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Bhutia ND, Sureja AK, Verma M, Gopala Krishnan S, Arya L, Bhardwaj R, Dash PK, Das Munshi A. Inheritance and molecular mapping of solitary/cluster fruit-bearing habit in Luffa. Mol Genet Genomics 2023:10.1007/s00438-023-02034-0. [PMID: 37231151 DOI: 10.1007/s00438-023-02034-0] [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: 11/07/2022] [Accepted: 05/15/2023] [Indexed: 05/27/2023]
Abstract
Fruiting behaviour and sex form are important goals for Luffa breeders and this study aimed to shed light upon inheritance patterns for both these traits. The hermaphrodite form of Luffa acutangula (known as Satputia) is an underutilized vegetable with a unique clustered fruiting habit. Its desirable traits, such as plant architecture, earliness, as well as contrasting traits like unique clustered fruiting, bisexual flower, and crossability with Luffa acutangula (monoecious ridge gourd with solitary fruits), make it a potential source for trait improvement and mapping of desirable traits in Luffa. In the present study, we have elucidated the inheritance pattern of fruiting behaviour in Luffa using F2 mapping population generated from a cross between Pusa Nutan (Luffa acutangula, monoecious, solitary fruiting) × DSat-116 (Luffa acutangula, hermaphrodite, cluster fruiting). In F2 generation, the observed distribution of plant phenotypes fitted in the expected ratio of 3:1 (solitary vs cluster) for fruit-bearing habit. This is the first report of monogenic recessive control for cluster fruit-bearing habit in Luffa. Herein, we designate for the first time the gene symbol cl for cluster fruit bearing in Luffa. Linkage analysis revealed that SRAP marker ME10 EM4-280 was linked to the fruiting trait at the distance of 4.6 cM from the Cl locus. In addition, the inheritance pattern of hermaphrodite sex form in Luffa was also studied in the F2 population of Pusa Nutan × DSat-116 that segregated into 9:3:3:1 ratio (monoecious:andromonoecious:gynoecious:hermaphrodite), suggesting a digenic recessive control of hermaphrodite sex form in Luffa, which was further confirmed by the test cross. The inheritance and identification of molecular marker for cluster fruiting trait provides a basis for breeding in Luffa species.
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Affiliation(s)
- Nangsol D Bhutia
- College of Horticulture and Forestry, Central Agricultural University, Pasighat, Arunachal Pradesh, 791102, India
| | - Amish K Sureja
- ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, 110012, India.
| | - Manjusha Verma
- ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012, India
| | - S Gopala Krishnan
- ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, 110012, India
| | - Lalit Arya
- ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012, India
| | - Rakesh Bhardwaj
- ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012, India
| | - Prasanta K Dash
- ICAR-National Institute of Plant Biotechnology, Pusa, New Delhi, 110012, India
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Liu L, Gan Y, Luo J, Li J, Zheng X, Gong H, Liu X, Deng L, Zhao G, Wu H. QTL mapping reveals candidate genes for main agronomic traits in Luffa based on a high-resolution genetic map. FRONTIERS IN PLANT SCIENCE 2022; 13:1069618. [PMID: 36466279 PMCID: PMC9716215 DOI: 10.3389/fpls.2022.1069618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
Luffa is an important medicinal and edible vegetable crop of Cucurbitaceae. Strong heterosis effects and strikingly complementary characteristics were found between the two domesticated Luffa cultivars, Luffa acutangula and Luffa cylindrica. To explore the genetic basis underlying their important agronomic traits, we constructed the first interspecific high-density genetic linkage map using a BC1 population of 110 lines derived from a cross between S1174 (Luffa acutangula) and P93075 (Luffa cylindrica). The map spanned a total of 2246.74 cM with an average distance of 0.48 cM between adjacent markers. Thereafter, a large-scale field-based quantitative trait loci (QTLs) mapping was conducted for 25 important agronomic traits and 40 significant genetic loci distributed across 11 chromosomes were detected. Notably, a vital QTL (qID2) located on chromosome 9 with a minimum distance of 23 kb was identified to be responsible for the internode diameter and explained 11% of the phenotypic variation. Lac09g006860 (LacCRWN3), encoding a nuclear lamina protein involved in the control of nuclear morphology, was the only gene harbored in qID2. Sequence alignment showed completely different promoter sequences between the two parental alleles of LacCRWN3 except for some nonsynonymous single nucleotide polymorphisms (SNPs) in exons, and the expression level in thick-stem P93075 was distinctively higher than that in thin-stem S1174. According to the natural variation analysis of a population of 183 inbred lines, two main haplotypes were found for LacCRWN3: the P93075-like and S1174-like, with the former haplotype lines exhibiting significantly thicker internode diameters than those of the latter haplotype lines. It showed that LacCRWN3, as the only CRWN3 gene in Cucurbitaceae, was the most likely candidate gene regulating the internode diameter of Luffa. Our findings will be beneficial for deciphering the molecular mechanism of key phenotypic traits and promoting maker-assisted breeding in Luffa.
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Affiliation(s)
- Lili Liu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yaqin Gan
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Jianning Luo
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Junxing Li
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiaoming Zheng
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Hao Gong
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiaoxi Liu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Liting Deng
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Gangjun Zhao
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Haibin Wu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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Lavale SA, Mathew D, Pradeepkumar T, Joseph John K, Joseph J. Mapping the QTL and tagging yield traits in bitter gourd (Momordica charantia L.) using microsatellite markers. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Ma M, Meng H, Lei E, Wang T, Zhang W, Lu B. De novo transcriptome assembly, gene annotation, and EST-SSR marker development of an important medicinal and edible crop, Amomum tsaoko (Zingiberaceae). BMC PLANT BIOLOGY 2022; 22:467. [PMID: 36171538 PMCID: PMC9519402 DOI: 10.1186/s12870-022-03827-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 08/30/2022] [Indexed: 05/14/2023]
Abstract
BACKGROUND Amomum tsaoko is a medicinal and food dual-use crop that belongs to the Zingiberaceae family. However, the lack of transcriptomic and genomic information has limited the understanding of the genetic basis of this species. Here, we performed transcriptome sequencing of samples from different A. tsaoko tissues, and identified and characterized the expressed sequence tag-simple sequence repeat (EST-SSR) markers. RESULTS A total of 58,278,226 high-quality clean reads were obtained and de novo assembled to generate 146,911 unigenes with an N50 length of 2002 bp. A total of 128,174 unigenes were successfully annotated by searching seven protein databases, and 496 unigenes were identified as annotated as putative terpenoid biosynthesis-related genes. Furthermore, a total of 55,590 EST-SSR loci were detected, and 42,333 primer pairs were successfully designed. We randomly selected 80 primer pairs to validate their polymorphism in A. tsaoko; 18 of these primer pairs produced distinct, clear, and reproducible polymorphisms. A total of 98 bands and 96 polymorphic bands were amplified by 18 pairs of EST-SSR primers for the 72 A. tsaoko accessions. The Shannon's information index (I) ranged from 0.477 (AM208) to 1.701 (AM242) with an average of 1.183, and the polymorphism information content (PIC) ranged from 0.223 (AM208) to 0.779 (AM247) with an average of 0.580, indicating that these markers had a high level of polymorphism. Analysis of molecular variance (AMOVA) indicated relatively low genetic differentiation among the six A. tsaoko populations. Cross-species amplification showed that 14 of the 18 EST-SSR primer pairs have transferability between 11 Zingiberaceae species. CONCLUSIONS Our study is the first to provide transcriptome data of this important medicinal and edible crop, and these newly developed EST-SSR markers are a very efficient tool for germplasm evaluation, genetic diversity, and molecular marker-assisted selection in A. tsaoko.
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Affiliation(s)
- Mengli Ma
- Key Laboratory for Research and Utilization of Characteristic Biological Resources in Southern Yunnan, Honghe University, Mengzi, 661199, China
| | - Hengling Meng
- Key Laboratory for Research and Utilization of Characteristic Biological Resources in Southern Yunnan, Honghe University, Mengzi, 661199, China
| | - En Lei
- College of Biological and Agricultural Sciences, Honghe University, Mengzi, 661199, China
| | - Tiantao Wang
- College of Biological and Agricultural Sciences, Honghe University, Mengzi, 661199, China
| | - Wei Zhang
- Key Laboratory for Research and Utilization of Characteristic Biological Resources in Southern Yunnan, Honghe University, Mengzi, 661199, China
- College of Biological and Agricultural Sciences, Honghe University, Mengzi, 661199, China
| | - Bingyue Lu
- Key Laboratory for Research and Utilization of Characteristic Biological Resources in Southern Yunnan, Honghe University, Mengzi, 661199, China.
- College of Biological and Agricultural Sciences, Honghe University, Mengzi, 661199, China.
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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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Zhao G, Wang M, Luo C, Li J, Gong H, Zheng X, Liu X, Luo J, Wu H. Metabolome and Transcriptome Analyses of Cucurbitacin Biosynthesis in Luffa ( Luffa acutangula). FRONTIERS IN PLANT SCIENCE 2022; 13:886870. [PMID: 35747880 PMCID: PMC9209774 DOI: 10.3389/fpls.2022.886870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/13/2022] [Indexed: 05/17/2023]
Abstract
Cucurbitacins are extremely bitter compounds mainly present in Cucurbitaceae, where Luffa belongs. However, there is no comprehensive analysis of cucurbitacin biosynthesis in Luffa fruit. Therefore, this study analyzed bitter (WM709) and non-bitter (S1174) genotypes of Luffa to reveal the underlying mechanism of cucurbitacin biosynthesis by integrating metabolome and transcriptome analyses. A total of 422 metabolites were detected, including vitamins, essential amino acids, antioxidants, and antitumor substances. Of these, 131 metabolites showed significant differences between bitter (WM709) and non-bitter (S1174) Luffa fruits. The levels of isocucurbitacin B, cucurbitacin D, 23,24-dihydro cucurbitacin E, cucurbitacin F were significantly higher in bitter than in non-bitter Luffa. Transcriptome analysis showed that Bi, cytochromes P450s (CYP450s), and acyltransferase (ACT) of the cucurbitacin biosynthesis pathway, were significantly up-regulated. Moreover, drought stress and abscisic acid (ABA) activated genes of the cucurbitacin biosynthesis pathway. Furthermore, dual-luciferase reporter and yeast one-hybrid assays demonstrated that ABA-response element binding factor 1 (AREB1) binds to the Bi promoter to activate Bi expression. Comparative analysis of the Luffa and cucumber genomes showed that Bi, CYP450s, and ACT are located in the conserved syntenic loci, and formed a cucurbitacin biosynthesis cluster. This study provides important insights into major genes and metabolites of the cucurbitacin biosynthetic pathway, deepening the understanding of regulatory mechanisms of cucurbitacin biosynthesis in Luffa.
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Affiliation(s)
- Gangjun Zhao
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Meng Wang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Caixia Luo
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Junxing Li
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Hao Gong
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiaoming Zheng
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiaoxi Liu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jianning Luo
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Jianning Luo,
| | - Haibin Wu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- *Correspondence: Haibin Wu,
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Zhao G, Luo C, Luo J, Li J, Gong H, Zheng X, Liu X, Guo J, Zhou L, Wu H. A mutation in LacDWARF1 results in a GA-deficient dwarf phenotype in sponge gourd (Luffa acutangula). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3443-3457. [PMID: 34390352 PMCID: PMC8440308 DOI: 10.1007/s00122-021-03938-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 12/07/2020] [Indexed: 06/13/2023]
Abstract
KEY MESSAGE A dwarfism gene LacDWARF1 was mapped by combined BSA-Seq and comparative genomics analyses to a 65.4 kb physical genomic region on chromosome 05. Dwarf architecture is one of the most important traits utilized in Cucurbitaceae breeding because it saves labor and increases the harvest index. To our knowledge, there has been no prior research about dwarfism in the sponge gourd. This study reports the first dwarf mutant WJ209 with a decrease in cell size and internodes. A genetic analysis revealed that the mutant phenotype was controlled by a single recessive gene, which is designated Lacdwarf1 (Lacd1). Combined with bulked segregate analysis and next-generation sequencing, we quickly mapped a 65.4 kb region on chromosome 5 using F2 segregation population with InDel and SNP polymorphism markers. Gene annotation revealed that Lac05g019500 encodes a gibberellin 3β-hydroxylase (GA3ox) that functions as the most likely candidate gene for Lacd1. DNA sequence analysis showed that there is an approximately 4 kb insertion in the first intron of Lac05g019500 in WJ209. Lac05g019500 is transcribed incorrectly in the dwarf mutant owing to the presence of the insertion. Moreover, the bioactive GAs decreased significantly in WJ209, and the dwarf phenotype could be restored by exogenous GA3 treatment, indicating that WJ209 is a GA-deficient mutant. All these results support the conclusion that Lac05g019500 is the Lacd1 gene. In addition, RNA-Seq revealed that many genes, including those related to plant hormones, cellular process, cell wall, membrane and response to stress, were significantly altered in WJ209 compared with the wild type. This study will aid in the use of molecular marker-assisted breeding in the dwarf sponge gourd.
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Affiliation(s)
- Gangjun Zhao
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
| | - Caixia Luo
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
- College of Agriculture & Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
| | - Jianning Luo
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
| | - Junxing Li
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
| | - Hao Gong
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
| | - Xiaoming Zheng
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
| | - Xiaoxi Liu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
| | - Jinju Guo
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
| | - Lingyan Zhou
- College of Agriculture & Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
| | - Haibin Wu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China.
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Mkhize P, Mashilo J, Shimelis H. Progress on Genetic Improvement and Analysis of Bottle Gourd [Lagenaria siceraria (Molina) Standl.] for Agronomic Traits, Nutrient Compositions, and Stress Tolerance: A Review. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.683635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Bottle gourd [Lagenaria siceraria (Molina) Standl.] is an important multi-purpose cucurbit crop grown for its leaf, fruit, and seed. It is widely cultivated and used for human consumption in sub-Saharan Africa (SSA) providing vital human nutrition and serving as food security crop. There is wide genetic variation among bottle gourd genetic resources in Africa for diverse qualitative and quantitative attributes for effective variety design, product development, and marketing. However, the crop is under- researched and -utilized, and improved varieties are yet to be developed and commercialized in the region. Therefore, the objective of this review is to provide the progress on bottle gourd genetic improvement and genetic analysis targeting agronomic and horticultural attributes, nutritional composition, biotic, and abiotic stress tolerance to guide current and future cultivar development, germplasm access, and conservation in SSA. The first section of the paper presents progress on breeding of bottle gourd for horticultural traits, agronomic performance, nutritional and anti-nutritional composition, and biotic and abiotic stress tolerance. This is followed by important highlights on key genetic resources of cultivated and wild bottle gourd for demand driven breeding. Lastly, the review summaries advances in bottle gourd genomics, genetic engineering and genome editing. Information presented in this paper should aid bottle gourd breeders and agronomists to develop and deploy new generation and promising varieties with farmer- and market -preferred attributes.
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Pootakham W, Sonthirod C, Naktang C, Nawae W, Yoocha T, Kongkachana W, Sangsrakru D, Jomchai N, U-Thoomporn S, Sheedy JR, Buaboocha J, Mekiyanon S, Tangphatsornruang S. De novo assemblies of Luffa acutangula and Luffa cylindrica genomes reveal an expansion associated with substantial accumulation of transposable elements. Mol Ecol Resour 2020; 21:212-225. [PMID: 32841550 DOI: 10.1111/1755-0998.13240] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/30/2020] [Accepted: 08/04/2020] [Indexed: 01/22/2023]
Abstract
Luffa spp. (sponge gourd or ridge gourd) is an economically important vegetable crop widely cultivated in China, India and Southeast Asia. Here, we employed PacBio long-read single-molecule real-time (SMRT) sequencing to perform de novo genome assemblies of two commonly cultivated Luffa species, L. acutangula and L. cylindrica. We obtained preliminary draft genomes of 734.6 Mb and 689.8 Mb with scaffold N50 of 786,130 and 578,616 bases for L. acutangula and L. cylindrica, respectively. We also applied long-range Chicago and HiC techniques to obtain the first chromosome-scale whole-genome assembly of L. acutangula. The final assembly contained 13 pseudomolecules, corresponding to the haploid chromosome number in Luffa spp. (1n = 13, 2n = 26). The sizes of the assembled Luffa genomes are approximately twice as large as the genome assemblies of related Cucurbitaceae. A large proportion of L. acutangula (62.17%; 456.69 Mb) and L. cylindrica (56.78%; 391.65 Mb) genome assemblies contained repetitive elements. Phylogenetic analyses revealed that the substantial accumulation of transposable elements likely contributed to the expansion of the Luffa genomes. We also investigated alternative splicing events in Luffa using full-length transcript sequences obtained from PacBio Isoform Sequencing (Iso-seq). While the predominant form of alternative splicing in most plant species examined was intron retention, alternative 3' acceptor site selection appeared to be a major event observed in Luffa. High-quality genome assemblies for L. acutangula and L. cylindrica reported here provide valuable resources for Luffa breeding and future genetics and comparative genomics studies in Cucurbitaceae.
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Affiliation(s)
- Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chaiwat Naktang
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wanapinun Nawae
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Thippawan Yoocha
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wasitthee Kongkachana
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Duangjai Sangsrakru
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Nukoon Jomchai
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sonicha U-Thoomporn
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - John R Sheedy
- Chia Tai Company Limited, Phra Khanong District, Bangkok, Thailand
| | | | - Supat Mekiyanon
- Chia Tai Company Limited, Phra Khanong District, Bangkok, Thailand
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10
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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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11
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Lou L, Su X, Liu X, Liu Z. Construction of a high-density genetic linkage map and identification of gene controlling resistance to cucumber mosaic virus in Luffa cylindrica (L.) Roem. based on specific length amplified fragment sequencing. Mol Biol Rep 2020; 47:5831-5841. [PMID: 32700128 DOI: 10.1007/s11033-020-05652-8] [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: 02/24/2020] [Accepted: 07/08/2020] [Indexed: 10/23/2022]
Abstract
Luffa cylindrica L. is a cash crop which has important health, medicinal and industrial value, but no high saturation genetic map has been constructed owing to a lack of efficient markers. Furthermore, no genes were reportedly responsible for CMV resistance in Luffa spp. Specific length amplified fragment sequencing (SLAF-seq) is a valuable tool for large-scale discovery of markers and genetic mapping. The present study reported the construction of a high-density genetic map and the mapping of CMV resistant genes by using an F2 population of 130 individuals and their two inbred line parents. A total of 271.01 Mb pair-end reads were generated. 100,077 high-quality SLAFs were detected, and 7404 of them were polymorphic. Finally, 3701 of the polymorphic markers were selected for genetic map construction, and 13 linkage groups were generated. The map spanned 1518.56 cM with an average distance of 0.41 cM between adjacent markers. Based on the newly constructed high-density map, one gene located on chromosome 1 (100.072-100.457 cM) was identified to regulate CMV resistance in L. cylindrica. A gag-polypeptide of LTR copia-type retrotransposon was predicted as the candidate gene responsible for CMV resistance in L. cylindrica. The high-density genetic map and the CMV resistant gene mapped and predicted in this study will be useful in future research.
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Affiliation(s)
- Lina Lou
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences/Laboratory for Horticultural Crop Genetic Improvement, Zhongling Street 50, Nanjing, 210014, Jiangsu Province, China.
| | - Xiaojun Su
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences/Laboratory for Horticultural Crop Genetic Improvement, Zhongling Street 50, Nanjing, 210014, Jiangsu Province, China
| | - Xiaohong Liu
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences/Laboratory for Horticultural Crop Genetic Improvement, Zhongling Street 50, Nanjing, 210014, Jiangsu Province, China
| | - Zhe Liu
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences/Laboratory for Horticultural Crop Genetic Improvement, Zhongling Street 50, Nanjing, 210014, Jiangsu Province, China
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12
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Feng C, Yi H, Yang L, Kang M. The genetic basis of hybrid male sterility in sympatric Primulina species. BMC Evol Biol 2020; 20:49. [PMID: 32349663 PMCID: PMC7191819 DOI: 10.1186/s12862-020-01617-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 04/21/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Sympatric sister species provide an opportunity to investigate the genetic mechanisms and evolutionary forces that maintain species boundaries. The persistence of morphologically and genetically distinct populations in sympatry can only occur if some degree of reproductive isolation exists. A pair of sympatric sister species of Primulina (P. depressa and P. danxiaensis) was used to explore the genetic architecture of hybrid male sterility. RESULTS We mapped one major- and seven minor-effect quantitative trait loci (QTLs) that underlie pollen fertility rate (PFR). These loci jointly explained 55.4% of the phenotypic variation in the F2 population. A Bateson-Dobzhansky-Muller (BDM) model involving three loci was observed in this system. We found genotypic correlations between hybrid male sterility and flower morphology, consistent with the weak but significant phenotypic correlations between PFR and floral traits. CONCLUSIONS Hybrid male sterility in Primulina is controlled by a polygenic genetic basis with a complex pattern. The genetic incompatibility involves a three-locus BDM model. Hybrid male sterility is genetically correlated with floral morphology and divergence hitchhiking may occur between them.
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Affiliation(s)
- Chen Feng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650 China
| | - Huiqin Yi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Lihua Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650 China
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650 China
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13
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Zhang T, Ren X, Zhang Z, Ming Y, Yang Z, Hu J, Li S, Wang Y, Sun S, Sun K, Piao F, Sun Z. Long‐read sequencing and de novo assembly of the
Luffa cylindrica
(L.) Roem. genome. Mol Ecol Resour 2020; 20:511-519. [DOI: 10.1111/1755-0998.13129] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/27/2019] [Accepted: 12/18/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Tao Zhang
- College of Horticulture Henan Agricultural University Zhengzhou China
| | - Xuyan Ren
- College of Horticulture Henan Agricultural University Zhengzhou China
| | - Zhao Zhang
- College of Horticulture China Agricultural University Beijing China
| | - Yao Ming
- BGI‐Genomics BGI‐Shenzhen Shenzhen Guangdong China
| | - Zhe Yang
- College of Horticulture Henan Agricultural University Zhengzhou China
| | - Jianbin Hu
- College of Horticulture Henan Agricultural University Zhengzhou China
| | - Shengli Li
- College of Horticulture Henan Agricultural University Zhengzhou China
| | - Yong Wang
- Zhumadian City Academy of Agricultural Sciences Henan Agricultural Academy of Sciences Zhumadian China
| | - Shouru Sun
- College of Horticulture Henan Agricultural University Zhengzhou China
| | - Kaile Sun
- College of Horticulture Henan Agricultural University Zhengzhou China
| | - Fengzhi Piao
- College of Horticulture Henan Agricultural University Zhengzhou China
| | - Zhiqiang Sun
- College of Horticulture Henan Agricultural University Zhengzhou China
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Genome Survey Sequencing of Luffa Cylindrica L. and Microsatellite High Resolution Melting (SSR-HRM) Analysis for Genetic Relationship of Luffa Genotypes. Int J Mol Sci 2017; 18:ijms18091942. [PMID: 28891982 PMCID: PMC5618591 DOI: 10.3390/ijms18091942] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 08/25/2017] [Accepted: 09/07/2017] [Indexed: 12/20/2022] Open
Abstract
Luffa cylindrica (L.) Roem. is an economically important vegetable crop in China. However, the genomic information on this species is currently unknown. In this study, for the first time, a genome survey of L. cylindrica was carried out using next-generation sequencing (NGS) technology. In total, 43.40 Gb sequence data of L. cylindrica, about 54.94× coverage of the estimated genome size of 789.97 Mb, were obtained from HiSeq 2500 sequencing, in which the guanine plus cytosine (GC) content was calculated to be 37.90%. The heterozygosity of genome sequences was only 0.24%. In total, 1,913,731 contigs (>200 bp) with 525 bp N50 length and 1,410,117 scaffolds (>200 bp) with 885.01 Mb total length were obtained. From the initial assembled L. cylindrica genome, 431,234 microsatellites (SSRs) (≥5 repeats) were identified. The motif types of SSR repeats included 62.88% di-nucleotide, 31.03% tri-nucleotide, 4.59% tetra-nucleotide, 0.96% penta-nucleotide and 0.54% hexa-nucleotide. Eighty genomic SSR markers were developed, and 51/80 primers could be used in both “Zheda 23” and “Zheda 83”. Nineteen SSRs were used to investigate the genetic diversity among 32 accessions through SSR-HRM analysis. The unweighted pair group method analysis (UPGMA) dendrogram tree was built by calculating the SSR-HRM raw data. SSR-HRM could be effectively used for genotype relationship analysis of Luffa species.
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