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Ning Y, Liu Z, Liu J, Qi R, Xia P, Yuan X, Xu H, Chen L. Comparative transcriptomics analysis of tolerant and sensitive genotypes reveals genes involved in the response to cold stress in bitter gourd (Momordica charantia L.). Sci Rep 2024; 14:16564. [PMID: 39019887 PMCID: PMC11255239 DOI: 10.1038/s41598-024-58754-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 04/02/2024] [Indexed: 07/19/2024] Open
Abstract
Bitter gourd is an economically important horticultural crop for its edible and medicinal value. However, the regulatory mechanisms of bitter gourd in response to cold stress are still poorly elucidated. In this study, phytohormone determination and comparative transcriptome analyses in XY (cold-tolerant) and QF (cold-sensitive) after low temperature treatment were conducted. Under cold stress, the endogenous contents of abscisic acid (ABA), jasmonic acid (JA) and salicylic acid (SA) in XY were significantly increased at 24 h after treatment (HAT), indicating that ABA, JA and SA might function in regulating cold resistance. RNA-seq results revealed that more differentially expressed genes were identified at 6 HAT in QF and 24 HAT in XY, respectively. KEGG analysis suggested that the plant hormone signal transduction pathway was significantly enriched in both genotypes at all the time points. In addition, transcription factors showing different expression patterns between XY and QF were identified, including CBF3, ERF2, NAC90, WRKY51 and WRKY70. Weighted gene co-expression network analysis suggested MARK1, ERF17, UGT74E2, GH3.1 and PPR as hub genes. These results will deepen the understanding of molecular mechanism of bitter gourd in response to cold stress and the identified genes may help to facilitate the genetic improvement of cold-resistant cultivars.
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Affiliation(s)
- Yu Ning
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Zhiyang Liu
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Jing Liu
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Renjie Qi
- College of Pharmacy, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Pengfei Xia
- Nanjing Innovation Vegetable Molecular Breeding Research Institute, Nanjing, 211899, China
| | - Xihan Yuan
- Nanjing Innovation Vegetable Molecular Breeding Research Institute, Nanjing, 211899, China
| | - Hai Xu
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Longzheng Chen
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
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Yan K, Zhu H, Cao G, Meng L, Li J, Zhang J, Liu S, Wang Y, Feng R, Soaud SA, Elhamid MAA, Heakel RMY, Wei Q, El-Sappah AH, Ru D. Chromosome genome assembly of the Camphora longepaniculata (Gamble) with PacBio and Hi-C sequencing data. FRONTIERS IN PLANT SCIENCE 2024; 15:1372127. [PMID: 38993944 PMCID: PMC11238478 DOI: 10.3389/fpls.2024.1372127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/21/2024] [Indexed: 07/13/2024]
Abstract
Introduction Camphora longepaniculata, a crucial commercial crop and a fundamental component of traditional Chinese medicine, is renowned for its abundant production of volatile terpenoids. However, the lack of available genomic information has hindered pertinent research efforts in the past. Methods To bridge this gap, the present study aimed to use PacBio HiFi, short-read, and highthroughput chromosome conformation capture sequencing to construct a chromosome-level assembly of the C. longepaniculata genome. Results and discussion With twelve chromosomes accounting for 99.82% (766.69 Mb) of the final genome assembly, which covered 768.10 Mb, it was very complete. Remarkably, the assembly's contig and scaffold N50 values are exceptional as well-41.12 and 63.78 Mb, respectively-highlighting its excellent quality and intact structure. Furthermore, a total of 39,173 protein-coding genes were predicted, with 38,766 (98.96%) of them being functionally annotated. The completeness of the genome was confirmed by the Benchmarking Universal Single-Copy Ortholog evaluation, which revealed 99.01% of highly conserved plant genes. As the first comprehensive assembly of the C. longepaniculata genome, it provides a crucial starting point for deciphering the complex pathways involved in terpenoid production. Furthermore, this excellent genome serves as a vital resource for upcoming research on the breeding and genetics of C. longepaniculata.
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Affiliation(s)
- Kuan Yan
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Sichuan Oil Cinnamon Engineering Technology Research Center, Yibin University, Yibin, China
| | - Hui Zhu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Guiling Cao
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Sichuan Oil Cinnamon Engineering Technology Research Center, Yibin University, Yibin, China
| | - Lina Meng
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Sichuan Oil Cinnamon Engineering Technology Research Center, Yibin University, Yibin, China
| | - Junqiang Li
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Sichuan Oil Cinnamon Engineering Technology Research Center, Yibin University, Yibin, China
| | - Jian Zhang
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Sichuan Oil Cinnamon Engineering Technology Research Center, Yibin University, Yibin, China
| | - Sicen Liu
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Sichuan Oil Cinnamon Engineering Technology Research Center, Yibin University, Yibin, China
| | - Yujie Wang
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Sichuan Oil Cinnamon Engineering Technology Research Center, Yibin University, Yibin, China
| | - Ruizhang Feng
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Sichuan Oil Cinnamon Engineering Technology Research Center, Yibin University, Yibin, China
| | - Salma A. Soaud
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | | | - Rania M. Y. Heakel
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Qin Wei
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Sichuan Oil Cinnamon Engineering Technology Research Center, Yibin University, Yibin, China
| | - Ahmed H. El-Sappah
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Sichuan Oil Cinnamon Engineering Technology Research Center, Yibin University, Yibin, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Dafu Ru
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
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Shen C, Lu Q, Yang D, Zhang X, Huang X, Li R, Que Z, Chen N. Genome-wide identification analysis in wild-type Solanum pinnatisectum reveals some genes defending against Phytophthora infestans. Front Genet 2024; 15:1379784. [PMID: 38812971 PMCID: PMC11134371 DOI: 10.3389/fgene.2024.1379784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/15/2024] [Indexed: 05/31/2024] Open
Abstract
Solanum pinnatisectum exhibits strong resistance to late blight caused by Phytophthora infestans but only an incomplete genome assembly based on short Illumina reads has been published. In this study, we generated the first chromosome-level draft genome for the wild-type potato species S. pinnatisectum in China using Oxford Nanopore technology sequencing and Hi-C technology. The high-quality assembled genome size is 664 Mb with a scaffold N50 value of 49.17 Mb, of which 65.87% was occupied by repetitive sequences, and predominant long terminal repeats (42.51% of the entire genome). The genome of S. pinnatisectum was predicted to contain 34,245 genes, of which 99.34% were functionally annotated. Moreover, 303 NBS-coding disease resistance (R) genes were predicted in the S. pinnatisectum genome to investigate the potential mechanisms of resistance to late blight disease. The high-quality chromosome-level reference genome of S. pinnatisectum is expected to provide potential valuable resources for intensively and effectively investigating molecular breeding and genetic research in the future.
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Affiliation(s)
- Chunxiu Shen
- Jiangxi Key Laboratory of Crop Growth and Development Regulation, College of Life Sciences, Resources and Environment Sciences, Yichun University, Yichun, China
| | - Qineng Lu
- Jiangxi Key Laboratory of Crop Growth and Development Regulation, College of Life Sciences, Resources and Environment Sciences, Yichun University, Yichun, China
| | - Di Yang
- Jiangxi Key Laboratory of Crop Growth and Development Regulation, College of Life Sciences, Resources and Environment Sciences, Yichun University, Yichun, China
| | | | | | - Rungen Li
- Jiangxi Key Laboratory of Crop Growth and Development Regulation, College of Life Sciences, Resources and Environment Sciences, Yichun University, Yichun, China
| | - Zhiqun Que
- Jiangxi Key Laboratory of Crop Growth and Development Regulation, College of Life Sciences, Resources and Environment Sciences, Yichun University, Yichun, China
| | - Na Chen
- Jiangxi Key Laboratory of Crop Growth and Development Regulation, College of Life Sciences, Resources and Environment Sciences, Yichun University, Yichun, China
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Wei Z, Zhang L, Gao L, Chen J, Peng L, Yang L. Chromosome-level genome assembly and annotation of the Yunling cattle with PacBio and Hi-C sequencing data. Sci Data 2024; 11:233. [PMID: 38395911 PMCID: PMC10891105 DOI: 10.1038/s41597-024-03066-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Yunling cattle is a new breed of beef cattle bred in Yunnan Province, China. It is bred by crossing the Brahman, the Murray Grey and the Yunnan Yellow cattle. Yunling cattle can adapt to the tropical and subtropical climate environment, and has good reproductive ability and growth speed under high temperature and high humidity conditions, it also has strong resistance to internal and external parasites and with good beef performance. In this study, we generated a high-quality chromosome-level genome assembly of a male Yunling cattle using a combination of short reads sequencing, PacBio HiFi sequencing and Hi-C scaffolding technologies. The genome assembly(3.09 Gb) is anchored to 31 chromosomes(29 autosomes plus one X and Y), with a contig N50 of 35.97 Mb and a scaffold N50 of 112.01 Mb. It contains 1.62 Gb of repetitive sequences and 20,660 protein-coding genes. This first construction of the Yunling cattle genome provides a valuable genetic resource that will facilitate further study of the genetic diversity of bovine species and accelerate Yunling cattle breeding efforts.
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Affiliation(s)
- Zaichao Wei
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, China
- College of Big Data, Baoshan University, Baoshan, China
| | - Lilian Zhang
- College of Big Data, Yunnan Agricultural University, Kunming, China
- Yunnan Engineering Technology Research Center of Agricultural Big Data, Kunming, China
- Yunnan Engineering Research Center for Big Data Intelligent Information Processing of Green Agricultural Products, Kunming, China
| | - Lutao Gao
- College of Big Data, Yunnan Agricultural University, Kunming, China
- Yunnan Engineering Technology Research Center of Agricultural Big Data, Kunming, China
- Yunnan Engineering Research Center for Big Data Intelligent Information Processing of Green Agricultural Products, Kunming, China
| | - Jian Chen
- College of Big Data, Yunnan Agricultural University, Kunming, China
- Yunnan Engineering Technology Research Center of Agricultural Big Data, Kunming, China
- Yunnan Engineering Research Center for Big Data Intelligent Information Processing of Green Agricultural Products, Kunming, China
| | - Lin Peng
- College of Big Data, Yunnan Agricultural University, Kunming, China
- Yunnan Engineering Technology Research Center of Agricultural Big Data, Kunming, China
- Yunnan Engineering Research Center for Big Data Intelligent Information Processing of Green Agricultural Products, Kunming, China
| | - Linnan Yang
- College of Big Data, Yunnan Agricultural University, Kunming, China.
- Yunnan Engineering Technology Research Center of Agricultural Big Data, Kunming, China.
- Yunnan Engineering Research Center for Big Data Intelligent Information Processing of Green Agricultural Products, Kunming, China.
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Vinay ND, Singh K, Ellur RK, Chinnusamy V, Jaiswal S, Iquebal MA, Munshi AD, Matsumura H, Boopalakrishnan G, Jat GS, Kole C, Gaikwad AB, Kumar D, Dey SS, Behera TK. High-quality Momordica balsamina genome elucidates its potential use in improving stress resilience and therapeutic properties of bitter gourd. FRONTIERS IN PLANT SCIENCE 2024; 14:1258042. [PMID: 38333042 PMCID: PMC10851156 DOI: 10.3389/fpls.2023.1258042] [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: 07/13/2023] [Accepted: 12/29/2023] [Indexed: 02/10/2024]
Abstract
Introduction Momordica balsamina is the closest wild species that can be crossed with an important fruit vegetable crop, Momordica charantia, has immense medicinal value, and placed under II subclass of primary gene pool of bitter gourd. M. balsamina is tolerant to major biotic and abiotic stresses. Genome characterization of Momordica balsamina as a wild relative of bitter gourd will contribute to the knowledge of the gene pool available for improvement in bitter gourd. There is potential to transfer gene/s related to biotic resistance and medicinal importance from M. balsamina to M. charantia to produce high-quality, better yielding and stress tolerant bitter gourd genotypes. Methods The present study provides the first and high-quality chromosome-level genome assembly of M. balsamina with size 384.90 Mb and N50 30.96 Mb using sequence data from 10x Genomics, Nanopore, and Hi-C platforms. Results A total of 6,32,098 transposons elements; 2,15,379 simple sequence repeats; 5,67,483 transcription factor binding sites; 3,376 noncoding RNA genes; and 41,652 protein-coding genes were identified, and 4,347 disease resistance, 67 heat stress-related, 05 carotenoid-related, 15 salt stress-related, 229 cucurbitacin-related, 19 terpenes-related, 37 antioxidant activity, and 06 sex determination-related genes were characterized. Conclusion Genome sequencing of M. balsamina will facilitate interspecific introgression of desirable traits. This information is cataloged in the form of webgenomic resource available at http://webtom.cabgrid.res.in/mbger/. Our finding of comparative genome analysis will be useful to get insights into the patterns and processes associated with genome evolution and to uncover functional regions of cucurbit genomes.
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Affiliation(s)
- N. D. Vinay
- Division of Vegetable Science, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Kalpana Singh
- Division of Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ranjith Kumar Ellur
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anilabha Das Munshi
- Division of Vegetable Science, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | | | - G. Boopalakrishnan
- Division of Vegetable Science, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Gograj Singh Jat
- Division of Vegetable Science, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | | | - Ambika Baladev Gaikwad
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Dinesh Kumar
- Division of Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Shyam Sundar Dey
- Division of Vegetable Science, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Tusar Kanti Behera
- Division of Vegetable Science, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
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Jin C, Ma JX, Wang H, Tang LX, Ye YF, Li X, Si J. First genome assembly and annotation of Sanghuangporus weigelae uncovers its medicinal functions, metabolic pathways, and evolution. Front Cell Infect Microbiol 2024; 13:1325418. [PMID: 38264724 PMCID: PMC10803629 DOI: 10.3389/fcimb.2023.1325418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 12/18/2023] [Indexed: 01/25/2024] Open
Abstract
Sanghuangporus, also known as "Sanghuang" in China, is a well-known genus of traditional Chinese medicinal macrofungi. To make more effective use of Sanghuangporus resources, we completed the first genome assembly and annotation of a monokaryon strain of S. weigelae in the present study. A 33.96-Mb genome sequence was assembled as 13 contigs, leading to prediction of 9377 protein-coding genes. Phylogenetic and average nucleotide identity analyses indicated that the S. weigelae genome is closely related to those of other Sanghuangporus species in evolutionary tree, which clustered in one clade. Collinearity analysis revealed a high level of collinearity of S. weigelae with S. baumii, S. vaninii, and S. sanghuang. Biosynthesis pathways potentially involved in medicinal properties, including terpenoid and polysaccharide synthesis, were identified in S. weigelae, while polysaccharides were identified as the main medicinal metabolites in S. weigelae, with flavonoids more important in Sanghuangporus than other medicinal mushroom groups. Genes encoding 332 carbohydrate-active enzymes were identified in the S. weigelae genome, including major glycoside hydrolases and glycosyltransferases predicted, revealing the robust lignocellulose degradation capacity of S. weigelae. Further, 130 genes, clustered in seven classes were annotated to encode cytochromes P450 in the S. weigelae genome. Overall, our results reveal the remarkably medicinal capacity of S. weigelae and provide new insights that will inform the study of evolution and medicinal application of S. weigelae. The data are a reference resource for the formulation of scientific and rational ecological protection policies for Sanghuangporus species.
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Affiliation(s)
| | | | | | | | | | | | - Jing Si
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
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Singh D, Mittal N, Verma S, Singh A, Siddiqui MH. Applications of some advanced sequencing, analytical, and computational approaches in medicinal plant research: a review. Mol Biol Rep 2023; 51:23. [PMID: 38117315 DOI: 10.1007/s11033-023-09057-1] [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: 05/18/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023]
Abstract
The potential active chemicals found in medicinal plants, which have long been employed as natural medicines, are abundant. Exploring the genes responsible for producing these compounds has given new insights into medicinal plant research. Previously, the authentication of medicinal plants was done via DNA marker sequencing. With the advancement of sequencing technology, several new techniques like next-generation sequencing, single molecule sequencing, and fourth-generation sequencing have emerged. These techniques enshrined the role of molecular approaches for medicinal plants because all the genes involved in the biosynthesis of medicinal compound(s) could be identified through RNA-seq analysis. In several research insights, transcriptome data have also been used for the identification of biosynthesis pathways. miRNAs in several medicinal plants and their role in the biosynthesis pathway as well as regulation of the disease-causing genes were also identified. In several research articles, an in silico study was also found to be effective in identifying the inhibitory effect of medicinal plant-based compounds against virus' gene(s). The use of advanced analytical methods like spectroscopy and chromatography in metabolite proofing of secondary metabolites has also been reported in several recent research findings. Furthermore, advancement in molecular and analytic methods will give new insight into studying the traditionally important medicinal plants that are still unexplored.
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Affiliation(s)
- Dhananjay Singh
- Department of Biosciences, Integral University, Lucknow, Uttar Pradesh, 226026, India
| | - Nishu Mittal
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, Uttar Pradesh, 225003, India
| | - Swati Verma
- College of Horticulture and Forestry Thunag, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan, Himachal Pradesh, 173230, India
| | - Anjali Singh
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, Uttar Pradesh, 225003, India
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Zhong J, Cui J, Miao M, Hu F, Dong J, Liu J, Zhong C, Cheng J, Hu K. A point mutation in MC06g1112 encoding FLOWERING LOCUS T decreases the first flower node in bitter gourd ( Momordica charantia L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1153208. [PMID: 37881613 PMCID: PMC10595031 DOI: 10.3389/fpls.2023.1153208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 09/25/2023] [Indexed: 10/27/2023]
Abstract
In Cucurbitaceae crops, the first flower node (FFN) is an important agronomic trait which can impact the onset of maturity, the production of female flowers, and yield. However, the gene responsible for regulating FFN in bitter gourd is unknown. Here, we used a gynoecious line (S156G) with low FFN as the female parent and a monoecious line (K8-201) with high FFN as the male parent to obtain F1 and F2 generations. Genetic analysis indicated that the low FFN trait was incompletely dominant over the high FFN trait. A major quantitative trait locus (QTL)-Mcffn and four minor effect QTLs-Mcffn1.1, Mcffn1.2, Mcffn1.3, and Mcffn1.4 were detected by whole-genome re-sequencing-based QTL mapping in the S156G×K8-201 F2 population (n=234) cultivated in autumn 2019. The Mcffn locus was further supported by molecular marker-based QTL mapping in three S156G×K8-201 F2 populations planted in autumn 2019 (n=234), autumn 2020 (n=192), and spring 2022 (n=205). Then, the Mcffn locus was fine-mapped into a 77.98-kb physical region on pseudochromosome MC06 using a large S156G×K8-201 F2 population (n=2,402). MC06g1112, which is a homolog of FLOWERING LOCUS T (FT), was considered as the most likely Mcffn candidate gene according to both expression and sequence variation analyses between parental lines. A point mutation (C277T) in MC06g1112, which results in a P93S amino acid mutation between parental lines, may be responsible for decreasing FFN in bitter gourd. Our findings provide a helpful resource for the molecular marker-assisted selective breeding of bitter gourd.
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Affiliation(s)
- Jian Zhong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), College of Horticulture, South China Agricultural University, Guangzhou, China
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Junjie Cui
- Department of Horticulture, Foshan University, Foshan, China
| | - Mingjun Miao
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Fang Hu
- Henry Fok School of Biology and Agricultural, Shaoguan University, Shaoguan, China
| | - Jichi Dong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Jia Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Chunfeng Zhong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Jiaowen Cheng
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Kailin Hu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), College of Horticulture, South China Agricultural University, Guangzhou, China
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Wang Z, Peng C, Wu W, Yan C, Lv Y, Li JT. Developmental regulation of conserved non-coding element evolution provides insights into limb loss in squamates. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2399-2414. [PMID: 37256419 DOI: 10.1007/s11427-023-2362-5] [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: 04/14/2023] [Accepted: 05/09/2023] [Indexed: 06/01/2023]
Abstract
Limb loss shows recurrent phenotypic evolution across squamate lineages. Here, based on three de novo-assembled genomes of limbless lizards from different lineages, we showed that divergence of conserved non-coding elements (CNEs) played an important role in limb development. These CNEs were associated with genes required for limb initiation and outgrowth, and with regulatory signals in the early stage of limb development. Importantly, we identified the extensive existence of insertions and deletions (InDels) in the CNEs, with the numbers ranging from 111 to 756. Most of these CNEs with InDels were lineage-specific in the limbless squamates. Nearby genes of these InDel CNEs were important to early limb formation, such as Tbx4, Fgf10, and Gli3. Based on functional experiments, we found that nucleotide mutations and InDels both affected the regulatory function of the CNEs. Our study provides molecular evidence underlying limb loss in squamate reptiles from a developmental perspective and sheds light on the importance of regulatory element InDels in phenotypic evolution.
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Affiliation(s)
- Zeng Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & h Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Changjun Peng
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & h Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Wu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & h Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chaochao Yan
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & h Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yunyun Lv
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & h Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- College of Life Science, Neijiang Normal University, Neijiang, 641100, China
| | - Jia-Tang Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & h Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin Nay Pyi Taw, 05282, Myanmar.
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Selvakumar R, Jat GS, Manjunathagowda DC. Allele mining through TILLING and EcoTILLING approaches in vegetable crops. PLANTA 2023; 258:15. [PMID: 37311932 DOI: 10.1007/s00425-023-04176-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/01/2023] [Indexed: 06/15/2023]
Abstract
MAIN CONCLUSION The present review illustrates a comprehensive overview of the allele mining for genetic improvement in vegetable crops, and allele exploration methods and their utilization in various applications related to pre-breeding of economically important traits in vegetable crops. Vegetable crops have numerous wild descendants, ancestors and terrestrial races that could be exploited to develop high-yielding and climate-resilient varieties resistant/tolerant to biotic and abiotic stresses. To further boost the genetic potential of economic traits, the available genomic tools must be targeted and re-opened for exploitation of novel alleles from genetic stocks by the discovery of beneficial alleles from wild relatives and their introgression to cultivated types. This capability would be useful for giving plant breeders direct access to critical alleles that confer higher production, improve bioactive compounds, increase water and nutrient productivity as well as biotic and abiotic stress resilience. Allele mining is a new sophisticated technique for dissecting naturally occurring allelic variants in candidate genes that influence important traits which could be used for genetic improvement of vegetable crops. Target-induced local lesions in genomes (TILLINGs) is a sensitive mutation detection avenue in functional genomics, particularly wherein genome sequence information is limited or not available. Population exposure to chemical mutagens and the absence of selectivity lead to TILLING and EcoTILLING. EcoTILLING may lead to natural induction of SNPs and InDels. It is anticipated that as TILLING is used for vegetable crops improvement in the near future, indirect benefits will become apparent. Therefore, in this review we have highlighted the up-to-date information on allele mining for genetic enhancement in vegetable crops and methods of allele exploration and their use in pre-breeding for improvement of economic traits.
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Affiliation(s)
- Raman Selvakumar
- ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110 012, India
| | - Gograj Singh Jat
- ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110 012, India.
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11
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Zhan J, Zhong J, Cheng J, Wang Y, Hu K. Map-based cloning of the APRR2 gene controlling green stigma in bitter gourd ( Momordica charantia). FRONTIERS IN PLANT SCIENCE 2023; 14:1128926. [PMID: 37235005 PMCID: PMC10208069 DOI: 10.3389/fpls.2023.1128926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/20/2023] [Indexed: 05/28/2023]
Abstract
Bitter gourd is an economically important vegetable and medicinal crop distinguished by its bitter fruits. Its stigma color is widely used to assess the distinctiveness, uniformity, and stability of bitter gourd varieties. However, limited researches have been dedicated to genetic basis of its stigma color. In this study, we employed bulked segregant analysis (BSA) sequencing to identify a single dominant locus McSTC1 located on pseudochromosome 6 through genetic mapping of an F2 population (n =241) derived from the cross between green and yellow stigma parental lines. An F2-derived F3 segregation population (n = 847) was further adopted for fine mapping, which delimited the McSTC1 locus to a 13.87 kb region containing one predicted gene McAPRR2 (Mc06g1638), a homolog of the Arabidopsis two-component response regulator-like gene AtAPRR2. Sequence alignment analysis of McAPRR2 revealed that a 15 bp insertion at exon 9 results in a truncated GLK domain of its encoded protein, which existed in 19 bitter gourd varieties with yellow stigma. A genome-wide synteny search of the bitter gourd McAPRR2 genes in Cucurbitaceae family revealed its close relationship with other cucurbits APRR2 genes that are corresponding to white or light green fruit skin. Our findings provide insights into the molecular marker-assisted breeding of bitter gourd stigma color and the mechanism of gene regulation for stigma color.
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Affiliation(s)
- Jinyi Zhan
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jian Zhong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Jiaowen Cheng
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Yuhui Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Kailin Hu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
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12
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Niu Y, Zhang T, Chen M, Chen G, Liu Z, Yu R, Han X, Chen K, Huang A, Chen C, Yang Y. Analysis of the Complete Mitochondrial Genome of the Bitter Gourd ( Momordica charantia). PLANTS (BASEL, SWITZERLAND) 2023; 12:1686. [PMID: 37111909 PMCID: PMC10143269 DOI: 10.3390/plants12081686] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/16/2023] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
Bitter gourd (Momordica charantia L.) is a significant vegetable. Although it has a special bitter taste, it is still popular with the public. The industrialization of bitter gourd could be hampered by a lack of genetic resources. The bitter gourd's mitochondrial and chloroplast genomes have not been extensively studied. In the present study, the mitochondrial genome of bitter gourd was sequenced and assembled, and its substructure was investigated. The mitochondrial genome of bitter gourd is 331,440 bp with 24 unique core genes, 16 variable genes, 3 rRNAs, and 23 tRNAs. We identified 134 SSRs and 15 tandem repeats in the entire mitochondrial genome of bitter gourd. Moreover, 402 pairs of repeats with a length greater than or equal to 30 were observed in total. The longest palindromic repeat was 523 bp, and the longest forward repeat was 342 bp. We found 20 homologous DNA fragments in bitter gourd, and the summary insert length was 19,427 bp, accounting for 5.86% of the mitochondrial genome. We predicted a total of 447 potential RNA editing sites in 39 unique PCGs and also discovered that the ccmFN gene has been edited the most often, at 38 times. This study provides a basis for a better understanding and analysis of differences in the evolution and inheritance patterns of cucurbit mitochondrial genomes.
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Affiliation(s)
- Yu Niu
- Tropical Crops Genetic Resources Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Ting Zhang
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Muxi Chen
- Guangdong Helinong Biological Seeds Co., Ltd., Shantou 515800, China
- Guangdong Helinong Agricultural Research Institute Co., Ltd., Shantou 515800, China
| | - Guoju Chen
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Zhaohua Liu
- Tropical Crops Genetic Resources Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Renbo Yu
- Tropical Crops Genetic Resources Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Xu Han
- Tropical Crops Genetic Resources Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Kunhao Chen
- Guangdong Helinong Biological Seeds Co., Ltd., Shantou 515800, China
- Guangdong Helinong Agricultural Research Institute Co., Ltd., Shantou 515800, China
| | - Aizheng Huang
- Institute of Agricultural Science Research of Jiangmen, Jiangmen 529060, China
| | - Changming Chen
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Yan Yang
- Tropical Crops Genetic Resources Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
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Mangal V, Lal MK, Tiwari RK, Altaf MA, Sood S, Gahlaut V, Bhatt A, Thakur AK, Kumar R, Bhardwaj V, Kumar V, Singh B, Singh R, Kumar D. A comprehensive and conceptual overview of omics-based approaches for enhancing the resilience of vegetable crops against abiotic stresses. PLANTA 2023; 257:80. [PMID: 36913037 DOI: 10.1007/s00425-023-04111-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
Abiotic stresses adversely affect the productivity and production of vegetable crops. The increasing number of crop genomes that have been sequenced or re-sequenced provides a set of computationally anticipated abiotic stress-related responsive genes on which further research may be focused. Knowledge of omics approaches and other advanced molecular tools have all been employed to understand the complex biology of these abiotic stresses. A vegetable can be defined as any component of a plant that is eaten for food. These plant parts may be celery stems, spinach leaves, radish roots, potato tubers, garlic bulbs, immature cauliflower flowers, cucumber fruits, and pea seeds. Abiotic stresses, such as deficient or excessive water, high temperature, cold, salinity, oxidative, heavy metals, and osmotic stress, are responsible for the adverse activity in plants and, ultimately major concern for decreasing yield in many vegetable crops. At the morphological level, altered leaf, shoot and root growth, altered life cycle duration and fewer or smaller organs can be observed. Likewise different physiological and biochemical/molecular processes are also affected in response to these abiotic stresses. In order to adapt and survive in a variety of stressful situations, plants have evolved physiological, biochemical, and molecular response mechanisms. A comprehensive understanding of the vegetable's response to different abiotic stresses and the identification of tolerant genotypes are essential to strengthening each vegetable's breeding program. The advances in genomics and next-generation sequencing have enabled the sequencing of many plant genomes over the last twenty years. A combination of modern genomics (MAS, GWAS, genomic selection, transgenic breeding, and gene editing), transcriptomics, and proteomics along with next-generation sequencing provides an array of new powerful approaches to the study of vegetable crops. This review examines the overall impact of major abiotic stresses on vegetables, adaptive mechanisms and functional genomic, transcriptomic, and proteomic processes used by researchers to minimize these challenges. The current status of genomics technologies for developing adaptable vegetable cultivars that will perform better in future climates is also examined.
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Affiliation(s)
- Vikas Mangal
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India.
| | - Milan Kumar Lal
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India.
| | - Rahul Kumar Tiwari
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India.
| | | | - Salej Sood
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Vijay Gahlaut
- CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- Department of Biotechnology and University Center for Research and Development, Chandigarh University, Mohali, Punjab, India
| | | | - Ajay Kumar Thakur
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Ravinder Kumar
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Vinay Bhardwaj
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Vinod Kumar
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Brajesh Singh
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Rajender Singh
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Devendra Kumar
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
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14
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Tang CY, Zhang X, Xu X, Sun S, Peng C, Song MH, Yan C, Sun H, Liu M, Xie L, Luo SJ, Li JT. Genetic mapping and molecular mechanism behind color variation in the Asian vine snake. Genome Biol 2023; 24:46. [PMID: 36895044 PMCID: PMC9999515 DOI: 10.1186/s13059-023-02887-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 02/27/2023] [Indexed: 03/11/2023] Open
Abstract
BACKGROUND Reptiles exhibit a wide variety of skin colors, which serve essential roles in survival and reproduction. However, the molecular basis of these conspicuous colors remains unresolved. RESULTS We investigate color morph-enriched Asian vine snakes (Ahaetulla prasina), to explore the mechanism underpinning color variations. Transmission electron microscopy imaging and metabolomics analysis indicates that chromatophore morphology (mainly iridophores) is the main basis for differences in skin color. Additionally, we assemble a 1.77-Gb high-quality chromosome-anchored genome of the snake. Genome-wide association study and RNA sequencing reveal a conservative amino acid substitution (p.P20S) in SMARCE1, which may be involved in the regulation of chromatophore development initiated from neural crest cells. SMARCE1 knockdown in zebrafish and immunofluorescence verify the interactions among SMARCE1, iridophores, and tfec, which may determine color variations in the Asian vine snake. CONCLUSIONS This study reveals the genetic associations of color variation in Asian vine snakes, providing insights and important resources for a deeper understanding of the molecular and genetic mechanisms related to reptilian coloration.
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Affiliation(s)
- Chen-Yang Tang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiaohu Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- Sichuan University-The Chinese University of Hong Kong Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiao Xu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Shijie Sun
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- Sichuan University-The Chinese University of Hong Kong Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Changjun Peng
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meng-Huan Song
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chaochao Yan
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Huaqin Sun
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- Sichuan University-The Chinese University of Hong Kong Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Mingfeng Liu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- Sichuan University-The Chinese University of Hong Kong Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Liang Xie
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Shu-Jin Luo
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Jia-Tang Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin Nay Pyi Taw, 05282, Myanmar.
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15
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N. D. V, Matsumura H, Munshi AD, Ellur RK, Chinnusamy V, Singh A, Iquebal MA, Jaiswal S, Jat GS, Panigrahi I, Gaikwad AB, Rao AR, Dey SS, Behera TK. Molecular mapping of genomic regions and identification of possible candidate genes associated with gynoecious sex expression in bitter gourd. FRONTIERS IN PLANT SCIENCE 2023; 14:1071648. [PMID: 36938036 PMCID: PMC10017754 DOI: 10.3389/fpls.2023.1071648] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Bitter gourd is an important vegetable crop grown throughout the tropics mainly because of its high nutritional value. Sex expression and identification of gynoecious trait in cucurbitaceous vegetable crops has facilitated the hybrid breeding programme in a great way to improve productivity. In bitter gourd, gynoecious sex expression is poorly reported and detailed molecular pathways involve yet to be studied. The present experiment was conducted to study the inheritance, identify the genomic regions associated with gynoecious sex expression and to reveal possible candidate genes through QTL-seq. Segregation for the gynoecious and monoecious sex forms in the F2 progenies indicated single recessive gene controlling gynoecious sex expression in the genotype, PVGy-201. Gynoecious parent, PVGy-201, Monoecious parent, Pusa Do Mausami (PDM), and two contrasting bulks were constituted for deep-sequencing. A total of 10.56, 23.11, 15.07, and 19.38 Gb of clean reads from PVGy-201, PDM, gynoecious bulk and monoecious bulks were generated. Based on the ΔSNP index, 1.31 Mb regions on the chromosome 1 was identified to be associated with gynoecious sex expression in bitter gourd. In the QTL region 293,467 PVGy-201 unique variants, including SNPs and indels, were identified. In the identified QTL region, a total of 1019 homozygous variants were identified between PVGy1 and PDM genomes and 71 among them were non-synonymous variants (SNPS and INDELs), out of which 11 variants (7 INDELs, 4 SNPs) were classified as high impact variants with frame shift/stop gain effect. In total twelve genes associated with male and female gametophyte development were identified in the QTL-region. Ethylene-responsive transcription factor 12, Auxin response factor 6, Copper-transporting ATPase RAN1, CBL-interacting serine/threonine-protein kinase 23, ABC transporter C family member 2, DEAD-box ATP-dependent RNA helicase 1 isoform X2, Polygalacturonase QRT3-like isoform X2, Protein CHROMATIN REMODELING 4 were identified with possible role in gynoecious sex expression. Promoter region variation in 8 among the 12 genes indicated their role in determining gynoecious sex expression in bitter gourd genotype, DBGy-1. The findings in the study provides insight about sex expression in bitter gourd and will facilitate fine mapping and more precise identification of candidate genes through their functional validation.
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Affiliation(s)
- Vinay N. D.
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Hideo Matsumura
- Gene Research Centre, Shinshu University, Ueda, Nagano, Japan
| | - Anilabha Das Munshi
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ranjith Kumar Ellur
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ankita Singh
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Gograj Singh Jat
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ipsita Panigrahi
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ambika Baladev Gaikwad
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - A. R. Rao
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Shyam Sundar Dey
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Tusar Kanti Behera
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
- ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
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16
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She CW, Jiang XH, He CP. Comparative karyotype analysis of eight Cucurbitaceae crops using fluorochrome banding and 45S rDNA-FISH. COMPARATIVE CYTOGENETICS 2023; 17:31-58. [PMID: 37305810 PMCID: PMC10252140 DOI: 10.3897/compcytogen.v17.i1.99236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 01/23/2023] [Indexed: 06/13/2023]
Abstract
To have an insight into the karyotype variation of eight Cucurbitaceae crops including Cucumissativus Linnaeus, 1753, Cucumismelo Linnaeus, 1753, Citrulluslanatus (Thunberg, 1794) Matsumura et Nakai, 1916, Benincasahispida (Thunberg, 1784) Cogniaux, 1881, Momordicacharantia Linnaeus, 1753, Luffacylindrica (Linnaeus, 1753) Roemer, 1846, Lagenariasicerariavar.hispida (Thunberg, 1783) Hara, 1948 and Cucurbitamoschata Duchesne ex Poiret, 1819, well morphologically differentiated mitotic metaphase chromosomes were prepared using the enzymatic maceration and flame-drying method, and the chromosomal distribution of heterochromatin and 18S-5.8S-26S rRNA genes (45S rDNA) was investigated using sequential combined PI and DAPI (CPD) staining and fluorescence in situ hybridization (FISH) with 45S rDNA probe. Detailed karyotypes were established using the dataset of chromosome measurements, fluorochrome bands and rDNA FISH signals. Four karyotype asymmetry indices, CVCI, CVCL, MCA and Stebbins' category, were measured to elucidate the karyological relationships among species. All the species studied had symmetrical karyotypes composed of metacentric and submetacentric or only metacentric chromosomes, but their karyotype structure can be discriminated by the scatter plot of MCA vs. CVCL. The karyological relationships among these species revealed by PCoA based on x, 2n, TCL, MCA, CVCL and CVCI was basically in agreement with the phylogenetic relationships revealed by DNA sequences. CPD staining revealed all 45S rDNA sites in all species, (peri)centromeric GC-rich heterochromatin in C.sativus, C.melo, C.lanatus, M.charantia and L.cylindrica, terminal GC-rich heterochromatin in C.sativus. DAPI counterstaining after FISH revealed pericentromeric DAPI+ heterochromatin in C.moschata. rDNA FISH detected two 45S loci in five species and five 45S loci in three species. Among these 45S loci, most were located at the terminals of chromosome arms, and a few in the proximal regions. In C.sativus, individual chromosomes can be precisely distinguished by the CPD band and 45S rDNA signal patterns, providing an easy method for chromosome identification of cucumber. The genome differentiation among these species was discussed in terms of genome size, heterochromatin, 45S rDNA site, and karyotype asymmetry based on the data of this study and previous reports.
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Affiliation(s)
- Chao-Wen She
- Key Laboratory of Research and Utilization of
Ethnomedicinal Plant Resources of Hunan Province, Huaihua University, Huaihua, Hunan,
418008, ChinaHuaihua UniversityHuaihuaChina
- College of Life Sciences and Chemistry, Hunan University
of Technology, Zhuzhou, Hunan, 412007, ChinaHunan University of TechnologyZhuzhouChina
| | - Xiang-Hui Jiang
- Key Laboratory of Research and Utilization of
Ethnomedicinal Plant Resources of Hunan Province, Huaihua University, Huaihua, Hunan,
418008, ChinaHuaihua UniversityHuaihuaChina
| | - Chun-Ping He
- College of Life Sciences and Chemistry, Hunan University
of Technology, Zhuzhou, Hunan, 412007, ChinaHunan University of TechnologyZhuzhouChina
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17
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Baluchamy N, Thayyil P, Mathew D, Minimol JS, Koorathodi V. Candidate gene based SSR and SNP markers for gynoecy in bitter gourd (Momordica charantia L.). Mol Biol Rep 2023; 50:1125-1132. [PMID: 36401706 DOI: 10.1007/s11033-022-08098-2] [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: 02/02/2022] [Accepted: 11/08/2022] [Indexed: 11/20/2022]
Abstract
BACKGROUND Even though the bitter gourd hybrids are shown to have significant heterosis for many of the economic traits, processes such as manual bagging and hand pollination make the hybrid seed production labour-intensive. Use of gynoecious line as female parent makes hybrid seed production more economical. This work was performed with the objective to identify the candidate gene based molecular markers for gynoecy in bitter gourd. METHODS AND RESULTS Seven putative genes for flowering and sex expression, isolated from the monoecious (MC-136) and gynoecious (KAU-MCGy-101) bitter gourd accessions, were sequence characterized. MADS-box transcription factor genes AG6 and McAG2 had nucleotide polymorphisms at five sites each and were potential candidates for marker development. An In/Del polymorphism of 48 bp ([TC]24) in AG6 gene was used to develop an SSR marker and a transition mutation of [A/G] in this gene was used to develop a set of SNP markers. These markers have developed distinct polymorphism between the monoecious and gynoecious genotypes and were found suited for the marker assisted selection. CONCLUSIONS MADS box transcription factor genes AG6 and McAG2 are identified as candidates for sex expression in bitter gourd. Based on the InDels and transition in the intronic region of AG6, SSR marker BGAG6 and an SNP marker set segregating with the sex forms were developed. The markers have been validated using four other monoecious lines and are routinely used in our bitter gourd hybrid seed production programmes.
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Affiliation(s)
- Nivethitha Baluchamy
- Centre for Plant Biotechnology and Molecular Biology, Kerala Agricultural University, Thrissur, 680 656, India
| | - Pradeepkumar Thayyil
- Department of Vegetable Science, College of Agriculture, Kerala Agricultural University, Thrissur, 680 656, India
| | - Deepu Mathew
- Centre for Plant Biotechnology and Molecular Biology, Kerala Agricultural University, Thrissur, 680 656, India.
| | | | - Veni Koorathodi
- Department of Vegetable Science, College of Agriculture, Kerala Agricultural University, Thrissur, 680 656, India
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18
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Fu A, Zheng Y, Guo J, Grierson D, Zhao X, Wen C, Liu Y, Li J, Zhang X, Yu Y, Ma H, Wang Q, Zuo J. Telomere-to-telomere genome assembly of bitter melon ( Momordica charantia L. var. abbreviata Ser.) reveals fruit development, composition and ripening genetic characteristics. HORTICULTURE RESEARCH 2023; 10:uhac228. [PMID: 36643758 PMCID: PMC9832870 DOI: 10.1093/hr/uhac228] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/26/2022] [Indexed: 05/19/2023]
Abstract
Momordica charantia L. var. abbreviata Ser. (Mca), known as bitter gourd or bitter melon, is a Momordica variety with medicinal value and belongs to the Cucurbitaceae family. In view of the lack of genomic information on bitter gourd and other Momordica species and to promote Mca genomic research, we assembled a 295.6-Mb telomere-to-telomere (T2T) high-quality Mca genome with six gap-free chromosomes after Hi-C correction. This genome is anchored to 11 chromosomes, which is consistent with the karyotype information, and comprises 98 contigs (N50 of 25.4 Mb) and 95 scaffolds (N50 of 25.4 Mb). The Mca genome harbors 19 895 protein-coding genes, of which 45.59% constitute predicted repeat sequences. Synteny analysis revealed variations involved in fruit quality during the divergence of bitter gourd. In addition, assay for transposase-accessible chromatin by high-throughput sequencing and metabolic analysis showed that momordicosides and other substances are characteristic of Mca fruit pulp. A combined transcriptomic and metabolomic analysis revealed the mechanisms of pigment accumulation and cucurbitacin biosynthesis in Mca fruit peels, providing fundamental molecular information for further research on Mca fruit ripening. This report provides a new genetic resource for Momordica genomic studies and contributes additional insights into Cucurbitaceae phylogeny.
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Affiliation(s)
| | | | - Jing Guo
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Donald Grierson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
| | - Xiaoyan Zhao
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agricultural and Forestry Sciences, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Vegetable Postharvest Processing of Ministry of Agriculture and Rural Areas, Beijing 100097, China
| | - Changlong Wen
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agricultural and Forestry Sciences, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Vegetable Postharvest Processing of Ministry of Agriculture and Rural Areas, Beijing 100097, China
| | - Ye Liu
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Advanced Innovation Center for Food Nutrition and Human Health, School of Food and Health, Beijing Technology and Business University (BTBU), Beijing, 100048, China
| | - Jian Li
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Advanced Innovation Center for Food Nutrition and Human Health, School of Food and Health, Beijing Technology and Business University (BTBU), Beijing, 100048, China
| | - Xuewen Zhang
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Ying Yu
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Hong Ma
- Corresponding authors: Jinhua Zuo, +861051503058; Qing Wang, ; Hong Ma,
| | - Qing Wang
- Corresponding authors: Jinhua Zuo, +861051503058; Qing Wang, ; Hong Ma,
| | - Jinhua Zuo
- Corresponding authors: Jinhua Zuo, +861051503058; Qing Wang, ; Hong Ma,
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19
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Li X, He SG, Li WR, Luo LY, Yan Z, Mo DX, Wan X, Lv FH, Yang J, Xu YX, Deng J, Zhu QH, Xie XL, Xu SS, Liu CX, Peng XR, Han B, Li ZH, Chen L, Han JL, Ding XZ, Dingkao R, Chu YF, Wu JY, Wang LM, Zhou P, Liu MJ, Li MH. Genomic analyses of wild argali, domestic sheep, and their hybrids provide insights into chromosome evolution, phenotypic variation, and germplasm innovation. Genome Res 2022; 32:1669-1684. [PMID: 35948368 PMCID: PMC9528982 DOI: 10.1101/gr.276769.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/29/2022] [Indexed: 11/24/2022]
Abstract
Understanding the genetic mechanisms of phenotypic variation in hybrids between domestic animals and their wild relatives may aid germplasm innovation. Here, we report the high-quality genome assemblies of a male Pamir argali (O ammon polii, 2n = 56), a female Tibetan sheep (O aries, 2n = 54), and a male hybrid of Pamir argali and domestic sheep, and the high-throughput sequencing of 425 ovine animals, including the hybrids of argali and domestic sheep. We detected genomic synteny between Chromosome 2 of sheep and two acrocentric chromosomes of argali. We revealed consistent satellite repeats around the chromosome breakpoints, which could have resulted in chromosome fusion. We observed many more hybrids with karyotype 2n = 54 than with 2n = 55, which could be explained by the selfish centromeres, the possible decreased rate of normal/balanced sperm, and the increased incidence of early pregnancy loss in the aneuploid ewes or rams. We identified genes and variants associated with important morphological and production traits (e.g., body weight, cannon circumference, hip height, and tail length) that show significant variations. We revealed a strong selective signature at the mutation (c.334C > A, p.G112W) in TBXT and confirmed its association with tail length among sheep populations of wide geographic and genetic origins. We produced an intercross population of 110 F2 offspring with varied number of vertebrae and validated the causal mutation by whole-genome association analysis. We verified its function using CRISPR-Cas9 genome editing. Our results provide insights into chromosomal speciation and phenotypic evolution and a foundation of genetic variants for the breeding of sheep and other animals.
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Affiliation(s)
- Xin Li
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - San-Gang He
- MOA Key Laboratory of Ruminant Genetics, Breeding and Reproduction, Ministry of Agriculture (MOA); Key Laboratory of Animal Technology of Xinjiang, Xinjiang Academy of Animal Science, Urumqi, 830000, China
| | - Wen-Rong Li
- MOA Key Laboratory of Ruminant Genetics, Breeding and Reproduction, Ministry of Agriculture (MOA); Key Laboratory of Animal Technology of Xinjiang, Xinjiang Academy of Animal Science, Urumqi, 830000, China
| | - Ling-Yun Luo
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Ze Yan
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Dong-Xin Mo
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xing Wan
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Feng-Hua Lv
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Ji Yang
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Ya-Xi Xu
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Juan Deng
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiang-Hui Zhu
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Song-Song Xu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Chen-Xi Liu
- MOA Key Laboratory of Ruminant Genetics, Breeding and Reproduction, Ministry of Agriculture (MOA); Key Laboratory of Animal Technology of Xinjiang, Xinjiang Academy of Animal Science, Urumqi, 830000, China
| | - Xin-Rong Peng
- MOA Key Laboratory of Ruminant Genetics, Breeding and Reproduction, Ministry of Agriculture (MOA); Key Laboratory of Animal Technology of Xinjiang, Xinjiang Academy of Animal Science, Urumqi, 830000, China
| | - Bin Han
- MOA Key Laboratory of Ruminant Genetics, Breeding and Reproduction, Ministry of Agriculture (MOA); Key Laboratory of Animal Technology of Xinjiang, Xinjiang Academy of Animal Science, Urumqi, 830000, China
| | - Zhong-Hui Li
- MOA Key Laboratory of Ruminant Genetics, Breeding and Reproduction, Ministry of Agriculture (MOA); Key Laboratory of Animal Technology of Xinjiang, Xinjiang Academy of Animal Science, Urumqi, 830000, China
| | - Lei Chen
- MOA Key Laboratory of Ruminant Genetics, Breeding and Reproduction, Ministry of Agriculture (MOA); Key Laboratory of Animal Technology of Xinjiang, Xinjiang Academy of Animal Science, Urumqi, 830000, China
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, 00100, Kenya
| | - Xue-Zhi Ding
- MOA Key Laboratory of Veterinary Pharmaceutical Development of Ministry of Agriculture (MOA), Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Renqing Dingkao
- Institute of Animal Science and Veterinary Medicine, Gannan Tibetan Autonomous Prefecture, Hezuo, 747000, China
| | - Yue-Feng Chu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Jin-Yan Wu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Li-Min Wang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Ping Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Ming-Jun Liu
- MOA Key Laboratory of Ruminant Genetics, Breeding and Reproduction, Ministry of Agriculture (MOA); Key Laboratory of Animal Technology of Xinjiang, Xinjiang Academy of Animal Science, Urumqi, 830000, China
| | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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20
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Epidermal Patterning Factor 2-like (McEPFL2): A Putative Candidate for the Continuous Ridge (cr) Fruit Skin Locus in Bitter Gourd (Momordica charantia L.). Genes (Basel) 2022; 13:genes13071148. [PMID: 35885929 PMCID: PMC9316824 DOI: 10.3390/genes13071148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/17/2022] [Accepted: 06/22/2022] [Indexed: 02/04/2023] Open
Abstract
Bitter gourd (Momordica charantia L.) is an economically important vegetable and medicinal crop in many Asian countries. Limited work has been conducted in understanding the genetic basis of horticulturally important traits in bitter gourd. Bitter gourd is consumed primarily for its young, immature fruit, and fruit appearance plays an important role in market acceptability. One such trait is the ridges on the fruit skin. In the present study, molecular mapping of a locus underlying fruit ridge continuity was conducted. Genetic analysis in segregating populations, derived from the crosses between two inbred lines Y1 with continuous ridges (CR) and Z-1-4 with discontinuous ridges (DCR), suggested that CR was controlled by a single recessive gene (cr). High-throughput genome sequencing of CR and DCR bulks combined with high-resolution genetic mapping in an F2 population delimited cr into a 108 kb region with 16 predicted genes. Sequence variation analysis and expression profiling supported the epidermal patterning factor 2-like (McEPFL2) gene as the best candidate of the cr locus. A 1 bp deletion in the first exon of McEPFL2 in Y1 which would result in a truncated McEPFL2 protein may be the causal polymorphism for the phenotypic difference between Y1 and Z-1-4. The association of this 1 bp deletion with CR was further supported by gDNA sequencing of McEPFL2 among 31 bitter gourd accessions. This work provides a foundation for understanding the genetic and molecular control of fruit epidermal pattering and development, which also facilitates marker-assisted selection in bitter melon breeding.
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21
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Zhong J, Cheng J, Cui J, Hu F, Dong J, Liu J, Zou Y, Hu K. MC03g0810, an Important Candidate Gene Controlling Black Seed Coat Color in Bitter Gourd ( Momordica spp.). FRONTIERS IN PLANT SCIENCE 2022; 13:875631. [PMID: 35574132 PMCID: PMC9094142 DOI: 10.3389/fpls.2022.875631] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/25/2022] [Indexed: 06/01/2023]
Abstract
Seed coat color is one of the most intuitive phenotypes in bitter gourd (Momordica spp.). Although the inheritance of the seed coat color has been reported, the gene responsible for it is still unknown. This study used two sets of parents, representing, respectively, the intersubspecific and intraspecific materials of bitter gourd, and their respective F1 and F2 progenies for genetic analysis and primary mapping of the seed coat color. A large F2:3 population comprising 2,975 seedlings from intraspecific hybridization was used to fine-map the seed coat color gene. The results inferred that a single gene, named McSC1, controlled the seed coat color and that the black color was dominant over the yellow color. The McSC1 locus was mapped to a region with a physical length of ∼7.8 Mb and 42.7 kb on pseudochromosome 3 via bulked segregant analysis with whole-genome resequencing (BSA-seq) and linkage analysis, respectively. Subsequently, the McSC1 locus was further fine-mapped to a 13.2-kb region containing only one candidate gene, MC03g0810, encoding a polyphenol oxidase (PPO). Additionally, the variations of MC03g0810 in the 89 bitter gourd germplasms showed a complete correlation with the seed coat color. Expression and PPO activity analyses showed a positive correlation between the expression level of MC03g0810 and its product PPO and the seed coat color. Therefore, MC03g0810 was proposed as the causal gene of McSC1. Our results provide an important reference for molecular marker-assisted breeding based on the seed coat color and uncover molecular mechanisms of the seed coat color formation in bitter gourd.
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Affiliation(s)
- Jian Zhong
- College of Horticulture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, Guangzhou, China
- Guangdong Vegetables Engineering Research Center, Guangzhou, China
| | - Jiaowen Cheng
- College of Horticulture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, Guangzhou, China
- Guangdong Vegetables Engineering Research Center, Guangzhou, China
| | - Junjie Cui
- Department of Horticulture, Foshan University, Foshan, China
| | - Fang Hu
- Henry Fok School of Biology and Agricultural, Shaoguan University, Shaoguan, China
| | - Jichi Dong
- College of Horticulture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, Guangzhou, China
- Guangdong Vegetables Engineering Research Center, Guangzhou, China
| | - Jia Liu
- College of Horticulture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, Guangzhou, China
- Guangdong Vegetables Engineering Research Center, Guangzhou, China
| | - Yichao Zou
- College of Horticulture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, Guangzhou, China
- Guangdong Vegetables Engineering Research Center, Guangzhou, China
| | - Kailin Hu
- College of Horticulture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, Guangzhou, China
- Guangdong Vegetables Engineering Research Center, Guangzhou, China
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22
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Zhao G, Wang M, Gan Y, Gong H, Li J, Zheng X, Liu X, Zhao S, Luo J, Wu H. Identification of suitable reference genes for quantitative reverse transcription PCR in Luffa ( Luffa cylindrica). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:737-747. [PMID: 35592479 PMCID: PMC9110621 DOI: 10.1007/s12298-022-01182-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 04/20/2022] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
UNLABELLED Reverse transcription real-time quantitative PCR is widely used to quantify gene expression. Reference genes are usually used as internal controls to measure the target gene expression level. To date, there is no consensus on the use of systematically validated reference genes in different tissues of Luffa. This study evaluated the expression stability of 11 candidate reference genes in different tissues using five algorithms (BestKeeper, comparative delta-Ct method, GeNorm, NormFinder, and RefFinder). Protein phosphatase 2A was the most stable gene, while alpha Tubulin was the least stable. The relative expression of ethylene-related genes in different tissues was also analyzed to reveal their role in sex determination. This study provides the basis for using suitable reference genes to evaluate targeted gene expression. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-022-01182-8.
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Affiliation(s)
- Gangjun Zhao
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640 China
| | - Meng Wang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640 China
| | - Yaqin Gan
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640 China
| | - Hao Gong
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Junxing Li
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Xiaoming Zheng
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Xiaoxi Liu
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Siying Zhao
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640 China
| | - Jianning Luo
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Haibin Wu
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642 China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640 China
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23
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Ma L, Wang Q, Zheng Y, Guo J, Yuan S, Fu A, Bai C, Zhao X, Zheng S, Wen C, Guo S, Gao L, Grierson D, Zuo J, Xu Y. Cucurbitaceae genome evolution, gene function and molecular breeding. HORTICULTURE RESEARCH 2022; 9:uhab057. [PMID: 35043161 PMCID: PMC8969062 DOI: 10.1093/hr/uhab057] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/28/2021] [Indexed: 05/07/2023]
Abstract
The Cucurbitaceae is one of the most genetically diverse plant families in the world. Many of them are important vegetables or medicinal plants and are widely distributed worldwide. The rapid development of sequencing technologies and bioinformatic algorithms has enabled the generation of genome sequences of numerous important Cucurbitaceae species. This has greatly facilitated research on gene identification, genome evolution, genetic variation and molecular breeding of cucurbit crops. So far, genome sequences of 18 different cucurbit species belonging to tribes Benincaseae, Cucurbiteae, Sicyoeae, Momordiceae and Siraitieae have been deciphered. This review summarizes the genome sequence information, evolutionary relationship, and functional genes associated with important agronomic traits (e.g., fruit quality). The progress of molecular breeding in cucurbit crops and prospects for future applications of Cucurbitaceae genome information are also discussed.
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Affiliation(s)
- Lili Ma
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Qing Wang
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yanyan Zheng
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Jing Guo
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Shuzhi Yuan
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Anzhen Fu
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Chunmei Bai
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xiaoyan Zhao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Shufang Zheng
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Changlong Wen
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Shaogui Guo
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Lipu Gao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Donald Grierson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
| | - Jinhua Zuo
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yong Xu
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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24
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Ren B, Ru D, Chen L, Duan N, Li Y, Shi J, Cao J, Liu B. Genome Sequence of Elaeagnus mollis, the First Chromosome-Level Genome of the Family Elaeagnaceae. Genome Biol Evol 2021; 13:evab266. [PMID: 34864990 PMCID: PMC8691057 DOI: 10.1093/gbe/evab266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2021] [Indexed: 11/25/2022] Open
Abstract
Elaeagnus mollis Diels (Elaeagnaceae) is a species of shrubs and/or dwarf trees that produces highly nutritious nuts with abundant oil and pharmaceutical properties. It is endemic to China but endangered. Therefore, to facilitate the protection of its genetic resources and the development of its commercially attractive traits we generated a high-quality genome of E. mollis. The contig version of the genome (630.96 Mb long) was assembled into 14 chromosomes using Hi-C data, with contig and scaffold N50 values of 18.40 and 38.86 Mb, respectively. Further analyses identified 397.49 Mb (63.0%) of repetitive sequences and 27,130 protein-coding genes, of which 26,725 (98.5%) were functionally annotated. Benchmarking Universal Single-Copy Ortholog assessment indicated that 98.0% of highly conserved plant genes are completely present in the genome. This is the first reference genome for any species of Elaeagnaceae and should greatly facilitate future efforts to conserve, utilize, and elucidate the evolution of this endangered endemic species.
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Affiliation(s)
| | - Dafu Ru
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, China
| | | | - Na Duan
- Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | - Yong Li
- Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | - Jianwei Shi
- Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | | | - Bingbing Liu
- Institute of Loess Plateau, Shanxi University, Taiyuan, China
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Ajinath LS, Mathew D. Genome-wide mining of potentially-hypervariable microsatellites and validation of markers in Momordica charantia L. Genetica 2021; 150:77-85. [PMID: 34822037 DOI: 10.1007/s10709-021-00142-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 11/18/2021] [Indexed: 11/26/2022]
Abstract
Relatively large number of bitter melon microsatellite markers have been reported; however, only few resulted in successful PCR amplification and a small fraction shown polymorphisms. This limited chance of recovering polymorphic markers makes the primer screening a cost-demanding process. To test the hypothesis that microsatellites with longer motifs as well as shorter motifs repeated substantially shall have better prospects to be polymorphic, we performed a genome-wide microsatellite mining. We selected a sample of genome-wide microsatellites with prescribed motif lengths or satisfying a target repeat number, which were considered potentially-hyper variable, for primer designing and validation. Seventy five microsatellites satisfying these criteria were identified, of which 69 were validated through successful PCR amplification. Among them, 40 (53.33% of the markers identified) were polymorphic. This result showed a significantly higher success compared to our initial results of 51 (20.64%) polymorphic markers out of the 188 amplified when 247 previously reported markers were screened. The screening of two cultivars revealed that markers were efficient to identify up to three alleles. The characterization of these 69 new markers with 247 markers previously reported showed that di-nucleotide motifs were most abundant, followed by tri- and tetra-nucleotide motifs. TC motif markers were most polymorphic (12.08%) followed by AG and CT motifs (both 9.89%). Similarly, AGA (6.59%) and TATT (3.29%) were most polymorphic among the tri- and tetra-nucleotide motifs. These 69 hypervariable microsatellite markers along with 188 markers initially validated in this study shall be useful for phylogenetic analyses, studies of linkage, QTL, and association mapping in bitter melon.
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Affiliation(s)
- Lavale Shivaji Ajinath
- Centre for Plant Biotechnology and Molecular Biology, Kerala Agricultural University, 680 656, Thrissur, Kerala, India
| | - Deepu Mathew
- Centre for Plant Biotechnology and Molecular Biology, Kerala Agricultural University, 680 656, Thrissur, Kerala, India.
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Zhou J, Wu P, Xiong Z, Liu N, Zhao N, Ji M, Qiu Y, Yang B. Chromosome-Level Genome Assembly Reveals Significant Gene Expansion in the Toll and IMD Signaling Pathways of Dendrolimus kikuchii. Front Genet 2021; 12:728418. [PMID: 34777464 PMCID: PMC8589036 DOI: 10.3389/fgene.2021.728418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/28/2021] [Indexed: 12/12/2022] Open
Abstract
A high-quality genome is of significant value when seeking to control forest pests such as Dendrolimus kikuchii, a destructive member of the order Lepidoptera that is widespread in China. Herein, a high quality, chromosome-level reference genome for D. kikuchii based on Nanopore, Pacbio HiFi sequencing and the Hi-C capture system is presented. Overall, a final genome assembly of 705.51 Mb with contig and scaffold N50 values of 20.89 and 24.73 Mb, respectively, was obtained. Of these contigs, 95.89% had unique locations on 29 chromosomes. In silico analysis revealed that the genome contained 15,323 protein-coding genes and 63.44% repetitive sequences. Phylogenetic analyses indicated that D. kikuchii may diverged from the common ancestor of Thaumetopoea. Pityocampa, Thaumetopoea ni, Heliothis virescens, Hyphantria armigera, Spodoptera frugiperda, and Spodoptera litura approximately 122.05 million years ago. Many gene families were expanded in the D. kikuchii genome, particularly those of the Toll and IMD signaling pathway, which included 10 genes in peptidoglycan recognition protein, 19 genes in MODSP, and 11 genes in Toll. The findings from this study will help to elucidate the mechanisms involved in protection of D. kikuchii against foreign substances and pathogens, and may highlight a potential channel to control this pest.
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Affiliation(s)
- Jielong Zhou
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Peifu Wu
- College of Life Science, Southwest Forestry University, Kunming, China
| | - Zhongping Xiong
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Naiyong Liu
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Ning Zhao
- College of Life Science, Southwest Forestry University, Kunming, China
| | - Mei Ji
- Yunnan Academy of Forestry and Grassland, Kunming, China
| | - Yu Qiu
- College of Life Science, Southwest Forestry University, Kunming, China
| | - Bin Yang
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
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Wang Y. A draft genome, resequencing, and metabolomes reveal the genetic background and molecular basis of the nutritional and medicinal properties of loquat (Eriobotrya japonica (Thunb.) Lindl). HORTICULTURE RESEARCH 2021; 8:231. [PMID: 34719689 PMCID: PMC8558328 DOI: 10.1038/s41438-021-00657-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 06/21/2021] [Accepted: 07/04/2021] [Indexed: 05/06/2023]
Abstract
Loquat (Eriobotrya japonica) is a popular fruit and medicinal plant. Here, a high-quality draft genome of the E. japonica 'Big Five-pointed Star' cultivar that covers ~98% (733.32 Mb) of the estimated genome size (749.25 Mb) and contains a total of 45,492 protein-coding genes is reported. Comparative genomic analysis suggests that the loquat genome has evolved a unique genetic mechanism of chromosome repair. Resequencing data from 52 loquat cultivars, including 16 white-fleshed and 36 yellow-fleshed variants, were analyzed, and the flower, leaf, and root metabolomes of 'Big Five-pointed Star' were determined using a UPLC-ESI-MS/M system. A genome-wide association study identified several candidate genes associated with flesh color in E. japonica, linking these phenotypes to sugar metabolism. A total of 577 metabolites, including 98 phenolic acids, 95 flavonoids, and 28 terpenoids, were found, and 191 metabolites, including 46 phenolic acids, 33 flavonoids, and 7 terpenoids, showed no differences in concentration among the leaves, roots, and flowers. Candidate genes related to the biosynthesis of various medicinal ingredients, such as phenolics, flavonoids, terpenoids, and polysaccharides, were identified. Some of these genes were confirmed to be members of expanding gene families, suggesting that the high concentrations of beneficial metabolites in loquat may be associated with the number of biosynthetic genes in this plant. In summary, this study provides fundamental molecular insights into the nutritional and medical properties of E. japonica.
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Affiliation(s)
- Yunsheng Wang
- School of Life and Health Science, Kaili University, Kaili City, Guizhou Province, 556011, China.
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Voshall A, Behera S, Li X, Yu XH, Kapil K, Deogun JS, Shanklin J, Cahoon EB, Moriyama EN. A consensus-based ensemble approach to improve transcriptome assembly. BMC Bioinformatics 2021; 22:513. [PMID: 34674629 PMCID: PMC8532302 DOI: 10.1186/s12859-021-04434-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 10/10/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Systems-level analyses, such as differential gene expression analysis, co-expression analysis, and metabolic pathway reconstruction, depend on the accuracy of the transcriptome. Multiple tools exist to perform transcriptome assembly from RNAseq data. However, assembling high quality transcriptomes is still not a trivial problem. This is especially the case for non-model organisms where adequate reference genomes are often not available. Different methods produce different transcriptome models and there is no easy way to determine which are more accurate. Furthermore, having alternative-splicing events exacerbates such difficult assembly problems. While benchmarking transcriptome assemblies is critical, this is also not trivial due to the general lack of true reference transcriptomes. RESULTS In this study, we first provide a pipeline to generate a set of the simulated benchmark transcriptome and corresponding RNAseq data. Using the simulated benchmarking datasets, we compared the performance of various transcriptome assembly approaches including both de novo and genome-guided methods. The results showed that the assembly performance deteriorates significantly when alternative transcripts (isoforms) exist or for genome-guided methods when the reference is not available from the same genome. To improve the transcriptome assembly performance, leveraging the overlapping predictions between different assemblies, we present a new consensus-based ensemble transcriptome assembly approach, ConSemble. CONCLUSIONS Without using a reference genome, ConSemble using four de novo assemblers achieved an accuracy up to twice as high as any de novo assemblers we compared. When a reference genome is available, ConSemble using four genome-guided assemblies removed many incorrectly assembled contigs with minimal impact on correctly assembled contigs, achieving higher precision and accuracy than individual genome-guided methods. Furthermore, ConSemble using de novo assemblers matched or exceeded the best performing genome-guided assemblers even when the transcriptomes included isoforms. We thus demonstrated that the ConSemble consensus strategy both for de novo and genome-guided assemblers can improve transcriptome assembly. The RNAseq simulation pipeline, the benchmark transcriptome datasets, and the script to perform the ConSemble assembly are all freely available from: http://bioinfolab.unl.edu/emlab/consemble/ .
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Affiliation(s)
- Adam Voshall
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.,Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.,Department of Pediatrics, Division of Genetics and Genomics, Boston Children's Hospital/Harvard Medical School, Boston, MA, 02115, USA
| | - Sairam Behera
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xiangjun Li
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.,Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Xiao-Hong Yu
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Kushagra Kapil
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Jitender S Deogun
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - John Shanklin
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Edgar B Cahoon
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.,Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Etsuko N Moriyama
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA. .,Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
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Wang J, Xu S, Mei Y, Cai S, Gu Y, Sun M, Liang Z, Xiao Y, Zhang M, Yang S. A high-quality genome assembly of Morinda officinalis, a famous native southern herb in the Lingnan region of southern China. HORTICULTURE RESEARCH 2021; 8:135. [PMID: 34059651 PMCID: PMC8166937 DOI: 10.1038/s41438-021-00551-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 02/23/2021] [Accepted: 03/22/2021] [Indexed: 05/03/2023]
Abstract
Morinda officinalis is a well-known medicinal and edible plant that is widely cultivated in the Lingnan region of southern China. Its dried roots (called bajitian in traditional Chinese medicine) are broadly used to treat various diseases, such as impotence and rheumatism. Here, we report a high-quality chromosome-scale genome assembly of M. officinalis using Nanopore single-molecule sequencing and Hi-C technology. The assembled genome size was 484.85 Mb with a scaffold N50 of 40.97 Mb, and 90.77% of the assembled sequences were anchored on eleven pseudochromosomes. The genome includes 27,698 protein-coding genes, and most of the assemblies are repetitive sequences. Genome evolution analysis revealed that M. officinalis underwent core eudicot γ genome triplication events but no recent whole-genome duplication (WGD). Likewise, comparative genomic analysis showed no large-scale structural variation after species divergence between M. officinalis and Coffea canephora. Moreover, gene family analysis indicated that gene families associated with plant-pathogen interactions and sugar metabolism were significantly expanded in M. officinalis. Furthermore, we identified many candidate genes involved in the biosynthesis of major active components such as anthraquinones, iridoids and polysaccharides. In addition, we also found that the DHQS, GGPPS, TPS-Clin, TPS04, sacA, and UGDH gene families-which include the critical genes for active component biosynthesis-were expanded in M. officinalis. This study provides a valuable resource for understanding M. officinalis genome evolution and active component biosynthesis. This work will facilitate genetic improvement and molecular breeding of this commercially important plant.
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Affiliation(s)
- Jihua Wang
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, China
| | - Shiqiang Xu
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, China
| | - Yu Mei
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, China
| | - Shike Cai
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, China
| | - Yan Gu
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, China
| | - Minyang Sun
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, China
| | - Zhan Liang
- DongFuhang High-tech Agricultural Planting and Management Co., Ltd, 526000, Zhaoqing, China
| | - Yong Xiao
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, China.
| | - Muqing Zhang
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources, Guangxi University, 530005, Nanning, China.
| | - Shaohai Yang
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, China.
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Crosstalk of Multi-Omics Platforms with Plants of Therapeutic Importance. Cells 2021; 10:cells10061296. [PMID: 34071113 PMCID: PMC8224614 DOI: 10.3390/cells10061296] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/25/2021] [Accepted: 05/10/2021] [Indexed: 02/06/2023] Open
Abstract
From time immemorial, humans have exploited plants as a source of food and medicines. The World Health Organization (WHO) has recorded 21,000 plants with medicinal value out of 300,000 species available worldwide. The promising modern "multi-omics" platforms and tools have been proven as functional platforms able to endow us with comprehensive knowledge of the proteome, genome, transcriptome, and metabolome of medicinal plant systems so as to reveal the novel connected genetic (gene) pathways, proteins, regulator sequences and secondary metabolite (molecule) biosynthetic pathways of various drug and protein molecules from a variety of plants with therapeutic significance. This review paper endeavors to abridge the contemporary advancements in research areas of multi-omics and the information involved in decoding its prospective relevance to the utilization of plants with medicinal value in the present global scenario. The crosstalk of medicinal plants with genomics, transcriptomics, proteomics, and metabolomics approaches will be discussed.
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Development and validation of genome-wide InDel markers with high levels of polymorphism in bitter gourd (Momordica charantia). BMC Genomics 2021; 22:190. [PMID: 33726664 PMCID: PMC7968231 DOI: 10.1186/s12864-021-07499-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 03/02/2021] [Indexed: 11/21/2022] Open
Abstract
Background The preferred choice for molecular marker development is identifying existing variation in populations through DNA sequencing. With the genome resources currently available for bitter gourd (Momordica charantia), it is now possible to detect genome-wide insertion-deletion (InDel) polymorphisms among bitter gourd populations, which guides the efficient development of InDel markers. Results Here, using bioinformatics technology, we detected 389,487 InDels from 61 Chinese bitter gourd accessions with an average density of approximately 1298 InDels/Mb. Then we developed a total of 2502 unique InDel primer pairs with a polymorphism information content (PIC) ≥0.6 distributed across the whole genome. Amplification of InDels in two bitter gourd lines ‘47–2–1-1-3’ and ‘04–17,’ indicated that the InDel markers were reliable and accurate. To highlight their utilization, the InDel markers were employed to construct a genetic map using 113 ‘47–2–1-1-3’ × ‘04–17’ F2 individuals. This InDel genetic map of bitter gourd consisted of 164 new InDel markers distributed on 15 linkage groups with a coverage of approximately half of the genome. Conclusions This is the first report on the development of genome-wide InDel markers for bitter gourd. The validation of the amplification and genetic map construction suggests that these unique InDel markers may enhance the efficiency of genetic studies and marker-assisted selection for bitter gourd. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07499-0.
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Rao PG, Behera TK, Gaikwad AB, Munshi AD, Srivastava A, Boopalakrishnan G, Vinod. Genetic analysis and QTL mapping of yield and fruit traits in bitter gourd (Momordica charantia L.). Sci Rep 2021; 11:4109. [PMID: 33603131 PMCID: PMC7893057 DOI: 10.1038/s41598-021-83548-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/19/2021] [Indexed: 11/17/2022] Open
Abstract
Bitter gourd (Momordica charantia L.) is an economically important vegetable crop grown in tropical parts of the world. In this study, a high-density linkage map of M. charantia was constructed through genotyping-by-sequencing (GBS) technology using F2:3 mapping population generated from the cross DBGy-201 × Pusa Do Mausami. About 2013 high-quality SNPs were assigned on a total of 20 linkage groups (LGs) spanning over 2329.2 CM with an average genetic distance of 1.16 CM. QTL analysis was performed for six major yield-contributing traits such as fruit length, fruit diameter, fruit weight, fruit flesh thickness, number of fruits per plant and yield per plant. These six quantitative traits were mapped with 19 QTLs (9 QTLs with LOD > 3) using composite interval mapping (CIM). Among 19 QTLs, 12 QTLs derived from 'Pusa Do Mausami' revealed a negative additive effect when its allele increased trait score whereas 7 QTLs derived from 'DBGy-201' revealed a positive additive effect when its allele trait score increased. The phenotypic variation (R2%) elucidated by these QTLs ranged from 0.09% (fruit flesh thickness) on LG 14 to 32.65% (fruit diameter) on LG 16 and a total of six major QTLs detected. Most QTLs detected in the present study were located relatively very close, maybe due to the high correlation among the traits. This information will serve as a significant basis for marker-assisted selection and molecular breeding in bitter gourd crop improvement.
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Affiliation(s)
- P Gangadhara Rao
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - T K Behera
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Ambika B Gaikwad
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - A D Munshi
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Arpita Srivastava
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - G Boopalakrishnan
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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Fu A, Wang Q, Mu J, Ma L, Wen C, Zhao X, Gao L, Li J, Shi K, Wang Y, Zhang X, Zhang X, Wang F, Grierson D, Zuo J. Combined genomic, transcriptomic, and metabolomic analyses provide insights into chayote (Sechium edule) evolution and fruit development. HORTICULTURE RESEARCH 2021; 8:35. [PMID: 33517348 PMCID: PMC7847470 DOI: 10.1038/s41438-021-00487-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 01/07/2021] [Accepted: 01/07/2021] [Indexed: 05/11/2023]
Abstract
Chayote (Sechium edule) is an agricultural crop in the Cucurbitaceae family that is rich in bioactive components. To enhance genetic research on chayote, we used Nanopore third-generation sequencing combined with Hi-C data to assemble a draft chayote genome. A chromosome-level assembly anchored on 14 chromosomes (N50 contig and scaffold sizes of 8.40 and 46.56 Mb, respectively) estimated the genome size as 606.42 Mb, which is large for the Cucurbitaceae, with 65.94% (401.08 Mb) of the genome comprising repetitive sequences; 28,237 protein-coding genes were predicted. Comparative genome analysis indicated that chayote and snake gourd diverged from sponge gourd and that a whole-genome duplication (WGD) event occurred in chayote at 25 ± 4 Mya. Transcriptional and metabolic analysis revealed genes involved in fruit texture, pigment, flavor, flavonoids, antioxidants, and plant hormones during chayote fruit development. The analysis of the genome, transcriptome, and metabolome provides insights into chayote evolution and lays the groundwork for future research on fruit and tuber development and genetic improvements in chayote.
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Affiliation(s)
- Anzhen Fu
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, The Collaborative Innovation Center of Cucurbits Crops, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China
| | - Qing Wang
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, The Collaborative Innovation Center of Cucurbits Crops, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jianlou Mu
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China
| | - Lili Ma
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, The Collaborative Innovation Center of Cucurbits Crops, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China
| | - Changlong Wen
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, The Collaborative Innovation Center of Cucurbits Crops, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xiaoyan Zhao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, The Collaborative Innovation Center of Cucurbits Crops, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Lipu Gao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, The Collaborative Innovation Center of Cucurbits Crops, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jian Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, 100048, China
| | - Kai Shi
- Department of Horticulture, Zhejiang University, Hangzhou, 310058, China
| | - Yunxiang Wang
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100093, China
| | - Xuechuan Zhang
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Xuewen Zhang
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Fengling Wang
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Donald Grierson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK.
| | - Jinhua Zuo
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, The Collaborative Innovation Center of Cucurbits Crops, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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Kaur G, Pathak M, Singla D, Chhabra G, Chhuneja P, Kaur Sarao N. Quantitative Trait Loci Mapping for Earliness, Fruit, and Seed Related Traits Using High Density Genotyping-by-Sequencing-Based Genetic Map in Bitter Gourd ( Momordica charantia L.). FRONTIERS IN PLANT SCIENCE 2021; 12:799932. [PMID: 35211132 PMCID: PMC8863046 DOI: 10.3389/fpls.2021.799932] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/28/2021] [Indexed: 05/17/2023]
Abstract
Bitter gourd (Momordica charantia L.) is an important vegetable crop having numerous medicinal properties. Earliness and yield related traits are main aims of bitter gourd breeding program. High resolution quantitative trait loci (QTLs) mapping can help in understanding the molecular basis of phenotypic variation of these traits and thus facilitate marker-assisted breeding. The aim of present study was to identify genetic loci controlling earliness, fruit, and seed related traits. To achieve this, genotyping-by-sequencing (GBS) approach was used to genotype 101 individuals of F4 population derived from a cross between an elite cultivar Punjab-14 and PAUBG-6. This population was phenotyped under net-house conditions for three years 2018, 2019, and 2021. The linkage map consisting of 15 linkage groups comprising 3,144 single nucleotide polymorphism (SNP) markers was used to detect the QTLs for nine traits. A total of 50 QTLs for these traits were detected which were distributed on 11 chromosomes. The QTLs explained 5.09-29.82% of the phenotypic variance. The highest logarithm of the odds (LOD) score for a single QTL was 8.68 and the lowest was 2.50. For the earliness related traits, a total of 22 QTLs were detected. For the fruit related traits, a total of 16 QTLs and for seed related traits, a total of 12 QTLs were detected. Out of 50 QTLs, 20 QTLs were considered as frequent QTLs (FQ-QTLs). The information generated in this study is very useful in the future for fine-mapping and marker-assisted selection for these traits in bitter gourd improvement program.
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Affiliation(s)
- Gurpreet Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Mamta Pathak
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, India
| | - Deepak Singla
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Gautam Chhabra
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Navraj Kaur Sarao
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
- *Correspondence: Navraj Kaur Sarao,
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Cheng QQ, Ouyang Y, Tang ZY, Lao CC, Zhang YY, Cheng CS, Zhou H. Review on the Development and Applications of Medicinal Plant Genomes. FRONTIERS IN PLANT SCIENCE 2021; 12:791219. [PMID: 35003182 PMCID: PMC8732986 DOI: 10.3389/fpls.2021.791219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/23/2021] [Indexed: 05/04/2023]
Abstract
With the development of sequencing technology, the research on medicinal plants is no longer limited to the aspects of chemistry, pharmacology, and pharmacodynamics, but reveals them from the genetic level. As the price of next-generation sequencing technology becomes affordable, and the long-read sequencing technology is established, the medicinal plant genomes with large sizes have been sequenced and assembled more easily. Although the review of plant genomes has been reported several times, there is no review giving a systematic and comprehensive introduction about the development and application of medicinal plant genomes that have been reported until now. Here, we provide a historical perspective on the current situation of genomes in medicinal plant biology, highlight the use of the rapidly developing sequencing technologies, and conduct a comprehensive summary on how the genomes apply to solve the practical problems in medicinal plants, like genomics-assisted herb breeding, evolution history revelation, herbal synthetic biology study, and geoherbal research, which are important for effective utilization, rational use and sustainable protection of medicinal plants.
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Affiliation(s)
- Qi-Qing Cheng
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Yue Ouyang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Zi-Yu Tang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Chi-Chou Lao
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Yan-Yu Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Chun-Song Cheng
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Hua Zhou
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
- Joint Laboratory for Translational Cancer Research of Chinese Medicine, The Ministry of Education of the People’s Republic of China, Macau University of Science and Technology, Taipa, Macao SAR, China
- *Correspondence: Hua Zhou,
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Kaur G, Pathak M, Singla D, Sharma A, Chhuneja P, Sarao NK. High-Density GBS-Based Genetic Linkage Map Construction and QTL Identification Associated With Yellow Mosaic Disease Resistance in Bitter Gourd ( Momordica charantia L.). FRONTIERS IN PLANT SCIENCE 2021; 12:671620. [PMID: 34249043 PMCID: PMC8264296 DOI: 10.3389/fpls.2021.671620] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/30/2021] [Indexed: 05/14/2023]
Abstract
Yellow mosaic disease (YMD) in bitter gourd (Momordica charantia) is a devastating disease that seriously affects its yield. Although there is currently no effective method to control the disease, breeding of resistant varieties is the most effective and economic option. Moreover, quantitative trait locus (QTL) associated with resistance to YMD has not yet been reported. With the objective of mapping YMD resistance in bitter gourd, the susceptible parent "Punjab-14" and the resistant parent "PAUBG-6" were crossed to obtain F4 mapping population comprising 101 individuals. In the present study, the genotyping by sequencing (GBS) approach was used to develop the genetic linkage map. The map contained 3,144 single nucleotide polymorphism (SNP) markers, consisted of 15 linkage groups, and it spanned 2415.2 cM with an average marker distance of 0.7 cM. By adopting the artificial and field inoculation techniques, F4:5 individuals were phenotyped for disease resistance in Nethouse (2019), Rainy (2019), and Spring season (2020). The QTL analysis using the genetic map and phenotyping data identified three QTLs qYMD.pau_3.1, qYMD.pau_4.1, and qYMD.pau_5.1 on chromosome 3, 4, and 5 respectively. Among these, qYMD.pau_3.1, qYMD.pau_4.1 QTLs were identified during the rainy season, explaining the 13.5 and 21.6% phenotypic variance respectively, whereas, during the spring season, qYMD.pau_4.1 and qYMD.pau_5.1 QTLs were observed with 17.5 and 22.1% phenotypic variance respectively. Only one QTL qYMD.pau_5.1 was identified for disease resistance under nethouse conditions with 15.6% phenotypic variance. To our knowledge, this is the first report on the identification of QTLs associated with YMD resistance in bitter gourd using SNP markers. The information generated in this study is very useful in the future for fine-mapping and marker-assisted selection for disease resistance.
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Affiliation(s)
- Gurpreet Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Mamta Pathak
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, India
| | - Deepak Singla
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Abhishek Sharma
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Navraj Kaur Sarao
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
- *Correspondence: Navraj Kaur Sarao,
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Ma L, Wang Q, Mu J, Fu A, Wen C, Zhao X, Gao L, Li J, Shi K, Wang Y, Zhang X, Zhang X, Fei Z, Grierson D, Zuo J. The genome and transcriptome analysis of snake gourd provide insights into its evolution and fruit development and ripening. HORTICULTURE RESEARCH 2020; 7:199. [PMID: 33328440 PMCID: PMC7704671 DOI: 10.1038/s41438-020-00423-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 05/03/2023]
Abstract
Snake gourd (Trichosanthes anguina L.), which belongs to the Cucurbitaceae family, is a popular ornamental and food crop species with medicinal value and is grown in many parts of the world. Although progress has been made in its genetic improvement, the organization, composition, and evolution of the snake gourd genome remain largely unknown. Here, we report a high-quality genome assembly for snake gourd, comprising 202 contigs, with a total size of 919.8 Mb and an N50 size of 20.1 Mb. These findings indicate that snake gourd has one of the largest genomes of Cucurbitaceae species sequenced to date. The snake gourd genome assembly harbors 22,874 protein-coding genes and 80.0% of the genome consists of repetitive sequences. Phylogenetic analysis reveals that snake gourd is closely related to sponge gourd but diverged from their common ancestor ~33-47 million years ago. The genome sequence reported here serves as a valuable resource for snake gourd genetic research and comparative genomic studies in Cucurbitaceae and other plant species. In addition, fruit transcriptome analysis reveals the candidate genes related to quality traits during snake gourd fruit development and provides a basis for future research on snake gourd fruit development and ripening at the transcript level.
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Affiliation(s)
- Lili Ma
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, The Collaborative Innovation Center of Cucurbit Crops, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China
| | - Qing Wang
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, The Collaborative Innovation Center of Cucurbit Crops, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jianlou Mu
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China
| | - Anzhen Fu
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, The Collaborative Innovation Center of Cucurbit Crops, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China
| | - Changlong Wen
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, The Collaborative Innovation Center of Cucurbit Crops, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xiaoyan Zhao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, The Collaborative Innovation Center of Cucurbit Crops, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Lipu Gao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, The Collaborative Innovation Center of Cucurbit Crops, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jian Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, 100048, China
| | - Kai Shi
- Department of Horticulture, Zhejiang University, Hangzhou, 310058, China
| | - Yunxiang Wang
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Xuewen Zhang
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Xuechuan Zhang
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA.
- U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA.
| | - Donald Grierson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK.
| | - Jinhua Zuo
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, The Collaborative Innovation Center of Cucurbit Crops, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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Ding Z, Cui H, Zhu Q, Wu Y, Zhang T, Qiu B, Gao P. Complete sequence of mitochondrial genome of Cucumis melo L. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3176-3177. [PMID: 33458102 PMCID: PMC7782283 DOI: 10.1080/23802359.2020.1808543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Cucumis melo L. is one of the most important fruit-type vegetables in the world. This genome is divided into a main loop and two small loops. The length of the main loop is 2,709,526 bp, and the two small loops are 149,555 bp and 47,592 bp long, respectively. There are 88 coding genes in the melon mitochondrial genome, including 40 protein-coding genes (which accounted for about 1.23% of the whole genome), 8 rRNAs, and 40 tRNAs. The total length of rRNAs and tRNAs spans 0.31% of the total genome sequence. Among the 88 mitochondrial coding genes, only 5 tRNAs were located into the second largest circular DNA molecule. The complete mitogenome sequence provided herein would help understand C. melo evolution.
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Affiliation(s)
- Zhuo Ding
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China.,Ministry of Agriculture, Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Harbin, Heilongjiang, China
| | - Haonan Cui
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China.,Ministry of Agriculture, Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Harbin, Heilongjiang, China
| | - Qianglong Zhu
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Yue Wu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China.,Ministry of Agriculture, Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Harbin, Heilongjiang, China
| | - Taifeng Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China.,Ministry of Agriculture, Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Harbin, Heilongjiang, China
| | - Boyan Qiu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China.,Ministry of Agriculture, Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Harbin, Heilongjiang, China
| | - Peng Gao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China.,Ministry of Agriculture, Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Harbin, Heilongjiang, China
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Wu H, Zhao G, Gong H, Li J, Luo C, He X, Luo S, Zheng X, Liu X, Guo J, Chen J, Luo J. A high-quality sponge gourd ( Luffa cylindrica) genome. HORTICULTURE RESEARCH 2020; 7:128. [PMID: 32821411 PMCID: PMC7395165 DOI: 10.1038/s41438-020-00350-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 05/27/2020] [Accepted: 05/31/2020] [Indexed: 05/06/2023]
Abstract
Sponge gourd (Luffa cylindrica) is an important cultivated vegetable and medicinal plant in the family Cucurbitaceae. In this study, a draft genome sequence of the sponge gourd inbred line P93075 was analyzed. Using Illumina, PacBio, and 10× Genomics sequencing techniques as well as new assembly techniques such as FALCON and chromatin interaction mapping (Hi-C), a chromosome-scale genome of approximately 656.19 Mb, with an N50 scaffold length of 48.76 Mb, was generated. From this assembly, 25,508 protein-coding gene loci were identified, and 63.81% of the whole-genome consisted of transposable elements, which are major contributors to the expansion of the sponge gourd genome. According to a phylogenetic analysis of conserved genes, the sponge gourd lineage diverged from the bitter gourd lineage approximately 41.6 million years ago. Additionally, many genes that respond to biotic and abiotic stresses were found to be lineage specific or expanded in the sponge gourd genome, as demonstrated by the presence of 462 NBS-LRR genes, a much greater number than are found in the genomes of other cucurbit species; these results are consistent with the high stress resistance of sponge gourd. Collectively, our study provides insights into genome evolution and serves as a valuable reference for the genetic improvement of sponge gourd.
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Affiliation(s)
- Haibin Wu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640 China
| | - Gangjun Zhao
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640 China
| | - Hao Gong
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640 China
| | - Junxing Li
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640 China
| | - Caixia Luo
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640 China
| | - Xiaoli He
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640 China
| | - Shaobo Luo
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640 China
| | - Xiaoming Zheng
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640 China
| | - Xiaoxi Liu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640 China
| | - Jinju Guo
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640 China
| | - Junqiu Chen
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640 China
| | - Jianning Luo
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640 China
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40
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Long-read bitter gourd ( Momordica charantia) genome and the genomic architecture of nonclassic domestication. Proc Natl Acad Sci U S A 2020; 117:14543-14551. [PMID: 32461376 DOI: 10.1073/pnas.1921016117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genetic architecture of quantitative traits is determined by both Mendelian and polygenic factors, yet classic examples of plant domestication focused on selective sweep of newly mutated Mendelian genes. Here we report the chromosome-level genome assembly and the genomic investigation of a nonclassic domestication example, bitter gourd (Momordica charantia), an important Asian vegetable and medicinal plant of the family Cucurbitaceae. Population resequencing revealed the divergence between wild and South Asian cultivars about 6,000 y ago, followed by the separation of the Southeast Asian cultivars about 800 y ago, with the latter exhibiting more extreme trait divergence from wild progenitors and stronger signs of selection on fruit traits. Unlike some crops where the largest phenotypic changes and traces of selection happened between wild and cultivar groups, in bitter gourd large differences exist between two regional cultivar groups, likely reflecting the distinct consumer preferences in different countries. Despite breeding efforts toward increasing female flower proportion, a gynoecy locus exhibits complex patterns of balanced polymorphism among haplogroups, with potential signs of selective sweep within haplogroups likely reflecting artificial selection and introgression from cultivars back to wild accessions. Our study highlights the importance to investigate such nonclassic example of domestication showing signs of balancing selection and polygenic trait architecture in addition to classic selective sweep in Mendelian factors.
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Guo Y, Gao M, Liang X, Xu M, Liu X, Zhang Y, Liu X, Liu J, Gao Y, Qu S, Luan F. Quantitative Trait Loci for Seed Size Variation in Cucurbits - A Review. FRONTIERS IN PLANT SCIENCE 2020; 11:304. [PMID: 32265957 PMCID: PMC7099056 DOI: 10.3389/fpls.2020.00304] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 03/03/2020] [Indexed: 05/17/2023]
Abstract
Cucurbits (Cucurbitaceae family) include many economically important fruit vegetable crops such as watermelon, pumpkin/squash, cucumber, and melon. Seed size (SS) is an important trait in cucurbits breeding, which is controlled by quantitative trait loci (QTL). Recent advances have deciphered several signaling pathways underlying seed size variation in model plants such as Arabidopsis and rice, but little is known on the genetic basis of SS variation in cucurbits. Here we conducted literature review on seed size QTL identified in watermelon, pumpkin/squash, cucumber and melon, and inferred 14, 9 and 13 consensus SS QTL based on their physical positions in respective draft genomes. Among them, four from watermelon (ClSS2.2, ClSS6.1, ClSS6.2, and ClSS8.2), two from cucumber (CsSS4.1 and CsSS5.1), and one from melon (CmSS11.1) were major-effect, stable QTL for seed size and weight. Whole genome sequence alignment revealed that these major-effect QTL were located in syntenic regions across different genomes suggesting possible structural and functional conservation of some important genes for seed size control in cucurbit crops. Annotation of genes in the four watermelon consensus SS QTL regions identified genes that are known to play important roles in seed size control including members of the zinc finger protein and the E3 ubiquitin-protein ligase families. The present work highlights the utility of comparative analysis in understanding the genetic basis of seed size variation, which may help future mapping and cloning of seed size QTL in cucurbits.
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Affiliation(s)
- Yu Guo
- College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar, China
- Heilongjiang Provincial Key Laboratory of Resistance Gene Engineering and Preservation of Biodiversity in Cold Areas, Qiqihar, China
| | - Meiling Gao
- College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar, China
- Heilongjiang Provincial Key Laboratory of Resistance Gene Engineering and Preservation of Biodiversity in Cold Areas, Qiqihar, China
| | - Xiaoxue Liang
- College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar, China
| | - Ming Xu
- College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar, China
| | - Xiaosong Liu
- College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar, China
| | - Yanling Zhang
- College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar, China
| | - Xiujie Liu
- Qiqihar Horticultural Research Institute, Qiqihar, China
| | - Jixiu Liu
- Qiqihar Horticultural Research Institute, Qiqihar, China
| | - Yue Gao
- Qiqihar Horticultural Research Institute, Qiqihar, China
| | - Shuping Qu
- College of Horticulture, Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Feishi Luan
- College of Horticulture, Landscape Architecture, Northeast Agricultural University, Harbin, China
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Cui J, Yang Y, Luo S, Wang L, Huang R, Wen Q, Han X, Miao N, Cheng J, Liu Z, Zhang C, Feng C, Zhu H, Su J, Wan X, Hu F, Niu Y, Zheng X, Yang Y, Shan D, Dong Z, He W, Dhillon NPS, Hu K. Whole-genome sequencing provides insights into the genetic diversity and domestication of bitter gourd ( Momordica spp.). HORTICULTURE RESEARCH 2020; 7:85. [PMID: 32528697 PMCID: PMC7261802 DOI: 10.1038/s41438-020-0305-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/14/2020] [Accepted: 03/23/2020] [Indexed: 05/06/2023]
Abstract
Bitter gourd (Momordica charantia) is a popular cultivated vegetable in Asian and African countries. To reveal the characteristics of the genomic structure, evolutionary trajectory, and genetic basis underlying the domestication of bitter gourd, we performed whole-genome sequencing of the cultivar Dali-11 and the wild small-fruited line TR and resequencing of 187 bitter gourd germplasms from 16 countries. The major gene clusters (Bi clusters) for the biosynthesis of cucurbitane triterpenoids, which confer a bitter taste, are highly conserved in cucumber, melon, and watermelon. Comparative analysis among cucurbit genomes revealed that the Bi cluster involved in cucurbitane triterpenoid biosynthesis is absent in bitter gourd. Phylogenetic analysis revealed that the TR group, including 21 bitter gourd germplasms, may belong to a new species or subspecies independent from M. charantia. Furthermore, we found that the remaining 166 M. charantia germplasms are geographically differentiated, and we identified 710, 412, and 290 candidate domestication genes in the South Asia, Southeast Asia, and China populations, respectively. This study provides new insights into bitter gourd genetic diversity and domestication and will facilitate the future genomics-enabled improvement of bitter gourd.
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Affiliation(s)
- Junjie Cui
- College of Horticulture, South China Agricultural University/State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, 510642 Guangzhou, China
| | - Yan Yang
- Tropical Crop Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, 571737 Danzhou, China
| | - Shaobo Luo
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, 510640 Guangzhou, China
| | - Le Wang
- BGI Genomics, BGI-Shenzhen, 518083 Shenzhen, China
| | - Rukui Huang
- Vegetable Research Institute, Guangxi Academy of Agricultural Sciences, 530007 Nanning, China
| | - Qingfang Wen
- Crop Research Institute, Fujian Academy of Agricultural Sciences, 350013 Fuzhou, China
| | - Xiaoxia Han
- Institute of Vegetable Research, Hunan Academy of Agricultural Sciences, 410125 Changsha, China
| | - Nansheng Miao
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, 330200 Nanchang, China
| | - Jiaowen Cheng
- College of Horticulture, South China Agricultural University/State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, 510642 Guangzhou, China
| | - Ziji Liu
- Tropical Crop Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, 571737 Danzhou, China
| | - Changyuan Zhang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, 510640 Guangzhou, China
| | - Chengcheng Feng
- Vegetable Research Institute, Guangxi Academy of Agricultural Sciences, 530007 Nanning, China
| | - Haisheng Zhu
- Crop Research Institute, Fujian Academy of Agricultural Sciences, 350013 Fuzhou, China
| | - Jianwen Su
- Institute of Vegetable Research, Hunan Academy of Agricultural Sciences, 410125 Changsha, China
| | - Xinjian Wan
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, 330200 Nanchang, China
| | - Fang Hu
- College of Horticulture, South China Agricultural University/State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, 510642 Guangzhou, China
| | - Yu Niu
- Tropical Crop Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, 571737 Danzhou, China
| | - Xiaoming Zheng
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, 510640 Guangzhou, China
| | - Yulan Yang
- BGI Genomics, BGI-Shenzhen, 518083 Shenzhen, China
| | - Dai Shan
- BGI Genomics, BGI-Shenzhen, 518083 Shenzhen, China
| | | | - Weiming He
- BGI Genomics, BGI-Shenzhen, 518083 Shenzhen, China
| | - Narinder P. S. Dhillon
- World Vegetable Center, East and Southeast Asia, Research and Training Station, Kasetsart University, Kamphaeng Saen, Nakhon Pathom, 73140 Thailand
| | - Kailin Hu
- College of Horticulture, South China Agricultural University/State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, 510642 Guangzhou, China
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Pan Y, Wang Y, McGregor C, Liu S, Luan F, Gao M, Weng Y. Genetic architecture of fruit size and shape variation in cucurbits: a comparative perspective. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1-21. [PMID: 31768603 DOI: 10.1007/s00122-019-03481-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 11/11/2019] [Indexed: 05/28/2023]
Abstract
The Cucurbitaceae family hosts many economically important fruit vegetables (cucurbits) such as cucumber, melon, watermelon, pumpkin/squash, and various gourds. The cucurbits are probably best known for the diverse fruit sizes and shapes, but little is known about their genetic basis and molecular regulation. Here, we reviewed the literature on fruit size (FS), shape (FSI), and fruit weight (FW) QTL identified in cucumber, melon, and watermelon, from which 150 consensus QTL for these traits were inferred. Genome-wide survey of the three cucurbit genomes identified 253 homologs of eight classes of fruit or grain size/weight-related genes cloned in Arabidopsis, tomato, and rice that encode proteins containing the characteristic CNR (cell number regulator), CSR (cell size regulator), CYP78A (cytochrome P450), SUN, OVATE, TRM (TONNEAU1 Recruiting Motif), YABBY, and WOX domains. Alignment of the consensus QTL with candidate gene homologs revealed widespread structure and function conservation of fruit size/shape gene homologs in cucurbits, which was exemplified with the fruit size/shape candidate genes CsSUN25-26-27a and CsTRM5 in cucumber, CmOFP1a in melon, and ClSUN25-26-27a in watermelon. In cucurbits, the andromonoecy (for 1-aminocyclopropane-1-carboxylate synthase) and the carpel number (for CLAVATA3) loci are known to have pleiotropic effects on fruit shape, which may complicate identification of fruit size/shape candidate genes in these regions. The present work illustrates the power of comparative analysis in understanding the genetic architecture of fruit size/shape variation, which may facilitate QTL mapping and cloning for fruit size-related traits in cucurbits. The limitations and perspectives of this approach are also discussed.
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Affiliation(s)
- Yupeng Pan
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
| | - Yuhui Wang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Cecilia McGregor
- Department of Horticulture and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
| | - Shi Liu
- College of Horticulture and, Landscape Architecture at Northeast Agricultural University, Harbin, 150030, China
| | - Feishi Luan
- College of Horticulture and, Landscape Architecture at Northeast Agricultural University, Harbin, 150030, China
| | - Meiling Gao
- College of Life Science, Agriculture and Forestry, Qiqihar University, Qiqihar, 161006, China
| | - Yiqun Weng
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- USDA-ARS Vegetable Crops Research Unit, 1575 Linden Dr., Madison, WI, 53706, USA.
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Hendre PS, Muthemba S, Kariba R, Muchugi A, Fu Y, Chang Y, Song B, Liu H, Liu M, Liao X, Sahu SK, Wang S, Li L, Lu H, Peng S, Cheng S, Xu X, Yang H, Wang J, Liu X, Simons A, Shapiro HY, Mumm RH, Van Deynze A, Jamnadass R. African Orphan Crops Consortium (AOCC): status of developing genomic resources for African orphan crops. PLANTA 2019; 250:989-1003. [PMID: 31073657 DOI: 10.1007/s00425-019-03156-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 04/01/2019] [Indexed: 05/28/2023]
Abstract
The African Orphan Crops Consortium (AOCC) successfully initiated the ambitious genome sequencing project of 101 African orphan crops/trees with 6 genomes sequenced, 6 near completion, and 20 currently in progress. Addressing stunting, malnutrition, and hidden hunger through nutritious, economic, and resilient agri-food system is one of the major agricultural challenges of this century. As sub-Saharan Africa harbors a large portion of the severely malnourished population, the African Orphan Crops Consortium (AOCC) was established in 2011 with an aim to reduce stunting and malnutrition by providing nutritional security through improving locally adapted nutritious, but neglected, under-researched or orphan African food crops. Foods from these indigenous or naturalized crops and trees are rich in minerals, vitamins, and antioxidant, and are an integral part of the dietary portfolio and cultural, social, and economic milieu of African farmers. Through stakeholder consultations supported by the African Union, 101 African orphan and under-researched crop species were prioritized to mainstream into African agri-food systems. The AOCC, through a network of international-regional-public-private partnerships and collaborations, is generating genomic resources of three types, i.e., reference genome sequence, transcriptome sequence, and re-sequencing 100 accessions/species, using next-generation sequencing (NGS) technology. Furthermore, the University of California Davis African Plant Breeding Academy under the AOCC banner is training 150 lead African scientists to breed high yielding, nutritious, and climate-resilient (biotic and abiotic stress tolerant) crop varieties that meet African farmer and consumer needs. To date, one or more forms of sequence data have been produced for 60 crops. Reference genome sequences for six species have already been published, 6 are almost near completion, and 19 are in progress.
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Affiliation(s)
- Prasad S Hendre
- African Orphan Crops Consortium, World Agroforestry Centre (ICRAF), Nairobi, Kenya.
| | - Samuel Muthemba
- African Orphan Crops Consortium, World Agroforestry Centre (ICRAF), Nairobi, Kenya
| | - Robert Kariba
- African Orphan Crops Consortium, World Agroforestry Centre (ICRAF), Nairobi, Kenya
| | - Alice Muchugi
- African Orphan Crops Consortium, World Agroforestry Centre (ICRAF), Nairobi, Kenya
| | - Yuan Fu
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Yue Chang
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Bo Song
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Huan Liu
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Min Liu
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Xuezhu Liao
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Sunil Kumar Sahu
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Sibo Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Linzhou Li
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Haorong Lu
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Shufeng Peng
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Shifeng Cheng
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Xin Liu
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Anthony Simons
- African Orphan Crops Consortium, World Agroforestry Centre (ICRAF), Nairobi, Kenya
| | - Howard-Yana Shapiro
- African Orphan Crops Consortium, World Agroforestry Centre (ICRAF), Nairobi, Kenya
- University of California, 1 Shields Ave, Davis, CA, 95616, USA
| | - Rita H Mumm
- University of Illinois, Urbana, IL, 61801, USA
| | | | - Ramni Jamnadass
- African Orphan Crops Consortium, World Agroforestry Centre (ICRAF), Nairobi, Kenya
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Kiryushkin AS, Ilina EL, Puchkova VA, Guseva ED, Pawlowski K, Demchenko KN. Lateral Root Initiation in the Parental Root Meristem of Cucurbits: Old Players in a New Position. FRONTIERS IN PLANT SCIENCE 2019; 10:365. [PMID: 31110507 PMCID: PMC6499211 DOI: 10.3389/fpls.2019.00365] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/08/2019] [Indexed: 05/12/2023]
Abstract
While in most higher plants, including the model system Arabidopsis thaliana, the formation of lateral root primordia is induced in the elongation zone of the parental root, in seven plant families, including Cucurbitaceae, an alternative root branching mechanism is established such that lateral roots are initiated directly in the apical meristem of the parental root. In Arabidopsis, the transcription factor GATA23 and MEMBRANE-ASSOCIATED KINASE REGULATOR4 (MAKR4) are involved in the gene regulatory network of lateral root initiation. Among all marker genes examined, these are the earliest known marker genes up-regulated by auxin during lateral root initiation. In this study, putative functional orthologs of Arabidopsis GATA23 and MAKR4 were identified in cucumber (Cucumis sativus) and squash (Cucurbita pepo). Both cucurbits contained 26 genes encoding GATA family transcription factors and only one MAKR4 gene. Phylogenetic and transcriptional analysis of up-regulation by auxin led to the identification of GATA23 putative functional orthologs in Cucurbitaceae - CpGATA24 and CsGATA24. In squash, CpMAKR4 was up-regulated by naphthylacetic acid (NAA) and, similar to MAKR4 in Arabidopsis, indole-3-butyric acid (IBA). A detailed analysis of the expression pattern of CpGATA24 and CpMAKR4 in squash roots from founder cell specification until emergence of lateral root primordia was carried out using promoter-fluorescent reporter gene fusions and confocal microscopy. Their expression was induced in the protoxylem, and then expanded to founder cells in the pericycle. Thus, while the overall expression pattern of these genes was significantly different from that in Arabidopsis, in founder cells their expression was induced in the same order as in Arabidopsis. Altogether, these findings suggest that in Cucurbitaceae the putative functional orthologs of GATA23 and MAKR4 might play a role in founder cell specification and primordium positioning during lateral root initiation. The role of the protoxylem in auxin transport as a trigger of founder cells specification and lateral root initiation is discussed.
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Affiliation(s)
- Alexey S. Kiryushkin
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Elena L. Ilina
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Vera A. Puchkova
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Elizaveta D. Guseva
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Kirill N. Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, Saint Petersburg, Russia
- Laboratory of Molecular and Cellular Biology, All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
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Chen F, Song Y, Li X, Chen J, Mo L, Zhang X, Lin Z, Zhang L. Genome sequences of horticultural plants: past, present, and future. HORTICULTURE RESEARCH 2019; 6:112. [PMID: 31645966 PMCID: PMC6804536 DOI: 10.1038/s41438-019-0195-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/27/2019] [Accepted: 08/10/2019] [Indexed: 05/18/2023]
Abstract
Horticultural plants play various and critical roles for humans by providing fruits, vegetables, materials for beverages, and herbal medicines and by acting as ornamentals. They have also shaped human art, culture, and environments and thereby have influenced the lifestyles of humans. With the advent of sequencing technologies, there has been a dramatic increase in the number of sequenced genomes of horticultural plant species in the past decade. The genomes of horticultural plants are highly diverse and complex, often with a high degree of heterozygosity and a high ploidy due to their long and complex history of evolution and domestication. Here we summarize the advances in the genome sequencing of horticultural plants, the reconstruction of pan-genomes, and the development of horticultural genome databases. We also discuss past, present, and future studies related to genome sequencing, data storage, data quality, data sharing, and data visualization to provide practical guidance for genomic studies of horticultural plants. Finally, we propose a horticultural plant genome project as well as the roadmap and technical details toward three goals of the project.
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Affiliation(s)
- Fei Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yunfeng Song
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xiaojiang Li
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Junhao Chen
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300 China
| | - Lan Mo
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300 China
| | - Xingtan Zhang
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, MO 63103 USA
| | - Liangsheng Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology and Quality Science and Processing Technology in Special Starch, Key Laboratory of Ministry of Education for Genetics & Breeding and Multiple Utilization of Crops, College of Crop Science, Fuzhou, China
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Xia M, Han X, He H, Yu R, Zhen G, Jia X, Cheng B, Deng XW. Improved de novo genome assembly and analysis of the Chinese cucurbit Siraitia grosvenorii, also known as monk fruit or luo-han-guo. Gigascience 2018; 7:5034949. [PMID: 29893829 PMCID: PMC6007378 DOI: 10.1093/gigascience/giy067] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 05/29/2018] [Indexed: 11/20/2022] Open
Abstract
Background Luo-han-guo (Siraitia grosvenorii), also called monk fruit, is a member of the Cucurbitaceae family. Monk fruit has become an important area for research because of the pharmacological and economic potential of its noncaloric, extremely sweet components (mogrosides). It is also commonly used in traditional Chinese medicine for the treatment of lung congestion, sore throat, and constipation. Recently, a single reference genome became available for monk fruit, assembled from 36.9x genome coverage reads via Illumina sequencing platforms. This genome assembly has a relatively short (34.2 kb) contig N50 length and lacks integrated annotations. These drawbacks make it difficult to use as a reference in assembling transcriptomes and discovering novel functional genes. Findings Here, we offer a new high-quality draft of the S. grosvenorii genome assembled using 31 Gb (∼73.8x) long single molecule real time sequencing reads and polished with ∼50 Gb Illumina paired-end reads. The final genome assembly is approximately 469.5 Mb, with a contig N50 length of 432,384 bp, representing a 12.6-fold improvement. We further annotated 237.3 Mb of repetitive sequence and 30,565 consensus protein coding genes with combined evidence. Phylogenetic analysis showed that S. grosvenorii diverged from members of the Cucurbitaceae family approximately 40.9 million years ago. With comprehensive transcriptomic analysis and differential expression testing, we identified 4,606 up-regulated genes in the early fruit compared to the leaf, a number of which were linked to metabolic pathways regulating fruit development and ripening. Conclusions The availability of this new monk fruit genome assembly, as well as the annotations, will facilitate the discovery of new functional genes and the genetic improvement of monk fruit.
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Affiliation(s)
- Mian Xia
- Key Laboratory of Crop biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Xue Han
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China
| | - Hang He
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China
| | - Renbo Yu
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China
| | - Gang Zhen
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China
| | - Xiping Jia
- National Demonstration Area of Modern Agriculture in Cangxi, Sichuan Province, China
| | - Beijiu Cheng
- Key Laboratory of Crop biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Xing Wang Deng
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China
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Mozaniel SDO, Wanessa ADC, Fernanda WFB, Marilena EA, Gracialda CF, Raul NDCJ. Phytochemical profile and biological activities of Momordica charantia L. (Cucurbitaceae): A review. ACTA ACUST UNITED AC 2018. [DOI: 10.5897/ajb2017.16374] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Cui J, Luo S, Niu Y, Huang R, Wen Q, Su J, Miao N, He W, Dong Z, Cheng J, Hu K. A RAD-Based Genetic Map for Anchoring Scaffold Sequences and Identifying QTLs in Bitter Gourd ( Momordica charantia). FRONTIERS IN PLANT SCIENCE 2018; 9:477. [PMID: 29706980 PMCID: PMC5906717 DOI: 10.3389/fpls.2018.00477] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 03/27/2018] [Indexed: 05/22/2023]
Abstract
Genetic mapping is a basic tool necessary for anchoring assembled scaffold sequences and for identifying QTLs controlling important traits. Though bitter gourd (Momordica charantia) is both consumed and used as a medicinal, research on its genomics and genetic mapping is severely limited. Here, we report the construction of a restriction site associated DNA (RAD)-based genetic map for bitter gourd using an F2 mapping population comprising 423 individuals derived from two cultivated inbred lines, the gynoecious line 'K44' and the monoecious line 'Dali-11.' This map comprised 1,009 SNP markers and spanned a total genetic distance of 2,203.95 cM across the 11 linkage groups. It anchored a total of 113 assembled scaffolds that covered about 251.32 Mb (85.48%) of the 294.01 Mb assembled genome. In addition, three horticulturally important traits including sex expression, fruit epidermal structure, and immature fruit color were evaluated using a combination of qualitative and quantitative data. As a result, we identified three QTL/gene loci responsible for these traits in three environments. The QTL/gene gy/fffn/ffn, controlling sex expression involved in gynoecy, first female flower node, and female flower number was detected in the reported region. Particularly, two QTLs/genes, Fwa/Wr and w, were found to be responsible for fruit epidermal structure and white immature fruit color, respectively. This RAD-based genetic map promotes the assembly of the bitter gourd genome and the identified genetic loci will accelerate the cloning of relevant genes in the future.
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Affiliation(s)
- Junjie Cui
- College of Horticulture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Shaobo Luo
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yu Niu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
| | - Rukui Huang
- Vegetable Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Qingfang Wen
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Jianwen Su
- Hunan Vegetable Research Institute, Changsha, China
| | - Nansheng Miao
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Weiming He
- Beijing Genomics Institute, Shenzhen, China
| | | | - Jiaowen Cheng
- College of Horticulture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Kailin Hu
- College of Horticulture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, China
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Kyriakidou M, Tai HH, Anglin NL, Ellis D, Strömvik MV. Current Strategies of Polyploid Plant Genome Sequence Assembly. FRONTIERS IN PLANT SCIENCE 2018; 9:1660. [PMID: 30519250 PMCID: PMC6258962 DOI: 10.3389/fpls.2018.01660] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 10/25/2018] [Indexed: 05/14/2023]
Abstract
Polyploidy or duplication of an entire genome occurs in the majority of angiosperms. The understanding of polyploid genomes is important for the improvement of those crops, which humans rely on for sustenance and basic nutrition. As climate change continues to pose a potential threat to agricultural production, there will increasingly be a demand for plant cultivars that can resist biotic and abiotic stresses and also provide needed and improved nutrition. In the past decade, Next Generation Sequencing (NGS) has fundamentally changed the genomics landscape by providing tools for the exploration of polyploid genomes. Here, we review the challenges of the assembly of polyploid plant genomes, and also present recent advances in genomic resources and functional tools in molecular genetics and breeding. As genomes of diploid and less heterozygous progenitor species are increasingly available, we discuss the lack of complexity of these currently available reference genomes as they relate to polyploid crops. Finally, we review recent approaches of haplotyping by phasing and the impact of third generation technologies on polyploid plant genome assembly.
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Affiliation(s)
- Maria Kyriakidou
- Department of Plant Science, McGill University, Montreal, QC, Canada
| | - Helen H. Tai
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
| | | | | | - Martina V. Strömvik
- Department of Plant Science, McGill University, Montreal, QC, Canada
- *Correspondence: Martina V. Strömvik
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