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Thakro V, Varshney N, Malik N, Daware A, Srivastava R, Mohanty JK, Basu U, Narnoliya L, Jha UC, Tripathi S, Tyagi AK, Parida SK. Functional allele of a MATE gene selected during domestication modulates seed color in chickpea. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:53-71. [PMID: 37738381 DOI: 10.1111/tpj.16469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/14/2023] [Accepted: 08/29/2023] [Indexed: 09/24/2023]
Abstract
Seed color is one of the key target traits of domestication and artificial selection in chickpeas due to its implications on consumer preference and market value. The complex seed color trait has been well dissected in several crop species; however, the genetic mechanism underlying seed color variation in chickpea remains poorly understood. Here, we employed an integrated genomics strategy involving QTL mapping, high-density mapping, map-based cloning, association analysis, and molecular haplotyping in an inter-specific RIL mapping population, association panel, wild accessions, and introgression lines (ILs) of Cicer gene pool. This delineated a MATE gene, CaMATE23, encoding a Transparent Testa (TT) and its natural allele (8-bp insertion) and haplotype underlying a major QTL governing seed color on chickpea chromosome 4. Signatures of selective sweep and a strong purifying selection reflected that CaMATE23, especially its 8-bp insertion natural allelic variant, underwent selection during chickpea domestication. Functional investigations revealed that the 8-bp insertion containing the third cis-regulatory RY-motif element in the CaMATE23 promoter is critical for enhanced binding of CaFUSCA3 transcription factor, a key regulator of seed development and flavonoid biosynthesis, thereby affecting CaMATE23 expression and proanthocyanidin (PA) accumulation in the seed coat to impart varied seed color in chickpea. Consequently, overexpression of CaMATE23 in Arabidopsis tt12 mutant partially restored the seed color phenotype to brown pigmentation, ascertaining its functional role in PA accumulation in the seed coat. These findings shed new light on the seed color regulation and evolutionary history, and highlight the transcriptional regulation of CaMATE23 by CaFUSCA3 in modulating seed color in chickpea. The functionally relevant InDel variation, natural allele, and haplotype from CaMATE23 are vital for translational genomic research, including marker-assisted breeding, for developing chickpea cultivars with desirable seed color that appeal to consumers and meet global market demand.
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Affiliation(s)
- Virevol Thakro
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Nidhi Varshney
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Naveen Malik
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, 303002, India
| | - Anurag Daware
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rishi Srivastava
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Jitendra K Mohanty
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Udita Basu
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Laxmi Narnoliya
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Uday Chand Jha
- Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India
| | - Shailesh Tripathi
- Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
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Verma SK, Mittal S, Gayacharan, Wankhede DP, Parida SK, Chattopadhyay D, Prasad G, Mishra DC, Joshi DC, Singh M, Singh K, Singh AK. Transcriptome Analysis Reveals Key Pathways and Candidate Genes Controlling Seed Development and Size in Ricebean ( Vigna umbellata). Front Genet 2022; 12:791355. [PMID: 35126460 PMCID: PMC8815620 DOI: 10.3389/fgene.2021.791355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/23/2021] [Indexed: 11/27/2022] Open
Abstract
Ricebean (Vigna umbellata) is a lesser known pulse with well-recognized potential. Recently, it has emerged as a legume with endowed nutritional potential because of high concentration of quality protein and other vital nutrients in its seeds. However, the genes and pathways involved in regulating seed development and size are not understood in this crop. In our study, we analyzed the transcriptome of two genotypes with contrasting grain size (IC426787: large seeded and IC552985: small seeded) at two different time points, namely, 5 and 10 days post-anthesis (DPA). The bold seeded genotype across the time points (B5_B10) revealed 6,928 differentially expressed genes (DEGs), whereas the small seeded genotype across the time point (S5_S10) contributed to 14,544 DEGs. We have also identified several candidate genes for seed development-related traits like seed size and 100-seed weight. On the basis of similarity search and domain analysis, some candidate genes (PHO1, cytokinin dehydrogenase, A-type cytokinin, and ARR response negative regulator) related to 100-seed weight and seed size showed downregulation in the small seeded genotype. The MapMan and KEGG analysis confirmed that auxin and cytokinin pathways varied in both the contrasting genotypes and can therefore be the regulators of the seed size and other seed development-related traits in ricebeans. A total of 51 genes encoding SCF TIR1/AFB , Aux/IAA, ARFs, E3 ubiquitin transferase enzyme, and 26S proteasome showing distinct expression dynamics in bold and small genotypes were also identified. We have also validated randomly selected SSR markers in eight accessions of the Vigna species (V. umbellata: 6; Vigna radiata: 1; and Vigna mungo: 1). Cross-species transferability pattern of ricebean-derived SSR markers was higher in V. radiata (73.08%) than V. mungo (50%). To the best of our knowledge, this is the first transcriptomic study conducted in this crop to understand the molecular basis of any trait. It would provide us a comprehensive understanding of the complex transcriptome dynamics during the seed development and gene regulatory mechanism of the seed size determination in ricebeans.
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Affiliation(s)
| | - Shikha Mittal
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Gayacharan
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | | | | | | | - Geeta Prasad
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | | | | | - Mohar Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Kuldeep Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Amit Kumar Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
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Tiwari M, Yadav M, Singh B, Pandey V, Nawaz K, Bhatia S. Evolutionary and functional analysis of two-component system in chickpea reveals CaRR13, a TypeB RR, as positive regulator of symbiosis. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2415-2427. [PMID: 34146435 PMCID: PMC8633487 DOI: 10.1111/pbi.13649] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/02/2021] [Accepted: 06/06/2021] [Indexed: 05/19/2023]
Abstract
The critical role of cytokinin in early nodulation in legumes is well known. In our study, exogenous cytokinin application to roots of the important crop legume, chickpea (Cicer arietinum L.), led to the formation of pseudo-nodules even in the absence of rhizobia. Hence, a genome-wide analysis of the cytokinin signalling, two-component system (TCS) genes, was conducted in chickpea, Medicago and Cajanus cajan. The integrated phylogenetic, evolutionary and expression analysis of the TCS genes was carried out, which revealed that histidine kinases (HKs) were highly conserved, whereas there was diversification leading to neofunctionalization at the level of response regulators (RRs) especially the TypeB RRs. Further, the functional role of the CaHKs in nodulation was established by complementation of the sln1Δ mutant of yeast and cre1 mutants of (Medicago) which led to restoration of the nodule-deficient phenotype. Additionally, the highest expressing TypeB RR of chickpea, CaRR13, was functionally characterized. Its localization in the nucleus and its Y1H assay-based interaction with the promoter of the early nodulation gene CaNSP2 indicated its role as a transcription factor regulating early nodulation. Overexpression, RNAi lines and complementation of cre1 mutants with CaRR13 revealed its critical involvement as an important signalling molecule regulating early events of nodule organogenesis in chickpea.
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Affiliation(s)
- Manish Tiwari
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Manisha Yadav
- National Institute of Plant Genome ResearchNew DelhiIndia
| | | | - Vimal Pandey
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Kashif Nawaz
- National Institute of Plant Genome ResearchNew DelhiIndia
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Admas S, Tesfaye K, Haileselassie T, Shiferaw E, Flynn KC. Genetic variability and population structure of Ethiopian chickpea (Cicer arietinum L.) germplasm. PLoS One 2021; 16:e0260651. [PMID: 34843606 PMCID: PMC8629288 DOI: 10.1371/journal.pone.0260651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/12/2021] [Indexed: 11/21/2022] Open
Abstract
Evaluation of the genetic diversity and an understanding of the genetic structure and relationships of chickpea genotypes are valuable to design efficient germplasm conservation strategies and crop breeding programs. Information is limited, in these regards, for Ethiopian chickpea germplasms. Therefore, the present study was carried out to estimate the genetic diversity, population structure, and relationships of 152 chickpea genotypes using simple sequence repeats (SSR) markers. Twenty three SSR markers exhibited polymorphism producing a total of 133 alleles, with a mean of 5.8 alleles per locus. Analyses utilizing various genetic-based statistics included pairwise population Nei’s genetic distance, heterozygosity, Shannon’s information index, polymorphic information content, and percent polymorphism. These analyses exemplified the existence of high genetic variation within and among chickpea genotypes. The 152 genotypes were divided into two major clusters based on Nei’s genetic distances. The exotic genotypes were grouped in one cluster exclusively showing that these genotypes are distinct to Ethiopian genotypes, while the patterns of clustering of Ethiopian chickpea genotypes based on their geographic region were not consistent because of the seed exchange across regions. Model-based population structure clustering identified two discrete populations. These finding provides useful insight for chickpea collections and ex-situ conservation and national breeding programs for widening the genetic base of chickpea.
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Affiliation(s)
- Sintayehu Admas
- Ethiopian Biodiversity Institute, Addis Ababa, Ethiopia
- College of Natural Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- * E-mail:
| | - Kassahun Tesfaye
- College of Natural Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Biotechnology Institute, Addis Ababa, Ethiopia
| | | | | | - K. Colton Flynn
- Grassland Soil and Water Research Laboratory, USDA-ARS, Temple, Texas, United States of America
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Tiwari M, Pandey V, Singh B, Yadav M, Bhatia S. Evolutionary and expression dynamics of LRR-RLKs and functional establishment of KLAVIER homolog in shoot mediated regulation of AON in chickpea symbiosis. Genomics 2021; 113:4313-4326. [PMID: 34801685 DOI: 10.1016/j.ygeno.2021.11.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 04/10/2021] [Accepted: 11/16/2021] [Indexed: 11/29/2022]
Abstract
Chickpea shoot exogenously treated with cytokinin showed stunted phenotype of root, shoot and significantly reduced nodule numbers. Genome-wide identification of LRR-RLKs in chickpea and Medicago resulted in 200 and 371 genes respectively. Gene duplication analysis revealed that LRR-RLKs family expanded through segmental duplications in chickpea and tandem duplications in Medicago. Expression profiling of LRR-RLKs revealed their involvement in cytokinin signaling and plant organ development. Overexpression of KLAVIER ortholog of chickpea, Ca_LRR-RLK147, in roots revealed its localization in the membrane but showed no effect on root nodulation despite increased cle peptide levels. Two findings (i) drastic effect on nodule number by exogenous cytokinin treatment to only shoot and restoration to normal nodulation by treatment to both root and shoot tissue and (ii) no effect on nodule number by overexpression of Ca_LRR-RLK147 establishes the fact that despite presence of cle peptides in root, the function of Ca_LRR-RLK147 was shoot mediated during AON.
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Affiliation(s)
- Manish Tiwari
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Vimal Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Baljinder Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Manisha Yadav
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sabhyata Bhatia
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
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Asadi-Aghbolaghi M, Dedicova B, Ranade SS, Le KC, Sharifzadeh F, Omidi M, Egertsdotter U. Protocol development for somatic embryogenesis, SSR markers and genetic modification of Stipagrostis pennata (Trin.) De Winter. PLANT METHODS 2021; 17:70. [PMID: 34193231 PMCID: PMC8247082 DOI: 10.1186/s13007-021-00768-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/12/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Stipagrostis pennata (Trin.) De Winter is an important species for fixing sand in shifting and semi-fixed sandy lands, for grazing, and potentially as a source of lignocellulose fibres for pulp and paper industry. The seeds have low viability, which limits uses for revegetation. Somatic embryogenesis offers an alternative method for obtaining large numbers of plants from limited seed sources. RESULTS A protocol for plant regeneration from somatic embryos of S. pennata was developed. Somatic embryogenesis was induced on Murashige & Skoog (MS) medium supplemented with 3 mg·L-1 2,4-D subsequently shoots were induced on MS medium and supplemented with 5 mg·L-1 zeatin riboside. The highest shoots induction was obtained when embryogenic callus derived from mature embryos (96%) in combination with MS filter-sterilized medium was used from Khuzestan location. The genetic stability of regenerated plants was analysed using ten simple sequence repeats (SSR) markers from S. pennata which showed no somaclonal variation in regenerated plants from somatic embryos of S. pennata. The regenerated plants of S. pennata showed genetic stability without any somaclonal variation for the four pairs of primers that gave the expected amplicon sizes. This data seems very reliable as three of the PCR products belonged to the coding region of the genome. Furthermore, stable expression of GUS was obtained after Agrobacterium-mediated transformation using a super binary vector carried by a bacterial strain LBA4404. CONCLUSION To our knowledge, the current work is the first attempt to develop an in vitro protocol for somatic embryogenesis including the SSR marker analyses of regenerated plants, and Agrobacterium-mediated transformation of S. pennata that can be used for its large-scale production for commercial purposes.
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Affiliation(s)
- Masoumeh Asadi-Aghbolaghi
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, 14174, Karaj, Iran
| | - Beata Dedicova
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden.
| | - Sonali Sachi Ranade
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Kim-Cuong Le
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Farzad Sharifzadeh
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, 14174, Karaj, Iran
| | - Mansoor Omidi
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, 14174, Karaj, Iran
| | - Ulrika Egertsdotter
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
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Pradhan S, Verma S, Chakraborty A, Bhatia S. Identification and molecular characterization of miRNAs and their target genes associated with seed development through small RNA sequencing in chickpea. Funct Integr Genomics 2021; 21:283-298. [PMID: 33630193 DOI: 10.1007/s10142-021-00777-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/12/2021] [Accepted: 02/09/2021] [Indexed: 11/30/2022]
Abstract
Multiple studies have attempted to dissect the molecular mechanism underlying seed development in chickpea (Cicer arietinum L.). These studies highlight the need to focus on the role of miRNAs in regulating storage protein accumulation in seeds. Therefore, a total of 8,856,691 short-read sequences were generated from a small RNA library of developing chickpea seeds and were analyzed using miRDeep-P to identify 74 known and 26 novel miRNA sequences. Known miRNAs were classified into 22 miRNA families with miRNA156 family being most abundant. Of the 26 putative novel miRNAs identified, only 22 could be experimentally validated using stem loop end point PCR. Differential expression analyses led to the identification of known as well as novel miRNAs that could regulate various stages of chickpea seed development. In silico target prediction revealed several important target genes and transcription factors like SPL, mediator of RNA Polymerase II transcription subunit 12, aspartic proteinase and NACs, which were further validated by real-time PCR analysis. A comparative expression analysis in chickpea genotypes with contrasting seed protein content revealed one known (Car-miR156h) and two novel miRNA (Car-novmiR7 and Car-novmiR23) candidates to be highly expressed in the LPC (low protein content) chickpea genotypes, targets of which are known to regulate seed storage protein accumulation. Therefore, this study provides a useful resource in the form of miRNA and their targets which can be further utilized to understand and manipulate various regulatory mechanisms involved in seed development with the overall aim of improving yield and nutrition attributes in chickpea.
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Affiliation(s)
- Seema Pradhan
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Subodh Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Anirban Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Sabhyata Bhatia
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Discerning molecular diversity and association mapping for phenological, physiological and yield traits under high temperature stress in chickpea (Cicer arietinum L.). J Genet 2021. [DOI: 10.1007/s12041-020-01254-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Naik A, Mishra SK, Nag A, Soren GK, Panda AK, Panda SK, Panigrahi J. Cross-genera amplification of Cajanus spp. specific SSR markers in Clitoria ternatea (L.) and their application in genetic diversity studies. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:2371-2390. [PMID: 33424153 PMCID: PMC7772131 DOI: 10.1007/s12298-020-00907-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/08/2020] [Accepted: 10/26/2020] [Indexed: 06/12/2023]
Abstract
Clitoria ternatea (L.) is a medicinal leguminous plant and is cultivated to cater the need of herbal industries and asthetic purposes. The unavailability of steady molecular marker impedes the genetic improvement of C. ternatea. In the present study, transferability of 98 pairs of Cajanus spp. specific SSR primers were assessed among 14 genotypes of C. ternatea, varied for their flower color, floral architecture and bio-metabolite (taraxerol and delphinidin) content, and out of them 43 had successfully amplified the fragments. Among them, 36 pairs of primers showed 100% transferability, whereas rest seven varied from 42.86 to 92.85% transferability. The transferable 43 pairs of SSR primers generated 196 alleles across the 14 genotypes and the AMOVA analysis showed moderate genetic variation (55.1%) among the genotypes of C. ternatea, which was also reinforced by Nei's genetic distance and gene identity estimates derived haplotype matrix. Similarly, both the principal coordinate analysis and dendrogram grouped these 14 genotypes of C. ternatea into two major clusters based on SSR allele distribution and frequency, and the clustering pattern is in accordance with petal color but in contrast to floral architecture. MCheza based outlier analysis revealed 16 alleles for balancing selection, which are putatively involved in the maintenance of genetic polymorphism in C. ternatea. Moreover, the estimates of molecular diversity and bio-metabolite content revealed the possible use of these genotypes in future breeding programme of this species.
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Affiliation(s)
- Aparupa Naik
- Department of Bioscience and Bioinformatics, Khallikote University, Konishi, Berhampur, Odisha 761008 India
- Department of Biotechnology and Bioinformatics, Sambalpur University, Jyoti Vihar, Burla, Odisha 768019 India
| | - Sujit K. Mishra
- Department of Biotechnology and Bioinformatics, Sambalpur University, Jyoti Vihar, Burla, Odisha 768019 India
- Department of Zoology, Centurion University of Technology and Management, Bhubaneswar, Odisha India
| | - Atul Nag
- Department of Biotechnology and Bioinformatics, Sambalpur University, Jyoti Vihar, Burla, Odisha 768019 India
| | - Gopal K. Soren
- Department of Bioscience and Bioinformatics, Khallikote University, Konishi, Berhampur, Odisha 761008 India
| | - Aditya K. Panda
- Department of Bioscience and Bioinformatics, Khallikote University, Konishi, Berhampur, Odisha 761008 India
| | - Sanjib K. Panda
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Ajmer, Rajasthan 305817 India
| | - Jogeswar Panigrahi
- Department of Bioscience and Bioinformatics, Khallikote University, Konishi, Berhampur, Odisha 761008 India
- Department of Biotechnology and Bioinformatics, Sambalpur University, Jyoti Vihar, Burla, Odisha 768019 India
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Kumar R, Kaundal SP, Sharma V, Sharma A, Singh G, Sharma RK, Chahota RK, Sharma TR. Development of transcriptome-wide SSR markers for genetic diversity and structure analysis in Macrotyloma uniflorum (Lam.) Verdc. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:2255-2266. [PMID: 33268927 PMCID: PMC7688872 DOI: 10.1007/s12298-020-00898-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/16/2020] [Accepted: 10/13/2020] [Indexed: 06/12/2023]
Abstract
Horsegram is an important drought resistant pulse crop from Fabaceae and can be easily grown in dry lands with no irrigation facilities. However, it remained neglected since long and has been considered as orphan legume which requires immediate attention for its improvement and for the development of new promising varieties in future. In the present study, 7352 simple sequence repeat (SSR) markers were developed from the transcriptome data and 150 SSR were randomly synthesized for validation and diversity analysis in a panel of 58 horsegram genotypes. The synthesized primers included all types of repeats spanning direpeats to hexarepeats. Of the validated SSR markers, 33 markers were polymorphic and produced 40 loci which were used to analyze the genetic diversity and structure of horsegram. In total, 130 alleles were produced in a range of 2-9 alleles with maximum alleles produced by primer HTSSR 155. Expected heterozygosity (He) ranged from 0.03 to 1.00 and observed heterozygosity (Ho) ranged from 0.13 to 0.81. Polymorphism information content value ranged from 0.065 to 0.78. Dendrogram based on UPGMA and principal component analysis showed four groups of the 58 genotypes of horsegram. Structure analysis showed three genetic stocks for the analyzed germplasm. Thus, the developed SSRs can be useful in future population genetics analysis, molecular breeding studies and mapping works in horsegram germplasm as well as in related legume species.
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Affiliation(s)
| | | | - Vikas Sharma
- Sant Baba Bhag Singh University, Khiala, Jalandhar, Punjab, India
| | | | - Gagandeep Singh
- Central University of Himachal Pradesh, Dharamshala (H.P), India
| | - Ram Kumar Sharma
- CSIR-Institute of Himalayan Bioresource Technology, Palampur (H.P), India
| | | | - Tilak Raj Sharma
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India
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Asadi A, Ebrahimi A, Rashidi-Monfared S, Basiri M, Akbari-Afjani J. Comprehensive functional analysis and mapping of SSR markers in the chickpea genome (Cicer arietinum L.). Comput Biol Chem 2019; 84:107169. [PMID: 31812779 DOI: 10.1016/j.compbiolchem.2019.107169] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 11/16/2019] [Accepted: 11/18/2019] [Indexed: 11/19/2022]
Abstract
Plant molecular breeding largely depends on the relationship between molecular markers and major traits. Herein, a total of 32,962 genomic simple sequence repeats (SSRs) were detected in the whole genome of chickpea with an average density of 94.93 SSRs/Mb. Chickpea chromosomes uniformity test indicated that the genomic SSRs (gSSRs) were steadily distributed across the genome. Moreover, 48,667 transcriptome sequences were analyzed and 1949 SSR-containing transcript assembly contigs (TACs) were identified. The analysis showed that di- and trinucleotide SSRs were the most frequent SSR motifs within the transcriptome sequences. Among them, AT and TTA and AG and TTC motifs within the transcriptome showed the highest frequencies among di- and trinucleotide repeat motifs, respectively. The SSRs-containing TACs were compared to the GenBank non-redundant database using BLASTX, and subsequently, gene ontology (GO) analysis was performed using QuickGO browser to reduce complexity and highlight biological processes associated with the SSRs-containing TACs. The identified SSRs-containing TACs were categorized into 35 enriched functional-related gene group. The mapping of characterized SSRs-containing TACs onto chickpea chromosomes was performed using BLASTN. The mapping result showed that, a total of 1798 SSRs-containing TACs were mapped onto the chickpea genome. Based on the functional analysis result, 249 and 242 of the mapped SSRs-containing TACs were found in the genes encoding for putative stress-related proteins and transcription factors, respectively. The results presented here can be applied to improve and speed up the chickpea breeding programs.
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Affiliation(s)
- AliAkbar Asadi
- Agricultural Biotechnology Department, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Amin Ebrahimi
- Agronomy and Plant Breeding Department, Faculty of Agriculture, Shahrood University of Technology, Semnan, Iran
| | - Sajad Rashidi-Monfared
- Agricultural Biotechnology Department, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
| | - Mohammad Basiri
- Agricultural Biotechnology Department, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Javad Akbari-Afjani
- Agricultural Biotechnology Department, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
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A comprehensive analysis of the B3 superfamily identifies tissue-specific and stress-responsive genes in chickpea ( Cicer arietinum L.). 3 Biotech 2019; 9:346. [PMID: 31497464 DOI: 10.1007/s13205-019-1875-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 08/14/2019] [Indexed: 12/31/2022] Open
Abstract
The aim of this study was to provide a comprehensive analysis of the plant-specific B3 domain-containing transcription factors (TFs) in chickpea. Scanning of the chickpea genome resulted in the identification of 51 B3 domain-containing TFs that were located on seven out of eight chickpea chromosomes. Based on the presence of additional domains other than the B3 domain, the candidates were classified into four subfamilies, i.e., ARF (24), REM (19), LAV (6) and RAV (2). Phylogenetic analysis classified them into four groups in which members of the same group had similar intron-exon organization and motif composition. Genome duplication analysis of the candidate B3 genes revealed an event of segmental duplication that was instrumental in the expansion of the B3 gene family. Ka/Ks analysis showed that the B3 gene family was under purifying selection. Further, chickpea B3 genes showed maximum orthology with Medicago followed by soybean and Arabidopsis. Promoter analyses of the B3 genes led to the identification of several tissue-specific and stress-responsive cis-regulatory elements. Expression profiling of the candidate B3 genes using publicly available RNA-seq data of several chickpea tissues indicated their putative role in plant development and abiotic stress response. These findings were further validated by real-time expression analysis. Overall, this study provides a comprehensive analysis of the B3 domain-containing proteins in chickpea that would aid in devising strategies for crop manipulation in chickpea.
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Pandey S, Kumari A, Shree M, Kumar V, Singh P, Bharadwaj C, Loake GJ, Parida SK, Masakapalli SK, Gupta KJ. Nitric oxide accelerates germination via the regulation of respiration in chickpea. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4539-4555. [PMID: 31162578 PMCID: PMC6735774 DOI: 10.1093/jxb/erz185] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 04/11/2019] [Indexed: 05/11/2023]
Abstract
Seed germination is crucial for the plant life cycle. We investigated the role of nitric oxide (NO) in two chickpea varieties that differ in germination capacity: Kabuli, which has a low rate of germination and germinates slowly, and Desi, which shows improved germination properties. Desi produced more NO than Kabuli and had lower respiratory rates. As a result of the high respiration rates, Kabuli had higher levels of reactive oxygen species (ROS). Treatment with the NO donor S-nitroso-N-acetyl-D,L-penicillamine (SNAP) reduced respiration in Kabuli and decreased ROS levels, resulting in accelerated germination rates. These findings suggest that NO plays a key role in the germination of Kabuli. SNAP increased the levels of transcripts encoding enzymes involved in carbohydrate metabolism and the cell cycle. Moreover, the levels of amino acids and organic acids were increased in Kabuli as a result of SNAP treatment. 1H-nuclear magnetic resonance analysis revealed that Kabuli has a higher capacity for glucose oxidation than Desi. An observed SNAP-induced increase in 13C incorporation into soluble alanine may result from enhanced oxidation of exogenous [13C]glucose via glycolysis and the pentose phosphate pathway. A homozygous hybrid that originated from a recombinant inbred line population of a cross between Desi and Kabuli germinated faster and had increased NO levels and a reduced accumulation of ROS compared with Kabuli. Taken together, these findings demonstrate the importance of NO in chickpea germination via the control of respiration and ROS accumulation.
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Affiliation(s)
- Sonika Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, 110067, New Delhi, India
| | - Aprajita Kumari
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, 110067, New Delhi, India
| | - Manu Shree
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand 175005, HP, India
| | - Vinod Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, 110067, New Delhi, India
| | - Pooja Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, 110067, New Delhi, India
| | | | - Gary J Loake
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, The King’s Buildings, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Swarup K Parida
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, 110067, New Delhi, India
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Raizada A, Souframanien J. Transcriptome sequencing, de novo assembly, characterisation of wild accession of blackgram (Vigna mungo var. silvestris) as a rich resource for development of molecular markers and validation of SNPs by high resolution melting (HRM) analysis. BMC PLANT BIOLOGY 2019; 19:358. [PMID: 31419947 PMCID: PMC6697964 DOI: 10.1186/s12870-019-1954-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/31/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND Blackgram [Vigna mungo (L.) Hepper], is an important legume crop of Asia with limited genomic resources. We report a comprehensive set of genic simple sequence repeat (SSR) and single nucleotide polymorphism (SNPs) markers using Illumina MiSeq sequencing of transcriptome and its application in genetic variation analysis and mapping. RESULTS Transcriptome sequencing of immature seeds of wild blackgram, V. mungo var. silvestris by Illumina MiSeq technology generated 1.9 × 107 reads, which were assembled into 40,178 transcripts (TCS) with an average length of 446 bp covering 2.97 GB of the genome. A total of 38,753 CDS (Coding sequences) were predicted from 40,178 TCS and 28,984 CDS were annotated through BLASTX and mapped to GO and KEGG database resulting in 140 unique pathways. The tri-nucleotides were most abundant (39.9%) followed by di-nucleotide (30.2%). About 60.3 and 37.6% of SSR motifs were present in the coding sequences (CDS) and untranslated regions (UTRs) respectively. Among SNPs, the most abundant substitution type were transitions (Ts) (61%) followed by transversions (Tv) type (39%), with a Ts/Tv ratio of 1.58. A total of 2306 DEGs were identified by RNA Seq between wild and cultivar and validation was done by quantitative reverse transcription polymerase chain reaction. In this study, we genotyped SNPs with a validation rate of 78.87% by High Resolution Melting (HRM) Assay. CONCLUSION In the present study, 1621genic-SSR and 1844 SNP markers were developed from immature seed transcriptome sequence of blackgram and 31 genic-SSR markers were used to study genetic variations among different blackgram accessions. Above developed markers contribute towards enriching available genomic resources for blackgram and aid in breeding programmes.
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Affiliation(s)
- Avi Raizada
- Nuclear Agriculture and Biotechnology Division, BARC, Trombay, Mumbai, Trombay, 400085, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Anushakti Nagar, 400094, India
| | - J Souframanien
- Nuclear Agriculture and Biotechnology Division, BARC, Trombay, Mumbai, Trombay, 400085, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Anushakti Nagar, 400094, India.
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Tiwari B, Kalim S, Tyagi N, Kumari R, Bangar P, Barman P, Kumar S, Gaikwad A, Bhat KV. Identification of genes associated with stress tolerance in moth bean [ Vigna aconitifolia (Jacq.) Marechal], a stress hardy crop. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:551-561. [PMID: 30042612 PMCID: PMC6041239 DOI: 10.1007/s12298-018-0525-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 12/15/2017] [Accepted: 03/14/2018] [Indexed: 05/24/2023]
Abstract
Moth bean is the most drought and heat tolerant cultigens among Asian Vigna. We performed comparative transcriptome analysis of moth bean cultivar "Marumoth" under control and stress condition. De novo transcriptome assembly was carried out by using Velvet followed by Oases softwares. Differential expression analyses, SSR identification and validation and mapping of pathways and transcription factors were conducted. A total of 179,979 and 201,888 reads were generated on Roche 454 platform and 48,617,205 and 45,449,053 reads were generated on ABI Solid platform for the control and stressed samples. Combined assembly from Roche and ABI Solid platforms generated 16,090 and 15,096 transcripts for control and stressed samples. We found 1287 SSRs and 5606 transcripts involved in 179 pathways. The 55 transcription factor families represented 19.42% of total mothbean transcripts. In expression profiling, ten transcripts were found to be up-regulated and 41 down-regulated while 490 showed no major change under moisture stress condition. Stress inducible genes like Catalase, Cyt P450 monooxygenase, heat shock proteins (HSP 90 and HSP 70), oxidoreductase, protein kinases, dehydration responsive protein (DRP), universal stress protein and ferridoxin NADH oxidoreductase genes were up-regulated in stressed sample. Genes which might be involved in moisture stress tolerance in moth bean were identified and these might be useful for stress tolerance breeding in moth bean and other related crops.
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Affiliation(s)
- Bhavana Tiwari
- Genomic Resources Division, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | | | - Neetu Tyagi
- Genomic Resources Division, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Ratna Kumari
- Genomic Resources Division, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Pooja Bangar
- Genomic Resources Division, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Paramananda Barman
- Genomic Resources Division, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sanjay Kumar
- Genomic Resources Division, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Ambika Gaikwad
- Genomic Resources Division, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - K. V. Bhat
- Genomic Resources Division, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
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Jha UC, Jha R, Bohra A, Parida SK, Kole PC, Thakro V, Singh D, Singh NP. Population structure and association analysis of heat stress relevant traits in chickpea ( Cicer arietinum L.). 3 Biotech 2018; 8:43. [PMID: 29354354 PMCID: PMC5750240 DOI: 10.1007/s13205-017-1057-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 12/19/2017] [Indexed: 12/27/2022] Open
Abstract
Understanding genetic diversity and population structure is prerequisite to broaden the cultivated base of any crop. In the current investigation, we report discovery of a total of 319 alleles by assaying 81 SSRs on 71 chickpea genotypes. The cluster analysis based on Jaccard coefficient and unweighted neighbor joining algorithm categorized all genotypes into two major clusters. Cultivars grown within the same agro-climatic zones were clustered together, whereas the remaining genotypes particularly advanced breeding lines and accessions assigned to another cluster. Population structure analysis separated the entire collection into two subpopulations (K = 2) and the clustering pattern remained in close agreement with those of distance-based methods. Importantly, we also discovered marker trait association for membrane stability index (MSI) and leaf chlorophyll content measured as SPAD chlorophyll meter reading (SCMR), the two important physiological parameters indicative of heat stress (HS) tolerance in chickpea. Association analysis using both general linear and mixed linear models of the mean phenotypic data of traits recorded in 2016 and 2017 uncovered significant association of NCPGR206 and H2L102 with the MSI trait. Likewise, SSR markers GA9, TR31 and TA113 exhibited significant association with SCMR trait. The genomic regions putatively linked with two traits may be investigated in greater detail to further improve knowledge about the genetic architecture of HS tolerance in chickpea.
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Affiliation(s)
- Uday Chand Jha
- Indian Institute of Pulses Research (IIPR), Kanpur, UP 208 024 India
| | - Rintu Jha
- Indian Institute of Pulses Research (IIPR), Kanpur, UP 208 024 India
| | - Abhishek Bohra
- Indian Institute of Pulses Research (IIPR), Kanpur, UP 208 024 India
| | - Swarup Kumar Parida
- National Institute of Plant Genome Research (NIPGR), New Delhi, 110067 India
| | - Paresh Chandra Kole
- Department of Genetics & Plant Breeding and Crop Physiology, Institute of Agriculture, Visva Bharati University, Sriniketan, Bolpur, West Bengal 731236 India
| | - Virevol Thakro
- National Institute of Plant Genome Research (NIPGR), New Delhi, 110067 India
| | - Deepak Singh
- Indian Agricultural Statistical Research Institute (IASRI), New Delhi, India
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Jha UC, Jha R, Bohra A, Parida SK, Kole PC, Thakro V, Singh D, Singh NP. Population structure and association analysis of heat stress relevant traits in chickpea ( Cicer arietinum L.). 3 Biotech 2018. [PMID: 29354354 DOI: 10.1007/s1320] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Understanding genetic diversity and population structure is prerequisite to broaden the cultivated base of any crop. In the current investigation, we report discovery of a total of 319 alleles by assaying 81 SSRs on 71 chickpea genotypes. The cluster analysis based on Jaccard coefficient and unweighted neighbor joining algorithm categorized all genotypes into two major clusters. Cultivars grown within the same agro-climatic zones were clustered together, whereas the remaining genotypes particularly advanced breeding lines and accessions assigned to another cluster. Population structure analysis separated the entire collection into two subpopulations (K = 2) and the clustering pattern remained in close agreement with those of distance-based methods. Importantly, we also discovered marker trait association for membrane stability index (MSI) and leaf chlorophyll content measured as SPAD chlorophyll meter reading (SCMR), the two important physiological parameters indicative of heat stress (HS) tolerance in chickpea. Association analysis using both general linear and mixed linear models of the mean phenotypic data of traits recorded in 2016 and 2017 uncovered significant association of NCPGR206 and H2L102 with the MSI trait. Likewise, SSR markers GA9, TR31 and TA113 exhibited significant association with SCMR trait. The genomic regions putatively linked with two traits may be investigated in greater detail to further improve knowledge about the genetic architecture of HS tolerance in chickpea.
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Affiliation(s)
- Uday Chand Jha
- 1Indian Institute of Pulses Research (IIPR), Kanpur, UP 208 024 India
| | - Rintu Jha
- 1Indian Institute of Pulses Research (IIPR), Kanpur, UP 208 024 India
| | - Abhishek Bohra
- 1Indian Institute of Pulses Research (IIPR), Kanpur, UP 208 024 India
| | - Swarup Kumar Parida
- 2National Institute of Plant Genome Research (NIPGR), New Delhi, 110067 India
| | - Paresh Chandra Kole
- 3Department of Genetics & Plant Breeding and Crop Physiology, Institute of Agriculture, Visva Bharati University, Sriniketan, Bolpur, West Bengal 731236 India
| | - Virevol Thakro
- 2National Institute of Plant Genome Research (NIPGR), New Delhi, 110067 India
| | - Deepak Singh
- Indian Agricultural Statistical Research Institute (IASRI), New Delhi, India
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Singh A, Sharma V, Dikshit HK, Aski M, Kumar H, Thirunavukkarasu N, Patil BS, Kumar S, Sarker A. Association mapping unveils favorable alleles for grain iron and zinc concentrations in lentil (Lens culinaris subsp. culinaris). PLoS One 2017; 12:e0188296. [PMID: 29161321 PMCID: PMC5697819 DOI: 10.1371/journal.pone.0188296] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 11/04/2017] [Indexed: 11/18/2022] Open
Abstract
Lentil is a major cool-season grain legume grown in South Asia, West Asia, and North Africa. Populations in developing countries of these regions have micronutrient deficiencies; therefore, breeding programs should focus more on improving the micronutrient content of food. In the present study, a set of 96 diverse germplasm lines were evaluated at three different locations in India to examine the variation in iron (Fe) and zinc (Zn) concentration and identify simple sequence repeat (SSR) markers that associate with the genetic variation. The genetic variation among genotypes of the association mapping (AM) panel was characterized using a genetic distance-based and a general model-based clustering method. The model-based analysis identified six subpopulations, which satisfactorily explained the genetic structure of the AM panel. AM analysis identified three SSRs (PBALC 13, PBALC 206, and GLLC 563) associated with grain Fe concentration explaining 9% to 11% of phenotypic variation and four SSRs (PBALC 353, SSR 317-1, PLC 62, and PBALC 217) were associated with grain Zn concentration explaining 14%, to 21% of phenotypic variation. These identified SSRs exhibited consistent performance across locations. These candidate SSRs can be used in marker-assisted genetic improvement for developing Fe and Zn fortified lentil varieties. Favorable alleles and promising genotypes identified in this study can be utilized for lentil biofortification.
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Affiliation(s)
- Akanksha Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
- Department of Bioscience and Biotechnology, Banasthali University, Banasthali, Rajasthan, India
| | - Vinay Sharma
- Department of Bioscience and Biotechnology, Banasthali University, Banasthali, Rajasthan, India
| | - Harsh Kumar Dikshit
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Muraleedhar Aski
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Harish Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
- Punjab Agriculture University, RRS, Faridkot, Punjab, India
| | | | | | - Shiv Kumar
- ICARDA, B.P. 6299, Station Experiment, INRA-Quich, Rue Hafiane Cherkaoui Agdal, Rabat-Institutes, Rabat, Morocco
| | - Ashutosh Sarker
- South Asia and China Program (ICARDA), NASC Complex, New Delhi, India
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Chen H, Chen H, Hu L, Wang L, Wang S, Wang ML, Cheng X. Genetic diversity and a population structure analysis of accessions in the Chinese cowpea [ Vigna unguiculata (L.) Walp.] germplasm collection. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.cj.2017.04.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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Chen H, Wang L, Liu X, Hu L, Wang S, Cheng X. De novo transcriptomic analysis of cowpea (Vigna unguiculata L. Walp.) for genic SSR marker development. BMC Genet 2017; 18:65. [PMID: 28693419 PMCID: PMC5504845 DOI: 10.1186/s12863-017-0531-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 06/28/2017] [Indexed: 01/14/2023] Open
Abstract
Background Cowpea [Vigna unguiculata (L.) Walp.] is one of the most important legumes in tropical and semi-arid regions. However, there is relatively little genomic information available for genetic research on and breeding of cowpea. The objectives of this study were to analyse the cowpea transcriptome and develop genic molecular markers for future genetic studies of this genus. Results Approximately 54 million high-quality cDNA sequence reads were obtained from cowpea based on Illumina paired-end sequencing technology and were de novo assembled to generate 47,899 unigenes with an N50 length of 1534 bp. Sequence similarity analysis revealed 36,289 unigenes (75.8%) with significant similarity to known proteins in the non-redundant (Nr) protein database, 23,471 unigenes (49.0%) with BLAST hits in the Swiss-Prot database, and 20,654 unigenes (43.1%) with high similarity in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Further analysis identified 5560 simple sequence repeats (SSRs) as potential genic molecular markers. Validating a random set of 500 SSR markers yielded 54 polymorphic markers among 32 cowpea accessions. Conclusions This transcriptomic analysis of cowpea provided a valuable set of genomic data for characterizing genes with important agronomic traits in Vigna unguiculata and a new set of genic SSR markers for further genetic studies and breeding in cowpea and related Vigna species. Electronic supplementary material The online version of this article (doi:10.1186/s12863-017-0531-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Honglin Chen
- The National Key Facility for Crop Gene, Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lixia Wang
- The National Key Facility for Crop Gene, Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaoyan Liu
- The National Key Facility for Crop Gene, Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Liangliang Hu
- The National Key Facility for Crop Gene, Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Suhua Wang
- The National Key Facility for Crop Gene, Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xuzhen Cheng
- The National Key Facility for Crop Gene, Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Wang Y, Liu K, Bi D, Zhou S, Shao J. Characterization of the transcriptome and EST-SSR development in Boea clarkeana, a desiccation-tolerant plant endemic to China. PeerJ 2017; 5:e3422. [PMID: 28630801 PMCID: PMC5474092 DOI: 10.7717/peerj.3422] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/16/2017] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Desiccation-tolerant (DT) plants can recover full metabolic competence upon rehydration after losing most of their cellular water (>95%) for extended periods of time. Functional genomic approaches such as transcriptome sequencing can help us understand how DT plants survive and respond to dehydration, which has great significance for plant biology and improving the drought tolerance of crops. Boea clarkeana Hemsl. (Gesneriaceae) is a DT dicotyledonous herb. Its genomic sequences characteristics remain unknown. Based on transcriptomic analyses, polymorphic EST-SSR (simple sequence repeats in expressed sequence tags) molecular primers can be designed, which will greatly facilitate further investigations of the population genetics and demographic histories of DT plants. METHODS In the present study, we used the platform Illumina HiSeq™2000 and de novo assembly technology to obtain leaf transcriptomes of B. clarkeana and conducted a BLASTX alignment of the sequencing data and protein databases for sequence classification and annotation. Then, based on the sequence information, the EST-SSR markers were developed, and the functional annotation of ESTs containing polymorphic SSRs were obtained through BLASTX. RESULTS A total of 91,449 unigenes were generated from the leaf cDNA library of B. clarkeana. Based on a sequence similarity search with a known protein database, 72,087 unigenes were annotated. Among the annotated unigenes, a total of 71,170 unigenes showed significant similarity to the known proteins of 463 popular model species in the Nr database, and 59,962 unigenes and 32,336 unigenes were assigned to Gene Ontology (GO) classifications and Cluster of Orthologous Groups (COG), respectively. In addition, 44,924 unigenes were mapped in 128 KEGG pathways. Furthermore, a total of 7,610 unigenes with 8,563 microsatellites were found. Seventy-four primer pairs were selected from 436 primer pairs designed for polymorphism validation. SSRs with higher polymorphism rates were concentrated on dinucleotides, pentanucleotides and hexanucleotides. Finally, 17 pairs with stable, highly polymorphic loci were selected for polymorphism screening. There was a total of 65 alleles, with 2-6 alleles at each locus. Primarily due to the unique biological characteristics of plants, the HE (0-0.196), HO (0.082-0.14) and PIC (0-0.155) per locus were very low. The functional annotation distribution centered on ESTs containing di- and tri-nucleotide SSRs, and the ESTs containing primers BC2, BC4 and BC12 were annotated to vegetative dehydration/desiccation pathways. DISCUSSION This work is the first genetic study of B. clarkeana as a new plant resource of DT genes. A substantial number of transcriptome sequences were generated in this study. These sequences are valuable resources for gene annotation and discovery as well as molecular marker development. These sequences could also provide a valuable basis for future molecular studies of B. clarkeana.
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Affiliation(s)
- Ying Wang
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu, Anhui, China
| | - Kun Liu
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu, Anhui, China
| | - De Bi
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Shoubiao Zhou
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- College of Environmental Science and Engineering, Anhui Normal University, Wuhu, Anhui, China
| | - Jianwen Shao
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu, Anhui, China
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Jadhav AA, Rayate SJ, Mhase LB, Thudi M, Chitikineni A, Harer PN, Jadhav AS, Varshney RK, Kulwal PL. Marker-trait association study for protein content in chickpea (Cicer arietinum L.). J Genet 2016; 94:279-86. [PMID: 26174675 DOI: 10.1007/s12041-015-0529-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Chickpea (Cicer arietinum L.) is the second most important cool season food legume cultivated in arid and semiarid regions of the world. The objective of the present study was to study variation for protein content in chickpea germplasm, and to find markers associated with it. A set of 187 genotypes comprising both international and exotic collections, and representing both desi and kabuli types with protein content ranging from 13.25% to 26.77% was used. Twenty-three SSR markers representing all eight linkage groups (LG) amplifying 153 loci were used for the analysis. Population structure analysis identified three subpopulations, and corresponding Q values of principal components were used to take care of population structure in the analysis which was performed using general linear and mixed linear models. Marker-trait association (MTA) analysis identified nine significant associations representing four QTLs in the entire population. Subpopulation analyses identified ten significant MTAs representing five QTLs, four of which were common with that of the entire population. Two most significant QTLs linked with markers TR26.205 and CaM1068.195 were present on LG3 and LG5. Gene ontology search identified 29 candidate genes in the region of significant MTAs on LG3. The present study will be helpful in concentrating on LG3 and LG5 for identification of closely linked markers for protein content in chickpea and for their use in molecular breeding programme for nutritional quality improvement.
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Affiliation(s)
- A A Jadhav
- State Level Biotechnology Centre, Mahatma Phule Agricultural University, Rahuri 413 722, India.
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Chen H, Chen X, Tian J, Yang Y, Liu Z, Hao X, Wang L, Wang S, Liang J, Zhang L, Yin F, Cheng X. Development of Gene-Based SSR Markers in Rice Bean (Vigna umbellata L.) Based on Transcriptome Data. PLoS One 2016; 11:e0151040. [PMID: 26950544 PMCID: PMC4780709 DOI: 10.1371/journal.pone.0151040] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 02/23/2016] [Indexed: 11/24/2022] Open
Abstract
Rice bean (Vigna umbellata (Thunb.) Ohwi & Ohashi) is a warm season annual legume mainly grown in East Asia. Only scarce genomic resources are currently available for this legume crop species and no simple sequence repeat (SSR) markers have been specifically developed for rice bean yet. In this study, approximately 26 million high quality cDNA sequence reads were obtained from rice bean using Illumina paired-end sequencing technology and assembled into 71,929 unigenes with an average length of 986 bp. Of these unigenes, 38,840 (33.2%) showed significant similarity to proteins in the NCBI non-redundant protein and nucleotide sequence databases. Furthermore, 30,170 (76.3%) could be classified into gene ontology categories, 25,451 (64.4%) into Swiss-Prot categories and 21,982 (55.6%) into KOG database categories (E-value < 1.0E-5). A total of 9,301 (23.5%) were mapped onto 118 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway database. A total of 3,011 genic SSRs were identified as potential molecular markers. AG/CT (30.3%), AAG/CTT (8.1%) and AGAA/TTCT (20.0%) are the three main repeat motifs. A total of 300 SSR loci were randomly selected for validation by using PCR amplification. Of these loci, 23 primer pairs were polymorphic among 32 rice bean accessions. A UPGMA dendrogram revealed three major clusters among 32 rice bean accessions. The large number of SSR-containing sequences and genic SSRs in this study will be valuable for the construction of high-resolution genetic linkage maps, association or comparative mapping and genetic analyses of various Vigna species.
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Affiliation(s)
- Honglin Chen
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- * E-mail: (HLC); (XZC)
| | - Xin Chen
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China
| | - Jing Tian
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, Hebei, China
| | - Yong Yang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, Anhui, China
| | - Zhenxing Liu
- Tangshan Academy of Agricultural Sciences, Tangshan 036001, Hebei, China
| | - Xiyu Hao
- Baicheng Academy of Agricultural Sciences, Baicheng 137000, Jilin, China
| | - Lixia Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Suhua Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jie Liang
- Baicheng Academy of Agricultural Sciences, Baicheng 137000, Jilin, China
| | - Liya Zhang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, Anhui, China
| | - Fengxiang Yin
- Baicheng Academy of Agricultural Sciences, Baicheng 137000, Jilin, China
| | - Xuzhen Cheng
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- * E-mail: (HLC); (XZC)
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Duan C, Li W, Zhu Z, Li D, Sun S, Wang X. Genetic differentiation and diversity of Callosobruchus chinensis collections from China. BULLETIN OF ENTOMOLOGICAL RESEARCH 2016; 106:124-34. [PMID: 26548842 PMCID: PMC4762245 DOI: 10.1017/s0007485315000863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Callosobruchus chinensis (Linnaeus) is one of the most destructive pests of leguminous seeds. Genetic differentiation and diversity analysis of 345 C. chinensis individuals from 23 geographic populations using 20 polymorphic simple sequence repeats revealed a total of 149 alleles with an average of 7.45 alleles per locus. The average Shannon's information index was 1.015. The gene flow and genetic differentiation rate values at the 20 loci ranged from 0.201 to 1.841 and 11.0-47.2%, with averages of 0.849 and 24.4%, respectively. In the 23 geographic populations, the effective number of alleles and observed heterozygosity ranged from 1.441 to 2.218 and 0.191-0.410, respectively. Shannon's information index ranged from 0.357 to 0.949, with the highest value in Hohhot and the lowest in Rudong. In all comparisons, the fixation index (F ST ) values ranged from 0.049 to 0.441 with a total F ST value of 0.254 among the 23 C. chinensis populations, indicating a moderate level of genetic differentiation and gene flow among these populations. Analysis of molecular variance revealed that the genetic variation within populations accounted for 76.7% of the total genetic variation. The genetic similarity values between populations varied from 0.617 to 0.969, whereas genetic distances varied from 0.032 to 0.483. Using unweighted pair-group method using arithmetical averages cluster analysis, the 23 geographic collections were classified into four distinct genetic groups but most of them were clustered into a single group. The pattern of the three concentrated groups from polymerase chain reactions analysis showed a somewhat different result with cluster.
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Affiliation(s)
- C.X. Duan
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
- Author for correspondence Tel: +86-10-8210-9609 Fax: +86-10-8210-9608 E-mail:
| | - W.C. Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Z.D. Zhu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - D.D. Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - S.L. Sun
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - X.M. Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
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De Novo Transcriptome Sequencing Analysis of cDNA Library and Large-Scale Unigene Assembly in Japanese Red Pine (Pinus densiflora). Int J Mol Sci 2015; 16:29047-59. [PMID: 26690126 PMCID: PMC4691086 DOI: 10.3390/ijms161226139] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/13/2015] [Accepted: 11/26/2015] [Indexed: 01/28/2023] Open
Abstract
Japanese red pine (Pinus densiflora) is extensively cultivated in Japan, Korea, China, and Russia and is harvested for timber, pulpwood, garden, and paper markets. However, genetic information and molecular markers were very scarce for this species. In this study, over 51 million sequencing clean reads from P. densiflora mRNA were produced using Illumina paired-end sequencing technology. It yielded 83,913 unigenes with a mean length of 751 bp, of which 54,530 (64.98%) unigenes showed similarity to sequences in the NCBI database. Among which the best matches in the NCBI Nr database were Picea sitchensis (41.60%), Amborella trichopoda (9.83%), and Pinus taeda (4.15%). A total of 1953 putative microsatellites were identified in 1784 unigenes using MISA (MicroSAtellite) software, of which the tri-nucleotide repeats were most abundant (50.18%) and 629 EST-SSR (expressed sequence tag- simple sequence repeats) primer pairs were successfully designed. Among 20 EST-SSR primer pairs randomly chosen, 17 markers yielded amplification products of the expected size in P. densiflora. Our results will provide a valuable resource for gene-function analysis, germplasm identification, molecular marker-assisted breeding and resistance-related gene(s) mapping for pine for P. densiflora.
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CNMS: The preferred genic markers for comparative genomic, molecular phylogenetic, functional genetic diversity and differential gene regulatory expression analyses in chickpea. J Biosci 2015; 40:579-92. [PMID: 26333404 DOI: 10.1007/s12038-015-9545-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The intra/inter-genomic comparative mapping-based phylogenetic footprinting identified 5 paralogous and 656 orthologous genome-wide CNMS markers in the upstream sequences of chickpea genes. These CNMS markers revealed a high-degree of gene-based syntenic relationship between chickpea and Medicago genomes while minimum between chickpea and Vitis genomes. The time of divergence and duplication estimated using CNMS markers highlight the expected phylogenetic relationships between chickpea and six dicot (legume) species as well as occurrence of ancient genome (approximately 53 Mya) with small-scale recent segmental (approximately 10 Mya) duplication events in chickpea. A wider level of functional molecular diversity (14 to 88 percent) and admixed population genetic structure was detected among desi, kabuli and wild genotypes by genic CNMS markers at a genome-wide scale suggesting their utility in large-scale genetic analysis in chickpea. The subfunctionalization at the cis-regulatory element region and TFBS (transcription factor binding site) motif levels in the upstream sequences of CNMS marker-associated orthologous genes than the paralogues was predominant. Functional constraint might have considerable effect on these CNMScontaining regulatory elements controlling consistent orthologous gene expression in dicots. A rapid subfunctionalization based on diverge differential expression of paralogous CNMS marker-associated genes particularly those that underwent recent small-scale segmental duplication events in chickpea was apparent. The differential regulation of expression and subfunctionalization potential of Ultra CNMS marker-associated genes suggest their utility in deciphering the complex gene regulatory function as well as identification and targeted mapping of potential genes/QTLs governing vital agronomic traits in chickpea. The gene-based CNMS markers with desirable inherent genetic attributes like higher degree of comparative genome mapping, functional genetic diversity and differential gene regulatory expression potential can significantly propel the genomics-assisted chickpea crop improvement.
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Parida SK, Verma M, Yadav SK, Ambawat S, Das S, Garg R, Jain M. Development of genome-wide informative simple sequence repeat markers for large-scale genotyping applications in chickpea and development of web resource. FRONTIERS IN PLANT SCIENCE 2015; 6:645. [PMID: 26347762 PMCID: PMC4543896 DOI: 10.3389/fpls.2015.00645] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 08/03/2015] [Indexed: 05/18/2023]
Abstract
Development of informative polymorphic simple sequence repeat (SSR) markers at a genome-wide scale is essential for efficient large-scale genotyping applications. We identified genome-wide 1835 SSRs showing polymorphism between desi and kabuli chickpea. A total of 1470 polymorphic SSR markers from diverse coding and non-coding regions of the chickpea genome were developed. These physically mapped SSR markers exhibited robust amplification efficiency (73.9%) and high intra- and inter-specific polymorphic potential (63.5%), thereby suggesting their immense use in various genomics-assisted breeding applications. The SSR markers particularly derived from intergenic and intronic sequences revealed high polymorphic potential. Using the mapped SSR markers, a wider functional molecular diversity (16-94%, mean: 68%), and parentage- and cultivar-specific admixed domestication pattern and phylogenetic relationships in a structured population of desi and kabuli chickpea genotypes was evident. The intra-specific polymorphism (47.6%) and functional molecular diversity (65%) potential of polymorphic SSR markers developed in our study is much higher than that of previous documentations. Finally, we have developed a user-friendly web resource, Chickpea Microsatellite Database (CMsDB; http://www.nipgr.res.in/CMsDB.html), which provides public access to the data and results reported in this study. The developed informative SSR markers can serve as a resource for various genotyping applications, including genetic enhancement studies in chickpea.
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Affiliation(s)
| | | | | | | | | | | | - Mukesh Jain
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome ResearchNew Delhi, India
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Bajaj D, Das S, Badoni S, Kumar V, Singh M, Bansal KC, Tyagi AK, Parida SK. Genome-wide high-throughput SNP discovery and genotyping for understanding natural (functional) allelic diversity and domestication patterns in wild chickpea. Sci Rep 2015; 5:12468. [PMID: 26208313 PMCID: PMC4513697 DOI: 10.1038/srep12468] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 06/29/2015] [Indexed: 12/22/2022] Open
Abstract
We identified 82489 high-quality genome-wide SNPs from 93 wild and cultivated Cicer accessions through integrated reference genome- and de novo-based GBS assays. High intra- and inter-specific polymorphic potential (66-85%) and broader natural allelic diversity (6-64%) detected by genome-wide SNPs among accessions signify their efficacy for monitoring introgression and transferring target trait-regulating genomic (gene) regions/allelic variants from wild to cultivated Cicer gene pools for genetic improvement. The population-specific assignment of wild Cicer accessions pertaining to the primary gene pool are more influenced by geographical origin/phenotypic characteristics than species/gene-pools of origination. The functional significance of allelic variants (non-synonymous and regulatory SNPs) scanned from transcription factors and stress-responsive genes in differentiating wild accessions (with potential known sources of yield-contributing and stress tolerance traits) from cultivated desi and kabuli accessions, fine-mapping/map-based cloning of QTLs and determination of LD patterns across wild and cultivated gene-pools are suitably elucidated. The correlation between phenotypic (agromorphological traits) and molecular diversity-based admixed domestication patterns within six structured populations of wild and cultivated accessions via genome-wide SNPs was apparent. This suggests utility of whole genome SNPs as a potential resource for identifying naturally selected trait-regulating genomic targets/functional allelic variants adaptive to diverse agroclimatic regions for genetic enhancement of cultivated gene-pools.
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Affiliation(s)
- Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shouvik Das
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Saurabh Badoni
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Vinod Kumar
- National Research Centre on Plant Biotechnology (NRCPB), New Delhi-110012, India
| | - Mohar Singh
- National Bureau of Plant Genetic Resources (NBPGR), New Delhi-110012, India
| | - Kailash C. Bansal
- National Bureau of Plant Genetic Resources (NBPGR), New Delhi-110012, India
| | - Akhilesh K. Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Swarup K. Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
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Development and Validation of EST-SSR Markers from the Transcriptome of Adzuki Bean (Vigna angularis). PLoS One 2015; 10:e0131939. [PMID: 26146990 PMCID: PMC4492930 DOI: 10.1371/journal.pone.0131939] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 06/08/2015] [Indexed: 11/28/2022] Open
Abstract
The adzuki bean (Vigna angularis (Ohwi) Ohwi and Ohashi) is an important grain legume of Asia. It is cultivated mainly in China, Japan and Korea. Despite its importance, few genomic resources are available for molecular genetic research of adzuki bean. In this study, we developed EST-SSR markers for the adzuki bean through next-generation sequencing. More than 112 million high-quality cDNA sequence reads were obtained from adzuki bean using Illumina paired-end sequencing technology, and the sequences were de novo assembled into 65,950 unigenes. The average length of the unigenes was 1,213 bp. Among the unigenes, 14,547 sequences contained a unique simple sequence repeat (SSR) and 3,350 sequences contained more than one SSR. A total of 7,947 EST-SSRs were identified as potential molecular markers, with mono-nucleotide A/T repeats (99.0%) as the most abundant motif class, followed by AG/CT (68.4%), AAG/CTT (30.0%), AAAG/CTTT (26.2%), AAAAG/CTTTT (16.1%), and AACGGG/CCCGTT (6.0%). A total of 500 SSR markers were randomly selected for validation, of which 296 markers produced reproducible amplicons with 38 polymorphic markers among the 32 adzuki bean genotypes selected from diverse geographical locations across China. The large number of SSR-containing sequences and EST-SSR markers will be valuable for genetic analysis of the adzuki bean and related Vigna species.
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Souframanien J, Reddy KS. De novo Assembly, Characterization of Immature Seed Transcriptome and Development of Genic-SSR Markers in Black Gram [Vigna mungo (L.) Hepper]. PLoS One 2015; 10:e0128748. [PMID: 26042595 PMCID: PMC4456365 DOI: 10.1371/journal.pone.0128748] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 05/01/2015] [Indexed: 12/02/2022] Open
Abstract
Black gram [V. mungo (L.) Hepper] is an important legume crop extensively grown in south and south-east Asia, where it is a major source of dietary protein for its predominantly vegetarian population. However, lack of genomic information and markers has become a limitation for genetic improvement of this crop. Here, we report the transcriptome sequencing of the immature seeds of black gram cv. TU94-2, by Illumina paired end sequencing technology to generate transcriptome sequences for gene discovery and genic-SSR marker development. A total of 17.2 million paired-end reads were generated and 48,291 transcript contigs (TCS) were assembled with an average length of 443 bp. Based on sequence similarity search, 33,766 TCS showed significant similarity to known proteins. Among these, only 29,564 TCS were annotated with gene ontology (GO) functional categories. A total number of 138 unique KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were identified, of which majority of TCS are grouped into purine metabolism (678) followed by pyrimidine metabolism (263). A total of 48,291 TCS were searched for SSRs and 1,840 SSRs were identified in 1,572 TCS with an average frequency of one SSR per 11.9 kb. The tri-nucleotide repeats were most abundant (35%) followed by di-nucleotide repeats (32%). PCR primer pairs were successfully designed for 933 SSR loci. Sequences analyses indicate that about 64.4% and 35.6% of the SSR motifs were present in the coding sequences (CDS) and untranslated regions (UTRs) respectively. Tri-nucleotide repeats (57.3%) were preferentially present in the CDS. The rate of successful amplification and polymorphism were investigated using selected primers among 18 black gram accessions. Genic-SSR markers developed from the Illumina paired end sequencing of black gram immature seed transcriptome will provide a valuable resource for genetic diversity, evolution, linkage mapping, comparative genomics and marker-assisted selection in black gram.
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Affiliation(s)
- J. Souframanien
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai-400085, India
- * E-mail:
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Chen H, Qiao L, Wang L, Wang S, Blair MW, Cheng X. Assessment of genetic diversity and population structure of mung bean (Vigna radiata) germplasm using EST-based and genomic SSR markers. Gene 2015; 566:175-83. [PMID: 25895480 DOI: 10.1016/j.gene.2015.04.043] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 04/15/2015] [Accepted: 04/16/2015] [Indexed: 01/30/2023]
Abstract
Mung bean is an important legume crop in tropical and subtropical countries of Asia and has high nutritional and economic value. However the genetic diversity of mung bean is poorly characterized. In this study, our goal was to develop and use microsatellite simple sequence repeat (SSR) markers for germplasm evaluation. In total, 500 novel expression sequence tag EST-based SSRs (eSSRs) and genomic SSRs (gSSRs) were developed from mung bean transcriptome and genome sequences. Of these, only 58 were useful for diversity evaluation in a panel of 157 cultivated and wild mung bean accessions from different collection sites in East Asia. A total of 2.66 alleles were detected on average per locus which shows that polymorphism is generally low for the species. The average polymorphic information content (PIC) of gSSRs was higher than eSSRs and most of the polymorphic gSSRs were composed of di- and tri-nucleotide repeats (52.4% and 38.1% of all loci, respectively). The genotypes were differentiated into nine subgroups by cluster analysis, and the wild mung bean accessions separated well from the cultivated accessions. Analysis of molecular variance indicated that 22% of variance was observed among populations and 78% was due to differences within populations. Clustering, population structure analyses showed that non-Chinese cultivated and wild mung bean accessions were separated from Chinese accessions, but no geographical distinctions existed between genotypes collected in China. Interestingly, the average PIC value of cultivated mung bean (0.36) was higher than that of wild mung bean (0.25) showing that further collecting and wide crosses are necessary for mung bean improvement.
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Affiliation(s)
- Honglin Chen
- National Key Facility for Crop Gene Resources Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ling Qiao
- National Key Facility for Crop Gene Resources Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Lixia Wang
- National Key Facility for Crop Gene Resources Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Suhua Wang
- National Key Facility for Crop Gene Resources Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Matthew Wohlgemuth Blair
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN 37209, USA
| | - Xuzhen Cheng
- National Key Facility for Crop Gene Resources Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Transcriptome sequencing of mung bean (Vigna radiate L.) genes and the identification of EST-SSR markers. PLoS One 2015; 10:e0120273. [PMID: 25830701 PMCID: PMC4382333 DOI: 10.1371/journal.pone.0120273] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 02/02/2015] [Indexed: 11/19/2022] Open
Abstract
Mung bean (Vigna radiate (L.) Wilczek) is an important traditional food legume crop, with high economic and nutritional value. It is widely grown in China and other Asian countries. Despite its importance, genomic information is currently unavailable for this crop plant species or some of its close relatives in the Vigna genus. In this study, more than 103 million high quality cDNA sequence reads were obtained from mung bean using Illumina paired-end sequencing technology. The processed reads were assembled into 48,693 unigenes with an average length of 874 bp. Of these unigenes, 25,820 (53.0%) and 23,235 (47.7%) showed significant similarity to proteins in the NCBI non-redundant protein and nucleotide sequence databases, respectively. Furthermore, 19,242 (39.5%) could be classified into gene ontology categories, 18,316 (37.6%) into Swiss-Prot categories and 10,918 (22.4%) into KOG database categories (E-value < 1.0E-5). A total of 6,585 (8.3%) were mapped onto 244 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway database. Among the unigenes, 10,053 sequences contained a unique simple sequence repeat (SSR), and 2,303 sequences contained more than one SSR together in the same expressed sequence tag (EST). A total of 13,134 EST-SSRs were identified as potential molecular markers, with mono-nucleotide A/T repeats being the most abundant motif class and G/C repeats being rare. In this SSR analysis, we found five main repeat motifs: AG/CT (30.8%), GAA/TTC (12.6%), AAAT/ATTT (6.8%), AAAAT/ATTTT (6.2%) and AAAAAT/ATTTTT (1.9%). A total of 200 SSR loci were randomly selected for validation by PCR amplification as EST-SSR markers. Of these, 66 marker primer pairs produced reproducible amplicons that were polymorphic among 31 mung bean accessions selected from diverse geographical locations. The large number of SSR-containing sequences found in this study will be valuable for the construction of a high-resolution genetic linkage maps, association or comparative mapping and genetic analyses of various Vigna species.
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Bajaj D, Saxena MS, Kujur A, Das S, Badoni S, Tripathi S, Upadhyaya HD, Gowda CLL, Sharma S, Singh S, Tyagi AK, Parida SK. Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1271-90. [PMID: 25504138 PMCID: PMC4339591 DOI: 10.1093/jxb/eru478] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Phylogenetic footprinting identified 666 genome-wide paralogous and orthologous CNMS (conserved non-coding microsatellite) markers from 5'-untranslated and regulatory regions (URRs) of 603 protein-coding chickpea genes. The (CT)n and (GA)n CNMS carrying CTRMCAMV35S and GAGA8BKN3 regulatory elements, respectively, are abundant in the chickpea genome. The mapped genic CNMS markers with robust amplification efficiencies (94.7%) detected higher intraspecific polymorphic potential (37.6%) among genotypes, implying their immense utility in chickpea breeding and genetic analyses. Seventeen differentially expressed CNMS marker-associated genes showing strong preferential and seed tissue/developmental stage-specific expression in contrasting genotypes were selected to narrow down the gene targets underlying seed weight quantitative trait loci (QTLs)/eQTLs (expression QTLs) through integrative genetical genomics. The integration of transcript profiling with seed weight QTL/eQTL mapping, molecular haplotyping, and association analyses identified potential molecular tags (GAGA8BKN3 and RAV1AAT regulatory elements and alleles/haplotypes) in the LOB-domain-containing protein- and KANADI protein-encoding transcription factor genes controlling the cis-regulated expression for seed weight in the chickpea. This emphasizes the potential of CNMS marker-based integrative genetical genomics for the quantitative genetic dissection of complex seed weight in chickpea.
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Affiliation(s)
- Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Maneesha S Saxena
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Alice Kujur
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shouvik Das
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Saurabh Badoni
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi 110012, India
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - C L L Gowda
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Shivali Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Sube Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
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Kumar S, Rajendran K, Kumar J, Hamwieh A, Baum M. Current knowledge in lentil genomics and its application for crop improvement. FRONTIERS IN PLANT SCIENCE 2015; 6:78. [PMID: 25755659 PMCID: PMC4337236 DOI: 10.3389/fpls.2015.00078] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/30/2015] [Indexed: 05/24/2023]
Abstract
Most of the lentil growing countries face a certain set of abiotic and biotic stresses causing substantial reduction in crop growth, yield, and production. Until-to date, lentil breeders have used conventional plant breeding techniques of selection-recombination-selection cycle to develop improved cultivars.These techniques have been successful in mainstreaming some of the easy-to-manage monogenic traits. However, in case of complex quantitative traits, these conventional techniques are less precise. As most of the economic traits are complex, quantitative, and often influenced by environments and genotype-environment interaction, the genetic improvement of these traits becomes difficult. Genomics assisted breeding is relatively powerful and fast approach to develop high yielding varieties more suitable to adverse environmental conditions. New tools such as molecular markers and bioinformatics are expected to generate new knowledge and improve our understanding on the genetics of complex traits. In the past, the limited availability of genomic resources in lentil could not allow breeders to employ these tools in mainstream breeding program.The recent application of the next generation sequencing and genotyping by sequencing technologies has facilitated to speed up the lentil genome sequencing project and large discovery of genome-wide single nucleotide polymorphism (SNP) markers. Currently, several linkage maps have been developed in lentil through the use of expressed sequenced tag (EST) derived simple sequence repeat (SSR) and SNP markers.These maps have emerged as useful genomic resources to identify quantitative trait loci imparting tolerance to biotic and abiotic stresses in lentil. In this review, the current knowledge on available genomic resources and its application in lentil breeding program are discussed.
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Affiliation(s)
- Shiv Kumar
- Biodiversity and Integrated Gene Management Program, International Center for Agricultural Research in the Dry Areas, RabatMorocco
| | - Karthika Rajendran
- Biodiversity and Integrated Gene Management Program, International Center for Agricultural Research in the Dry Areas, RabatMorocco
| | - Jitendra Kumar
- Division of Crop Improvement, Indian Institute of Pulses Research, KanpurIndia
| | - Aladdin Hamwieh
- International Center for Agricultural Research in the Dry Areas, CairoEgypt
| | - Michael Baum
- International Center for Agricultural Research in the Dry Areas, AmmanJordan
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Raveendar S, Lee GA, Jeon YA, Lee YJ, Lee JR, Cho GT, Cho JH, Park JH, Ma KH, Chung JW. Cross-amplification of Vicia sativa subsp. sativa microsatellites across 22 other Vicia species. Molecules 2015; 20:1543-50. [PMID: 25608853 PMCID: PMC6272350 DOI: 10.3390/molecules20011543] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 01/14/2015] [Indexed: 11/16/2022] Open
Abstract
The temperate and herbaceous genus Vicia L. is a member of the legume tribe Fabeae of the subfamily Papilionoideae. The genus Vicia comprises 166 annual or perennial species distributed mainly in Europe, Asia, and North America, but also extending to the temperate regions of South America and tropical Africa. The use of simple sequence repeat (SSR) markers for Vicia species has not been investigated as extensively as for other crop species. In this study, we assessed the potential for cross-species amplification of cDNA microsatellite markers developed from common vetch (Vicia sativa subsp. sativa). For cross-species amplification of the SSRs, amplification was carried out with genomic DNA isolated from two to eight accessions of 22 different Vicia species. For individual species or subspecies, the transferability rates ranged from 33% for V. ervilia to 82% for V. sativa subsp. nigra with an average rate of 52.0%. Because the rate of successful SSR marker amplification generally correlates with genetic distance, these SSR markers are potentially useful for analyzing genetic relationships between or within Vicia species.
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Affiliation(s)
- Sebastin Raveendar
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea
| | - Gi-An Lee
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea
| | - Young-Ah Jeon
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea
| | - Yun Jeong Lee
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea
| | - Jung-Ro Lee
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea
| | - Gyu-Taek Cho
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea
| | - Joon-Hyeong Cho
- Department of Biological and Environmental Science, Dongguk University, Seoul 100-175, Korea
| | - Jong-Hyun Park
- Food Grain Policy Division, Ministry of Agriculture, Food and Rural Affairs, Sejong-si 339-012, Korea
| | - Kyung-Ho Ma
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea
| | - Jong-Wook Chung
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
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Saxena MS, Bajaj D, Das S, Kujur A, Kumar V, Singh M, Bansal KC, Tyagi AK, Parida SK. An integrated genomic approach for rapid delineation of candidate genes regulating agro-morphological traits in chickpea. DNA Res 2014; 21:695-710. [PMID: 25335477 PMCID: PMC4263302 DOI: 10.1093/dnares/dsu031] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The identification and fine mapping of robust quantitative trait loci (QTLs)/genes governing important agro-morphological traits in chickpea still lacks systematic efforts at a genome-wide scale involving wild Cicer accessions. In this context, an 834 simple sequence repeat and single-nucleotide polymorphism marker-based high-density genetic linkage map between cultivated and wild parental accessions (Cicer arietinum desi cv. ICC 4958 and Cicer reticulatum wild cv. ICC 17160) was constructed. This inter-specific genetic map comprising eight linkage groups spanned a map length of 949.4 cM with an average inter-marker distance of 1.14 cM. Eleven novel major genomic regions harbouring 15 robust QTLs (15.6–39.8% R2 at 4.2–15.7 logarithm of odds) associated with four agro-morphological traits (100-seed weight, pod and branch number/plant and plant hairiness) were identified and mapped on chickpea chromosomes. Most of these QTLs showed positive additive gene effects with effective allelic contribution from ICC 4958, particularly for increasing seed weight (SW) and pod and branch number. One robust SW-influencing major QTL region (qSW4.2) has been narrowed down by combining QTL mapping with high-resolution QTL region-specific association analysis, differential expression profiling and gene haplotype-based association/LD mapping. This enabled to delineate a strong SW-regulating ABI3VP1 transcription factor (TF) gene at trait-specific QTL interval and consequently identified favourable natural allelic variants and superior high seed weight-specific haplotypes in the upstream regulatory region of this gene showing increased transcript expression during seed development. The genes (TFs) harbouring diverse trait-regulating QTLs, once validated and fine-mapped by our developed rapid integrated genomic approach and through gene/QTL map-based cloning, can be utilized as potential candidates for marker-assisted genetic enhancement of chickpea.
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Affiliation(s)
- Maneesha S Saxena
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shouvik Das
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Alice Kujur
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Vinod Kumar
- National Research Centre on Plant Biotechnology (NRCPB), New Delhi 110012, India
| | - Mohar Singh
- National Bureau of Plant Genetic Resources (NBPGR), New Delhi 110012, India
| | - Kailash C Bansal
- National Bureau of Plant Genetic Resources (NBPGR), New Delhi 110012, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
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Identification and characterization of microsatellites in expressed sequence tags and their cross transferability in different plants. Int J Genomics 2014; 2014:863948. [PMID: 25389527 PMCID: PMC4217358 DOI: 10.1155/2014/863948] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 08/31/2014] [Accepted: 09/22/2014] [Indexed: 12/20/2022] Open
Abstract
Expressed sequence tags (EST) are potential source for the development of genic microsatellite markers, gene discovery, comparative genomics, and other genomic studies. In the present study, 7630 ESTs were examined from NCBI for SSR identification and characterization. A total of 263 SSRs were identified with an average density of one SSR/4.2 kb (3.4% frequency). Analysis revealed that trinucleotide repeats (47.52%) were most abundant followed by tetranucleotide (19.77%), dinucleotide (19.01%), pentanucleotide (9.12%), and hexanucleotide repeats (4.56%). Functional annotation was done through homology search and gene ontology, and 35 EST-SSRs were selected. Primer pairs were designed for evaluation of cross transferability and polymorphism among 11 plants belonging to five different families. Total 402 alleles were generated at 155 loci with an average of 2.6 alleles/locus and the polymorphic information content (PIC) ranged from 0.15 to 0.92 with an average of 0.75. The cross transferability ranged from 34.84% to 98.06% in different plants, with an average of 67.86%. Thus, the validation study of annotated 35 EST-SSR markers which correspond to particular metabolic activity revealed polymorphism and evolutionary nature in different families of Angiospermic plants.
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Saxena MS, Bajaj D, Kujur A, Das S, Badoni S, Kumar V, Singh M, Bansal KC, Tyagi AK, Parida SK. Natural allelic diversity, genetic structure and linkage disequilibrium pattern in wild chickpea. PLoS One 2014; 9:e107484. [PMID: 25222488 PMCID: PMC4164632 DOI: 10.1371/journal.pone.0107484] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 08/11/2014] [Indexed: 01/23/2023] Open
Abstract
Characterization of natural allelic diversity and understanding the genetic structure and linkage disequilibrium (LD) pattern in wild germplasm accessions by large-scale genotyping of informative microsatellite and single nucleotide polymorphism (SNP) markers is requisite to facilitate chickpea genetic improvement. Large-scale validation and high-throughput genotyping of genome-wide physically mapped 478 genic and genomic microsatellite markers and 380 transcription factor gene-derived SNP markers using gel-based assay, fluorescent dye-labelled automated fragment analyser and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass array have been performed. Outcome revealed their high genotyping success rate (97.5%) and existence of a high level of natural allelic diversity among 94 wild and cultivated Cicer accessions. High intra- and inter-specific polymorphic potential and wider molecular diversity (11-94%) along with a broader genetic base (13-78%) specifically in the functional genic regions of wild accessions was assayed by mapped markers. It suggested their utility in monitoring introgression and transferring target trait-specific genomic (gene) regions from wild to cultivated gene pool for the genetic enhancement. Distinct species/gene pool-wise differentiation, admixed domestication pattern, and differential genome-wide recombination and LD estimates/decay observed in a six structured population of wild and cultivated accessions using mapped markers further signifies their usefulness in chickpea genetics, genomics and breeding.
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Affiliation(s)
- Maneesha S. Saxena
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Alice Kujur
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Shouvik Das
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Saurabh Badoni
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Vinod Kumar
- National Research Centre on Plant Biotechnology (NRCPB), New Delhi, India
| | - Mohar Singh
- National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| | - Kailash C. Bansal
- National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| | - Akhilesh K. Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Swarup K. Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
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Chankaew S, Isemura T, Isobe S, Kaga A, Tomooka N, Somta P, Hirakawa H, Shirasawa K, Vaughan DA, Srinives P. Detection of genome donor species of neglected tetraploid crop Vigna reflexo-pilosa (créole bean), and genetic structure of diploid species based on newly developed EST-SSR markers from azuki bean (Vigna angularis). PLoS One 2014; 9:e104990. [PMID: 25153330 PMCID: PMC4143246 DOI: 10.1371/journal.pone.0104990] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 07/16/2014] [Indexed: 11/18/2022] Open
Abstract
Vigna reflexo-pilosa, which includes a neglected crop, is the only one tetraploid species in genus Vigna. The ancestral species that make up this allotetraploid species have not conclusively been identified, although previous studies suggested that a donor genome of V. reflexo-pilosa is V. trinervia. In this study, 1,429 azuki bean EST-SSR markers were developed of which 38 EST-SSR primer pairs that amplified one product in diploid species and two discrete products in tetraploid species were selected to analyze 268 accessions from eight taxa of seven Asian Vigna species including V. reflexo-pilosa var. glabra, V. reflexo-pilosa var. reflexo-pilosa, V. exilis, V. hirtella, V. minima, V. radiata var. sublobata, V. tenuicaulis and V. trinervia to identify genome donor of V. reflexo-pilosa. Since both diploid and tetraploid species were analyzed and each SSR primer pair detected two loci in the tetraploid species, we separated genomes of the tetraploid species into two different diploid types, viz. A and B. In total, 445 alleles were detected by 38 EST-SSR markers. The highest gene diversity was observed in V. hirtella. By assigning the discrete PCR products of V. reflexo-pilosa into two distinguished genomes, we were able to identify the two genome donor parents of créole bean. Phylogenetic and principal coordinate analyses suggested that V. hirtella is a species complex and may be composed of at least three distinct taxa. Both analyses also clearly demonstrated that V. trinervia and one taxon of V. hirtella are the genome donors of V. reflexo-pilosa. Gene diversity indicates that the evolution rate of EST-SSRs on genome B of créole bean might be faster than that on genome A. Species relationship among the Vigna species in relation to genetic data, morphology and geographical distribution are presented.
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Affiliation(s)
- Sompong Chankaew
- Program in Plant Breeding, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom, Thailand
| | - Takehisa Isemura
- Genetic Resources Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Akito Kaga
- Genetic Resources Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Norihiko Tomooka
- Genetic Resources Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
- * E-mail: (NT); (PS)
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom, Thailand
| | | | | | - Duncan A. Vaughan
- Genetic Resources Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Peerasak Srinives
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom, Thailand
- * E-mail: (NT); (PS)
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Gaur R, Bhatia S, Gupta M. Generation of expressed sequence tags under cadmium stress for gene discovery and development of molecular markers in chickpea. PROTOPLASMA 2014; 251:955-72. [PMID: 24414095 DOI: 10.1007/s00709-013-0609-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 12/27/2013] [Indexed: 06/03/2023]
Abstract
Chickpea is the world's third most important legume crop and belongs to Fabaceae family but suffered from severe yield loss due to various biotic and abiotic stresses. Development of modern genomic tools such as molecular markers and identification of resistant genes associated with these stresses facilitate improvement in chickpea breeding towards abiotic stress tolerance. In this study, 1597 high-quality expressed sequence tags (ESTs) were generated from a cDNA library of variety Pusa 1105 root tissue after cadmium (Cd) treatment. Assembly of ESTs resulted in a total of 914 unigenes of which putative homology was obtained for 38.8 % of unigenes after BLASTX search. In terms of species distribution, majority of sequences found similarity with Medicago truncatula followed by Glycine max, Vitis vinifera and Populus trichocarpa and Pisum sativum sequences. Functional annotation was assigned using Blast2Go, and the Gene Ontology (GO) terms were categorized into biological process, molecular function and cellular component. Approximately 10.83 % of unigenes were assigned at least one GO term. Moreover, in the distribution of transcripts into various biological pathways, 20 of the annotated transcripts were assigned to ten pathways in KEGG database. A majority of the genes were found to be involved in sulphur and nitrogen metabolism. In the quantitative real-time PCR analysis, five of the transcription factors and three of the transporter genes were found to be highly expressed after Cd treatment. Besides, the utility of ESTs was demonstrated by exploiting them for the development of 83 genic molecular markers including EST-simple sequence repeats and intron targeted polymorphism that would assist in tagging of genes related to metal stress for future prospects.
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Affiliation(s)
- Rashmi Gaur
- Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India,
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Doddamani D, Katta MAVSK, Khan AW, Agarwal G, Shah TM, Varshney RK. CicArMiSatDB: the chickpea microsatellite database. BMC Bioinformatics 2014; 15:212. [PMID: 24952649 PMCID: PMC4230034 DOI: 10.1186/1471-2105-15-212] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 06/17/2014] [Indexed: 01/12/2023] Open
Abstract
Background Chickpea (Cicer arietinum) is a widely grown legume crop in tropical, sub-tropical and temperate regions. Molecular breeding approaches seem to be essential for enhancing crop productivity in chickpea. Until recently, limited numbers of molecular markers were available in the case of chickpea for use in molecular breeding. However, the recent advances in genomics facilitated the development of large scale markers especially SSRs (simple sequence repeats), the markers of choice in any breeding program. Availability of genome sequence very recently opens new avenues for accelerating molecular breeding approaches for chickpea improvement. Description In order to assist genetic studies and breeding applications, we have developed a user friendly relational database named the Chickpea Microsatellite Database (CicArMiSatDB http://cicarmisatdb.icrisat.org). This database provides detailed information on SSRs along with their features in the genome. SSRs have been classified and made accessible through an easy-to-use web interface. Conclusions This database is expected to help chickpea community in particular and legume community in general, to select SSRs of particular type or from a specific region in the genome to advance both basic genomics research as well as applied aspects of crop improvement.
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Affiliation(s)
| | | | | | | | | | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India.
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Expanding the repertoire of microsatellite markers for polymorphism studies in Indian accessions of mung bean (Vigna radiata L. Wilczek). Mol Biol Rep 2014; 41:5669-80. [PMID: 24913033 DOI: 10.1007/s11033-014-3436-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 05/26/2014] [Indexed: 10/25/2022]
Abstract
Limited availability of validated, polymorphic microsatellite markers in mung bean (Vigna radiata), an important food legume of India, has been a major hurdle towards its improvement and higher yield. The present study was undertaken in order to develop a new set of microsatellite markers and utilize them for the analysis of genetic diversity within mung bean accessions from India. A GA/CT enriched library was constructed from V. radiata which resulted in 1,250 putative recombinant clones of which 850 were sequenced. SSR motifs were identified and their flanking sequences were utilized to design 328 SSR primer pairs. Of these, 48 SSR markers were employed for assessing genetic diversity among 76 mung bean accessions from various geographical locations in India. Two hundred and thirty four alleles with an average of 4.85 alleles per locus were detected at 48 loci. The polymorphic information content (PIC) per locus varied from 0.1 to 0.88 (average: 0.49 per locus). The observed and expected heterozygosities ranged from 0.40 to 0.95 and 0.40 to 0.81 respectively. Based on Jaccard's similarity matrix, a dendrogram was constructed using the unweighted pair-group method with arithmetic averages (UPGMA) analysis which revealed that one accession from Bundi, Rajasthan was clustered out separately while remaining accessions were grouped into two major clusters. The markers generated in this study will help in expanding the repertoire of the available SSR markers thereby facilitating analysis of genetic diversity, molecular mapping and ultimately broadening the scope for genetic improvement of this legume.
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Duan CX, Li DD, Sun SL, Wang XM, Zhu ZD. Rapid development of microsatellite markers for Callosobruchus chinensis using Illumina paired-end sequencing. PLoS One 2014; 9:e95458. [PMID: 24835431 PMCID: PMC4023940 DOI: 10.1371/journal.pone.0095458] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 03/27/2014] [Indexed: 11/26/2022] Open
Abstract
Background The adzuki bean weevil, Callosobruchus chinensis L., is one of the most destructive pests of stored legume seeds such as mungbean, cowpea, and adzuki bean, which usually cause considerable loss in the quantity and quality of stored seeds during transportation and storage. However, a lack of genetic information of this pest results in a series of genetic questions remain largely unknown, including population genetic structure, kinship, biotype abundance, and so on. Co-dominant microsatellite markers offer a great resolving power to determine these events. Here, we report rapid microsatellite isolation from C. chinensis via high-throughput sequencing. Principal Findings In this study, 94,560,852 quality-filtered and trimmed reads were obtained for the assembly of genome using Illumina paired-end sequencing technology. In total, the genome with total length of 497,124,785 bp, comprising 403,113 high quality contigs was generated with de novo assembly. More than 6800 SSR loci were detected and a suit of 6303 primer pair sequences were designed and 500 of them were randomly selected for validation. Of these, 196 pair of primers, i.e. 39.2%, produced reproducible amplicons that were polymorphic among 8 C. chinensis genotypes collected from different geographical regions. Twenty out of 196 polymorphic SSR markers were used to analyze the genetic diversity of 18 C. chinensis populations. The results showed the twenty SSR loci were highly polymorphic among these populations. Conclusions This study presents a first report of genome sequencing and de novo assembly for C. chinensis and demonstrates the feasibility of generating a large scale of sequence information and SSR loci isolation by Illumina paired-end sequencing. Our results provide a valuable resource for C. chinensis research. These novel markers are valuable for future genetic mapping, trait association, genetic structure and kinship among C. chinensis.
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Affiliation(s)
- Can-xing Duan
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Dan-dan Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Su-li Sun
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Xiao-ming Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Zhen-dong Zhu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
- * E-mail:
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Südüpak MA. SSR-Based Genetic Diversity Assessment of Turkish Chickpea Varieties. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/bbeq.2013.0070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Wang Z, Yu G, Shi B, Wang X, Qiang H, Gao H. Development and characterization of simple sequence repeat (SSR) markers based on RNA-sequencing of Medicago sativa and in silico mapping onto the M. truncatula genome. PLoS One 2014; 9:e92029. [PMID: 24642969 PMCID: PMC3958398 DOI: 10.1371/journal.pone.0092029] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 02/17/2014] [Indexed: 11/18/2022] Open
Abstract
Sufficient codominant genetic markers are needed for various genetic investigations in alfalfa since the species is an outcrossing autotetraploid. With the newly developed next generation sequencing technology, a large amount of transcribed sequences of alfalfa have been generated and are available for identifying SSR markers by data mining. A total of 54,278 alfalfa non-redundant unigenes were assembled through the Illumina HiSeqTM 2000 sequencing technology. Based on 3,903 unigene sequences, 4,493 SSRs were identified. Tri-nucleotide repeats (56.71%) were the most abundant motif class while AG/CT (21.7%), AGG/CCT (19.8%), AAC/GTT (10.3%), ATC/ATG (8.8%), and ACC/GGT (6.3%) were the subsequent top five nucleotide repeat motifs. Eight hundred and thirty- seven EST-SSR primer pairs were successfully designed. Of these, 527 (63%) primer pairs yielded clear and scored PCR products and 372 (70.6%) exhibited polymorphisms. High transferability was observed for ssp falcata at 99.2% (523) and 71.7% (378) in M. truncatula. In addition, 313 of 527 SSR marker sequences were in silico mapped onto the eight M. truncatula chromosomes. Thirty-six polymorphic SSR primer pairs were used in the genetic relatedness analysis of 30 Chinese alfalfa cultivated accessions generating a total of 199 scored alleles. The mean observed heterozygosity and polymorphic information content were 0.767 and 0.635, respectively. The codominant markers not only enriched the current resources of molecular markers in alfalfa, but also would facilitate targeted investigations in marker-trait association, QTL mapping, and genetic diversity analysis in alfalfa.
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Affiliation(s)
- Zan Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail: (ZW); (HG)
| | - Guohui Yu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Department of Grassland Science, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Binbin Shi
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuemin Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haiping Qiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongwen Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail: (ZW); (HG)
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Pradhan S, Bandhiwal N, Shah N, Kant C, Gaur R, Bhatia S. Global transcriptome analysis of developing chickpea (Cicer arietinum L.) seeds. FRONTIERS IN PLANT SCIENCE 2014; 5:698. [PMID: 25566273 PMCID: PMC4267183 DOI: 10.3389/fpls.2014.00698] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 11/24/2014] [Indexed: 05/20/2023]
Abstract
Understanding developmental processes, especially in non-model crop plants, is extremely important in order to unravel unique mechanisms regulating development. Chickpea (C. arietinum L.) seeds are especially valued for their high carbohydrate and protein content. Therefore, in order to elucidate the mechanisms underlying seed development in chickpea, deep sequencing of transcriptomes from four developmental stages was undertaken. In this study, next generation sequencing platform was utilized to sequence the transcriptome of four distinct stages of seed development in chickpea. About 1.3 million reads were generated which were assembled into 51,099 unigenes by merging the de novo and reference assemblies. Functional annotation of the unigenes was carried out using the Uniprot, COG and KEGG databases. RPKM based digital expression analysis revealed specific gene activities at different stages of development which was validated using Real time PCR analysis. More than 90% of the unigenes were found to be expressed in at least one of the four seed tissues. DEGseq was used to determine differentially expressing genes which revealed that only 6.75% of the unigenes were differentially expressed at various stages. Homology based comparison revealed 17.5% of the unigenes to be putatively seed specific. Transcription factors were predicted based on HMM profiles built using TF sequences from five legume plants and analyzed for their differential expression during progression of seed development. Expression analysis of genes involved in biosynthesis of important secondary metabolites suggested that chickpea seeds can serve as a good source of antioxidants. Since transcriptomes are a valuable source of molecular markers like simple sequence repeats (SSRs), about 12,000 SSRs were mined in chickpea seed transcriptome and few of them were validated. In conclusion, this study will serve as a valuable resource for improved chickpea breeding.
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Affiliation(s)
| | | | | | | | | | - Sabhyata Bhatia
- *Correspondence: Sabhyata Bhatia, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India e-mail:
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Assessment of genetic diversity in Indian rice germplasm (Oryza sativa L.): use of random versus trait-linked microsatellite markers. J Genet 2013; 92:545-57. [DOI: 10.1007/s12041-013-0312-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Kujur A, Saxena MS, Bajaj D, Laxmi, Parida SK. Integrated genomics and molecular breeding approaches for dissecting the complex quantitative traits in crop plants. J Biosci 2013; 38:971-87. [DOI: 10.1007/s12038-013-9388-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Muthamilarasan M, Venkata Suresh B, Pandey G, Kumari K, Parida SK, Prasad M. Development of 5123 intron-length polymorphic markers for large-scale genotyping applications in foxtail millet. DNA Res 2013; 21:41-52. [PMID: 24086082 PMCID: PMC3925393 DOI: 10.1093/dnares/dst039] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Generating genomic resources in terms of molecular markers is imperative in molecular breeding for crop improvement. Though development and application of microsatellite markers in large-scale was reported in the model crop foxtail millet, no such large-scale study was conducted for intron-length polymorphic (ILP) markers. Considering this, we developed 5123 ILP markers, of which 4049 were physically mapped onto 9 chromosomes of foxtail millet. BLAST analysis of 5123 expressed sequence tags (ESTs) suggested the function for ∼71.5% ESTs and grouped them into 5 different functional categories. About 440 selected primer pairs representing the foxtail millet genome and the different functional groups showed high-level of cross-genera amplification at an average of ∼85% in eight millets and five non-millet species. The efficacy of the ILP markers for distinguishing the foxtail millet is demonstrated by observed heterozygosity (0.20) and Nei's average gene diversity (0.22). In silico comparative mapping of physically mapped ILP markers demonstrated substantial percentage of sequence-based orthology and syntenic relationship between foxtail millet chromosomes and sorghum (∼50%), maize (∼46%), rice (∼21%) and Brachypodium (∼21%) chromosomes. Hence, for the first time, we developed large-scale ILP markers in foxtail millet and demonstrated their utility in germplasm characterization, transferability, phylogenetics and comparative mapping studies in millets and bioenergy grass species.
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Abstract
Microsatellites are codominant molecular genetic markers, which are universally dispersed within genomes. These markers are highly popular because of their high level of polymorphism, relatively small size, and rapid detection protocols. They are widely used in a variety of fundamental and applied fields of biological sciences for plants and animal studies. Microsatellites are also extensively used in the field of agriculture, where they are used in characterizing genetic materials, plant selection, constructing dense linkage maps, mapping economically important quantitative traits, identifying genes responsible for these traits. In addition microsatellites are used for marker-assisted selection in breeding programs, thus speeding up the process. In this chapter, genomic distribution, evolution, and practical applications of microsatellites are considered, with special emphasis on plant breeding and agriculture. Moreover, novel advances in microsatellite technologies are also discussed.
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