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Xu X, Du Y, Li S, Tan M, Sohail H, Liu X, Qi X, Yang X, Chen X. A genome-wide association study reveals molecular mechanism underlying powdery mildew resistance in cucumber. Genome Biol 2024; 25:252. [PMID: 39358737 PMCID: PMC11445940 DOI: 10.1186/s13059-024-03402-8] [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: 08/03/2023] [Accepted: 09/24/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND Powdery mildew is a disease with one of the most substantial impacts on cucumber production globally. The most efficient approach for controlling powdery mildew is the development of genetic resistance; however, few genes associated with inherent variations in cucumber powdery mildew resistance have been identified as of yet. RESULTS In this study, we re-sequence 299 cucumber accessions, which are divided into four geographical groups. A genome-wide association study identifies 50 sites significantly associated with natural variations in powdery mildew resistance. Linkage disequilibrium analysis further divides these 50 sites into 32 linkage disequilibrium blocks containing 41 putative genes. Virus-induced gene silencing and gene expression analysis implicate CsGy5G015960, which encodes a phosphate transporter, as the candidate gene regulating powdery mildew resistance. On the basis of the resequencing data, we generate five CsGy5G015960 haplotypes, identifying Hap.1 as the haplotype most likely associated with powdery mildew resistance. In addition, we determine that a 29-bp InDel in the 3' untranslated region of CsGy5G015960 is responsible for mRNA stability. Overexpression of CsGy5G015960Hap.1 in the susceptible line enhances powdery mildew resistance and phosphorus accumulation. Further comparative RNA-seq analysis demonstrates that CsGy5G015960Hap.1 may regulate cucumber powdery mildew resistance by maintaining a higher H2O2 level through the depletion of multiple class III peroxidases. CONCLUSIONS Here we identify a candidate powdery mildew-resistant gene in cucumber using GWAS. The identified gene may be a promising target for molecular breeding and genetic engineering in cucumber to enhance powdery mildew resistance.
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Affiliation(s)
- Xuewen Xu
- School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the, Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Yujiao Du
- School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Suhao Li
- School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Ming Tan
- School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Hamza Sohail
- School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Xueli Liu
- School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Xiaohua Qi
- School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Xiaodong Yang
- School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu, 225009, China.
| | - Xuehao Chen
- School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the, Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, China.
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Li S, Lu K, Zhang L, Fan L, Lv W, Liu DJ, Feng G. Low-dose 60Co-γ-ray irradiation promotes the growth of cucumber seedlings by inducing CsSAUR37 expression. PLANT MOLECULAR BIOLOGY 2024; 114:107. [PMID: 39333431 DOI: 10.1007/s11103-024-01504-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 09/03/2024] [Indexed: 09/29/2024]
Abstract
Cucumber (Cucumis sativus L.) is a major vegetable crop grown globally, with a cultivation history of more than 3000 years. The limited genetic diversity, low rate of intraspecific variation, and extended periods of traditional breeding have resulted in slow progress in their genetic research and the development of new varieties. Gamma (γ)-ray irradiation potentially accelerates the breeding progress; however, the biological and molecular effects of γ-ray irradiation on cucumbers are unknown. Exposing cucumber seeds to 0, 50, 100, 150, 200, and 250 Gy doses of 60Co-γ-ray irradiation, this study aimed to investigate the resulting phenotype and physiological characteristics of seedling treatment to determine the optimal irradiation dose. The results showed that low irradiation doses (50-100 Gy) enhanced root growth, hypocotyl elongation, and lateral root numbers, promoting seedling growth. However, high irradiation doses (150-250 Gy) significantly inhibited seed germination and growth, decreasing the survival rate of seedlings. More than 100 Gy irradiation significantly decreased the total chlorophyll content while increasing the malondialdehyde (MDA) and H2O2 content in cucumber. Transcriptome sequencing analysis at 0, 50, 100, 150, 200, and 250 Gy doses showed that gene expression significantly differed between low and high irradiation doses. Gene Ontology enrichment and functional pathway enrichment analyses revealed that the auxin response pathway played a crucial role in seedling growth under low irradiation doses. Further, gene function analysis revealed that small auxin up-regulated gene CsSAUR37 was a key gene that was overexpressed in response to low irradiation doses, promoting primary root elongation and enhancing lateral root numbers by regulating the expression of protein phosphatase 2Cs (PP2Cs) and auxin synthesis genes.
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Affiliation(s)
- Shengnan Li
- Key Laboratory of Sugar Beet Genetic Breeding, College of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, China
- Sugar Beet Engineering Research Center of Heilongjiang Province, Harbin, 150080, China
| | - Ke Lu
- Key Laboratory of Sugar Beet Genetic Breeding, College of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, China
- Sugar Beet Engineering Research Center of Heilongjiang Province, Harbin, 150080, China
| | - La Zhang
- Key Laboratory of Sugar Beet Genetic Breeding, College of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, China
- Sugar Beet Engineering Research Center of Heilongjiang Province, Harbin, 150080, China
| | - Lianxue Fan
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Wei Lv
- Key Laboratory of Sugar Beet Genetic Breeding, College of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, China
- Sugar Beet Engineering Research Center of Heilongjiang Province, Harbin, 150080, China
| | - Da Jun Liu
- Key Laboratory of Sugar Beet Genetic Breeding, College of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, China.
- Sugar Beet Engineering Research Center of Heilongjiang Province, Harbin, 150080, China.
| | - Guojun Feng
- Key Laboratory of Sugar Beet Genetic Breeding, College of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, China.
- Sugar Beet Engineering Research Center of Heilongjiang Province, Harbin, 150080, China.
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Fang Y, Xiao X, Lin J, Lin Q, Wang J, Liu K, Li Z, Xing J, Liu Z, Wang B, Qi Y, Long X, Zeng X, Hu Y, Qi J, Qin Y, Yang J, Zhang Y, Zhang S, Ye D, Zhang J, Liu J, Tang C. Pan-genome and phylogenomic analyses highlight Hevea species delineation and rubber trait evolution. Nat Commun 2024; 15:7232. [PMID: 39174505 PMCID: PMC11341782 DOI: 10.1038/s41467-024-51031-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 07/28/2024] [Indexed: 08/24/2024] Open
Abstract
The para rubber tree (Hevea brasiliensis) is the world's sole commercial source of natural rubber, a vital industrial raw material. However, the narrow genetic diversity of this crop poses challenges for rubber breeding. Here, we generate high-quality de novo genome assemblies for three H. brasiliensis cultivars, two H. brasiliensis wild accessions, and three other Hevea species (H. nitida, H. pauciflora, and H. benthamiana). Through analyzing genomes of 94 Hevea accessions, we identify five distinct lineages that do not align with their previous species delineations. We discover multiple accessions with hybrid origins between these lineages, indicating incomplete reproductive isolation between them. Only two out of four wild lineages have been introduced to commercial rubber cultivars. Furthermore, we reveal that the rubber production traits emerged following the development of a large REF/SRPP gene cluster and its functional specialization in rubber-producing laticifers within this genus. These findings would enhance rubber breeding and benefit research communities.
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Affiliation(s)
- Yongjun Fang
- National Key Laboratory for Tropical Crop Breeding, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya/Haikou, China
| | - Xiaohu Xiao
- National Key Laboratory for Tropical Crop Breeding, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya/Haikou, China
| | - Jishan Lin
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China
| | - Qiang Lin
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jiang Wang
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China
- Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC, Haikou, China
| | - Kaiye Liu
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China
- Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC, Haikou, China
| | - Zhonghua Li
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China
- Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC, Haikou, China
| | - Jianfeng Xing
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China
| | - Zhenglin Liu
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China
| | - Baiyu Wang
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Yiying Qi
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiangyu Long
- National Key Laboratory for Tropical Crop Breeding, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya/Haikou, China
| | - Xia Zeng
- National Key Laboratory for Tropical Crop Breeding, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya/Haikou, China
| | - Yanshi Hu
- National Key Laboratory for Tropical Crop Breeding, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya/Haikou, China
| | - Jiyan Qi
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China
- Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC, Haikou, China
| | - Yunxia Qin
- National Key Laboratory for Tropical Crop Breeding, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya/Haikou, China
| | - Jianghua Yang
- National Key Laboratory for Tropical Crop Breeding, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya/Haikou, China
| | - Yi Zhang
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China
- Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC, Haikou, China
| | - Shengmin Zhang
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China
- Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC, Haikou, China
| | - De Ye
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China
- Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC, Haikou, China
| | - Jisen Zhang
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, China.
| | - Chaorong Tang
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China.
- Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC, Haikou, China.
- Yunnan Institute of Tropical Crops, Xishuangbanna, China.
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Guan J, Miao H, Zhang Z, Dong S, Zhou Q, Liu X, Beckles DM, Gu X, Huang S, Zhang S. A near-complete cucumber reference genome assembly and Cucumber-DB, a multi-omics database. MOLECULAR PLANT 2024; 17:1178-1182. [PMID: 38907525 DOI: 10.1016/j.molp.2024.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/05/2024] [Accepted: 06/19/2024] [Indexed: 06/24/2024]
Affiliation(s)
- Jiantao Guan
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Han Miao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhonghua Zhang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Shaoyun Dong
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qi Zhou
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoping Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Diane M Beckles
- Department of Plant Sciences, University of California, Davis, One Shield Avenue, Davis, CA 95616, USA
| | - Xingfang Gu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shengping Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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5
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Ge T, Luo X, Wang Y, Sedlmair M, Cheng Z, Zhao Y, Liu X, Deussen O, Chen B. Optimally Ordered Orthogonal Neighbor Joining Trees for Hierarchical Cluster Analysis. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2024; 30:5034-5046. [PMID: 37294655 DOI: 10.1109/tvcg.2023.3284499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We propose to use optimally ordered orthogonal neighbor-joining (O 3 NJ) trees as a new way to visually explore cluster structures and outliers in multi-dimensional data. Neighbor-joining (NJ) trees are widely used in biology, and their visual representation is similar to that of dendrograms. The core difference to dendrograms, however, is that NJ trees correctly encode distances between data points, resulting in trees with varying edge lengths. We optimize NJ trees for their use in visual analysis in two ways. First, we propose to use a novel leaf sorting algorithm that helps users to better interpret adjacencies and proximities within such a tree. Second, we provide a new method to visually distill the cluster tree from an ordered NJ tree. Numerical evaluation and three case studies illustrate the benefits of this approach for exploring multi-dimensional data in areas such as biology or image analysis.
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Shen J, Jiang Y, Pan J, Sun L, Li Q, He W, Sun P, Zhao B, Zhao H, Ke X, Guo Y, Yang T, Li Z. The GRAS transcription factor CsTL regulates tendril formation in cucumber. THE PLANT CELL 2024; 36:2818-2833. [PMID: 38630900 PMCID: PMC11289639 DOI: 10.1093/plcell/koae123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/13/2024] [Accepted: 03/23/2024] [Indexed: 04/19/2024]
Abstract
Cucumber (Cucumis sativus, Cs) tendrils are slender vegetative organs that typically require manual removal to ensure orderly growth during greenhouse cultivation. Here, we identified cucumber tendril-less (tl), a Tnt1 retrotransposon-induced insertion mutant lacking tendrils. Map-based cloning identified the mutated gene, CsaV3_3G003590, which we designated as CsTL, which is homologous to Arabidopsis thaliana LATERAL SUPPRESSOR (AtLAS). Knocking out CsTL repressed tendril formation but did not affect branch initiation, whereas overexpression (OE) of CsTL resulted in the formation of two or more tendrils in one leaf axil. Although expression of two cucumber genes regulating tendril formation, Tendril (CsTEN) and Unusual Floral Organs (CsUFO), was significantly decreased in CsTL knockout lines, these two genes were not direct downstream targets of CsTL. Instead, CsTL physically interacted with CsTEN, an interaction that further enhanced CsTEN-mediated expression of CsUFO. In Arabidopsis, the CsTL homolog AtLAS acts upstream of REVOLUTA (REV) to regulate branch initiation. Knocking out cucumber CsREV inhibited branch formation without affecting tendril initiation. Furthermore, genomic regions containing CsTL and AtLAS were not syntenic between the cucumber and Arabidopsis genomes, whereas REV orthologs were found on a shared syntenic block. Our results revealed not only that cucumber CsTL possesses a divergent function in promoting tendril formation but also that CsREV retains its conserved function in shoot branching.
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Affiliation(s)
- Junjun Shen
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanxin Jiang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jian Pan
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Linhan Sun
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Qingqing Li
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wenjing He
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Piaoyun Sun
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Bosi Zhao
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hongjiao Zhao
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xubo Ke
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yalu Guo
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tongwen Yang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zheng Li
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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Dai Z, Dong S, Cai H, Beckles DM, Guan J, Liu X, Gu X, Miao H, Zhang S. Genome-wide association analysis reveal candidate genes and haplotypes related to root weight in cucumber ( Cucumis sativus L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1417314. [PMID: 39086910 PMCID: PMC11288866 DOI: 10.3389/fpls.2024.1417314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Accepted: 06/25/2024] [Indexed: 08/02/2024]
Abstract
Background The plant root system is critical for the absorption of water and nutrients, and have a direct influence on growth and yield. In cucumber, a globally consumed crop, the molecular mechanism of root development remains unclear, and this has implications for developing stress tolerant varieties. This study sought to determine the genetic patterns and related genes of cucumber root weight. A core cucumber germplasms population was used to do the GWAS analysis in three environments. Results Here, we investigated four root-weight related traits including root fresh weight (RFW), root dry weight (RDW), ratio of root dry weight to root fresh weight (RDFW) and the comprehensive evaluation index, D-value of root weight (DRW) deduced based on the above three traits for the core germplasm of the cucumber global repository. According to the D-value, we identified 21 and 16 accessions with light and heavy-root, respectively. We also found that the East Asian ecotype accessions had significantly heavier root than other three ecotypes. The genome-wide association study (GWAS) for these four traits reveals that 4 of 10 significant loci (gDRW3.1, gDRW3.2, gDRW4.1 and gDRW5.1) were repeatedly detected for at least two traits. Further haplotype and expression analysis for protein-coding genes positioned within these 4 loci between light and heavy-root accessions predicted five candidate genes (i.e., Csa3G132020 and Csa3G132520 both encoding F-box protein PP2-B1 for gDRW3.1, Csa3G629240 encoding a B-cell receptor-associated protein for gDRW3.2, Csa4G499330 encodes a GTP binding protein for gDRW4.1, and Csa5G286040 encodes a proteinase inhibitor for gDRW5.1). Conclusions We conducted a systematic analysis of the root genetic basis and characteristics of cucumber core germplasms population. We detected four novel loci, which regulate the root weight in cucumber. Our study provides valuable candidate genes and haplotypes for the improvement of root system in cucumber breeding.
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Affiliation(s)
- Zhuonan Dai
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shaoyun Dong
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hexu Cai
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Diane M. Beckles
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Jiantao Guan
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoping Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xingfang Gu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Han Miao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shengping Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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8
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Shigita G, Shimomura K, Dung TP, Haque NP, Duong TT, Imoh ON, Monden Y, Nishida H, Tanaka K, Sugiyama M, Kawazu Y, Tomooka N, Kato K. Genetic characterization of cucumber genetic resources in the NARO Genebank indicates their multiple dispersal trajectories to the East. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:174. [PMID: 38954043 PMCID: PMC11219412 DOI: 10.1007/s00122-024-04683-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 06/22/2024] [Indexed: 07/04/2024]
Abstract
KEY MESSAGE Genotyping-by-sequencing of 723 worldwide cucumber genetic resources revealed that cucumbers were dispersed eastward via at least three distinct routes, one to Southeast Asia and two from different directions to East Asia. The cucumber (Cucumis sativus) is an economically important vegetable crop cultivated and consumed worldwide. Despite its popularity, the manner in which cucumbers were dispersed from their origin in South Asia to the rest of the world, particularly to the east, remains a mystery due to the lack of written records. In this study, we performed genotyping-by-sequencing (GBS) on 723 worldwide cucumber accessions, mainly deposited in the Japanese National Agriculture and Food Research Organization (NARO) Genebank, to characterize their genetic diversity, relationships, and population structure. Analyses based on over 60,000 genome-wide single-nucleotide polymorphisms identified by GBS revealed clear genetic differentiation between Southeast and East Asian populations, suggesting that they reached their respective region independently, not progressively. A deeper investigation of the East Asian population identified two subpopulations with different fruit characteristics, supporting the traditional classification of East Asian cucumbers into two types thought to have been introduced by independent routes. Finally, we developed a core collection of 100 accessions representing at least 93.2% of the genetic diversity present in the entire collection. The genetic relationships and population structure, their associations with geographic distribution and phenotypic traits, and the core collection presented in this study are valuable resources for elucidating the dispersal history and promoting the efficient use and management of genetic resources for research and breeding in cucumber.
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Affiliation(s)
- Gentaro Shigita
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
- Department of Life Science Systems, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Strasse 2, 85354, Freising, Germany
| | - Koichiro Shimomura
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
| | - Tran Phuong Dung
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
| | - Naznin Pervin Haque
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
| | - Thuy Thanh Duong
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
- Faculty of Agronomy, University of Agriculture and Forestry, Hue University, 102 Phung Hung Street, Hue, Vietnam
| | - Odirich Nnennaya Imoh
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
| | - Yuki Monden
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
| | - Hidetaka Nishida
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
| | - Katsunori Tanaka
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori, 036-8561, Japan
| | - Mitsuhiro Sugiyama
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
| | - Yoichi Kawazu
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
| | - Norihiko Tomooka
- Genetic Resources Center, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Kenji Kato
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan.
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Du W, Xia L, Li R, Zhao X, Jin D, Wang X, Pei Y, Zhou R, Chen J, Yu X. Updated Gene Prediction of the Cucumber (9930) Genome through Manual Annotation. PLANTS (BASEL, SWITZERLAND) 2024; 13:1604. [PMID: 38931036 PMCID: PMC11207753 DOI: 10.3390/plants13121604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024]
Abstract
Thorough and precise gene structure annotations are essential for maximizing the benefits of genomic data and unveiling valuable genetic insights. The cucumber genome was first released in 2009 and updated in 2019. To increase the accuracy of the predicted gene models, 64 published RNA-seq data and 9 new strand-specific RNA-seq data from multiple tissues were used for manual comparison with the gene models. The updated annotation file (V3.1) contains an increased number (24,145) of predicted genes compared to the previous version (24,317 genes), with a higher BUSCO value of 96.9%. A total of 6231 and 1490 transcripts were adjusted and newly added, respectively, accounting for 31.99% of the overall gene tally. These newly added and adjusted genes were renamed (CsaV3.1_XGXXXXX), while genes remaining unaltered preserved their original designations. A random selection of 21 modified/added genes were validated using RT-PCR analyses. Additionally, tissue-specific patterns of gene expression were examined using the newly obtained transcriptome data with the revised gene prediction model. This improved annotation of the cucumber genome will provide essential and accurate resources for studies in cucumber.
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Affiliation(s)
- Weixuan Du
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China (J.C.)
| | - Lei Xia
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China (J.C.)
| | - Rui Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China (J.C.)
| | - Xiaokun Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China (J.C.)
| | - Danna Jin
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China (J.C.)
| | - Xiaoning Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China (J.C.)
| | - Yun Pei
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China (J.C.)
- College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Rong Zhou
- Department of Food Science, Plant, Food & Climate, Aarhus University, Agro Food Park 48, DK-8200 Aarhus, Denmark;
| | - Jinfeng Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China (J.C.)
| | - Xiaqing Yu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China (J.C.)
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10
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Wang M, Cao Z, Jiang B, Wang K, Xie D, Chen L, Shi S, Yang S, Lu H, Peng Q. Chromosome-level genome assembly and population genomics reveals crucial selection for subgynoecy development in chieh-qua. HORTICULTURE RESEARCH 2024; 11:uhae113. [PMID: 38898961 PMCID: PMC11186066 DOI: 10.1093/hr/uhae113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 04/10/2024] [Indexed: 06/21/2024]
Abstract
Chieh-qua is an important cucurbit crop and very popular in South China and Southeast Asia. Despite its significance, its genetic basis and domestication history are unclear. In this study, we have successfully generated a chromosome-level reference genome assembly for the chieh-qua 'A36' using a hybrid assembly strategy that combines PacBio long reads and Illumina short reads. The assembled genome of chieh-qua is approximately 953.3 Mb in size and is organized into 12 chromosomes, with contig N50 of 6.9 Mb and scaffold N50 of 68.2 Mb. Notably, the chieh-qua genome is comparable in size to the wax gourd genome. Through gene prediction analysis, we have identified a total of 24 593 protein-coding genes in the A36 genome. Additionally, approximately 56.6% (539.3 Mb) of the chieh-qua genome consists of repetitive sequences. Comparative genome analysis revealed that chieh-qua and wax gourd are closely related, indicating a close evolutionary relationship between the two species. Population genomic analysis, employing 129 chieh-qua accessions and 146 wax gourd accessions, demonstrated that chieh-qua exhibits greater genetic diversity compared to wax gourd. We also employed the GWAS method to identify related QTLs associated with subgynoecy, an interested and important trait in chieh-qua. The MYB59 (BhiCQ0880026447) exhibited relatively high expression levels in the shoot apex of four subgynoecious varieties compared with monoecious varieties. Overall, this research provides insights into the domestication history of chieh-qua and offers valuable genomic resources for further molecular research.
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Affiliation(s)
- Min Wang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Zhenqiang Cao
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Biao Jiang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Kejian Wang
- China National Rice Research Institute, Hangzhou 310012, China
| | - Dasen Xie
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Lin Chen
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Shaoqi Shi
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Songguang Yang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Hongwei Lu
- China National Rice Research Institute, Hangzhou 310012, China
| | - Qingwu Peng
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
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11
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Wang C, Li J, Fang K, Yao H, Chai X, Du Y, Wang J, Hao N, Cao J, Li B, Wu T. CsHLS1-CsSCL28 module regulates compact plant architecture in cucumber. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1724-1739. [PMID: 38261466 PMCID: PMC11123426 DOI: 10.1111/pbi.14298] [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: 11/30/2023] [Revised: 01/05/2024] [Accepted: 01/12/2024] [Indexed: 01/25/2024]
Abstract
Increased planting densities boost crop yields. A compact plant architecture facilitates dense planting. However, the mechanisms regulating compact plant architecture in cucurbits remain unclear. In this study, we identified a cucumber (Cucumis sativus) compact plant architecture (cpa1) mutant from an ethyl methane sulfonate (EMS)-mutagenized library that exhibited distinctive phenotypic traits, including reduced leaf petiole angle and leaf size. The candidate mutation causes a premature stop codon in CsaV3_1G036420, which shares similarity to Arabidopsis HOOKLESS 1 (HLS1) encoding putative histone N-acetyltransferase (HAT) protein and was named CsHLS1. Consistent with the mutant phenotype, CsHLS1 was predominantly expressed in leaf petiole bases and leaves. Constitutive overexpressing CsHLS1 in cpa1 restored the wild-type plant architecture. Knockout of CsHLS1 resulted in reduces leaf petiole angle and leaf size and as well as decreased acetylation levels. Furthermore, CsHLS1 directly interacted with CsSCL28 and negatively regulated compact plant architecture in cucumber. Importantly, CsHLS1 knockout increased the photosynthesis rate and leaf nitrogen in cucumbers, thereby maintaining cucumber yield at normal density. Overall, our research provides valuable genetic breeding resource and gene target for creating a compact plant architecture for dense cucumber planting.
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Affiliation(s)
- Chunhua Wang
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research InstituteHunan Agricultural UniversityChangshaHunanChina
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of ChinaChangshaChina
| | - Jie Li
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research InstituteHunan Agricultural UniversityChangshaHunanChina
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of ChinaChangshaChina
| | - Kai Fang
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research InstituteHunan Agricultural UniversityChangshaHunanChina
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of ChinaChangshaChina
| | - Hongxin Yao
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research InstituteHunan Agricultural UniversityChangshaHunanChina
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of ChinaChangshaChina
| | - Xingwen Chai
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research InstituteHunan Agricultural UniversityChangshaHunanChina
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of ChinaChangshaChina
| | - Yalin Du
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research InstituteHunan Agricultural UniversityChangshaHunanChina
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of ChinaChangshaChina
| | - Junwei Wang
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research InstituteHunan Agricultural UniversityChangshaHunanChina
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of ChinaChangshaChina
| | - Ning Hao
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research InstituteHunan Agricultural UniversityChangshaHunanChina
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of ChinaChangshaChina
| | - Jiajian Cao
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research InstituteHunan Agricultural UniversityChangshaHunanChina
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of ChinaChangshaChina
| | - Baohai Li
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource ScienceZhejiang UniversityHangzhouChina
| | - Tao Wu
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research InstituteHunan Agricultural UniversityChangshaHunanChina
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of ChinaChangshaChina
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12
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Ma M, Yang L, Hu Z, Mo C, Geng S, Zhao X, He Q, Xiao L, Lu L, Wang D, Li S, Kong Q, Li D, Bie Z. Multiplex gene editing reveals cucumber MILDEW RESISTANCE LOCUS O family roles in powdery mildew resistance. PLANT PHYSIOLOGY 2024; 195:1069-1088. [PMID: 38330431 DOI: 10.1093/plphys/kiae047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 02/10/2024]
Abstract
Powdery mildew (PM) is one of the most widespread and prevalent diseases that affects a wide range of crops. In cucumber (Cucumis sativus L.), previous forward genetic studies have identified MILDEW RESISTANCE LOCUS O 8 (CsMLO8) as necessary but alone insufficient for cucumber PM resistance (PMR) and suggested the involvement of other members of the CsMLO family. However, the function of other CsMLO family members in cucumber remains largely unknown. Here, we developed a highly efficient multiplex gene editing system in cucumber to generate a series of Csmlo mutants from all the 13 family members. Systematic analysis of these mutants revealed growth effects of these CsMLO family members on development and PMR. Importantly, we obtained the Csmlo1/8/11 triple mutant with complete resistance to PM. Transcriptome and proteome analysis of PM-resistant Csmlo mutants suggested that the kinesin-like calmodulin-binding protein (KCBP)-interacting Ca2+-binding protein (CsKIC), calmodulin-like protein 28 (CsCML28), and Ca2+-dependent protein kinase 11 (CsCPK11)-mediated calcium signaling pathway is involved in PMR. CsMLO8 interacted directly with CsKIC, and the simultaneous silencing of both genes resulted in a phenotype that resembled the silencing of CsKIC alone. Silencing CsCML28 and CsCPK11 increased susceptibility to PM, whereas overexpressing CsCPK11 through genetic transformation enhanced cucumber's PMR, demonstrating their positive regulatory roles in PMR. Given the importance of PMR for cucurbit crops, this research provides unprecedented insights into the function of the proteins encoded by the CsMLO gene family as well as the plant defense response to PM pathogen.
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Affiliation(s)
- Mingru Ma
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Li Yang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhenzhu Hu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Changjuan Mo
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Shouyu Geng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin Zhao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiuyu He
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Li Xiao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Liurong Lu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Dan Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Shanggui Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiusheng Kong
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Dawei Li
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Zhilong Bie
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Department of Science and Technology of Hubei Province, Wuhan 430070, China
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13
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Liu B, Shen CC, Xia SW, Song SS, Su LH, Li Y, Hao Q, Liu YJ, Guan DL, Wang N, Wang WJ, Zhao X, Li HX, Li XX, Lai YS. A nanopore-based cucumber genome assembly reveals structural variations at two QTLs controlling hypocotyl elongation. PLANT PHYSIOLOGY 2024; 195:970-985. [PMID: 38478469 DOI: 10.1093/plphys/kiae153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 02/06/2024] [Indexed: 06/02/2024]
Abstract
The Xishuangbanna (XIS) cucumber (Cucumis sativus var. xishuangbannanesis) is a semiwild variety that has many distinct agronomic traits. Here, long reads generated by Nanopore sequencing technology helped assembling a high-quality genome (contig N50 = 8.7 Mb) of landrace XIS49. A total of 10,036 structural/sequence variations (SVs) were identified when comparing with Chinese Long (CL), and known SVs controlling spines, tubercles, and carpel number were confirmed in XIS49 genome. Two QTLs of hypocotyl elongation under low light, SH3.1 and SH6.1, were fine-mapped using introgression lines (donor parent, XIS49; recurrent parent, CL). SH3.1 encodes a red-light receptor Phytochrome B (PhyB, CsaV3_3G015190). A ∼4 kb region with large deletion and highly divergent regions (HDRs) were identified in the promoter of the PhyB gene in XIS49. Loss of function of this PhyB caused a super-long hypocotyl phenotype. SH6.1 encodes a CCCH-type zinc finger protein FRIGIDA-ESSENTIAL LIKE (FEL, CsaV3_6G050300). FEL negatively regulated hypocotyl elongation but it was transcriptionally suppressed by long terminal repeats retrotransposon insertion in CL cucumber. Mechanistically, FEL physically binds to the promoter of CONSTITUTIVE PHOTOMORPHOGENIC 1a (COP1a), regulating the expression of COP1a and the downstream hypocotyl elongation. These above results demonstrate the genetic mechanism of cucumber hypocotyl elongation under low light.
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Affiliation(s)
- Bin Liu
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
- Hami-melon Research Center, Xinjiang Academy of Agricultural Sciences, 830091 Urumqi, China
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Cheng-Cheng Shen
- College of Horticulture, Shanxi Agricultural University, 030801 Jinzhong, China
| | - Shi-Wei Xia
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
| | - Shan-Shan Song
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
| | - Li-Hong Su
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
| | - Yu Li
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
| | - Qian Hao
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
| | - Yan-Jun Liu
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
| | - Dai-Lu Guan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Ning Wang
- College of Horticulture, Shanxi Agricultural University, 030801 Jinzhong, China
| | - Wen-Jiao Wang
- College of Horticulture, Shanxi Agricultural University, 030801 Jinzhong, China
| | - Xiang Zhao
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
| | - Huan-Xiu Li
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
| | - Xi-Xiang Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100080 Beijing, China
| | - Yun-Song Lai
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
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14
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Wang C, Yao H, Wang C, Gao L, Chai X, Fang K, Du Y, Hao N, Cao J, Wu T. Transcription factor CsMYB36 regulates fruit neck length via mediating cell expansion in cucumber. PLANT PHYSIOLOGY 2024; 195:958-969. [PMID: 38447074 DOI: 10.1093/plphys/kiae140] [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] [Revised: 02/06/2024] [Accepted: 02/11/2024] [Indexed: 03/08/2024]
Abstract
The fruit neck is an important agronomic trait of cucumber (Cucumis sativus). However, the underlying genes and regulatory mechanisms involved in fruit neck development are poorly understood. We previously identified a cucumber yellow-green peel (ygp) mutant, whose causal gene is MYB DOMAIN PROTEIN 36 (CsMYB36). This study showed that the ygp mutant exhibited a shortened fruit neck and repressed cell expansion in the fruit neck. Further functional analysis showed that CsMYB36 was also a target gene, and its expression was enriched in the fruit neck. Overexpression of CsMYB36 in the ygp mutant rescued shortened fruit necks. Furthermore, transcriptome analysis and reverse transcription quantitative PCR (RT-qPCR) assays revealed that CsMYB36 positively regulates the expression of an expansin-like A3 (CsEXLA3) in the fruit neck, which is essential for cell expansion. Yeast 1-hybrid and dual-luciferase assays revealed that CsMYB36 regulates fruit neck elongation by directly binding to the promoter of CsEXLA3. Collectively, these findings demonstrate that CsMYB36 is an important gene in the regulation of fruit neck length in cucumber plants.
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Affiliation(s)
- Chunhua Wang
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research Institute, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of China, Changsha 410128, China
| | - Hongxin Yao
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research Institute, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of China, Changsha 410128, China
| | - Chen Wang
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research Institute, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of China, Changsha 410128, China
| | - Luyao Gao
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research Institute, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of China, Changsha 410128, China
| | - Xingwen Chai
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research Institute, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of China, Changsha 410128, China
| | - Kai Fang
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research Institute, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of China, Changsha 410128, China
| | - Yalin Du
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research Institute, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of China, Changsha 410128, China
| | - Ning Hao
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research Institute, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of China, Changsha 410128, China
| | - Jiajian Cao
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research Institute, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of China, Changsha 410128, China
| | - Tao Wu
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research Institute, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of China, Changsha 410128, China
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15
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Chen J, Liu L, Chen G, Wang S, Liu Y, Zhang Z, Li H, Wang L, Zhou Z, Zhao J, Zhang X. CsRAXs negatively regulate leaf size and fruiting ability through auxin glycosylation in cucumber. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1024-1037. [PMID: 38578173 DOI: 10.1111/jipb.13655] [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: 12/24/2023] [Accepted: 03/13/2024] [Indexed: 04/06/2024]
Abstract
Leaves are the main photosynthesis organ that directly determines crop yield and biomass. Dissecting the regulatory mechanism of leaf development is crucial for food security and ecosystem turn-over. Here, we identified the novel function of R2R3-MYB transcription factors CsRAXs in regulating cucumber leaf size and fruiting ability. Csrax5 single mutant exhibited enlarged leaf size and stem diameter, and Csrax1/2/5 triple mutant displayed further enlargement phenotype. Overexpression of CsRAX1 or CsRAX5 gave rise to smaller leaf and thinner stem. The fruiting ability of Csrax1/2/5 plants was significantly enhanced, while that of CsRAX5 overexpression lines was greatly weakened. Similarly, cell number and free auxin level were elevated in mutant plants while decreased in overexpression lines. Biochemical data indicated that CsRAX1/5 directly promoted the expression of auxin glucosyltransferase gene CsUGT74E2. Therefore, our data suggested that CsRAXs function as repressors for leaf size development by promoting auxin glycosylation to decrease free auxin level and cell division in cucumber. Our findings provide new gene targets for cucumber breeding with increased leaf size and crop yield.
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Affiliation(s)
- Jiacai Chen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Liu Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Guangxin Chen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Shaoyun Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Ye Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Zeqin Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Hongfei Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Liming Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhaoyang Zhou
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Jianyu Zhao
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiaolan Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
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16
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Liu M, Li Z, Kang Y, Lv J, Jin Z, Mu S, Yue H, Li L, Chen P, Li Y. A mutation in CsGME encoding GDP-mannose 3,5-epimerase results in little and wrinkled leaf in cucumber. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:114. [PMID: 38678513 DOI: 10.1007/s00122-024-04600-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/13/2024] [Indexed: 05/01/2024]
Abstract
KEY MESSAGE Map-based cloning revealed that a mutation in a highly conserved amino acid of the CsGME gene encoding GDP-mannose 3,5-epimerase, causes the phenotype of little and wrinkled leaves in cucumbers. Leaf size is a critical determinant of plant architecture in cucumbers, yet only a few genes associated with this trait have been mapped or cloned. Here, we identified and characterized a mutant with little and wrinkled leaves, named lwl-1. Genetic analysis revealed that the phenotype of the lwl-1 was controlled by a single recessive gene. Through map-based cloning, the lwl-1 locus was narrowed down to a 12.22-kb region exclusively containing one fully annotated gene CsGME (CsaV3_2G004170). CsGME encodes GDP-mannose 3,5-epimerase, which is involved in the synthesis of ascorbic acid (ASA) and one of the components of pectin, RG-II. Whole-length sequencing of the 12.22 kb DNA fragment revealed the presence of only a non-synonymous mutation located in the sixth exon of CsGME in lwl-1, resulting in an amino acid alteration from Pro363 to Leu363. This mutation was unique among 118 inbred lines from cucumber natural populations. CsGME expression significantly reduced in various organs of lwl-1, accompanied by a significant decrease in ASA and pectin content in leaves. Both CsGME and Csgme proteins were localized to the cytoplasm. The mutant phenotype exhibited partial recovery after the application of exogenous boric acid. Silencing CsGME in cucumber through VIGS confirmed its role as the causal gene for lwl-1. Transcriptome profiling revealed that CsGME greatly affected the expression of genes related to the cell division process and cell plate formation. This study represents the first report to characterize and clone the CsGME in cucumber, indicating its crucial role in regulating leaf size and development.
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Affiliation(s)
- Mengying Liu
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhaowei Li
- College of Life Science, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yunfeng Kang
- College of Life Science, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jinzhao Lv
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhuoshuai Jin
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Siyu Mu
- College of Life Science, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hongzhong Yue
- Vegetable Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, Gansu, China
| | - Lixia Li
- College of Horticulture, Shanxi Agricultural University, Taigu, 030801, China
| | - Peng Chen
- College of Life Science, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Yuhong Li
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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17
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Zhao X, Yu J, Chanda B, Zhao J, Wu S, Zheng Y, Sun H, Levi A, Ling KS, Fei Z. Genomic and pangenomic analyses provide insights into the population history and genomic diversification of bottle gourd. THE NEW PHYTOLOGIST 2024. [PMID: 38503725 DOI: 10.1111/nph.19673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 02/27/2024] [Indexed: 03/21/2024]
Abstract
Bottle gourd (Lagenaria siceraria (Mol.) Strandl.) is an economically important vegetable crop and one of the earliest domesticated crops. However, the population history and genomic diversification of bottle gourd have not been extensively studied. We generated a comprehensive bottle gourd genome variation map from genome sequences of 197 world-wide representative accessions, which enables a genome-wide association study for identifying genomic loci associated with resistance to zucchini yellow mosaic virus, and constructed a bottle gourd pangenome that harbors 1534 protein-coding genes absent in the reference genome. Demographic analyses uncover that domesticated bottle gourd originated in Southern Africa c. 12 000 yr ago, and subsequently radiated to the New World via the Atlantic drift and to Eurasia through the efforts of early farmers in the initial Holocene. The identified highly differentiated genomic regions among different bottle gourd populations harbor many genes contributing to their local adaptations such as those related to disease resistance and stress tolerance. Presence/absence variation analysis of genes in the pangenome reveals numerous genes including those involved in abiotic/biotic stress responses that have been under selection during the world-wide expansion of bottle gourds. The bottle gourd variation map and pangenome provide valuable resources for future functional studies and genomics-assisted breeding.
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Affiliation(s)
- Xuebo Zhao
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Jingyin Yu
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Bidisha Chanda
- USDA-ARS, US Vegetable Laboratory, Charleston, SC, 29414, USA
| | - Jiantao Zhao
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Shan Wu
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Yi Zheng
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Honghe Sun
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Amnon Levi
- USDA-ARS, US Vegetable Laboratory, Charleston, SC, 29414, USA
| | - Kai-Shu Ling
- USDA-ARS, US Vegetable Laboratory, Charleston, SC, 29414, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
- USDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
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18
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Li C, Ma H, Li P, Zhang S, Xu J, Wang L, Sheng W, Xu T, Shen L, Wang W, Xia T. Cucumber (Cucumis sativus L.) with heterologous poly-γ-glutamic acid has skin moisturizing, whitening and anti-wrinkle effects. Int J Biol Macromol 2024; 262:130026. [PMID: 38336313 DOI: 10.1016/j.ijbiomac.2024.130026] [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: 10/23/2023] [Revised: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
Three genes involved in poly-γ-glutamic acid(γ-PGA)synthesis cloned from Bacillus licheniformis were transformed into cucumber for the first time. Compared with control, its water content increased by 6-14 % and water loss rate decreased by 11-12 %. In zebrafish and human skin experiments, the moisturizing effect of transgenic cucumber was significantly higher than that of CK, γ-PGA and hyaluronic acid group. Transgenic cucumber reduced facial wrinkles and roughness by 19.58 % and 24.97 %, reduced skin melanin content by 5.27 %, increased skin topological angle and L-value by 5.89 % and 2.49 %, and increased the R2 and Q1 values of facial elasticity by 7.67 % and 5.64 %, respectively. The expressions of aqp3, Tyr, silv and OCA2 were down-regulated, eln1, eln2, col1a1a and col1a1b were up-regulated in zebrafish after treated with transgenic cucumber. This study provides an important reference for the endogenous synthesis of important skin care functional molecules in plants.
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Affiliation(s)
- Can Li
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China; State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Haizhen Ma
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China; State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Panpan Li
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Shengkui Zhang
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China; State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Jieting Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Ling Wang
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Wenlong Sheng
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Tianyu Xu
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Lu Shen
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Wanxia Wang
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Tao Xia
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China; State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China.
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19
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Li X, Wang Y, Cai C, Ji J, Han F, Zhang L, Chen S, Zhang L, Yang Y, Tang Q, Bucher J, Wang X, Yang L, Zhuang M, Zhang K, Lv H, Bonnema G, Zhang Y, Cheng F. Large-scale gene expression alterations introduced by structural variation drive morphotype diversification in Brassica oleracea. Nat Genet 2024; 56:517-529. [PMID: 38351383 PMCID: PMC10937405 DOI: 10.1038/s41588-024-01655-4] [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: 06/16/2023] [Accepted: 01/03/2024] [Indexed: 02/21/2024]
Abstract
Brassica oleracea, globally cultivated for its vegetable crops, consists of very diverse morphotypes, characterized by specialized enlarged organs as harvested products. This makes B. oleracea an ideal model for studying rapid evolution and domestication. We constructed a B. oleracea pan-genome from 27 high-quality genomes representing all morphotypes and their wild relatives. We identified structural variations (SVs) among these genomes and characterized these in 704 B. oleracea accessions using graph-based genome tools. We show that SVs exert bidirectional effects on the expression of numerous genes, either suppressing through DNA methylation or promoting probably by harboring transcription factor-binding elements. The following examples illustrate the role of SVs modulating gene expression: SVs promoting BoPNY and suppressing BoCKX3 in cauliflower/broccoli, suppressing BoKAN1 and BoACS4 in cabbage and promoting BoMYBtf in ornamental kale. These results provide solid evidence for the role of SVs as dosage regulators of gene expression, driving B. oleracea domestication and diversification.
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Affiliation(s)
- Xing Li
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yong Wang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chengcheng Cai
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Jialei Ji
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fengqing Han
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lei Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shumin Chen
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lingkui Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yinqing Yang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qi Tang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Johan Bucher
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Xuelin Wang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Limei Yang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mu Zhuang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kang Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Honghao Lv
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Guusje Bonnema
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands.
| | - Yangyong Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Feng Cheng
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
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20
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Lian Q, Li S, Kan S, Liao X, Huang S, Sloan DB, Wu Z. Association Analysis Provides Insights into Plant Mitonuclear Interactions. Mol Biol Evol 2024; 41:msae028. [PMID: 38324417 PMCID: PMC10875325 DOI: 10.1093/molbev/msae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/17/2024] [Accepted: 02/01/2024] [Indexed: 02/09/2024] Open
Abstract
Cytonuclear interaction refers to the complex and ongoing process of coevolution between nuclear and organelle genomes, which are responsible for cellular respiration, photosynthesis, lipid metabolism, etc. and play a significant role in adaptation and speciation. There have been a large number of studies to detect signatures of cytonuclear interactions. However, identification of the specific nuclear and organelle genetic polymorphisms that are involved in these interactions within a species remains relatively rare. The recent surge in whole genome sequencing has provided us an opportunity to explore cytonuclear interaction from a population perspective. In this study, we analyzed a total of 3,439 genomes from 7 species to identify signals of cytonuclear interactions by association (linkage disequilibrium) analysis of variants in both the mitochondrial and nuclear genomes across flowering plants. We also investigated examples of nuclear loci identified based on these association signals using subcellular localization assays, gene editing, and transcriptome sequencing. Our study provides a novel perspective on the investigation of cytonuclear coevolution, thereby enriching our understanding of plant fitness and offspring sterility.
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Affiliation(s)
- Qun Lian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Shuai Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shenglong Kan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Marine College, Shandong University, Weihai 264209, China
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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21
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Zhang RJ, Liu B, Song SS, Salah R, Song CJ, Xia SW, Hao Q, Liu YJ, Li Y, Lai YS. Lipid-Related Domestication Accounts for the Extreme Cold Sensitivity of Semiwild and Tropic Xishuangbanna Cucumber ( Cucumis sativus L. var. xishuangbannanesis). Int J Mol Sci 2023; 25:79. [PMID: 38203249 PMCID: PMC10779220 DOI: 10.3390/ijms25010079] [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: 09/02/2023] [Revised: 12/10/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024] Open
Abstract
Xishuangbanna (XIS) cucumber (Cucumis sativus L. var. xishuangbannanesis) is a semiwild variety originating from low latitude tropic areas, and therefore shows extreme cold sensitivity and heat tolerance. Here, we mapped the quantitative trait loci (QTLs) that control the cold sensitivity and heat tolerance of XIS cucumber seedlings. Using bulked segregant analysis (BSA), we identified three QTLs (HTT1.1, HTT3.1, and HTT3.2, with a total length of 11.98 Mb) for heat tolerance and two QTLs (LTT6.1 and LTT6.2, with a total length of 8.74 Mb) for cold sensitivity. The QTL LTT6.1 was then narrowed down to a length of 641 kb by using kompetitive allele-specific PCR (KASP) markers. Based on structural variants (SVs) and single-nucleotide polymorphisms (SNPs), we found the LTT6.1 is covered by a high divergent region including a 50 kb deletion in the XIS49 genome, which affects the gene structure of lipase abhydrolase domain containing 6 (ABHD6, Csa_6G032560). Accordingly, there is a very big difference in lipid composition, but not in other osmoprotectants like free amino acids and fatty acids, between XIS49 and cultivated cucumber CL. Moreover, we calculated the composite likelihood ratio (CLR) and identified selective sweeps from 115 resequencing data, and found that lipid- and fatty-acid-related processes are major aspects in the domestication of the XIS group cucumber. LTT6.1 is a particularly special region positioned nearby lipid-related selective sweeps. These studies above suggested that the lipid-related domestication of XIS cucumbers should account for their extreme cold sensitivity.
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Affiliation(s)
- Rui-Jing Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China (R.S.)
| | - Bin Liu
- Hami-Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
| | - Shan-Shan Song
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China (R.S.)
| | - Radwa Salah
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China (R.S.)
| | - Chang-Jiang Song
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China (R.S.)
| | - Shi-Wei Xia
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China (R.S.)
| | - Qian Hao
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China (R.S.)
| | - Yan-Jun Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China (R.S.)
| | - Yu Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China (R.S.)
| | - Yun-Song Lai
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China (R.S.)
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22
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Lin YC, Mansfeld BN, Tang X, Colle M, Chen F, Weng Y, Fei Z, Grumet R. Identification of QTL associated with resistance to Phytophthora fruit rot in cucumber ( Cucumis sativus L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1281755. [PMID: 38046614 PMCID: PMC10693349 DOI: 10.3389/fpls.2023.1281755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/30/2023] [Indexed: 12/05/2023]
Abstract
Phytophthora fruit rot (PFR) caused by the soilborne oomycete pathogen, Phytophthora capsici, can cause severe yield loss in cucumber. With no resistant variety available, genetic resources are needed to develop resistant varieties. The goal of this work was to identify quantitative trait loci (QTL) associated with resistance to PFR using multiple genomic approaches and populations. Two types of resistances have been identified: age-related resistance (ARR) and young fruit resistance. ARR occurs at 12-16 days post pollination (dpp), coinciding with the end of exponential fruit growth. A major QTL for ARR was discovered on chromosome 3 and a candidate gene identified based on comparative transcriptomic analysis. Young fruit resistance, which is observed during the state of rapid fruit growth prior to commercial harvest, is a quantitative trait for which multiple QTL were identified. The largest effect QTL, qPFR5.1, located on chromosome 5 was fine mapped to a 1-Mb region. Genome-wide association studies (GWAS) and extreme-phenotype genome-wide association study (XP-GWAS) for young fruit resistance were also performed on a cucumber core collection representing > 96% of the genetic diversity of the USDA cucumber germplasm. Several SNPs overlapped with the QTL identified from QTL-seq analysis on biparental populations. In addition, novel SNPs associated with the resistance were identified from the germplasm. The resistant alleles were found mostly in accessions from India and South Asia, the center of diversity for cucumber. The results from this work can be applied to future disease resistance studies and marker-assisted selection in breeding programs.
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Affiliation(s)
- Ying-Chen Lin
- Department of Horticulture, Graduate Program in Plant Breeding, Genetics and Biotechnology, Michigan State University, East Lansing, MI, United States
| | - Ben N. Mansfeld
- Department of Horticulture, Graduate Program in Plant Breeding, Genetics and Biotechnology, Michigan State University, East Lansing, MI, United States
| | - Xuemei Tang
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Marivi Colle
- Department of Horticulture, Graduate Program in Plant Breeding, Genetics and Biotechnology, Michigan State University, East Lansing, MI, United States
| | - Feifan Chen
- Department of Plant and Agroecosystem Sciences, University of Wisconsin, Madison, WI, United States
| | - Yiqun Weng
- Department of Plant and Agroecosystem Sciences, University of Wisconsin, Madison, WI, United States
- Vegetable Crops Research Unit, United States Department of Agriculture-Agriculture Research Service (USDA-ARS), Madison, WI, United States
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agriculture Research Service (USDA-ARS), Ithaca, NY, United States
| | - Rebecca Grumet
- Department of Horticulture, Graduate Program in Plant Breeding, Genetics and Biotechnology, Michigan State University, East Lansing, MI, United States
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23
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Wang Y, Dong Z, Ma Y, Zheng Y, Huang S, Yang X. Comprehensive dissection of meiotic DNA double-strand breaks and crossovers in cucumber. PLANT PHYSIOLOGY 2023; 193:1913-1932. [PMID: 37530486 PMCID: PMC10602612 DOI: 10.1093/plphys/kiad432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/21/2023] [Accepted: 07/14/2023] [Indexed: 08/03/2023]
Abstract
Meiotic recombination drives genetic diversity and crop genome optimization. In plant breeding, parents with favorable traits are crossed to create elite varieties. Different hybridizations produce diverse types of segment reshuffling between homologous chromosomes. However, little is known about the factors that cause hybrid-specific changes in crossovers (COs). Here, we constructed 2 F2 populations from crosses between a semiwild and 2 domesticated cucumber (Cucumis sativus) accessions and examined CO events. COs mainly occurred around genes and differed unevenly along chromosomes between the 2 hybrids. Fine-scale CO distributions were suppressed in regions of heterozygous structural variations (SVs) and were accelerated by high sequence polymorphism. C. sativus RADiation sensitive 51A (CsRAD51A) binding, histone H3 lysine 4 trimethylation (H3K4me3) modification, chromatin accessibility, and hypomethylation were positively associated with global CO landscapes and in local DNA double-strand break (DSB) hotspots and genes. The frequency and suppression of COs could be roughly predicted based on multiomic information. Differences in CO events between hybrids could be partially traced to distinct genetic and epigenetic features and were significantly associated with specific DSB hotspots and heterozygous SVs. Our findings identify the genomic and epigenetic features that contribute to CO formation and hybrid-specific divergence in cucumber and provide theoretical support for selecting parental combinations and manipulating recombination events at target genomic regions during plant breeding.
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Affiliation(s)
- Yanling Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhaonian Dong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yalin Ma
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yi Zheng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xueyong Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Gao L, Cao J, Gong S, Hao N, Du Y, Wang C, Wu T. The COPII subunit CsSEC23 mediates fruit glossiness in cucumber. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:524-540. [PMID: 37460197 DOI: 10.1111/tpj.16389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/07/2023] [Indexed: 07/28/2023]
Abstract
To improve our understanding of the mechanism underlying cucumber glossiness regulation, a novel cucumber mutant with a glossy peel (Csgp) was identified. MutMap, genotyping, and gene editing results demonstrated that CsSEC23, which is the core component of COPII vesicles, mediates the glossiness of cucumber fruit peel. CsSEC23 is functionally conserved and located in the Golgi and endoplasmic reticulum. CsSEC23 could interact with CsSEC31, but this interaction was absent in the Csgp mutant, which decreased the efficiency of COPII vesicle transportation. Genes related to wax and cutin transport were upregulated in the Csgp mutant, and the cuticle structure of the Csgp-mutant peel became thinner. Moreover, the wax and cutin contents were also changed due to CsSEC23 mutation. Taken together, the results obtained from this study revealed that CsSEC23 mediates cucumber glossiness, and this mediating might be affected by COPII vesicle transportation.
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Affiliation(s)
- Luyao Gao
- College of Horticulture, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (vegetables, tea, etc.), Ministry of Agriculture and Rural Affairs of China, Changsha, 410128, China
- Yuelushan Lab, Changsha, 410128, China
| | - Jiajian Cao
- College of Horticulture, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (vegetables, tea, etc.), Ministry of Agriculture and Rural Affairs of China, Changsha, 410128, China
- Yuelushan Lab, Changsha, 410128, China
- Whampoa Innovation Research Institute, Hunan Agricultural University, Changsha, 410128, China
| | - Siyu Gong
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Ning Hao
- College of Horticulture, Hunan Agricultural University, Changsha, 410128, China
- Laboratory of Plant Nutrition and Fertilizers, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Yalin Du
- College of Horticulture, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (vegetables, tea, etc.), Ministry of Agriculture and Rural Affairs of China, Changsha, 410128, China
- Yuelushan Lab, Changsha, 410128, China
- Whampoa Innovation Research Institute, Hunan Agricultural University, Changsha, 410128, China
| | - Chunhua Wang
- College of Horticulture, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (vegetables, tea, etc.), Ministry of Agriculture and Rural Affairs of China, Changsha, 410128, China
- Yuelushan Lab, Changsha, 410128, China
- Whampoa Innovation Research Institute, Hunan Agricultural University, Changsha, 410128, China
| | - Tao Wu
- College of Horticulture, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (vegetables, tea, etc.), Ministry of Agriculture and Rural Affairs of China, Changsha, 410128, China
- Yuelushan Lab, Changsha, 410128, China
- Whampoa Innovation Research Institute, Hunan Agricultural University, Changsha, 410128, China
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25
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Gasser M, Keller J, Fournier P, Pujic P, Normand P, Boubakri H. Identification and evolution of nsLTPs in the root nodule nitrogen fixation clade and molecular response of Frankia to AgLTP24. Sci Rep 2023; 13:16020. [PMID: 37749152 PMCID: PMC10520049 DOI: 10.1038/s41598-023-41117-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 08/22/2023] [Indexed: 09/27/2023] Open
Abstract
Non-specific lipid transfer proteins (nsLTPs) are antimicrobial peptides, involved in several plant biological processes including root nodule nitrogen fixation (RNF). Nodulating plants belonging to the RNF clade establish symbiosis with the nitrogen-fixing bacteria rhizobia (legumes symbiosis model) and Frankia (actinorhizal symbiosis model) leading to root nodule formation. nsLTPs are involved in processes active in early step of symbiosis and functional nodule in both models. In legumes, nsLTPs have been shown to regulate symbiont entry, promote root cortex infection, membrane biosynthesis, and improve symbiosis efficiency. More recently, a nsLTP, AgLTP24 has been described in the context of actinorhizal symbiosis between Alnus glutinosa and Frankia alni ACN14a. AgLTP24 is secreted at an early step of symbiosis on the deformed root hairs and targets the symbiont in the nitrogen-fixing vesicles in functional nodules. nsLTPs are involved in RNF, but their functions and evolutionary history are still largely unknown. Numerous putative nsLTPs were found up-regulated in functional nodules compared to non-infected roots in different lineages within the RNF clade. Here, results highlight that nodulating plants that are co-evolving with their nitrogen-fixing symbionts appear to have independently specialized nsLTPs for this interaction, suggesting a possible convergence of function, which opens perspectives to investigate nsLTPs functions in RNF.
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Affiliation(s)
- Mélanie Gasser
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622, Villeurbanne, France
| | - Jean Keller
- LRSV, Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France
| | - Pascale Fournier
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622, Villeurbanne, France
| | - Petar Pujic
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622, Villeurbanne, France
| | - Philippe Normand
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622, Villeurbanne, France
| | - Hasna Boubakri
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622, Villeurbanne, France.
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26
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Wang X, Jin B, Yan W, Wang J, Xu J, Cai C, Qi X, Xu Q, Yang X, Xu X, Chen X. Cucumber abscisic acid 8'-hydroxylase Csyf2 regulates yellow flesh by modulating carotenoid biosynthesis. PLANT PHYSIOLOGY 2023; 193:1001-1015. [PMID: 37394925 DOI: 10.1093/plphys/kiad383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/13/2023] [Accepted: 04/24/2023] [Indexed: 07/04/2023]
Abstract
Cucumber (Cucumis sativus L.) flesh is typically colorless or pale green. Flesh with yellow or orange pigment, determined mainly by carotenoid content and composition, is mostly found in semi-wild Xishuangbanna cucumber, which has a very narrow genetic background. Here, we identified a spontaneous cucumber mutant with yellow flesh (yf-343), which accumulated more β-cryptoxanthin and less lutein than regular cultivated European glasshouse-type cucumbers. Genetic analysis revealed that the yellow flesh phenotype was controlled by a single recessive gene. Through fine mapping and gene sequencing, we identified the candidate gene C. sativus yellow flesh 2 (Csyf2), encoding an abscisic acid (ABA) 8'-hydroxylase. Overexpression and RNAi-silencing of Csyf2 in cucumber hairy roots produced lower and higher ABA contents than in non-transgenic controls, respectively. Further, RNA-seq analysis suggested that genes related to ABA signal transduction were differentially expressed in fruit flesh between yf-343 and its wild type, BY, with white flesh. The carotenoid biosynthesis pathway was specifically enriched in fruit flesh at 30 days after pollination when yf-343 fruit flesh turns yellow. Our findings highlight a promising target for gene editing to increase carotenoid content, expanding our genetic resources for pigmented cucumber flesh breeding for improving the nutritional quality of cucumber.
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Affiliation(s)
- Xueting Wang
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Boyan Jin
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Wenjing Yan
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Jiaxi Wang
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Jun Xu
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Congxi Cai
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Xiaohua Qi
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Qiang Xu
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Xiaodong Yang
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Xuewen Xu
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Xuehao Chen
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
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27
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Tian X, Sang Z, Lan Z, Liu W, Feng Y, Hu J, Chen F, Liu Y. Fine-Scale analysis of both wild and cultivated horned galls provides insight into their quality differentiation. BMC PLANT BIOLOGY 2023; 23:426. [PMID: 37710158 PMCID: PMC10500821 DOI: 10.1186/s12870-023-04442-1] [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: 10/06/2022] [Accepted: 09/06/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND Galla chinensis is a traditional Chinese medicine (TCM) produced due to the interaction between the Fordinae aphids and the Rhus plant species. Horned galls with high tannin content are the most widely cultivated gall type, and Wufeng county of Hubei province in China is the center of cultivation. However, long-term artificial cultivation and domestication of horned galls to meet the increasing production demand have led to quality degradation. Understanding the reasons underlying quality degradation is urgent for horned gall production and application. The present study used a combination of metabolic, genetic, and ecological analyses to investigate the quality and genetic differentiation of the horned galls under long-term domestication as well as the potential relationships between them. RESULTS Analysis of gallic acid content and other three phenotypic traits (fresh weight, gall size, and wall thickness) revealed quality differentiation of horned galls collected from five locations in Wufeng, in which the cultivated samples from Wang Jiaping (WJP) showed the highest degradation. Genetic differentiation between the cultivated and wild Rhus chinensis trees in WJP, and between WJP and the other populations was detected based on SSR molecular markers, however, no significant difference in genetic structure was seen for the aphid populations. Among the various ecological factors examined, temperature was identified as the primary one affecting the quality of horned galls. CONCLUSIONS Both genetic and ecological factors caused quality differentiation of horned galls. The collection of diverse germplasm of host trees and aphids will help reduce the quality degradation of horned galls in Wufeng.
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Affiliation(s)
- Xufang Tian
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, People's Republic of China
| | - Ziyang Sang
- Forestry Science Research Institute of Wufeng County, Yichang, 443400, People's Republic of China
| | - Zhaohui Lan
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, People's Republic of China
| | - Wei Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, People's Republic of China
| | - Ying Feng
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, People's Republic of China
| | - Juan Hu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, People's Republic of China
| | - Faju Chen
- Biotechnology Research Center, China Three Gorges University, Yichang, 443002, People's Republic of China
| | - Yifei Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, People's Republic of China.
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28
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Xing Y, Cao Y, Ma Y, Wang F, Xin S, Zhu W. QTL mapping and transcriptomic analysis of fruit length in cucumber. FRONTIERS IN PLANT SCIENCE 2023; 14:1208675. [PMID: 37670860 PMCID: PMC10475832 DOI: 10.3389/fpls.2023.1208675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/21/2023] [Indexed: 09/07/2023]
Abstract
A total of 151 recombinant inbred lines (RILs) were derived from the cross between 'Cucumis sativus L. hardwickii' (HW) and a cultivated Northern Chinese inbred line 'XinTaiMiCi' (XTMC). We used resequencing to construct the genetic map and analyze the genetic background of RIL population, and combined with the phenotypes of RIL population and the analysis of RNA-seq data, we located the major loci controlling the fruit length of cucumber and related analysis. A genetic map containing 600 bin markers was constructed via re-sequencing. Based on the phenotype data collected in two different seasons (spring 2021 and autumn 2022), the major quantitative trait loci (QTLs) controlling cucumber fruit length were located and their transcriptomic analysis carried out. The results revealed three QTLs (Fl2.1, Fl4.1, and Fl6.1) detected repeatedly in the two seasons, of which Fl4.1 was the dominant QTL. From the functional annotation of corresponding genes there, we discovered the gene Csa4G337340 encoding an auxin efflux carrier family protein. The expression of that gene was significantly lower in XTMC and the long-fruit RIL lines than in HW and the short-fruit RIL lines; hence, we speculated the gene could be negatively correlated with the fruit length of cucumber. Transcriptomic analysis showed that 259 differentially expressed genes (DEGs) were enriched in the plant hormone signal transduction pathway. In addition, among those DEGs, 509 transcription factors were detected, these distributed in several transcription factor gene families, such as bHLH, AP2/ErF -ERF, C2H2, and NAC. Therefore, we concluded that the major gene controlling the fruit length of cucumber is located in the interval of Fl4.1, whose gene Csa4G337340 may be involved in the negative regulation of fruit length. Further, genes related to plant hormone signal transduction and several transcription factors were also found involved in the regulation of cucumber fruit length. Our results provide a reference for the fine mapping of major genes and analyzing the mechanism of cucumber fruit length.
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Affiliation(s)
- Yanan Xing
- Qingdao Agricultural University, Qingdao, China
| | - Yilin Cao
- Qingdao Agricultural University, Qingdao, China
| | - Yanan Ma
- Qingdao Agricultural University, Qingdao, China
| | - Fu Wang
- Qingdao Agricultural University, Qingdao, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao, China
| | - Shijie Xin
- Yantai Yeda Investment Development Group Co., Ltd, Yantai, China
| | - Wenying Zhu
- Qingdao Agricultural University, Qingdao, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao, China
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29
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Xia L, Wang H, Zhao X, Obel HO, Yu X, Lou Q, Chen J, Cheng C. Chloroplast Pan-Genomes and Comparative Transcriptomics Reveal Genetic Variation and Temperature Adaptation in the Cucumber. Int J Mol Sci 2023; 24:ijms24108943. [PMID: 37240287 DOI: 10.3390/ijms24108943] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
Although whole genome sequencing, genetic variation mapping, and pan-genome studies have been done on a large group of cucumber nuclear genomes, organelle genome information is largely unclear. As an important component of the organelle genome, the chloroplast genome is highly conserved, which makes it a useful tool for studying plant phylogeny, crop domestication, and species adaptation. Here, we have constructed the first cucumber chloroplast pan-genome based on 121 cucumber germplasms, and investigated the genetic variations of the cucumber chloroplast genome through comparative genomic, phylogenetic, haplotype, and population genetic structure analysis. Meanwhile, we explored the changes in expression of cucumber chloroplast genes under high- and low-temperature stimulation via transcriptome analysis. As a result, a total of 50 complete chloroplast genomes were successfully assembled from 121 cucumber resequencing data, ranging in size from 156,616-157,641 bp. The 50 cucumber chloroplast genomes have typical quadripartite structures, consisting of a large single copy (LSC, 86,339-86,883 bp), a small single copy (SSC, 18,069-18,363 bp), and two inverted repeats (IRs, 25,166-25,797 bp). Comparative genomic, haplotype, and population genetic structure results showed that there is more genetic variation in Indian ecotype cucumbers compared to other cucumber cultivars, which means that many genetic resources remain to be explored in Indian ecotype cucumbers. Phylogenetic analysis showed that the 50 cucumber germplasms could be classified into 3 types: East Asian, Eurasian + Indian, and Xishuangbanna + Indian. The transcriptomic analysis showed that matK were significantly up-regulated under high- and low-temperature stresses, further demonstrating that cucumber chloroplasts respond to temperature adversity by regulating lipid metabolism and ribosome metabolism. Further, accD has higher editing efficiency under high-temperature stress, which may contribute to the heat tolerance. These studies provide useful insight into genetic variation in the chloroplast genome, and established the foundation for exploring the mechanisms of temperature-stimulated chloroplast adaptation.
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Affiliation(s)
- Lei Xia
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Han Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaokun Zhao
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hesbon Ochieng Obel
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaqing Yu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Qunfeng Lou
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinfeng Chen
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunyan Cheng
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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30
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Song H, Wang Q, Zhang Z, Lin K, Pang E. Identification of clade-wide putative cis-regulatory elements from conserved non-coding sequences in Cucurbitaceae genomes. HORTICULTURE RESEARCH 2023; 10:uhad038. [PMID: 37799630 PMCID: PMC10548412 DOI: 10.1093/hr/uhad038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 02/20/2023] [Indexed: 10/07/2023]
Abstract
Cis-regulatory elements regulate gene expression and play an essential role in the development and physiology of organisms. Many conserved non-coding sequences (CNSs) function as cis-regulatory elements. They control the development of various lineages. However, predicting clade-wide cis-regulatory elements across several closely related species remains challenging. Based on the relationship between CNSs and cis-regulatory elements, we present a computational approach that predicts the clade-wide putative cis-regulatory elements in 12 Cucurbitaceae genomes. Using 12-way whole-genome alignment, we first obtained 632 112 CNSs in Cucurbitaceae. Next, we identified 16 552 Cucurbitaceae-wide cis-regulatory elements based on collinearity among all 12 Cucurbitaceae plants. Furthermore, we predicted 3 271 potential regulatory pairs in the cucumber genome, of which 98 were verified using integrative RNA sequencing and ChIP sequencing datasets from samples collected during various fruit development stages. The CNSs, Cucurbitaceae-wide cis-regulatory elements, and their target genes are accessible at http://cmb.bnu.edu.cn/cisRCNEs_cucurbit/. These elements are valuable resources for functionally annotating CNSs and their regulatory roles in Cucurbitaceae genomes.
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Affiliation(s)
- Hongtao Song
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Qi Wang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Zhonghua Zhang
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Kui Lin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Erli Pang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
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31
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Li B, Wei A, Tong X, Han Y, Liu N, Chen Z, Yang H, Wu H, Lv M, Wang NN, Du S. A Genome-Wide Association Study to Identify Novel Candidate Genes Related to Low-Nitrogen Tolerance in Cucumber (Cucumis sativus L.). Genes (Basel) 2023; 14:genes14030662. [PMID: 36980933 PMCID: PMC10048605 DOI: 10.3390/genes14030662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/09/2023] Open
Abstract
Cucumber is one of the most important vegetables, and nitrogen is essential for the growth and fruit production of cucumbers. It is crucial to develop cultivars with nitrogen limitation tolerance or high nitrogen efficiency for green and efficient development in cucumber industry. To reveal the genetic basis of cucumber response to nitrogen starvation, a genome-wide association study (GWAS) was conducted on a collection of a genetically diverse population of cucumber (Cucumis sativus L.) comprising 88 inbred and DH accessions including the North China type, the Eurasian type, the Japanese and South China type mixed subtype, and the South China type subtype. Phenotypic evaluation of six traits under control (14 mM) and treatment (3.5 mM) N conditions depicted the presence of broad natural variation in the studied population. The GWAS results showed that there were significant differences in the population for nitrogen limitation treatment. Nine significant loci were identified corresponding to six LD blocks, three of which overlapped. Sixteen genes were selected by GO annotation associated with nitrogen. Five low-nitrogen stress tolerance genes were finally identified by gene haplotype analysis: CsaV3_3G003630 (CsNRPD1), CsaV3_3G002970 (CsNRT1.1), CsaV3_4G030260 (CsSnRK2.5), CsaV3_4G026940, and CsaV3_3G011820 (CsNPF5.2). Taken together, the experimental data and identification of candidate genes presented in this study offer valuable insights and serve as a useful reference for the genetic enhancement of nitrogen limitation tolerance in cucumbers.
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Affiliation(s)
- Bowen Li
- College of Life Science, Nankai University, Tianjin 300071, China
| | - Aimin Wei
- Cucumber Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin 300192, China
- State Key Laboratory of Vegetable Biobreeding, Tianjin 300192, China
| | - Xueqiang Tong
- College of Life Science, Nankai University, Tianjin 300071, China
| | - Yike Han
- Cucumber Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin 300192, China
- State Key Laboratory of Vegetable Biobreeding, Tianjin 300192, China
| | - Nan Liu
- Cucumber Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin 300192, China
| | - Zhengwu Chen
- Cucumber Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin 300192, China
- State Key Laboratory of Vegetable Biobreeding, Tianjin 300192, China
| | - Hongyu Yang
- College of Life Science, Nankai University, Tianjin 300071, China
| | - Huaxiang Wu
- College of Life Science, Nankai University, Tianjin 300071, China
| | - Mingjie Lv
- Institute of Germplasm Resources and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin 300061, China
| | - Ning Ning Wang
- College of Life Science, Nankai University, Tianjin 300071, China
- College of Agricultural Science, Nankai University, Tianjin 300071, China
| | - Shengli Du
- College of Life Science, Nankai University, Tianjin 300071, China
- Cucumber Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin 300192, China
- State Key Laboratory of Vegetable Biobreeding, Tianjin 300192, China
- Correspondence:
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Che G, Pan Y, Liu X, Li M, Zhao J, Yan S, He Y, Wang Z, Cheng Z, Song W, Zhou Z, Wu T, Weng Y, Zhang X. Natural variation in CRABS CLAW contributes to fruit length divergence in cucumber. THE PLANT CELL 2023; 35:738-755. [PMID: 36427253 PMCID: PMC9940877 DOI: 10.1093/plcell/koac335] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/18/2022] [Indexed: 06/16/2023]
Abstract
Fruit length is a key domestication trait that affects crop yield and appearance. Cucumber (Cucumis sativus) fruits vary from 5 to 60 cm in length. Despite the identification of several regulators and multiple quantitative trait loci (QTLs) underlying fruit length, the natural variation, and molecular mechanisms underlying differences in fruit length are poorly understood. Through map-based cloning, we identified a nonsynonymous polymorphism (G to A) in CRABS CLAW (CsCRC) as underlying the major-effect fruit size/shape QTL FS5.2 in cucumber. The short-fruit allele CsCRCA is a rare allele that has only been found in round-fruited semi-wild Xishuangbanna cucumbers. A near-isogenic line (NIL) homozygous for CsCRCA exhibited a 34∼39% reduction in fruit length. Introducing CsCRCG into this NIL rescued the short-fruit phenotype, and knockdown of CsCRCG resulted in shorter fruit and smaller cells. In natural cucumber populations, CsCRCG expression was positively correlated with fruit length. Further, CsCRCG, but not CsCRCA, targets the downstream auxin-responsive protein gene CsARP1 to regulate its expression. Knockout of CsARP1 produced shorter fruit with smaller cells. Hence, our work suggests that CsCRCG positively regulates fruit elongation through transcriptional activation of CsARP1 and thus enhances cell expansion. Using different CsCRC alleles provides a strategy to manipulate fruit length in cucumber breeding.
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Affiliation(s)
- Gen Che
- State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
- School of Life Science, Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, Inner Mongolia University, Hohhot 010070, China
| | - Yupeng Pan
- Horticulture Department, University of Wisconsin-Madison, 1575 Linden Drive, Madison, Wisconsin 53706, USA
| | - Xiaofeng Liu
- State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Min Li
- State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Jianyu Zhao
- State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Shuangshuang Yan
- State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Yuting He
- State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Zhongyi Wang
- State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Zhihua Cheng
- State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Weiyuan Song
- State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Zhaoyang Zhou
- State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Tao Wu
- College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin-Madison, 1575 Linden Drive, Madison, Wisconsin 53706, USA
- USDA-ARS, Vegetable Crops Research Unit, 1575 Linden Drive, Madison, Wisconsin 53706, USA
| | - Xiaolan Zhang
- State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
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Vegetable biology and breeding in the genomics era. SCIENCE CHINA. LIFE SCIENCES 2023; 66:226-250. [PMID: 36508122 DOI: 10.1007/s11427-022-2248-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022]
Abstract
Vegetable crops provide a rich source of essential nutrients for humanity and represent critical economic values to global rural societies. However, genetic studies of vegetable crops have lagged behind major food crops, such as rice, wheat and maize, thereby limiting the application of molecular breeding. In the past decades, genome sequencing technologies have been increasingly applied in genetic studies and breeding of vegetables. In this review, we recapitulate recent progress on reference genome construction, population genomics and the exploitation of multi-omics datasets in vegetable crops. These advances have enabled an in-depth understanding of their domestication and evolution, and facilitated the genetic dissection of numerous agronomic traits, which jointly expedites the exploitation of state-of-the-art biotechnologies in vegetable breeding. We further provide perspectives of further directions for vegetable genomics and indicate how the ever-increasing omics data could accelerate genetic, biological studies and breeding in vegetable crops.
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Pollen tube emergence is mediated by ovary-expressed ALCATRAZ in cucumber. Nat Commun 2023; 14:258. [PMID: 36650145 PMCID: PMC9845374 DOI: 10.1038/s41467-023-35936-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/09/2023] [Indexed: 01/18/2023] Open
Abstract
Pollen tube guidance within female tissues of flowering plants can be divided into preovular guidance, ovular guidance and a connecting stage called pollen tube emergence. As yet, no female factor has been identified to positively regulate this transition process. In this study, we show that an ovary-expressed bHLH transcription factor Cucumis sativus ALCATRAZ (CsALC) functions in pollen tube emergence in cucumber. CsALC knockout mutants showed diminished pollen tube emergence, extremely reduced entry into ovules, and a 95% reduction in female fertility. Further examination showed two rapid alkalinization factors CsRALF4 and CsRALF19 were less expressed in Csalc ovaries compared to WT. Besides the loss of male fertility derived from precocious pollen tube rupture as in Arabidopsis, Csralf4 Csralf19 double mutants exhibited a 60% decrease in female fertility due to reduced pollen tube distribution and decreased ovule targeting efficiency. In brief, CsALC regulates female fertility and promotes CsRALF4/19 expression in the ovary during pollen tube guidance in cucumber.
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35
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Yu J, Wu S, Sun H, Wang X, Tang X, Guo S, Zhang Z, Huang S, Xu Y, Weng Y, Mazourek M, McGregor C, Renner SS, Branham S, Kousik C, Wechter W, Levi A, Grumet R, Zheng Y, Fei Z. CuGenDBv2: an updated database for cucurbit genomics. Nucleic Acids Res 2023; 51:D1457-D1464. [PMID: 36271794 PMCID: PMC9825510 DOI: 10.1093/nar/gkac921] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 01/30/2023] Open
Abstract
The Cucurbitaceae (cucurbit) family consists of about 1,000 species in 95 genera, including many economically important and popular fruit and vegetable crops. During the past several years, reference genomes have been generated for >20 cucurbit species, and variome and transcriptome profiling data have been rapidly accumulated for cucurbits. To efficiently mine, analyze and disseminate these large-scale datasets, we have developed an updated version of Cucurbit Genomics Database. The updated database, CuGenDBv2 (http://cucurbitgenomics.org/v2), currently hosts 34 reference genomes from 27 cucurbit species/subspecies belonging to 10 different genera. Protein-coding genes from these genomes have been comprehensively annotated by comparing their protein sequences to various public protein and domain databases. A novel 'Genotype' module has been implemented to facilitate mining and analysis of the functionally annotated variome data including SNPs and small indels from large-scale genome sequencing projects. An updated 'Expression' module has been developed to provide a comprehensive gene expression atlas for cucurbits. Furthermore, synteny blocks between any two and within each of the 34 genomes, representing a total of 595 pair-wise genome comparisons, have been identified and can be explored and visualized in the database.
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Affiliation(s)
- Jingyin Yu
- Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Shan Wu
- Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Honghe Sun
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Xin Wang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuemei Tang
- Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - 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 100097, China
| | - Zhonghua Zhang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Sanwen Huang
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, 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 100097, China
| | - Yiqun Weng
- U.S. Department of Agriculture-Agricultural Research Service, Vegetable Crops Research Unit, Madison, WI 53706, USA
- Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA
| | - Michael Mazourek
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Cecilia McGregor
- Department of Horticulture, University of Georgia, Athens, GA 30602, USA
| | - Susanne S Renner
- Faculty of Biology, Systematic Botany and Mycology, University of Munich (LMU), 80638 Munich, Germany
- Department of Biology, Washington University, Saint Louis, MO 63130, USA
| | - Sandra Branham
- Coastal Research and Educational Center, Clemson University, Charleston, SC 29414, USA
| | - Chandrasekar Kousik
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - W Patrick Wechter
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - Amnon Levi
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - Rebecca Grumet
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Yi Zheng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
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36
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Grumet R, Lin YC, Rett-Cadman S, Malik A. Morphological and Genetic Diversity of Cucumber ( Cucumis sativus L.) Fruit Development. PLANTS (BASEL, SWITZERLAND) 2022; 12:23. [PMID: 36616152 PMCID: PMC9824707 DOI: 10.3390/plants12010023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/30/2022] [Accepted: 12/04/2022] [Indexed: 06/03/2023]
Abstract
Cucumber (Cucumis sativus L.) fruits, which are eaten at an immature stage of development, can vary extensively in morphological features such as size, shape, waxiness, spines, warts, and flesh thickness. Different types of cucumbers that vary in these morphological traits are preferred throughout the world. Numerous studies in recent years have added greatly to our understanding of cucumber fruit development and have identified a variety of genetic factors leading to extensive diversity. Candidate genes influencing floral organ establishment, cell division and cell cycle regulation, hormone biosynthesis and response, sugar transport, trichome development, and cutin, wax, and pigment biosynthesis have all been identified as factors influencing cucumber fruit morphology. The identified genes demonstrate complex interplay between structural genes, transcription factors, and hormone signaling. Identification of genetic factors controlling these traits will facilitate breeding for desired characteristics to increase productivity, improve shipping, handling, and storage traits, and enhance consumer-desired qualities. The following review examines our current understanding of developmental and genetic factors driving diversity of cucumber fruit morphology.
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Affiliation(s)
- Rebecca Grumet
- Graduate Program in Plant Breeding, Genetics and Biotechnology, Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Ying-Chen Lin
- Graduate Program in Plant Breeding, Genetics and Biotechnology, Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Stephanie Rett-Cadman
- Graduate Program in Plant Breeding, Genetics and Biotechnology, Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Ajaz Malik
- Department of Horticulture-Vegetable Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar 190 025, India
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37
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Wang S, Wang K, Li Z, Li Y, He J, Li H, Wang B, Xin T, Tian H, Tian J, Zhang G, Li H, Huang S, Yang X. Architecture design of cucurbit crops for enhanced productivity by a natural allele. NATURE PLANTS 2022; 8:1394-1407. [PMID: 36509843 DOI: 10.1038/s41477-022-01297-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 10/31/2022] [Indexed: 05/12/2023]
Abstract
Increasing production efficiency is a top priority in agriculture. Optimal plant architecture is the biological basis of dense planting, high crop yield and labour cost savings, and is thus critical for improving agricultural productivity. In cucurbit crops, most species have elongated internodes, but the path to architecture improvement is still not clear. Here we identified a pumpkin accession with a dominant bushy trait, and found that the associated Bush locus harbours a cucurbit-conserved cis-regulatory element in the 5' untranslated region of a transcription factor gene YABBY1. In cucurbit crops, various B-region deletions enhance the translation of YABBY1, with consequent proportional suppression of stem length in a dose-dependent manner. Depending on different cultivation patterns, the precise deployment of these alleles has significant effects on yield improvement or labour cost saving. Our findings demonstrate that the engineering of the YABBY1 B-region is an efficient strategy to customize plant architecture in cucurbit crops.
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Affiliation(s)
- Shenhao Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Kun Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zheng Li
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Yangyang Li
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Jiao He
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Hongbo Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Bowen Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tongxu Xin
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haojie Tian
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiaxing Tian
- Beijing Vegetable Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Guoyu Zhang
- Beijing Vegetable Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Haizhen Li
- Beijing Vegetable Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Xueyong Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
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Jian L, Yan J, Liu J. De Novo Domestication in the Multi-Omics Era. PLANT & CELL PHYSIOLOGY 2022; 63:1592-1606. [PMID: 35762778 DOI: 10.1093/pcp/pcac077] [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: 01/14/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Most cereal crops were domesticated within the last 12,000 years and subsequently spread around the world. These crops have been nourishing the world by supplying a primary energy and nutrient source, thereby playing a critical role in determining the status of human health and sustaining the global population. Here, we review the major challenges of future agriculture and emphasize the utilization of wild germplasm. De novo domestication is one of the most straightforward strategies to manipulate domestication-related and/or other genes with known function, and thereby introduce desired traits into wild plants. We also summarize known causal variations and their corresponding pathways in order to better understand the genetic basis of crop evolution, and how this knowledge could facilitate de novo domestication. Indeed knowledge-driven de novo domestication has great potential for the development of new sustainable crops that have climate-resilient high yield with low resource input and meet individual nutrient needs. Finally, we discuss current opportunities for and barriers to knowledge-driven de novo domestication.
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Affiliation(s)
- Liumei Jian
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jie Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Feng H, Guo C, Li Z, Gao Y, Zhang Q, Geng Z, Wang J, Chen G, Liu K, Li H, Yang W. Machine learning assisted dynamic phenotypes and genomic variants help understand the ecotype divergence in rapeseed. FRONTIERS IN PLANT SCIENCE 2022; 13:1028779. [PMID: 36457523 PMCID: PMC9705987 DOI: 10.3389/fpls.2022.1028779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/14/2022] [Indexed: 06/17/2023]
Abstract
Three ecotypes of rapeseed, winter, spring, and semi-winter, have been formed to enable the plant to adapt to different geographic areas. Although several major loci had been found to contribute to the flowering divergence, the genomic footprints and associated dynamic plant architecture in the vegetative growth stage underlying the ecotype divergence remain largely unknown in rapeseed. Here, a set of 41 dynamic i-traits and 30 growth-related traits were obtained by high-throughput phenotyping of 171 diverse rapeseed accessions. Large phenotypic variation and high broad-sense heritability were observed for these i-traits across all developmental stages. Of these, 19 i-traits were identified to contribute to the divergence of three ecotypes using random forest model of machine learning approach, and could serve as biomarkers to predict the ecotype. Furthermore, we analyzed genomic variations of the population, QTL information of all dynamic i-traits, and genomic basis of the ecotype differentiation. It was found that 213, 237, and 184 QTLs responsible for the differentiated i-traits overlapped with the signals of ecotype divergence between winter and spring, winter and semi-winter, and spring and semi-winter, respectively. Of which, there were four common divergent regions between winter and spring/semi-winter and the strongest divergent regions between spring and semi-winter were found to overlap with the dynamic QTLs responsible for the differentiated i-traits at multiple growth stages. Our study provides important insights into the divergence of plant architecture in the vegetative growth stage among the three ecotypes, which was contributed to by the genetic differentiation, and might contribute to environmental adaption and yield improvement.
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Affiliation(s)
- Hui Feng
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Chaocheng Guo
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zongyi Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yuan Gao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zedong Geng
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Jing Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Guoxing Chen
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Haitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, School of Life Sciences, Hubei University, Wuhan, China
| | - Wanneng Yang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
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Transcriptomic and Physiological Analyses Reveal Potential Genes Involved in Photoperiod-Regulated β-Carotene Accumulation Mechanisms in the Endocarp of Cucumber ( Cucumis sativus L.) Fruit. Int J Mol Sci 2022; 23:ijms232012650. [PMID: 36293506 PMCID: PMC9604348 DOI: 10.3390/ijms232012650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/07/2022] [Accepted: 10/12/2022] [Indexed: 01/24/2023] Open
Abstract
The accumulation of carotenoids in plants is a key nutritional quality in many horticultural crops. Although the structural genes encoding the biosynthetic enzymes are well-characterized, little is known regarding photoperiod-mediated carotenoid accumulation in the fruits of some horticultural crops. Herein, we performed physiological and transcriptomic analyses using two cucumber genotypes, SWCC8 (XIS-orange-fleshed and photoperiod-sensitive) and CC3 (white-fleshed and photoperiod-non-sensitive), established under two photoperiod conditions (8L/16D vs. 12L/12D) at four fruit developmental stages. Day-neutral treatments significantly increased fruit β-carotene content by 42.1% compared to short day (SD) treatments in SWCC8 at 40 DAP with no significant changes in CC3. Day-neutral condition elevated sugar levels of fruits compared to short-day treatments. According to GO and KEGG analyses, the predominantly expressed genes were related to photosynthesis, carotenoid biosynthesis, plant hormone signaling, circadian rhythms, and carbohydrates. Consistent with β-carotene accumulation in SWCC8, the day-neutral condition elevated the expression of key carotenoid biosynthesis genes such as PSY1, PDS, ZDS1, LYCB, and CHYB1 during later stages between 30 to 40 days of fruit development. Compared to SWCC8, CC3 showed an expression of DEGs related to carotenoid cleavage and oxidative stresses, signifying reduced β-carotene levels in CC3 cucumber. Further, a WGCNA analysis revealed co-expression between carbohydrate-related genes (pentose-phosphatase synthase, β-glucosidase, and trehalose-6-phosphatase), photoperiod-signaling genes (LHY, APRR7/5, FKF1, PIF3, COP1, GIGANTEA, and CK2) and carotenoid-biosynthetic genes, thus suggesting that a cross-talk mechanism between carbohydrates and light-related genes induces β-carotene accumulation. The results highlighted herein provide a framework for future gene functional analyses and molecular breeding towards enhanced carotenoid accumulation in edible plant organs.
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41
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Multi-omics study revealed the genetic basis of beer flavor quality in yeast. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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42
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Guan J, Zhang J, Gong D, Zhang Z, Yu Y, Luo G, Somta P, Hu Z, Wang S, Yuan X, Zhang Y, Wang Y, Chen Y, Laosatit K, Chen X, Chen H, Sha A, Cheng X, Xie H, Wang L. Genomic analyses of rice bean landraces reveal adaptation and yield related loci to accelerate breeding. Nat Commun 2022; 13:5707. [PMID: 36175442 PMCID: PMC9523027 DOI: 10.1038/s41467-022-33515-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/21/2022] [Indexed: 11/29/2022] Open
Abstract
Rice bean (Vigna umbellata) is an underexploited domesticated legume crop consumed for dietary protein in Asia, yet little is known about the genetic diversity of this species. Here, we present a high-quality reference genome for a rice bean landrace (FF25) built using PacBio long-read data and a Hi-C chromatin interaction map, and assess the phylogenetic position and speciation time of rice bean within the Vigna genus. We sequence 440 landraces (two core collections), and GWAS based on data for growth sites at three widely divergent latitudes reveal loci associated with flowering and yield. Loci harboring orthologs of FUL (FRUITFULL), FT (FLOWERING LOCUS T), and PRR3 (PSEUDO-RESPONSE REGULATOR 3) contribute to the adaptation of rice bean from its low latitude center of origin towards higher latitudes, and the landraces which pyramid early-flowering alleles for these loci display maximally short flowering times. We also demonstrate that copy-number-variation for VumCYP78A6 can regulate seed-yield traits. Intriguingly, 32 landraces collected from a mountainous region in South-Central China harbor a recently acquired InDel in TFL1 (TERMINAL FLOWER1) affecting stem determinacy; these materials also have exceptionally high values for multiple human-desired traits and could therefore substantially advance breeding efforts to improve rice bean. Rice bean is an underexploited legume crop that has many desirable properties against bio and abiotic stresses. Here, the authors report the genome assembly of this species, conduct population genetics studies and reveal the genetic variations associated with adaptation and yield traits.
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Affiliation(s)
- Jiantao Guan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.,Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jintao Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agriculture, Yangtze University, Jingzhou, China
| | - Dan Gong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agriculture, Yangtze University, Jingzhou, China
| | - Zhengquan Zhang
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yang Yu
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Gaoling Luo
- Institute of Rice Research, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Zheng Hu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Suhua Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xingxing Yuan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yaowen Zhang
- College of Agriculture, Shanxi Agricultural University, Taiyuan, China
| | - Yanlan Wang
- Crop Research Institute of Hunan Province, Changsha, China
| | - Yanhua Chen
- Institute of Rice Research, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Kularb Laosatit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Honglin Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Aihua Sha
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Xuzhen Cheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hua Xie
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
| | - Lixia Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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The CsHEC1-CsOVATE module contributes to fruit neck length variation via modulating auxin biosynthesis in cucumber. Proc Natl Acad Sci U S A 2022; 119:e2209717119. [PMID: 36122223 PMCID: PMC9522363 DOI: 10.1073/pnas.2209717119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fruit neck is the proximal portion of the fruit with undesirable taste that has detrimental effects on fruit shape and commercial value in cucumber. Despite the dramatic variations in fruit neck length of cucumber germplasms, the genes and regulatory mechanisms underlying fruit neck elongation remain mysterious. In this study, we found that Cucumis sativus HECATE1 (CsHEC1) was highly expressed in fruit neck. Knockout of CsHEC1 resulted in shortened fruit neck and decreased auxin accumulation, whereas overexpression of CsHEC1 displayed the opposite effects, suggesting that CsHEC1 positively regulated fruit neck length by modulating local auxin level. Further analysis showed that CsHEC1 directly bound to the promoter of the auxin biosynthesis gene YUCCA4 (CsYUC4) and activated its expression. Enhanced expression of CsYUC4 resulted in elongated fruit neck and elevated auxin content. Moreover, knockout of CsOVATE resulted in longer fruit neck and higher auxin. Genetic and biochemical data showed that CsOVATE physically interacted with CsHEC1 to antagonize its function by attenuating the CsHEC1-mediated CsYUC4 transcriptional activation. In cucumber germplasms, the expression of CsHEC1 and CsYUC4 positively correlated with fruit neck length, while that of CsOVATE showed a negative correlation. Together, our results revealed a CsHEC1-CsOVATE regulatory module that confers fruit neck length variation via CsYUC4-mediated auxin biosynthesis in cucumber.
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Li N, Zhang X, Sun X, Zhu S, Cheng Y, Liu M, Gao S, Zhang J, Wang Y, Yang X, Chen J, Li F, He Q, Zeng Z, Yuan X, Zhou Z, Ma L, Wang T, Li X, Liu H, Pan Y, Zhou M, Gao C, Zhou G, Han Z, Liu S, Su J, Cheng Z, Tian S, Liu T. Genomic insights into the evolutionary history and diversification of bulb traits in garlic. Genome Biol 2022; 23:188. [PMID: 36071507 PMCID: PMC9450234 DOI: 10.1186/s13059-022-02756-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/22/2022] [Indexed: 11/24/2022] Open
Abstract
Background Garlic is an entirely sterile crop with important value as a vegetable, condiment, and medicine. However, the evolutionary history of garlic remains largely unknown. Results Here we report a comprehensive map of garlic genomic variation, consisting of amazingly 129.4 million variations. Evolutionary analysis indicates that the garlic population diverged at least 100,000 years ago, and the two groups cultivated in China were domesticated from two independent routes. Consequently, 15.0 and 17.5% of genes underwent an expression change in two cultivated groups, causing a reshaping of their transcriptomic architecture. Furthermore, we find independent domestication leads to few overlaps of deleterious substitutions in these two groups due to separate accumulation and selection-based removal. By analysis of selective sweeps, genome-wide trait associations and associated transcriptomic analysis, we uncover differential selections for the bulb traits in these two garlic groups during their domestication. Conclusions This study provides valuable resources for garlic genomics-based breeding, and comprehensive insights into the evolutionary history of this clonal-propagated crop. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02756-1.
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Affiliation(s)
- Ningyang Li
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.,Shandong Agricultural University, Tai'an, 271018, China
| | - Xueyu Zhang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Xiudong Sun
- Shandong Agricultural University, Tai'an, 271018, China
| | - Siyuan Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Yi Cheng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Meng Liu
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Song Gao
- Shandong Agricultural University, Tai'an, 271018, China.,Yangzhou University, Yangzhou, 225009, China
| | - Jiangjiang Zhang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Yanzhou Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.,Industrial Research Institute of garlic (IBFC-Jinxiang), Jinxiang, 272200, China
| | - Xiai Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.,Industrial Research Institute of garlic (IBFC-Jinxiang), Jinxiang, 272200, China
| | | | - Fu Li
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Qiaoyun He
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Zheng Zeng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Xiaoge Yuan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Zhiman Zhou
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Longchuan Ma
- Shandong Dongyun Research Center of garlic Engineering, JinXiang, 272200, China
| | - Taotao Wang
- Shandong Dongyun Research Center of garlic Engineering, JinXiang, 272200, China
| | - Xiang Li
- Shandong Agricultural University, Tai'an, 271018, China
| | - Hanqiang Liu
- Northwest A&F University, Yangling, 712100, China
| | - Yupeng Pan
- Northwest A&F University, Yangling, 712100, China
| | - Mengyan Zhou
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Chunsheng Gao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Gang Zhou
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Zhenlin Han
- University of Hawaii at Manoa, Honolulu, 96822, USA
| | - Shiqi Liu
- Shandong Agricultural University, Tai'an, 271018, China
| | - Jianguang Su
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.
| | - Zhihui Cheng
- Northwest A&F University, Yangling, 712100, China.
| | - Shilin Tian
- Novogene Bioinformatics Institute, Beijing, 100083, China.
| | - Touming Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China. .,Industrial Research Institute of garlic (IBFC-Jinxiang), Jinxiang, 272200, China.
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45
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Combination of Genomics, Transcriptomics Identifies Candidate Loci Related to Cold Tolerance in Dongxiang Wild Rice. PLANTS 2022; 11:plants11182329. [PMID: 36145730 PMCID: PMC9506393 DOI: 10.3390/plants11182329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/22/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022]
Abstract
Rice, a cold-sensitive crop, is a staple food for more than 50% of the world’s population. Low temperature severely compromises the growth of rice and challenges China’s food safety. Dongxiang wild rice (DXWR) is the most northerly common wild rice in China and has strong cold tolerance, but the genetic basis of its cold tolerance is still unclear. Here, we report quantitative trait loci (QTLs) analysis for seedling cold tolerance (SCT) using a high-density single nucleotide polymorphism linkage map in the backcross recombinant inbred lines that were derived from a cross of DXWR, and an indica cultivar, GZX49. A total of 10 putative QTLs were identified for SCT under 4 °C cold treatment, each explaining 2.0–6.8% of the phenotypic variation in this population. Furthermore, transcriptome sequencing of DXWR seedlings before and after cold treatment was performed, and 898 and 3413 differentially expressed genes (DEGs) relative to 0 h in cold-tolerant for 4 h and 12 h were identified, respectively. Gene ontology and Kyoto encyclopedia of genes and genomes (KEGG) analysis were performed on these DEGs. Using transcriptome data and genetic linkage analysis, combined with qRT-PCR, sequence comparison, and bioinformatics, LOC_Os08g04840 was putatively identified as a candidate gene for the major effect locus qSCT8. These findings provided insights into the genetic basis of SCT for the improvement of cold stress potential in rice breeding programs.
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46
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Monnot S, Cantet M, Mary-Huard T, Moreau L, Lowdon R, Van Haesendonck M, Ricard A, Boissot N. Unravelling cucumber resistance to several viruses via genome-wide association studies highlighted resistance hotspots and new QTLs. HORTICULTURE RESEARCH 2022; 9:uhac184. [PMID: 36338844 PMCID: PMC9627523 DOI: 10.1093/hr/uhac184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/10/2022] [Indexed: 06/16/2023]
Abstract
The mapping and introduction of sustainable resistance to viruses in crops is a major challenge in modern breeding, especially regarding vegetables. We hence assembled a panel of cucumber elite lines and landraces from different horticultural groups for testing with six virus species. We mapped 18 quantitative trait loci (QTL) with a multiloci genome wide association studies (GWAS), some of which have already been described in the literature. We detected two resistance hotspots, one on chromosome 5 for resistance to the cucumber mosaic virus (CMV), cucumber vein yellowing virus (CVYV), cucumber green mottle mosaic virus (CGMMV) and watermelon mosaic virus (WMV), colocalizing with the RDR1 gene, and another on chromosome 6 for resistance to the zucchini yellowing mosaic virus (ZYMV) and papaya ringspot virus (PRSV) close to the putative VPS4 gene location. We observed clear structuring of resistance among horticultural groups due to plant virus coevolution and modern breeding which have impacted linkage disequilibrium (LD) in resistance QTLs. The inclusion of genetic structure in GWAS models enhanced the GWAS accuracy in this study. The dissection of resistance hotspots by local LD and haplotype construction helped gain insight into the panel's resistance introduction history. ZYMV and CMV resistance were both introduced from different donors in the panel, resulting in multiple resistant haplotypes at same locus for ZYMV, and in multiple resistant QTLs for CMV.
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Affiliation(s)
- Severine Monnot
- INRAE, Génétique et Amélioration des Fruits et Légumes, 84143, Montfavet, France
- Bayer Crop Science, 13670, Saint-Andiol, France
| | | | - Tristan Mary-Huard
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Laurence Moreau
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Rebecca Lowdon
- Université Paris-Saclay, INRAE, AgroParisTech, Mathématiques et Informatique Appliquées-Paris, 75005 Paris, France
| | | | | | - Nathalie Boissot
- INRAE, Génétique et Amélioration des Fruits et Légumes, 84143, Montfavet, France
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47
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Yang A, Xu Q, Hong Z, Wang X, Zeng K, Yan L, Liu Y, Zhu Z, Wang H, Xu Y. Modified photoperiod response of CsFT promotes day neutrality and early flowering in cultivated cucumber. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2735-2746. [PMID: 35710636 DOI: 10.1007/s00122-022-04146-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 05/28/2022] [Indexed: 06/15/2023]
Abstract
Map-based cloning and photoperiod response detection suggested that CsFT is the critical gene for cucumber photoperiod domestication. Photoperiod sensitivity is important for sensing seasonal changes and local adaptation. However, day-length sensitivity limits crop geographical adaptation and it should be modified during domestication. Cucumber was domesticated in southern Asia and is currently cultivated worldwide across a wide range of latitudes, but its photoperiod sensitivity and its change during cucumber domestication are unknown. Here, we confirmed wild cucumber (Hardwickii) was a short-day plant, and its flowering depends on short-day (SD) conditions, while the cultivated cucumber (9930) is a day-neutral plant that flowers independently of day length. A photoperiod sensitivity locus (ps-1) was identified by the 9930 × Hardwickii F2 segregating populations, which span a ~ 970 kb region and contain 60 predicted genes. RNA-seq analysis showed that the critical photoperiod pathway gene FLOWERING LOCUS T (CsFT) within the ps-1 locus exhibits differential expression between 9930 and Hardwickii, which was confirmed by qRT-PCR detection. CsFT in Hardwickii was sensitive to day length and could be significantly induced by SD conditions, whereas CsFT was highly expressed in 9930 and was insensitive to day length. Moreover, the role of CsFT in promoting flowering was verified by overexpression of CsFT in Arabidopsis. We also identified the genetic variations existing in the promoter of CsFT among the different geographic cucumbers and suggest they have possible roles in photoperiod domestication. The results of this study suggest that a variation in photoperiod sensitivity of CsFT is associated with day neutrality and early flowering in cultivated cucumber and could contribute to cucumber cultivation in diverse regions throughout the world.
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Affiliation(s)
- Aiyi Yang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China
| | - Qinglan Xu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China
| | - Zezhou Hong
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China
| | - Xinrui Wang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China
| | - Kang Zeng
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China
| | - Ling Yan
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China
| | - Yuanyuan Liu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China
| | - Zhujun Zhu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China.
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Hangzhou, 311300, Zhejiang, China.
| | - Huasen Wang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China.
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Hangzhou, 311300, Zhejiang, China.
| | - Yunmin Xu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China.
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Hangzhou, 311300, Zhejiang, China.
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Chen SY, Zhou QYJ, Chen L, Li JY, Xie T, Zhang SH. Screening and identifying cucurbitacins and cucurbitacin glycosides in Cucumis sativus using high-performance liquid chromatography/quadrupole-time-of-flight mass spectrometry combined with in-source fragmentation and alkali adduct ions. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2022; 36:e9323. [PMID: 35560736 DOI: 10.1002/rcm.9323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/15/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
RATIONALE Cucumber, as a popular fruit and vegetable, has tremendously contributed to providing a sufficient and high-quality food supply. However, the cucumber plant metabolites, which may possess potential benefits for human health, were rarely reported. In addition, rapid detection of these metabolites from the complex biological matrix of cucumber samples is a tremendous challenge. METHODS A rapid detection method was established to systematically screen cucurbitacins and cucurbitacin glycosides in cucumber plants by combining high-performance liquid chromatography/quadrupole-time-of-flight mass spectrometry (HPLC-Q-TOF-MS) with in-source fragmentation (ISF). Moreover, the alkali cations, including acetic acid, 0.1% LiCl, 0.1% NH4 Cl, 0.1% NaCl, and 0.1% KCl, were added to the mobile phase for improving the ion response. RESULTS The fragmentation pathways of seven cucurbitacins and cucurbitacin glycosides were primarily investigated. The characteristic ISF ions at m/z 501.3211 and 503.3367 were identified and employed to screen 40 cucurbitacins and cucurbitacin glycosides from the complex biological matrix. Their structures were identified by their tandem mass spectrometry (MS/MS) spectra and fragmentation pathways of references. Finally, the metabolic distribution and network of cucurbitacins and cucurbitacin glycosides in cucumber plants were also proposed. CONCLUSIONS This work marks the first systematic and comprehensive study of the metabolites in cucumber plants using HPLC-Q-TOF-MS technology, providing a template for screening and identifying the triterpenoids from other plant-derived medicines or food.
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Affiliation(s)
- Si-Yuan Chen
- The First Hospital of Hunan University of Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
| | - Qing Yi-Jun Zhou
- Institute of Chinese Materia Medica, Hunan Academy of Chinese Medicine, Changsha, China
| | - Lin Chen
- Institute of Chinese Materia Medica, Hunan Academy of Chinese Medicine, Changsha, China
| | - Jia-Yu Li
- Institute of Chinese Materia Medica, Hunan Academy of Chinese Medicine, Changsha, China
| | - Tao Xie
- Department of Acupuncture and Rehabilitation, Changsha Traditional Chinese Medicine Hospital, Changsha, China
| | - Shui-Han Zhang
- Institute of Chinese Materia Medica, Hunan Academy of Chinese Medicine, Changsha, China
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49
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Lin X, Zhang N, Song H, Lin K, Pang E. Population-specific, recent positive selection signatures in cultivated Cucumis sativus L. (cucumber). G3 GENES|GENOMES|GENETICS 2022; 12:6585339. [PMID: 35554526 PMCID: PMC9258548 DOI: 10.1093/g3journal/jkac119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/03/2022] [Indexed: 11/13/2022]
Abstract
Population-specific, positive selection promotes the diversity of populations and drives local adaptations in the population. However, little is known about population-specific, recent positive selection in the populations of cultivated cucumber (Cucumis sativus L.). Based on a genomic variation map of individuals worldwide, we implemented a Fisher’s combination method by combining 4 haplotype-based approaches: integrated haplotype score (iHS), number of segregating sites by length (nSL), cross-population extended haplotype homozygosity (XP-EHH), and Rsb. Overall, we detected 331, 2,147, and 3,772 population-specific, recent positive selective sites in the East Asian, Eurasian, and Xishuangbanna populations, respectively. Moreover, we found that these sites were related to processes for reproduction, response to abiotic and biotic stress, and regulation of developmental processes, indicating adaptations to their microenvironments. Meanwhile, the selective genes associated with traits of fruits were also observed, such as the gene related to the shorter fruit length in the Eurasian population and the gene controlling flesh thickness in the Xishuangbanna population. In addition, we noticed that soft sweeps were common in the East Asian and Xishuangbanna populations. Genes involved in hard or soft sweeps were related to developmental regulation and abiotic and biotic stress resistance. Our study offers a comprehensive candidate dataset of population-specific, selective signatures in cultivated cucumber populations. Our methods provide guidance for the analysis of population-specific, positive selection. These findings will help explore the biological mechanisms of adaptation and domestication of cucumber.
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Affiliation(s)
- Xinrui Lin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University , Beijing 100875, China
| | - Ning Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University , Beijing 100875, China
| | - Hongtao Song
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University , Beijing 100875, China
| | - Kui Lin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University , Beijing 100875, China
| | - Erli Pang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University , Beijing 100875, China
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50
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Hill MJ, Penning BW, McCann MC, Carpita NC. COMPILE: a GWAS computational pipeline for gene discovery in complex genomes. BMC PLANT BIOLOGY 2022; 22:315. [PMID: 35778686 PMCID: PMC9250234 DOI: 10.1186/s12870-022-03668-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Genome-Wide Association Studies (GWAS) are used to identify genes and alleles that contribute to quantitative traits in large and genetically diverse populations. However, traits with complex genetic architectures create an enormous computational load for discovery of candidate genes with acceptable statistical certainty. We developed a streamlined computational pipeline for GWAS (COMPILE) to accelerate identification and annotation of candidate maize genes associated with a quantitative trait, and then matches maize genes to their closest rice and Arabidopsis homologs by sequence similarity. RESULTS COMPILE executed GWAS using a Mixed Linear Model that incorporated, without compression, recent advancements in population structure control, then linked significant Quantitative Trait Loci (QTL) to candidate genes and RNA regulatory elements contained in any genome. COMPILE was validated using published data to identify QTL associated with the traits of α-tocopherol biosynthesis and flowering time, and identified published candidate genes as well as additional genes and non-coding RNAs. We then applied COMPILE to 274 genotypes of the maize Goodman Association Panel to identify candidate loci contributing to resistance of maize stems to penetration by larvae of the European Corn Borer (Ostrinia nubilalis). Candidate genes included those that encode a gene of unknown function, WRKY and MYB-like transcriptional factors, receptor-kinase signaling, riboflavin synthesis, nucleotide-sugar interconversion, and prolyl hydroxylation. Expression of the gene of unknown function has been associated with pathogen stress in maize and in rice homologs closest in sequence identity. CONCLUSIONS The relative speed of data analysis using COMPILE allowed comparison of population size and compression. Limitations in population size and diversity are major constraints for a trait and are not overcome by increasing marker density. COMPILE is customizable and is readily adaptable for application to species with robust genomic and proteome databases.
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Affiliation(s)
- Matthew J Hill
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
- Present address: Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA, 02142, USA
- Present address: Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Bryan W Penning
- USDA-ARS Corn, Soybean and Wheat Quality Research Unit, Wooster, OH, 44691, USA
| | - Maureen C McCann
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907, USA
- Present address: Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Nicholas C Carpita
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA.
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907, USA.
- Present address: Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA.
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