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Zhang Z, Zhang H, Liu J, Chen K, Wang Y, Zhang G, Li L, Yue H, Weng Y, Li Y, Chen P. The mutation of CsSUN, an IQD family protein, is responsible for the short and fat fruit (sff) in cucumber (Cucumis sativus L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112177. [PMID: 38964612 DOI: 10.1016/j.plantsci.2024.112177] [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: 05/11/2024] [Revised: 06/20/2024] [Accepted: 06/30/2024] [Indexed: 07/06/2024]
Abstract
The fruit shape of cucumber is an important agronomic trait, and mining regulatory genes, especially dominant ones, is vital for cucumber breeding. In this study, we identified a short and fat fruit mutant, named sff, from an EMS mutagenized population. Compared to the CCMC (WT), sff (MT) exhibited reduced fruit length and increased dimeter. Segregation analysis revealed that the sff phenotype is controlled by a semi-dominant single gene with dosage effects. Through map-based cloning, the SFF locus was narrowed down to a 52.6 kb interval with two SNPs (G651A and C1072T) in the second and third exons of CsaV3_1G039870, which encodes an IQD family protein, CsSUN. The G651A within the IQ domain of CsSUN was identified as the unique SNP among 114 cucumber accessions, and it was the primary cause of the functional alteration in CsSUN. By generating CsSUN knockout lines in cucumber, we confirmed that CsSUN was responsible for sff mutant phenotype. The CsSUN is localized to the plasma membrane. CsSUN exhibited the highest expression in the fruit with lower expression in sff compared to WT. Histological observations suggest that the sff mutant phenotype is due to increased transverse cell division and inhibited longitudinal cell division. Transcriptome analysis revealed that CsSUN significantly affected the expression of genes related to cell division, expansion, and auxin signal transduction. This study unveils CsSUN's crucial role in shaping cucumber fruit and offers novel insights for cucumber breeding.
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Affiliation(s)
- Zhengao Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Haiqiang Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Junyan Liu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kang Chen
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yixin Wang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gaoyuan Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Lixia Li
- College of Horticulture, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| | - Hongzhong Yue
- Vegetable Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu 730070, China
| | - Yiqun Weng
- USDA-ARS Vegetable Crops Research Unit, University of Wisconsin, Madison, WI 53706, USA
| | - Yuhong Li
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Peng Chen
- College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, 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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Liu T, Dong Y, Gao S, Zhou Y, Liu D, Wang J, Liu Z, Deng Y, Li F. Identification of CaPCR1, an OFP gene likely involved in pointed versus concave fruit tip regulation in pepper (Capsicum annuum L.) using recombinant inbred lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:161. [PMID: 38874630 DOI: 10.1007/s00122-024-04675-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 06/09/2024] [Indexed: 06/15/2024]
Abstract
KEY MESSAGE CaPCR1 (Capana12g002165) was a candidate gene regulating fruit concave/pointed tip shape in pepper. The concave shape of the fruit tip in pepper plants is highly susceptible to drought and low temperature stresses, resulting in the appearance of a pointed tip fruit, which affects its commercial value. However, few studies on the process of fruit tip development and regulatory genes in pepper have been reported. Herein, the developmental process of the ovary before anthesis, especially changes in the shape of the ovary tip, was studied in detail. The results showed that the final fruit tip shape was consistent with the ovary tip shape before anthesis, and a concave tip shape gradually developed. F4 recombinant inbred lines (RILs) were constructed to map the genes regulating fruit tip shape through hybridization of the LRS and SBS pepper inbred lines. CaPCR1 (Capana12g002165), an OFP (OVATE Family Protein) family gene, was located in the candidate region on chr12. Three SNPs were found in the protein coding sequence of CaPCR1 between SBS and LRS, but only one SNP led to amino acid variation. Sequence variations, including base replacements, deletions and insertions, were also detected in the gene promoter region. The relative expression level of the CaPCR1 gene was significantly greater in the concave tip ovary than in the pointed tip ovary. qRT‒PCR analysis revealed that the CaPCR1 gene was expressed mainly in the gynoecium, placenta and green fruit pericarp, which was consistent with its function in ovary and fruit development. Taken together, these results suggested that CaPCR1 is a candidate gene involved in fruit tip shape determination in pepper.
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Affiliation(s)
- Tingting Liu
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Traditional Chinese Medicine College, Bozhou University, Bozhou, 236800, Anhui, China
| | - Yiping Dong
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Shenting Gao
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yingjia Zhou
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Dan Liu
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jubin Wang
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhenya Liu
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yingtian Deng
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Feng Li
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, Hubei, China.
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Panda M, Pradhan S, Mukherjee PK. Transcriptomics reveal useful resources for examining fruit development and variation in fruit size in Coccinia grandis. FRONTIERS IN PLANT SCIENCE 2024; 15:1386041. [PMID: 38863541 PMCID: PMC11165041 DOI: 10.3389/fpls.2024.1386041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 05/09/2024] [Indexed: 06/13/2024]
Abstract
Introduction The Cucurbitaceae family comprises many agronomically important members, that bear nutritious fruits and vegetables of great economic importance. Coccinia grandis, commonly known as Ivy gourd, belongs to this family and is widely consumed as a vegetable. Members of this family are known to display an impressive range of variation in fruit morphology. Although there have been studies on flower development in Ivy gourd, fruit development remains unexplored in this crop. Methods In this study, comparative transcriptomics of two Ivy gourd cultivars namely "Arka Neelachal Kunkhi" (larger fruit size) and "Arka Neelachal Sabuja" (smaller fruit size) differing in their average fruit size was performed. A de novo transcriptome assembly for Ivy gourd was developed by collecting fruits at different stages of development (5, 10, 15, and 20 days after anthesis i.e. DAA) from these two varieties. The transcriptome was analyzed to identify differentially expressed genes, transcription factors, and molecular markers. Results The transcriptome of Ivy gourd consisted of 155205 unigenes having an average contig size of 1472bp. Unigenes were annotated on publicly available databases to categorize them into different biological functions. Out of these, 7635 unigenes were classified into 38 transcription factor (TF) families, of which Trihelix TFs were most abundant. A total of 11,165 unigenes were found to be differentially expressed in both the varieties and the in silico expression results were validated through real-time PCR. Also, 98768 simple sequence repeats (SSRs) were identified in the transcriptome of Ivy gourd. Discussion This study has identified a number of genes, including transcription factors, that could play a crucial role in the determination of fruit shape and size in Ivy gourd. The presence of polymorphic SSRs indicated a possibility for marker-assisted selection for crop breeding in Ivy gourd. The information obtained can help select candidate genes that may be implicated in regulating fruit development and size in other fruit crops.
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Affiliation(s)
- Mitrabinda Panda
- Biotechnology Research Innovation Council-Institute of Life Sciences (BRIC-ILS), Bhubaneswar, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Seema Pradhan
- Biotechnology Research Innovation Council-Institute of Life Sciences (BRIC-ILS), Bhubaneswar, India
| | - Pulok K. Mukherjee
- Biotechnology Research Innovation Council-Institute of Bioresources and Sustainable Development (BRIC-IBSD), Imphal, India
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Zhou Y, Zhao M, Shen Q, Zhang M, Wang C, Zhang Y, Yang Q, Bo Y, Hu Z, Yang J, Zhang M, Lyu X. Genetic mapping reveals a candidate gene CmoFL1 controlling fruit length in pumpkin. FRONTIERS IN PLANT SCIENCE 2024; 15:1408602. [PMID: 38867882 PMCID: PMC11168575 DOI: 10.3389/fpls.2024.1408602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/06/2024] [Indexed: 06/14/2024]
Abstract
Fruit length (FL) is an important economical trait that affects fruit yield and appearance. Pumpkin (Cucurbita moschata Duch) contains a wealth genetic variation in fruit length. However, the natural variation underlying differences in pumpkin fruit length remains unclear. In this study, we constructed a F2 segregate population using KG1 producing long fruit and MBF producing short fruit as parents to identify the candidate gene for fruit length. By bulked segregant analysis (BSA-seq) and Kompetitive Allele-Specific PCR (KASP) approach of fine mapping, we obtained a 50.77 kb candidate region on chromosome 14 associated with the fruit length. Then, based on sequence variation, gene expression and promoter activity analyses, we identified a candidate gene (CmoFL1) encoding E3 ubiquitin ligase in this region may account for the variation of fruit length. One SNP variation in promoter of CmoFL1 changed the GT1CONSENSUS, and DUAL-LUC assay revealed that this variation significantly affected the promoter activity of CmoFL1. RNA-seq analysis indicated that CmoFL1 might associated with the cell division process and negatively regulate fruit length. Collectively, our work identifies an important allelic affecting fruit length, and provides a target gene manipulating fruit length in future pumpkin 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
| | - Meng Zhao
- 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
| | - Mengyi Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
| | - Chenhao Wang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yutong Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Qinrong Yang
- 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, 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, 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, Sanya, China
- Key laboratory of Horticultural Plant growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, China
| | - Xiaolong Lyu
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
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Xiao J, Huang J, Xiao K, Li G, Yang S, He Y. How different of the rhizospheric and endophytic microbial compositions in watermelons with different fruit shapes. PLoS One 2024; 19:e0302462. [PMID: 38753836 PMCID: PMC11098346 DOI: 10.1371/journal.pone.0302462] [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: 11/06/2023] [Accepted: 04/03/2024] [Indexed: 05/18/2024] Open
Abstract
Fruit shape is an important character of watermelon. And the compositions of rhizospheric and endophytic microorganisms of watermelon with different fruit shape also remains unclear. To elucidate the biological mechanism of watermelon fruit shape formations, the rhizospheric and endophytic microbial community compositions between oval (OW) and circular watermelons (CW) were analyzed. The results showed that except of the rhizospheric bacterial richness (P < 0.05), the rhizospheric and endophytic microbial (bacterial and fungal) diversity were not statistically significant between OW and CW (P > 0.05). However, the endophytic microbial (bacterial and fungal) compositions were significantly different. Firstly, Bacillus, Rhodanobacter, Cupriavidus, Luteimonas, and Devosia were the unique soil dominant bacterial genera in rhizospheres of circular watermelon (CW); In contrast, Nocardioides, Ensifer, and Saccharomonospora were the special soil dominant bacterial genera in rhizospheres of oval watermelons (OW); Meanwhile, Cephalotrichum, Neocosmospora, Phialosimplex, and Papulaspora were the unique soil dominant fungal genera in rhizospheres of circular watermelon (CW); By contrast, Acremonium, Cladosporium, Cryptococcus_f__Tremellaceae, Sodiomyces, Microascus, Conocybe, Sporidiobolus, and Acremonium were the unique soil dominant fungal genera in rhizospheres of oval watermelons (OW). Additionally, Lechevalieria, Pseudorhodoferax, Pseudomonas, Massilia, Flavobacterium, Aeromicrobium, Stenotrophomonas, Pseudonocardia, Novosphingobium, Melittangium, and Herpetosiphon were the unique dominant endophytic bacterial genera in stems of CW; In contrast, Falsirhodobacter, Kocuria, and Kineosporia were the special dominant endophytic genera in stems of OW; Moreover, Lectera and Fusarium were the unique dominant endophytic fungal genera in stems of CW; By contrast, Cercospora only was the special dominant endophytic fungal genus in stems of OW. All above results suggested that watermelons with different fruit shapes exactly recruited various microorganisms in rhizospheres and stems. Meanwhile, the enrichments of the different rhizosphric and endophytic microorganisms could be speculated in relating to watermelon fruit shapes formation.
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Affiliation(s)
- Jian Xiao
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, National Demonstration Center for Experimental Plant Science Education, Agricultural College, Guangxi University, Nanning, 530004, P. R. China
- Longping Branch, College of Biology, Hunan University, Changsha, 410125, Hunan, P. R. China
| | - Jinyan Huang
- Horticultural Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, P. R. China
| | - Kezhuo Xiao
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, National Demonstration Center for Experimental Plant Science Education, Agricultural College, Guangxi University, Nanning, 530004, P. R. China
| | - Guifen Li
- Horticultural Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, P. R. China
| | - Shangdong Yang
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, National Demonstration Center for Experimental Plant Science Education, Agricultural College, Guangxi University, Nanning, 530004, P. R. China
| | - Yi He
- Horticultural Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, P. R. China
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Jiang Q, Wang P, Xu Y, Zou B, Huang S, Wu Y, Li Y, Zhong C, Yu W. Fine mapping of TFL, a major gene regulating fruit length in snake gourd (Trichosanthes anguina L). BMC PLANT BIOLOGY 2024; 24:286. [PMID: 38627660 PMCID: PMC11020775 DOI: 10.1186/s12870-024-04952-6] [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: 11/08/2023] [Accepted: 03/27/2024] [Indexed: 04/19/2024]
Abstract
Fruit length is a crucial agronomic trait of snake gourd (Trichosanthes anguina L); however, genes associated with fruit length have not been characterised. In this study, F2 snake gourd populations were generated by crossing the inbred lines, S1 and S2 (fruit lengths: 110 and 20 cm, respectively). Subsequently, bulk segregant analysis, sequencing, and fine-mapping were performed on the F2 population to identify target genes. Our findings suggest that the fruit length of snake gourd is regulated by a major-effect regulatory gene. Mining of genes regulating fruit length in snake gourd to provide a basis for subsequent selection and breeding of new varieties. Genotype-phenotype association analysis was performed on the segregating F2 population comprising 6,000 plants; the results indicate that the target gene is located on Chr4 (61,846,126-61,865,087 bp, 18.9-kb interval), which only carries the annotated candidate gene, Tan0010544 (designated TFL). TFL belongs to the MADS-box family, one of the largest transcription factor families. Sequence analysis revealed a non-synonymous mutation of base C to G at position 202 in the coding sequence of TFL, resulting in the substitution of amino acid Gln to Glu at position 68 in the protein sequence. Subsequently, an InDel marker was developed to aid the marker-assisted selection of TFL. The TFL in the expression parents within the same period was analysed using quantitative real-time PCR; the TFL expression was significantly higher in short fruits than long fruits. Therefore, TFL can be a candidate gene for determining the fruit length in snake gourd. Collectively, these findings improve our understanding of the genetic components associated with fruit length in snake gourds, which could aid the development of enhanced breeding strategies for plant species.
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Affiliation(s)
- Qingwei Jiang
- College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
- Yulin Normal College, Yulin, Guangxi, 537000, China
| | - Peng Wang
- College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
| | - Yuanchao Xu
- Shenzhen Key Laboratory of Agricultural Synthetic Biology, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Bingying Zou
- College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
| | - Shishi Huang
- College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
| | - Yuancai Wu
- College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
| | - Yongqiang Li
- College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
| | - Chuan Zhong
- College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
| | - Wenjin Yu
- College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China.
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Bao Z, Guo Y, Deng Y, Zang J, Zhang J, Deng Y, Ouyang B, Qu X, Bürstenbinder K, Wang P. Microtubule-associated protein SlMAP70 interacts with IQ67-domain protein SlIQD21a to regulate fruit shape in tomato. THE PLANT CELL 2023; 35:4266-4283. [PMID: 37668409 PMCID: PMC10689142 DOI: 10.1093/plcell/koad231] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/01/2023] [Accepted: 08/06/2023] [Indexed: 09/06/2023]
Abstract
Tomato (Solanum lycopersicum) fruit shape is related to microtubule organization and the activity of microtubule-associated proteins (MAPs). However, insights into the mechanism of fruit shape formation from a cell biology perspective remain limited. Analysis of the tissue expression profiles of different microtubule regulators revealed that functionally distinct classes of MAPs, including members of the plant-specific MICROTUBULE-ASSOCIATED PROTEIN 70 (MAP70) and IQ67 DOMAIN (IQD, also named SUN in tomato) families, are differentially expressed during fruit development. SlMAP70-1-3 and SlIQD21a are highly expressed during fruit initiation, which relates to the dramatic microtubule pattern rearrangements throughout this developmental stage of tomato fruits. Transgenic tomato lines overexpressing SlMAP70-1 or SlIQD21a produced elongated fruits with reduced cell circularity and microtubule anisotropy, while their loss-of-function mutants showed the opposite phenotype, harboring flatter fruits. Fruits were further elongated in plants coexpressing both SlMAP70-1 and SlIQD21a. We demonstrated that SlMAP70s and SlIQD21a physically interact and that the elongated fruit phenotype is likely due to microtubule stabilization induced by the SlMAP70-SlIQD21a interaction. Together, our results identify SlMAP70 proteins and SlIQD21a as important regulators of fruit elongation and demonstrate that manipulating microtubule function during early fruit development provides an effective approach to alter fruit shape.
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Affiliation(s)
- Zhiru Bao
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Ye Guo
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yaling Deng
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jingze Zang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Junhong Zhang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingtian Deng
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Bo Ouyang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaolu Qu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Katharina Bürstenbinder
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle (Saale) 06120, Germany
| | - Pengwei Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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9
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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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10
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Ding H, Zhou G, Zhao L, Li X, Wang Y, Xia C, Xia Z, Wan Y. Genome-Wide Association Analysis of Fruit Shape-Related Traits in Areca catechu. Int J Mol Sci 2023; 24:ijms24054686. [PMID: 36902116 PMCID: PMC10003628 DOI: 10.3390/ijms24054686] [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: 02/02/2023] [Revised: 02/20/2023] [Accepted: 02/24/2023] [Indexed: 03/04/2023] Open
Abstract
The areca palm (Areca catechu L.) is one of the most economically important palm trees in tropical areas. To inform areca breeding programs, it is critical to characterize the genetic bases of the mechanisms that regulate areca fruit shape and to identify candidate genes related to fruit-shape traits. However, few previous studies have mined candidate genes associated with areca fruit shape. Here, the fruits produced by 137 areca germplasms were divided into three categories (spherical, oval, and columnar) based on the fruit shape index. A total of 45,094 high-quality single-nucleotide polymorphisms (SNPs) were identified across the 137 areca cultivars. Phylogenetic analysis clustered the areca cultivars into four subgroups. A genome-wide association study that used a mixed linear model identified the 200 loci that were the most significantly associated with fruit-shape traits in the germplasms. In addition, 86 candidate genes associated with areca fruit-shape traits were further mined. Among the proteins encoded by these candidate genes were UDP-glucosyltransferase 85A2, the ABA-responsive element binding factor GBF4, E3 ubiquitin-protein ligase SIAH1, and LRR receptor-like serine/threonine-protein kinase ERECTA. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed that the gene that encoded UDP-glycosyltransferase, UGT85A2, was significantly upregulated in columnar fruits as compared to spherical and oval fruits. The identification of molecular markers that are closely related to fruit-shape traits not only provides genetic data for areca breeding, but it also provides new insights into the shape formation mechanisms of drupes.
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Chen J, Pan B, Li Z, Xu Y, Cao X, Jia J, Shen H, Sun L. Fruit shape loci sun, ovate, fs8.1 and their interactions affect seed size and shape in tomato. FRONTIERS IN PLANT SCIENCE 2023; 13:1091639. [PMID: 36714752 PMCID: PMC9879704 DOI: 10.3389/fpls.2022.1091639] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
Seed size and shape are not only critical for plant reproduction and dispersal, but also important agronomic traits. Tomato fruit shape loci sun, ovate and fs8.1 regulate the morphology of fruit, flower, leaf and stem, and recently their functions in seed morphogenesis have also been noticed. However, mechanism underlying seed morphology variation has not been systematically investigated yet. Thus, using the near isogenic lines (NILs) harboring one, two or three of the fruit shape loci, histological, physiological and transcriptional bases of seed morphology change have been studied. sun and ovate showed potential abilities in decreasing seed size, whereas, fs8.1 had a potential ability in increasing this parameter. Interactions between two loci and the interaction among three loci all led to significant decrease of seed size. All the loci significantly down-regulated seed shape index (SSI), except for sun/fs8.1 double NIL, which resulted in the reductions in both seed length and width and finally led to a decreased trend of SSI. Histologically, seed morphological changes were mainly attributed to the cell number variations. Transcriptional and physiological analyses discovered that phytohormone-, cytoskeleton- as well as sugar transportation- and degradation-related genes were involved in the regulation of seed morphology by the fruit shape loci.
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Affiliation(s)
- Jie Chen
- College of Horticulture, China Agricultural University, Beijing, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Bingqing Pan
- College of Horticulture, China Agricultural University, Beijing, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Zixiong Li
- College of Horticulture, China Agricultural University, Beijing, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Yue Xu
- College of Horticulture, China Agricultural University, Beijing, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Xiaomeng Cao
- College of Horticulture, China Agricultural University, Beijing, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Jingjing Jia
- College of Horticulture, China Agricultural University, Beijing, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Huolin Shen
- College of Horticulture, China Agricultural University, Beijing, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Liang Sun
- College of Horticulture, China Agricultural University, Beijing, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
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12
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Amanullah S, Li S, Osae BA, Yang T, Abbas F, Gao M, Wang X, Liu H, Gao P, Luan F. Primary mapping of quantitative trait loci regulating multivariate horticultural phenotypes of watermelon ( Citrullus lanatus L.). FRONTIERS IN PLANT SCIENCE 2023; 13:1034952. [PMID: 36714694 PMCID: PMC9877429 DOI: 10.3389/fpls.2022.1034952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
Watermelon fruits exhibit a remarkable diversity of important horticultural phenotypes. In this study, we initiated a primary quantitative trait loci (QTL) mapping to identify the candidate regions controlling the ovary, fruit, and seed phenotypes. Whole genome sequencing (WGS) was carried out for two differentiated watermelon lines, and 350 Mb (96%) and 354 Mb (97%) of re-sequenced reads covered the reference de novo genome assembly, individually. A total of 45.53% non-synonymous single nucleotide polymorphism (nsSNPs) and 54.47% synonymous SNPs (sSNPs) were spotted, which produced 210 sets of novel SNP-based cleaved amplified polymorphism sequence (CAPS) markers by depicting 46.25% co-dominant polymorphism among parent lines and offspring. A biparental F2:3 mapping population comprised of 100 families was used for trait phenotyping and CAPS genotyping, respectively. The constructed genetic map spanned a total of 2,398.40 centimorgans (cM) in length and averaged 11.42 cM, with 95.99% genome collinearity. A total of 33 QTLs were identified at different genetic positions across the eight chromosomes of watermelon (Chr-01, Chr-02, Chr-04, Chr-05, Chr-06, Chr-07, Chr-10, and Chr-11); among them, eight QTLs of the ovary, sixteen QTLs of the fruit, and nine QTLs of the seed related phenotypes were classified with 5.32-25.99% phenotypic variance explained (PVE). However, twenty-four QTLs were identified as major-effect and nine QTLs were mapped as minor-effect QTLs across the flanking regions of CAPS markers. Some QTLs were exhibited as tightly localized across the nearby genetic regions and explained the pleiotropic effects of multigenic nature. The flanking QTL markers also depicted significant allele specific contributions and accountable genes were predicted for respective traits. Gene Ontology (GO) functional enrichment was categorized in molecular function (MF), cellular components (CC), and biological process (BP); however, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were classified into three main classes of metabolism, genetic information processing, and brite hierarchies. The principal component analysis (PCA) of multivariate phenotypes widely demonstrated the major variability, consistent with the identified QTL regions. In short, we assumed that our identified QTL regions provide valuable genetic insights regarding the watermelon phenotypes and fine genetic mapping could be used to confirm them.
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Affiliation(s)
- Sikandar Amanullah
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Shenglong Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Benjamin Agyei Osae
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Tiantian Yang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Farhat Abbas
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Meiling Gao
- College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar, China
| | - Xuezheng Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Hongyu Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Peng Gao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Feishi Luan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
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13
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Gebremeskel H, Umer MJ, Hongju Z, Li B, Shengjie Z, Yuan P, Xuqiang L, Nan H, Wenge L. Genetic mapping and molecular characterization of the delayed green gene dg in watermelon ( Citrullus lanatus). FRONTIERS IN PLANT SCIENCE 2023; 14:1152644. [PMID: 37152178 PMCID: PMC10158938 DOI: 10.3389/fpls.2023.1152644] [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: 01/28/2023] [Accepted: 04/03/2023] [Indexed: 05/09/2023]
Abstract
Leaf color mutants are common in higher plants that can be used as markers in crop breeding and are important tools in understanding regulatory mechanisms of chlorophyll biosynthesis and chloroplast development. Genetic analysis was performed by evaluating F1, F2 and BC1 populations derived from two parental lines (Charleston gray with green leaf color and Houlv with delayed green leaf color), suggesting that a single recessive gene controls the delayed green leaf color. In this study, the delayed green mutant showed a conditional pale green leaf color at the early leaf development but turned to green as the leaf development progressed. Delayed green leaf plants showed reduced pigment content, photosynthetic, chlorophyll fluorescence parameters, and impaired chloroplast development compared with green leaf plants. The delayed green (dg) locus was mapped to 7.48 Mb on chromosome 3 through bulk segregant analysis approach, and the gene controlling delayed green leaf color was narrowed to 53.54 kb between SNP130 and SNP135 markers containing three candidate genes. Sequence alignment of the three genes indicated that there was a single SNP mutation (G/A) in the coding region of ClCG03G010030 in the Houlv parent, which causes an amino acid change from Arginine to Lysine. The ClCG03G010030 gene encoded FtsH extracellular protease protein family is involved in early delayed green leaf development. The expression level of ClCG03G010030 was significantly reduced in delayed green leaf plants than in green leaf plants. These results indicated that the ClCG03G010030 might control watermelon green leaf color and the single SNP variation in ClCG03G010030 may result in early delayed green leaf color development during evolutionary process.
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Affiliation(s)
- Haileslassie Gebremeskel
- Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- Department of Horticulture, Ethiopian Institute of Agricultural Research, Addis Ababa, Ethiopia
| | - Muhammad Jawad Umer
- Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhu Hongju
- Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Bingbing Li
- Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Zhao Shengjie
- Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Pingli Yuan
- Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Lu Xuqiang
- Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - He Nan
- Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Liu Wenge
- Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- *Correspondence: Liu Wenge,
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14
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Zheng Q, Takei-Hoshi R, Okumura H, Ito M, Kawaguchi K, Otagaki S, Matsumoto S, Luo Z, Zhang Q, Shiratake K. Genome editing of SlMYB3R3, a cell cycle transcription factor gene of tomato, induces elongated fruit shape. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7312-7325. [PMID: 36070755 PMCID: PMC9730800 DOI: 10.1093/jxb/erac352] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
Fruit shape is an important trait that attracts consumers, and the regulation of genes related to cell division is crucial for shaping multicellular organs. In Arabidopsis, MYB3R transcription factors, which harbor three imperfect repeats in the N-terminus, control organ growth by regulating cell division. However, the function of MYB3Rs in tomato remains unknown. Here, we characterized tomato SlMYB3R3, which was preferentially expressed in flowers and placed in a subclade with two Arabidopsis cell cycle suppressors (MYB3R3/5). slmyb3r3 knockout mutants were generated using the CRISPR/Cas9 system. Morphological observation of the slmyb3r3 mutants showed that fruits that were elongated and occasionally peanut-like in shape were formed, which was caused by significantly increased cell numbers in the longitudinal direction. Transcriptome and yeast one-hybrid assay results suggested that SlMYB3R3 acted as a suppressor of cell-cycle-related genes by binding to the mitosis-specific activator (MSA) motifs in their promoters. Taken together, knock out of the suppressor SlMYB3R3 leads to elongated fruit, which results from the altered cell division pattern at the ovary stage, by regulating cell-cycle-related genes in an MSA-dependent manner. Our results suggest that SlMYB3R3 and its orthologs have the potential to change fruit shape as part of the molecular breeding of fruit crops.
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Affiliation(s)
- Qingyou Zheng
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan 430070, China
| | - Rie Takei-Hoshi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Hitomi Okumura
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Masaki Ito
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kanazawa 920-1192, Japan
| | - Kohei Kawaguchi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Shungo Otagaki
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Shogo Matsumoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Zhengrong Luo
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qinglin Zhang
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan 430070, China
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15
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Gong C, Lu X, Zhu H, Anees M, He N, Liu W. Genome-wide association study provides genetic insights into natural variation in watermelon rind thickness and single fruit weight. FRONTIERS IN PLANT SCIENCE 2022; 13:1074145. [PMID: 36561452 PMCID: PMC9763438 DOI: 10.3389/fpls.2022.1074145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Rind thickness and fruit weight are agronomic traits closely related to quality and yield, which have attracted much attention from consumers and breeders. However, the genetic mechanism of these two traits is still not well understood in natural populations. In this study, rind thickness and single fruit weight in 151 watermelon accessions were determined in 2019 and 2020, and genome-wide association analysis was performed by integrating phenotypic and genotype data. Abundant phenotypic variation was found in the test population, and the watermelon with thinner rind thickness tended to have smaller fruit weights. Five significant SNPs were closely associated with rind thickness on chromosome 2 by Genome-wide association study (GWAS), i.e., 32344170, 32321308, 32304738, 32328501, and 32311192. And there were 21 genes were annotated in the candidate interval, most notably, Cla97C02G044160 belonged to the MADS family, and part of the genes in this family played an important role in regulating organ size, further analysis of gene structure, gene expression level, and phylogenetic tree showed that Cla97C02G044160 was a candidate gene for regulating target traits. In conclusion, our study provides molecular insights into the natural variation of watermelon rind thickness and single fruit weight, meanwhile, providing data support for molecular marker-assisted breeding.
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Affiliation(s)
- Chengsheng Gong
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xuqiang Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Hongju Zhu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Muhammad Anees
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Nan He
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Wenge Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
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16
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Strygina KV, Elatskova AG, Elatskov YA, Tekhanovich GA, Khlestkina EK. Analysis of the Genes That Determine the Dwarf Form of Watermelon Citrullus lanatus (Thunb.) Matsum. & Nakai in the VIR Collection. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422120134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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17
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Liu L, Gan Y, Luo J, Li J, Zheng X, Gong H, Liu X, Deng L, Zhao G, Wu H. QTL mapping reveals candidate genes for main agronomic traits in Luffa based on a high-resolution genetic map. FRONTIERS IN PLANT SCIENCE 2022; 13:1069618. [PMID: 36466279 PMCID: PMC9716215 DOI: 10.3389/fpls.2022.1069618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
Luffa is an important medicinal and edible vegetable crop of Cucurbitaceae. Strong heterosis effects and strikingly complementary characteristics were found between the two domesticated Luffa cultivars, Luffa acutangula and Luffa cylindrica. To explore the genetic basis underlying their important agronomic traits, we constructed the first interspecific high-density genetic linkage map using a BC1 population of 110 lines derived from a cross between S1174 (Luffa acutangula) and P93075 (Luffa cylindrica). The map spanned a total of 2246.74 cM with an average distance of 0.48 cM between adjacent markers. Thereafter, a large-scale field-based quantitative trait loci (QTLs) mapping was conducted for 25 important agronomic traits and 40 significant genetic loci distributed across 11 chromosomes were detected. Notably, a vital QTL (qID2) located on chromosome 9 with a minimum distance of 23 kb was identified to be responsible for the internode diameter and explained 11% of the phenotypic variation. Lac09g006860 (LacCRWN3), encoding a nuclear lamina protein involved in the control of nuclear morphology, was the only gene harbored in qID2. Sequence alignment showed completely different promoter sequences between the two parental alleles of LacCRWN3 except for some nonsynonymous single nucleotide polymorphisms (SNPs) in exons, and the expression level in thick-stem P93075 was distinctively higher than that in thin-stem S1174. According to the natural variation analysis of a population of 183 inbred lines, two main haplotypes were found for LacCRWN3: the P93075-like and S1174-like, with the former haplotype lines exhibiting significantly thicker internode diameters than those of the latter haplotype lines. It showed that LacCRWN3, as the only CRWN3 gene in Cucurbitaceae, was the most likely candidate gene regulating the internode diameter of Luffa. Our findings will be beneficial for deciphering the molecular mechanism of key phenotypic traits and promoting maker-assisted breeding in Luffa.
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Affiliation(s)
- Lili Liu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yaqin Gan
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Jianning Luo
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Junxing Li
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiaoming Zheng
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Hao Gong
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiaoxi Liu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Liting Deng
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Gangjun Zhao
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Haibin Wu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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18
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Dou J, Duan S, Umer MJ, Xie K, Wang Y, Kang Q, Yang S, Yang L, Liu D, Liu L, Zhao F. Genome-wide analysis of IQD proteins and ectopic expression of watermelon ClIQD24 in tomato suggests its important role in regulating fruit shape. Front Genet 2022; 13:993218. [PMID: 36186419 PMCID: PMC9515400 DOI: 10.3389/fgene.2022.993218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/19/2022] [Indexed: 11/23/2022] Open
Abstract
The plant-specific IQ67 domain (IQD) is the largest class of calmodulin targets found in plants, and plays an important role in many biological processes, especially fruit development processes. However, the functional role of IQD proteins in the development of watermelon (Citrullus lanatus) shape remains unknown, as the IQD protein family in watermelon has not been systematically characterized. Herein, we elucidated the gene structures, chromosomal locations, evolutionary divergence, and functions of 35 IQD genes in the watermelon genome. The transcript profiles and quantitative real-time PCR analysis at different stages of fruit development showed that the ClIQD24 gene was highly expressed on 0 days after pollination. Furthermore, we found that the ectopic overexpression of ClIQD24 promoted tomato fruit elongation, thereby revealing the significance of ClIQD24 in the progression of watermelon shape. Our study will serve as a reference for further investigations on the molecular mechanisms underlying watermelon fruit shape formation.
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Affiliation(s)
- Junling Dou
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Shixiang Duan
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Muhammad Jawad Umer
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Kuixi Xie
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Yinping Wang
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Qishuai Kang
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Sen Yang
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Luming Yang
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Dongming Liu
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
- *Correspondence: Dongming Liu, ; Lifeng Liu, ; Fengli Zhao,
| | - Lifeng Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- *Correspondence: Dongming Liu, ; Lifeng Liu, ; Fengli Zhao,
| | - Fengli Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Dongming Liu, ; Lifeng Liu, ; Fengli Zhao,
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19
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Zheng H, Dong Y, Nong H, Huang L, Liu J, Yu X, Zhang Y, Yang L, Hong B, Wang W, Tao J. VvSUN may act in the auxin pathway to regulate fruit shape in grape. HORTICULTURE RESEARCH 2022; 9:uhac200. [PMID: 36382226 PMCID: PMC9647697 DOI: 10.1093/hr/uhac200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
Fruit shape is an essential agronomic feature in many crops. We identified and functionally characterized an auxin pathway-related gene, VvSUN. VvSUN, which belongs to the SUN/IQ67-DOMAIN (IQD) family, localizes to the plasma membrane and chloroplast and may be involved in controlling fruit shape through auxin. It is highly expressed in the ovary, and the expression level 1 week before the anthesis stage is positively correlated with the fruit shape index. Functional analyses illustrated that VvSUN gene overexpression in tomato and tobacco plants changed fruit/pod shape. The VvSUN promoter directly bound to VvARF6 in yeast and activated ß-glucuronidase (GUS) activity by indole-3-acetic acid (IAA) treatments in grapevine leaves, indicating that VvSUN functions are in coordination with auxin. Further analysis of 35S::VvSUN transgenic tomato ovaries showed that the fruit shape changes caused by VvSUN were predominantly caused by variations in cell number in longitudinal directions by regulating endogenous auxin levels via polar transport and/or auxin signal transduction process variations. Moreover, enrichment of the 35S::VvSUN transgenic tomato differentially expressed genes was found in a variety of biological processes, including primary metabolic process, transmembrane transport, calcium ion binding, cytoskeletal protein binding, tubulin binding, and microtubule-based movement. Using weighted gene co-expression network analysis (WGCNA), we confirmed that this plant hormone signal transduction may play a crucial role in controlling fruit shape. As a consequence, it is possible that VvSUN acts as a hub gene, altering cellular auxin levels and the plant hormone signal transduction pathway, which plays a role in cell division patterns, leading to anisotropic growth of the ovary and, ultimately, an elongated fruit shape.
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Affiliation(s)
- Huan Zheng
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yang Dong
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Huilan Nong
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Liyuan Huang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jing Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Yu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yaguan Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Lina Yang
- Charles River Laboratories International, Inc., Michigan, 49071, USA
| | - Ben Hong
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wu Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
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20
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Huang X, Wu W, Su L, Lv H, Cheng Z, Yang W, Nong L, Liu T, Chen Y, Wang P, Liu Z. Development and Application of InDel Markers Linked to Fruit-Shape and Peel-Colour Genes in Wax Gourd. Genes (Basel) 2022; 13:genes13091567. [PMID: 36140735 PMCID: PMC9498789 DOI: 10.3390/genes13091567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/22/2022] [Accepted: 08/29/2022] [Indexed: 12/03/2022] Open
Abstract
The wax gourd is commonly grown in many countries because of its high nutritional and economic value. While the genes for the fruit shape and peel colour of wax gourd have been reported, the InDel markers linked to these genes remain undeveloped. In this study, the InDel markers linked to fruit-shape (Bch02G016830) and peel-colour (Bch05G003950) genes were developed from resequenced data. We used 120 inbred lines, 536 isolated populations, and 4 commercial hybrids to evaluate the validity and application value of the InDel markers. The accuracy rates of nine pairs of fruit-shape InDel markers (GX1-GX9) were 84.16–91.66% in 120 inbred lines. The accuracy rates of 27 pairs of peel-colour InDel markers (PS1-PS27) within approximately 3.0 Mb upstream and 3.0 Mb downstream of the peel-colour gene were 100% and those of 6 pairs of peel-colour InDel markers (PS28-PS33) within 3.0–20 Mb upstream and downstream of the peel-colour gene were 55.83–90% in 120 inbred lines. The purity of four commercial hybrids determined using GX1, GX2, PS13, and PS14 was highly consistent with the field results for purity determination. Our results provide important information for genetic linkage map construction, molecular-marker-assisted selective breeding, and purity determination of wax gourd hybrids.
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Affiliation(s)
- Xiaochun Huang
- College of Agricultural, Guangxi University, Nanning 530004, China
| | - Wenting Wu
- College of Agricultural, Guangxi University, Nanning 530004, China
| | - Liwen Su
- College of Agricultural, Guangxi University, Nanning 530004, China
| | - Haixuan Lv
- College of Agricultural, Guangxi University, Nanning 530004, China
| | - Zhikui Cheng
- College of Agricultural, Guangxi University, Nanning 530004, China
| | - Wenrui Yang
- College of Agricultural, Guangxi University, Nanning 530004, China
| | - Lifeng Nong
- College of Agricultural, Guangxi University, Nanning 530004, China
| | - Ting Liu
- College of Agricultural, Guangxi University, Nanning 530004, China
| | - Yong Chen
- Institute for New Rural Development, Guangxi University, Nanning 530004, China
| | - Peng Wang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530004, China
| | - Zhengguo Liu
- College of Agricultural, Guangxi University, Nanning 530004, China
- Correspondence:
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21
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Deng Y, Liu S, Zhang Y, Tan J, Li X, Chu X, Xu B, Tian Y, Sun Y, Li B, Xu Y, Deng XW, He H, Zhang X. A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene discovery and breeding. MOLECULAR PLANT 2022; 15:1268-1284. [PMID: 35746868 DOI: 10.1016/j.molp.2022.06.010] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 05/30/2022] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
Watermelon, Citrullus lanatus, is the world's third largest fruit crop. Reference genomes with gaps and a narrow genetic base hinder functional genomics and genetic improvement of watermelon. Here, we report the assembly of a telomere-to-telomere gap-free genome of the elite watermelon inbred line G42 by incorporating high-coverage and accurate long-read sequencing data with multiple assembly strategies. All 11 chromosomes have been assembled into single-contig pseudomolecules without gaps, representing the highest completeness and assembly quality to date. The G42 reference genome is 369 321 829 bp in length and contains 24 205 predicted protein-coding genes, with all 22 telomeres and 11 centromeres characterized. Furthermore, we established a pollen-EMS mutagenesis protocol and obtained over 200 000 M1 seeds from G42 . In a sampling pool, 48 monogenic phenotypic mutations, selected from 223 M1 and 78 M2 mutants with morphological changes, were confirmed. The average mutation density was 1 SNP/1.69 Mb and 1 indel/4.55 Mb per M1 plant and 1 SNP/1.08 Mb and 1 indel/6.25 Mb per M2 plant. Taking advantage of the gap-free G42 genome, 8039 mutations from 32 plants sampled from M1 and M2 families were identified with 100% accuracy, whereas only 25% of the randomly selected mutations identified using the 97103v2 reference genome could be confirmed. Using this library and the gap-free genome, two genes responsible for elongated fruit shape and male sterility (ClMS1) were identified, both caused by a single base change from G to A. The validated gap-free genome and its EMS mutation library provide invaluable resources for functional genomics and genetic improvement of watermelon.
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Affiliation(s)
- Yun Deng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Shoucheng Liu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Yilin Zhang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China; School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China
| | - Jingsheng Tan
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Xiaopeng Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Xiao Chu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Binghua Xu
- Jiangsu Xuhuai Area Huaiyin Institute of Agricultural Science, Huaian, Jiangsu 223300, China
| | - Yao Tian
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Yudong Sun
- Jiangsu Xuhuai Area Huaiyin Institute of Agricultural Science, Huaian, Jiangsu 223300, China
| | - Bosheng Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Yunbi Xu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Xing Wang Deng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China; School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China
| | - Hang He
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China; School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China.
| | - Xingping Zhang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China.
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Li L, Cui S, Dang P, Yang X, Wei X, Chen K, Liu L, Chen CY. GWAS and bulked segregant analysis reveal the Loci controlling growth habit-related traits in cultivated Peanut (Arachis hypogaea L.). BMC Genomics 2022; 23:403. [PMID: 35624420 PMCID: PMC9145184 DOI: 10.1186/s12864-022-08640-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 05/05/2022] [Indexed: 11/10/2022] Open
Abstract
Background Peanut (Arachis hypogaea L.) is a grain legume crop that originated from South America and is now grown around the world. Peanut growth habit affects the variety’s adaptability, planting patterns, mechanized harvesting, disease resistance, and yield. The objective of this study was to map the quantitative trait locus (QTL) associated with peanut growth habit-related traits by combining the genome-wide association analysis (GWAS) and bulked segregant analysis sequencing (BSA-seq) methods. Results GWAS was performed with 17,223 single nucleotide polymorphisms (SNPs) in 103 accessions of the U.S. mini core collection genotyped using an Affymetrix version 2.0 SNP array. With a total of 12,342 high-quality polymorphic SNPs, the 90 suggestive and significant SNPs associated with lateral branch angle (LBA), main stem height (MSH), lateral branch height (LBL), extent radius (ER), and the index of plant type (IOPT) were identified. These SNPs were distributed among 15 chromosomes. A total of 597 associated candidate genes may have important roles in biological processes, hormone signaling, growth, and development. BSA-seq coupled with specific length amplified fragment sequencing (SLAF-seq) method was used to find the association with LBA, an important trait of the peanut growth habit. A 4.08 Mb genomic region on B05 was associated with LBA. Based on the linkage disequilibrium (LD) decay distance, we narrowed down and confirmed the region within the 160 kb region (144,193,467–144,513,467) on B05. Four candidate genes in this region were involved in plant growth. The expression levels of Araip.E64SW detected by qRT-PCR showed significant difference between ‘Jihua 5’ and ‘M130’. Conclusions In this study, the SNP (AX-147,251,085 and AX-144,353,467) associated with LBA by GWAS was overlapped with the results in BSA-seq through combined analysis of GWAS and BSA-seq. Based on LD decay distance, the genome range related to LBA on B05 was shortened to 144,193,467–144,513,467. Three candidate genes related to F-box family proteins (Araip.E64SW, Araip.YG1LK, and Araip.JJ6RA) and one candidate gene related to PPP family proteins (Araip.YU281) may be involved in plant growth and development in this genome region. The expression analysis revealed that Araip.E64SW was involved in peanut growth habits. These candidate genes will provide molecular targets in marker-assisted selection for peanut growth habits. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08640-3.
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Affiliation(s)
- Li Li
- State Key Laboratory for Crop Improvement and Regulation in North China, College of Agronomy, Hebei Agricultural University, Baoding, 071001, The People's Republic of China.,Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, 36948, USA.,School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, 056038, The People's Republic of China
| | - Shunli Cui
- State Key Laboratory for Crop Improvement and Regulation in North China, College of Agronomy, Hebei Agricultural University, Baoding, 071001, The People's Republic of China
| | - Phat Dang
- USDA-ARS National Peanut Research Laboratory, Dawson, GA, 39842, USA
| | - Xinlei Yang
- State Key Laboratory for Crop Improvement and Regulation in North China, College of Agronomy, Hebei Agricultural University, Baoding, 071001, The People's Republic of China
| | - Xuejun Wei
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, 056038, The People's Republic of China
| | - Kai Chen
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, 056038, The People's Republic of China
| | - Lifeng Liu
- State Key Laboratory for Crop Improvement and Regulation in North China, College of Agronomy, Hebei Agricultural University, Baoding, 071001, The People's Republic of China.
| | - Charles Y Chen
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, 36948, USA.
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23
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Gao L, Hao N, Wu T, Cao J. Advances in Understanding and Harnessing the Molecular Regulatory Mechanisms of Vegetable Quality. FRONTIERS IN PLANT SCIENCE 2022; 13:836515. [PMID: 35371173 PMCID: PMC8964363 DOI: 10.3389/fpls.2022.836515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
The quality of vegetables is facing new demands in terms of diversity and nutritional health. Given the improvements in living standards and the quality of consumed products, consumers are looking for vegetable products that maintain their nutrition, taste, and visual qualities. These requirements are directing scientists to focus on vegetable quality in breeding research. Thus, in recent years, research on vegetable quality has been widely carried out, and many applications have been developed via gene manipulation. In general, vegetable quality traits can be divided into three parts. First, commodity quality, which is most related to the commerciality of plants, refers to the appearance of the product. The second is flavor quality, which usually represents the texture and flavor of vegetables. Third, nutritional quality mainly refers to the contents of nutrients and health ingredients such as soluble solids (sugar), vitamin C, and minerals needed by humans. With biotechnological development, researchers can use gene manipulation technologies, such as molecular markers, transgenes and gene editing to improve the quality of vegetables. This review attempts to summarize recent studies on major vegetable crops species, with Brassicaceae, Solanaceae, and Cucurbitaceae as examples, to analyze the present situation of vegetable quality with the development of modern agriculture.
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Affiliation(s)
- Luyao Gao
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, China
- Key Laboratory for Vegetable Biology of Hunan Province, Changsha, China
| | - Ning Hao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Tao Wu
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, China
- Key Laboratory for Vegetable Biology of Hunan Province, Changsha, China
| | - Jiajian Cao
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, China
- Key Laboratory for Vegetable Biology of Hunan Province, Changsha, China
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24
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Ma J, Li C, Zong M, Qiu Y, Liu Y, Huang Y, Xie Y, Zhang H, Wang J. CmFSI8/CmOFP13 encoding an OVATE family protein controls fruit shape in melon. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1370-1384. [PMID: 34849737 DOI: 10.1093/jxb/erab510] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 11/20/2021] [Indexed: 06/13/2023]
Abstract
Fruit shape is an important quality and yield trait in melon (Cucumis melo). Although some quantitative trait loci for fruit shape have been reported in in this species, the genes responsible and the underlying mechanisms remain poorly understood. Here, we identified and characterized a gene controlling fruit shape from two melon inbred lines, B8 with long-horn fruit and HP22 with flat-round fruit. Genetic analysis suggested that the shape was controlled by a single and incompletely dominant locus, which we designate as CmFSI8/CmOFP13. This gene was finely mapped to a 53.7-kb interval on chromosome 8 based on bulked-segregant analysis sequencing and map-based cloning strategies. CmFSI8/CmOFP13 encodes an OVATE family protein (OFP) and is orthologous to AtOFP1 and SlOFP20. The transcription level of CmFSI8/CmOFP13 in the ovary of HP22 was significantly higher than that in B8, and sequence analysis showed that a 12.5-kb genomic variation with a retrotransposon insertion identified in the promoter was responsible for elevating the expression, and this ultimately caused the differences in fruit shape. Ectopic overexpression of CmFSI8/CmOFP13 in Arabidopsis led to multiple phenotypic changes, including kidney-shaped leaves and shortened siliques. Taken together, our results demonstrate the involvement of an OFP in regulating fruit shape in melon, and our improved understanding of the molecular mechanisms will enable us to better manipulate fruit shape in breeding.
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Affiliation(s)
- Jian Ma
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Congcong Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mei Zong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yanhong Qiu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yuemin Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yating Huang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yuli Xie
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Huijun Zhang
- School of Life Science, Huaibei Normal University, Huaibei, Anhui, 235000, China
| | - Jianshe Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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25
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Genetic and Molecular Regulation Mechanisms in the Formation and Development of Vegetable Fruit Shape. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12031514] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Vegetable crops have a long history of cultivation worldwide and rich germplasm resources. With its continuous development and progress, molecular biology technology has been applied to various fields of vegetable crop research. Fruit is an important organ in vegetable crops, and fruit shape can affect the yield and commercialization of vegetables. In nature, fruits show differences in size and shape. Based on fruit shape diversity, the growth direction and coordination mechanism of fruits remain unclear. In this review, we discuss the latest research on fruit shape. In addition, we compare the current theories on the molecular mechanisms that regulate fruit growth, size, and shape in different vegetable families.
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26
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Zhang C, Cui L, Fang J. Genome-wide association study of the candidate genes for grape berry shape-related traits. BMC PLANT BIOLOGY 2022; 22:42. [PMID: 35057757 PMCID: PMC8772106 DOI: 10.1186/s12870-022-03434-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND In the breeding of new horticultural crops, fruit shape is an important selection characteristic. A variety of fruit shapes appeared during the gradual process of selection and domestication. However, few studies have been conducted on grape berry shape, especially studies related to mining candidate genes. To discover candidate genes related to grape berry shape, the present study first took the berry shape parameters analyzed by Tomato Analyzer as the target traits and used a genome-wide association analysis to analyze candidate genes. RESULTS In total, 122 single-nucleotide polymorphism (SNP) loci had significant correlations with multiple berry shape traits in both years, and some candidate genes were further mined. These genes were mainly related to LRR receptor-like serine/threonine-protein kinase (At1g05700 and At1g07650), transcription factors (GATA transcription factor 23-like, transcription factor VIP1, transcription initiation factor TFIID, and MADS-box transcription factor 6), ubiquitin ligases (F-box protein SKIP19 and RING finger protein 44), and plant hormones (indole-3-acetic acid-amido synthetase GH3.6 and ethylene-responsive transcription factor ERF061). In addition, some important SNP loci were associated with multiple berry-shape traits. The study further revealed some genes that control multiple traits simultaneously, indicating that these berry shape traits are subject to the coordinated regulation of some genes in controlling berry shape. CONCLUSIONS In the present work, we identified interesting genetic determinants of grape berry shape-related traits. The identification of molecular markers that are closely related to these berry-shape traits is of great significance for breeding specific berry-shaped grape varieties.
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Affiliation(s)
- Chuan Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Liwen Cui
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jinggui Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
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27
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Gong C, Zhao S, Yang D, Lu X, Anees M, He N, Zhu H, Zhao Y, Liu W. Genome-wide association analysis provides molecular insights into the natural variation of watermelon seed size. HORTICULTURE RESEARCH 2022; 9:uhab074. [PMID: 35043154 PMCID: PMC8923815 DOI: 10.1093/hr/uhab074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 05/31/2023]
Abstract
Seed-consumption watermelon tend to have larger-sized seeds, while flesh-consumed watermelon often require relatively smaller seed. Therefore, the seed size of watermelon has received extensive attention from consumers and breeders. However, the study on the natural variation and genetic mechanism of watermelon seed size is not clear enough. In the present study, 100 seed weight, seed hilum length, seed length, seed width, and seed thickness in 197 watermelon accessions were examined. Furthermore, association analysis was conducted between seed size traits and high-quality SNP data. The results revealed that there was a strong correlation between the five seed traits. And seed enlargement was an important feature during watermelon seed size domestication. Meanwhile, the seed consumption biological species C. mucosospermu and C. lanatus edible seed watermelon had a significantly bigger seed size than other species's. Eleven non-repeating significant SNPs above the threshold line were obtained by GWAS analysis. Four of them on chromosome 5 were considered to be closely associated with seed size traits, i.e. S5: 32250307, S5: 32250454, S5: 32256177, S5: 32260870, which could be used as potential molecular markers for the breeding of watermelon cultivars with target seed size. In addition, combined with gene annotation information and previous reports, five genes near the four significant SNPs may regulate seed size. And qRT-PCR analysis showed that two genes Cla97C05G104360 and Cla97C05G104380, which may be involved in abscisic acid metabolism, may play an important role in regulating the seed size of watermelon. Our findings provide molecular insights into natural variation in watermelon seed size, and gives valuable information of molecular marker-assisted breeding.
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Affiliation(s)
- Chengsheng Gong
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Shengjie Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Dongdong Yang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Xuqiang Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Muhammad Anees
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Nan He
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Hongju Zhu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Yong Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Wenge Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
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Borovsky Y, Raz A, Doron-Faigenboim A, Zemach H, Karavani E, Paran I. Pepper Fruit Elongation Is Controlled by Capsicum annuum Ovate Family Protein 20. FRONTIERS IN PLANT SCIENCE 2022; 12:815589. [PMID: 35058962 PMCID: PMC8763684 DOI: 10.3389/fpls.2021.815589] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/02/2021] [Indexed: 05/28/2023]
Abstract
Fruit shape is one of the most important quality traits of pepper (Capsicum spp.) and is used as a major attribute for the classification of fruit types. Wide natural variation in fruit shape exists among the major cultivated species Capsicum annuum, allowing the identification of several QTLs controlling the trait. However, to date, no genes underlying fruit shape QTLs have been conclusively identified, nor has their function been verified in pepper. We constructed a mapping population from a cross of round- and elongated-fruited C. annuum parents and identified a single major QTL on chromosome 10, termed fs10, explaining 68 and 70% of the phenotypic variation for fruit shape index and for distal fruit end angle, respectively. The QTL was mapped in several generations and was localized to a 5 Mbp region containing the ortholog of SlOFP20 that suppresses fruit elongation in tomato. Virus-induced gene silencing of the pepper ortholog CaOFP20 resulted in increased fruit elongation on two independent backgrounds. Furthermore, CaOFP20 exhibited differential expression in fs10 near-isogenic lines, as well as in an association panel of elongated- and round-fruited accessions. A 42-bp deletion in the upstream region of CaOFP20 was most strongly associated with fruit shape variation within the locus. Histological observations in ovaries and fruit pericarps indicated that fs10 exerts its effect on fruit elongation by controlling cell expansion and replication. Our results indicate that CaOFP20 functions as a suppressor of fruit elongation in C. annuum and is the most likely candidate gene underlying fs10.
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Dou J, Yang H, Sun D, Yang S, Sun S, Zhao S, Lu X, Zhu H, Liu D, Ma C, Liu W, Yang L. The branchless gene Clbl in watermelon encoding a TERMINAL FLOWER 1 protein regulates the number of lateral branches. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:65-79. [PMID: 34562124 DOI: 10.1007/s00122-021-03952-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
A SNP mutation in Clbl gene encoding TERMINAL FLOWER 1 protein is responsible for watermelon branchless. Lateral branching is one of the most important traits, which directly determines plant architecture and crop productivity. Commercial watermelon has the characteristics of multiple lateral branches, and it is time-consuming and labor-costing to manually remove the lateral branches in traditional watermelon cultivation. In our present study, a lateral branchless trait was identified in watermelon material WCZ, and genetic analysis revealed that it was controlled by a single recessive gene, which named as Clbl (Citrullus lanatus branchless). A bulked segregant sequencing (BSA-seq) and linkage analysis was conducted to primarily map Clbl on watermelon chromosome 4. Next-generation sequencing-aided marker discovery and a large mapping population consisting of 1406 F2 plants were used to further map Clbl locus into a 9011-bp candidate region, which harbored only one candidate gene Cla018392 encoding a TERMINAL FLOWER 1 protein. Sequence comparison of Cla018392 between two parental lines revealed that there was a SNP detected from C to A in the coding region in the branchless inbred line WCZ, which resulted in a mutation from alanine (GCA) to glutamate (GAA) at the fourth exon. A dCAPS marker was developed from the SNP locus, which was co-segregated with the branchless phenotype in both BC1 and F2 population, and it was further validated in 152 natural watermelon accessions. qRT-PCR and in situ hybridization showed that the expression level of Cla018392 was significantly reduced in the axillary bud and apical bud in branchless line WCZ. Ectopic expression of ClTFL1 in Arabidopsis showed an increased number of lateral branches. The results of this study will be helpful for better understanding the molecular mechanism of lateral branch development in watermelon and for the development of marker-assisted selection (MAS) for new branchless watermelon cultivars.
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Affiliation(s)
- Junling Dou
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Huihui Yang
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
| | - Dongling Sun
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
| | - Sen Yang
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
| | - Shouru Sun
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
| | - Shengjie Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Xuqiang Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Huayu Zhu
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
| | - Dongming Liu
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
| | - Changsheng Ma
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
| | - Wenge Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China.
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou, 450002, China.
| | - Luming Yang
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China.
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou, 450002, China.
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Identification of yield-related genes through genome-wide association: case study of weeping forsythia, an emerging medicinal crop. Genes Genomics 2022; 44:145-154. [PMID: 34767154 PMCID: PMC8586636 DOI: 10.1007/s13258-021-01186-w] [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: 09/08/2021] [Accepted: 11/02/2021] [Indexed: 11/12/2022]
Abstract
KEY MESSAGE This study identified candidate genes related to fruit yield for an emerging medicinal crop, weeping forsythia. BACKGROUND The genetic basis of crop yield is an agricultural research hotspot. Identifying the genes related to yield traits is the key to increase the yield. Weeping forsythia is an emerging medicinal crop that currently lacks excellent varieties. The genes related to fruit yield in weeping forsythia have not been identified. OBJECTIVE Thus, we aimed to screen the candidate genes related to fruit yield of weeping forsythia by using genome-wide association analysis. METHODS Here, 60 samples from the same field and source of weeping forsythia were collected to identify its yield-related candidate genes. Association analysis was performed on the variant loci and the traits related to yield, i.e., fruit length, width, thickness, and weight. RESULTS Results from admixture, neighbor-joining, and kinship matrix analyses supported the non-significant genetic differentiation of these samples. Significant association was found between 2 variant loci and fruit length, 8 loci and fruit width, 24 loci and fruit thickness, and 13 loci and fruit weight. Further search on the 20 kb up/downstream of these variant loci revealed 1 gene related to fruit length, 16 genes related to fruit width, 12 genes related to fruit thickness, and 13 genes related to fruit weight. Among which, 4 genes, namely, WRKY transcription factor 35, salicylic acid-binding protein, auxin response factor 6, and alpha-mannosidase were highly related to the fruit development of weeping forsythia. CONCLUSION This study identify four candidate genes related to fruit development, which will provide useful information for the subsequent molecular-assisted and genetic breeding of weeping forsythia.
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Cheng Z, Liu Z, Xu Y, Ma L, Chen J, Gou J, Su L, Wu W, Chen Y, Yu W, Wang P. Fine mapping and identification of the candidate gene BFS for fruit shape in wax gourd (Benincasa hispida). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3983-3995. [PMID: 34480584 DOI: 10.1007/s00122-021-03942-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/18/2021] [Indexed: 05/18/2023]
Abstract
Non-synonymous mutations in the BFS gene, which encodes the IQD protein, are responsible for the shape of wax gourd fruits. Fruit shape is an important agronomic trait in wax gourds. Therefore, in this study, we employed bulked segregant analysis (BSA) to identify a candidate gene for fruit shape in wax gourds within F2 populations derived by crossing GX-71 (long cylindrical fruit, fruit shape index = 4.56) and MY-1 (round fruit, fruit shape index = 1.06) genotypes. According to BSA, the candidate gene is located in the 17.18 Mb region on chromosome 2. Meanwhile, kompetitive allele-specific PCR (KASP) markers were used to reduce it to a 19.6 Kb region. Only one gene was present within the corresponding region of the reference genome, namely Bch02G016830 (designated BFS). Subsequently, BFS was sequenced in six wax gourd varieties with different fruit shapes. Sequence analysis revealed two non-synonymous mutations in the round wax gourd and one non-synonymous mutation in the cylindrical wax gourd. Quantitative real‑time PCR (qRT-PCR) analysis further showed that the expression of BFS in round fruits was significantly higher than in long cylindrical fruits at the ovary formation stage. Therefore, BFS is a candidate gene for determination wax gourd shape. The predicted protein encoded by the BFS gene belongs to the IQ67-domain protein family, which have the structural characteristics of scaffold proteins and coordinate Ca2+ CaM signaling from the membrane to the nucleus. Ultimately, two derived cleaved amplified polymorphic sequence (dCAPS) markers were developed to facilitate marker-assisted selection for wax gourds breeding.
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Affiliation(s)
- Zhikui Cheng
- College of Agriculture, Guangxi University, Guangxi, 530004, China
| | - Zhengguo Liu
- College of Agriculture, Guangxi University, Guangxi, 530004, China
| | - Yuanchao Xu
- SinoDutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lianlian Ma
- College of Agriculture, Guangxi University, Guangxi, 530004, China
| | - Jieying Chen
- College of Agriculture, Guangxi University, Guangxi, 530004, China
| | - Jiquan Gou
- College of Agriculture, Guangxi University, Guangxi, 530004, China
| | - Liwen Su
- College of Agriculture, Guangxi University, Guangxi, 530004, China
| | - Wenting Wu
- College of Agriculture, Guangxi University, Guangxi, 530004, China
| | - Yong Chen
- Institute for New Rural Development, Guangxi University, Guangxi, 530004, China
| | - Wenjin Yu
- College of Agriculture, Guangxi University, Guangxi, 530004, China
| | - Peng Wang
- College of Agriculture, Guangxi University, Guangxi, 530004, China.
- Institute of Vegetables, Guangxi Academy of Agricultural Sciences, Guangxi, 530004, China.
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Yuan P, Umer MJ, He N, Zhao S, Lu X, Zhu H, Gong C, Diao W, Gebremeskel H, Kuang H, Liu W. Transcriptome regulation of carotenoids in five flesh-colored watermelons (Citrullus lanatus). BMC PLANT BIOLOGY 2021; 21:203. [PMID: 33910512 PMCID: PMC8082968 DOI: 10.1186/s12870-021-02965-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 04/07/2021] [Indexed: 05/15/2023]
Abstract
BACKGROUND Fruit flesh color in watermelon (Citrullus lanatus) is a great index for evaluating the appearance quality and a key contributor influencing consumers' preferences. But the molecular mechanism of this intricate trait remains largely unknown. Here, the carotenoids and transcriptome dynamics during the fruit development of cultivated watermelon with five different flesh colors were analyzed. RESULTS A total of 13 carotenoids and 16,781 differentially expressed genes (DEGs), including 1295 transcription factors (TFs), were detected in five watermelon genotypes during the fruit development. The comprehensive accumulation patterns of carotenoids were closely related to flesh color. A number of potential structural genes and transcription factors were found to be associated with the carotenoid biosynthesis pathway using comparative transcriptome analysis. The differentially expressed genes were divided into six subclusters and distributed in different GO terms and metabolic pathways. Furthermore, we performed weighted gene co-expression network analysis and predicted the hub genes in six main modules determining carotenoid contents. Cla018406 (a chaperone protein dnaJ-like protein) may be a candidate gene for β-carotene accumulation and highly expressed in orange flesh-colored fruit. Cla007686 (a zinc finger CCCH domain-containing protein) was highly expressed in the red flesh-colored watermelon, maybe a key regulator of lycopene accumulation. Cla003760 (membrane protein) and Cla021635 (photosystem I reaction center subunit II) were predicted to be the hub genes and may play an essential role in yellow flesh formation. CONCLUSIONS The composition and contents of carotenoids in five watermelon genotypes vary greatly. A series of candidate genes were revealed through combined analysis of metabolites and transcriptome. These results provide an important data resource for dissecting candidate genes and molecular basis governing flesh color formation in watermelon fruit.
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Affiliation(s)
- Pingli Yuan
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Muhammad Jawad Umer
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Nan He
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Shengjie Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Xuqiang Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Hongju Zhu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Chengsheng Gong
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Weinan Diao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Haileslassie Gebremeskel
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Hanhui Kuang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Wenge Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China.
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Bao Z, Xu Z, Zang J, Bürstenbinder K, Wang P. The Morphological Diversity of Plant Organs: Manipulating the Organization of Microtubules May Do the Trick. Front Cell Dev Biol 2021; 9:649626. [PMID: 33842476 PMCID: PMC8033015 DOI: 10.3389/fcell.2021.649626] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/08/2021] [Indexed: 12/02/2022] Open
Affiliation(s)
- Zhiru Bao
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China.,Interdisciplinary Sciences Research Institute, Huazhong Agricultural University, Wuhan, China.,National R&D Centre for Citrus Preservation, Huazhong Agricultural University, Wuhan, China
| | - Zhijing Xu
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China.,Interdisciplinary Sciences Research Institute, Huazhong Agricultural University, Wuhan, China.,National R&D Centre for Citrus Preservation, Huazhong Agricultural University, Wuhan, China
| | - Jingze Zang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China.,Interdisciplinary Sciences Research Institute, Huazhong Agricultural University, Wuhan, China.,National R&D Centre for Citrus Preservation, Huazhong Agricultural University, Wuhan, China
| | - Katharina Bürstenbinder
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Pengwei Wang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China.,Interdisciplinary Sciences Research Institute, Huazhong Agricultural University, Wuhan, China.,National R&D Centre for Citrus Preservation, Huazhong Agricultural University, Wuhan, China
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Wang H, Wang Z, Liu Z, Wang K, Xu W. Membrane disruption of Fusarium oxysporum f. sp. niveum induced by myriocin from Bacillus amyloliquefaciens LZN01. Microb Biotechnol 2021; 14:517-534. [PMID: 32954686 PMCID: PMC7936314 DOI: 10.1111/1751-7915.13659] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 08/10/2020] [Accepted: 08/14/2020] [Indexed: 12/28/2022] Open
Abstract
Myriocin, which is produced by Bacillus amyloliquefaciens LZN01, can inhibit the growth of Fusarium oxysporum f. sp. niveum (Fon). In the present study, the antifungal mechanism of myriocin against Fon was investigated with a focus on the effects of myriocin on the cell membrane. Myriocin decreased the membrane fluidity and destroyed the membrane integrity of Fon. Significant microscopic morphological changes, including conidial shrinkage, the appearance of larger vacuoles and inhomogeneity of electron density, were observed in myriocin-treated cells. A membrane-targeted mechanism of action was also supported by transcriptomic and proteomic analyses; a total of 560 common differentially expressed genes (DEGs) and 285 common differentially expressed proteins (DEPs) were identified. The DEGs were further verified by using RT-qPCR. The combined analysis between the transcriptome and proteome revealed that the expression of some membrane-related genes and proteins, mainly those related to sphingolipid metabolism, glycerophospholipid metabolism, steroid biosynthesis, ABC transporters and protein processing in the endoplasmic reticulum, was disordered. Myriocin affected the serine palmitoyl transferase (SPT) activity as evidenced through molecular docking. Our results indicate that myriocin has significant antifungal activity owing to its ability to induce membrane damage in Fon.
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Affiliation(s)
- Hengxu Wang
- College of Life Science and AgroforestryQiqihar UniversityQiqihar161006China
- Key Laboratory of Urban AgricultureMinistry of Agriculture and Rural AffairsShanghai200240China
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation IndustrializationQiqihar161006China
| | - Zhigang Wang
- College of Life Science and AgroforestryQiqihar UniversityQiqihar161006China
- Key Laboratory of Urban AgricultureMinistry of Agriculture and Rural AffairsShanghai200240China
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation IndustrializationQiqihar161006China
| | - Zeping Liu
- College of Life Science and AgroforestryQiqihar UniversityQiqihar161006China
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation IndustrializationQiqihar161006China
| | - Kexin Wang
- College of Life Science and AgroforestryQiqihar UniversityQiqihar161006China
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation IndustrializationQiqihar161006China
| | - Weihui Xu
- College of Life Science and AgroforestryQiqihar UniversityQiqihar161006China
- Key Laboratory of Urban AgricultureMinistry of Agriculture and Rural AffairsShanghai200240China
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation IndustrializationQiqihar161006China
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Sun Y, Zhang H, Fan M, He Y, Guo P. A mutation in the intron splice acceptor site of a GA3ox gene confers dwarf architecture in watermelon (Citrullus lanatus L.). Sci Rep 2020; 10:14915. [PMID: 32913219 PMCID: PMC7483442 DOI: 10.1038/s41598-020-71861-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 08/18/2020] [Indexed: 12/24/2022] Open
Abstract
Dwarf architecture is an important trait associated with plant yield, lodging resistance and labor cost. Here, we aimed to identify a gene causing dwarfism in watermelon. The ‘w106’ (dwarf) and ‘Charleston Gray’ (vine) were used as parents to construct F1 and F2 progeny. Dwarf architecture of ‘w106’ was mainly caused by longitudinal cell length reduction and was controlled by a single recessive gene. Whole-genome sequencing of two parents and two bulk DNAs of F2 population localized this gene to a 2.63-Mb region on chromosome 9; this was further narrowed to a 541-kb region. Within this region, Cla015407, encoding a gibberellin 3β-hydroxylase (GA3ox), was the candidate gene. Cla015407 had a SNP mutation (G → A) in the splice acceptor site of the intron, leading to altered splicing event and generating two splicing isoforms in dwarf plants. One splicing isoform retained the intron sequences, while the other had a 13-bp deletion in the second exon of GA3ox transcript, both resulting in truncated proteins and loss of the functional Fe2OG dioxygenase domain in dwarf plants. RNA-Seq analysis indicated that expression of Cla015407 and other GA biosynthetic and metabolic genes were mostly up-regulated in the shoots of dwarf plants compared with vine plants in F2 population. Measurement of endogenous GA levels indicated that bioactive GA4 was significantly decreased in the shoots of dwarf plants. Moreover, the dwarf phenotype can be rescued by exogenous applications of GA3 or GA4+7, with the latter having a more distinct effect than the former. Subcellular localization analyses of GA3ox proteins from two parents revealed their subcellular targeting in nucleus and cytosol. Here, a GA3ox gene controlling dwarf architecture was identified, and loss function of GA3ox leads to GA4 reduction and dwarfism phenotype in watermelon.
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Affiliation(s)
- Yuyan Sun
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Huiqing Zhang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Min Fan
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| | - Yanjun He
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Pingan Guo
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
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Wang H, Yan A, Sun L, Zhang G, Wang X, Ren J, Xu H. Novel stable QTLs identification for berry quality traits based on high-density genetic linkage map construction in table grape. BMC PLANT BIOLOGY 2020; 20:411. [PMID: 32883214 PMCID: PMC7470616 DOI: 10.1186/s12870-020-02630-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/30/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND Aroma, berry firmness and berry shape are three main quality traits in table grape production, and also the important target traits in grapevine breeding. However, the information about their genetic mechanisms is limited, which results in low accuracy and efficiency of quality breeding in grapevine. Mapping and isolation of quantitative trait locus (QTLs) based on the construction of genetic linkage map is a powerful approach to decipher the genetic determinants of complex quantitative traits. RESULTS In the present work, a final integrated map consisting of 3411 SLAF markers on 19 linkage groups (LGs) with an average distance of 0.98 cM between adjacent markers was generated using the specific length amplified fragment sequencing (SLAF-seq) technique. A total of 9 significant stable QTLs for Muscat flavor, berry firmness and berry shape were identified on two linkage groups among the hybrids analyzed over three consecutive years from 2016 to 2018. Notably, new stable QTLs for berry firmness and berry shape were found on LG 8 respectively for the first time. Based on biological function and expression profiles of candidate genes in the major QTL regions, 3 genes (VIT_08s0007g00440, VIT_08s0040g02740 and VIT_08s0040g02350) related to berry firmness and 3 genes (VIT_08s0032g01110, VIT_08s0032g01150 and VIT_08s0105g00200) linked to berry shape were highlighted. Overexpression of VIT_08s0032g01110 in transgenic Arabidopsis plants caused the change of pod shape. CONCLUSIONS A new high-density genetic map with total 3411 markers was constructed with SLAF-seq technique, and thus enabled the detection of narrow interval QTLs for relevant traits in grapevine. VIT_08s0007g00440, VIT_08s0040g02740 and VIT_08s0040g02350 were found to be related to berry firmness, while VIT_08s0032g01110, VIT_08s0032g01150 and VIT_08s0105g00200 were linked to berry shape.
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Affiliation(s)
- Huiling Wang
- Beijing Academy of Forestry and Pomology Sciences, Beijing, 100093, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, 100093, P.R. China
| | - Ailing Yan
- Beijing Academy of Forestry and Pomology Sciences, Beijing, 100093, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, P.R. China
| | - Lei Sun
- Beijing Academy of Forestry and Pomology Sciences, Beijing, 100093, China
| | - Guojun Zhang
- Beijing Academy of Forestry and Pomology Sciences, Beijing, 100093, China
| | - Xiaoyue Wang
- Beijing Academy of Forestry and Pomology Sciences, Beijing, 100093, China
| | - Jiancheng Ren
- Beijing Academy of Forestry and Pomology Sciences, Beijing, 100093, China
| | - Haiying Xu
- Beijing Academy of Forestry and Pomology Sciences, Beijing, 100093, China.
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Aguado E, García A, Iglesias-Moya J, Romero J, Wehner TC, Gómez-Guillamón ML, Picó B, Garcés-Claver A, Martínez C, Jamilena M. Mapping a Partial Andromonoecy Locus in Citrullus lanatus Using BSA-Seq and GWAS Approaches. FRONTIERS IN PLANT SCIENCE 2020; 11:1243. [PMID: 32973825 PMCID: PMC7466658 DOI: 10.3389/fpls.2020.01243] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/29/2020] [Indexed: 05/11/2023]
Abstract
The sexual expression of watermelon plants is the result of the distribution and occurrence of male, female, bisexual and hermaphrodite flowers on the main and secondary stems. Plants can be monoecious (producing male and female flowers), andromonoecious (producing male and hermaphrodite flowers), or partially andromonoecious (producing male, female, bisexual, and hermaphrodite flowers) within the same plant. Sex determination of individual floral buds and the distribution of the different flower types on the plant, are both controlled by ethylene. A single missense mutation in the ethylene biosynthesis gene CitACS4, is able to promote the conversion of female into hermaphrodite flowers, and therefore of monoecy (genotype MM) into partial andromonoecy (genotype Mm) or andromonoecy (genotype mm). We phenotyped and genotyped, for the M/m locus, a panel of 207 C. lanatus accessions, including five inbreds and hybrids, and found several accessions that were repeatedly phenotyped as PA (partially andromonoecious) in several locations and different years, despite being MM. A cosegregation analysis between a SNV in CitACS4 and the PA phenotype, demonstrated that the occurrence of bisexual and hermaphrodite flowers in a PA line is not dependent on CitACS4, but conferred by an unlinked recessive gene which we called pa. Two different approaches were performed to map the pa gene in the genome of C. lanatus: bulk segregant analysis sequencing (BSA-seq) and genome wide association analysis studies (GWAS). The BSA-seq study was performed using two contrasting bulks, the monoecious M-bulk and the partially andromonoecious PA-bulk, each one generated by pooling DNA from 20 F2 plants. For GWAS, 122 accessions from USDA gene bank, already re-sequenced by genotyping by sequencing (GBS), were used. The combination of the two approaches indicates that pa maps onto a genomic region expanding across 32.24-36.44 Mb in chromosome 1 of watermelon. Fine mapping narrowed down the pa locus to a 867 Kb genomic region containing 101 genes. A number of candidate genes were selected, not only for their function in ethylene biosynthesis and signalling as well as their role in flower development and sex determination, but also by the impact of the SNPs and indels differentially detected in the two sequenced bulks.
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Affiliation(s)
- Encarnación Aguado
- Department of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, Almería, Spain
| | - Alicia García
- Department of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, Almería, Spain
| | - Jessica Iglesias-Moya
- Department of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, Almería, Spain
| | - Jonathan Romero
- Department of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, Almería, Spain
| | - Todd C. Wehner
- Departament of Horticultural Science, North Carolina State University, Raleigh, NC, United States
| | | | - Belén Picó
- COMAV—Universidad Politécnica de Valencia, Valencia, Spain
| | | | - Cecilia Martínez
- Department of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, Almería, Spain
| | - Manuel Jamilena
- Department of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, Almería, Spain
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Yang B, Wendrich JR, De Rybel B, Weijers D, Xue H. Rice microtubule-associated protein IQ67-DOMAIN14 regulates grain shape by modulating microtubule cytoskeleton dynamics. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1141-1152. [PMID: 31622529 PMCID: PMC7152617 DOI: 10.1111/pbi.13279] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 10/10/2019] [Accepted: 10/15/2019] [Indexed: 05/07/2023]
Abstract
Cortical microtubule (MT) arrays play a critical role in plant cell shape determination by defining the direction of cell expansion. As plants continuously adapt to ever-changing environmental conditions, multiple environmental and developmental inputs need to be translated into changes of the MT cytoskeleton. Here, we identify and functionally characterize an auxin-inducible and MT-localized protein OsIQ67-DOMAIN14 (OsIQD14), which is highly expressed in rice seed hull cells. We show that while deficiency of OsIQD14 results in short and wide seeds and increases overall yield, overexpression leads to narrow and long seeds, caused by changed MT alignment. We further show that OsIQD14-mediated MT reordering is regulated by specifically affecting MT dynamics, and ectopic expression of OsIQD14 in Arabidopsis could change the cell shape both in pavement cells and in hypocotyl cells. Additionally, OsIQD14 activity is tightly controlled by calmodulin proteins, providing an alternative way to modify the OsIQD14 activity. Our results indicate that OsIQD14 acts as a key factor in regulating MT rearrangements in rice hull cells and hence the grain shape, and allows effective local cell shape manipulation to improve the rice yield trait.
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Affiliation(s)
- BaoJun Yang
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Jos R. Wendrich
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
- Laboratory of BiochemistryWageningen UniversityWageningenThe Netherlands
| | - Bert De Rybel
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Dolf Weijers
- Laboratory of BiochemistryWageningen UniversityWageningenThe Netherlands
| | - Hong‐Wei Xue
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
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Hao N, Han D, Huang K, Du Y, Yang J, Zhang J, Wen C, Wu T. Genome-based breeding approaches in major vegetable crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1739-1752. [PMID: 31728564 DOI: 10.1007/s00122-019-03477-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/09/2019] [Indexed: 05/09/2023]
Abstract
Vegetable crops are major nutrient sources for humanity and have been well-cultivated since thousands of years of domestication. With the rapid development of next-generation sequencing and high-throughput genotyping technologies, the reference genome of more than 20 vegetables have been well-assembled and published. Resequencing approaches on large-scale germplasm resources have clarified the domestication and improvement of vegetable crops by human selection; its application on genetic mapping and quantitative trait locus analysis has led to the discovery of key genes and molecular markers linked to important traits in vegetables. Moreover, genome-based breeding has been utilized in many vegetable crops, including Solanaceae, Cucurbitaceae, Cruciferae, and other families, thereby promoting molecular breeding at a single-nucleotide level. Thus, genome-wide SNP markers have been widely used, and high-throughput genotyping techniques have become one of the most essential methods in vegetable breeding. With the popularization of gene editing technology research on vegetable crops, breeding efficiency can be rapidly increased, especially by combining the genomic and variomic information of vegetable crops. This review outlines the present genome-based breeding approaches used for major vegetable crops to provide insights into next-generation molecular breeding for the increasing global population.
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Affiliation(s)
- Ning Hao
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, 410128, China
- College of Horticulture and Landscape, Northeast Agricultural University, Harbin, 150030, China
| | - Deguo Han
- College of Horticulture and Landscape, Northeast Agricultural University, Harbin, 150030, China
| | - Ke Huang
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, 410128, China
| | - Yalin Du
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, 410128, China
| | - Jingjing Yang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Jian Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Changlong Wen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China.
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China.
| | - Tao Wu
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, 410128, China.
- College of Horticulture and Landscape, Northeast Agricultural University, Harbin, 150030, China.
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Liao N, Hu Z, Li Y, Hao J, Chen S, Xue Q, Ma Y, Zhang K, Mahmoud A, Ali A, Malangisha GK, Lyu X, Yang J, Zhang M. Ethylene-responsive factor 4 is associated with the desirable rind hardness trait conferring cracking resistance in fresh fruits of watermelon. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1066-1077. [PMID: 31610078 PMCID: PMC7061880 DOI: 10.1111/pbi.13276] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 09/26/2019] [Accepted: 10/06/2019] [Indexed: 05/11/2023]
Abstract
Fruit rind plays a pivotal role in alleviating water loss and disease and particularly in cracking resistance as well as the transportability, storability and shelf-life quality of the fruit. High susceptibility to cracking due to low rind hardness is largely responsible for severe annual yield losses of fresh fruits such as watermelon in the field and during the postharvest process. However, the candidate gene controlling the rind hardness phenotype remains unclear to date. Herein, we report, for the first time, an ethylene-responsive transcription factor 4 (ClERF4) associated with variation in rind hardness via a combinatory genetic map with bulk segregant analysis (BSA). Strikingly, our fine-mapping approach revealed an InDel of 11 bp and a neighbouring SNP in the ClERF4 gene on chromosome 10, conferring cracking resistance in F2 populations with variable rind hardness. Furthermore, the concomitant kompetitive/competitive allele-specific PCR (KASP) genotyping data sets of 104 germplasm accessions strongly supported candidate ClERF4 as a causative gene associated with fruit rind hardness variability. In conclusion, our results provide new insight into the underlying mechanism controlling rind hardness, a desirable trait in fresh fruit. Moreover, the findings will further enable the molecular improvement of fruit cracking resistance in watermelon via precisely targeting the causative gene relevant to rind hardness, ClERF4.
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Affiliation(s)
- Nanqiao Liao
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
| | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
- Key laboratory of Horticultural Plant growthDevelopment and Quality ImprovementMinistry of AgricultureHangzhouChina
| | - Yingying Li
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
| | - Junfang Hao
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
| | - Shuna Chen
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
| | - Qin Xue
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
| | - Yuyuan Ma
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
| | - Kejia Zhang
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
| | - Ahmed Mahmoud
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
| | - Abid Ali
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
| | - Guy Kateta Malangisha
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
| | - Xiaolong Lyu
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
- Key laboratory of Horticultural Plant growthDevelopment and Quality ImprovementMinistry of AgricultureHangzhouChina
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
- Key laboratory of Horticultural Plant growthDevelopment and Quality ImprovementMinistry of AgricultureHangzhouChina
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Liu Z, Haider MS, Khan N, Fang J. Comprehensive Sequence Analysis of IQD Gene Family and their Expression Profiling in Grapevine ( Vitis vinifera). Genes (Basel) 2020; 11:genes11020235. [PMID: 32102395 PMCID: PMC7073947 DOI: 10.3390/genes11020235] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/14/2020] [Accepted: 02/19/2020] [Indexed: 12/25/2022] Open
Abstract
The plant-specific IQ67-domain (IQD) protein family members are downstream targets of calcium sensors, known to regulate plant growth and lateral organ polarity, and basal defense response against environmental cues. No systematic study of IQD gene family has been performed on grapevine. The public availability of grapevine genome enables us to perform identification, phylogeny, chromosomal orientation, and gene structure analysis of the IQD genes in grapevine. We identified 49 VvIQD genes (VvIQD1–VvIQD49) and further classified them into eight subgroups based on phylogenetic relationships. The 49 VvIQD genes were assigned to 19 different chromosomal positions. The collinear relationship between grapevine and Arabidopsis IQDs (VvIQD and AtIQD), and within grapevine VvIQDs, was highly conserved. In addition, most of duplicated gene pairs showed Ka/Ks ratio less than 1.00, indicating purifying selection within these gene pairs, implying functional discrepancy after duplication. Transcription profiling of VvIQD genes shed light on their specific role in grapevine tissue and organ development. The qRT-PCR validation of the 49 VvIQD genes in grape berry tissue from cultivars with distinct berry shape during developmental phases suggested candidate genes involved in the shape of grape berries. The subcellular prediction of VvIQD22, VvIQD23, VvIQD38, and VvIQD49 genes validated their localization in the nucleus and plasma membrane. The VvIQD49 protein interaction with VvCaM2 was also verified by bimolecular fluorescence complementation (BiFC) analysis in the plasma membrane. Our findings will be valuable for the functional genomic studies for desirable shape development of grape berries.
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Affiliation(s)
- Zhongjie Liu
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.L.); (M.S.H.)
| | - Muhammad Salman Haider
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.L.); (M.S.H.)
| | - Nadeem Khan
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada;
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada
| | - Jinggui Fang
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.L.); (M.S.H.)
- Correspondence: ; Tel.: +86-02584395217; Fax: +86-02584395217
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42
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Su W, Tao R, Liu W, Yu C, Yue Z, He S, Lavelle D, Zhang W, Zhang L, An G, Zhang Y, Hu Q, Larkin RM, Michelmore RW, Kuang H, Chen J. Characterization of four polymorphic genes controlling red leaf colour in lettuce that have undergone disruptive selection since domestication. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:479-490. [PMID: 31325407 PMCID: PMC6953203 DOI: 10.1111/pbi.13213] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 07/06/2019] [Accepted: 07/14/2019] [Indexed: 05/18/2023]
Abstract
Anthocyanins protect plants from biotic and abiotic stressors and provide great health benefits to consumers. In this study, we cloned four genes (Red Lettuce Leaves 1 to 4: RLL1 to RLL4) that contribute to colour variations in lettuce. The RLL1 gene encodes a bHLH transcription factor, and a 5-bp deletion in some cultivars abolishes its function to activate the anthocyanin biosynthesis pathway. The RLL2 gene encodes an R2R3-MYB transcription factor, which was derived from a duplication followed by mutations in its promoter region. The RLL3 gene encodes an R2-MYB transcription factor, which down-regulates anthocyanin biosynthesis through competing with RLL2 for interaction with RLL1; a mis-sense mutation compromises the capacity of RLL3 to bind RLL1. The RLL4 gene encodes a WD-40 transcription factor, homologous to the RUP genes suppressing the UV-B signal transduction pathway in Arabidopsis; a mis-sense mutation in rll4 attenuates its suppressing function, leading to a high concentration of anthocyanins. Sequence analysis of the RLL1-RLL4 genes from wild and cultivated lettuce showed that their function-changing mutations occurred after domestication. The mutations in rll1 disrupt anthocyanin biosynthesis, while the mutations in RLL2, rll3 and rll4 activate anthocyanin biosynthesis, showing disruptive selection for leaf colour during domestication of lettuce. The characterization of multiple polymorphic genes in this study provides the necessary molecular resources for the rational breeding of lettuce cultivars with distinct levels of red pigments and green cultivars with high levels of health-promoting flavonoids.
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Affiliation(s)
- Wenqing Su
- Key Laboratory of Horticultural Plant BiologyMinistry of EducationKey Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region)MOACollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Rong Tao
- Key Laboratory of Horticultural Plant BiologyMinistry of EducationKey Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region)MOACollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Wenye Liu
- Key Laboratory of Horticultural Plant BiologyMinistry of EducationKey Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region)MOACollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Changchun Yu
- Key Laboratory of Horticultural Plant BiologyMinistry of EducationKey Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region)MOACollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Zhen Yue
- Key Laboratory of Horticultural Plant BiologyMinistry of EducationKey Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region)MOACollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Shuping He
- Key Laboratory of Horticultural Plant BiologyMinistry of EducationKey Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region)MOACollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Dean Lavelle
- Genome Center and Department of Plant SciencesUniversity of CaliforniaDavisCAUSA
| | - Weiyi Zhang
- Key Laboratory of Horticultural Plant BiologyMinistry of EducationKey Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region)MOACollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Lei Zhang
- Key Laboratory of Horticultural Plant BiologyMinistry of EducationKey Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region)MOACollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Guanghui An
- Key Laboratory of Horticultural Plant BiologyMinistry of EducationKey Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region)MOACollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Yu Zhang
- Key Laboratory of Horticultural Plant BiologyMinistry of EducationKey Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region)MOACollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Qun Hu
- Key Laboratory of Horticultural Plant BiologyMinistry of EducationKey Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region)MOACollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Robert M. Larkin
- Key Laboratory of Horticultural Plant BiologyMinistry of EducationKey Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region)MOACollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | | | - Hanhui Kuang
- Key Laboratory of Horticultural Plant BiologyMinistry of EducationKey Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region)MOACollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Jiongjiong Chen
- Key Laboratory of Horticultural Plant BiologyMinistry of EducationKey Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region)MOACollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
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Pan Y, Wang Y, McGregor C, Liu S, Luan F, Gao M, Weng Y. Genetic architecture of fruit size and shape variation in cucurbits: a comparative perspective. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1-21. [PMID: 31768603 DOI: 10.1007/s00122-019-03481-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 11/11/2019] [Indexed: 05/28/2023]
Abstract
The Cucurbitaceae family hosts many economically important fruit vegetables (cucurbits) such as cucumber, melon, watermelon, pumpkin/squash, and various gourds. The cucurbits are probably best known for the diverse fruit sizes and shapes, but little is known about their genetic basis and molecular regulation. Here, we reviewed the literature on fruit size (FS), shape (FSI), and fruit weight (FW) QTL identified in cucumber, melon, and watermelon, from which 150 consensus QTL for these traits were inferred. Genome-wide survey of the three cucurbit genomes identified 253 homologs of eight classes of fruit or grain size/weight-related genes cloned in Arabidopsis, tomato, and rice that encode proteins containing the characteristic CNR (cell number regulator), CSR (cell size regulator), CYP78A (cytochrome P450), SUN, OVATE, TRM (TONNEAU1 Recruiting Motif), YABBY, and WOX domains. Alignment of the consensus QTL with candidate gene homologs revealed widespread structure and function conservation of fruit size/shape gene homologs in cucurbits, which was exemplified with the fruit size/shape candidate genes CsSUN25-26-27a and CsTRM5 in cucumber, CmOFP1a in melon, and ClSUN25-26-27a in watermelon. In cucurbits, the andromonoecy (for 1-aminocyclopropane-1-carboxylate synthase) and the carpel number (for CLAVATA3) loci are known to have pleiotropic effects on fruit shape, which may complicate identification of fruit size/shape candidate genes in these regions. The present work illustrates the power of comparative analysis in understanding the genetic architecture of fruit size/shape variation, which may facilitate QTL mapping and cloning for fruit size-related traits in cucurbits. The limitations and perspectives of this approach are also discussed.
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Affiliation(s)
- Yupeng Pan
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
| | - Yuhui Wang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Cecilia McGregor
- Department of Horticulture and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
| | - Shi Liu
- College of Horticulture and, Landscape Architecture at Northeast Agricultural University, Harbin, 150030, China
| | - Feishi Luan
- College of Horticulture and, Landscape Architecture at Northeast Agricultural University, Harbin, 150030, China
| | - Meiling Gao
- College of Life Science, Agriculture and Forestry, Qiqihar University, Qiqihar, 161006, China
| | - Yiqun Weng
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- USDA-ARS Vegetable Crops Research Unit, 1575 Linden Dr., Madison, WI, 53706, USA.
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Wang C, Zhang H, Xia Q, Yu J, Zhu D, Zhao Q. ZmGLR, a cell membrane localized microtubule-associated protein, mediated leaf morphogenesis in maize. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 289:110248. [PMID: 31623783 DOI: 10.1016/j.plantsci.2019.110248] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/28/2019] [Accepted: 08/30/2019] [Indexed: 06/10/2023]
Abstract
Microtubule arrays play notable roles in cell division, cell movement, cell morphogenesis and signal transduction. Due to their important regulation of microtubule dynamic instability and array-ordering processes, microtubule-associated proteins have been a cutting-edge issue in research. Here, a new maize microtubule-associated protein, ZmGLR (Zea mays glutamic acid- and lysine-rich), was found. ZmGLR bundles microtubules in vitro and targets the cell membrane through an interaction between 24 conserved N-terminal amino acids and specific phosphatidylinositol phosphates (PtdInsPs). Increased Ca2+ levels in the cytoplasm lead to ZmGLR partially dissociating from the cell membrane and moving into the cytoplasm to associate with microtubule. Overexpression and RNAi of ZmGLR both resulted in misoriented microtubule arrays, which led to dwarf maize plants and curved leaves. In addition, the expression of ZmGLR was regulated by BR and auxin through ZmBES1 and ZmARF9, respectively. This study reveals that the microtubule-associated protein ZmGLR plays a crucial role in cortical microtubule reorientation and maize leaf morphogenesis.
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Affiliation(s)
- Chenchen Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Hua Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Qi Xia
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Jingjuan Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Dengyun Zhu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Qian Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China.
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Wu S, Wang X, Reddy U, Sun H, Bao K, Gao L, Mao L, Patel T, Ortiz C, Abburi VL, Nimmakayala P, Branham S, Wechter P, Massey L, Ling K, Kousik C, Hammar SA, Tadmor Y, Portnoy V, Gur A, Katzir N, Guner N, Davis A, Hernandez AG, Wright CL, McGregor C, Jarret R, Zhang X, Xu Y, Wehner TC, Grumet R, Levi A, Fei Z. Genome of 'Charleston Gray', the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:2246-2258. [PMID: 31022325 PMCID: PMC6835170 DOI: 10.1111/pbi.13136] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 04/16/2019] [Accepted: 04/18/2019] [Indexed: 05/14/2023]
Abstract
Years of selection for desirable fruit quality traits in dessert watermelon (Citrullus lanatus) has resulted in a narrow genetic base in modern cultivars. Development of novel genomic and genetic resources offers great potential to expand genetic diversity and improve important traits in watermelon. Here, we report a high-quality genome sequence of watermelon cultivar 'Charleston Gray', a principal American dessert watermelon, to complement the existing reference genome from '97103', an East Asian cultivar. Comparative analyses between genomes of 'Charleston Gray' and '97103' revealed genomic variants that may underlie phenotypic differences between the two cultivars. We then genotyped 1365 watermelon plant introduction (PI) lines maintained at the U.S. National Plant Germplasm System using genotyping-by-sequencing (GBS). These PI lines were collected throughout the world and belong to three Citrullus species, C. lanatus, C. mucosospermus and C. amarus. Approximately 25 000 high-quality single nucleotide polymorphisms (SNPs) were derived from the GBS data using the 'Charleston Gray' genome as the reference. Population genomic analyses using these SNPs discovered a close relationship between C. lanatus and C. mucosospermus and identified four major groups in these two species correlated to their geographic locations. Citrullus amarus was found to have a distinct genetic makeup compared to C. lanatus and C. mucosospermus. The SNPs also enabled identification of genomic regions associated with important fruit quality and disease resistance traits through genome-wide association studies. The high-quality 'Charleston Gray' genome and the genotyping data of this large collection of watermelon accessions provide valuable resources for facilitating watermelon research, breeding and improvement.
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Affiliation(s)
- Shan Wu
- Boyce Thompson InstituteCornell UniversityIthacaNYUSA
| | - Xin Wang
- Boyce Thompson InstituteCornell UniversityIthacaNYUSA
| | - Umesh Reddy
- Department of BiologyWest Virginia State UniversityInstituteWVUSA
| | - Honghe Sun
- Boyce Thompson InstituteCornell UniversityIthacaNYUSA
- National Engineering Research Center for VegetablesBeijing Academy of Agriculture and Forestry SciencesKey Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)BeijingChina
| | - Kan Bao
- Boyce Thompson InstituteCornell UniversityIthacaNYUSA
| | - Lei Gao
- Boyce Thompson InstituteCornell UniversityIthacaNYUSA
| | - Linyong Mao
- Boyce Thompson InstituteCornell UniversityIthacaNYUSA
- Department of Biochemistry and Molecular BiologyHoward University College of MedicineWashingtonDCUSA
| | - Takshay Patel
- Horticultural Science DepartmentNorth Carolina State UniversityRaleighNCUSA
| | - Carlos Ortiz
- Department of BiologyWest Virginia State UniversityInstituteWVUSA
| | | | | | - Sandra Branham
- U.S. Department of Agriculture‐Agricultural Research ServiceU.S. Vegetable LaboratoryCharlestonSCUSA
| | - Pat Wechter
- U.S. Department of Agriculture‐Agricultural Research ServiceU.S. Vegetable LaboratoryCharlestonSCUSA
| | - Laura Massey
- U.S. Department of Agriculture‐Agricultural Research ServiceU.S. Vegetable LaboratoryCharlestonSCUSA
| | - Kai‐Shu Ling
- U.S. Department of Agriculture‐Agricultural Research ServiceU.S. Vegetable LaboratoryCharlestonSCUSA
| | - Chandrasekar Kousik
- U.S. Department of Agriculture‐Agricultural Research ServiceU.S. Vegetable LaboratoryCharlestonSCUSA
| | - Sue A. Hammar
- Department of HorticultureMichigan State UniversityEast LansingMIUSA
| | - Yaakov Tadmor
- Department of Vegetable ResearchAgricultural Research OrganizationNewe Ya'ar Research CenterRamat YishayIsrael
| | - Vitaly Portnoy
- Department of Vegetable ResearchAgricultural Research OrganizationNewe Ya'ar Research CenterRamat YishayIsrael
| | - Amit Gur
- Department of Vegetable ResearchAgricultural Research OrganizationNewe Ya'ar Research CenterRamat YishayIsrael
| | - Nurit Katzir
- Department of Vegetable ResearchAgricultural Research OrganizationNewe Ya'ar Research CenterRamat YishayIsrael
| | | | - Angela Davis
- Sakata Seed AmericaWoodland Research StationWoodlandCAUSA
| | - Alvaro G. Hernandez
- Roy J. Carver Biotechnology CenterUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Chris L. Wright
- Roy J. Carver Biotechnology CenterUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | | | - Robert Jarret
- U.S. Department of Agriculture‐Agricultural Research ServicePlant Genetic Resources Conservation UnitGriffinGAUSA
| | | | - Yong Xu
- National Engineering Research Center for VegetablesBeijing Academy of Agriculture and Forestry SciencesKey Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)BeijingChina
| | - Todd C. Wehner
- Horticultural Science DepartmentNorth Carolina State UniversityRaleighNCUSA
| | - Rebecca Grumet
- Department of HorticultureMichigan State UniversityEast LansingMIUSA
| | - Amnon Levi
- U.S. Department of Agriculture‐Agricultural Research ServiceU.S. Vegetable LaboratoryCharlestonSCUSA
| | - Zhangjun Fei
- Boyce Thompson InstituteCornell UniversityIthacaNYUSA
- U.S. Department of Agriculture‐Agricultural Research ServiceRobert W. Holley Center for Agriculture and HealthIthacaNYUSA
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Guo S, Zhao S, Sun H, Wang X, Wu S, Lin T, Ren Y, Gao L, Deng Y, Zhang J, Lu X, Zhang H, Shang J, Gong G, Wen C, He N, Tian S, Li M, Liu J, Wang Y, Zhu Y, Jarret R, Levi A, Zhang X, Huang S, Fei Z, Liu W, Xu Y. Resequencing of 414 cultivated and wild watermelon accessions identifies selection for fruit quality traits. Nat Genet 2019; 51:1616-1623. [PMID: 31676863 DOI: 10.1038/s41588-019-0518-4] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/23/2019] [Indexed: 12/31/2022]
Abstract
Fruit characteristics of sweet watermelon are largely the result of human selection. Here we report an improved watermelon reference genome and whole-genome resequencing of 414 accessions representing all extant species in the Citrullus genus. Population genomic analyses reveal the evolutionary history of Citrullus, suggesting independent evolutions in Citrullus amarus and the lineage containing Citrullus lanatus and Citrullus mucosospermus. Our findings indicate that different loci affecting watermelon fruit size have been under selection during speciation, domestication and improvement. A non-bitter allele, arising in the progenitor of sweet watermelon, is largely fixed in C. lanatus. Selection for flesh sweetness started in the progenitor of C. lanatus and continues through modern breeding on loci controlling raffinose catabolism and sugar transport. Fruit flesh coloration and sugar accumulation might have co-evolved through shared genetic components including a sugar transporter gene. This study provides valuable genomic resources and sheds light on watermelon speciation and breeding history.
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Affiliation(s)
- Shaogui Guo
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Shengjie Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Honghe Sun
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China.,Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, USA
| | - Xin Wang
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, USA
| | - Shan Wu
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, USA
| | - Tao Lin
- Lingnan Guangdong Laboratory of Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yi Ren
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Lei Gao
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, USA
| | - Yun Deng
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Jie Zhang
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Xuqiang Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Haiying Zhang
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Jianli Shang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Guoyi Gong
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Changlong Wen
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Nan He
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Shouwei Tian
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Maoying Li
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Junpu Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Yanping Wang
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Yingchun Zhu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Robert Jarret
- U.S. Department of Agriculture-Agricultural Research Service, Plant Genetic Resources Conservation Unit, Griffin, GA, USA
| | - Amnon Levi
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Lab, Charleston, SC, USA
| | - Xingping Zhang
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Sanwen Huang
- Lingnan Guangdong Laboratory of Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 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, China.
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, USA. .,U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA.
| | - Wenge Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China.
| | - Yong Xu
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China.
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47
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Feng X, Cheng H, Zuo D, Zhang Y, Wang Q, Liu K, Ashraf J, Yang Q, Li S, Chen X, Song G. Fine mapping and identification of the fuzzless gene GaFzl in DPL972 (Gossypium arboreum). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2169-2179. [PMID: 30941465 PMCID: PMC6647196 DOI: 10.1007/s00122-019-03330-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 09/14/2018] [Indexed: 05/15/2023]
Abstract
KEY MESSAGE The fuzzless gene GaFzl was fine mapped to a 70-kb region containing a GIR1 gene, Cotton_A_11941, responsible for the fuzzless trait in Gossypium arboreum DPL972. Cotton fiber is the most important natural textile resource. The fuzzless mutant DPL972 (Gossypium arboreum) provides a useful germplasm resource to explore the molecular mechanism underlying fiber and fuzz initiation and development. In our previous research, the fuzzless gene in DPL972 was identified as a single dominant gene and named GaFzl. In the present study, we fine mapped this gene using F2 and BC1 populations. By combining traditional map-based cloning and next-generation sequencing, we mapped GaFzl to a 70-kb region containing seven annotated genes. RNA-Sequencing and re-sequencing analysis narrowed these candidates to two differentially expressed genes, Cotton_A_11941 and Cotton_A_11942. Sequence alignment uncovered no variation in coding or promoter regions of Cotton_A_11942 between DPL971 and DPL972, whereas two single-base mutations in the promoter region and a TTG insertion in the coding region were detected in Cotton_A_11941 in DPL972. Cotton_A_11941 encoding a homologous gene of GIR1 (GLABRA2-interacting repressor) in Arabidopsis thaliana is thus the candidate gene most likely responsible for the fuzzless trait in DPL972. Our findings should lead to a better understanding of cotton fuzz formation, thereby accelerating marker-assisted selection during cotton breeding.
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Affiliation(s)
- Xiaoxu Feng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Plant Genetics, Gembloux Agro Bio Tech, University of Liège, Gembloux, Belgium
| | - Hailiang Cheng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Dongyun Zuo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Youping Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Qiaolian Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Ke Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Javaria Ashraf
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Qiuhong Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Simin Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xiaoqin Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Guoli Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
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48
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Kölling M, Kumari P, Bürstenbinder K. Calcium- and calmodulin-regulated microtubule-associated proteins as signal-integration hubs at the plasma membrane-cytoskeleton nexus. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:387-396. [PMID: 30590729 DOI: 10.1093/jxb/ery397] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 12/06/2018] [Indexed: 05/09/2023]
Abstract
Plant growth and development are a genetically predetermined series of events but can change dramatically in response to environmental stimuli, involving perpetual pattern formation and reprogramming of development. The rate of growth is determined by cell division and subsequent cell expansion, which are restricted and controlled by the cell wall-plasma membrane-cytoskeleton continuum, and are coordinated by intricate networks that facilitate intra- and intercellular communication. An essential role in cellular signaling is played by calcium ions, which act as universal second messengers that transduce, integrate, and multiply incoming signals during numerous plant growth processes, in part by regulation of the microtubule cytoskeleton. In this review, we highlight recent advances in the understanding of calcium-mediated regulation of microtubule-associated proteins, their function at the microtubule cytoskeleton, and their potential role as hubs in crosstalk with other signaling pathways.
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Affiliation(s)
- Malte Kölling
- Leibniz Institute of Plant Biochemistry, Weinberg, Halle/Saale, Germany
| | - Pratibha Kumari
- Leibniz Institute of Plant Biochemistry, Weinberg, Halle/Saale, Germany
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49
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Mitra D, Klemm S, Kumari P, Quegwer J, Möller B, Poeschl Y, Pflug P, Stamm G, Abel S, Bürstenbinder K. Microtubule-associated protein IQ67 DOMAIN5 regulates morphogenesis of leaf pavement cells in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:529-543. [PMID: 30407556 PMCID: PMC6322583 DOI: 10.1093/jxb/ery395] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/22/2018] [Indexed: 05/14/2023]
Abstract
Plant microtubules form a highly dynamic intracellular network with important roles for regulating cell division, cell proliferation, and cell morphology. Their organization and dynamics are co-ordinated by various microtubule-associated proteins (MAPs) that integrate environmental and developmental stimuli to fine-tune and adjust cytoskeletal arrays. IQ67 DOMAIN (IQD) proteins recently emerged as a class of plant-specific MAPs with largely unknown functions. Here, using a reverse genetics approach, we characterize Arabidopsis IQD5 in terms of its expression domains, subcellular localization, and biological functions. We show that IQD5 is expressed mostly in vegetative tissues, where it localizes to cortical microtubule arrays. Our phenotypic analysis of iqd5 loss-of-function lines reveals functions of IQD5 in pavement cell (PC) shape morphogenesis. Histochemical analysis of cell wall composition further suggests reduced rates of cellulose deposition in anticlinal cell walls, which correlate with reduced anisotropic expansion. Lastly, we demonstrate IQD5-dependent recruitment of calmodulin calcium sensors to cortical microtubule arrays and provide first evidence for important roles for calcium in regulation of PC morphogenesis. Our work identifies IQD5 as a novel player in PC shape regulation and, for the first time, links calcium signaling to developmental processes that regulate anisotropic growth in PCs.
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Affiliation(s)
- Dipannita Mitra
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry (IPB),Halle (Saale), Germany
| | - Sandra Klemm
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry (IPB),Halle (Saale), Germany
| | - Pratibha Kumari
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry (IPB),Halle (Saale), Germany
| | - Jakob Quegwer
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry (IPB),Halle (Saale), Germany
| | - Birgit Möller
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Yvonne Poeschl
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- iDiv, German Integrative Research Center for Biodiversity, Leipzig, Germany
| | - Paul Pflug
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry (IPB),Halle (Saale), Germany
| | - Gina Stamm
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry (IPB),Halle (Saale), Germany
| | - Steffen Abel
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry (IPB),Halle (Saale), Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Katharina Bürstenbinder
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry (IPB),Halle (Saale), Germany
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50
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Xanthopoulou A, Montero-Pau J, Mellidou I, Kissoudis C, Blanca J, Picó B, Tsaballa A, Tsaliki E, Dalakouras A, Paris HS, Ganopoulou M, Moysiadis T, Osathanunkul M, Tsaftaris A, Madesis P, Kalivas A, Ganopoulos I. Whole-genome resequencing of Cucurbita pepo morphotypes to discover genomic variants associated with morphology and horticulturally valuable traits. HORTICULTURE RESEARCH 2019; 6:94. [PMID: 31645952 PMCID: PMC6804688 DOI: 10.1038/s41438-019-0176-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 06/18/2019] [Accepted: 06/19/2019] [Indexed: 05/20/2023]
Abstract
Cucurbita pepo contains two cultivated subspecies, each of which encompasses four fruit-shape morphotypes (cultivar groups). The Pumpkin, Vegetable Marrow, Cocozelle, and Zucchini Groups are of subsp. pepo and the Acorn, Crookneck, Scallop, and Straightneck Groups are of subsp. ovifera. Recently, a de novo assembly of the C. pepo subsp. pepo Zucchini genome was published, providing insights into its evolution. To expand our knowledge of evolutionary processes within C. pepo and to identify variants associated with particular morphotypes, we performed whole-genome resequencing of seven of these eight C. pepo morphotypes. We report for the first time whole-genome resequencing of the four subsp. pepo (Pumpkin, Vegetable Marrow, Cocozelle, green Zucchini, and yellow Zucchini) morphotypes and three of the subsp. ovifera (Acorn, Crookneck, and Scallop) morphotypes. A high-depth resequencing approach was followed, using the BGISEQ-500 platform that enables the identification of rare variants, with an average of 33.5X. Approximately 94.5% of the clean reads were mapped against the reference Zucchini genome. In total, 3,823,977 high confidence single-nucleotide polymorphisms (SNPs) were identified. Within each accession, SNPs varied from 636,918 in green Zucchini to 2,656,513 in Crookneck, and were distributed homogeneously along the chromosomes. Clear differences between subspecies pepo and ovifera in genetic variation and linkage disequilibrium are highlighted. In fact, comparison between subspecies pepo and ovifera indicated 5710 genes (22.5%) with Fst > 0.80 and 1059 genes (4.1%) with Fst = 1.00 as potential candidate genes that were fixed during the independent evolution and domestication of the two subspecies. Linkage disequilibrium was greater in subsp. ovifera than in subsp. pepo, perhaps reflective of the earlier differentiation of morphotypes within subsp. ovifera. Some morphotype-specific genes have been localized. Our results offer new clues that may provide an improved understanding of the underlying genomic regions involved in the independent evolution and domestication of the two subspecies. Comparisons among SNPs unique to particular subspecies or morphotypes may provide candidate genes responsible for traits of high economic importance.
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Affiliation(s)
- Aliki Xanthopoulou
- Department of Genetics and Plant Breeding, Aristotle University of Thessaloniki, Thessaloniki, 54124 Greece
| | - Javier Montero-Pau
- Department of Biochemistry and Molecular Biology, Universitat de València, 46022 Valencia, Spain
| | - Ifigeneia Mellidou
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DEMETER (ex NAGREF), Thermi, Macedonia 57001 Greece
| | | | - José Blanca
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Belén Picó
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Aphrodite Tsaballa
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DEMETER (ex NAGREF), Thermi, Macedonia 57001 Greece
| | - Eleni Tsaliki
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DEMETER (ex NAGREF), Thermi, Macedonia 57001 Greece
| | - Athanasios Dalakouras
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DEMETER (ex NAGREF), Thermi, Macedonia 57001 Greece
| | - Harry S. Paris
- Department of Vegetable Crops and Plant Genetics, Agricultural Research Organization, Newe Ya’ar Research Center, Ramat Yishay, Israel
| | - Maria Ganopoulou
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DEMETER (ex NAGREF), Thermi, Macedonia 57001 Greece
| | - Theodoros Moysiadis
- Institute of Applied Biosciences (INAB), CERTH, Thermi-Thessaloniki, 57001 Greece
| | - Maslin Osathanunkul
- Department of Biology, Faculty of Science Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Bioresources for Agriculture, Industry and MedicineChiang Mai University, Chiang Mai, Thailand
| | | | - Panagiotis Madesis
- Institute of Applied Biosciences (INAB), CERTH, Thermi-Thessaloniki, 57001 Greece
| | - Apostolos Kalivas
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DEMETER (ex NAGREF), Thermi, Macedonia 57001 Greece
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DEMETER (ex NAGREF), Thermi, Macedonia 57001 Greece
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