]
Abstract
Agave species are widely cultivated crassulacean acid metabolism (CAM) plants for alcoholic beverages, food and fiber production. Among these, the Agave hybrid H11648 ((A. amaniensis × A. angustifolia) × A. amaniensis) is the main cultivar for sisal fiber in the tropical areas of Brazil, China, and African countries. The plants of Agave hybrid H11648 have a long life cycle and large leaves, which require a huge amount of nitrogen nutrient. However, the molecular basis of nitrogen transport and allocation has not been well understood in agave. In this study, we identified 19 NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER FAMILY(NPF) genes (called AhNPFs) with full-length coding sequences in Agave hybrid H11648. Our analysis of gene expression in various types of tissues revealed the tissue-specific expression pattern of AhNPFs. We further examined their expression patterns at different leaf developmental stages, under abiotic/biotic stresses and nutrient deficiency. The results reveal several candidate regulators in the agave NPF family, including AhNPF4.3/5.2/7.1. We first characterized the NPF genes in agave based on published leaf transcriptome datasets and emphasized their potential functions. The study will benefit future studies related to nitrogen nutrient in agave.
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Affiliation(s)
- Shibei Tan
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (S.T.); (Y.L.); (J.X.)
| | - Yanqiong Liang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (S.T.); (Y.L.); (J.X.)
| | - Yanlei Huang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Jingen Xi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (S.T.); (Y.L.); (J.X.)
| | - Xing Huang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (S.T.); (Y.L.); (J.X.)
- Correspondence: (X.H.); (X.Y.); (K.Y.)
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Correspondence: (X.H.); (X.Y.); (K.Y.)
| | - Kexian Yi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (S.T.); (Y.L.); (J.X.)
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou 571101, China
- Correspondence: (X.H.); (X.Y.); (K.Y.)
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6
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Tian Z, Han J, Che G, Hasi A. Genome-wide characterization and expression analysis of SAUR gene family in Melon (Cucumis melo L.). PLANTA 2022; 255:123. [PMID: 35552537 DOI: 10.1007/s00425-022-03908-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
We identified 66 melon SAUR genes by bioinformatic analyses. CmSAUR19, 38, 58, 62 genes are specifically expressed in different stages of fruit growth, suggesting their participation in regulating fruit development. Auxin plays a crucial role in plant growth by regulating the multiple auxin response genes. However, in melon (Cucumis melo L.), the functions of the auxin early response gene family SAUR (Small auxin up RNA) genes in fruit development are still poorly understood. Through genome-wide characterization of CmSAUR family in melon, we identified a total of 66 CmSAUR genes. The open reading frames of the CmSAUR genes ranged from 234 to 525 bp, containing only one exon and lacking introns. Chromosomal position and phylogenetic tree analyses found that the two gene clusters in the melon chromosome are highly homologous in the Cucurbitaceae plants. Among the four conserved motifs in CmSAUR proteins, motif 1, motif 2, and motif 3 located in most of the family protein sequences, and motif 4 showed a close correlation with the two gene clusters. The CmSAUR28 and CmSAUR58 genes have auxin response elements located in the promoters, suggesting they may be involved in the auxin signaling pathway to regulate fruit development. Through transcriptomic profiling in the four developmental stages of fruit and different lateral organs, we selected 16 differentially-expressed SAUR genes for performing further expression analyses. qRT-PCR results showed that five SAUR genes are specifically expressed in flower organs and ovaries. CmSAUR19 and CmSAUR58 were significantly accumulated in the early developmental stage of the fruit. CmSAUR38 and CmAUR62 showed high expression in the climacteric and post-climacteric stages, suggesting their specific role in controlling fruit ripening. This work provides a foundation for further exploring the function of the SAUR gene in fruit development.
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Affiliation(s)
- Ze Tian
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Jiadi Han
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Gen Che
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
| | - Agula Hasi
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
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Li M, Chen R, Gu H, Cheng D, Guo X, Shi C, Li L, Xu G, Gu S, Wu Z, Chen J. Grape Small Auxin Upregulated RNA ( SAUR) 041 Is a Candidate Regulator of Berry Size in Grape. Int J Mol Sci 2021; 22:ijms222111818. [PMID: 34769249 PMCID: PMC8584205 DOI: 10.3390/ijms222111818] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 11/25/2022] Open
Abstract
Grape (Vitis vinifera) is an important horticultural crop that can be used to make juice and wine. However, the small size of the berry limits its yield. Cultivating larger berry varieties can be an effective way to solve this problem. As the largest family of auxin early response genes, SAUR (small auxin upregulated RNA) plays an important role in the growth and development of plants. Berry size is one of the important factors that determine grape quality. However, the SAUR gene family’s function in berry size of grape has not been studied systematically. We identified 60 SAUR members in the grape genome and divided them into 12 subfamilies based on phylogenetic analysis. Subsequently, we conducted a comprehensive and systematic analysis on the SAUR gene family by analyzing distribution of key amino acid residues in the domain, structural features, conserved motifs, and protein interaction network, and combined with the heterologous expression in Arabidopsis and tomato. Finally, the member related to grape berry size in SAUR gene family were screened. This genome-wide study provides a systematic analysis of grape SAUR gene family, further understanding the potential functions of candidate genes, and provides a new idea for grape breeding.
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Affiliation(s)
- Ming Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (M.L.); (H.G.); (D.C.); (X.G.); (C.S.); (L.L.); (G.X.); (S.G.); (Z.W.)
| | - Rui Chen
- Biotechnology Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin 300192, China;
| | - Hong Gu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (M.L.); (H.G.); (D.C.); (X.G.); (C.S.); (L.L.); (G.X.); (S.G.); (Z.W.)
| | - Dawei Cheng
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (M.L.); (H.G.); (D.C.); (X.G.); (C.S.); (L.L.); (G.X.); (S.G.); (Z.W.)
| | - Xizhi Guo
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (M.L.); (H.G.); (D.C.); (X.G.); (C.S.); (L.L.); (G.X.); (S.G.); (Z.W.)
| | - Caiyun Shi
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (M.L.); (H.G.); (D.C.); (X.G.); (C.S.); (L.L.); (G.X.); (S.G.); (Z.W.)
| | - Lan Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (M.L.); (H.G.); (D.C.); (X.G.); (C.S.); (L.L.); (G.X.); (S.G.); (Z.W.)
| | - Guoyi Xu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (M.L.); (H.G.); (D.C.); (X.G.); (C.S.); (L.L.); (G.X.); (S.G.); (Z.W.)
| | - Shicao Gu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (M.L.); (H.G.); (D.C.); (X.G.); (C.S.); (L.L.); (G.X.); (S.G.); (Z.W.)
| | - Zhiyong Wu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (M.L.); (H.G.); (D.C.); (X.G.); (C.S.); (L.L.); (G.X.); (S.G.); (Z.W.)
| | - Jinyong Chen
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (M.L.); (H.G.); (D.C.); (X.G.); (C.S.); (L.L.); (G.X.); (S.G.); (Z.W.)
- Correspondence:
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Maceda-López LF, Villalpando-Aguilar JL, García-Hernández E, Ávila de Dios E, Andrade-Canto SB, Morán-Velázquez DC, Rodríguez-López L, Hernández-Díaz D, Chablé-Vega MA, Trejo L, Góngora-Castillo E, López-Rosas I, Simpson J, Alatorre-Cobos F. Improved method for isolation of high-quality total RNA from Agave tequilana Weber roots. 3 Biotech 2021; 11:75. [PMID: 33505830 DOI: 10.1007/s13205-020-02620-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 12/26/2020] [Indexed: 12/30/2022] Open
Abstract
Together with their undeniable role in the ecology of arid and semiarid ecosystems, Agave species are emerging as a model to dissect the relationships between crassulacean acid metabolism and high efficiency of light and water use, and as an energy crop for bioethanol production. Transcriptome resources from economically valuable Agaves species, such as Agave tequilana and A. salmiana, as well as hybrids for fibers, are now available, and multiple gene expression landscape analyses have been reported. Key components in molecular mechanisms underlying drought tolerance could be uncovered by analyzing gene expression patterns of roots. This study describes an efficient protocol for high-quality total RNA isolation from phenolic compounds-rich Agave roots. Our methodology involves suitable root handling and collecting in the field and using saving-time commercial kits available. RNA isolated from roots free of lignified out-layers and clean cortex showed high values of quality and integrity according to electrophoresis and microfluidics-based platform. Synthesis of long full-length cDNAs and PCR amplification tested the suitability for downstream applications of extracted RNA. The protocol was applied successfully to A. tequilana roots but can be used for other Agave species that also develop lignified epidermis/exodermis in roots.
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Affiliation(s)
- Luis F Maceda-López
- Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
| | - José L Villalpando-Aguilar
- Tecnológico Nacional de México, Instituto Tecnológico de Chiná, Calle 11entre 22 y 28, 24050 Chiná, Mexico
| | - Eleazar García-Hernández
- Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
| | - Emmanuel Ávila de Dios
- Departmento de Ingeniería Genetica, Centro de Investigación y Estudios Avanzados, 3681 Irapuato, Mexico
| | - Silvia B Andrade-Canto
- Centro de Investigacion Cientifica de Yucatan, A.C., Calle 43 No.130 x 32 y 34, Chuburna de Hidalgo, 97205 Mérida, Yucatan Mexico
| | - Dalia C Morán-Velázquez
- Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
| | - Lorena Rodríguez-López
- Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
| | - Demetrio Hernández-Díaz
- Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
| | - Manuel A Chablé-Vega
- Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
| | - Laura Trejo
- CONACYT Research Fellow, Laboratorio de Biodiversidad y Cultivo de Tejidos Vegetales, Instituto de Biología, UNAM, 90640 Santa Cruz Tlaxcala, Tlaxcala Mexico
| | - Elsa Góngora-Castillo
- CONACYT Research Fellow, Centro de Investigacion Cientifica de Yucatan, A.C., Calle 43 No.130 x 32 y 34, Chuburna de Hidalgo, 97205 Mérida, Yucatan Mexico
| | - Itzel López-Rosas
- CONACYT Research Fellow, Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
| | - June Simpson
- Departmento de Ingeniería Genetica, Centro de Investigación y Estudios Avanzados, 3681 Irapuato, Mexico
| | - Fulgencio Alatorre-Cobos
- CONACYT Research Fellow, Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
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