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Xu Y, Yu F, Feng W, Wei J, Su S, Li J, Hua G, Li W, Tang Y. Genetic variation mining of the Chinese mitten crab (Eriocheir sinensis) based on transcriptome data from public databases. Brief Funct Genomics 2024:elae030. [PMID: 38984674 DOI: 10.1093/bfgp/elae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/02/2024] [Accepted: 06/25/2024] [Indexed: 07/11/2024] Open
Abstract
At present, public databases house an extensive repository of transcriptome data, with the volume continuing to grow at an accelerated pace. Utilizing these data effectively is a shared interest within the scientific community. In this study, we introduced a novel strategy that harnesses SNPs and InDels identified from transcriptome data, combined with sample metadata from databases, to effectively screen for molecular markers correlated with traits. We utilized 228 transcriptome datasets of Eriocheir sinensis from the NCBI database and employed the Genome Analysis Toolkit software to identify 96 388 SNPs and 20 645 InDels. Employing the genome-wide association study analysis, in conjunction with the gender information from databases, we identified 3456 sex-biased SNPs and 639 sex-biased InDels. The KOG and KEGG annotations of the sex-biased SNPs and InDels revealed that these genes were primarily involved in the metabolic processes of E. sinensis. Combined with SnpEff annotation and PCR experimental validation, a highly sex-biased SNP located in the Kelch domain containing 4 (Klhdc4) gene, CHR67-6415071, was found to alter the splicing sites of Klhdc4, generating two splice variants, Klhdc4_a and Klhdc4_b. Additionally, Klhdc4 exhibited robust expression across the ovaries, testes, and accessory glands. The sex-biased SNPs and InDels identified in this study are conducive to the development of unisexual cultivation methods for E. sinensis, and the alternative splicing event caused by the sex-biased SNP in Klhdc4 may serve as a potential mechanism for sex regulation in E. sinensis. The analysis strategy employed in this study represents a new direction for the rational exploitation and utilization of transcriptome data in public databases.
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Affiliation(s)
- Yuanfeng Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214128, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Fan Yu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214128, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Wenrong Feng
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214128, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Jia Wei
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214128, China
| | - Shengyan Su
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214128, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Jianlin Li
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214128, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Guoan Hua
- Jiangsu Haorun Biological Industry Group Co., Ltd, Taizhou 225309, China
| | - Wenjing Li
- Jiangsu Haorun Biological Industry Group Co., Ltd, Taizhou 225309, China
| | - Yongkai Tang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214128, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
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Nair RM, Chaudhari S, Devi N, Shivanna A, Gowda A, Boddepalli VN, Pradhan H, Schafleitner R, Jegadeesan S, Somta P. Genetics, genomics, and breeding of black gram [ Vigna mungo (L.) Hepper]. FRONTIERS IN PLANT SCIENCE 2024; 14:1273363. [PMID: 38288416 PMCID: PMC10822891 DOI: 10.3389/fpls.2023.1273363] [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: 08/06/2023] [Accepted: 12/18/2023] [Indexed: 01/31/2024]
Abstract
Black gram [Vigna mungo (L.) Hepper] is a highly nutritious grain legume crop, mainly grown in South and Southeast Asia, with the largest area in India, where the crop is challenged by several biotic and abiotic stresses leading to significant yield losses. Improving genetic gains to increase on-farm yields is the primary goal of black gram breeding programs. This could be achieved by developing varieties resistant to major diseases like mungbean yellow mosaic disease, urdbean leaf crinkle virus, Cercospora leaf spot, anthracnose, powdery mildew, and insect pests such as whitefly, cowpea aphids, thrips, stem flies, and bruchids. Along with increasing on-farm yields, incorporating market-preferred traits ensures the adoption of improved varieties. Black gram breeding programs rely upon a limited number of parental lines, leading to a narrow genetic base of the developed varieties. For accelerating genetic gain, there is an urgent need to include more diverse genetic material for improving traits for better adaptability and stress resistance in breeding populations. The present review summarizes the importance of black gram, the major biotic and abiotic stresses, available genetic and genomic resources, major traits for potential crop improvement, their inheritance, and the breeding approaches being used in black gram for the development of new varieties.
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Hazra A, Pal A, Kundu A. Alternative splicing shapes the transcriptome complexity in blackgram [Vigna mungo (L.) Hepper]. Funct Integr Genomics 2023; 23:144. [PMID: 37133618 DOI: 10.1007/s10142-023-01066-4] [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: 01/26/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 05/04/2023]
Abstract
Vigna mungo, a highly consumed crop in the pan-Asian countries, is vulnerable to several biotic and abiotic stresses. Understanding the post-transcriptional gene regulatory cascades, especially alternative splicing (AS), may underpin large-scale genetic improvements to develop stress-resilient varieties. Herein, a transcriptome based approach was undertaken to decipher the genome-wide AS landscape and splicing dynamics in order to establish the intricacies of their functional interactions in various tissues and stresses. RNA sequencing followed by high-throughput computational analyses identified 54,526 AS events involving 15,506 AS genes that generated 57,405 transcripts isoforms. Enrichment analysis revealed their involvement in diverse regulatory functions and demonstrated that transcription factors are splicing-intensive, splice variants of which are expressed differentially across tissues and environmental cues. Increased expression of a splicing regulator NHP2L1/SNU13 was found to co-occur with lower intron retention events. The host transcriptome is significantly impacted by differential isoform expression of 1172 and 765 AS genes that resulted in 1227 (46.8% up and 53.2% downregulated) and 831 (47.5% up and 52.5% downregulated) transcript isoforms under viral pathogenesis and Fe2+ stressed condition, respectively. However, genes experiencing AS operate differently from the differentially expressed genes, suggesting AS is a unique and independent mode of regulatory mechanism. Therefore, it can be inferred that AS mediates a crucial regulatory role across tissues and stressful situations and the results would provide an invaluable resource for future endeavours in V. mungo genomics.
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Affiliation(s)
- Anjan Hazra
- Agricultural and Ecological Research Unit, Indian Statistical Institute, 203, B. T. Road, Kolkata, 700108, India
- Department of Genetics, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, India
| | - Amita Pal
- Division of Plant Biology, Bose Institute, Kolkata, 700091, India.
| | - Anirban Kundu
- Plant Genomics and Bioinformatics Laboratory, P.G. Department of Botany, Ramakrishna Mission Vivekananda Centenary College (Autonomous), Rahara, Kolkata, 700118, India.
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Majhi S, Sikdar (née Bhakta) M. How heavy metal stress affects the growth and development of pulse crops: insights into germination and physiological processes. 3 Biotech 2023; 13:155. [PMID: 37138782 PMCID: PMC10149436 DOI: 10.1007/s13205-023-03585-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 04/23/2023] [Indexed: 05/05/2023] Open
Abstract
The current work is an extensive review addressing the effects of heavy metals in major pulse crops such as Chickpea (Cicer arietinum L.), Pea (Pisum sativum L.), Pigeonpea (Cajanus cajan L.), Mung bean (Vigna radiata L.), Black gram (Vigna mungo L.) and Lentil (Lens culinaris Medik.). Pulses are important contributors to the global food supply in the world, due to their vast beneficial properties in providing protein, nutritional value and health benefits to the human population. Several studies have reported that heavy metals are injurious to plants causing inhibition in plant germination, a decrease in the root and shoot length, reduction in respiration rate and photosynthesis. Properly disposing of heavy metal wastes has become an increasingly difficult task to solve in developed countries. Heavy metals pose one of the substantial constraints to pulse crops growth and productivity even at low concentrations. This article attempts to present the morphological, biochemical and various physiological changes induced on the pulse crops grown under various heavy metal stress such as As, Cd, Cr, Cu, Pb, and Ni.
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Affiliation(s)
- Sudipta Majhi
- Microbiology, Nutrition and Dietetics Laboratory, Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, West Bengal 700073 India
| | - Mausumi Sikdar (née Bhakta)
- Microbiology, Nutrition and Dietetics Laboratory, Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, West Bengal 700073 India
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Liu C, Zhang M, Zhao X. Development of unigene-derived SSR markers from RNA-seq data of Uraria lagopodioides (Fabaceae) and their application in the genus Uraria Desv. (Fabaceae). BMC PLANT BIOLOGY 2023; 23:87. [PMID: 36759771 PMCID: PMC9912670 DOI: 10.1186/s12870-023-04086-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Uraria Desv. belongs to the tribe Desmodieae (Fabaceae), a group of legume plants, some of which have medicinal properties. However, due to a lack of genomic information, the interspecific relationships, genetic diversity, population genetics, and identification of functional genes within Uraria species are still unclear. RESULTS Using RNA-Seq, a total of 66,026 Uraria lagopodioides unigenes with a total sequence content of 52,171,904 bp were obtained via de novo assembly and annotated using GO, KEGG, and KOG databases. 17,740 SSRs were identified from a set of 66,026 unigenes. Cross-species amplification showed that 54 out of 150 potential unigene-derived SSRs were transferable in Uraria, of which 19 polymorphic SSRs were developed. Cluster analysis based on polymorphisms successfully distinguished seven Uraria species and revealed their interspecific relationships. Seventeen samples of seven Uraria species were clustered into two monophyletic clades, and phylogenetic relationships of Uraria species based on unigene-derived SSRs were consistent with classifications based on morphological characteristics. CONCLUSIONS Unigenes annotated in the present study will provide new insights into the functional genomics of Uraria species. Meanwhile, the unigene-derived SSR markers developed here will be invaluable for assessing the genetic diversity and evolutionary history of Uraria and relatives.
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Affiliation(s)
- Chaoyu Liu
- College of Forestry, Southwest Forestry University, Kunming, 650224, China
| | - Maomao Zhang
- College of Forestry, Southwest Forestry University, Kunming, 650224, China
| | - Xueli Zhao
- College of Forestry, Southwest Forestry University, Kunming, 650224, China.
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China, Southwest Forestry University, Kunming, 650224, China.
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Dossou SSK, Song S, Liu A, Li D, Zhou R, Berhe M, Zhang Y, Sheng C, Wang Z, You J, Wang L. Resequencing of 410 Sesame Accessions Identifies SINST1 as the Major Underlying Gene for Lignans Variation. Int J Mol Sci 2023; 24:ijms24021055. [PMID: 36674569 PMCID: PMC9860558 DOI: 10.3390/ijms24021055] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 01/06/2023] Open
Abstract
Sesame is a promising oilseed crop that produces specific lignans of clinical importance. Hence, a molecular description of the regulatory mechanisms of lignan biosynthesis is essential for crop improvement. Here, we resequence 410 sesame accessions and identify 5.38 and 1.16 million SNPs (single nucleotide polymorphisms) and InDels, respectively. Population genomic analyses reveal that sesame has evolved a geographic pattern categorized into northern (NC), middle (MC), and southern (SC) groups, with potential origin in the southern region and subsequent introduction to the other regions. Selective sweeps analysis uncovers 120 and 75 significant selected genomic regions in MC and NC groups, respectively. By screening these genomic regions, we unveiled 184 common genes positively selected in these subpopulations for exploitation in sesame improvement. Genome-wide association study identifies 17 and 72 SNP loci for sesamin and sesamolin variation, respectively, and 11 candidate causative genes. The major pleiotropic SNPC/A locus for lignans variation is located in the exon of the gene SiNST1. Further analyses revealed that this locus was positively selected in higher lignan content sesame accessions, and the "C" allele is favorable for a higher accumulation of lignans. Overexpression of SiNST1C in sesame hairy roots significantly up-regulated the expression of SiMYB58, SiMYB209, SiMYB134, SiMYB276, and most of the monolignol biosynthetic genes. Consequently, the lignans content was significantly increased, and the lignin content was slightly increased. Our findings provide insights into lignans and lignin regulation in sesame and will facilitate molecular breeding of elite varieties and marker-traits association studies.
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Affiliation(s)
- Senouwa Segla Koffi Dossou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Laboratory of Plant Physiology and Biotechnologies, Faculty of Sciences, University of Lomé, Lomé 01BP 1515, Togo
| | - Shengnan Song
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Aili Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Donghua Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Rong Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Muez Berhe
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Yanxin Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Chen Sheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Zhijian Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Correspondence: (J.Y.); (L.W.); Tel.: +86-18607147952 (J.Y.); +86-15926338805 (L.W.)
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Correspondence: (J.Y.); (L.W.); Tel.: +86-18607147952 (J.Y.); +86-15926338805 (L.W.)
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Verma SK, Singh CK, Taunk J, Gayacharan, Chandra Joshi D, Kalia S, Dey N, Singh AK. Vignette of Vigna domestication: From archives to genomics. Front Genet 2022; 13:960200. [PMID: 36338960 PMCID: PMC9634637 DOI: 10.3389/fgene.2022.960200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 09/27/2022] [Indexed: 06/26/2024] Open
Abstract
The genus Vigna comprises fast-growing, diploid legumes, cultivated in tropical and subtropical parts of the world. It comprises more than 200 species among which Vigna angularis, Vigna radiata, Vigna mungo, Vigna aconitifolia, Vigna umbellata, Vigna unguiculata, and Vigna vexillata are of enormous agronomic importance. Human selection along with natural variability within these species encompasses a vital source for developing new varieties. The present review convokes the early domestication history of Vigna species based on archeological pieces of evidence and domestication-related traits (DRTs) together with genetics of domestication. Traces of early domestication of Vigna have been evidenced to spread across several temperate and tropical regions of Africa, Eastern Asia, and few parts of Europe. Several DRTs of Vigna species, such as pod shattering, pod and seed size, dormancy, seed coat, seed color, maturity, and pod dehiscence, can clearly differentiate wild species from their domesticates. With the advancement in next-generation high-throughput sequencing techniques, exploration of genetic variability using recently released reference genomes along with de novo sequencing of Vigna species have provided a framework to perform genome-wide association and functional studies to figure out different genes related to DRTs. In this review, genes and quantitative trait loci (QTLs) related to DRTs of different Vigna species have also been summarized. Information provided in this review will enhance the in-depth understanding of the selective pressures that causes crop domestication along with nature of evolutionary selection made in unexplored Vigna species. Furthermore, correlated archeological and domestication-related genetic evidence will facilitate Vigna species to be considered as suitable model plants.
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Affiliation(s)
| | | | - Jyoti Taunk
- Department of Biotechnology, University Centre for Research and Development, Chandigarh University, Mohali, Punjab, India
| | - Gayacharan
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Dinesh Chandra Joshi
- ICAR-Vivekananda Institute of Hill Agriculture (Vivekananda Parvatiya Krishi Anusandhan Sansthan), Uttarakhand, Almora, India
| | - Sanjay Kalia
- Department of Biotechnology, Ministry of Science and Technology, New Delhi, India
| | - Nrisingha Dey
- Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Amit Kumar Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
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Jha UC, Nayyar H, Parida SK, Bakır M, von Wettberg EJB, Siddique KHM. Progress of Genomics-Driven Approaches for Sustaining Underutilized Legume Crops in the Post-Genomic Era. Front Genet 2022; 13:831656. [PMID: 35464848 PMCID: PMC9021634 DOI: 10.3389/fgene.2022.831656] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/24/2022] [Indexed: 12/22/2022] Open
Abstract
Legume crops, belonging to the Fabaceae family, are of immense importance for sustaining global food security. Many legumes are profitable crops for smallholder farmers due to their unique ability to fix atmospheric nitrogen and their intrinsic ability to thrive on marginal land with minimum inputs and low cultivation costs. Recent progress in genomics shows promise for future genetic gains in major grain legumes. Still it remains limited in minor legumes/underutilized legumes, including adzuki bean, cluster bean, horse gram, lathyrus, red clover, urd bean, and winged bean. In the last decade, unprecedented progress in completing genome assemblies of various legume crops and resequencing efforts of large germplasm collections has helped to identify the underlying gene(s) for various traits of breeding importance for enhancing genetic gain and contributing to developing climate-resilient cultivars. This review discusses the progress of genomic resource development, including genome-wide molecular markers, key breakthroughs in genome sequencing, genetic linkage maps, and trait mapping for facilitating yield improvement in underutilized legumes. We focus on 1) the progress in genomic-assisted breeding, 2) the role of whole-genome resequencing, pangenomes for underpinning the novel genomic variants underlying trait gene(s), 3) how adaptive traits of wild underutilized legumes could be harnessed to develop climate-resilient cultivars, 4) the progress and status of functional genomics resources, deciphering the underlying trait candidate genes with putative function in underutilized legumes 5) and prospects of novel breeding technologies, such as speed breeding, genomic selection, and genome editing. We conclude the review by discussing the scope for genomic resources developed in underutilized legumes to enhance their production and play a critical role in achieving the "zero hunger" sustainable development goal by 2030 set by the United Nations.
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Affiliation(s)
- Uday Chand Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, India
| | | | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Melike Bakır
- Department of Agricultural Biotechnology, Faculty of Agriculture, Erciyes University, Kayseri, Turkey
| | - Eric J. B. von Wettberg
- Plant and Soil Science and Gund Institute for the Environment, The University of Vermont, Burlington, VT, United States
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
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Sen Gupta D, Basu PS, Souframanien J, Kumar J, Dhanasekar P, Gupta S, Pandiyan M, Geetha S, Shanthi P, Kumar V, Pratap Singh N. Morpho-Physiological Traits and Functional Markers Based Molecular Dissection of Heat-Tolerance in Urdbean. FRONTIERS IN PLANT SCIENCE 2021; 12:719381. [PMID: 34659290 PMCID: PMC8511409 DOI: 10.3389/fpls.2021.719381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Urdbean (Vigna mungo L. Hepper) is one of the important pulse crops. Its cultivation is not so popular during summer seasons because this crop is unable to withstand excessive heat stress beside lack of humidity in the atmosphere. Therefore, a panel of 97 urdbean diverse genotypes was assessed for yield under stress and non-stress conditions with an aim to identify heat tolerant genotypes. This study identified 8 highly heat tolerant and 35 highly heat sensitive genotypes based on heat susceptibility index. Further, physiological and biochemical traits-based characterization of a group of six highly heat sensitive and seven highly heat tolerant urdbean genotypes showed genotypic variability for leaf nitrogen balance index (NBI), chlorophyll (SPAD), epidermal flavnols, and anthocyanin contents under 42/25°C max/min temperature. Our results showed higher membrane stability index among heat tolerant genotypes compared to sensitive genotypes. Significant differences among genotypes for ETR at different levels of PAR irradiances and PAR × genotypes interactions indicated high photosynthetic ability of a few genotypes under heat stress. Further, the most highly sensitive genotype PKGU-1 showed a decrease in different fluorescence parameters indicating distortion of PS II. Consequently, reduction in the quantum yield of PS II was observed in a sensitive one as compared to a tolerant genotype. Fluorescence kinetics showed the delayed and fast quenching of Fm in highly heat sensitive (PKGU 1) and tolerant (UPU 85-86) genotypes, respectively. Moreover, tolerant genotype (UPU 85-86) had high antioxidant activities explaining their role for scavenging superoxide radicals (ROS) protecting delicate membranes from oxidative damage. Molecular characterization further pinpointed genetic differences between heat tolerant (UPU 85-86) and heat sensitive genotypes (PKGU 1). These findings will contribute to the breeding toward the development of heat tolerant cultivars in urdbean.
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Affiliation(s)
- Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
- All India Coordinated Research Project on Mungbean, Urdbean, Lentil, Lathyrus, Rajmash, and Fieldpea, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Partha S. Basu
- Division of Basic Sciences, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - J. Souframanien
- Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - P. Dhanasekar
- Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Sanjeev Gupta
- All India Coordinated Research Project on Mungbean, Urdbean, Lentil, Lathyrus, Rajmash, and Fieldpea, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | | | - S. Geetha
- National Pulses Research Centre, Vamban, India
| | - P. Shanthi
- National Pulses Research Centre, Vamban, India
| | - Vaibhav Kumar
- Division of Basic Sciences, ICAR-Indian Institute of Pulses Research, Kanpur, India
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Zhang K, He M, Fan Y, Zhao H, Gao B, Yang K, Li F, Tang Y, Gao Q, Lin T, Quinet M, Janovská D, Meglič V, Kwiatkowski J, Romanova O, Chrungoo N, Suzuki T, Luthar Z, Germ M, Woo SH, Georgiev MI, Zhou M. Resequencing of global Tartary buckwheat accessions reveals multiple domestication events and key loci associated with agronomic traits. Genome Biol 2021; 22:23. [PMID: 33430931 PMCID: PMC7802136 DOI: 10.1186/s13059-020-02217-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 12/03/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Tartary buckwheat (Fagopyrum tataricum) is a nutritionally balanced and flavonoid-rich crop plant that has been in cultivation for 4000 years and is now grown globally. Despite its nutraceutical and agricultural value, the characterization of its genetics and its domestication history is limited. RESULTS Here, we report a comprehensive database of Tartary buckwheat genomic variation based on whole-genome resequencing of 510 germplasms. Our analysis suggests that two independent domestication events occurred in southwestern and northern China, resulting in diverse characteristics of modern Tartary buckwheat varieties. Genome-wide association studies for important agricultural traits identify several candidate genes, including FtUFGT3 and FtAP2YT1 that significantly correlate with flavonoid accumulation and grain weight, respectively. CONCLUSIONS We describe the domestication history of Tartary buckwheat and provide a detailed resource of genomic variation to allow for genomic-assisted breeding in the improvement of elite cultivars.
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Affiliation(s)
- Kaixuan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Room 107, Ziyuan North Building, Xueyuan South Road No. 80, Haidian District, Beijing, 100081 China
| | - Ming He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Room 107, Ziyuan North Building, Xueyuan South Road No. 80, Haidian District, Beijing, 100081 China
| | - Yu Fan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Room 107, Ziyuan North Building, Xueyuan South Road No. 80, Haidian District, Beijing, 100081 China
| | - Hui Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Room 107, Ziyuan North Building, Xueyuan South Road No. 80, Haidian District, Beijing, 100081 China
| | - Bin Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Room 107, Ziyuan North Building, Xueyuan South Road No. 80, Haidian District, Beijing, 100081 China
| | - Keli Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Room 107, Ziyuan North Building, Xueyuan South Road No. 80, Haidian District, Beijing, 100081 China
| | - Faliang Li
- Research Station of Alpine Crop, Xichang Institute of Agricultural Sciences, Liangshan, 616150 Sichuan China
| | - Yu Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Room 107, Ziyuan North Building, Xueyuan South Road No. 80, Haidian District, Beijing, 100081 China
| | - Qiang Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen, 58083 Guangdong China
| | - Tao Lin
- College of Horticulture, China Agricultural University, Beijing, 100083 China
| | - Muriel Quinet
- Groupe de Recherche en Physiologie Végétale (GRPV), Earth and Life Institute-Agronomy (ELI-A), Université catholique de Louvain, Croix du Sud 45, boîte L7.07.13, B-1348 Louvain-la-Neuve, Belgium
| | - Dagmar Janovská
- Gene Bank, Crop Research Institute, Drnovská 507, Prague 6, Czech Republic
| | - Vladimir Meglič
- Agricultural Institute of Slovenia, Hacquetova ulica, Ljubljana, Slovenia
| | - Jacek Kwiatkowski
- Department of Plant Breeding and Seed Production, University of Warmia and Mazury in Olsztyn, Plac Łódzki 3, 10-724 Olsztyn, Poland
| | - Olga Romanova
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), Bol’shaya Morskaya, 42-44, St. Petersburg, Russia 190000
| | - Nikhil Chrungoo
- Department of Botany, North Eastern Hill University, Shillong, 793022 India
| | - Tatsuro Suzuki
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Suya 2421, Koshi, Kumamoto 861-1192 Japan
| | - Zlata Luthar
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Mateja Germ
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Sun-Hee Woo
- Department of Crop Science, Chungbuk National University, Cheong-ju, Republic of Korea
| | - Milen I. Georgiev
- Group of Plant Cell Biotechnology and Metabolomics, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Plovdiv, Bulgaria
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Meiliang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Room 107, Ziyuan North Building, Xueyuan South Road No. 80, Haidian District, Beijing, 100081 China
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11
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Pootakham W, Nawae W, Naktang C, Sonthirod C, Yoocha T, Kongkachana W, Sangsrakru D, Jomchai N, U-Thoomporn S, Somta P, Laosatit K, Tangphatsornruang S. A chromosome-scale assembly of the black gram (Vigna mungo) genome. Mol Ecol Resour 2020; 21:238-250. [PMID: 32794377 DOI: 10.1111/1755-0998.13243] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/05/2020] [Accepted: 08/10/2020] [Indexed: 02/06/2023]
Abstract
Black gram (Vigna mungo) is an important short duration grain legume crop. Black gram seeds provide an inexpensive source of dietary protein. Here, we applied the 10X Genomics linked-read technology to obtain a de novo whole genome assembly of V. mungo cultivated variety Chai Nat 80 (CN80). The preliminary assembly contained 12,228 contigs and had an N50 length of 5.2 Mb. Subsequent scaffolding using the long-range Chicago and HiC techniques yielded the first high-quality, chromosome-level assembly of 499 Mb comprising 11 pseudomolecules. Comparative genomics analyses based on sequence information from single-copy orthologous genes revealed that black gram and mungbean (Vigna radiata) diverged about 2.7 million years ago . The transversion rate (4DTv) analysis in V. mungo revealed no evidence supporting a recent genome-wide duplication event observed in the tetraploid créole bean (Vigna reflexo-pilosa). The proportion of repetitive elements in the black gram genome is slightly lower than the numbers reported for related Vigna species. The majority of long terminal repeat retrotransposons appeared to integrate into the genome within the last five million years. We also examined alternative splicing events in V. mungo using full-length transcript sequences. While intron retention was the most prevalent mode of alternative splicing in several plant species, alternative 3' acceptor site selection represented the majority of events in black gram. Our high-quality genome assembly along with the genomic variation information from the germplasm provides valuable resources for accelerating the development of elite varieties through marker-assisted breeding and for future comparative genomics and phylogenetic studies in legume species.
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Affiliation(s)
- Wirulda Pootakham
- 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
| | - Chaiwat Naktang
- 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
| | - 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
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Kularb Laosatit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
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12
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Manimekalai R, Suresh G, Govinda Kurup H, Athiappan S, Kandalam M. Role of NGS and SNP genotyping methods in sugarcane improvement programs. Crit Rev Biotechnol 2020; 40:865-880. [PMID: 32508157 DOI: 10.1080/07388551.2020.1765730] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Sugarcane (Saccharum spp.) is one of the most economically significant crops because of its high sucrose content and it is a promising biomass feedstock for biofuel production. Sugarcane genome sequencing and analysis is a difficult task due to its heterozygosity and polyploidy. Long sequence read technologies, PacBio Single-Molecule Real-Time (SMRT) sequencing, the Illumina TruSeq, and the Oxford Nanopore sequencing could solve the problem of genome assembly. On the applications side, next generation sequencing (NGS) technologies played a major role in the discovery of single nucleotide polymorphism (SNP) and the development of low to high throughput genotyping platforms. The two mainstream high throughput genotyping platforms are the SNP microarray and genotyping by sequencing (GBS). This paper reviews the NGS in sugarcane genomics, genotyping methodologies, and the choice of these methods. Array-based SNP genotyping is robust, provides consistent SNPs, and relatively easier downstream data analysis. The GBS method identifies large scale SNPs across the germplasm. A combination of targeted GBS and array-based genotyping methods should be used to increase the accuracy of genomic selection and marker-assisted breeding.
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Affiliation(s)
- Ramaswamy Manimekalai
- Crop Improvement Division, ICAR - Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, India
| | - Gayathri Suresh
- Crop Improvement Division, ICAR - Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, India
| | - Hemaprabha Govinda Kurup
- Crop Improvement Division, ICAR - Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, India
| | - Selvi Athiappan
- Crop Improvement Division, ICAR - Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, India
| | - Mallikarjuna Kandalam
- Business Development, Asia Pacific Japan region, Thermo Fisher Scientific, Waltham, MA, USA
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13
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Papaioannou C, Zeliou K, Trigas P, Papasotiropoulos V. High Resolution Melting (HRM) Genotyping in the Genus Origanum: Molecular Identification and Discrimination for Authentication Purposes. Biochem Genet 2020; 58:725-737. [PMID: 32394225 DOI: 10.1007/s10528-020-09970-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 05/04/2020] [Indexed: 12/25/2022]
Abstract
Origanum L. (Lamiaceae) is an important genus of medicinal and aromatic plants used since ancient times as culinary herbs and remedies in traditional medicine. Although it is a relatively small genus, intra-generic species delineation, as well as its inter-generic relationships within tribe Mentheae, are still poorly understood. High resolution melting (HRM) analysis, coupled with microsatellite markers (SSRs), could facilitate the molecular identification and characterization of certain genotypes more efficiently and relatively faster when compared to other analytical methods. In this study, 38 Origanum samples corresponding to six Origanum taxa (O. dictamnus, O. majorana, O. onites, O. scabrum, O. sipyleum, and O. vulgare subsp. hirtum) were analyzed, using six microsatellite loci. Our goal was to molecularly identify and discriminate among the selected samples and to evaluate the ability of the HRM technique as an analytical tool for the discrimination of Origanum species from Greece. The temperature-shifted melting curves produced by the HRM analysis, resulted in 98 unique HRM profiles, which enabled the discrimination of the Origanum genotypes studied. According to the similarity dendrogram based on the HRM profiles, six unique clusters were formed, each one corresponding to a single taxon. In conclusion, HRM genotyping provided a fast, cost-effective method, well suited for the molecular characterization and identification of Origanum taxa and for the authentication of the original genetic material.
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Affiliation(s)
- Charikleia Papaioannou
- Department of Agriculture, University of Patras, Theodoropoulou Str, 27200, Amaliada, Greece.,Laboratory of Genetics, Department of Biology, University of Patras, 26504, Patras, Greece
| | - Konstantina Zeliou
- Laboratory of Pharmacognosy and Chemistry of Natural Products, Department of Pharmacy, University of Patras, 26504, Patras, Greece
| | - Panayiotis Trigas
- Laboratory of Systematic Botany, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
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