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Lv D, Wang G, You J, Zhu L, Yang H, Cao B, Gu W, Li C. Genome-Wide Analysis and Expression Profiling of Lectin Receptor-like Kinase Genes in Watermelon ( Citrullus lanatus). Int J Mol Sci 2024; 25:8257. [PMID: 39125826 PMCID: PMC11312183 DOI: 10.3390/ijms25158257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 07/24/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024] Open
Abstract
Watermelon is one of the most important edible plants worldwide. Owing to its special cultivation conditions, watermelon is exposed to many biological and abiotic stresses during its development. Lectin receptor-like kinases (LecRLKs) are plant-specific membrane proteins that play important roles in sensing and responding to environmental stimuli. Although the LecRLK gene family has been identified in a variety of plants, a comprehensive analysis has not yet been undertaken in watermelon. In this study, 61 putative LecRLK genes were identified in watermelon, consisting of 36 G-type, 24 L-type, and 1 C-type LecRLK genes. They were distributed in clusters on chromosomes, and members from the same subfamily were mostly clustered together. The analysis of the phylogenetic tree and conserved motif indicated that there were obvious differences among three ClaLecRLK subfamilies, and there was also rich diversity in the C-terminal within subfamilies. A collinear analysis revealed that the evolution of the ClaLecRLK gene family in different Cucurbitaceae crops was asynchronous. Furthermore, the analysis of the ClaLecRLK protein structure showed that not all proteins contained signal peptides and a single transmembrane domain. A subcellular localization assay confirmed that the number and position of transmembrane domains did not affect ClaLecRLK protein localization in cells. Transcriptome data revealed distinct expression patterns of LecRLK genes of watermelon in various tissues, and their responses to different fungi infection were also significantly different. Finally, the potential binding sites of the ClaLecRLK genes targeted by miRNA were predicted. This study enhances the understanding of the characteristics and functions of the LecRLK gene family in watermelon and opens up the possibility of exploring the roles that LecRLK genes may play in the life cycle of Cucurbitaceae plants.
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Affiliation(s)
- Duo Lv
- Shanghai Key Lab of Protected Horticultural Technology, Horticultural Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (D.L.); (J.Y.); (L.Z.); (H.Y.); (B.C.)
| | - Gang Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Jiaqi You
- Shanghai Key Lab of Protected Horticultural Technology, Horticultural Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (D.L.); (J.Y.); (L.Z.); (H.Y.); (B.C.)
| | - Lihua Zhu
- Shanghai Key Lab of Protected Horticultural Technology, Horticultural Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (D.L.); (J.Y.); (L.Z.); (H.Y.); (B.C.)
| | - Hongjuan Yang
- Shanghai Key Lab of Protected Horticultural Technology, Horticultural Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (D.L.); (J.Y.); (L.Z.); (H.Y.); (B.C.)
| | - Biting Cao
- Shanghai Key Lab of Protected Horticultural Technology, Horticultural Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (D.L.); (J.Y.); (L.Z.); (H.Y.); (B.C.)
| | - Weihong Gu
- Shanghai Key Lab of Protected Horticultural Technology, Horticultural Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (D.L.); (J.Y.); (L.Z.); (H.Y.); (B.C.)
| | - Chaohan Li
- Shanghai Key Lab of Protected Horticultural Technology, Horticultural Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (D.L.); (J.Y.); (L.Z.); (H.Y.); (B.C.)
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Shi R, Cao Y, Yang T, Wang Y, Xiang Y, Chen F, Zhang W, Zhou X, Sun C, Fu S, Hu M, Zhang J, Wang X. Genome-Wide Association Study Reveals the Genetic Basis of Crude Fiber Components in Brassica napus L. Shoots at Stem Elongation Stage. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:16530-16540. [PMID: 39001851 DOI: 10.1021/acs.jafc.4c03032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/15/2024]
Abstract
Brassica napus is currently the principal field crop for producing materials for primary, secondary and tertiary industries. B. napus shoots at stem elongation stage are rich in anthocyanins, vitamin C and mineral elements such as selenium, calcium and zinc, and represent a new type of green vegetable. However, the high crude fiber (CF) content of B. napus shoots affects their taste, and few studies have focused on the quality traits of these vegetables. In this study, we investigated five traits related to the CF components, including neutral detergent fiber (NDF), acid detergent fiber (ADF), acid detergent lignin (ADL), hemicellulose (Hem) and cellulose (Cel), of B. napus shoots. Whole-genome resequencing at a depth of ∼20× was utilized to genotype an association panel of 202 diverse accessions, which resulted in the identification of 6,093,649 single nucleotide polymorphisms (SNPs) and 996,252 indels, respectively. A genome-wide association study (GWAS) was performed for the five CF-related traits based on the phenotypic data observed in four environments. A total of 1,285 significant SNPs were detected at the threshold of -log10 (p) = 5.16, and 97 significant association regions were obtained. In addition, seven candidate genes located on chromosomes A2 (one gene), A8 (three genes), A9 (two genes) and C9 (one gene) related to CF traits were identified, and ten lines containing low CF contents were selected as excellent germplasm resources for breeding. Our results contributed new insights into the genetic basis of CF traits and suggested germplasm resources for the quality improvement of B. napus shoots.
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Affiliation(s)
- Rui Shi
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, PR China
| | - Yu Cao
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
- Yili Kazakh Autonmoous Prefecture Institure of Agricultural Science, Yining, Xinjiang 835000, PR China
| | - Tinghai Yang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
| | - Yaping Wang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
| | - Yanan Xiang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
| | - Feng Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
| | - Wei Zhang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
| | - Xiaoying Zhou
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
| | - Chengming Sun
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
| | - Sanxiong Fu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
- Yili Kazakh Autonmoous Prefecture Institure of Agricultural Science, Yining, Xinjiang 835000, PR China
| | - Maolong Hu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
- Yili Kazakh Autonmoous Prefecture Institure of Agricultural Science, Yining, Xinjiang 835000, PR China
| | - Jiefu Zhang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
- Yili Kazakh Autonmoous Prefecture Institure of Agricultural Science, Yining, Xinjiang 835000, PR China
| | - Xiaodong Wang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
- Yili Kazakh Autonmoous Prefecture Institure of Agricultural Science, Yining, Xinjiang 835000, PR China
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Guo S, Tian M, Du H, Liu S, Yu R, Shen H. Quantitative Trait Loci Mapping and Comparative Transcriptome Analysis of Fruit Weight (FW) in Watermelon ( Citrullus lanatus L.). Genes (Basel) 2024; 15:933. [PMID: 39062712 PMCID: PMC11276344 DOI: 10.3390/genes15070933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/08/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
The watermelon (Citrullus lanatus L.) holds substantial economic value as a globally cultivated horticultural crop. However, the genetic architecture of watermelon fruit weight (FW) remains poorly understood. In this study, we used sh14-11 with small fruit and N14 with big fruit to construct 100 recombinant inbred lines (RILs). Based on whole-genome resequencing (WGR), 218,127 single nucleotide polymorphisms (SNPs) were detected to construct a high-quality genetic map. After quantitative trait loci (QTL) mapping, a candidate interval of 31-38 Mb on chromosome 2 was identified for FW. Simultaneously, the bulked segregant analysis (BSA) in the F2 population corroborated the identification of the same interval, encompassing the homologous gene linked to the known FW-related gene fas. Additionally, RNA-seq was carried out across 11 tissues from sh14-11 and N14, revealing expression profiles that identified 1695 new genes and corrected the annotation of 2941 genes. Subsequent differential expression analysis unveiled 8969 differentially expressed genes (DEGs), with 354 of these genes exhibiting significant differences across four key developmental stages. The integration of QTL mapping and differential expression analysis facilitated the identification of 14 FW-related genes, including annotated TGA and NAC transcription factors implicated in fruit development. This combined approach offers valuable insights into the genetic basis of FW, providing crucial resources for enhancing watermelon cultivation.
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Affiliation(s)
- Song Guo
- Horticulture College, China Agricultural University, Beijing 100193, China;
| | - Mei Tian
- Institute of Horticultural Research, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China; (M.T.); (H.D.); (S.L.)
| | - Huiying Du
- Institute of Horticultural Research, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China; (M.T.); (H.D.); (S.L.)
| | - Shengfeng Liu
- Institute of Horticultural Research, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China; (M.T.); (H.D.); (S.L.)
| | - Rong Yu
- Institute of Horticultural Research, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China; (M.T.); (H.D.); (S.L.)
| | - Huolin Shen
- Horticulture College, China Agricultural University, Beijing 100193, China;
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Zhang Y, Zhao M, Tan J, Huang M, Chu X, Li Y, Han X, Fang T, Tian Y, Jarret R, Lu D, Chen Y, Xue L, Li X, Qin G, Li B, Sun Y, Deng XW, Deng Y, Zhang X, He H. Telomere-to-telomere Citrullus super-pangenome provides direction for watermelon breeding. Nat Genet 2024:10.1038/s41588-024-01823-6. [PMID: 38977857 DOI: 10.1038/s41588-024-01823-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 06/04/2024] [Indexed: 07/10/2024]
Abstract
To decipher the genetic diversity within the cucurbit genus Citrullus, we generated telomere-to-telomere (T2T) assemblies of 27 distinct genotypes, encompassing all seven Citrullus species. This T2T super-pangenome has expanded the previously published reference genome, T2T-G42, by adding 399.2 Mb and 11,225 genes. Comparative analysis has unveiled gene variants and structural variations (SVs), shedding light on watermelon evolution and domestication processes that enhanced attributes such as bitterness and sugar content while compromising disease resistance. Multidisease-resistant loci from Citrullus amarus and Citrullus mucosospermus were successfully introduced into cultivated Citrullus lanatus. The SVs identified in C. lanatus have not only been inherited from cordophanus but also from C. mucosospermus, suggesting additional ancestors beyond cordophanus in the lineage of cultivated watermelon. Our investigation substantially improves the comprehension of watermelon genome diversity, furnishing comprehensive reference genomes for all Citrullus species. This advancement aids in the exploration and genetic enhancement of watermelon using its wild relatives.
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Affiliation(s)
- Yilin Zhang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Mingxia Zhao
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Jingsheng Tan
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Minghan Huang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Xiao Chu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Yan Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Xue Han
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Taohong Fang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Yao Tian
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | | | - Dongdong Lu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Yijun Chen
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Lifang Xue
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Xiaoni Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Guochen Qin
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Bosheng Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Yudong Sun
- Vegetable Research and Development Center, Huaiyin Institute of Agricultural Sciences of Xuhuai Region in Jiangsu, Huai'an, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Yun Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China.
| | - Xingping Zhang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China.
| | - Hang He
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China.
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China.
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Huang A, Feng S, Ye Z, Zhang T, Chen S, Chen C, Chen S. Genome Assembly and Structural Variation Analysis of Luffa acutangula Provide Insights on Flowering Time and Ridge Development. PLANTS (BASEL, SWITZERLAND) 2024; 13:1828. [PMID: 38999668 PMCID: PMC11243878 DOI: 10.3390/plants13131828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/21/2024] [Accepted: 06/21/2024] [Indexed: 07/14/2024]
Abstract
Luffa spp. is an important worldwide cultivated vegetable and medicinal plant from the Cucurbitaceae family. In this study, we report a high-quality chromosome-level genome of the high-generation inbred line SG261 of Luffa acutangula. The genomic sequence was determined by PacBio long reads, Hi-C sequencing reads, and 10× Genomics sequencing, with an assembly size of 739.82 Mb, contig N50 of 18.38 Mb, and scaffold N50 of 56.08 Mb. The genome of L. acutangula SG261 was predicted to contain 27,312 protein-coding genes and 72.56% repetitive sequences, of which long terminal repeats (LTRs) were an important form of repetitive sequences, accounting for 67.84% of the genome. Phylogenetic analysis reveals that L. acutangula evolved later than Luffa cylindrica, and Luffa is closely related to Momodica charantia. Comparing the genome of L. acutangula SG261 and L. cylindrica with PacBio data, 67,128 high-quality structural variations (SVs) and 55,978 presence-absence variations (PAVs) were identified in SG261, resulting in 2424 and 1094 genes with variation in the CDS region, respectively, and there are 287 identical genes affected by two different structural variation analyses. In addition, we found that the transcription factor FY (FLOWERING LOCUS Y) families had a large expansion in L. acutangula SG261 (flowering in the morning) compared to L. cylindrica (flowering in the afternoon), which may result in the early flowering time in L. acutangula SG261. This study provides valuable reference for the breeding of and pan-genome research into Luffa species.
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Affiliation(s)
- Aizheng Huang
- Institute of Agricultural Science Research of Jiangmen, Jiangmen 529060, China;
| | - Shuo Feng
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (S.F.)
| | - Zhuole Ye
- Dongguan Agricultural Scientific Research Center, Dongguan 523086, China
| | - Ting Zhang
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (S.F.)
| | - Shenglong Chen
- Dongguan Agricultural Scientific Research Center, Dongguan 523086, China
| | - Changming Chen
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (S.F.)
| | - Shijun Chen
- Institute of Agricultural Science Research of Jiangmen, Jiangmen 529060, China;
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Park SY, Kim JE, Kang HM, Park KH, Je BI, Lee KW, Hwang DY, Choi YW. Citrullus mucosospermus Extract Exerts Protective Effects against Methionine- and Choline-Deficient Diet-Induced Nonalcoholic Steatohepatitis in Mice. Foods 2024; 13:2101. [PMID: 38998607 PMCID: PMC11240977 DOI: 10.3390/foods13132101] [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: 06/05/2024] [Revised: 06/25/2024] [Accepted: 06/28/2024] [Indexed: 07/14/2024] Open
Abstract
In recent years, there has been increasing interest in exploring the potential therapeutic advantages of Citrullus mucosospermus extracts (CME) for nonalcoholic steatohepatitis (NASH). In this study, we investigated the therapeutic effects of CME on NASH using a mice model. High-performance liquid chromatography (HPLC) was employed to identify cucurbitacin E and cucurbitacin E-2-O-glucoside from the CME. Although CME did not significantly alter the serum lipid levels in methionine- and choline-deficient (MCD) mice, it demonstrated a protective effect against MCD diet-induced liver damage. CME reduced histological markers, reduced alanine transaminase (ALT) and aspartame transaminase (AST) levels, and modulated key NASH-related genes, including C/EBPα, PPARγ, Fas, and aP2. In addition, CME was found to restore hormone-sensitive lipase (HSL) and adipose triglyceride lipase (ATGL) activity, both crucial for fat catabolism, and reduced the levels of pro-inflammatory cytokines. Furthermore, CME demonstrated the potential to mitigate oxidative stress by maintaining or enhancing the activation and expression of nuclear factor erythroid 2-related factor 2 (Nrf2) and superoxide dismutase (SOD), both pivotal players in antioxidant defense mechanisms. These findings underscore the promising therapeutic potential of CME in ameliorating liver damage, inflammation, and oxidative stress associated with NASH.
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Affiliation(s)
- Sun Young Park
- Institute of Nano-Bio Convergence, Pusan National University, Busan 46241, Republic of Korea
| | - Ji Eun Kim
- Department of Biomaterials Science (BK21 FOUR Program)/Life and Industry Convergence Research Institute/Laboratory Animals Resources Center, Pusan National University, Miryang 50463, Republic of Korea
| | - He Mi Kang
- Department of Horticultural Bioscience/Life and Industry Convergence Research Institute, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Republic of Korea
| | - Ki Ho Park
- Department of Biomaterials Science (BK21 FOUR Program)/Life and Industry Convergence Research Institute/Laboratory Animals Resources Center, Pusan National University, Miryang 50463, Republic of Korea
| | - Byoung Il Je
- Department of Horticultural Bioscience/Life and Industry Convergence Research Institute, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Republic of Korea
| | - Ki Won Lee
- Natural Products Convergence R&D Division, Kwangdong Pharm. Co., Ltd., Seoul 08381, Republic of Korea
| | - Dae Youn Hwang
- Department of Biomaterials Science (BK21 FOUR Program)/Life and Industry Convergence Research Institute/Laboratory Animals Resources Center, Pusan National University, Miryang 50463, Republic of Korea
| | - Young Whan Choi
- Department of Horticultural Bioscience/Life and Industry Convergence Research Institute, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Republic of Korea
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Li XX, Lai YS. The Development and Application of Vegetable Genomics Increase the Efficiency of Exploring New Gene Resources for Vegetables. Int J Mol Sci 2024; 25:6906. [PMID: 39000015 PMCID: PMC11241489 DOI: 10.3390/ijms25136906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 05/29/2024] [Indexed: 07/14/2024] Open
Abstract
Vegetables, as indispensable non-staple foods in people's daily diet, provide a variety of essential vitamins, minerals, and other nutrients, as well as special phytochemicals, which are recognized as functional components for human nutritional balance or medicinal purposes [...].
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Affiliation(s)
- Xi-Xiang Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yun-Song Lai
- College of Horticulture, Sichuan Agricultural University, Chengdu 611100, China
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Wang M, Cao Z, Jiang B, Wang K, Xie D, Chen L, Shi S, Yang S, Lu H, Peng Q. Chromosome-level genome assembly and population genomics reveals crucial selection for subgynoecy development in chieh-qua. HORTICULTURE RESEARCH 2024; 11:uhae113. [PMID: 38898961 PMCID: PMC11186066 DOI: 10.1093/hr/uhae113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 04/10/2024] [Indexed: 06/21/2024]
Abstract
Chieh-qua is an important cucurbit crop and very popular in South China and Southeast Asia. Despite its significance, its genetic basis and domestication history are unclear. In this study, we have successfully generated a chromosome-level reference genome assembly for the chieh-qua 'A36' using a hybrid assembly strategy that combines PacBio long reads and Illumina short reads. The assembled genome of chieh-qua is approximately 953.3 Mb in size and is organized into 12 chromosomes, with contig N50 of 6.9 Mb and scaffold N50 of 68.2 Mb. Notably, the chieh-qua genome is comparable in size to the wax gourd genome. Through gene prediction analysis, we have identified a total of 24 593 protein-coding genes in the A36 genome. Additionally, approximately 56.6% (539.3 Mb) of the chieh-qua genome consists of repetitive sequences. Comparative genome analysis revealed that chieh-qua and wax gourd are closely related, indicating a close evolutionary relationship between the two species. Population genomic analysis, employing 129 chieh-qua accessions and 146 wax gourd accessions, demonstrated that chieh-qua exhibits greater genetic diversity compared to wax gourd. We also employed the GWAS method to identify related QTLs associated with subgynoecy, an interested and important trait in chieh-qua. The MYB59 (BhiCQ0880026447) exhibited relatively high expression levels in the shoot apex of four subgynoecious varieties compared with monoecious varieties. Overall, this research provides insights into the domestication history of chieh-qua and offers valuable genomic resources for further molecular research.
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Affiliation(s)
- Min Wang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Zhenqiang Cao
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Biao Jiang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Kejian Wang
- China National Rice Research Institute, Hangzhou 310012, China
| | - Dasen Xie
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Lin Chen
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Shaoqi Shi
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Songguang Yang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Hongwei Lu
- China National Rice Research Institute, Hangzhou 310012, China
| | - Qingwu Peng
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
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Jiao D, Zhao H, Sun H, Zhang J, Zhang H, Gong G, Anees M, Zhu H, Liu W, Xu Y. Identification of allelic relationship and translocation region among chromosomal translocation lines that leads to less-seed watermelon. HORTICULTURE RESEARCH 2024; 11:uhae087. [PMID: 38799123 PMCID: PMC11116901 DOI: 10.1093/hr/uhae087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/20/2024] [Indexed: 05/29/2024]
Abstract
Less-seed and seedless traits are desirable characteristics in watermelon (Citrullus lanatus). Hybridization between watermelon chromosomal translocated lines and wild lines significantly reduced seed counts in the hybrid fruits, approaching even seedless. However, the allelic relationships and the chromosomal translocation breakpoints from different sources are unclear, which limits their utility in breeding practices. This study focused on three groups of chromosomal translocation materials from different sources and conducted inheritance and allelic relationship analysis of translocation points. The results from third-generation genome sequencing and fluorescence in situ hybridization (FISH) revealed that the specific translocations in the naturally mutated material MT-a involved reciprocal translocations between Chr6 and Chr10. The Co60γ radiation-induced mutant material MT-b involved reciprocal translocations between Chr1 and Chr5, Chr4 and Chr8. The Co60γ radiation-induced mutant material MT-c involved complex translocations among Chr1, Chr5, and Chr11. Cytological observation showed that heterozygous translocation hybrids showed chromosomal synapsis abnormalities during meiotic diakinesis. Further, dominant and codominant molecular markers were developed on both sides of the translocation breakpoints, which could facilitate rapid and efficient identification of chromosome translocation lines. This study provides technical guidance for utilizing chromosomal translocation materials in the development of less-seed watermelon varieties.
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Affiliation(s)
- Di Jiao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Hanghai East Road, Guancheng District, Zhengzhou, Henan 450009, China
- State Key Laboratory of Vegetable Biobreeding, Tianjin Academy of Agriculture Sciences, Jinjing Road, Xiqing District, Tianjin 300192, China
| | - Hong Zhao
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Zhanghua Road, Haidian Districk, Beijing 100097, China
| | - Honghe Sun
- Plant Biology Section, School of Integrative Plant Science, Cornell University, 236 Tower Road, Ithaca, New York 14853, USA
- Boyce Thompson Institute, 533 Tower Road, Ithaca, New York 14853, USA
| | - Jie Zhang
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Zhanghua Road, Haidian Districk, Beijing 100097, China
| | - Haiying Zhang
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Zhanghua Road, Haidian Districk, Beijing 100097, China
| | - Guoyi Gong
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Zhanghua Road, Haidian Districk, Beijing 100097, China
| | - Muhammad Anees
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Hanghai East Road, Guancheng District, Zhengzhou, Henan 450009, China
| | - Hongju Zhu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Hanghai East Road, Guancheng District, Zhengzhou, Henan 450009, China
| | - Wenge Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Hanghai East Road, Guancheng District, Zhengzhou, Henan 450009, China
| | - Yong Xu
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Zhanghua Road, Haidian Districk, Beijing 100097, China
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10
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Guo D, Jiang H, Xie L. An R2R3-MYB Transcriptional Factor LuMYB314 Associated with the Loss of Petal Pigmentation in Flax ( Linum usitatissimum L.). Genes (Basel) 2024; 15:511. [PMID: 38674445 PMCID: PMC11050253 DOI: 10.3390/genes15040511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
The loss of anthocyanin pigments is one of the most common evolutionary transitions in petal color, yet the genetic basis for these changes in flax remains largely unknown. In this study, we used crossing studies, a bulk segregant analysis, genome-wide association studies, a phylogenetic analysis, and transgenic testing to identify genes responsible for the transition from blue to white petals in flax. This study found no correspondence between the petal color and seed color, refuting the conclusion that a locus controlling the seed coat color is associated with the petal color, as reported in previous studies. The locus controlling the petal color was mapped using a BSA-seq analysis based on the F2 population. However, no significantly associated genomic regions were detected. Our genome-wide association study identified a highly significant QTL (BP4.1) on chromosome 4 associated with flax petal color in the natural population. The combination of a local Manhattan plot and an LD heat map identified LuMYB314, an R2R3-MYB transcription factor, as a potential gene responsible for the natural variations in petal color in flax. The overexpression of LuMYB314 in both Arabidopsis thaliana and Nicotiana tabacum resulted in anthocyanin deposition, indicating that LuMYB314 is a credible candidate gene for controlling the petal color in flax. Additionally, our study highlights the limitations of the BSA-seq method in low-linkage genomic regions, while also demonstrating the powerful detection capabilities of GWAS based on high-density genomic variation mapping. This study enhances our genetic insight into petal color variations and has potential breeding value for engineering LuMYB314 to develop colored petals, bast fibers, and seeds for multifunctional use in flax.
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Affiliation(s)
- Dongliang Guo
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China;
| | - Haixia Jiang
- Key Laboratory of Plant Stress Biology in Arid Land, College of Life Science, Xinjiang Normal University, Urumqi 830017, China;
| | - Liqiong Xie
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China;
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11
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Zhou Y, Shen Q, Cai L, Zhao H, Zhang K, Ma Y, Bo Y, Lyu X, Yang J, Hu Z, Zhang M. Promoter variations of ClERF1 gene determines flesh firmness in watermelon. BMC PLANT BIOLOGY 2024; 24:290. [PMID: 38627629 PMCID: PMC11020897 DOI: 10.1186/s12870-024-05000-z] [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: 03/08/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Flesh firmness is a critical factor that influences fruit storability, shelf-life and consumer's preference as well. However, less is known about the key genetic factors that are associated with flesh firmness in fresh fruits like watermelon. RESULTS In this study, through bulk segregant analysis (BSA-seq), we identified a quantitative trait locus (QTL) that influenced variations in flesh firmness among recombinant inbred lines (RIL) developed from cross between the Citrullus mucosospermus accession ZJU152 with hard-flesh and Citrullus lanatus accession ZJU163 with soft-flesh. Fine mapping and sequence variations analyses revealed that ethylene-responsive factor 1 (ClERF1) was the most likely candidate gene for watermelon flesh firmness. Furthermore, several variations existed in the promoter region between ClERF1 of two parents, and significantly higher expressions of ClERF1 were found in hard-flesh ZJU152 compared with soft-flesh ZJU163 at key developmental stages. DUAL-LUC and GUS assays suggested much stronger promoter activity in ZJU152 over ZJU163. In addition, the kompetitive allele-specific PCR (KASP) genotyping datasets of RIL populations and germplasm accessions further supported ClERF1 as a possible candidate gene for fruit flesh firmness variability and the hard-flesh genotype might only exist in wild species C. mucosospermus. Through yeast one-hybrid (Y1H) and dual luciferase assay, we found that ClERF1 could directly bind to the promoters of auxin-responsive protein (ClAux/IAA) and exostosin family protein (ClEXT) and positively regulated their expressions influencing fruit ripening and cell wall biosynthesis. CONCLUSIONS Our results indicate that ClERF1 encoding an ethylene-responsive factor 1 is associated with flesh firmness in watermelon and provide mechanistic insight into the regulation of flesh firmness, and the ClERF1 gene is potentially applicable to the molecular improvement of fruit-flesh firmness by design breeding.
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Affiliation(s)
- Yimei Zhou
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Qinghui Shen
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Lingmin Cai
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Haoshun Zhao
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Kejia Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yuyuan Ma
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | | | - Xiaolong Lyu
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Zhejiang Engineering Research Center for Precision Crop Design Breeding, Hanghzou, China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, China
- Key laboratory of Horticultural Plant growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, China
| | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Zhejiang Engineering Research Center for Precision Crop Design Breeding, Hanghzou, China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, China
- Key laboratory of Horticultural Plant growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, China
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Zhejiang Engineering Research Center for Precision Crop Design Breeding, Hanghzou, China.
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, China.
- Key laboratory of Horticultural Plant growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, China.
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12
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Cao H, Wang R, Zhao J, Shi L, Huang Y, Wu T, Zhang C. Genome-wide identification and expression analysis of the cryptochromes reveal the CsCRY1 role under low-light-stress in cucumber. FRONTIERS IN PLANT SCIENCE 2024; 15:1371435. [PMID: 38660445 PMCID: PMC11040678 DOI: 10.3389/fpls.2024.1371435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024]
Abstract
Introduction Low-light-stress is a common meteorological disaster that can result in slender seedlings. The photoreceptors play a crucial role in perceiving and regulating plants' tolerance to low-light-stress. However, the low-light-stress tolerance of cucumber has not been effectively evaluated, and the functions of these photoreceptor genes in cucumber, particularly under low-light-stress conditions, are not clear. Methods Herein, we evaluated the growth characteristics of cucumber seedlings under various LED light treatment. The low-light-stress tolerant cucumber CR and intolerant cucumber CR were used as plant materials for gene expression analysis, and then the function of CsCRY1 was analyzed. Results The results revealed that light treatment below 40 μmol m-2 s-1 can quickly and effectively induce low-light-stress response. Then, cucumber CR exhibited remarkable tolerance to low-light-stress was screened. Moreover, a total of 11 photoreceptor genes were identified and evaluated. Among them, the cryptochrome 1 (CRY1) had the highest expression level and was only induced in the low-light sensitive cucumber CS. The transcript CsaV3_3G047490.1 is predicted to encode a previously unknown CsCRY1 protein, which lacks 70 amino acids at its C-terminus due to alternative 5' splice sites within the final intron of the CsCRY1 gene. Discussion CRY1 is a crucial photoreceptor that plays pivotal roles in regulating plants' tolerance to low-light stress. In this study, we discovered that alternative splicing of CsCRY1 generates multiple transcripts encoding distinct CsCRY1 protein variants, providing valuable insights for future exploration and utilization of CsCRY1 in cucumber.
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Affiliation(s)
- Haishun Cao
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Rui Wang
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Junhong Zhao
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Liangliang Shi
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yuan Huang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Tingquan Wu
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Changyuan Zhang
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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13
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Ma Y, Wang Y, Zhou Z, Zhang R, Xie Y, Zhang Y, Bo Y, Lyu X, Yang J, Zhang M, Hu Z. A large presence/absence variation in the promotor of the ClLOG gene determines trichome elongation in watermelon. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:98. [PMID: 38592431 DOI: 10.1007/s00122-024-04601-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/13/2024] [Indexed: 04/10/2024]
Abstract
KEY MESSAGE The ClLOG gene encoding a cytokinin riboside 5'-monophosphate phosphoribohydrolase determines trichome length in watermelon, which is associated with its promoter variations. Trichomes, which are differentiated from epidermal cells, are special accessory structures that cover the above-ground organs of plants and possibly contribute to biotic and abiotic stress resistance. Here, a bulked segregant analysis (BSA) of an F2 population with significant variations in trichome length was undertaken. A 1.84-Mb candidate region on chromosome 10 was associated with trichome length. Resequencing and fine-mapping analyses indicated that a 12-kb structural variation in the promoter of Cla97C10G203450 (ClLOG) led to a significant expression difference in this gene in watermelon lines with different trichome lengths. In addition, a virus-induced gene silencing analysis confirmed that ClLOG positively regulated trichome elongation. These findings provide new information and identify a potential target gene for controlling multicellular trichome elongation in watermelon.
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Affiliation(s)
- Yuyuan Ma
- Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, Zhejiang, People's Republic of China
| | - Yu Wang
- Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, Zhejiang, People's Republic of China
| | - Zhiqin Zhou
- Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, Zhejiang, People's Republic of China
| | - Runqin Zhang
- Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, Zhejiang, People's Republic of China
| | - Yiru Xie
- Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, Zhejiang, People's Republic of China
| | - Yihan Zhang
- Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China
| | - Yongming Bo
- Key Laboratory of Vegetable Breeding, Ningbo Weimeng Seed Co., Ltd, Ningbo, 315100, People's Republic of China
| | - Xiaolong Lyu
- Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, Zhejiang, People's Republic of China
| | - Jinghua Yang
- Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, Zhejiang, People's Republic of China
| | - Mingfang Zhang
- Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, Zhejiang, People's Republic of China
- Key Laboratory of Vegetable Breeding, Ningbo Weimeng Seed Co., Ltd, Ningbo, 315100, People's Republic of China
| | - Zhongyuan Hu
- Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, People's Republic of China.
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China.
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, Zhejiang, People's Republic of China.
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14
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Zhang Y, Zhang W, Liu Y, Zheng Y, Nie X, Wu Q, Yu W, Wang Y, Wang X, Fang K, Qin L, Xing Y. GWAS identifies two important genes involved in Chinese chestnut weight and leaf length regulation. PLANT PHYSIOLOGY 2024; 194:2387-2399. [PMID: 38114094 DOI: 10.1093/plphys/kiad674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/21/2023]
Abstract
There are many factors that affect the yield of Chinese chestnut (Castanea mollissima), with single nut weight (SNW) being one of the most important. Leaf length is also related to Chinese chestnut yield. However, the genetic architecture and gene function associated with Chinese chestnut nut yield have not been fully explored. In this study, we performed genotyping by sequencing 151 Chinese chestnut cultivars, followed by a genome-wide association study (GWAS) on six horticultural traits. First, we analyzed the phylogeny of the Chinese chestnut and found that the Chinese chestnut cultivars divided into two ecotypes, a northern and southern cultivar group. Differences between the cultivated populations were found in the pathways of plant growth and adaptation to the environment. In the selected regions, we also found interesting tandemly arrayed genes that may influence Chinese chestnut traits and environmental adaptability. To further investigate which horticultural traits were selected, we performed a GWAS using six horticultural traits from 151 cultivars. Forty-five loci that strongly associated with horticultural traits were identified, and six genes highly associated with these traits were screened. In addition, a candidate gene associated with SNW, APETALA2 (CmAP2), and another candidate gene associated with leaf length (LL), CRYPTOCHROME INTERACTING BASIC HELIX-LOOP-HELIX 1 (CmCIB1), were verified in Chinese chestnut and Arabidopsis (Arabidopsis thaliana). Our results showed that CmAP2 affected SNW by negatively regulating cell size. CmCIB1 regulated the elongation of new shoots and leaves by inducing cell elongation, potentially affecting photosynthesis. This study provided valuable information and insights for Chinese chestnut breeding research.
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Affiliation(s)
- Yu Zhang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Weiwei Zhang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Yang Liu
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Yi Zheng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Xinghua Nie
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Qinyi Wu
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Wenjie Yu
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Yafeng Wang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Xuefeng Wang
- Longtan Forestry Station, Liyang Bureau of Natural Resources and Planning, Liyang, Jiangsu 213300, China
| | - Kefeng Fang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China
| | - Ling Qin
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Yu Xing
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
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15
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Zhao X, Yu J, Chanda B, Zhao J, Wu S, Zheng Y, Sun H, Levi A, Ling KS, Fei Z. Genomic and pangenomic analyses provide insights into the population history and genomic diversification of bottle gourd. THE NEW PHYTOLOGIST 2024. [PMID: 38503725 DOI: 10.1111/nph.19673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 02/27/2024] [Indexed: 03/21/2024]
Abstract
Bottle gourd (Lagenaria siceraria (Mol.) Strandl.) is an economically important vegetable crop and one of the earliest domesticated crops. However, the population history and genomic diversification of bottle gourd have not been extensively studied. We generated a comprehensive bottle gourd genome variation map from genome sequences of 197 world-wide representative accessions, which enables a genome-wide association study for identifying genomic loci associated with resistance to zucchini yellow mosaic virus, and constructed a bottle gourd pangenome that harbors 1534 protein-coding genes absent in the reference genome. Demographic analyses uncover that domesticated bottle gourd originated in Southern Africa c. 12 000 yr ago, and subsequently radiated to the New World via the Atlantic drift and to Eurasia through the efforts of early farmers in the initial Holocene. The identified highly differentiated genomic regions among different bottle gourd populations harbor many genes contributing to their local adaptations such as those related to disease resistance and stress tolerance. Presence/absence variation analysis of genes in the pangenome reveals numerous genes including those involved in abiotic/biotic stress responses that have been under selection during the world-wide expansion of bottle gourds. The bottle gourd variation map and pangenome provide valuable resources for future functional studies and genomics-assisted breeding.
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Affiliation(s)
- Xuebo Zhao
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Jingyin Yu
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Bidisha Chanda
- USDA-ARS, US Vegetable Laboratory, Charleston, SC, 29414, USA
| | - Jiantao Zhao
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Shan Wu
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Yi Zheng
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Honghe Sun
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Amnon Levi
- USDA-ARS, US Vegetable Laboratory, Charleston, SC, 29414, USA
| | - Kai-Shu Ling
- USDA-ARS, US Vegetable Laboratory, Charleston, SC, 29414, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
- USDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
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16
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Zheng YP. Global characteristics and trends of researches on watermelon: Based on bibliometric and visualized analysis. Heliyon 2024; 10:e26824. [PMID: 38434322 PMCID: PMC10907791 DOI: 10.1016/j.heliyon.2024.e26824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 02/17/2024] [Accepted: 02/20/2024] [Indexed: 03/05/2024] Open
Abstract
Watermelon is an important horticultural plant. A bibliometric analysis of the watermelon literature was carried out in order to analyze the research state, hotspots, and trends, as well as to highlight the overall watermelon research development from a holistic viewpoint. The summary of watermelon research is given via metrological analysis based on a set of indices using a newly built Bibliometrix R-package tool. This study gathered 6,632 documents indexed in the Core Collection of Web of Science (WoS) in the domain of watermelon from 1992 to 2022 using bibliometrix. The results indicated that the number of published articles showed an apparently upward trend. The United States was in the first place, with Plant Disease being the most productive journal. Levi A from the United States Department of Agriculture-Agricultural Research Service is the most prolific author, and Levi A is the most cited; The most frequently used keywords by authors are "growth", "resistance", "identification", "yield", "quality" "plants", "watermelon stomach" and "expression"; The most talked-about issues in this subject are resistance, yield, and quality, which highlight the crucial research areas. To effectively comprehend the turning moments for future research, it is useful to monitor the hotspots and frontiers of watermelon studies. The results highlight the future paths for study in the field of watermelon and provide useful information for researchers interested in the topic.
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Affiliation(s)
- Yu-Ping Zheng
- Library of Henan University of Science and Technology, China
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17
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Ye Q, Zhang L, Li Q, Ji Y, Zhou Y, Wu Z, Hu Y, Ma Y, Wang J, Zhang C. Genome and GWAS analysis identified genes significantly related to phenotypic state of Rhododendron bark. HORTICULTURE RESEARCH 2024; 11:uhae008. [PMID: 38487544 PMCID: PMC10939351 DOI: 10.1093/hr/uhae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 01/01/2024] [Indexed: 03/17/2024]
Abstract
As an important horticultural plant, Rhododendron is often used in urban greening and landscape design. However, factors such as the high rate of genetic recombination, frequent outcrossing in the wild, weak linkage disequilibrium, and the susceptibility of gene expression to environmental factors limit further exploration of functional genes related to important horticultural traits, and make the breeding of new varieties require a longer time. Therefore, we choose bark as the target trait which is not easily affected by environmental factors, but also has ornamental properties. Genome-wide association study (GWAS) of Rhododendron delavayi (30 samples), R. irroratum (30 samples) and their F1 generation R. agastum (200 samples) was conducted on the roughness of bark phenotypes. Finally, we obtained 2416.31 Gbp of clean data and identified 5 328 800 high-quality SNPs. According to the P-value and the degree of linkage disequilibrium of SNPs, we further identified 4 out of 11 candidate genes that affect bark roughness. The results of gene differential expression analysis further indicated that the expression levels of Rhdel02G0243600 and Rhdel08G0220700 in different bark phenotypes were significantly different. Our study identified functional genes that influence important horticultural traits of Rhododendron, and illustrated the powerful utility and great potential of GWAS in understanding and exploiting wild germplasm genetic resources of Rhododendron.
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Affiliation(s)
- Qiannan Ye
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lu Zhang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Yunnan Academy of Agricultural Sciences Kunming 650000, China
| | - Qing Li
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaliang Ji
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Yanli Zhou
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan 650201, China
| | - Zhenzhen Wu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanting Hu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan 650201, China
| | - Yongpeng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Jihua Wang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Yunnan Academy of Agricultural Sciences Kunming 650000, China
| | - Chengjun Zhang
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan 650201, China
- Haiyan Engineering & Technology Center, Zhejiang Institute of Advanced Technology, Jiaxing 314022, China
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
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18
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Deng Y, Liu X, Liu S, Li X, Xue L, Bai T, Xu B, Li G, Sun Y, Zhang X. Fine mapping of ClLOX, a QTL for powdery mildew resistance in watermelon (Citrullus lanatus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:51. [PMID: 38369666 DOI: 10.1007/s00122-023-04520-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/07/2023] [Indexed: 02/20/2024]
Abstract
KEY MESSAGE ClLOX, is located on chromosome 2 and encodes a lipoxygenase gene, which induced watermelon powdery mildew resistance by inhibiting pathogen spread. Powdery mildew is one of the most severe fungal diseases reducing yield and quality of watermelon (Citrullus lanatus L.) and other cucurbit crops. Genes responsible for powdery mildew resistance in watermelon are highly valuable. In this study, we first identified the QTL pm-lox for powdery mildew resistance in watermelon, located within a 0.93 Mb interval of chromosome 2, via XP-GWAS method using two F2 populations. The F2:3 families from one of the F2 populations were then used for fine-mapping the pm-lox locus into a 9,883 bp physical region between 29,581,906 and 29,591,789, containing only two annotated genes. Of these, only ClG42_02g0161300 showed a significant differential expression between the resistant and susceptible lines after powdery mildew inoculation based on RNA sequencing (RNA-seq) and qRT-PCR analysis, and is designated ClLOX. Derived Cleaved Amplified Polymorphic Sequence (dCAPs) markers were developed and validated. In addition, our tests showed that the resistance was anti-spread rather than anti-infection of the pathogen. This study identified a new resistance gene (ClLOX), provided insights into the mechanism of powdery mildew resistance, and developed a molecular marker for watermelon breeding.
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Affiliation(s)
- Yun Deng
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Xin Liu
- Vegetable Research and Development Center, Huaiyin Institute of Agricultural Sciences of Xuhuai Region in Jiangsu, Huai'an, Jiangsu, 223001, China
| | - Shoucheng Liu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Xiaoni Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Lifang Xue
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Tian Bai
- Vegetable Research and Development Center, Huaiyin Institute of Agricultural Sciences of Xuhuai Region in Jiangsu, Huai'an, Jiangsu, 223001, China
| | - Binghua Xu
- Vegetable Research and Development Center, Huaiyin Institute of Agricultural Sciences of Xuhuai Region in Jiangsu, Huai'an, Jiangsu, 223001, China
| | - Guoqing Li
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yudong Sun
- Vegetable Research and Development Center, Huaiyin Institute of Agricultural Sciences of Xuhuai Region in Jiangsu, Huai'an, Jiangsu, 223001, China.
| | - Xingping Zhang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, 261325, China.
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19
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Lian Q, Li S, Kan S, Liao X, Huang S, Sloan DB, Wu Z. Association Analysis Provides Insights into Plant Mitonuclear Interactions. Mol Biol Evol 2024; 41:msae028. [PMID: 38324417 PMCID: PMC10875325 DOI: 10.1093/molbev/msae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/17/2024] [Accepted: 02/01/2024] [Indexed: 02/09/2024] Open
Abstract
Cytonuclear interaction refers to the complex and ongoing process of coevolution between nuclear and organelle genomes, which are responsible for cellular respiration, photosynthesis, lipid metabolism, etc. and play a significant role in adaptation and speciation. There have been a large number of studies to detect signatures of cytonuclear interactions. However, identification of the specific nuclear and organelle genetic polymorphisms that are involved in these interactions within a species remains relatively rare. The recent surge in whole genome sequencing has provided us an opportunity to explore cytonuclear interaction from a population perspective. In this study, we analyzed a total of 3,439 genomes from 7 species to identify signals of cytonuclear interactions by association (linkage disequilibrium) analysis of variants in both the mitochondrial and nuclear genomes across flowering plants. We also investigated examples of nuclear loci identified based on these association signals using subcellular localization assays, gene editing, and transcriptome sequencing. Our study provides a novel perspective on the investigation of cytonuclear coevolution, thereby enriching our understanding of plant fitness and offspring sterility.
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Affiliation(s)
- Qun Lian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Shuai Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shenglong Kan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Marine College, Shandong University, Weihai 264209, China
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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20
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Kumar P, Kayastha A, Singh VK, Kayastha AM. In Silico Structural and Functional Insight into the Binding Interactions of the Modeled Structure of Watermelon Urease with Urea. ACS OMEGA 2024; 9:2272-2285. [PMID: 38250402 PMCID: PMC10795036 DOI: 10.1021/acsomega.3c05993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 01/23/2024]
Abstract
Urease (EC 3.5.1.5) is an amidohydrolase. This nickel-dependent metalloenzyme converts urea into NH3 and CO2. Despite their vital role in plants, the structure and function of watermelon (Citrullus lanatus) urease are unknown. We used third- and fourth-generation gene prediction algorithms to annotate the C. lanatus urease sequence in this investigation. The solved urease structure from Canavalia ensiformis (PDB ID: 4GY7) was utilized as a template model to identify the target 3-D model structure of the unknown C. lanatus urease for the first time. Cluretox, the C. lanatus urease intrinsic disordered area identical to Jaburetox, was also found. The C. lanatus urease structure was docked with urea to study atom interaction, amino acid interactions, and binding analyses in the urease-urea complex at 3.5 Å. This study found that amino acids His517, Gly548, Asp631, Ala634, Thr569, His543, Met635, His407, His490, and Ala438 of C. lanatus urease bind urea. To study the molecular basis and mode of action of C. lanatus urease, molecular dynamics simulation was performed and RMSD, RMSF, Rg, SAS, and H-bond analyses were done. The calculated binding free energy (ΔG) for the urea-urease complex at 100 ns using the MM/PBSA method is -7.61 kJ/mol. Understanding its catalytic principles helps scientists construct more efficient enzymes, tailor fertilization to boost agricultural output, and create sustainable waste management solutions.
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Affiliation(s)
- Prince Kumar
- School
of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Arpan Kayastha
- Department
of Biosciences and Bioengineering, IIT Roorkee, Roorkee 247667, India
| | - Vinay Kumar Singh
- School
of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Arvind M. Kayastha
- School
of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
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21
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Chen J, Tan C, Zhu M, Zhang C, Wang Z, Ni X, Liu Y, Wei T, Wei X, Fang X, Xu Y, Huang X, Qiu J, Liu H. CropGS-Hub: a comprehensive database of genotype and phenotype resources for genomic prediction in major crops. Nucleic Acids Res 2024; 52:D1519-D1529. [PMID: 38000385 PMCID: PMC10767954 DOI: 10.1093/nar/gkad1062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/15/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023] Open
Abstract
The explosive amount of multi-omics data has brought a paradigm shift both in academic research and further application in life science. However, managing and reusing the growing resources of genomic and phenotype data points presents considerable challenges for the research community. There is an urgent need for an integrated database that combines genome-wide association studies (GWAS) with genomic selection (GS). Here, we present CropGS-Hub, a comprehensive database comprising genotype, phenotype, and GWAS signals, as well as a one-stop platform with built-in algorithms for genomic prediction and crossing design. This database encompasses a comprehensive collection of over 224 billion genotype data and 434 thousand phenotype data generated from >30 000 individuals in 14 representative populations belonging to 7 major crop species. Moreover, the platform implemented three complete functional genomic selection related modules including phenotype prediction, user model training and crossing design, as well as a fast SNP genotyper plugin-in called SNPGT specifically built for CropGS-Hub, aiming to assist crop scientists and breeders without necessitating coding skills. CropGS-Hub can be accessed at https://iagr.genomics.cn/CropGS/.
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Affiliation(s)
- Jiaxin Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Cong Tan
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Research, Wuhan 430074, China
| | - Min Zhu
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Chenyang Zhang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Bioverse, Shenzhen 518083, China
| | - Zhihan Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xuemei Ni
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Bioverse, Shenzhen 518083, China
| | - Yanlin Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Tong Wei
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Research, Wuhan 430074, China
| | - XiaoFeng Wei
- China National GeneBank, BGI, Shenzhen 518120, China
| | - Xiaodong Fang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Research, Sanya 572025, China
| | - Yang Xu
- Agricultural College, Yangzhou University, Yangzhou 225009, China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Bioverse, Shenzhen 518083, China
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22
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Zhou L, Tian Y, Ren L, Yan Z, Jiang J, Shi Q, Geng C, Li X. A natural substitution of a conserved amino acid in eIF4E confers resistance against multiple potyviruses. MOLECULAR PLANT PATHOLOGY 2024; 25:e13418. [PMID: 38279849 PMCID: PMC10777747 DOI: 10.1111/mpp.13418] [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: 11/13/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/29/2024]
Abstract
Eukaryotic translation initiation factor 4E (eIF4E), which plays a pivotal role in initiating translation in eukaryotic organisms, is often hijacked by the viral genome-linked protein to facilitate the infection of potyviruses. In this study, we found that the naturally occurring amino acid substitution D71G in eIF4E is widely present in potyvirus-resistant watermelon accessions and disrupts the interaction between watermelon eIF4E and viral genome-linked protein of papaya ringspot virus-watermelon strain, zucchini yellow mosaic virus or watermelon mosaic virus. Multiple sequence alignment and protein modelling showed that the amino acid residue D71 located in the cap-binding pocket of eIF4E is strictly conserved in many plant species. The mutation D71G in watermelon eIF4E conferred resistance against papaya ringspot virus-watermelon strain and zucchini yellow mosaic virus, and the equivalent mutation D55G in tobacco eIF4E conferred resistance to potato virus Y. Therefore, our finding provides a potential precise target for breeding plants resistant to multiple potyviruses.
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Affiliation(s)
- Ling‐Xi Zhou
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
| | - Yan‐Ping Tian
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
| | - Li‐Li Ren
- Science and Technology Research Center of China CustomsBeijingChina
| | - Zhi‐Yong Yan
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
| | - Jun Jiang
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
| | - Qing‐Hua Shi
- College of Horticulture Science and EngineeringShandong Agricultural UniversityTai'anChina
| | - Chao Geng
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
| | - Xiang‐Dong Li
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
- Institute of Plant ProtectionShandong Academy of Agricultural SciencesJi'nanChina
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23
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He S, Li G, Zhang J, Ding Y, Wu H, Xie J, Wu H, Yang Z. The effect of environmental factors on the genetic differentiation of Cucurbita ficifolia populations based on whole-genome resequencing. BMC PLANT BIOLOGY 2023; 23:647. [PMID: 38102604 PMCID: PMC10722772 DOI: 10.1186/s12870-023-04602-3] [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: 07/29/2023] [Accepted: 11/10/2023] [Indexed: 12/17/2023]
Abstract
BACKGROUND Cucurbita ficifolia is one of the squash species most resistant to fungal pathogens, and has especially high resistance to melon Fusarium wilt. This species is therefore an important germplasm resource for the breeding of squash and melon cultivars. RESULTS Whole-genome resequencing of 223 individuals from 32 populations in Yunnan Province, the main cucurbit production area in China, was performed and 3,855,120 single-nucleotide polymorphisms (SNPs) and 1,361,000 InDels were obtained. SNP analysis suggested that levels of genetic diversity in C. ficifolia were high, but that different populations showed no significant genetic differentiation or geographical structure, and that individual C. ficifolia plants with fruit rinds of a similar color did not form independent clusters. A Mantel test conducted in combination with geographical distance and environmental factors suggested that genetic distance was not correlated with geographical distance, but had a significant correlation with environmental distance. Further associations between the genetic data and five environmental factors were analyzed using whole-genome association analysis. SNPs associated with each environmental factor were investigated and genes 250 kb upstream and downstream from associated SNPs were annotated. Overall, 15 marker-trait-associated SNPs (MTAs) and 293 genes under environmental selection were identified. The identified genes were involved in cell membrane lipid metabolism, macromolecular complexes, catalytic activity and other related aspects. Ecological niche modeling was used to simulate the distribution of C. ficifolia across time, from the present and into the future. We found that the area suitable for C. ficifolia changed with the changing climate in different periods. CONCLUSIONS Resequencing of the C. ficifolia accessions has allowed identification of genetic markers, such as SNPs and InDels. The SNPs identified in this study suggest that environmental factors mediated the formation of the population structure of C. ficifolia in China. These SNPs and Indels might also contribute to the variation in important pathways of genes for important agronomic traits such as yield, disease resistance and stress tolerance. Moreover, the genome resequencing data and the genetic markers identified from 223 accessions provide insight into the genetic variation of the C. ficifolia germplasm and will facilitate a broad range of genetic studies.
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Affiliation(s)
- Shuilian He
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Gengyun Li
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Jing Zhang
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Yumei Ding
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Hongzhi Wu
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Junjun Xie
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Hang Wu
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Zhengan Yang
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
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24
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Ganaparthi VR, Rennberger G, Wechter P, Levi A, Branham SE. Genome-Wide Association Mapping and Genomic Prediction of Fusarium Wilt Race 2 Resistance in the USDA Citrullus amarus Collection. PLANT DISEASE 2023; 107:3836-3842. [PMID: 37386705 DOI: 10.1094/pdis-02-23-0400-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Fusarium wilt caused by Fusarium oxysporum f. sp. niveum (Fon) race 2 is a serious disease in watermelon and can reduce yields by 80%. Genome-wide association studies (GWAS) are a valuable tool in dissecting the genetic basis of traits. Citrullus amarus accessions (n = 120) from the USDA germplasm collection were genotyped with whole-genome resequencing, resulting in 2,126,759 single nucleotide polymorphic (SNP) markers that were utilized for GWAS. Three models were used for GWAS with the R package GAPIT. Mixed linear model (MLM) analysis did not identify any significant marker associations. FarmCPU identified four quantitative trait nucleotides (QTN) on three different chromosomes (i.e., chromosomes 1, 5, and 9), and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) identified one QTN on chromosome 10 as significantly associated with Fon race 2 resistance. FarmCPU identified four QTN that explained 60% of Fon race 2 resistance, and the single QTN from BLINK explained 27%. Relevant candidate genes were found within the linkage disequilibrium (LD) blocks of these significant SNPs, including genes encoding aquaporins, expansins, 2S albumins, and glutathione S-transferases which have been shown to be involved in imparting resistance to Fusarium spp. Genomic predictions (GP) for Fon race 2 resistance using all 2,126,759 SNPs resulted in a mean prediction accuracy of 0.08 with five-fold cross-validation employing genomic best linear unbiased prediction (gBLUP) or ridge-regression best linear unbiased prediction (rrBLUP). Mean prediction accuracy with gBLUP leave-one-out cross-validation was 0.48. Thus, along with identifying genomic regions associated with Fon race 2 resistance among the accessions, this study observed prediction accuracies that were strongly influenced by population size.
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Affiliation(s)
| | | | - Patrick Wechter
- Coastal Research and Education Center, Clemson University, Charleston, SC
| | - Amnon Levi
- U.S. Vegetable Laboratory, USDA-ARS, Charleston, SC 29414
| | - Sandra E Branham
- Coastal Research and Education Center, Clemson University, Charleston, SC
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25
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Rennberger G, Branham SE, Wechter WP. Genome-Wide Association Study of Resistance to Pseudomonas syringae in the USDA Collection of Citrullus amarus. PLANT DISEASE 2023; 107:3464-3474. [PMID: 37129351 DOI: 10.1094/pdis-04-23-0795-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Pseudomonas leaf spot (PLS), caused by Pseudomonas syringae pv. syringae, is an emerging disease of watermelon in the United States with the potential to severely reduce yield under humid conditions. The genetic basis of resistance to this disease is not known and no resistant germplasm is available. Because Citrullus amarus is an important reservoir of resistance genes for the cultivated watermelon, C. lanatus, we screened the United States Department of Agriculture plant introduction collection of C. amarus for resistance to PLS. Accessions (n = 117) were phenotyped for their level of resistance to PLS in two separate tests. Accession means of percent leaf area affected ranged from 1.5 to 99.4%. The broad-sense heritability for the trait was 0.51. Whole-genome resequencing generated 2,126,759 single-nucleotide polymorphisms (SNPs) which were used to perform a genome-wide association study (GWAS) aimed at discovering molecular markers for resistance. Three different models-BLINK, FarmCPU, and MLM-were included in the GWAS analyses. BLINK and FarmCPU, which are multilocus models, found eight SNPs, located on chromosomes Ca01, Ca05, Ca06, Ca08, and Ca10, that were significantly associated with resistance to PLS. Two of these SNPs were found by both BLINK and FarmCPU. The MLM model did not detect any significant associations. BLINK and FarmCPU estimated an explained phenotypic variance of 43.6 and 28.5%, respectively, for SNP S6_19327000 and 25.0 and 26.0%, respectively, for SNP S1_33362258, the two most significant SNPs found. In total, 43 candidate genes with known involvement in disease resistance were discovered within the genomic intervals of seven of the eight peak SNPs. Eleven of the candidate genes that were found have been reported to be involved in resistance to P. syringae in other plant species. Two significant SNPs were within resistance genes previously documented to play important roles of plant resistance specific to P. syringae in other pathosystems. The SNPs identified in this study will be instrumental in finding causal genes involved in PLS resistance in watermelon and developing resistant germplasm through breeding.
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Affiliation(s)
- Gabriel Rennberger
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), U.S. Vegetable Laboratory, Charleston, SC 29414
| | - Sandra E Branham
- Clemson University, Department of Plant and Environmental Sciences, Coastal Research and Education Center, Charleston, SC 29414
| | - William P Wechter
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), U.S. Vegetable Laboratory, Charleston, SC 29414
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Yang T, Amanullah S, Li S, Cheng R, Zhang C, Zhao Z, Liu H, Luan F, Wang X. Molecular Mapping of Putative Genomic Regions Controlling Fruit and Seed Morphology of Watermelon. Int J Mol Sci 2023; 24:15755. [PMID: 37958737 PMCID: PMC10650541 DOI: 10.3390/ijms242115755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
The genetic regulatory basis of qualitative and quantitative phenotypes of watermelon is being investigated in different types of molecular and genetic breeding studies around the world. In this study, biparental F2 mapping populations were developed over two experimental years, and the collected datasets of fruit and seed traits exhibited highly significant correlations. Whole-genome resequencing of comparative parental lines was performed and detected single nucleotide polymorphism (SNP) loci were converted into cleaved amplified polymorphic sequence (CAPS) markers. The screened polymorphic markers were genotyped in segregating populations and two genetic linkage maps were constructed, which covered a total of 2834.28 and 2721.45 centimorgan (cM) genetic lengths, respectively. A total of 22 quantitative trait loci (QTLs) for seven phenotypic traits were mapped; among them, five stable and major-effect QTLs (PC-8-1, SL-9-1, SWi-9-1, SSi-9-1, and SW-6-1) and four minor-effect QTLs (PC-2-1 and PC-2-2; PT-2-1 and PT-2-2; SL-6-1 and SSi-6-2; and SWi-6-1 and SWi-6-2) were observed with 3.77-38.98% PVE. The adjacent QTL markers showed a good fit marker-trait association, and a significant allele-specific contribution was also noticed for genetic inheritance of traits. Further, a total of four candidate genes (Cla97C09G179150, Cla97C09G179350, Cla97C09G180040, and Cla97C09G180100) were spotted in the stable colocalized QTLs of seed size linked traits (SL-9-1 and SWi-9-1) that showed non-synonymous type mutations. The gene expression trends indicated that the seed morphology had been formed in the early developmental stage and showed the genetic regulation of seed shape formation. Hence, we think that our identified QTLs and genes would provide powerful genetic insights for marker-assisted breeding aimed at improving the quality traits of watermelon.
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Affiliation(s)
- Tiantian Yang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (R.C.); (Z.Z.); (H.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Sikandar Amanullah
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (R.C.); (Z.Z.); (H.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Shenglong Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (R.C.); (Z.Z.); (H.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Rui Cheng
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (R.C.); (Z.Z.); (H.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Chen Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (R.C.); (Z.Z.); (H.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Zhengxiang Zhao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (R.C.); (Z.Z.); (H.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Hongyu Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (R.C.); (Z.Z.); (H.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Feishi Luan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (R.C.); (Z.Z.); (H.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Xuezheng Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (R.C.); (Z.Z.); (H.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
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Fang X, Li S, Zhu Z, Zhang X, Xiong C, Wang X, Luan F, Liu S. Clorf Encodes Carotenoid Isomerase and Regulates Orange Flesh Color in Watermelon ( Citrullus lanatus L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:15445-15455. [PMID: 37815876 DOI: 10.1021/acs.jafc.3c02122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2023]
Abstract
Flesh color is a significant characteristic of watermelon. Although various flesh-color genes have been identified, the inheritance and molecular basis of the orange flesh trait remain relatively unexplored. In the present study, the genetic analysis of six generations derived from W1-1 (red flesh) and W1-61 (orange flesh) revealed that the orange flesh color trait was regulated by a single recessive gene, Clorf (orange flesh). Bulk segregant analysis (BSA) locked the range to ∼4.66 Mb, and initial mapping situated the Clorf locus within a 688.35-kb region of watermelon chromosome 10. Another 1,026 F2 plants narrowed the Clorf locus to a 304.62-kb region containing 32 candidate genes. Subsequently, genome sequence variations in this 304.62-kb region were extracted for in silico BSA strategy among 11 resequenced lines (one orange flesh and ten nonorange flesh) and finally narrowed the Clorf locus into an 82.51-kb region containing nine candidate genes. Sequence variation analysis of coding regions and gene expression levels supports Cla97C10G200950 as the most possible candidate for Clorf, which encodes carotenoid isomerase (Crtiso). This study provides a genetic resource for investigating the orange flesh color of watermelon, with Clorf malfunction resulting in low lycopene accumulation and, thus, orange flesh.
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Affiliation(s)
- Xufeng Fang
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Shenglong Li
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Zicheng Zhu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Xian Zhang
- College of Horticulture, Northwest of A&F University, Yangling 712100, China
| | - Cheng Xiong
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Xuezheng Wang
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Feishi Luan
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Shi Liu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
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Tian S, Yang J, Fu Y, Zhang X, Zhang J, Zhao H, Hu Q, Liu P, He W, Han X, Wen C. McAPRR2: The Key Regulator of Domesticated Pericarp Color in Bitter Gourd. PLANTS (BASEL, SWITZERLAND) 2023; 12:3585. [PMID: 37896048 PMCID: PMC10610206 DOI: 10.3390/plants12203585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/07/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023]
Abstract
Pericarp color is a crucial commercial trait influencing consumer preferences for bitter gourds. However, until now, the gene responsible for this trait has remained unidentified. In this study, we identified a gene (McAPRR2) controlling pericarp color via a genome-wide association study (GWAS) utilizing the resequencing data of 106 bitter gourd accessions. McAPRR2 exhibits three primary haplotypes: Hap1 is a wild type with a green pericarp, Hap2 is a SA (South Asian) and SEA (Southeast Asia) type with a green pericarp, and Hap3 is primarily a SEA type with a light green pericarp. The McAPRR2 haplotype is significantly correlated with both pericarp color and ecological type. Importantly, McAPRR2 with the light green pericarp demonstrated premature termination due to a 15 bp sequence insertion. The phylogenetic tree clustered according to pericarp color and ecological type, using SNPs located in the McAPRR2 gene and its promoter. High πwild/SEA and πSA/SEA values indicate high nucleotide diversity between wild and SEA types and between SA and SEA types in the McAPRR2 gene. The haplotypes, phylogenetic tree, and nucleotide diversity of McAPRR2 suggest that McAPRR2 has undergone domestication selection. This study identifies McAPRR2 as the key gene determining pericarp color in bitter gourds and introduces a novel insight that McAPRR2 is subject to domestication selection.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Changlong Wen
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China (J.Y.); (J.Z.); (H.Z.)
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Katuuramu DN, Levi A, Wechter WP. Genetic control of flowering time and fruit yield in citron watermelon. FRONTIERS IN PLANT SCIENCE 2023; 14:1236576. [PMID: 37881618 PMCID: PMC10595160 DOI: 10.3389/fpls.2023.1236576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/18/2023] [Indexed: 10/27/2023]
Abstract
Flowering time and fruit yield are important traits in watermelon crop improvement. There is limited information on the inheritance and genomic loci underlying flowering time and yield performance, especially in citron watermelon. A total of 125 citron watermelon accessions were evaluated in field trials over two growing seasons for days to male and female flowers, fruit count, fruit weight, and fruit yield. The germplasm was genotyped with more than two million single-nucleotide polymorphism (SNP) markers generated via whole-genome resequencing. Trait mapping was conducted using a genome-wide association study (GWAS). Broad-sense heritability for all traits ranged from moderate to high, indicating that genetic improvement through breeding and selection is feasible. Significant marker-trait associations were uncovered for days to female flower (chromosomes Ca04, Ca05, Ca08, and Ca09), fruit count (on Ca02, Ca03, and Ca05), fruit weight (on Ca02, Ca06, Ca08, Ca10, and Ca11), and fruit yield on chromosomes Ca05, Ca07, and Ca09. The phenotypic variation explained by the significant SNPs ranged from 1.6 to 25.4, highlighting the complex genetic architecture of the evaluated traits. Candidate genes relevant to flowering time and fruit yield component traits were uncovered on chromosomes Ca02, Ca04, Ca05, Ca06, Ca09, and Ca11. These results lay a foundation for marker-assisted trait introgression of flowering time and fruit yield component traits in watermelons.
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30
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Wu S, Sun H, Gao L, Branham S, McGregor C, Renner SS, Xu Y, Kousik C, Wechter WP, Levi A, Fei Z. A Citrullus genus super-pangenome reveals extensive variations in wild and cultivated watermelons and sheds light on watermelon evolution and domestication. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1926-1928. [PMID: 37490004 PMCID: PMC10502741 DOI: 10.1111/pbi.14120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/09/2023] [Accepted: 06/25/2023] [Indexed: 07/26/2023]
Affiliation(s)
- Shan Wu
- Boyce Thompson InstituteIthacaNew YorkUSA
| | - Honghe Sun
- Boyce Thompson InstituteIthacaNew YorkUSA
- Plant Biology Section, School of Integrative Plant ScienceCornell UniversityIthacaNew YorkUSA
| | - Lei Gao
- Boyce Thompson InstituteIthacaNew YorkUSA
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed DesignChinese Academy of SciencesWuhanHubeiChina
| | - Sandra Branham
- Coastal Research and Educational CenterClemson UniversityCharlestonSouth CarolinaUSA
| | | | | | - Yong Xu
- National Engineering Research Center for VegetablesBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | | | - W. Patrick Wechter
- Coastal Research and Educational CenterClemson UniversityCharlestonSouth CarolinaUSA
| | - Amnon Levi
- USDA‐ARSU.S. Vegetable LaboratoryCharlestonSouth CarolinaUSA
| | - Zhangjun Fei
- Boyce Thompson InstituteIthacaNew YorkUSA
- USDA‐ARS Robert W. Holley Center for Agriculture and HealthIthacaNew YorkUSA
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Wang J, Wang Y, Yu Y, Zhang J, Ren Y, Tian S, Li M, Liao S, Guo S, Gong G, Zhang H, Xu Y. ClSnRK2.3 negatively regulates watermelon fruit ripening and sugar accumulation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2336-2348. [PMID: 37219233 DOI: 10.1111/jipb.13535] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/23/2023] [Indexed: 05/24/2023]
Abstract
Watermelon (Citrullus lanatus) as non-climacteric fruit is domesticated from the ancestors with inedible fruits. We previously revealed that the abscisic acid (ABA) signaling pathway gene ClSnRK2.3 might influence watermelon fruit ripening. However, the molecular mechanisms are unclear. Here, we found that the selective variation of ClSnRK2.3 resulted in lower promoter activity and gene expression level in cultivated watermelons than ancestors, which indicated ClSnRK2.3 might be a negative regulator in fruit ripening. Overexpression (OE) of ClSnRK2.3 significantly delayed watermelon fruit ripening and suppressed the accumulation of sucrose, ABA and gibberellin GA4 . Furthermore, we determined that the pyrophosphate-dependent phosphofructokinase (ClPFP1) in sugar metabolism pathway and GA biosynthesis enzyme GA20 oxidase (ClGA20ox) could be phosphorylated by ClSnRK2.3 and thereby resulting in accelerated protein degradation in OE lines and finally led to low levels of sucrose and GA4 . Besides that, ClSnRK2.3 phosphorylated homeodomain-leucine zipper protein (ClHAT1) and protected it from degradation to suppress the expression of the ABA biosynthesis gene 9'-cis-epoxycarotenoid dioxygenase 3 (ClNCED3). These results indicated that ClSnRK2.3 negatively regulated watermelon fruit ripening by manipulating the biosynthesis of sucrose, ABA and GA4 . Altogether, these findings revealed a novel regulatory mechanism in non-climacteric fruit development and ripening.
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Affiliation(s)
- Jinfang Wang
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, 100097, China
| | - Yanping Wang
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, 100097, China
| | - Yongtao Yu
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, 100097, China
| | - Jie Zhang
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, 100097, China
| | - Yi Ren
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, 100097, China
| | - Shouwei Tian
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, 100097, China
| | - Maoying Li
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, 100097, China
| | - Shengjin Liao
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, 100097, China
| | - Shaogui Guo
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, 100097, China
| | - Guoyi Gong
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, 100097, China
| | - Haiying Zhang
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, 100097, China
| | - Yong Xu
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, 100097, China
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32
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Goldman IL, Wang Y, Alfaro AV, Brainard S, Oravec MW, McGregor CE, van der Knaap E. Form and contour: breeding and genetics of organ shape from wild relatives to modern vegetable crops. FRONTIERS IN PLANT SCIENCE 2023; 14:1257707. [PMID: 37841632 PMCID: PMC10568141 DOI: 10.3389/fpls.2023.1257707] [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: 07/12/2023] [Accepted: 08/28/2023] [Indexed: 10/17/2023]
Abstract
Shape is a primary determinant of consumer preference for many horticultural crops and it is also associated with many aspects of marketing, harvest mechanics, and postharvest handling. Perceptions of quality and preference often map to specific shapes of fruits, tubers, leaves, flowers, roots, and other plant organs. As a result, humans have greatly expanded the palette of shapes available for horticultural crops, in many cases creating a series of market classes where particular shapes predominate. Crop wild relatives possess organs shaped by natural selection, while domesticated species possess organs shaped by human desires. Selection for visually-pleasing shapes in vegetable crops resulted from a number of opportunistic factors, including modification of supernumerary cambia, allelic variation at loci that control fundamental processes such as cell division, cell elongation, transposon-mediated variation, and partitioning of photosynthate. Genes that control cell division patterning may be universal shape regulators in horticultural crops, influencing the form of fruits, tubers, and grains in disparate species. Crop wild relatives are often considered less relevant for modern breeding efforts when it comes to characteristics such as shape, however this view may be unnecessarily limiting. Useful allelic variation in wild species may not have been examined or exploited with respect to shape modifications, and newly emergent information on key genes and proteins may provide additional opportunities to regulate the form and contour of vegetable crops.
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Affiliation(s)
- Irwin L. Goldman
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Yanbing Wang
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Andrey Vega Alfaro
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Scott Brainard
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Madeline W. Oravec
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Cecilia Elizabeth McGregor
- Department of Horticulture, University of Georgia, Athens, GA, United States
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Department of Horticulture, University of Georgia, Athens, GA, United States
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
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Liu M, Kang B, Wu H, Aranda MA, Peng B, Liu L, Fei Z, Hong N, Gu Q. Transcriptomic and metabolic profiling of watermelon uncovers the role of salicylic acid and flavonoids in the resistance to cucumber green mottle mosaic virus. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5218-5235. [PMID: 37235634 DOI: 10.1093/jxb/erad197] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 05/24/2023] [Indexed: 05/28/2023]
Abstract
Understanding the mechanisms underlying plant resistance to virus infections is crucial for viral disease management in agriculture. However, the defense mechanism of watermelon (Citrullus lanatus) against cucumber green mottle mosaic virus (CGMMV) infection remains largely unknown. In this study, we performed transcriptomic, metabolomic, and phytohormone analyses of a CGMMV susceptible watermelon cultivar 'Zhengkang No.2' ('ZK') and a CGMMV resistant wild watermelon accession PI 220778 (PI) to identify the key regulatory genes, metabolites, and phytohormones responsible for CGMMV resistance. We then tested several phytohormones and metabolites for their roles in watermelon CGMMV resistance via foliar application, followed by CGMMV inoculation. Several phenylpropanoid metabolism-associated genes and metabolites, especially those involved in the flavonoid biosynthesis pathway, were found to be significantly enriched in the CGMMV-infected PI plants compared with the CGMMV-infected 'ZK' plants. We also identified a gene encoding UDP-glycosyltransferase (UGT) that is involved in kaempferol-3-O-sophoroside biosynthesis and controls disease resistance, as well as plant height. Additionally, salicylic acid (SA) biogenesis increased in the CGMMV-infected 'ZK' plants, resulting in the activation of a downstream signaling cascade. SA levels in the tested watermelon plants correlated with that of total flavonoids, and SA pre-treatment up-regulated the expression of flavonoid biosynthesis genes, thus increasing the total flavonoid content. Furthermore, application of exogenous SA or flavonoids extracted from watermelon leaves suppressed CGMMV infection. In summary, our study demonstrates the role of SA-induced flavonoid biosynthesis in plant development and CGMMV resistance, which could be used to breed for CGMMV resistance in watermelon.
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Affiliation(s)
- Mei Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Baoshan Kang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Huijie Wu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Miguel A Aranda
- Centro de Edafología y Biología Aplicada del Segura (CEBAS)- CSIC, Apdo. correos 164, 30100 Espinardo, Murcia, Spain
| | - Bin Peng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Liming Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Ni Hong
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qinsheng Gu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
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Wang D, Chen Y, Zhu T, Wang J, Liu M, Tian S, Wang J, Yuan L. Developing a highly efficient CGBE base editor in watermelon. HORTICULTURE RESEARCH 2023; 10:uhad155. [PMID: 37719272 PMCID: PMC10500149 DOI: 10.1093/hr/uhad155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/01/2023] [Indexed: 09/19/2023]
Abstract
Cytosine and adenosine base editors (CBEs and ABEs) are novel genome-editing tools that have been widely utilized in molecular breeding to precisely modify single-nucleotide polymorphisms (SNPs) critical for plant agronomic traits and species evolution. However, conventional BE editors are limited to achieve C-to-T and A-to-G substitutions, respectively. To enhance the applicability of base editing technology in watermelon, we developed an efficient CGBE editor (SCGBE2.0) by removing the uracil glycosylase inhibitor (UGI) unit from the commonly used hA3A-CBE and incorporating the uracil-DNA glycosylase (UNG) component. Seven specific guide RNAs (sgRNAs) targeting five watermelon genes were designed to assess the editing efficiency of SCGBE. The results obtained from stably transformed watermelon plants demonstrated that SCGBE2.0 could efficiently induce C-to-G mutations at positions C5-C9 in 43.2% transgenic plants (with a maximum base conversion efficiency of 46.1%) and C-to-A mutation at position C4 in 23.5% transgenic plants (with a maximum base conversion efficiency of 45.9%). These findings highlight the capability of our integrated SCGBE2.0 editor to achieve C-to-G/A mutations in a site-preferred manner, thus providing an efficient base editing tool for precise base modification and site-directed saturated mutagenesis in watermelon.
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Affiliation(s)
- Dong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yani Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Tao Zhu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Man Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shujuan Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jiafa Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Li Yuan
- Corresponding author. E-mail:
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Guo WJ, Pommerrenig B, Neuhaus HE, Keller I. Interaction between sugar transport and plant development. JOURNAL OF PLANT PHYSIOLOGY 2023; 288:154073. [PMID: 37603910 DOI: 10.1016/j.jplph.2023.154073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 08/23/2023]
Abstract
Endogenous programs and constant interaction with the environment regulate the development of the plant organism and its individual organs. Sugars are necessary building blocks for plant and organ growth and at the same time act as critical integrators of the metabolic state into the developmental program. There is a growing recognition that the specific type of sugar and its subcellular or tissue distribution is sensed and translated to developmental responses. Therefore, the transport of sugars across membranes is a key process in adapting plant organ properties and overall development to the nutritional state of the plant. In this review, we discuss how plants exploit various sugar transporters to signal growth responses, for example, to control the development of sink organs such as roots or fruits. We highlight which sugar transporters are involved in root and shoot growth and branching, how intracellular sugar allocation can regulate senescence, and, for example, control fruit development. We link the important transport processes to downstream signaling cascades and elucidate the factors responsible for the integration of sugar signaling and plant hormone responses.
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Affiliation(s)
- Woei-Jiun Guo
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Benjamin Pommerrenig
- Department of Plant Physiology, University of Kaiserslautern, Erwin Schrödinger Str., 67663, Kaiserslautern, Germany
| | - H Ekkehard Neuhaus
- Department of Plant Physiology, University of Kaiserslautern, Erwin Schrödinger Str., 67663, Kaiserslautern, Germany
| | - Isabel Keller
- Department of Plant Physiology, University of Kaiserslautern, Erwin Schrödinger Str., 67663, Kaiserslautern, Germany.
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Yan H, Wang K, Wang M, Feng L, Zhang H, Wei X. QTL Mapping and Genome-Wide Association Study Reveal Genetic Loci and Candidate Genes Related to Soluble Solids Content in Melon. Curr Issues Mol Biol 2023; 45:7110-7129. [PMID: 37754234 PMCID: PMC10530127 DOI: 10.3390/cimb45090450] [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: 08/01/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/28/2023] Open
Abstract
Melon (Cucumis melo L.) is an economically important Cucurbitaceae crop grown around the globe. The sweetness of melon is a significant factor in fruit quality and consumer appeal, and the soluble solids content (SSC) is a key index of melon sweetness. In this study, 146 recombinant inbred lines (RILs) derived from two oriental melon materials with different levels of sweetness containing 1427 bin markers, and 213 melon accessions containing 1,681,775 single nucleotide polymorphism (SNP) markers were used to identify genomic regions influencing SSC. Linkage mapping detected 10 quantitative trait loci (QTLs) distributed on six chromosomes, seven of which were overlapped with the reported QTLs. A total of 211 significant SNPs were identified by genome-wide association study (GWAS), 138 of which overlapped with the reported QTLs. Two new stable, co-localized regions on chromosome 3 were identified by QTL mapping and GWAS across multiple environments, which explained large phenotypic variance. Five candidate genes related to SSC were identified by QTL mapping, GWAS, and qRT-PCR, two of which were involved in hydrolysis of raffinose and sucrose located in the new stable loci. The other three candidate genes were involved in raffinose synthesis, sugar transport, and production of substrate for sugar synthesis. The genomic regions and candidate genes will be helpful for molecular breeding programs and elucidating the mechanisms of sugar accumulation.
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Zhang K, Gao W, Zhou Y, Zhao H, Xia Y, Zhang M, Bo Y, Lyu X, Hu Z, Yang J, Zhang M. Allelic variations of ClACO gene improve nitrogen uptake via ethylene-mediated root architecture in watermelon. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:199. [PMID: 37624448 DOI: 10.1007/s00122-023-04448-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023]
Abstract
KEY MESSAGE The ClACO gene encoding 1-aminocyclopropane-1-carboxylate oxidase enabled highly efficient 15N uptake in watermelon. Nitrogen is one of the most essential nutrient elements that play a pivotal role in regulating plant growth and development for crop productivity. Elucidating the genetic basis of high nitrogen uptake is the key to improve nitrogen use efficiency for sustainable agricultural productivity. Whereas previous researches on nitrogen absorption process are mainly focused on a few model plants or crops. To date, the causal genes that determine the efficient nitrogen uptake of watermelon have not been mapped and remains largely unknown. Here, we fine-mapped the 1-aminocyclopropane-1-carboxylate oxidase (ClACO) gene associated with nitrogen uptake efficiency in watermelon via bulked segregant analysis (BSA). The variations in the ClACO gene led to the changes of gene expression levels between two watermelon accessions with different nitrogen uptake efficiencies. Intriguingly, in terms of the transcript abundance of ClACO, it was concomitant with significant differences in ethylene evolutions in roots and root architectures between the two accessions and among the different genotypic offsprings of the recombinant BC2F1(ZJU132)-18. These findings suggest that ethylene as a negative regulator altered nitrogen uptake efficiency in watermelon by controlling root development. In conclusion, our current study will provide valuable target gene for precise breeding of 'green' watermelon varieties with high-nitrogen uptake efficiencies.
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Affiliation(s)
- Kejia Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Wei Gao
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yimei Zhou
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Haoshun Zhao
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yuelin Xia
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Mengyi Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | | | - Xiaolong Lyu
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, China
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, China
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, China.
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Song B, Ning W, Wei D, Jiang M, Zhu K, Wang X, Edwards D, Odeny DA, Cheng S. Plant genome resequencing and population genomics: Current status and future prospects. MOLECULAR PLANT 2023; 16:1252-1268. [PMID: 37501370 DOI: 10.1016/j.molp.2023.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 05/30/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023]
Abstract
Advances in DNA sequencing technology have sparked a genomics revolution, driving breakthroughs in plant genetics and crop breeding. Recently, the focus has shifted from cataloging genetic diversity in plants to exploring their functional significance and delivering beneficial alleles for crop improvement. This transformation has been facilitated by the increasing adoption of whole-genome resequencing. In this review, we summarize the current progress of population-based genome resequencing studies and how these studies affect crop breeding. A total of 187 land plants from 163 countries have been resequenced, comprising 54 413 accessions. As part of resequencing efforts 367 traits have been surveyed and 86 genome-wide association studies have been conducted. Economically important crops, particularly cereals, vegetables, and legumes, have dominated the resequencing efforts, leaving a gap in 49 orders, including Lycopodiales, Liliales, Acorales, Austrobaileyales, and Commelinales. The resequenced germplasm is distributed across diverse geographic locations, providing a global perspective on plant genomics. We highlight genes that have been selected during domestication, or associated with agronomic traits, and form a repository of candidate genes for future research and application. Despite the opportunities for cross-species comparative genomics, many population genomic datasets are not accessible, impeding secondary analyses. We call for a more open and collaborative approach to population genomics that promotes data sharing and encourages contribution-based credit policy. The number of plant genome resequencing studies will continue to rise with the decreasing DNA sequencing costs, coupled with advances in analysis and computational technologies. This expansion, in terms of both scale and quality, holds promise for deeper insights into plant trait genetics and breeding design.
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Affiliation(s)
- Bo Song
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Weidong Ning
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Huazhong Agricultural University, College of Informatics, Hubei Key Laboratory of Agricultural Bioinformatics, Wuhan, Hubei, China
| | - Di Wei
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 53007, China
| | - Mengyun Jiang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Kun Zhu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Xingwei Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, Nairobi, Kenya
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
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Liu M, Wu H, Hong N, Kang B, Peng B, Liu L, Gu Q. Argonaute 1 and 5 proteins play crucial roles in the defence against cucumber green mottle mosaic virus in watermelon. MOLECULAR PLANT PATHOLOGY 2023; 24:961-972. [PMID: 37118922 PMCID: PMC10346368 DOI: 10.1111/mpp.13344] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/04/2023] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
RNA silencing, a core part of plants' antiviral defence, requires the ARGONAUTE, DICER-like, and RNA-dependent RNA polymerase proteins. However, how these proteins contribute to watermelon's RNA interference (RNAi) pathway response to cucumber green mottle mosaic virus (CGMMV) has not been characterized. Here, we identify seven ClAGO, four ClDCL, and 11 ClRDR genes in watermelon and analyse their expression profiles when infected with CGMMV. ClAGO1 and ClAGO5 expression levels were highly induced by CGMMV infection. The results of ClAGO1 and ClAGO5 overexpression and silencing experiments suggest that these genes play central roles in watermelon's antiviral defence. Furthermore, co-immunoprecipitation and bimolecular fluorescence complementation experiments showed that ClAGO1 interacts with ClAGO5 in vivo, suggesting that ClAGO1 and ClAGO5 co-regulate watermelon defence against CGMMV infection. We also identified the ethylene response factor (ERF) binding site in the promoters of the ClAGO1 and ClAGO5 genes, and ethylene (ETH) treatment significantly increased ClAGO5 expression. Two ERF genes (Cla97C08G147180 and Cla97C06G122830) closely related to ClAGO5 expression were identified using co-expression analysis. Subcellular localization revealed that two ERFs and ClAGO5 predominantly localize at the nucleus, suggesting that enhancement of resistance to CGMMV by ETH is probably achieved through ClAGO5 but not ClAGO1. Our findings reveal aspects of the mechanisms underlying RNA silencing in watermelon against CGMMV.
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Affiliation(s)
- Mei Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Huijie Wu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Ni Hong
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Baoshan Kang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Bin Peng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Liming Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Qinsheng Gu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
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Perez de Souza L, Bitocchi E, Papa R, Tohge T, Fernie AR. Decreased metabolic diversity in common beans associated with domestication revealed by untargeted metabolomics, information theory, and molecular networking. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1021-1036. [PMID: 37272491 DOI: 10.1111/tpj.16277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 04/28/2023] [Accepted: 05/03/2023] [Indexed: 06/06/2023]
Abstract
The process of crop domestication leads to a dramatic reduction in the gene expression associated with metabolic diversity. Genes involved in specialized metabolism appear to be particularly affected. Although there is ample evidence of these effects at the genetic level, a reduction in diversity at the metabolite level has been taken for granted despite having never been adequately accessed and quantified. Here we leveraged the high coverage of ultra high performance liquid chromatography-high-resolution mass spectrometry based metabolomics to investigate the metabolic diversity in the common bean (Phaseolus vulgaris). Information theory highlights a shift towards lower metabolic diversity and specialization when comparing wild and domesticated bean accessions. Moreover, molecular networking approaches facilitated a broader metabolite annotation than achieved to date, and its integration with gene expression data uncovers a metabolic shift from specialized metabolism towards central metabolism upon domestication of this crop.
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Affiliation(s)
- Leonardo Perez de Souza
- Max-Planck-Institute of Molecular Plant Physiology, Am Müehlenberg 1, Potsdam-Golm, 14476, Germany
| | - Elena Bitocchi
- Department of Agricultural, Food, and Environmental Sciences, Università Politecnica delle Marche, 60131, Ancona, Italy
| | - Roberto Papa
- Department of Agricultural, Food, and Environmental Sciences, Università Politecnica delle Marche, 60131, Ancona, Italy
| | - Takayuki Tohge
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara, 630-0192, Japan
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Müehlenberg 1, Potsdam-Golm, 14476, Germany
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Liu HN, Pei MS, Ampomah-Dwamena C, He GQ, Wei TL, Shi QF, Yu YH, Guo DL. Genome-wide characterization of long terminal repeat retrotransposons provides insights into trait evolution of four cucurbit species. Funct Integr Genomics 2023; 23:218. [PMID: 37393305 DOI: 10.1007/s10142-023-01128-7] [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: 11/26/2022] [Revised: 05/22/2023] [Accepted: 06/07/2023] [Indexed: 07/03/2023]
Abstract
Cucurbits are a diverse plant family that includes economically important crops, such as cucumber, watermelon, melon, and pumpkin. Knowledge of the roles that long terminal repeat retrotransposons (LTR-RTs) have played in diversification of cucurbit species is limited; to add to understanding of the roles of LTR-RTs, we assessed their distributions in four cucurbit species. We identified 381, 578, 1086, and 623 intact LTR-RTs in cucumber (Cucumis sativus L. var. sativus cv. Chinese Long), watermelon (Citrullus lanatus subsp. vulgaris cv. 97103), melon (Cucumis melo cv. DHL92), and Cucurbita (Cucurbita moschata var. Rifu), respectively. Among these LTR-RTs, the Ale clade of the Copia superfamily was the most abundant in all the four cucurbit species. Insertion time and copy number analysis revealed that an LTR-RT burst occurred approximately 2 million years ago in cucumber, watermelon, melon, and Cucurbita, and may have contributed to their genome size variation. Phylogenetic and nucleotide polymorphism analyses suggested that most LTR-RTs were formed after species diversification. Analysis of gene insertions by LTR-RTs revealed that the most frequent insertions were of Ale and Tekay and that genes related to dietary fiber synthesis were the most commonly affected by LTR-RTs in Cucurbita. These results increase our understanding of LTR-RTs and their roles in genome evolution and trait characterization in cucurbits.
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Affiliation(s)
- Hai-Nan Liu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, China
| | - Mao-Song Pei
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, China
| | | | - Guang-Qi He
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, China
| | - Tong-Lu Wei
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, China
| | - Qiao-Fang Shi
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, China
| | - Yi-He Yu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, China
| | - Da-Long Guo
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China.
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, China.
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Sun Y, Kou DR, Li Y, Ni JP, Wang J, Zhang YM, Wang QN, Jiang B, Wang X, Sun YX, Xu XT, Tan XJ, Zhang YJ, Kong XD. Pan-genome of Citrullus genus highlights the extent of presence/absence variation during domestication and selection. BMC Genomics 2023; 24:332. [PMID: 37322453 DOI: 10.1186/s12864-023-09443-w] [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: 01/19/2023] [Accepted: 06/11/2023] [Indexed: 06/17/2023] Open
Abstract
The rich genetic diversity in Citrullus lanatus and the other six species in the Citrullus genus provides important sources in watermelon breeding. Here, we present the Citrullus genus pan-genome based on the 400 Citrullus genus resequencing data, showing that 477 Mb contigs and 6249 protein-coding genes were absent in the Citrullus lanatus reference genome. In the Citrullus genus pan-genome, there are a total of 8795 (30.5%) genes that exhibit presence/absence variations (PAVs). Presence/absence variation (PAV) analysis showed that a lot of gene PAV were selected during the domestication and improvement, such as 53 favorable genes and 40 unfavorable genes were identified during the C. mucosospermus to C. lanatus landrace domestication. We also identified 661 resistance gene analogs (RGAs) in the Citrullus genus pan-genome, which contains 90 RGAs (89 variable and 1 core gene) located on the pangenome additional contigs. By gene PAV-based GWAS, 8 gene presence/absence variations were found associated with flesh color. Finally, based on the results of gene PAV selection analysis between watermelon populations with different fruit colors, we identified four non-reference candidate genes associated with carotenoid accumulation, which had a significantly higher frequency in the white flesh. These results will provide an important source for watermelon breeding.
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Affiliation(s)
- Yang Sun
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China.
| | - Dou-Rong Kou
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Yan Li
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
- Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | | | - Jing Wang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
- Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yong-Mei Zhang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Qing-Nan Wang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Bin Jiang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Xu Wang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Yue-Xin Sun
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Xin-Tong Xu
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Xiao-Juan Tan
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Yong-Jun Zhang
- Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Chen X, Li Y, Ai G, Chen J, Guo D, Zhu Z, Zhu X, Tian S, Wang J, Liu M, Yuan L. Creation of a watermelon haploid inducer line via ClDMP3-mediated single fertilization of the central cell. HORTICULTURE RESEARCH 2023; 10:uhad081. [PMID: 37323231 PMCID: PMC10261877 DOI: 10.1093/hr/uhad081] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 04/18/2023] [Indexed: 06/17/2023]
Abstract
The use of doubled haploids is one of the most efficient breeding methods in modern agriculture. Irradiation of pollen grains has been shown to induce haploids in cucurbit crops, possibly because it causes preferential fertilization of the central cell over the egg cell. Disruption of the DMP gene is known to induce single fertilization of the central cell, which can lead to the formation of haploids. In the present study, a detailed method of creating a watermelon haploid inducer line via ClDMP3 mutation is described. The cldmp3 mutant induced haploids in multiple watermelon genotypes at rates of up to 1.12%. These haploids were confirmed via fluorescent markers, flow cytometry, molecular markers, and immuno-staining. The haploid inducer created by this method has the potential to greatly advance watermelon breeding in the future.
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Affiliation(s)
- Xiner Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shanxi, China
| | - Yuxiu Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shanxi, China
| | - Gongli Ai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shanxi, China
| | - Jinfan Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shanxi, China
| | - Dalong Guo
- College of Horticulture and Plant Protection Henan University of Science and Technology, 471000, Luoyang, China
| | - Zhonghou Zhu
- Luoyang Nongfa Agricultural Technology Co., LTD, 471100, Luoyang, China
| | - Xuejie Zhu
- Luoyang Nongfa Agricultural Technology Co., LTD, 471100, Luoyang, China
| | - Shujuan Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shanxi, China
- Shenzhen Research Institute, Northwest A&F University, Shenzhen, 518000, Guangdong, China
| | - Jiafa Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shanxi, China
- Shenzhen Research Institute, Northwest A&F University, Shenzhen, 518000, Guangdong, China
| | - Man Liu
- Corresponding author. E-mail: ,
| | - Li Yuan
- Corresponding author. E-mail: ,
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Zang F, Ma Y, Wu Q, Tu X, Xie X, Huang P, Tong B, Zheng Y, Zang D. Resequencing of Rosa rugosa accessions revealed the history of population dynamics, breed origin, and domestication pathways. BMC PLANT BIOLOGY 2023; 23:235. [PMID: 37142995 PMCID: PMC10158352 DOI: 10.1186/s12870-023-04244-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 04/23/2023] [Indexed: 05/06/2023]
Abstract
BACKGROUND Rosa rugosa is a shrub that originated in China and has economic and ecological value. However, during the development of R. rugosa, the genetic background was chaotic, and the genetic structure among different wild populations was unclear, as well as wild and cultivated accessions. Here, we report whole-genome resequencing of wild and cultivated R. rugosa accessions. RESULTS A total of 19,041,284 SNPs were identified in 188 R. rugosa accessions and 3 R. chinensis accessions by resequencing. Population genetic analysis revealed that cultivated and wild groups were separated very early. All R. rugosa accessions were divided into 8 categories based on genetic structure: (1) Weihai, Yantai, and Liaoning category, (2) Jilin category, and (3) Hammonasset category (above three are wild); (4) traditional varieties, (5) hybrids between R. rugosa and R. chinensis, (6) Zizhi Rose, (7) Kushui Rose, (8) hybrids between R. rugosa and R. multiflora. We found that the heterozygosity and genetic diversity of wild accessions were generally lower than those of cultivated individuals. The genes that were selected during cultivation were identified, and it was found that these genes were mainly related to environmental adaptation and growth. CONCLUSIONS The Jilin population was the oldest population and later migrated to Liaoning and then migrated to Yantai and Weihai by sea regression in the Bohai Basin. The Hammonasset naturalized population probably originated from the Jilin population and then experienced separate differentiation. The long-term asexual reproduction pattern of R. rugosa decreased genetic diversity in the wild population. During R. rugosa cultivation, the ancestors of the Jilin population were involved in breeding traditional varieties, after which almost no wild individuals were engaged in breeding. However, in recent decades, cross breeding of R. rugosa started the utilization of wild germplasms. In comparison, some other species play important roles in variety formation. Few genes related to economic traits were selected, suggesting no directional domestication in the R. rugosa cultivation process.
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Affiliation(s)
- Fengqi Zang
- State Key Laboratory of Tree Genetics and Breeding, Laboratory of Forest Silviculture and Tree Cultivation, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, P. R. China
| | - Yan Ma
- College of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural University, Tai'an, 271018, Shandong, P. R. China
| | - Qichao Wu
- College of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural University, Tai'an, 271018, Shandong, P. R. China
| | - Xiaolong Tu
- State Key Laboratory of Genetic Resources and Evolution, Center for excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, P. R. China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming Yunnan, 650204, P. R. China
| | - Xiaoman Xie
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, 250102, P. R. China
| | - Ping Huang
- State Key Laboratory of Tree Genetics and Breeding, Laboratory of Forest Silviculture and Tree Cultivation, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, P. R. China
| | - Boqiang Tong
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, 250102, P. R. China
| | - Yongqi Zheng
- State Key Laboratory of Tree Genetics and Breeding, Laboratory of Forest Silviculture and Tree Cultivation, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, P. R. China.
| | - Dekui Zang
- College of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural University, Tai'an, 271018, Shandong, P. R. China.
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45
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Zheng W, Zhang W, Liu D, Yin M, Wang X, Wang S, Shen S, Liu S, Huang Y, Li X, Zhao Q, Yan L, Xu Y, Yu S, Hu B, Yuan T, Mei Z, Guo L, Luo J, Deng X, Xu Q, Huang L, Ma Z. Evolution-guided multiomics provide insights into the strengthening of bioactive flavone biosynthesis in medicinal pummelo. PLANT BIOTECHNOLOGY JOURNAL 2023. [PMID: 37115171 PMCID: PMC10363765 DOI: 10.1111/pbi.14058] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/20/2023] [Accepted: 03/31/2023] [Indexed: 06/19/2023]
Abstract
Pummelo (Citrus maxima or Citrus grandis) is a basic species and an important type for breeding in Citrus. Pummelo is used not only for fresh consumption but also for medicinal purposes. However, the molecular basis of medicinal traits is unclear. Here, compared with wild citrus species/Citrus-related genera, the content of 43 bioactive metabolites and their derivatives increased in the pummelo. Furthermore, we assembled the genome sequence of a variety for medicinal purposes with a long history, Citrus maxima 'Huazhouyou-tomentosa' (HZY-T), at the chromosome level with a genome size of 349.07 Mb. Comparative genomics showed that the expanded gene family in the pummelo genome was enriched in flavonoids-, terpenoid-, and phenylpropanoid biosynthesis. Using the metabolome and transcriptome of six developmental stages of HZY-T and Citrus maxima 'Huazhouyou-smooth' (HZY-S) fruit peel, we generated the regulatory networks of bioactive metabolites and their derivatives. We identified a novel MYB transcription factor, CmtMYB108, as an important regulator of flavone pathways. Both mutations and expression of CmtMYB108, which targets the genes PAL (phenylalanine ammonia-lyase) and FNS (flavone synthase), displayed differential expression between Citrus-related genera, wild citrus species and pummelo species. This study provides insights into the evolution-associated changes in bioactive metabolism during the origin process of pummelo.
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Affiliation(s)
- Weikang Zheng
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Wang Zhang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Dahui Liu
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Minqiang Yin
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Xia Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | | | | | - Shengjun Liu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Yue Huang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Xinxin Li
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Qian Zhao
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Lu Yan
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Yuantao Xu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Shiqi Yu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Bin Hu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Tao Yuan
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Zhinan Mei
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Lanping Guo
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou, China
| | - Xiuxin Deng
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Qiang Xu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhaocheng Ma
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
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Zhou C, Wang P, Zeng Q, Zeng R, Hu W, Sun L, Liu S, Luan F, Zhu Q. Comparative chloroplast genome analysis of seven extant Citrullus species insight into genetic variation, phylogenetic relationships, and selective pressure. Sci Rep 2023; 13:6779. [PMID: 37185306 PMCID: PMC10130142 DOI: 10.1038/s41598-023-34046-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 04/23/2023] [Indexed: 05/17/2023] Open
Abstract
Citrullus ecirrhosus, Citrullus rehmii, and Citrullus naudinianus are three important related wild species of watermelon in the genus Citrullus, and their morphological differences are clear, however, their chloroplast genome differences remain unknown. This study is the first to assemble, analyze, and publish the complete chloroplast genomes of C. ecirrhosus, C. rehmii, and C. naudinianus. A comparative analysis was then conducted among the complete chloroplast genomes of seven extant Citrullus species, and the results demonstrated that the average genome sizes of Citrullus is 157,005 bp, a total of 130-133 annotated genes were identified, including 8 rRNA, 37 tRNA and 85-88 protein-encoding genes. Their gene content, order, and genome structure were similar. However, noncoding regions were more divergent than coding regions, and rps16-trnQ was a hypervariable fragment. Thirty-four polymorphic SSRs, 1,271 SNPs and 234 INDELs were identified. Phylogenetic trees revealed a clear phylogenetic relationship of Citrullus species, and the developed molecular markers (SNPs and rps16-trnQ) could be used for taxonomy in Citrullus. Three genes (atpB, clpP1, and rpoC2) were identified to undergo selection and would promote the environmental adaptation of Citrullus.
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Affiliation(s)
- Cong Zhou
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, NO. 1101 Zhimin Street, Qingshanhu District, Nanchang, 330045, People's Republic of China
| | - Putao Wang
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, NO. 1101 Zhimin Street, Qingshanhu District, Nanchang, 330045, People's Republic of China
| | - Qun Zeng
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, NO. 1101 Zhimin Street, Qingshanhu District, Nanchang, 330045, People's Republic of China
| | - Rongbin Zeng
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, NO. 1101 Zhimin Street, Qingshanhu District, Nanchang, 330045, People's Republic of China
| | - Wei Hu
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, NO. 1101 Zhimin Street, Qingshanhu District, Nanchang, 330045, People's Republic of China
| | - Lei Sun
- Department of Agronomy and Horticulture, Liaoning Agricultural Technical College, Yingkou, 115009, People's Republic of China
| | - Shi Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Feishi Luan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Qianglong Zhu
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, NO. 1101 Zhimin Street, Qingshanhu District, Nanchang, 330045, People's Republic of China.
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Mi Q, Pang H, Luan F, Gao P, Liu S. Integrated analysis of biparental and natural populations reveals CRIB domain-containing protein underlying seed coat crack trait in watermelon. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:95. [PMID: 37014431 DOI: 10.1007/s00122-023-04320-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/07/2023] [Indexed: 06/19/2023]
Abstract
The scc locus of the watermelon seed coat crack trait was fine mapped on chromosome 3. Cla97C03G056110 (annotated as CRIB domain-containing protein) was regarded as the most likely candidate gene Seed coat crack (scc) is a special characteristic of watermelon compared with other cucurbit crops. However, information regarding the genetic basis of this trait is limited. We conducted a genetic analysis of six generations derived from PI 192938 (scc) and Cream of Saskatchewan (COS) (non-scc) parental lines and found that the scc trait was regulated by a single recessive gene through two years. Bulk segregant analysis sequencing (BSA-seq) and initial mapping placed the scc locus into an 808.8 kb region on chromosome 3. Evaluation of another 1152 F2 plants narrowed the scc locus to a 277.11 kb region containing 37 candidate genes. Due to the lack of molecular markers in the fine-mapping interval, we extracted the genome sequence variations in this 277.11 kb region with in silico BSA among seventeen re-sequenced lines (6 scc and 11 non-scc) and finally delimited the scc locus to an 8.34 kb region with only one candidate gene Cla97C03G056110 (CRIB domain-containing protein). Three single nucleotide polymorphism loci in the promoter region of Cla97C03G056110 altered cis-acting elements that were highly correlated with the nature watermelon panel. The expression of Cla97C03G056110 in seed coat tissue was higher in non-scc than in scc lines and was specifically expressed in seed coat compared with fruit flesh.
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Affiliation(s)
- Qi Mi
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, Heilongjiang Province, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, Heilongjiang Province, China
| | - Hongqian Pang
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, Heilongjiang Province, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, Heilongjiang Province, China
| | - Feishi Luan
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, Heilongjiang Province, China.
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, Heilongjiang Province, China.
| | - Peng Gao
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, Heilongjiang Province, China.
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, Heilongjiang Province, China.
| | - Shi Liu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, Heilongjiang Province, China.
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, Heilongjiang Province, China.
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48
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Gong C, He N, Zhu H, Anees M, Lu X, Liu W. Multi-omics integration to explore the molecular insight into the volatile organic compounds in watermelon. Food Res Int 2023; 166:112603. [PMID: 36914327 DOI: 10.1016/j.foodres.2023.112603] [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: 11/04/2022] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023]
Abstract
A range of volatile organic compounds played an important role in the formation of watermelon fruit aroma, while due to the low content and difficulty in detection, it is often neglected in watermelon breeding programs, resulting in a decline in fruit flavor. VOCs in the flesh of 194 watermelon accessions and seven cultivars at four developmental stages were determined by SPME-GC-MS. Ten metabolites with significant differences in the natural population and positive accumulation during fruit development are considered to be the key metabolite related to watermelon fruit aroma. And the link between metabolite and, flesh color and sugar content by correlation analysis was established. The results of the genome-wide association study showed that (5E)-6,10-dimethylundeca-5,9-dien-2-one, and 1-(4-methylphenyl) ethanone were colocalized with watermelon flesh color on chromosome 4, which may be regulated by LCYB and CCD. (E)-4-(2,6,6-trimethylcyclohexen-1-yl)but-3-en-2-one is the VOC produced by the cleavage of carotenoids, which has a positive correlation with the sugar content of the fruit, and the candidate gene Cla97C05G092490 on chromosome 5 may interact with PSY to influence the accumulation of this metabolite. In addition, Cla97C02G049790 (enol reductase), Cla97C03G051490 (omega-3 fatty acid desaturase gene), LOX, and ADH may play important roles in the synthesis of fatty acids and their derived VOCs. Taken together, our findings provide molecular insights into the accumulation and natural variation of VOCs in watermelon, and give data support for breeding watermelon cultivars with better flavor.
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Affiliation(s)
- Chengsheng Gong
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
| | - Nan He
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Hongju Zhu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Muhammad Anees
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Xuqiang Lu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Wenge Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
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49
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Song H, Wang Q, Zhang Z, Lin K, Pang E. Identification of clade-wide putative cis-regulatory elements from conserved non-coding sequences in Cucurbitaceae genomes. HORTICULTURE RESEARCH 2023; 10:uhad038. [PMID: 37799630 PMCID: PMC10548412 DOI: 10.1093/hr/uhad038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 02/20/2023] [Indexed: 10/07/2023]
Abstract
Cis-regulatory elements regulate gene expression and play an essential role in the development and physiology of organisms. Many conserved non-coding sequences (CNSs) function as cis-regulatory elements. They control the development of various lineages. However, predicting clade-wide cis-regulatory elements across several closely related species remains challenging. Based on the relationship between CNSs and cis-regulatory elements, we present a computational approach that predicts the clade-wide putative cis-regulatory elements in 12 Cucurbitaceae genomes. Using 12-way whole-genome alignment, we first obtained 632 112 CNSs in Cucurbitaceae. Next, we identified 16 552 Cucurbitaceae-wide cis-regulatory elements based on collinearity among all 12 Cucurbitaceae plants. Furthermore, we predicted 3 271 potential regulatory pairs in the cucumber genome, of which 98 were verified using integrative RNA sequencing and ChIP sequencing datasets from samples collected during various fruit development stages. The CNSs, Cucurbitaceae-wide cis-regulatory elements, and their target genes are accessible at http://cmb.bnu.edu.cn/cisRCNEs_cucurbit/. These elements are valuable resources for functionally annotating CNSs and their regulatory roles in Cucurbitaceae genomes.
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Affiliation(s)
- Hongtao Song
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Qi Wang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Zhonghua Zhang
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Kui Lin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Erli Pang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
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50
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Liu S, Liu M, Cao Y, Xu Y, Liu H, Zhu Q, Zhang X, Luan F. Identification of chromosome region and candidate genes for canary-yellow flesh (Cyf) locus in watermelon (Citrullus lanatus). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 329:111594. [PMID: 36642105 DOI: 10.1016/j.plantsci.2023.111594] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Genetic control of fruit flesh color in watermelon is complex, and significant knowledge gaps still exist. In the present study, we investigated the genetic basis of canary-yellow flesh color in watermelon inbred line PI 635597 using a segregating population derived from a cross between PI 635597 and another inbred line, Cream of Saskatchewan (pale yellow flesh color). We showed that a single dominant gene controls the canary-yellow flesh color for the Cyf (canary-yellow flesh) trait. Bulk segregant analysis (BSA) and fine genetic mapping narrowed down the Cyf locus to a 79.62-kb region on chromosome 6, which harbors 10 predicted genes. Sequence variation analysis in the promoter and coding regions and gene expression analysis in both parental lines and selected watermelon accessions with diverse fruit flesh colors support Cla97C06G122050 (unknown protein) and Cla97C06G122120 (pentatricopeptide repeat) as predicted candidate genes for the Cyf locus. Marker-assisted selection and sequence alignment showed that the Cyf locus could differentiate canary-yellow flesh and pale-yellow flesh. Our results indicate that the Cyf locus might be responsible for canary-yellow flesh color and carotenoid accumulation levels.
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Affiliation(s)
- Shi Liu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, Heilongjiang Province, China; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang Province, China.
| | - Mengqiu Liu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, Heilongjiang Province, China; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang Province, China.
| | - Yue Cao
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, Heilongjiang Province, China; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang Province, China.
| | - Yan Xu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, Heilongjiang Province, China; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang Province, China.
| | - Hongyu Liu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, Heilongjiang Province, China; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang Province, China.
| | - Qianglong Zhu
- Agronomy College, Jiangxi Agricultural University, Nanchang, Jiangxi Province, China.
| | - Xian Zhang
- College of Horticulture, Northwest of A&F University, Yangling, Shaanxi Province, China.
| | - Feishi Luan
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, Heilongjiang Province, China; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang Province, China.
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