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Laisram N, Rahman Z, Singh VP. Antagonistic Activity of Pseudomonas fluorescens Strain X1 Against Different Fusaria and it's In Vivo Analysis Against Fusarium udum Infected Pigeon Pea. Curr Microbiol 2023; 80:98. [PMID: 36739341 DOI: 10.1007/s00284-023-03184-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/05/2023] [Indexed: 02/06/2023]
Abstract
A plant growth-promoting rhizobacterial strain, Pseudomonas fluorescens X1 isolated from the garden soil was employed for antagonistic activity against different species of fusaria. Strain X1 inhibited four different fusaria (Fusarium moniliforme, Fusarium oxysporum, Fusarium semitectum and Fusarium udum) in dual culture plate assay, and in broth culture using cell-free culture filtrate. Scanning electron microscopic (SEM) analysis revealed deformation and shrinkage in mycelia of fusaria after treatment with strain X1. Confocal micrographs showed degeneration of nuclei inside the cells of fusaria for the same effect. Strain X1 exhibited maximum antifungal activity, when it was grown in nutrient broth yeast (NBY) medium amended with 1 mM NH4MoO4 and 1% glucose. The antifungal extracts eluted from thin-layer chromatography (TLC) followed by high performance liquid chromatography (HPLC) showed two fractions active against different fusaria. Liquid chromatography-mass spectrometry (LCMS) analysis of the two fractions 1 and 2 corresponded to molecular ions at m/z 177.16 and m/z 177.09, respectively. Infra-red (IR) analysis showed five similar absorption bands in both the fractions analysed. In vivo analysis of strain X1 alone and along with fungicide inhibited the growth of F. udum and improved the biomass and growth of pigeon pea. These results indicated that strain X1 could be possibly used as a biocontrol agent to inhibit the growth of soil-borne diseases of different fusaria including F. udum that causes wilting in pigeon pea.
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Singh G, Gudi S, Amandeep, Upadhyay P, Shekhawat PK, Nayak G, Goyal L, Kumar D, Kumar P, Kamboj A, Thada A, Shekhar S, Koli GK, DP M, Halladakeri P, Kaur R, Kumar S, Saini P, Singh I, Ayoubi H. Unlocking the hidden variation from wild repository for accelerating genetic gain in legumes. Front Plant Sci 2022; 13:1035878. [PMID: 36438090 PMCID: PMC9682257 DOI: 10.3389/fpls.2022.1035878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 10/17/2022] [Indexed: 11/02/2023]
Abstract
The fluctuating climates, rising human population, and deteriorating arable lands necessitate sustainable crops to fulfil global food requirements. In the countryside, legumes with intriguing but enigmatic nitrogen-fixing abilities and thriving in harsh climatic conditions promise future food security. However, breaking the yield plateau and achieving higher genetic gain are the unsolved problems of legume improvement. Present study gives emphasis on 15 important legume crops, i.e., chickpea, pigeonpea, soybean, groundnut, lentil, common bean, faba bean, cowpea, lupin, pea, green gram, back gram, horse gram, moth bean, rice bean, and some forage legumes. We have given an overview of the world and India's area, production, and productivity trends for all legume crops from 1961 to 2020. Our review article investigates the importance of gene pools and wild relatives in broadening the genetic base of legumes through pre-breeding and alien gene introgression. We have also discussed the importance of integrating genomics, phenomics, speed breeding, genetic engineering and genome editing tools in legume improvement programmes. Overall, legume breeding may undergo a paradigm shift once genomics and conventional breeding are integrated in the near future.
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Affiliation(s)
- Gurjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Santosh Gudi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Amandeep
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Priyanka Upadhyay
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Pooja Kanwar Shekhawat
- Division of Crop Improvement, Plant Breeding and Genetics, Indian Council of Agricultural Research (ICAR)-Central Soil Salinity Research Institute, Karnal, Haryana, India
- Department of Plant Breeding and Genetics, Sri Karan Narendra Agriculture University, Jobner, Rajasthan, India
| | - Gyanisha Nayak
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Lakshay Goyal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Deepak Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, India
| | - Pradeep Kumar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Akashdeep Kamboj
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Antra Thada
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Shweta Shekhar
- Department of Plant Molecular Biology and Biotechnology, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Ganesh Kumar Koli
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, India
| | - Meghana DP
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Priyanka Halladakeri
- Department of Genetics and Plant Breeding, Anand Agricultural University, Anand, Gujarat, India
| | - Rajvir Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Sumit Kumar
- Department of Agronomy, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Pawan Saini
- CSB-Central Sericultural Research & Training Institute (CSR&TI), Ministry of Textiles, Govt. of India, Jammu- Kashmir, Pampore, India
| | - Inderjit Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Habiburahman Ayoubi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
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Yohane EN, Shimelis H, Laing M, Shayanowako A. Genetic diversity and grouping of pigeonpea [Cajanus cajan Millspaugh] Germplasm using SNP markers and agronomic traits. PLoS One 2022; 17:e0275060. [PMID: 36327283 DOI: 10.1371/journal.pone.0275060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 09/09/2022] [Indexed: 11/06/2022] Open
Abstract
Knowledge of genetic interrelationships and grouping among pigeonpea germplasm collections is fundamental to selecting breeding parents with unique genetic constitutions. The objectives of this study were to assess the genetic diversity and genetic grouping present among 81 pigeonpea genotypes collected from Malawi, Tanzania and Kenya using 4122 single nucleotide polymorphism (SNP) markers and complementary morphological traits. The SNP markers and phenotypic traits revealed significant genetic variation among the assessed genotypes. The test genotypes were resolved into three distinct clusters based on both marker systems. The mean gene diversity and the polymorphic information content (PIC) were 0.14 and 0.11, suggesting moderate genetic differentiation among the genotypes. The analysis of molecular variance revealed that differences among populations accounted for only 2.7% of the variation, while within the population (among individuals) accounted for 97.3% of the variation. The results based on the DArT SNP genotyping complemented the phenotypic data and led to the selection of unique pigeonpea genotypes for effective breeding programs in Malawi and related agroecologies. This suggested that unique breeding populations could be created by identifying and selecting divergent individuals as parental lines. There is a need to create a new genetic variation or introgress genes from genetically unrelated parents to increase the genetic base of the current pigeonpea breeding populations.
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Kinhoégbè G, Djèdatin G, Saxena RK, Chitikineni A, Bajaj P, Molla J, Agbangla C, Dansi A, Varshney RK. Genetic diversity and population structure of pigeonpea (Cajanus cajan [L.] Millspaugh) landraces grown in Benin revealed by Genotyping-By-Sequencing. PLoS One 2022; 17:e0271565. [PMID: 35857738 PMCID: PMC9299330 DOI: 10.1371/journal.pone.0271565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 07/04/2022] [Indexed: 11/18/2022] Open
Abstract
Genetic diversity studies provide important details on target trait availability and its variability, for the success of breeding programs. In this study, GBS approach was used to reveal a new structuration of genetic diversity and population structure of pigeonpea in Benin. We used a total of 688 high-quality Single Nucleotide Polymorphism markers for a total of 44 pigeonpea genotypes. The distribution of SNP markers on the 11 chromosomes ranged from 14 on chromosome 5 to 133 on chromosome 2. The Polymorphism Information Content and gene diversity values were 0.30 and 0.34 respectively. The analysis of population structure revealed four clear subpopulations. The Weighted Neighbor Joining tree agreed with structure analyses by grouping the 44 genotypes into four clusters. The PCoA revealed that genotypes from subpopulations 1, 2 and 3 intermixed among themselves. The Analysis of Molecular Variance showed 7% of the total variation among genotypes while the rest of variation (93%) was within genotypes from subpopulations indicating a high gene exchange (Nm = 7.13) and low genetic differentiation (PhiPT = 0.07) between subpopulations. Subpopulation 2 presented the highest mean values of number of different alleles (Na = 1.57), number of loci with private alleles (Pa = 0.11) and the percentage of polymorphic loci (P = 57.12%). We discuss our findings and demonstrate how the genetic diversity and the population structure of this specie can be used through the Genome Wide Association Studies and Marker-Assisted Selection to enhance genetic gain in pigeonpea breeding programs in Benin.
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Affiliation(s)
- Géofroy Kinhoégbè
- Laboratory of Molecular Biology and Bioinformatics Applied to Genomics, National University of Sciences, Technologies Engineering and Mathematics of Abomey, Dassa-Zoumé, Benin
- Centre of Excellence in Genomics and Systems Biology, International Crop Research Institute for the Semi-Arid Tropics, Hyderabad, India
- * E-mail:
| | - Gustave Djèdatin
- Laboratory of Molecular Biology and Bioinformatics Applied to Genomics, National University of Sciences, Technologies Engineering and Mathematics of Abomey, Dassa-Zoumé, Benin
| | - Rachit Kumar Saxena
- Centre of Excellence in Genomics and Systems Biology, International Crop Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Anu Chitikineni
- Centre of Excellence in Genomics and Systems Biology, International Crop Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Prasad Bajaj
- Centre of Excellence in Genomics and Systems Biology, International Crop Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Johiruddin Molla
- Centre of Excellence in Genomics and Systems Biology, International Crop Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Clément Agbangla
- Laboratory of Molecular Genetic and Genomes Analysis, University of Abomey-Calavi, Abomey-Calavi, Benin
| | - Alexandre Dansi
- Laboratory of Biotechnology, Genetic Resources and Plant and Animal Breeding, National University of Sciences Technologies Engineering and Mathematics of Abomey, Dassa-Zoumé, Benin
| | - Rajeev Kumar Varshney
- Centre of Excellence in Genomics and Systems Biology, International Crop Research Institute for the Semi-Arid Tropics, Hyderabad, India
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Jha UC, Nayyar H, Parida SK, Deshmukh R, von Wettberg EJB, Siddique KHM. Ensuring Global Food Security by Improving Protein Content in Major Grain Legumes Using Breeding and 'Omics' Tools. Int J Mol Sci 2022; 23:7710. [PMID: 35887057 PMCID: PMC9325250 DOI: 10.3390/ijms23147710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/05/2022] [Accepted: 07/05/2022] [Indexed: 11/16/2022] Open
Abstract
Grain legumes are a rich source of dietary protein for millions of people globally and thus a key driver for securing global food security. Legume plant-based 'dietary protein' biofortification is an economic strategy for alleviating the menace of rising malnutrition-related problems and hidden hunger. Malnutrition from protein deficiency is predominant in human populations with an insufficient daily intake of animal protein/dietary protein due to economic limitations, especially in developing countries. Therefore, enhancing grain legume protein content will help eradicate protein-related malnutrition problems in low-income and underprivileged countries. Here, we review the exploitable genetic variability for grain protein content in various major grain legumes for improving the protein content of high-yielding, low-protein genotypes. We highlight classical genetics-based inheritance of protein content in various legumes and discuss advances in molecular marker technology that have enabled us to underpin various quantitative trait loci controlling seed protein content (SPC) in biparental-based mapping populations and genome-wide association studies. We also review the progress of functional genomics in deciphering the underlying candidate gene(s) controlling SPC in various grain legumes and the role of proteomics and metabolomics in shedding light on the accumulation of various novel proteins and metabolites in high-protein legume genotypes. Lastly, we detail the scope of genomic selection, high-throughput phenotyping, emerging genome editing tools, and speed breeding protocols for enhancing SPC in grain legumes to achieve legume-based dietary protein security and thus reduce the global hunger risk.
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Affiliation(s)
- Uday C. Jha
- ICAR—Indian Institute of Pulses Research (IIPR), Kanpur 208024, India
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh 160014, India;
| | - Swarup K. Parida
- National Institute of Plant Genome Research, New Delhi 110067, India;
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute, Punjab 140308, India;
| | | | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia
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Chapman MA, He Y, Zhou M. Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security. New Phytol 2022; 234:1583-1597. [PMID: 35318683 PMCID: PMC9994440 DOI: 10.1111/nph.18021] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/22/2022] [Indexed: 04/14/2023]
Abstract
Underutilized crops are, by definition, under-researched compared to staple crops yet come with traits that may be especially important given climate change and the need to feed a globally increasing population. These crops are often stress-tolerant, and this combined with unique and beneficial nutritional profiles. Whilst progress is being made by generating reference genome sequences, in this Tansley Review, we show how this is only the very first step. We advocate that going 'beyond a reference genome' should be a priority, as it is only at this stage one can identify the specific genes and the adaptive alleles that underpin the valuable traits. We sum up how population genomic and pangenomic approaches have led to the identification of stress- and disease-tolerant alleles in staple crops and compare this to the small number of examples from underutilized crops. We also demonstrate how previously underutilized crops have benefitted from genomic advances and that many breeding targets in underutilized crops are often well studied in staple crops. This cross-crop population-level resequencing could lead to an understanding of the genetic basis of adaptive traits in underutilized crops. This level of investment may be crucial for fully understanding the value of these crops before they are lost.
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Affiliation(s)
- Mark A. Chapman
- Biological SciencesUniversity of SouthamptonLife Sciences Building 85, Highfield CampusSouthamptonSO17 1BJUK
| | - Yuqi He
- Institute of Crop SciencesChinese Academy of Agricultural SciencesRoom 405, National Crop Gene Bank BuildingZhongguancun South Street No. 12Haidian DistrictBeijing100081China
| | - Meiliang Zhou
- Institute of Crop SciencesChinese Academy of Agricultural SciencesRoom 405, National Crop Gene Bank BuildingZhongguancun South Street No. 12Haidian DistrictBeijing100081China
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Ganguly S, Purohit A, Ghosh S, Chaudhuri RK, Das S, Chakraborti D. Clean gene technology to develop selectable marker-free pod borer-resistant transgenic pigeon pea events involving the constitutive expression of Cry1Ac. Appl Microbiol Biotechnol 2022; 106:3051-3067. [PMID: 35441877 DOI: 10.1007/s00253-022-11922-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 04/04/2022] [Accepted: 04/08/2022] [Indexed: 11/29/2022]
Abstract
The most crucial yield constraint of pigeon pea is susceptibility to the pod borer Helicoverpa armigera, which causes extensive damage and severe economic losses every year. The Agrobacterium-mediated plumular meristem transformation technique was applied for the development of cry1Ac transgenic pigeon pea. Bioactivity of the cry1Ac gene was compared based on integration and expression driven by two promoters, the constitutive CaMV35S promoter and the green-tissue-specific ats1A promoter, in those transgenic events. The transgenic events also contained the selectable marker gene nptII flanked by loxP sites. Independent transgenic events expressing the Cre recombinase gene along with a linked bar selection marker were also developed. Integration and expression patterns of both cry1Ac and cre were confirmed through Southern and western blot analysis of T1 events. The constitutive expression of the Cry1Ac protein was found to be more effective for conferring resistant activity against H. armigera larvae in comparison to green-tissue-specific expression. Constitutively expressing Cry1Ac T1 events were crossed with Cre recombinase expressing T1 events. The crossing-based Cre/lox-mediated marker gene elimination strategy was demonstrated to generate nptII-free Cry1Ac-expressing T2 events. These events were subsequently analyzed in the T3 generation for the segregation of cre and bar genes. Five Cry1Ac-expressing T3 transgenic pigeon pea events were devoid of the nptII marker as well as cre-bar genes. H. armigera larval mortality in those marker-free T3 events was found to be 80-100%. The development of such nptII selectable marker-free Cry1Ac-expressing pigeon pea transgenics for the first time would greatly support the sustainable biotechnological breeding program for pod borer resistance in pigeon pea. KEY POINTS: • Constitutive expression of Cry1Ac conferred complete resistance against Helicoverpa armigera • Green-tissue-specific expression of Cry1Ac conferred partial pest resistance • Cre/lox-mediated nptII elimination was successful in constitutively expressing Cry1Ac transgenic pigeon pea events.
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Affiliation(s)
- Shreeparna Ganguly
- Department of Biotechnology, St. Xavier's College (Autonomous), 30, Mother Teresa Sarani, Kolkata - 700016, West Bengal, India.,Department of Genetics, University of Calcutta, 35, Ballygunge Circular Road, Kolkata - 700019, West Bengal, India
| | - Arnab Purohit
- Department of Genetics, University of Calcutta, 35, Ballygunge Circular Road, Kolkata - 700019, West Bengal, India
| | - Sanatan Ghosh
- Department of Genetics, University of Calcutta, 35, Ballygunge Circular Road, Kolkata - 700019, West Bengal, India
| | - Rituparna Kundu Chaudhuri
- Department of Botany, Barasat Govt. College, 10, K.N.C. Road, Barasat, Kolkata - 700124, West Bengal, India
| | - Sampa Das
- Division of Plant Biology, Bose Institute, C.I.T. Scheme VII M, P1/12, Kankurgachi, Kolkata- 700054, West Bengal, India
| | - Dipankar Chakraborti
- Department of Genetics, University of Calcutta, 35, Ballygunge Circular Road, Kolkata - 700019, West Bengal, India.
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Jorrin B, Maluk M, Atoliya N, Kumar SC, Chalasani D, Tkacz A, Singh P, Basu A, Pullabhotla SVSRN, Kumar M, Mohanty SR, East AK, Ramachandran VK, James EK, Podile AR, Saxena AK, Rao DLN, Poole PS. Genomic Diversity of Pigeon Pea ( Cajanus cajan L. Millsp.) Endosymbionts in India and Selection of Potential Strains for Use as Agricultural Inoculants. Front Plant Sci 2021; 12:680981. [PMID: 34557206 PMCID: PMC8453007 DOI: 10.3389/fpls.2021.680981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 08/06/2021] [Indexed: 05/27/2023]
Abstract
Pigeon pea (Cajanus cajan L. Millsp. ) is a legume crop resilient to climate change due to its tolerance to drought. It is grown by millions of resource-poor farmers in semiarid and tropical subregions of Asia and Africa and is a major contributor to their nutritional food security. Pigeon pea is the sixth most important legume in the world, with India contributing more than 70% of the total production and harbouring a wide variety of cultivars. Nevertheless, the low yield of pigeon pea grown under dry land conditions and its yield instability need to be improved. This may be done by enhancing crop nodulation and, hence, biological nitrogen fixation (BNF) by supplying effective symbiotic rhizobia through the application of "elite" inoculants. Therefore, the main aim in this study was the isolation and genomic analysis of effective rhizobial strains potentially adapted to drought conditions. Accordingly, pigeon pea endosymbionts were isolated from different soil types in Southern, Central, and Northern India. After functional characterisation of the isolated strains in terms of their ability to nodulate and promote the growth of pigeon pea, 19 were selected for full genome sequencing, along with eight commercial inoculant strains obtained from the ICRISAT culture collection. The phylogenomic analysis [Average nucleotide identity MUMmer (ANIm)] revealed that the pigeon pea endosymbionts were members of the genera Bradyrhizobium and Ensifer. Based on nodC phylogeny and nod cluster synteny, Bradyrhizobium yuanmingense was revealed as the most common endosymbiont, harbouring nod genes similar to those of Bradyrhizobium cajani and Bradyrhizobium zhanjiangense. This symbiont type (e.g., strain BRP05 from Madhya Pradesh) also outperformed all other strains tested on pigeon pea, with the notable exception of an Ensifer alkalisoli strain from North India (NBAIM29). The results provide the basis for the development of pigeon pea inoculants to increase the yield of this legume through the use of effective nitrogen-fixing rhizobia, tailored for the different agroclimatic regions of India.
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Affiliation(s)
- Beatriz Jorrin
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Marta Maluk
- The James Hutton Institute, Dundee, United Kingdom
| | | | - Shiv Charan Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Danteswari Chalasani
- Department of Plant Sciences, School of Life Science, University of Hyderabad, Hyderabad, India
| | - Andrzej Tkacz
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Prachi Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Anirban Basu
- Department of Plant Sciences, School of Life Science, University of Hyderabad, Hyderabad, India
| | - Sarma VSRN Pullabhotla
- Department of Plant Sciences, School of Life Science, University of Hyderabad, Hyderabad, India
| | - Murugan Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | | | - Alison K. East
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | | | | | - Appa Rao Podile
- Department of Plant Sciences, School of Life Science, University of Hyderabad, Hyderabad, India
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - DLN Rao
- ICAR-Indian Institute of Soil Science, Bhopal, India
| | - Philip S. Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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10
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Liu C, Wu Y, Liu Y, Yang L, Dong R, Jiang L, Liu P, Liu G, Wang Z, Luo L. Genome-wide analysis of tandem duplicated genes and their contribution to stress resistance in pigeonpea (Cajanus cajan). Genomics 2020; 113:728-735. [PMID: 33053410 DOI: 10.1016/j.ygeno.2020.10.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/11/2020] [Accepted: 10/08/2020] [Indexed: 01/23/2023]
Abstract
Pigeonpea is the main protein source for more than one billion people, and it shows a strong adaptation to biotic stress and abiotic stress. Gene duplication is a fundamental process in genome evolution. Although the draft sequence of the pigeonpea genome has been available since 2011, further analysis of tandem duplicated genes (TDGs) and their contribution to the evolution of pigeonpea has not been reported. In this study, we identify 3211 TDGs in the pigeonpea genome and KEGG enrichment analysis of these genes shows that the TDGs are significantly enriched in resistance-related pathways. In addition, we find that TDGs are more abundant in retrotransposon-related genes in pigeonpea than in the other species included in our study. These results indicate that stress resistance in pigeonpea may be ascribed to resistance-related pathways and retrotransposons originating from tandem duplications. Our study will provide an important basis for further research in pigeonpea breeding.
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Affiliation(s)
- Chun Liu
- College of Forestry & College of Tropical Crops, Hainan University, Haikou 570228, China; Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yuanhang Wu
- College of Forestry & College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Yunxi Liu
- College of Forestry & College of Tropical Crops, Hainan University, Haikou 570228, China; Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Liyun Yang
- College of Forestry & College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Rongshu Dong
- Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Lingyan Jiang
- College of Forestry & College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Pandao Liu
- Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Guodao Liu
- Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Zhiyong Wang
- College of Forestry & College of Tropical Crops, Hainan University, Haikou 570228, China.
| | - Lijuan Luo
- College of Forestry & College of Tropical Crops, Hainan University, Haikou 570228, China.
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Leisner CP. Review: Climate change impacts on food security- focus on perennial cropping systems and nutritional value. Plant Sci 2020; 293:110412. [PMID: 32081261 DOI: 10.1016/j.plantsci.2020.110412] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/09/2019] [Accepted: 01/08/2020] [Indexed: 05/18/2023]
Abstract
Anthropogenic increases in fossil fuel emissions have been a primary driver of increased concentrations of atmospheric carbon dioxide ([CO2]) and other greenhouse gases resulting in warmer temperatures, alterations in precipitation patterns, and increased occurrence of extreme weather events in terrestrial areas across the globe. In agricultural growing regions, alterations in climate can challenge plant productivity in ways that impact the ability of the world to sustain adequate food production for a growing and increasingly affluent population with shifting access to affordable and nutritious food. While the knowledge gap that exists regarding potential climate change impacts is large across agriculture, it is especially large in specialty cropping systems. This includes fruit and vegetable crops, and perennial cropping systems which also contribute (along with row crops) to our global diet. In order to obtain a comprehensive view of the true impact of climate change on our global food supply, we must expand our narrow focus from improving yield and plant productivity to include the impact of climate change on the nutritional value of these crops. In order to address these questions, we need a multi-faceted approach that integrates physiology and genomics tools and conducts comprehensive experiments under realistic depictions of future projected climate. This review describes gaps in our knowledge in relation to these responses, and future questions and actions that are needed to develop a sustainable future food supply in light of global climate change.
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Affiliation(s)
- Courtney P Leisner
- Department of Biological Sciences, Auburn University, Auburn AL 36849 USA.
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Fossou RK, Pothier JF, Zézé A, Perret X. Bradyrhizobium ivorense sp. nov. as a potential local bioinoculant for Cajanus cajan cultures in Côte d'Ivoire. Int J Syst Evol Microbiol 2020; 70:1421-1430. [PMID: 32122457 PMCID: PMC7397250 DOI: 10.1099/ijsem.0.003931] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
For many smallholder farmers of Sub-Saharan Africa, pigeonpea (Cajanus cajan) is an important crop to make ends meet. To ascertain the taxonomic status of pigeonpea isolates of Côte d’Ivoire previously identified as bradyrhizobia, a polyphasic approach was applied to strains CI-1BT, CI-14A, CI-19D and CI-41S. Phylogeny of 16S ribosomal RNA (rRNA) genes placed these nodule isolates in a separate lineage from current species of the B. elkanii super clade. In phylogenetic analyses of single and concatenated partial dnaK, glnII, gyrB, recA and rpoB sequences, the C. cajan isolates again formed a separate lineage, with strain CI-1BT sharing the highest sequence similarity (95.2 %) with B. tropiciagri SEMIA 6148T. Comparative genomic analyses corroborated the novel species status, with 86 % ANIb and 89 % ANIm as the highest average nucleotide identity (ANI) values with B. elkanii USDA 76T. Although CI-1BT, CI-14A, CI-19D and CI-41S shared similar phenotypic and metabolic properties, growth of CI-41S was slower in/on various media. Symbiotic efficacy varied significantly between isolates, with CI-1BT and CI-41S scoring on the C. cajan ‘Light-Brown’ landrace as the most and least proficient bacteria, respectively. Also proficient on Vigna radiata (mung bean), Vigna unguiculata (cowpea, niébé) and additional C. cajan cultivars, CI-1BT represents a potential bioinoculant adapted to local soil conditions and capable of fostering the growth of diverse legume crops in Côte d'Ivoire. Given the data presented here, we propose the 19 C. cajan isolates to belong to a novel species called Bradyrhizobium ivorense sp. nov., with CI-1BT (=CCOS 1862T=CCMM B1296T) as a type strain.
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Affiliation(s)
- Romain K Fossou
- Laboratoire de Biotechnologies Végétale et Microbienne, Unité Mixte de Recherche et d'Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Felix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire.,Department of Botany and Plant Biology, Microbiology Unit, University of Geneva, Sciences III, 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Joël F Pothier
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, CH-8820 Wädenswil, Switzerland
| | - Adolphe Zézé
- Laboratoire de Biotechnologies Végétale et Microbienne, Unité Mixte de Recherche et d'Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Felix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Xavier Perret
- Department of Botany and Plant Biology, Microbiology Unit, University of Geneva, Sciences III, 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
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Satheesh Naik SJ, Bohra A, Basavaraja T, Mishra RK, Padmaja G, Poornima KN. Diversity of Phytophthora Stem Blight of Pigeonpea and Its Sustainable Management. Fungal Biol 2020. [DOI: 10.1007/978-3-030-35947-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Ribeiro T, Vasconcelos E, Dos Santos KGB, Vaio M, Brasileiro-Vidal AC, Pedrosa-Harand A. Diversity of repetitive sequences within compact genomes of Phaseolus L. beans and allied genera Cajanus L. and Vigna Savi. Chromosome Res 2019; 28:139-153. [PMID: 31734754 DOI: 10.1007/s10577-019-09618-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/24/2019] [Accepted: 10/15/2019] [Indexed: 01/08/2023]
Abstract
Repetitive sequences are ubiquitous and fast-evolving elements responsible for size variation and large-scale organization of plant genomes. Within tribe Phaseoleae (Fabaceae), some genera, such as Phaseolus, Vigna, and Cajanus, show small genome and mostly stable chromosome number. Here, we applied a combined computational and cytological approach to study the organization and diversification of repetitive elements in some species of these genera. Sequences were classified in terms of type and repetitiveness and the most abundant were mapped to chromosomes. We identified long terminal repeat (LTR) retrotransposons, especially Ogre and Chromovirus elements, making up most of genomes, other than P. acutifolius and Vigna species. Satellite DNAs (SatDNAs) were less representative, but highly diverse among species, showing a clear phylogenetic relationship. In situ localization revealed preferential location at pericentromeres and centromeres for both types of sequences, suggesting a heterogeneous composition, especially for centromeres. Few elements showed subterminal accumulation. Copy number variation among chromosomes within and among species was observed for all nine identified SatDNAs. Altogether, our data pointed two main elements (Ty3/Gypsy retrotransponsons and SatDNAs) to the diversification on the repetitive landscape in Phaseoleae, with a typical set of repeats in each species. The high turnover of these sequences, however, did not affect total genome size.
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Affiliation(s)
- Tiago Ribeiro
- Integrative Plant Research Laboratory, Department of Botany and Ecology, Federal University of Mato Grosso, Av. Fernando Corrêa da Costa, 2367, Boa Esperança, Cuiabá, MT, 78060900, Brazil.
| | - Emanuelle Vasconcelos
- Laboratory of Plant Genetics and Biotechnology, Department of Genetics, Federal University of Pernambuco, Recife, PE, Brazil
| | - Karla G B Dos Santos
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Av. Prof. Moraes Rêgo, s/n, Cidade Universitária, Recife, PE, 50670420, Brazil
| | - Magdalena Vaio
- Laboratory of Plant Genome Evolution and Domestication, Department of Plant Biology, Faculty of Agronomy, University of the Republic, Montevideo, Uruguay
| | - Ana Christina Brasileiro-Vidal
- Laboratory of Plant Genetics and Biotechnology, Department of Genetics, Federal University of Pernambuco, Recife, PE, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Av. Prof. Moraes Rêgo, s/n, Cidade Universitária, Recife, PE, 50670420, Brazil.
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Olatoye MO, Hu Z, Aikpokpodion PO. Epistasis Detection and Modeling for Genomic Selection in Cowpea ( Vigna unguiculata L. Walp.). Front Genet 2019; 10:677. [PMID: 31417604 PMCID: PMC6682672 DOI: 10.3389/fgene.2019.00677] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 06/27/2019] [Indexed: 12/24/2022] Open
Abstract
Genetic architecture reflects the pattern of effects and interaction of genes underlying phenotypic variation. Most mapping and breeding approaches generally consider the additive part of variation but offer limited knowledge on the benefits of epistasis which explains in part the variation observed in traits. In this study, the cowpea multiparent advanced generation inter-cross (MAGIC) population was used to characterize the epistatic genetic architecture of flowering time, maturity, and seed size. In addition, consideration for epistatic genetic architecture in genomic-enabled breeding (GEB) was investigated using parametric, semi-parametric, and non-parametric genomic selection (GS) models. Our results showed that large and moderate effect-sized two-way epistatic interactions underlie the traits examined. Flowering time QTL colocalized with cowpea putative orthologs of Arabidopsis thaliana and Glycine max genes like PHYTOCLOCK1 (PCL1 [Vigun11g157600]) and PHYTOCHROME A (PHY A [Vigun01g205500]). Flowering time adaptation to long and short photoperiod was found to be controlled by distinct and common main and epistatic loci. Parametric and semi-parametric GS models outperformed non-parametric GS model, while using known quantitative trait nucleotide(s) (QTNs) as fixed effects improved prediction accuracy when traits were controlled by large effect loci. In general, our study demonstrated that prior understanding of the genetic architecture of a trait can help make informed decisions in GEB.
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Affiliation(s)
- Marcus O. Olatoye
- Department of Crop Sciences, University of Illinois, Urbana-Champaign, IL, United States
| | - Zhenbin Hu
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
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Singh A, Singh PK, Sharma AK, Singh NK, Sonah H, Deshmukh R, Sharma TR. Understanding the Role of the WRKY Gene Family under Stress Conditions in Pigeonpea ( Cajanus Cajan L.). Plants (Basel) 2019; 8:plants8070214. [PMID: 31295921 PMCID: PMC6681228 DOI: 10.3390/plants8070214] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 06/27/2019] [Accepted: 06/29/2019] [Indexed: 12/26/2022]
Abstract
Pigeonpea (Cajanus cajan L.), a protein-rich legume, is a major food component of the daily diet for residents in semi-arid tropical regions of the word. Pigeonpea is also known for its high level of tolerance against biotic and abiotic stresses. In this regard, understanding the genes involved in stress tolerance has great importance. In the present study, identification, and characterization of WRKY, a large transcription factor gene family involved in numerous biological processes like seed germination, metabolism, plant growth, biotic and abiotic stress responses was performed in pigeonpea. A total of 94 WRKY genes identified in the pigeonpea genome were extensively characterized for gene-structures, localizations, phylogenetic distribution, conserved motif organizations, and functional annotation. Phylogenetic analysis revealed three major groups (I, II, and III) of pigeonpea WRKY genes. Subsequently, expression profiling of 94 CcWRKY genes across different tissues like root, nodule, stem, petiole, petal, sepal, shoot apical meristem (SAM), mature pod, and mature seed retrieved from the available RNAseq data identified tissue-specific WRKY genes with preferential expression in the vegetative and reproductive stages. Gene co-expression networks identified four WRKY genes at the center of maximum interaction which may play a key role in the entire WRKY regulations. Furthermore, quantitative real-time polymerase chain reaction (qRT-PCR) expression analysis of WRKY genes in root and leaf tissue samples from plants under drought and salinity stress identified differentially expressed WRKY genes. The study will be helpful to understand the evolution, regulation, and distribution of the WRKY gene family, and additional exploration for the development of stress tolerance cultivars in pigeonpea and other legumes crops.
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Affiliation(s)
- Akshay Singh
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306 India
- Dr. A. P. J. Abdul Kalam Technical University, Lucknow, Uttar Pradesh 226031, India
| | | | - Ajay Kumar Sharma
- Meerut Institute of Engineering and Technology, Meerut, Uttar Pradesh 250005, India
| | | | - Humira Sonah
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306 India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306 India
| | - Tilak Raj Sharma
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306 India.
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Garg N, Sharma A. Role of putrescine (Put) in imparting salt tolerance through modulation of put metabolism, mycorrhizal and rhizobial symbioses in Cajanus cajan (L.) Millsp. Symbiosis 2019; 79:59-74. [DOI: 10.1007/s13199-019-00621-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Arora S, Mahato AK, Singh S, Mandal P, Bhutani S, Dutta S, Kumawat G, Singh BP, Chaudhary AK, Yadav R, Gaikwad K, Sevanthi AM, Datta S, Raje RS, Sharma TR, Singh NK. A high-density intraspecific SNP linkage map of pigeonpea (Cajanas cajan L. Millsp.). PLoS One 2017; 12:e0179747. [PMID: 28654689 PMCID: PMC5487049 DOI: 10.1371/journal.pone.0179747] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 06/02/2017] [Indexed: 01/09/2023] Open
Abstract
Pigeonpea (Cajanus cajan (L.) Millsp.) is a major food legume cultivated in semi-arid tropical regions including the Indian subcontinent, Africa, and Southeast Asia. It is an important source of protein, minerals, and vitamins for nearly 20% of the world population. Due to high carbon sequestration and drought tolerance, pigeonpea is an important crop for the development of climate resilient agriculture and nutritional security. However, pigeonpea productivity has remained low for decades because of limited genetic and genomic resources, and sparse utilization of landraces and wild pigeonpea germplasm. Here, we present a dense intraspecific linkage map of pigeonpea comprising 932 markers that span a total adjusted map length of 1,411.83 cM. The consensus map is based on three different linkage maps that incorporate a large number of single nucleotide polymorphism (SNP) markers derived from next generation sequencing data, using Illumina GoldenGate bead arrays, and genotyping with restriction site associated DNA (RAD) sequencing. The genotyping-by-sequencing enhanced the marker density but was met with limited success due to lack of common markers across the genotypes of mapping population. The integrated map has 547 bead-array SNP, 319 RAD-SNP, and 65 simple sequence repeat (SSR) marker loci. We also show here correspondence between our linkage map and published genome pseudomolecules of pigeonpea. The availability of a high-density linkage map will help improve the anchoring of the pigeonpea genome to its chromosomes and the mapping of genes and quantitative trait loci associated with useful agronomic traits.
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Affiliation(s)
- Sheetal Arora
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Ajay Kumar Mahato
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Sangeeta Singh
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Paritra Mandal
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Shefali Bhutani
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Sutapa Dutta
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Giriraj Kumawat
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Bikram Pratap Singh
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | | | - Rekha Yadav
- Division of Genetics, Indian Agricultural Research Institute, Pusa, New Delhi, India
| | - K. Gaikwad
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | | | | | - Ranjeet S. Raje
- Division of Genetics, Indian Agricultural Research Institute, Pusa, New Delhi, India
| | - Tilak R. Sharma
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Nagendra Kumar Singh
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
- * E-mail:
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Abstract
Pigeonpea (Cajanus cajan L.), a diploid legume crop, is a member of the tribe Phaseoleae. This tribe is descended from the millettioid (tropical) clade of the subfamily Papilionoideae, which includes many important legume crop species such as soybean (Glycine max), mung bean (Vigna radiata), cowpea (Vigna ungiculata), and common bean (Phaseolus vulgaris). It plays major role in food and nutritional security, being rich source of proteins, minerals and vitamins. We have developed a comprehensive Pigeonpea Transcription Factors Database (PpTFDB) that encompasses information about 1829 putative transcription factors (TFs) and their 55 TF families. PpTFDB provides a comprehensive information about each of the identified TFs that includes chromosomal location, protein physicochemical properties, sequence data, protein functional annotation, simple sequence repeats (SSRs) with primers derived from their motifs, orthology with related legume crops, and gene ontology (GO) assignment to respective TFs. (PpTFDB: http://14.139.229.199/PpTFDB/Home.aspx) is a freely available and user friendly web resource that facilitates users to retrieve the information of individual members of a TF family through a set of query interfaces including TF ID or protein functional annotation. In addition, users can also get the information by browsing interfaces, which include browsing by TF Categories and by, GO Categories. This PpTFDB will serve as a promising central resource for researchers as well as breeders who are working towards crop improvement of legume crops.
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Affiliation(s)
- Akshay Singh
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
- Dr. A. P. J. Abdul Kalam Technical University, Lucknow, Uttar Pradesh, India
| | - Ajay Kumar Sharma
- Meerut Institute of Engineering and Technology, Meerut, Uttar Pradesh, India
| | | | - Tilak Raj Sharma
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
- * E-mail: ,
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Krishnan HB, Natarajan SS, Oehrle NW, Garrett WM, Darwish O. Proteomic Analysis of Pigeonpea (Cajanus cajan) Seeds Reveals the Accumulation of Numerous Stress-Related Proteins. J Agric Food Chem 2017; 65:4572-4581. [PMID: 28532149 DOI: 10.1021/acs.jafc.7b00998] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Pigeonpea is one of the major sources of dietary protein for more than a billion people living in South Asia. This hardy legume is often grown in low-input and risk-prone marginal environments. Considerable research effort has been devoted by a global research consortium to develop genomic resources for the improvement of this legume crop. These efforts have resulted in the elucidation of the complete genome sequence of pigeonpea. Despite these developments, little is known about the seed proteome of this important crop. Here, we report the proteome of pigeonpea seed. To enable the isolation of maximum number of seed proteins, including those that are present in very low amounts, three different protein fractions were obtained by employing different extraction media. High-resolution two-dimensional (2-D) electrophoresis followed by MALDI-TOF-TOF-MS/MS analysis of these protein fractions resulted in the identification of 373 pigeonpea seed proteins. Consistent with the reported high degree of synteny between the pigeonpea and soybean genomes, a large number of pigeonpea seed proteins exhibited significant amino acid homology with soybean seed proteins. Our proteomic analysis identified a large number of stress-related proteins, presumably due to its adaptation to drought-prone environments. The availability of a pigeonpea seed proteome reference map should shed light on the roles of these identified proteins in various biological processes and facilitate the improvement of seed composition.
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Affiliation(s)
- Hari B Krishnan
- Plant Genetics Research Unit, Agricultural Research Service, U.S. Department of Agriculture, University of Missouri , Columbia, Missouri 65211, United States
| | - Savithiry S Natarajan
- Soybean Genomics and Improvement Laboratory, PSI, Agricultural Research Service, U.S. Department of Agriculture , Beltsville, Maryland 20705, United States
| | - Nathan W Oehrle
- Plant Genetics Research Unit, Agricultural Research Service, U.S. Department of Agriculture, University of Missouri , Columbia, Missouri 65211, United States
| | - Wesley M Garrett
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service, U.S. Department of Agriculture , Beltsville, Maryland 20705, United States
| | - Omar Darwish
- Department of Computer and Information Sciences, Towson University , Towson, Maryland 21252, United States
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Patil PG, Dubey J, Bohra A, Mishra RK, Saabale PR, Das A, Rathore M, Singh NP. Association mapping to discover significant marker-trait associations for resistance against fusarium wilt variant 2 in pigeonpea [Cajanus cajan (L.) Millspaugh] using SSR markers. J Appl Genet 2017; 58:307-19. [DOI: 10.1007/s13353-017-0400-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 04/28/2017] [Accepted: 05/16/2017] [Indexed: 10/19/2022]
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Saxena RK, Singh VK, Kale SM, Tathineni R, Parupalli S, Kumar V, Garg V, Das RR, Sharma M, Yamini KN, Muniswamy S, Ghanta A, Rathore A, Kumar CVS, Saxena KB, Kishor PBK, Varshney RK. Construction of genotyping-by-sequencing based high-density genetic maps and QTL mapping for fusarium wilt resistance in pigeonpea. Sci Rep 2017; 7:1911. [PMID: 28507291 DOI: 10.1038/s41598-017-01537-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 03/31/2017] [Indexed: 11/09/2022] Open
Abstract
Fusarium wilt (FW) is one of the most important biotic stresses causing yield losses in pigeonpea. Genetic improvement of pigeonpea through genomics-assisted breeding (GAB) is an economically feasible option for the development of high yielding FW resistant genotypes. In this context, two recombinant inbred lines (RILs) (ICPB 2049 × ICPL 99050 designated as PRIL_A and ICPL 20096 × ICPL 332 designated as PRIL_B) and one F2 (ICPL 85063 × ICPL 87119) populations were used for the development of high density genetic maps. Genotyping-by-sequencing (GBS) approach was used to identify and genotype SNPs in three mapping populations. As a result, three high density genetic maps with 964, 1101 and 557 SNPs with an average marker distance of 1.16, 0.84 and 2.60 cM were developed in PRIL_A, PRIL_B and F2, respectively. Based on the multi-location and multi-year phenotypic data of FW resistance a total of 14 quantitative trait loci (QTLs) including six major QTLs explaining >10% phenotypic variance explained (PVE) were identified. Comparative analysis across the populations has revealed three important QTLs (qFW11.1, qFW11.2 and qFW11.3) with upto 56.45% PVE for FW resistance. This is the first report of QTL mapping for FW resistance in pigeonpea and identified genomic region could be utilized in GAB.
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Saxena RK, Kale SM, Kumar V, Parupali S, Joshi S, Singh V, Garg V, Das RR, Sharma M, Yamini KN, Ghanta A, Rathore A, Sameerkumar CV, Saxena KB, Varshney RK. Genotyping-by-sequencing of three mapping populations for identification of candidate genomic regions for resistance to sterility mosaic disease in pigeonpea. Sci Rep 2017; 7:1813. [PMID: 28500330 PMCID: PMC5431754 DOI: 10.1038/s41598-017-01535-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 03/30/2017] [Indexed: 01/09/2023] Open
Abstract
Sterility mosaic disease (SMD) is one of the serious production constraints that may lead to complete yield loss in pigeonpea. Three mapping populations including two recombinant inbred lines and one F2, were used for phenotyping for SMD resistance at two locations in three different years. Genotyping-by-sequencing approach was used for simultaneous identification and genotyping of SNPs on above mentioned populations. In total, 212,464, 89,699 and 64,798 SNPs were identified in ICPL 20096 × ICPL 332 (PRIL_B), ICPL 20097 × ICP 8863 (PRIL_C) and ICP 8863 × ICPL 87119 (F2) respectively. By using high-quality SNPs, genetic maps were developed for PRIL_B (1,101 SNPs; 921.21 cM), PRIL_C (484 SNPs; 798.25 cM) and F2 (996 SNPs; 1,597.30 cM) populations. The average inter marker distance on these maps varied from 0.84 cM to 1.65 cM, which was lowest in all genetic mapping studies in pigeonpea. Composite interval mapping based QTL analysis identified a total of 10 QTLs including three major QTLs across the three populations. The phenotypic variance of the identified QTLs ranged from 3.6 to 34.3%. One candidate genomic region identified on CcLG11 seems to be promising QTL for molecular breeding in developing superior lines with enhanced resistance to SMD.
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Affiliation(s)
- Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - Sandip M Kale
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - Vinay Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - Swathi Parupali
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - Shourabh Joshi
- Institute of Biotechnology, Professor Jayshankar Telangana State Agricultural University (PJTSAU), Rajendranagar, Hyderabad, 500 030, India
| | - Vikas Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - Vanika Garg
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - Roma R Das
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - Mamta Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - K N Yamini
- Institute of Biotechnology, Professor Jayshankar Telangana State Agricultural University (PJTSAU), Rajendranagar, Hyderabad, 500 030, India
| | - Anuradha Ghanta
- Institute of Biotechnology, Professor Jayshankar Telangana State Agricultural University (PJTSAU), Rajendranagar, Hyderabad, 500 030, India
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - C V Sameerkumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - K B Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India.
- School of Plant Biology and Institute of Agriculture, The University of Western Australia, Crawley, WA, 6009, Australia.
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Muñoz N, Liu A, Kan L, Li MW, Lam HM. Potential Uses of Wild Germplasms of Grain Legumes for Crop Improvement. Int J Mol Sci 2017; 18:E328. [PMID: 28165413 DOI: 10.3390/ijms18020328] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 01/26/2017] [Accepted: 01/26/2017] [Indexed: 01/14/2023] Open
Abstract
Challenged by population increase, climatic change, and soil deterioration, crop improvement is always a priority in securing food supplies. Although the production of grain legumes is in general lower than that of cereals, the nutritional value of grain legumes make them important components of food security. Nevertheless, limited by severe genetic bottlenecks during domestication and human selection, grain legumes, like other crops, have suffered from a loss of genetic diversity which is essential for providing genetic materials for crop improvement programs. Illustrated by whole-genome-sequencing, wild relatives of crops adapted to various environments were shown to maintain high genetic diversity. In this review, we focused on nine important grain legumes (soybean, peanut, pea, chickpea, common bean, lentil, cowpea, lupin, and pigeonpea) to discuss the potential uses of their wild relatives as genetic resources for crop breeding and improvement, and summarized the various genetic/genomic approaches adopted for these purposes.
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Fossou RK, Ziegler D, Zézé A, Barja F, Perret X. Two Major Clades of Bradyrhizobia Dominate Symbiotic Interactions with Pigeonpea in Fields of Côte d'Ivoire. Front Microbiol 2016; 7:1793. [PMID: 27891120 PMCID: PMC5104742 DOI: 10.3389/fmicb.2016.01793] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/25/2016] [Indexed: 12/03/2022] Open
Abstract
In smallholder farms of Côte d'Ivoire, particularly in the northeast of the country, Cajanus cajan (pigeonpea) has become an important crop because of its multiple beneficial facets. Pigeonpea seeds provide food to make ends meet, are sold on local markets, and aerial parts serve as forage for animals. Since it fixes atmospheric nitrogen in symbiosis with soil bacteria collectively known as rhizobia, C. cajan also improves soil fertility and reduces fallow time. Yet, seed yields remain low mostly because farmers cannot afford chemical fertilizers. To identify local rhizobial strains susceptible to be used as bio-inoculants to foster pigeonpea growth, root nodules were collected in six fields of three geographically distant regions of Côte d'Ivoire. Nodule bacteria were isolated and characterized using various molecular techniques including matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry (MS) and DNA sequencing. These molecular analyses showed that 63 out of 85 nodule isolates belonged to two major clades of bradyrhizobia, one of which is known as the Bradyrhizobium elkanii super clade. Phylogenies of housekeeping (16S-ITS-23S, rpoB) and symbiotic (nifH) genes were not always congruent suggesting that lateral transfer of nitrogen fixation genes also contributed to define the genome of these bradyrhizobial isolates. Interestingly, no field-, plant-, or cultivar-specific effect was found to shape the profiles of symbiotic strains. In addition, nodule isolates CI-1B, CI-36E, and CI-41A that belong to distinct species, showed similar symbiotic efficiencies suggesting that any of these strains might serve as a proficient inoculant for C. cajan.
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Affiliation(s)
- Romain K Fossou
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva Geneva, Switzerland
| | - Dominik Ziegler
- Microbiology Unit, Department of Botany and Plant Biology, University of GenevaGeneva, Switzerland; Mabritec AGRiehen, Switzerland
| | - Adolphe Zézé
- Laboratoire de Biotechnologies Végétale et Microbienne, Unité Mixte de Recherche et d'Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Félix Houphouët-Boigny (INPHB) Yamoussoukro, Côte d'Ivoire
| | - François Barja
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva Geneva, Switzerland
| | - Xavier Perret
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva Geneva, Switzerland
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Kumar V, Khan AW, Saxena RK, Garg V, Varshney RK. First-generation HapMap in Cajanus spp. reveals untapped variations in parental lines of mapping populations. Plant Biotechnol J 2016; 14:1673-81. [PMID: 26821983 PMCID: PMC5066660 DOI: 10.1111/pbi.12528] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 12/06/2015] [Accepted: 12/10/2015] [Indexed: 05/02/2023]
Abstract
Whole genome re-sequencing (WGRS) was conducted on a panel of 20 Cajanus spp. accessions (crossing parentals of recombinant inbred lines, introgression lines, multiparent advanced generation intercross and nested association mapping population) comprising of two wild species and 18 cultivated species accessions. A total of 791.77 million paired-end reads were generated with an effective mapping depth of ~12X per accession. Analysis of WGRS data provided 5 465 676 genome-wide variations including 4 686 422 SNPs and 779 254 InDels across the accessions. Large structural variations in the form of copy number variations (2598) and presence and absence variations (970) were also identified. Additionally, 2 630 904 accession-specific variations comprising of 2 278 571 SNPs (86.6%), 166 243 deletions (6.3%) and 186 090 insertions (7.1%) were also reported. Identified polymorphic sites in this study provide the first-generation HapMap in Cajanus spp. which will be useful in mapping the genomic regions responsible for important traits.
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Affiliation(s)
- Vinay Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Aamir W Khan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vanika Garg
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- School of Plant Biology and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
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Kawashima CG, Guimarães GA, Nogueira SR, MacLean D, Cook DR, Steuernagel B, Baek J, Bouyioukos C, Melo BDVA, Tristão G, de Oliveira JC, Rauscher G, Mittal S, Panichelli L, Bacot K, Johnson E, Iyer G, Tabor G, Wulff BBH, Ward E, Rairdan GJ, Broglie KE, Wu G, van Esse HP, Jones JDG, Brommonschenkel SH. A pigeonpea gene confers resistance to Asian soybean rust in soybean. Nat Biotechnol 2016; 34:661-5. [PMID: 27111723 DOI: 10.1038/nbt.3554] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 03/24/2016] [Indexed: 12/31/2022]
Abstract
Asian soybean rust (ASR), caused by the fungus Phakopsora pachyrhizi, is one of the most economically important crop diseases, but is only treatable with fungicides, which are becoming less effective owing to the emergence of fungicide resistance. There are no commercial soybean cultivars with durable resistance to P. pachyrhizi, and although soybean resistance loci have been mapped, no resistance genes have been cloned. We report the cloning of a P. pachyrhizi resistance gene CcRpp1 (Cajanus cajan Resistance against Phakopsora pachyrhizi 1) from pigeonpea (Cajanus cajan) and show that CcRpp1 confers full resistance to P. pachyrhizi in soybean. Our findings show that legume species related to soybean such as pigeonpea, cowpea, common bean and others could provide a valuable and diverse pool of resistance traits for crop improvement.
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Affiliation(s)
| | | | | | | | - Doug R Cook
- Department of Plant Pathology, University of California Davis, Davis, California, USA
| | | | - Jongmin Baek
- Department of Plant Pathology, University of California Davis, Davis, California, USA
| | | | | | - Gustavo Tristão
- Dep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | - Gilda Rauscher
- Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA
| | - Shipra Mittal
- Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA
| | - Lisa Panichelli
- Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA
| | - Karen Bacot
- Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA
| | - Ebony Johnson
- Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA
| | - Geeta Iyer
- Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA
| | - Girma Tabor
- Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA
| | | | - Eric Ward
- 2Blades Foundation, Evanston, Illinois, USA
| | - Gregory J Rairdan
- Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA
| | - Karen E Broglie
- Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA
| | - Gusui Wu
- Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA
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Garg N, Pandey R. High effectiveness of exotic arbuscular mycorrhizal fungi is reflected in improved rhizobial symbiosis and trehalose turnover in Cajanus cajan genotypes grown under salinity stress. FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2016.04.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Njung'e V, Deshpande S, Siambi M, Jones R, Silim S, De Villiers S. SSR genetic diversity assessment of popular pigeonpea varieties in Malawi reveals unique fingerprints. ELECTRON J BIOTECHN 2016. [DOI: 10.1016/j.ejbt.2016.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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30
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Sahu AR, Mishra RR, Panigrahi J. Estimation of genetic diversity among 34 genotypes in the genus Cajanus with contrasting host response to the pod borer and its allied pests. ACTA ACUST UNITED AC 2016; 19:17-28. [DOI: 10.1007/s12892-015-0045-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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31
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Kole C, Muthamilarasan M, Henry R, Edwards D, Sharma R, Abberton M, Batley J, Bentley A, Blakeney M, Bryant J, Cai H, Cakir M, Cseke LJ, Cockram J, de Oliveira AC, De Pace C, Dempewolf H, Ellison S, Gepts P, Greenland A, Hall A, Hori K, Hughes S, Humphreys MW, Iorizzo M, Ismail AM, Marshall A, Mayes S, Nguyen HT, Ogbonnaya FC, Ortiz R, Paterson AH, Simon PW, Tohme J, Tuberosa R, Valliyodan B, Varshney RK, Wullschleger SD, Yano M, Prasad M. Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects. Front Plant Sci 2015; 6:563. [PMID: 26322050 PMCID: PMC4531421 DOI: 10.3389/fpls.2015.00563] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 07/08/2015] [Indexed: 05/19/2023]
Abstract
Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops, which can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful in enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.
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Affiliation(s)
| | - Mehanathan Muthamilarasan
- Department of Plant Molecular Genetics and Genomics, National Institute of Plant Genome ResearchNew Delhi, India
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of QueenslandSt Lucia, QLD, Australia
| | - David Edwards
- School of Agriculture and Food Sciences, University of QueenslandBrisbane, QLD, Australia
| | - Rishu Sharma
- Department of Plant Pathology, Faculty of Agriculture, Bidhan Chandra Krishi ViswavidyalayaMohanpur, India
| | - Michael Abberton
- Genetic Resources Centre, International Institute of Tropical AgricultureIbadan, Nigeria
| | - Jacqueline Batley
- Centre for Integrated Legume Research, University of QueenslandBrisbane, QLD, Australia
| | - Alison Bentley
- The John Bingham Laboratory, National Institute of Agricultural BotanyCambridge, UK
| | | | - John Bryant
- CLES, Hatherly Laboratories, University of ExeterExeter, UK
| | - Hongwei Cai
- Forage Crop Research Institute, Japan Grassland Agriculture and Forage Seed AssociationNasushiobara, Japan
- Department of Plant Genetics and Breeding, College of Agronomy and Biotechnology, China Agricultural UniversityBeijing, China
| | - Mehmet Cakir
- Faculty of Science and Engineering, School of Biological Sciences and Biotechnology, Murdoch UniversityMurdoch, WA, Australia
| | - Leland J. Cseke
- Department of Biological Sciences, The University of Alabama in HuntsvilleHuntsville, AL, USA
| | - James Cockram
- The John Bingham Laboratory, National Institute of Agricultural BotanyCambridge, UK
| | | | - Ciro De Pace
- Department of Agriculture, Forests, Nature and Energy, University of TusciaViterbo, Italy
| | - Hannes Dempewolf
- Global Crop Diversity Trust, Platz der Vereinten NationenBonn, Germany
| | - Shelby Ellison
- Department of Horticulture, University of WisconsinMadison, WI, USA
| | - Paul Gepts
- Section of Crop and Ecosystem Sciences, Department of Plant Sciences, University of California, DavisDavis, CA, USA
| | - Andy Greenland
- The John Bingham Laboratory, National Institute of Agricultural BotanyCambridge, UK
| | - Anthony Hall
- Department of Botany and Plant Sciences, University of CaliforniaRiverside, Riverside, USA
| | - Kiyosumi Hori
- Agrogenomics Research Center, National Institute of Agrobiological SciencesTsukuba, Japan
| | | | - Mike W. Humphreys
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityWales, UK
| | - Massimo Iorizzo
- Department of Horticulture, University of WisconsinMadison, WI, USA
| | | | - Athole Marshall
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityWales, UK
| | - Sean Mayes
- Biotechnology and Crop Genetics, Crops for the FutureSemenyih, Malaysia
| | - Henry T. Nguyen
- National Center for Soybean Biotechnology and Division of Plant Science, University of MissouriColumbia, MO, USA
| | | | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural SciencesSundvagen, Sweden
| | | | - Philipp W. Simon
- Department of Horticulture, USDA-ARS, University of WisconsinMadison, WI, USA
| | - Joe Tohme
- Agrobiodiversity and Biotechnology Project, Centro International de Agricultura TropicalCali, Columbia
| | | | - Babu Valliyodan
- National Center for Soybean Biotechnology and Division of Plant Science, University of MissouriColumbia, MO, USA
| | - Rajeev K. Varshney
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Stan D. Wullschleger
- Oak Ridge National Laboratory, Environmental Sciences Division, Climate Change Science InstituteOak Ridge, TN, USA
| | - Masahiro Yano
- National Agriculture and Food Research Organization, Institute of Crop ScienceTsukuba, Japan
| | - Manoj Prasad
- Department of Plant Molecular Genetics and Genomics, National Institute of Plant Genome ResearchNew Delhi, India
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Sinha P, Singh VK, Suryanarayana V, Krishnamurthy L, Saxena RK, Varshney RK. Evaluation and validation of housekeeping genes as reference for gene expression studies in pigeonpea (Cajanus cajan) under drought stress conditions. PLoS One 2015; 10:e0122847. [PMID: 25849964 DOI: 10.1371/journal.pone.0122847] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/23/2015] [Indexed: 12/27/2022] Open
Abstract
Gene expression analysis using quantitative real-time PCR (qRT-PCR) is a very sensitive technique and its sensitivity depends on the stable performance of reference gene(s) used in the study. A number of housekeeping genes have been used in various expression studies in many crops however, their expression were found to be inconsistent under different stress conditions. As a result, species specific housekeeping genes have been recommended for different expression studies in several crop species. However, such specific housekeeping genes have not been reported in the case of pigeonpea (Cajanus cajan) despite the fact that genome sequence has become available for the crop. To identify the stable housekeeping genes in pigeonpea for expression analysis under drought stress conditions, the relative expression variations of 10 commonly used housekeeping genes (EF1α, UBQ10, GAPDH, 18SrRNA, 25SrRNA, TUB6, ACT1, IF4α, UBC and HSP90) were studied on root, stem and leaves tissues of Asha (ICPL 87119). Three statistical algorithms geNorm, NormFinder and BestKeeper were used to define the stability of candidate genes. geNorm analysis identified IF4α and TUB6 as the most stable housekeeping genes however, NormFinder analysis determined IF4α and HSP90 as the most stable housekeeping genes under drought stress conditions. Subsequently validation of the identified candidate genes was undertaken in qRT-PCR based gene expression analysis of uspA gene which plays an important role for drought stress conditions in pigeonpea. The relative quantification of the uspA gene varied according to the internal controls (stable and least stable genes), thus highlighting the importance of the choice of as well as validation of internal controls in such experiments. The identified stable and validated housekeeping genes will facilitate gene expression studies in pigeonpea especially under drought stress conditions.
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Garg N, Pandey R. Effectiveness of native and exotic arbuscular mycorrhizal fungi on nutrient uptake and ion homeostasis in salt-stressed Cajanus cajan L. (Millsp.) genotypes. Mycorrhiza 2015; 25:165-180. [PMID: 25155616 DOI: 10.1007/s00572-014-0600-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 08/17/2014] [Indexed: 06/03/2023]
Abstract
Soil salinity is an increasing problem worldwide, restricting plant growth and production. Research findings show that arbuscular mycorrhizal (AM) fungi have the potential to reduce negative effects of salinity. However, plant growth responses to AM fungi vary as a result of genetic variation in mycorrhizal colonization and plant growth responsiveness. Thus, profitable use of AM requires selection of a suitable combination of host plant and fungal partner. A greenhouse experiment was conducted to compare effectiveness of a native AM fungal inoculum sourced from saline soil and two single exotic isolates, Funneliformis mossseae and Rhizophagus irregularis (single or dual mix), on Cajanus cajan (L.) Millsp. genotypes (Paras and Pusa 2002) under salt stress (0-100 mM NaCl). While salinity reduced plant biomass and disturbed ionic status in both genotypes, Pusa 2002 was more salt tolerant and ensured higher AM fungal colonization, plant biomass and nutrient content with favourable ion status under salinity. Although all AM fungi reduced negative effects of salt stress, R. irregularis (alone or in combination with F. mosseae) displayed highest efficiency under salinity, resulting in highest biomass, yield, nutrient uptake and improved membrane stability with favourable K(+)/Na(+) and Ca(2+)/Na(+) ratios in the host plant. Higher effectiveness of R. irregularis correlated with higher root colonization, indicating that the symbiosis formed by R. irregularis had more stable viability and efficiency under salt stress. These findings enhance understanding of the functional diversity of AM fungi in ameliorating plant salt stress tolerance and suggest the potential use of R. irregularis for increasing Cajanus cajan productivity in saline soils.
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Affiliation(s)
- Neera Garg
- Department of Botany, Panjab University, Chandigarh, 160014, India,
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Daspute A, Fakrudin B. Identification of Coupling and Repulsion Phase DNA Marker Associated With an Allele of a Gene Conferring Host Plant Resistance to Pigeonpea sterility mosaic virus (PPSMV) in Pigeonpea (Cajanus cajan L. Millsp.). Plant Pathol J 2015; 31:33-40. [PMID: 25774108 PMCID: PMC4356603 DOI: 10.5423/ppj.oa.07.2014.0064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 10/08/2014] [Accepted: 10/14/2014] [Indexed: 06/04/2023]
Abstract
Pigeonpea Sterility Mosaic Disease (PSMD) is an important foliar disease caused by Pigeonpea sterility mosaic virus (PPSMV) which is transmitted by eriophyid mites (Aceria cajani Channabasavanna). In present study, a F2 mapping population comprising 325 individuals was developed by crossing PSMD susceptible genotype (Gullyal white) and PSMD resistant genotype (BSMR 736). We identified a set of 32 out of 300 short decamer random DNA markers that showed polymorphism between Gullyal white and BSMR 736 parents. Among them, eleven DNA markers showed polymorphism including coupling and repulsion phase type of polymorphism across the parents. Bulked Segregant Analysis (BSA), revealed that the DNA marker, IABTPPN7, produced a single coupling phase marker (IABTPPN7414) and a repulsion phase marker (IABTPPN7983) co-segregating with PSMD reaction. Screening of 325 F2 population using IABTPPN7 revealed that the repulsion phase marker, IABTPPN7983, was co-segregating with the PSMD responsive SV1 at a distance of 23.9 cM for Bidar PPSMV isolate. On the other hand, the coupling phase marker IABTPPN7414 did not show any linkage with PSMD resistance. Additionally, single marker analysis both IABTPPN7983 (P<0.0001) and IABTPPN 7414 (P<0.0001) recorded a significant association with the PSMD resistance and explained a phenotypic variance of 31 and 36% respectively in F2 population. The repulsion phase marker, IABTPPN7983, could be of use in Marker-Assisted Selection (MAS) in the PPSMV resistance breeding programmes of pigeonpea.
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Affiliation(s)
| | - B. Fakrudin
- Corresponding author. Phone) +91-9480369274, FAX) +91-836-2747627, E-mail)
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35
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Sahu AR, Mishra RR, Rath SC, Panigrahi J. Construction of interspecific genetic linkage map of pigeonpea using SCoT, RAPD, ISSR markers and simple inherited trait loci. Nucleus 2015; 58:23-31. [DOI: 10.1007/s13237-015-0129-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Singh N, Jain N, Kumar R, Jain A, Singh NK, Rai V. A comparative method for protein extraction and 2-D gel electrophoresis from different tissues of Cajanus cajan. Front Plant Sci 2015; 6:606. [PMID: 26300903 PMCID: PMC4528993 DOI: 10.3389/fpls.2015.00606] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 07/23/2015] [Indexed: 05/14/2023]
Abstract
Pigeonpea is an important legume crop with high protein content. However, it is often subjected to various abiotic and biotic stresses. Proteomics is a state-of-the-art technique used to analyze the protein profiling of a tissue for deciphering the molecular entities that could be manipulated for developing crops resistant to these stresses. In this context, developing a comprehensive proteome profile from different vegetative and reproductive tissues has become mandatory. Although several protein extraction protocols from different tissues of diverse plant species have been reported, there is no report for pigeonpea. Here, we report tissue-specific protein extraction protocols representing vegetative (young leaves), and reproductive (flowers and seeds) organs and their subsequent analysis on 2-dimensional gel electrophoresis. The study explicitly demonstrated that the efficacy of a particular protein extraction protocol is dependent on the different tissues, such as leaves, flowers and seeds that differ in their structure and metabolic constituents. For instance, phenol-based protocol showed an efficacy toward higher protein yield, better spot resolution and a minimal streaking on 2-DE gel for both leaves and flowers. Protein extraction from seeds was best achieved by employing phosphate-TCA-acetone protocol.
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Affiliation(s)
| | | | | | | | | | - Vandna Rai
- *Correspondence: Vandna Rai, Functional Genomics, Genomics, National Research Centre on Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Campus, New Delhi-110012, India,
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Pazhamala L, Saxena RK, Singh VK, Sameerkumar CV, Kumar V, Sinha P, Patel K, Obala J, Kaoneka SR, Tongoona P, Shimelis HA, Gangarao NVPR, Odeny D, Rathore A, Dharmaraj PS, Yamini KN, Varshney RK. Genomics-assisted breeding for boosting crop improvement in pigeonpea (Cajanus cajan). Front Plant Sci 2015; 6:50. [PMID: 25741349 PMCID: PMC4330709 DOI: 10.3389/fpls.2015.00050] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/20/2015] [Indexed: 05/18/2023]
Abstract
Pigeonpea is an important pulse crop grown predominantly in the tropical and sub-tropical regions of the world. Although pigeonpea growing area has considerably increased, yield has remained stagnant for the last six decades mainly due to the exposure of the crop to various biotic and abiotic constraints. In addition, low level of genetic variability and limited genomic resources have been serious impediments to pigeonpea crop improvement through modern breeding approaches. In recent years, however, due to the availability of next generation sequencing and high-throughput genotyping technologies, the scenario has changed tremendously. The reduced sequencing costs resulting in the decoding of the pigeonpea genome has led to the development of various genomic resources including molecular markers, transcript sequences and comprehensive genetic maps. Mapping of some important traits including resistance to Fusarium wilt and sterility mosaic disease, fertility restoration, determinacy with other agronomically important traits have paved the way for applying genomics-assisted breeding (GAB) through marker assisted selection as well as genomic selection (GS). This would accelerate the development and improvement of both varieties and hybrids in pigeonpea. Particularly for hybrid breeding programme, mitochondrial genomes of cytoplasmic male sterile (CMS) lines, maintainers and hybrids have been sequenced to identify genes responsible for cytoplasmic male sterility. Furthermore, several diagnostic molecular markers have been developed to assess the purity of commercial hybrids. In summary, pigeonpea has become a genomic resources-rich crop and efforts have already been initiated to integrate these resources in pigeonpea breeding.
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Affiliation(s)
- Lekha Pazhamala
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Rachit K. Saxena
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Vikas K. Singh
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - C. V. Sameerkumar
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Vinay Kumar
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Pallavi Sinha
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Kishan Patel
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Jimmy Obala
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-NatalScottsville, South Africa
| | - Seleman R. Kaoneka
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-NatalScottsville, South Africa
| | - P. Tongoona
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-NatalScottsville, South Africa
| | - Hussein A. Shimelis
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-NatalScottsville, South Africa
| | | | - Damaris Odeny
- International Crops Research Institute for the Semi-Arid TropicsNairobi, Kenya
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - P. S. Dharmaraj
- Agricultural Research Station, University of Agricultural SciencesGulbarga, India
| | - K. N. Yamini
- Department of Agricultural Biotechnology, Acharya N. G. Ranga Agricultural UniversityHyderabad, India
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
- School of Plant Biology and Institute of Agriculture, The University of Western AustraliaCrawley, WA, Australia
- *Correspondence: Rajeev K. Varshney, Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics, Building 300, Patancheru, Hyderabad 502324, India e-mail:
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Saxena RK, Saxena KB, Pazhamala LT, Patel K, Parupalli S, Sameerkumar CV, Varshney RK. Genomics for greater efficiency in pigeonpea hybrid breeding. Front Plant Sci 2015; 6:793. [PMID: 26483810 PMCID: PMC4589649 DOI: 10.3389/fpls.2015.00793] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/12/2015] [Indexed: 05/20/2023]
Abstract
Cytoplasmic genic male sterility (CGMS) based hybrid technology has demonstrated its immense potential in increasing the productivity of various crops, including pigeonpea. This technology has shown promise for breaking the long-standing yield stagnation in pigeonpea. There are difficulties in commercial hybrid seed production due to non-availability of field-oriented technologies such as time-bound assessment of genetic purity of hybrid seeds. Besides this, there are other routine breeding activities which are labor oriented and need more resources. These include breeding and maintenance of new fertility restorers and maintainer lines, diversification of cytoplasm, and incorporation of biotic and abiotic stress resistances. The recent progress in genomics research could accelerate the existing traditional efforts to strengthen the hybrid breeding technology. Marker based seed purity assessment, identification of heterotic groups; selection of new fertility restorers are few areas which have already been initiated. In this paper efforts have been made to identify critical areas and opportunities where genomics can play a leading role and assist breeders in accelerating various activities related to breeding and commercialization of pigeonpea hybrids.
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Affiliation(s)
- Rachit K. Saxena
- *Correspondence: Rachit K. Saxena, International Crops Research Institute for the Semi-Arid Tropics, Building No. 300, Center of Excellence in Genomics, ICRISAT, Patancheru, Hyderabad 502324, India,
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Malviya N, Gupta S, Singh VK, Yadav MK, Bisht NC, Sarangi BK, Yadav D. Genome wide in silico characterization of Dof gene families of pigeonpea (Cajanus cajan (L) Millsp.). Mol Biol Rep 2014; 42:535-52. [PMID: 25344821 DOI: 10.1007/s11033-014-3797-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 10/14/2014] [Indexed: 11/24/2022]
Abstract
The DNA binding with One Finger (Dof) protein is a plant specific transcription factor involved in the regulation of wide range of processes. The analysis of whole genome sequence of pigeonpea has identified 38 putative Dof genes (CcDof) distributed on 8 chromosomes. A total of 17 out of 38 CcDof genes were found to be intronless. A comprehensive in silico characterization of CcDof gene family including the gene structure, chromosome location, protein motif, phylogeny, gene duplication and functional divergence has been attempted. The phylogenetic analysis resulted in 3 major clusters with closely related members in phylogenetic tree revealed common motif distribution. The in silico cis-regulatory element analysis revealed functional diversity with predominance of light responsive and stress responsive elements indicating the possibility of these CcDof genes to be associated with photoperiodic control and biotic and abiotic stress. The duplication pattern showed that tandem duplication is predominant over segmental duplication events. The comparative phylogenetic analysis of these Dof proteins along with 78 soybean, 36 Arabidopsis and 30 rice Dof proteins revealed 7 major clusters. Several groups of orthologs and paralogs were identified based on phylogenetic tree constructed. Our study provides useful information for functional characterization of CcDof genes.
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Affiliation(s)
- N Malviya
- Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur, 273 009, Uttar Pradesh, India
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Kumar RR, Yadav S, Joshi S, Bhandare PP, Patil VK, Kulkarni PB, Sonkawade S, Naik GR. Identification and Validation of Expressed Sequence Tags from Pigeonpea (Cajanus cajan L.) Root. Int J Plant Genomics 2014; 2014:651912. [PMID: 24895494 PMCID: PMC4033407 DOI: 10.1155/2014/651912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 04/15/2014] [Indexed: 06/03/2023]
Abstract
Pigeonpea (Cajanus cajan (L) Millsp.) is an important food legume crop of rain fed agriculture in the arid and semiarid tropics of the world. It has deep and extensive root system which serves a number of important physiological and metabolic functions in plant development and growth. In order to identify genes associated with pigeonpea root, ESTs were generated from the root tissues of pigeonpea (GRG-295 genotype) by normalized cDNA library. A total of 105 high quality ESTs were generated by sequencing of 250 random clones which resulted in 72 unigenes comprising 25 contigs and 47 singlets. The ESTs were assigned to 9 functional categories on the basis of their putative function. In order to validate the possible expression of transcripts, four genes, namely, S-adenosylmethionine synthetase, phosphoglycerate kinase, serine carboxypeptidase, and methionine aminopeptidase, were further analyzed by reverse transcriptase PCR. The possible role of the identified transcripts and their functions associated with root will also be a valuable resource for the functional genomics study in legume crop.
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Affiliation(s)
- Ravi Ranjan Kumar
- Vidya Pratishthan's School of Biotechnology, Vidyanagari, Baramati, Pune 413133, India
- Department of Biotechnology, Gulbarga University, Gulbarga, Karnataka 585106, India
| | - Shailesh Yadav
- Institute of Biotechnology, Acharya N. G. Ranga Agricultural University, Hyderabad 500030, India
| | - Shourabh Joshi
- Institute of Biotechnology, Acharya N. G. Ranga Agricultural University, Hyderabad 500030, India
| | | | - Vinod Kumar Patil
- Department of Biotechnology, Gulbarga University, Gulbarga, Karnataka 585106, India
| | - Pramod B. Kulkarni
- Department of Biotechnology, Gulbarga University, Gulbarga, Karnataka 585106, India
| | - Swati Sonkawade
- Department of Biotechnology, Gulbarga University, Gulbarga, Karnataka 585106, India
| | - G. R. Naik
- Department of Biotechnology, Gulbarga University, Gulbarga, Karnataka 585106, India
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Deeplanaik N, Kumaran RC, Venkatarangaiah K, Shivashankar SKH, Doddamani D, Telkar S. Expression of drought responsive genes in pigeonpea and in silico comparison with soybean cDNA library. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s12892-013-0069-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Mishra RR, Sahu AR, Rath SC, Behera B, Panigrahi J. Molecular mapping of locus controlling resistance to Helicoverpa armigera (Hubner) in Cajanus cajan L. (Millspaugh) using interspecific F2 mapping population. Nucleus 2013. [DOI: 10.1007/s13237-013-0086-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Varshney RK, Mohan SM, Gaur PM, Gangarao NVPR, Pandey MK, Bohra A, Sawargaonkar SL, Chitikineni A, Kimurto PK, Janila P, Saxena KB, Fikre A, Sharma M, Rathore A, Pratap A, Tripathi S, Datta S, Chaturvedi SK, Mallikarjuna N, Anuradha G, Babbar A, Choudhary AK, Mhase MB, Bharadwaj C, Mannur DM, Harer PN, Guo B, Liang X, Nadarajan N, Gowda CLL. Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics. Biotechnol Adv 2013; 31:1120-34. [PMID: 23313999 DOI: 10.1016/j.biotechadv.2013.01.001] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 12/16/2012] [Accepted: 01/03/2013] [Indexed: 10/27/2022]
Abstract
Advances in next-generation sequencing and genotyping technologies have enabled generation of large-scale genomic resources such as molecular markers, transcript reads and BAC-end sequences (BESs) in chickpea, pigeonpea and groundnut, three major legume crops of the semi-arid tropics. Comprehensive transcriptome assemblies and genome sequences have either been developed or underway in these crops. Based on these resources, dense genetic maps, QTL maps as well as physical maps for these legume species have also been developed. As a result, these crops have graduated from 'orphan' or 'less-studied' crops to 'genomic resources rich' crops. This article summarizes the above-mentioned advances in genomics and genomics-assisted breeding applications in the form of marker-assisted selection (MAS) for hybrid purity assessment in pigeonpea; marker-assisted backcrossing (MABC) for introgressing QTL region for drought-tolerance related traits, Fusarium wilt (FW) resistance and Ascochyta blight (AB) resistance in chickpea; late leaf spot (LLS), leaf rust and nematode resistance in groundnut. We critically present the case of use of other modern breeding approaches like marker-assisted recurrent selection (MARS) and genomic selection (GS) to utilize the full potential of genomics-assisted breeding for developing superior cultivars with enhanced tolerance to various environmental stresses. In addition, this article recommends the use of advanced-backcross (AB-backcross) breeding and development of specialized populations such as multi-parents advanced generation intercross (MAGIC) for creating new variations that will help in developing superior lines with broadened genetic base. In summary, we propose the use of integrated genomics and breeding approach in these legume crops to enhance crop productivity in marginal environments ensuring food security in developing countries.
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Affiliation(s)
- Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; CGIAR Generation Challenge Programme (GCP), c/o CIMMYT, DF 06600, Mexico; The University of Western Australia, Crawley 6009, Australia; Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou 510640, China.
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Kumawat G, Raje RS, Bhutani S, Pal JK, Mithra ASVCR, Gaikwad K, Sharma TR, Singh NK. Molecular mapping of QTLs for plant type and earliness traits in pigeonpea (Cajanus cajan L. Millsp.). BMC Genet 2012; 13:84. [PMID: 23043321 PMCID: PMC3504571 DOI: 10.1186/1471-2156-13-84] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 09/28/2012] [Indexed: 12/14/2022] Open
Abstract
Background Pigeonpea is an important grain legume of the semi-arid tropics and sub-tropical regions where it plays a crucial role in the food and nutritional security of the people. The average productivity of pigeonpea has remained very low and stagnant for over five decades due to lack of genomic information and intensive breeding efforts. Previous SSR-based linkage maps of pigeonpea used inter-specific crosses due to low inter-varietal polymorphism. Here our aim was to construct a high density intra-specific linkage map using genic-SNP markers for mapping of major quantitative trait loci (QTLs) for key agronomic traits, including plant height, number of primary and secondary branches, number of pods, days to flowering and days to maturity in pigeonpea. Results A population of 186 F2:3 lines derived from an intra-specific cross between inbred lines ‘Pusa Dwarf’ and ‘HDM04-1’ was used to construct a dense molecular linkage map of 296 genic SNP and SSR markers covering a total adjusted map length of 1520.22 cM for the 11 chromosomes of the pigeonpea genome. This is the first dense intra-specific linkage map of pigeonpea with the highest genome length coverage. Phenotypic data from the F2:3 families were used to identify thirteen QTLs for the six agronomic traits. The proportion of phenotypic variance explained by the individual QTLs ranged from 3.18% to 51.4%. Ten of these QTLs were clustered in just two genomic regions, indicating pleiotropic effects or close genetic linkage. In addition to the main effects, significant epistatic interaction effects were detected between the QTLs for number of pods per plant. Conclusions A large amount of information on transcript sequences, SSR markers and draft genome sequence is now available for pigeonpea. However, there is need to develop high density linkage maps and identify genes/QTLs for important agronomic traits for practical breeding applications. This is the first report on identification of QTLs for plant type and maturity traits in pigeonpea. The QTLs identified in this study provide a strong foundation for further validation and fine mapping for utilization in the pigeonpea improvement.
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Affiliation(s)
- Giriraj Kumawat
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India
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Bohra A, Saxena RK, Gnanesh BN, Saxena K, Byregowda M, Rathore A, KaviKishor PB, Cook DR, Varshney RK. An intra-specific consensus genetic map of pigeonpea [Cajanus cajan (L.) Millspaugh] derived from six mapping populations. Theor Appl Genet 2012; 125:1325-38. [PMID: 22772726 PMCID: PMC3442162 DOI: 10.1007/s00122-012-1916-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 06/05/2012] [Indexed: 05/21/2023]
Abstract
Pigeonpea (Cajanus cajan L.) is an important food legume crop of rainfed agriculture. Owing to exposure of the crop to a number of biotic and abiotic stresses, the crop productivity has remained stagnant for almost last five decades at ca. 750 kg/ha. The availability of a cytoplasmic male sterility (CMS) system has facilitated the development and release of hybrids which are expected to enhance the productivity of pigeonpea. Recent advances in genomics and molecular breeding such as marker-assisted selection (MAS) offer the possibility to accelerate hybrid breeding. Molecular markers and genetic maps are pre-requisites for deploying MAS in breeding. However, in the case of pigeonpea, only one inter- and two intra-specific genetic maps are available so far. Here, four new intra-specific genetic maps comprising 59-140 simple sequence repeat (SSR) loci with map lengths ranging from 586.9 to 881.6 cM have been constructed. Using these four genetic maps together with two recently published intra-specific genetic maps, a consensus map was constructed, comprising of 339 SSR loci spanning a distance of 1,059 cM. Furthermore, quantitative trait loci (QTL) analysis for fertility restoration (Rf) conducted in three mapping populations identified four major QTLs explaining phenotypic variances up to 24 %. To the best of our knowledge, this is the first report on construction of a consensus genetic map in pigeonpea and on the identification of QTLs for fertility restoration. The developed consensus genetic map should serve as a reference for developing new genetic maps as well as correlating with the physical map in pigeonpea to be developed in near future. The availability of more informative markers in the bins harbouring QTLs for sterility mosaic disease (SMD) and Rf will facilitate the selection of the most suitable markers for genetic analysis and molecular breeding applications in pigeonpea.
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Affiliation(s)
- Abhishek Bohra
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324 India
- Osmania University, Hyderabad, 500007 India
| | - Rachit K. Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324 India
- Osmania University, Hyderabad, 500007 India
| | - B. N. Gnanesh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324 India
- University of Agricultural Sciences, Bengaluru (UAS-B), 560065 India
| | - Kulbhushan Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324 India
| | - M. Byregowda
- University of Agricultural Sciences, Bengaluru (UAS-B), 560065 India
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324 India
| | | | | | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324 India
- CGIAR Generation Challenge Programme (GCP), c/o CIMMYT, 06600 Mexico DF, Mexico
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Kudapa H, Bharti AK, Cannon SB, Farmer AD, Mulaosmanovic B, Kramer R, Bohra A, Weeks NT, Crow JA, Tuteja R, Shah T, Dutta S, Gupta DK, Singh A, Gaikwad K, Sharma TR, May GD, Singh NK, Varshney RK. A comprehensive transcriptome assembly of Pigeonpea (Cajanus cajan L.) using sanger and second-generation sequencing platforms. Mol Plant 2012; 5:1020-8. [PMID: 22241453 PMCID: PMC3440007 DOI: 10.1093/mp/ssr111] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 11/29/2011] [Indexed: 05/18/2023]
Abstract
A comprehensive transcriptome assembly for pigeonpea has been developed by analyzing 128.9 million short Illumina GA IIx single end reads, 2.19 million single end FLX/454 reads, and 18 353 Sanger expressed sequenced tags from more than 16 genotypes. The resultant transcriptome assembly, referred to as CcTA v2, comprised 21 434 transcript assembly contigs (TACs) with an N50 of 1510 bp, the largest one being ~8 kb. Of the 21 434 TACs, 16 622 (77.5%) could be mapped on to the soybean genome build 1.0.9 under fairly stringent alignment parameters. Based on knowledge of intron junctions, 10 009 primer pairs were designed from 5033 TACs for amplifying intron spanning regions (ISRs). By using in silico mapping of BAC-end-derived SSR loci of pigeonpea on the soybean genome as a reference, putative mapping positions at the chromosome level were predicted for 6284 ISR markers, covering all 11 pigeonpea chromosomes. A subset of 128 ISR markers were analyzed on a set of eight genotypes. While 116 markers were validated, 70 markers showed one to three alleles, with an average of 0.16 polymorphism information content (PIC) value. In summary, the CcTA v2 transcript assembly and ISR markers will serve as a useful resource to accelerate genetic research and breeding applications in pigeonpea.
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Affiliation(s)
- Himabindu Kudapa
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India
| | - Arvind K. Bharti
- National Center for Genome Resources (NCGR), Santa Fe, NM 87505, USA
| | - Steven B. Cannon
- United States Department of Agriculture–Agricultural Research Service (USDA–ARS), Corn Insects and Crop Genetics Research Unit, Ames, IA, USA
- Department of Agronomy, Iowa State University, Amens, IA, USA
| | - Andrew D. Farmer
- National Center for Genome Resources (NCGR), Santa Fe, NM 87505, USA
| | - Benjamin Mulaosmanovic
- United States Department of Agriculture–Agricultural Research Service (USDA–ARS), Corn Insects and Crop Genetics Research Unit, Ames, IA, USA
| | - Robin Kramer
- National Center for Genome Resources (NCGR), Santa Fe, NM 87505, USA
| | - Abhishek Bohra
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India
| | - Nathan T. Weeks
- United States Department of Agriculture–Agricultural Research Service (USDA–ARS), Corn Insects and Crop Genetics Research Unit, Ames, IA, USA
| | - John A. Crow
- National Center for Genome Resources (NCGR), Santa Fe, NM 87505, USA
| | - Reetu Tuteja
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India
| | - Trushar Shah
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India
| | - Sutapa Dutta
- National Research Centre on Plant Biotechnology (NRCPB), Indian Agricultural Research Institute, New Delhi 110 012, India
| | - Deepak K. Gupta
- National Research Centre on Plant Biotechnology (NRCPB), Indian Agricultural Research Institute, New Delhi 110 012, India
| | - Archana Singh
- National Research Centre on Plant Biotechnology (NRCPB), Indian Agricultural Research Institute, New Delhi 110 012, India
| | - Kishor Gaikwad
- National Research Centre on Plant Biotechnology (NRCPB), Indian Agricultural Research Institute, New Delhi 110 012, India
| | - Tilak R. Sharma
- National Research Centre on Plant Biotechnology (NRCPB), Indian Agricultural Research Institute, New Delhi 110 012, India
| | - Gregory D. May
- National Center for Genome Resources (NCGR), Santa Fe, NM 87505, USA
| | - Nagendra K. Singh
- National Research Centre on Plant Biotechnology (NRCPB), Indian Agricultural Research Institute, New Delhi 110 012, India
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India
- CGIAR Generation Challenge Programme (GCP), c/o CIMMYT, 06600 Mexico DF, Mexico
- To whom correspondence should be addressed at address. E-mail , tel. +91 4030713305, fax +91 40 30713074
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Mishra RR, Sahu AR, Rath SC, Mishra SP, Panigrahi J. Cyto-morphological and molecular characterization of Cajanus cajan × C. scarabaeoides F1 hybrid. Nucleus 2012. [DOI: 10.1007/s13237-012-0050-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Sliwka J, Jakuczun H, Chmielarz M, Hara-Skrzypiec A, Tomczyńska I, Kilian A, Zimnoch-Guzowska E. Late blight resistance gene from Solanum ruiz-ceballosii is located on potato chromosome X and linked to violet flower colour. BMC Genet 2012; 13:11. [PMID: 22369123 PMCID: PMC3347998 DOI: 10.1186/1471-2156-13-11] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 02/27/2012] [Indexed: 11/10/2022] Open
Abstract
Background Phytophthora infestans (Mont.) de Bary, the causal organism of late blight, is economically the most important pathogen of potato and resistance against it has been one of the primary goals of potato breeding. Some potentially durable, broad-spectrum resistance genes against this disease have been described recently. However, to obtain durable resistance in potato cultivars more genes are needed to be identified to realize strategies such as gene pyramiding or use of genotype mixtures based on diverse genes. Results A major resistance gene, Rpi-rzc1, against P. infestans originating from Solanum ruiz-ceballosii was mapped to potato chromosome X using Diversity Array Technology (DArT) and sequence-specific PCR markers. The gene provided high level of resistance in both detached leaflet and tuber slice tests. It was linked, at a distance of 3.4 cM, to violet flower colour most likely controlled by the previously described F locus. The marker-trait association with the closest marker, violet flower colour, explained 87.1% and 85.7% of variance, respectively, for mean detached leaflet and tuber slice resistance. A genetic linkage map that consisted of 1,603 DArT markers and 48 reference sequence-specific PCR markers of known chromosomal localization with a total map length of 1204.8 cM was constructed. Conclusions The Rpi-rzc1 gene described here can be used for breeding potatoes resistant to P. infestans and the breeding process can be expedited using the molecular markers and the phenotypic marker, violet flower colour, identified in this study. Knowledge of the chromosomal localization of Rpi-rzc1 can be useful for design of gene pyramids. The genetic linkage map constructed in this study contained 1,149 newly mapped DArT markers and will be a valuable resource for future mapping projects using this technology in the Solanum genus.
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Affiliation(s)
- Jadwiga Sliwka
- Plant Breeding and Acclimatization Institute-National Research Institute, Młochów Research Centre, Młochów, Poland.
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Blair MW, Fernandez AC, Ishitani M, Moreta D, Seki M, Ayling S, Shinozaki K. Construction and EST sequencing of full-length, drought stress cDNA libraries for common beans (Phaseolus vulgaris L.). BMC Plant Biol 2011; 11:171. [PMID: 22118559 PMCID: PMC3240127 DOI: 10.1186/1471-2229-11-171] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 11/25/2011] [Indexed: 05/07/2023]
Abstract
BACKGROUND Common bean is an important legume crop with only a moderate number of short expressed sequence tags (ESTs) made with traditional methods. The goal of this research was to use full-length cDNA technology to develop ESTs that would overlap with the beginning of open reading frames and therefore be useful for gene annotation of genomic sequences. The library was also constructed to represent genes expressed under drought, low soil phosphorus and high soil aluminum toxicity. We also undertook comparisons of the full-length cDNA library to two previous non-full clone EST sets for common bean. RESULTS Two full-length cDNA libraries were constructed: one for the drought tolerant Mesoamerican genotype BAT477 and the other one for the acid-soil tolerant Andean genotype G19833 which has been selected for genome sequencing. Plants were grown in three soil types using deep rooting cylinders subjected to drought and non-drought stress and tissues were collected from both roots and above ground parts. A total of 20,000 clones were selected robotically, half from each library. Then, nearly 10,000 clones from the G19833 library were sequenced with an average read length of 850 nucleotides. A total of 4,219 unigenes were identified consisting of 2,981 contigs and 1,238 singletons. These were functionally annotated with gene ontology terms and placed into KEGG pathways. Compared to other EST sequencing efforts in common bean, about half of the sequences were novel or represented the 5' ends of known genes. CONCLUSIONS The present full-length cDNA libraries add to the technological toolbox available for common bean and our sequencing of these clones substantially increases the number of unique EST sequences available for the common bean genome. All of this should be useful for both functional gene annotation, analysis of splice site variants and intron/exon boundary determination by comparison to soybean genes or with common bean whole-genome sequences. In addition the library has a large number of transcription factors and will be interesting for discovery and validation of drought or abiotic stress related genes in common bean.
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Affiliation(s)
- Matthew W Blair
- Bean Program and Biotechnology Unit, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Andrea C Fernandez
- Bean Program and Biotechnology Unit, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Manabu Ishitani
- Bean Program and Biotechnology Unit, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Danilo Moreta
- Bean Program and Biotechnology Unit, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Motoaki Seki
- Plant Genomic Network Research Team and Director, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Sarah Ayling
- Bean Program and Biotechnology Unit, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Kazuo Shinozaki
- Plant Genomic Network Research Team and Director, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
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Varshney RK, Chen W, Li Y, Bharti AK, Saxena RK, Schlueter JA, Donoghue MTA, Azam S, Fan G, Whaley AM, Farmer AD, Sheridan J, Iwata A, Tuteja R, Penmetsa RV, Wu W, Upadhyaya HD, Yang SP, Shah T, Saxena KB, Michael T, McCombie WR, Yang B, Zhang G, Yang H, Wang J, Spillane C, Cook DR, May GD, Xu X, Jackson SA. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol 2011; 30:83-9. [PMID: 22057054 DOI: 10.1038/nbt.2022] [Citation(s) in RCA: 421] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 10/03/2011] [Indexed: 11/08/2022]
Abstract
Pigeonpea is an important legume food crop grown primarily by smallholder farmers in many semi-arid tropical regions of the world. We used the Illumina next-generation sequencing platform to generate 237.2 Gb of sequence, which along with Sanger-based bacterial artificial chromosome end sequences and a genetic map, we assembled into scaffolds representing 72.7% (605.78 Mb) of the 833.07 Mb pigeonpea genome. Genome analysis predicted 48,680 genes for pigeonpea and also showed the potential role that certain gene families, for example, drought tolerance-related genes, have played throughout the domestication of pigeonpea and the evolution of its ancestors. Although we found a few segmental duplication events, we did not observe the recent genome-wide duplication events observed in soybean. This reference genome sequence will facilitate the identification of the genetic basis of agronomically important traits, and accelerate the development of improved pigeonpea varieties that could improve food security in many developing countries.
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Affiliation(s)
- Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
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