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Zhang Y, Zhao M, Tan J, Huang M, Chu X, Li Y, Han X, Fang T, Tian Y, Jarret R, Lu D, Chen Y, Xue L, Li X, Qin G, Li B, Sun Y, Deng XW, Deng Y, Zhang X, He H. Telomere-to-telomere Citrullus super-pangenome provides direction for watermelon breeding. Nat Genet 2024; 56:1750-1761. [PMID: 38977857 PMCID: PMC11319210 DOI: 10.1038/s41588-024-01823-6] [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: 08/26/2023] [Accepted: 06/04/2024] [Indexed: 07/10/2024]
Abstract
To decipher the genetic diversity within the cucurbit genus Citrullus, we generated telomere-to-telomere (T2T) assemblies of 27 distinct genotypes, encompassing all seven Citrullus species. This T2T super-pangenome has expanded the previously published reference genome, T2T-G42, by adding 399.2 Mb and 11,225 genes. Comparative analysis has unveiled gene variants and structural variations (SVs), shedding light on watermelon evolution and domestication processes that enhanced attributes such as bitterness and sugar content while compromising disease resistance. Multidisease-resistant loci from Citrullus amarus and Citrullus mucosospermus were successfully introduced into cultivated Citrullus lanatus. The SVs identified in C. lanatus have not only been inherited from cordophanus but also from C. mucosospermus, suggesting additional ancestors beyond cordophanus in the lineage of cultivated watermelon. Our investigation substantially improves the comprehension of watermelon genome diversity, furnishing comprehensive reference genomes for all Citrullus species. This advancement aids in the exploration and genetic enhancement of watermelon using its wild relatives.
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Affiliation(s)
- Yilin Zhang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Mingxia Zhao
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Jingsheng Tan
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Minghan Huang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Xiao Chu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Yan Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Xue Han
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Taohong Fang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Yao Tian
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | | | - Dongdong Lu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Yijun Chen
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Lifang Xue
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Xiaoni Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Guochen Qin
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Bosheng Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Yudong Sun
- Vegetable Research and Development Center, Huaiyin Institute of Agricultural Sciences of Xuhuai Region in Jiangsu, Huai'an, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Yun Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China.
| | - Xingping Zhang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China.
| | - Hang He
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China.
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China.
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Baranov D, Dolgov S, Timerbaev V. New Advances in the Study of Regulation of Tomato Flowering-Related Genes Using Biotechnological Approaches. PLANTS (BASEL, SWITZERLAND) 2024; 13:359. [PMID: 38337892 PMCID: PMC10856997 DOI: 10.3390/plants13030359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/21/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024]
Abstract
The tomato is a convenient object for studying reproductive processes, which has become a classic. Such complex processes as flowering and fruit setting require an understanding of the fundamental principles of molecular interaction, the structures of genes and proteins, the construction of signaling pathways for transcription regulation, including the synchronous actions of cis-regulatory elements (promoter and enhancer), trans-regulatory elements (transcription factors and regulatory RNAs), and transposable elements and epigenetic regulators (DNA methylation and acetylation, chromatin structure). Here, we discuss the current state of research on tomatoes (2017-2023) devoted to studying the function of genes that regulate flowering and signal regulation systems using genome-editing technologies, RNA interference gene silencing, and gene overexpression, including heterologous expression. Although the central candidate genes for these regulatory components have been identified, a complete picture of their relationship has yet to be formed. Therefore, this review summarizes the latest achievements related to studying the processes of flowering and fruit set. This work attempts to display the gene interaction scheme to better understand the events under consideration.
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Affiliation(s)
- Denis Baranov
- Laboratory of Expression Systems and Plant Genome Modification, Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (D.B.); (S.D.)
- Laboratory of Plant Genetic Engineering, All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Sergey Dolgov
- Laboratory of Expression Systems and Plant Genome Modification, Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (D.B.); (S.D.)
- Laboratory of Plant Genetic Engineering, All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Vadim Timerbaev
- Laboratory of Expression Systems and Plant Genome Modification, Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (D.B.); (S.D.)
- Laboratory of Plant Genetic Engineering, All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
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Katuuramu DN, Levi A, Wechter WP. Genome-wide association study of soluble solids content, flesh color, and fruit shape in citron watermelon. THE PLANT GENOME 2023; 16:e20391. [PMID: 37718629 DOI: 10.1002/tpg2.20391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/01/2023] [Accepted: 08/29/2023] [Indexed: 09/19/2023]
Abstract
Fruit quality traits are crucial determinants of consumers' willingness to purchase watermelon produce, making them major goals for breeding programs. There is limited information on the genetic underpinnings of fruit quality traits in watermelon. A total of 125 citron watermelon (Citrullus amarus) accessions were genotyped using single nucleotide polymorphisms (SNPs) molecular markers generated via whole-genome resequencing. A total of 2,126,759 genome-wide SNP markers were used to uncover marker-trait associations using single and multi-locus GWAS models. High broad-sense heritability for fruit quality traits was detected. Correlation analysis among traits revealed positive relationships, with the exception of fruit diameter and fruit shape index (ratio of fruit length to fruit diameter), which was negative. A total of 37 significant SNP markers associated with soluble solids content, flesh color, fruit length, fruit diameter, and fruit shape index traits were uncovered. These peak SNPs accounted for 2.1%-23.4% of the phenotypic variation explained showing the quantitative inheritance nature of the evaluated traits. Candidate genes relevant to fruit quality traits were uncovered on chromosomes Ca01, Ca03, Ca06, and Ca07. These significant molecular markers and candidate genes will be useful in marker-assisted breeding of fruit quality traits in watermelon.
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Affiliation(s)
| | - Amnon Levi
- USDA-ARS, U.S. Vegetable Laboratory, Charleston, South Carolina, USA
| | - William P Wechter
- USDA-ARS, U.S. Vegetable Laboratory, Charleston, South Carolina, USA
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Goldman IL, Wang Y, Alfaro AV, Brainard S, Oravec MW, McGregor CE, van der Knaap E. Form and contour: breeding and genetics of organ shape from wild relatives to modern vegetable crops. FRONTIERS IN PLANT SCIENCE 2023; 14:1257707. [PMID: 37841632 PMCID: PMC10568141 DOI: 10.3389/fpls.2023.1257707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 08/28/2023] [Indexed: 10/17/2023]
Abstract
Shape is a primary determinant of consumer preference for many horticultural crops and it is also associated with many aspects of marketing, harvest mechanics, and postharvest handling. Perceptions of quality and preference often map to specific shapes of fruits, tubers, leaves, flowers, roots, and other plant organs. As a result, humans have greatly expanded the palette of shapes available for horticultural crops, in many cases creating a series of market classes where particular shapes predominate. Crop wild relatives possess organs shaped by natural selection, while domesticated species possess organs shaped by human desires. Selection for visually-pleasing shapes in vegetable crops resulted from a number of opportunistic factors, including modification of supernumerary cambia, allelic variation at loci that control fundamental processes such as cell division, cell elongation, transposon-mediated variation, and partitioning of photosynthate. Genes that control cell division patterning may be universal shape regulators in horticultural crops, influencing the form of fruits, tubers, and grains in disparate species. Crop wild relatives are often considered less relevant for modern breeding efforts when it comes to characteristics such as shape, however this view may be unnecessarily limiting. Useful allelic variation in wild species may not have been examined or exploited with respect to shape modifications, and newly emergent information on key genes and proteins may provide additional opportunities to regulate the form and contour of vegetable crops.
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Affiliation(s)
- Irwin L. Goldman
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Yanbing Wang
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Andrey Vega Alfaro
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Scott Brainard
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Madeline W. Oravec
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Cecilia Elizabeth McGregor
- Department of Horticulture, University of Georgia, Athens, GA, United States
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Department of Horticulture, University of Georgia, Athens, GA, United States
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
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