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Pradeepkumara N, Sharma PK, Munshi AD, Behera TK, Bhatia R, Kumari K, Singh J, Jaiswal S, Iquebal MA, Arora A, Rai A, Kumar D, Bhattacharya RC, Dey SS. Fruit transcriptional profiling of the contrasting genotypes for shelf life reveals the key candidate genes and molecular pathways regulating post-harvest biology in cucumber. Genomics 2022; 114:110273. [PMID: 35092817 DOI: 10.1016/j.ygeno.2022.110273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 02/07/2023]
Abstract
Cucumber fruits are perishable in nature and become unfit for market within 2-3 days of harvesting. A natural variant, DC-48 with exceptionally high shelf life was developed and used to dissect the genetic architecture and molecular mechanism for extended shelf life through RNA-seq for first time. A total of 1364 DEGs were identified and cell wall degradation, chlorophyll and ethylene metabolism related genes played key role. Polygalacturunase (PG), Expansin (EXP) and xyloglucan were down regulated determining fruit firmness and retention of fresh green colour was mainly attributed to the low expression level of the chlorophyll catalytic enzymes (CCEs). Gene regulatory networks revealed the hub genes and cross-talk associated with wide variety of the biological processes. Large number of SSRs (21524), SNPs (545173) and InDels (126252) identified will be instrumental in cucumber improvement. A web genomic resource, CsExSLDb developed will provide a platform for future investigation on cucumber post-harvest biology.
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Affiliation(s)
- N Pradeepkumara
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Parva Kumar Sharma
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - A D Munshi
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - T K Behera
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Reeta Bhatia
- Division of Floriculture and Landscaping, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Khushboo Kumari
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Jogendra Singh
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Sarika Jaiswal
- 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
| | - Ajay Arora
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - R C Bhattacharya
- ICAR-National Institute of Plant Biotechnology, New Delhi, India
| | - S S Dey
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India.
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Rakshita KN, Singh S, Verma VK, Sharma BB, Saini N, Iquebal MA, Behera TK. Correction to: Understanding population structure and detection of QTLs for curding related traits in Indian cauliflower by genotyping by sequencing analysis. Funct Integr Genomics 2021; 22:139. [PMID: 34800205 DOI: 10.1007/s10142-021-00817-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- K N Rakshita
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Shrawan Singh
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India.
| | | | - Brij Bihari Sharma
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Navinder Saini
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- ICAR-Indian Agricultural Statistical Research Institute, New Delhi, India
| | - T K Behera
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Rakshita KN, Singh S, Verma VK, Sharma BB, Saini N, Iquebal MA, Behera TK. Understanding population structure and detection of QTLs for curding-related traits in Indian cauliflower by genotyping by sequencing analysis. Funct Integr Genomics 2021; 21:679-693. [PMID: 34664160 DOI: 10.1007/s10142-021-00811-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 10/20/2022]
Abstract
Curd initiation and development are complex traits and highly responsive for different temperature ranges in cauliflower. The present study was aimed to identify QTLs for eight traits associated with curding behaviour in diverse germplasm of Indian cauliflower. For this, 92 genotypes of cauliflower and 2 each of tropical broccoli and cabbage were genotyped through genotyping by sequencing (GBS). It generated ≈302 million reads (9.1226E + 10 bp) and identified 35,381 SNPs, maximum from chromosome 3 (4735) with a mean value of 3981.1 SNPs. Ts/Tv ratio was 1.74, suggesting transition bias. STRUCTURE analysis revealed delta value of K = 4 and four subpopulations and prominence of population admixture. In total, 121 significant SNPs were detected for eight traits, 38 for Delhi (North Indian plain) and 83 for Barapani (North-East India). Twelve QTLs were detected for traits associated with regulation of curd formation and development, five of which were for marketable curd length, curd width, days to 50% curd harvest and marketable curd weight from Delhi region and seven for curd length, curd width, days to 50% curd harvest, gross plant weight, leaf length, marketable/net curd weight and number of leaves per plant for Barapani area of North East India. The SNPs identified will be useful for development of markers for curding-related traits and their use in breeding varieties with wider curding plasticity.
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Affiliation(s)
- K N Rakshita
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Shrawan Singh
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India.
| | | | - Brij Bihari Sharma
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Navinder Saini
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- ICAR-Indian Agricultural Statistical Research Institute, New Delhi, India
| | - T K Behera
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Rao PG, Behera TK, Gaikwad AB, Munshi AD, Srivastava A, Boopalakrishnan G, Vinod. Author Correction: Genetic analysis and QTL mapping of yield and fruit traits in bitter gourd (Momordica charantia L.). Sci Rep 2021; 11:12664. [PMID: 34112909 PMCID: PMC8192739 DOI: 10.1038/s41598-021-91764-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Singh S, Dey SS, Bhatia R, Kumar R, Behera TK. Current understanding of male sterility systems in vegetable Brassicas and their exploitation in hybrid breeding. Plant Reprod 2019; 32:231-256. [PMID: 31053901 DOI: 10.1007/s00497-019-00371-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 04/25/2019] [Indexed: 06/09/2023]
Abstract
Overview of the current status of GMS and CMS systems available in Brassica vegetables, their molecular mechanism, wild sources of sterile cytoplasm and exploitation of male sterility in hybrid breeding. The predominantly herbaceous family Brassicaceae (crucifers or mustard family) encompasses over 3700 species, and many of them are scientifically and economically important. The genus Brassica is an economically important genus within the tribe Brassicaceae that comprises important vegetable, oilseed and fodder crops. Brassica vegetables display strong hybrid vigor, and heterosis breeding is the integral part in their improvement. Commercial production of F1 hybrid seeds in Brassica vegetables requires an effective male sterility system. Among the available male sterility systems, cytoplasmic male sterility (CMS) is the most widely exploited in Brassica vegetables. This system is maternally inherited and studied intensively. A limited number of reports about the genic male sterility (GMS) are available in Brassica vegetables. The GMS system is reported to be dominant, recessive and trirecessive in nature in different species. In this review, we discuss the available male sterility systems in Brassica vegetables and their potential use in hybrid breeding. The molecular mechanism of mt-CMS and causal mitochondrial genes of CMS has been discussed in detail. Finally, the exploitation of male sterility system in heterosis breeding of Brassica vegetables, future prospects and need for further understanding of these systems are highlighted.
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Affiliation(s)
- Saurabh Singh
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - S S Dey
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India.
| | - Reeta Bhatia
- Division of Floriculture and Landscaping, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Raj Kumar
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - T K Behera
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
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Saxena S, Singh A, Archak S, Behera TK, John JK, Meshram SU, Gaikwad AB. Development of novel simple sequence repeat markers in bitter gourd (Momordica charantia L.) through enriched genomic libraries and their utilization in analysis of genetic diversity and cross-species transferability. Appl Biochem Biotechnol 2014; 175:93-118. [PMID: 25240849 DOI: 10.1007/s12010-014-1249-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 09/10/2014] [Indexed: 11/24/2022]
Abstract
Microsatellite or simple sequence repeat (SSR) markers are the preferred markers for genetic analyses of crop plants. The availability of a limited number of such markers in bitter gourd (Momordica charantia L.) necessitates the development and characterization of more SSR markers. These were developed from genomic libraries enriched for three dinucleotide, five trinucleotide, and two tetranucleotide core repeat motifs. Employing the strategy of polymerase chain reaction-based screening, the number of clones to be sequenced was reduced by 81 % and 93.7 % of the sequenced clones contained in microsatellite repeats. Unique primer-pairs were designed for 160 microsatellite loci, and amplicons of expected length were obtained for 151 loci (94.4 %). Evaluation of diversity in 54 bitter gourd accessions at 51 loci indicated that 20 % of the loci were polymorphic with the polymorphic information content values ranging from 0.13 to 0.77. Fifteen Indian varieties were clearly distinguished indicative of the usefulness of the developed markers. Markers at 40 loci (78.4 %) were transferable to six species, viz. Momordica cymbalaria, Momordica subangulata subsp. renigera, Momordica balsamina, Momordica dioca, Momordica cochinchinesis, and Momordica sahyadrica. The microsatellite markers reported will be useful in various genetic and molecular genetic studies in bitter gourd, a cucurbit of immense nutritive, medicinal, and economic importance.
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Affiliation(s)
- Swati Saxena
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
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Bharathi LK, Munshi AD, Chandrashekaran S, Behera TK, Das AB, John KJ. Cytotaxonomical analysis of Momordica L. (Cucurbitaceae) species of Indian occurrence. J Genet 2011; 90:21-30. [PMID: 21677385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Somatic chromosome number and detailed karyotype analysis were carried out in six Indian Momordica species viz. M. balsamina, M. charantia, M. cochinchinensis, M. dioica, M. sahyadrica and M. cymbalaria (syn. Luffa cymbalaria; a taxon of controversial taxonomic identity). The somatic chromosome number 2n = 22 was reconfirmed in monoecious species (M. balsamina and M. charantia). Out of four dioecious species, the chromosome number was reconfirmed in M. cochinchinensis (2n = 28), M. dioica (2n = 28) and M. subangulata subsp. renigera (2n = 56), while in M. sahyadrica (2n = 28) somatic chromosome number was reported for the first time. A new chromosome number of 2n = 18 was reported in M. cymbalaria against its previous reports of 2n = 16, 22. The karyotype analysis of all the species revealed significant numerical and structural variations of chromosomes. It was possible to distinguish chromosomes of M. cymbalaria from other Momordica species and also between monoecious and dioecious taxa of the genus. Morphology and crossability among the dioecious species was also studied. Evidence from morphology, crossability, pollen viability and chromosome synapsis suggests a segmental allopolyploid origin for M. subangulata subsp. renigera. The taxonomic status of the controversial taxon M. cymbalaria was also discussed using morphological, karyological and crossability data.
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Affiliation(s)
- L K Bharathi
- Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi 110 012, India.
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Mishra JM, Behera TK, Panda BK, Sarangi K. Twin lithopaedions: a rare entity. Singapore Med J 2007; 48:866-8. [PMID: 17728971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Lithopaedion (stone baby) is the name given to an extrauterine pregnancy that evolves to foetal death and calcification. There are around 300 cases reported in the world medical literature to date. We report the case of a 40-year-old woman who presented with features of acute intestinal obstruction (abdominal distention, vomiting and absolute constipation) for a week. She had a past history of a missed abortion in the fifth month of gestation, eight years prior to this presentation, one which we thought to be irrelevant to the present illness. However, complementary investigations, including scout abdominal radiographs and ultrasonography of the abdomen and pelvis, were done before the operation. The abdominal radiograph showed two opaque globular masses on either side of the lower abdomen with distended small intestinal loops. Exploratory laparotomy was performed and a portion of strangulated small bowel attached to a solid globular mass behind the left ovary was removed, with a subsequent resection of the gut and end-to-end anastomosis. Upon removal of a thick membrane from the globular mass, a dead five-month-old calcified foetus was recovered. In the right iliac fossa, a similar mass was removed and another dead calcified foetus of similar age was recovered.
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Affiliation(s)
- J M Mishra
- Post Graduate Department of General Surgery, VSS Medical College and Hospital, Burla, Orissa, India.
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