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Mangal V, Verma LK, Singh SK, Saxena K, Roy A, Karn A, Rohit R, Kashyap S, Bhatt A, Sood S. Triumphs of genomic-assisted breeding in crop improvement. Heliyon 2024; 10:e35513. [PMID: 39170454 PMCID: PMC11336775 DOI: 10.1016/j.heliyon.2024.e35513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 07/23/2024] [Accepted: 07/30/2024] [Indexed: 08/23/2024] Open
Abstract
Conventional breeding approaches have played a significant role in meeting the food demand remarkably well until now. However, the increasing population, yield plateaus in certain crops, and limited recombination necessitate using genomic resources for genomics-assisted crop improvement programs. As a result of advancements in the next-generation sequence technology, GABs have developed dramatically to characterize allelic variants and facilitate their rapid and efficient incorporation in crop improvement programs. Genomics-assisted breeding (GAB) has played an important role in harnessing the potential of modern genomic tools, exploiting allelic variation from genetic resources and developing cultivars over the past decade. The availability of pangenomes for major crops has been a significant development, albeit with varying degrees of completeness. Even though adopting these technologies is essentially determined on economic grounds and cost-effective assays, which create a wealth of information that can be successfully used to exploit the latent potential of crops. GAB has been instrumental in harnessing the potential of modern genomic resources and exploiting allelic variation for genetic enhancement and cultivar development. GAB strategies will be indispensable for designing future crops and are expected to play a crucial role in breeding climate-smart crop cultivars with higher nutritional value.
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Affiliation(s)
- Vikas Mangal
- ICAR-Central Potato Research Institute (CPRI), Shimla, Himachal Pradesh, 171001, India
| | | | - Sandeep Kumar Singh
- Department of Genetics and Plant Breeding, Faculty of Agricultural Sciences, Siksha ‘O’ Anusandhan University, Bhubaneswar, Odisha, 751030, India
| | - Kanak Saxena
- Department of Genetics and Plant Breeding, Rabindranath Tagore University, Raisen, Madhya Pradesh, India
| | - Anirban Roy
- Division of Genetics and Plant Breeding, Ramakrishna Mission Vivekananda Educational and Research Institute (RKMVERI), Narendrapur, Kolkata, 700103, India
| | - Anandi Karn
- Plant Breeding & Graduate Program, IFAS - University of Florida, Gainesville, USA
| | - Rohit Rohit
- Department of Genetics and Plant Breeding, GBPUA&T, Pantnagar, Uttarakhand, 263145, India
| | - Shruti Kashyap
- Department of Genetics and Plant Breeding, GBPUA&T, Pantnagar, Uttarakhand, 263145, India
| | - Ashish Bhatt
- Department of Genetics and Plant Breeding, GBPUA&T, Pantnagar, Uttarakhand, 263145, India
| | - Salej Sood
- ICAR-Central Potato Research Institute (CPRI), Shimla, Himachal Pradesh, 171001, India
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Bhutia KL, Kisku A, Lap B, Sahni S, Arya M, Bhutia ND, Ahmad M, Chaturvedi R, Sudhan RA, Sharma VK. Insight into a region of chickpea ( Cicer arietinum L.) Chromosome 2 revealed potential candidate genes linked to Foc4 Fusarium wilt resistance. FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:FP24068. [PMID: 39137292 DOI: 10.1071/fp24068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 07/16/2024] [Indexed: 08/15/2024]
Abstract
Two markers on Chromosome 2 of chickpea (Cicer arietinum ) are reportedly associated with resistance to race 4 Fusarium wilt, and are frequently used in breeding. However, the genes in this region that actually confer wilt resistance are unknown. We aimed to characterise them using both in silico approaches and marker trait association (MTA) analysis. Of the 225 protein-encoding genes in this region, 51 showed significant differential expression in two contrasting chickpea genotypes under wilt, with potential involvement in stress response. From a diverse set of 244 chickpea genotypes, two sets of 40 resistant and 40 susceptible genotypes were selected based on disease incidence and amplification pattern of the TA59 marker. All cultivars were further genotyped with 1238 single nucleotide polymorphisms (SNPs) specific to the 51 genes; only seven SNPs were significantly correlated with disease. SNP Ca2_24099002, specific to the LOC101498008 (Transmembrane protein 87A) gene, accounted for the highest phenotypic variance for disease incidence at 16.30%, whereas SNPs Ca2_25166118 and Ca2_27029215, specific to the LOC101494644 (β-glucosidase BoGH3B-like) and LOC101505289 (Putative tRNA pseudouridine synthase) genes, explained 10.51% and 10.50% of the variation, respectively, in the sets with contrasting disease susceptibility. Together with the TA59 and TR19 markers, these SNPs can be used in a chickpea breeding scheme to develop wilt resistance.
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Affiliation(s)
- Karma L Bhutia
- Department of Agricultural Biotechnology & Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar 848125, India
| | - Anima Kisku
- Department of Agricultural Biotechnology & Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar 848125, India
| | - Bharati Lap
- Department of Genetics & Plant Breeding, Rajiv Gandhi University, Doimukh, Arunachal Pradesh 791112, India
| | - Sangita Sahni
- Department of Plant Pathology, Tirhut College of Agriculture, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar 848125, India
| | - Madhuri Arya
- Department of Genetics & Plant Breeding, Tirhut College of Agriculture, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar 848125, India
| | - Nangsol D Bhutia
- College of Horticulture, Central Agricultural Univeristy (Imphal), Bermiok, Sikkim 737134, India
| | - Mahtab Ahmad
- Department of Agricultural Biotechnology & Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar 848125, India
| | - Rashmi Chaturvedi
- Department of Agricultural Biotechnology & Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar 848125, India
| | - Rajalingam Amutha Sudhan
- Department of Agricultural Biotechnology & Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar 848125, India
| | - Vinay Kumar Sharma
- Department of Agricultural Biotechnology & Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar 848125, India
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3
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Thudi M, Samineni S, Li W, Boer MP, Roorkiwal M, Yang Z, Ladejobi F, Zheng C, Chitikineni A, Nayak S, He Z, Valluri V, Bajaj P, Khan AW, Gaur PM, van Eeuwijk F, Mott R, Xin L, Varshney RK. Whole genome resequencing and phenotyping of MAGIC population for high resolution mapping of drought tolerance in chickpea. THE PLANT GENOME 2024; 17:e20333. [PMID: 37122200 DOI: 10.1002/tpg2.20333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/17/2023] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
Terminal drought is one of the major constraints to crop production in chickpea (Cicer arietinum L.). In order to map drought tolerance related traits at high resolution, we sequenced multi-parent advanced generation intercross (MAGIC) population using whole genome resequencing approach and phenotyped it under drought stress environments for two consecutive years (2013-14 and 2014-15). A total of 52.02 billion clean reads containing 4.67 TB clean data were generated on the 1136 MAGIC lines and eight parental lines. Alignment of clean data on to the reference genome enabled identification of a total, 932,172 of SNPs, 35,973 insertions, and 35,726 deletions among the parental lines. A high-density genetic map was constructed using 57,180 SNPs spanning a map distance of 1606.69 cM. Using compressed mixed linear model, genome-wide association study (GWAS) enabled us to identify 737 markers significantly associated with days to 50% flowering, days to maturity, plant height, 100 seed weight, biomass, and harvest index. In addition to the GWAS approach, an identity-by-descent (IBD)-based mixed model approach was used to map quantitative trait loci (QTLs). The IBD-based mixed model approach detected major QTLs that were comparable to those from the GWAS analysis as well as some exclusive QTLs with smaller effects. The candidate genes like FRIGIDA and CaTIFY4b can be used for enhancing drought tolerance in chickpea. The genomic resources, genetic map, marker-trait associations, and QTLs identified in the study are valuable resources for the chickpea community for developing climate resilient chickpeas.
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Affiliation(s)
- Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University (RPCAU), Pusa, India
| | - Srinivasan Samineni
- Crop Improvement Program-Asia, ICRISAT, Patancheru, India
- International Center for Biosaline Agriculture, Dubai, United Arab Emirates
| | - Wenhao Li
- Wageningen University and Research, Wageningen, The Netherlands
| | - Martin P Boer
- Wageningen University and Research, Wageningen, The Netherlands
| | - Manish Roorkiwal
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Khalifa Center for Genetic Engineering and Biotechnology (KCGEB), United Arab Emirates University, Al Ain, United Arab Emirates
| | | | - Funmi Ladejobi
- Department of Genetics, Evolution and Environment, Genetics Institute, University College London, London, UK
| | - Chaozhi Zheng
- Wageningen University and Research, Wageningen, The Netherlands
- BGI-Shenzhen, Shenzhen, China
| | - Annapurna Chitikineni
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Sourav Nayak
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | | | - Vinod Valluri
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Prasad Bajaj
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Aamir W Khan
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Pooran M Gaur
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University (RPCAU), Pusa, India
- The UWA Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia
| | | | - Richard Mott
- Department of Genetics, Evolution and Environment, Genetics Institute, University College London, London, UK
| | - Liu Xin
- BGI-Shenzhen, Shenzhen, China
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
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Yadav RK, Tripathi MK, Tiwari S, Tripathi N, Asati R, Patel V, Sikarwar RS, Payasi DK. Breeding and Genomic Approaches towards Development of Fusarium Wilt Resistance in Chickpea. Life (Basel) 2023; 13:life13040988. [PMID: 37109518 PMCID: PMC10144025 DOI: 10.3390/life13040988] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/29/2023] Open
Abstract
Chickpea is an important leguminous crop with potential to provide dietary proteins to both humans and animals. It also ameliorates soil nitrogen through biological nitrogen fixation. The crop is affected by an array of biotic and abiotic factors. Among different biotic stresses, a major fungal disease called Fusarium wilt, caused by Fusarium oxysporum f. sp. ciceris (FOC), is responsible for low productivity in chickpea. To date, eight pathogenic races of FOC (race 0, 1A, and 1B/C, 2-6) have been reported worldwide. The development of resistant cultivars using different conventional breeding methods is very time consuming and depends upon the environment. Modern technologies can improve conventional methods to solve these major constraints. Understanding the molecular response of chickpea to Fusarium wilt can help to provide effective management strategies. The identification of molecular markers closely linked to genes/QTLs has provided great potential for chickpea improvement programs. Moreover, omics approaches, including transcriptomics, metabolomics, and proteomics give scientists a vast viewpoint of functional genomics. In this review, we will discuss the integration of all available strategies and provide comprehensive knowledge about chickpea plant defense against Fusarium wilt.
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Affiliation(s)
- Rakesh Kumar Yadav
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Manoj Kumar Tripathi
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology & Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Sushma Tiwari
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology & Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Niraj Tripathi
- Directorate of Research Services, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Jabalpur 482004, India
| | - Ruchi Asati
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Vinod Patel
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - R S Sikarwar
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
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5
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Kumari G, Shanmugavadivel PS, Lavanya GR, Tiwari P, Singh D, Gore PG, Tripathi K, Madhavan Nair R, Gupta S, Pratap A. Association mapping for important agronomic traits in wild and cultivated Vigna species using cross-species and cross-genera simple sequence repeat markers. Front Genet 2022; 13:1000440. [PMID: 36406138 PMCID: PMC9669911 DOI: 10.3389/fgene.2022.1000440] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/06/2022] [Indexed: 10/10/2023] Open
Abstract
The genus Vigna is an agronomically important taxon, with many of its species inhabiting a wide range of environments and offering numerous useful genes for the improvement of the cultivated types. The present study aimed to detect the genomic regions associated with yield-attributing traits by genome-wide association mapping. A diverse panel of 98 wild and cultivated Vigna accessions (acc.) belonging to 13 different species was evaluated for yield and related traits during the kharif season of 2017 and 2018. The panel was also genotyped using 92 cross-genera and cross-species simple sequence repeat markers to study the population genetic structure and useful market-trait associations. The PCA and trait correlation established relationships amongst the traits during both seasons while 100-seed weight (HSW) had a positive correlation with pod length (PL), and days to first flowering (DFF) with days to maturity (DM). The population genetic structure analysis grouped different acc. into three genetically distinct sub-populations with SP-1 comprising 34 acc., SP-2 (24 acc.), and SP-3 (33 acc.) and one admixture group (7 acc.). Mixed linear model analysis revealed an association of 13 markers, namely, VR018, VR039, VR022, CEDG033, GMES0337, MBSSR008, CEDG220, VM27, CP1225, CP08695, CEDG100, CEDG008, and CEDG096A with nine traits. Seven of the aforementioned markers, namely, VR018 for plant height (PH) and terminal leaflet length (TLL), VR022 for HSW and pod length (PL), CEDG033 for DFF and DM, MBSSR008 for DFF and DM, CP1225 for CC at 30 days (CC30), DFF and DM, CEDG100 for PH and terminal leaflet length (TLL), and CEDG096A for CC30 and chlorophyll content at 45 days were associated with multiple traits. The marker CEDG100, associated with HSW, PH, and TLL, is co-localized in gene-encoding histone-lysine N-methyltransferase ATX5. Similarly, VR22, associated with PL and HSW, is co-located in gene-encoding SHOOT GRAVITROPISM 5 in mungbean. These associations may be highly useful for marker-assisted genetic improvement of mungbean and other related Vigna species.
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Affiliation(s)
- Gita Kumari
- ICAR-Indian Institute of Pulses Research, Kanpur, India
| | | | - G. Roopa Lavanya
- Sam Higginbottom University of Agricultural Technology and Sciences, Prayagraj, India
| | - Pravin Tiwari
- ICAR-Indian Institute of Pulses Research, Kanpur, India
| | | | - P. G. Gore
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Kuldeep Tripathi
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | | | - Sanjeev Gupta
- ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Aditya Pratap
- ICAR-Indian Institute of Pulses Research, Kanpur, India
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Choudhary AK, Jain SK, Dubey AK, Kumar J, Sharma M, Gupta KC, Sharma LD, Prakash V, Kumar S. Conventional and molecular breeding for disease resistance in chickpea: status and strategies. Biotechnol Genet Eng Rev 2022:1-32. [PMID: 35959728 DOI: 10.1080/02648725.2022.2110641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 12/21/2021] [Indexed: 11/02/2022]
Abstract
Chickpea (Cicer arietinum L.) is an important grain legume at the global level. Among different biotic stresses, diseases are the most important factor limiting its production, causing yield losses up to 100% in severe condition. The major diseases that adversely affect yield of chickpea include Fusarium wilt, Ascochyta blight and Botrytis gray mold. However, dry root rot, collar rot, Sclerotinia stem rot, rust, stunt disease and phyllody have been noted as emerging biotic threats to chickpea production in many production regions. Identification and incorporation of different morphological and biochemical traits are required through breeding to enhance genetic gain for disease resistance. In recent years, remarkable progress has been made in the development of trait-specific breeding lines, genetic and genomic resources in chickpea. Advances in genomics technologies have opened up new avenues to introgress genes from secondary and tertiary gene pools for improving disease resistance in chickpea. In this review, we have discussed important diseases, constraints and improvement strategies for enhancing disease resistance in chickpea.
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Affiliation(s)
- Arbind K Choudhary
- Division of Crop Research, ICAR Research Complex for Eastern Region, Patna, Bihar, India
| | - Shailesh Kumar Jain
- Department of Genetics and Plant Breeding, Rajasthan Agricultural Research Institute, Durgapura, Jaipur, Rajasthan, India
| | - Abhishek Kumar Dubey
- Division of Crop Research, ICAR Research Complex for Eastern Region, Patna, Bihar, India
| | - Jitendra Kumar
- Division of Crop Improvement, Indian Institute of Pulses Research (IIPR), Kanpur, Uttar Pradesh, India
| | - Mamta Sharma
- Crop Protection and Seed Health, International Crops Research Institute for the Semi-Arid-Tropics (ICRISAT), Patancheru, Telangana, India
| | - Kailash Chand Gupta
- Department of Genetics and Plant Breeding, Rajasthan Agricultural Research Institute, Durgapura, Jaipur, Rajasthan, India
| | - Leela Dhar Sharma
- Department of Genetics and Plant Breeding, Rajasthan Agricultural Research Institute, Durgapura, Jaipur, Rajasthan, India
| | - Ved Prakash
- Department of Genetics and Plant Breeding, Rajasthan Agricultural Research Institute, Durgapura, Jaipur, Rajasthan, India
| | - Saurabh Kumar
- Division of Crop Research, ICAR Research Complex for Eastern Region, Patna, Bihar, India
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Bharadwaj C, Jorben J, Rao A, Roorkiwal M, Patil BS, Jayalakshmi, Ahammed SK, Saxena DR, Yasin M, Jahagirdar JE, Sontakke PL, Pithia MS, Chudasama MK, Swarup I, Singh RK, Nitesh SD, Chitikineni A, Singh S, Singh I, Pratap A, Dixit GP, Srivastava AK, Varshney RK. Development of High Yielding Fusarium Wilt Resistant Cultivar by Pyramiding of “Genes” Through Marker-Assisted Backcrossing in Chickpea (Cicer arietinum L.). Front Genet 2022; 13:924287. [PMID: 35991541 PMCID: PMC9388742 DOI: 10.3389/fgene.2022.924287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/17/2022] [Indexed: 11/13/2022] Open
Abstract
Pusa 391, a mega desi chickpea variety with medium maturity duration is extensively cultivated in the Central Zone of India. Of late, this variety has become susceptible to Fusarium wilt (FW), which has drastic impact on its yield. Presence of variability in the wilt causing pathogen, Fusarium oxysporum f.sp. ciceri (foc) across geographical locations necessitates the role of pyramiding for FW resistance for different races (foc 1,2,3,4 and 5). Subsequently, the introgression lines developed in Pusa 391 genetic background were subjected to foreground selection using three SSR markers (GA16, TA 27 and TA 96) while 48 SSR markers uniformly distributed on all chromosomes, were used for background selection to observe the recovery of recurrent parent genome (RPG). BC1F1 lines with 75–85% RPG recovery were used to generate BC2F1. The plants that showed more than 90% RPG recovery in BC2F1 were used for generating BC3F1. The plants that showed more than 96% RPG recovery were selected and selfed to generate BC3F3. Multi-location evaluation of advanced introgression lines (BC2F3) in six locations for grain yield (kg/ha), days to fifty percent flowering, days to maturity, 100 seed weight and disease incidence was done. In case of disease incidence, the genotype IL1 (BGM 20211) was highly resistant to FW in Junagarh, Indore, New Delhi, Badnapur and moderately resistant at Sehore and Nandyal. GGE biplot analysis revealed that IL1(BGM20211) was the most stable genotype at Junagadh, Sehore and Nandyal. GGE biplot analysis revealed that IL1(BGM 20211) and IL4(BGM 20212) were the top performers in yield and highly stable across six environments and were nominated for Advanced Varietal Trials (AVT) of AICRP (All India Coordinated Research Project on Chickpea) in 2018–19. BGM20211 and BGM 20212 recorded 29 and 28.5% average yield gain over the recurrent parent Pusa 391, in the AVT-1 and AVT-2 over five environments. Thus, BGM20211 was identified for release and notified as Pusa Manav/Pusa Chickpea 20211 for Madhya Pradesh, Gujarat and Maharashtra, Southern Rajasthan, Bundhelkhand region of Uttar Pradesh states by the Central Sub-Committees on Crop Standards, Notification and Release of Varieties of Agricultural Crops, Ministry of Agriculture and Farmers Welfare, Government of India, for commercial cultivation in India (Gazette notification number S.O.500 (E) dt. 29-1-2021).Such pyramided lines give resilience to multiple races of fusarium wilt with added yield advantage.
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8
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Rohilla V, Yadav RK, Poonia A, Sheoran R, Kumari G, Shanmugavadivel PS, Pratap A. Association Mapping for Yield Attributing Traits and Yellow Mosaic Disease Resistance in Mung Bean [ Vigna radiata (L.) Wilczek]. FRONTIERS IN PLANT SCIENCE 2022; 12:749439. [PMID: 35111171 PMCID: PMC8801447 DOI: 10.3389/fpls.2021.749439] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Mung bean [Vigna radiata (L.) Wilczek] is an important short-duration grain legume widely known for its nutritional, soil ameliorative, and cropping system intensification properties. This study aims at evaluating genetic diversity among mung bean genotypes and detecting genomic regions associated with various yield attributing traits and yellow mosaic disease (YMD) resistance by association mapping. A panel of 80 cultivars and advanced breeding lines was evaluated for 10 yield-related and YMD resistance traits during kharif (monsoon) and summer seasons of 2018-2019 and 2019-2020. A total of 164 genome-wide simple sequence repeat (SSR) markers were initially screened, out of which 89 were found polymorphic which generated 317 polymorphic alleles with an average of 3.56 alleles per SSR locus. The number of alleles at each locus varied from 2 to 7. The population genetic structure analysis grouped different genotypes in three major clusters and three genetically distinct subpopulations (SPs) (i.e., SP-1, SP-2, and SP-3) with one admixture subpopulation (SP-4). Both cluster and population genetic structure analysis categorized the advanced mung bean genotypes in a single group/SP and the released varieties in other groups/SPs, suggesting that the studied genotypes may have common ancestral history at some level. The population genetic structure was also in agreement with the genetic diversity analysis. The estimate of the average degree of linkage disequilibrium (LD) present at the genome level in 80 mung bean genotypes unveiled significant LD blocks. Over the four seasons, 10 marker-trait associations were observed significant for YMD and four seed yield (SY)-related traits viz., days to flowering, days to maturity, plant height, and number of pods per plant using the mixed linear model (MLM) method. These associations may be useful for marker-assisted mung bean yield improvement programs and YMD resistance.
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Affiliation(s)
- Versha Rohilla
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Rajesh Kumar Yadav
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Atman Poonia
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Ravika Sheoran
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Gita Kumari
- ICAR-Indian Institute of Pulses Research, Kanpur, India
| | | | - Aditya Pratap
- ICAR-Indian Institute of Pulses Research, Kanpur, India
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9
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Palakurthi R, Jayalakshmi V, Kumar Y, Kulwal P, Yasin M, Kute NS, Laxuman C, Yeri S, Vemula A, Rathore A, Samineni S, Soren KR, Mondal B, Dixit GP, Bharadwaj C, Chaturvedi SK, Gaur PM, Roorkiwal M, Thudi M, Singh NP, Varshney RK. Translational Chickpea Genomics Consortium to Accelerate Genetic Gains in Chickpea (Cicer arietinum L.). PLANTS 2021; 10:plants10122583. [PMID: 34961053 PMCID: PMC8703834 DOI: 10.3390/plants10122583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/23/2021] [Accepted: 10/30/2021] [Indexed: 12/03/2022]
Abstract
The Translational Chickpea Genomics Consortium (TCGC) was set up to increase the production and productivity of chickpea (Cicer arietinum L.). It represents research institutes from six major chickpea growing states (Madhya Pradesh, Maharashtra, Andhra Pradesh, Telangana, Karnataka and Uttar Pradesh) of India. The TCGC team has been engaged in deploying modern genomics approaches in breeding and popularizing improved varieties in farmers’ fields across the states. Using marker-assisted backcrossing, introgression lines with enhanced drought tolerance and fusarium wilt resistance have been developed in the genetic background of 10 elite varieties of chickpea. Multi-location evaluation of 100 improved lines (70 desi and 30 kabuli) during 2016–2017 and 2018–2019 enabled the identification of top performing desi and kabuli lines. In total, 909 Farmer Participatory Varietal Selection trials were conducted in 158 villages in 16 districts of the five states, during 2017–2018, 2018–2019, and 2019–2020, involving 16 improved varieties. New molecular breeding lines developed in different genetic backgrounds are potential candidates for national trials under the ICAR-All India Coordinated Research Project on Chickpea. The comprehensive efforts of TCGC resulted in the development and adoption of high-yielding varieties that will increase chickpea productivity and the profitability of chickpea growing farmers.
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Affiliation(s)
- Ramesh Palakurthi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India; (R.P.); (A.V.); (A.R.); (S.S.); (P.M.G.); (M.R.)
| | - Veera Jayalakshmi
- Regional Agricultural Research Station (RARS), Acharya N.G. Ranga Agricultural University (ANGRAU), Nandyal 518501, India;
| | - Yogesh Kumar
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur 208024, India; (Y.K.); (K.R.S.); (B.M.); (G.P.D.); (S.K.C.)
| | - Pawan Kulwal
- Department Agricultural Botany, Mahatma Phule Krishi Vidyapeeth (MPKV), Rahuri 413722, India; (P.K.); (N.S.K.)
| | - Mohammad Yasin
- RAK College of Agriculture (RAKCA), Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya (RVSKVV), Sehore 466001, India;
| | - Nandkumar Surendra Kute
- Department Agricultural Botany, Mahatma Phule Krishi Vidyapeeth (MPKV), Rahuri 413722, India; (P.K.); (N.S.K.)
| | - Chinchole Laxuman
- Agricultural Research Station (ARS), University of Agricultural Sciences (UAS), Raichur 584104, India; (C.L.); (S.Y.)
| | - Sharanabasappa Yeri
- Agricultural Research Station (ARS), University of Agricultural Sciences (UAS), Raichur 584104, India; (C.L.); (S.Y.)
| | - Anilkumar Vemula
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India; (R.P.); (A.V.); (A.R.); (S.S.); (P.M.G.); (M.R.)
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India; (R.P.); (A.V.); (A.R.); (S.S.); (P.M.G.); (M.R.)
| | - Srinivasan Samineni
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India; (R.P.); (A.V.); (A.R.); (S.S.); (P.M.G.); (M.R.)
| | - Khela Ram Soren
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur 208024, India; (Y.K.); (K.R.S.); (B.M.); (G.P.D.); (S.K.C.)
| | - Biswajit Mondal
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur 208024, India; (Y.K.); (K.R.S.); (B.M.); (G.P.D.); (S.K.C.)
| | - Girish Prasad Dixit
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur 208024, India; (Y.K.); (K.R.S.); (B.M.); (G.P.D.); (S.K.C.)
| | - Chellapilla Bharadwaj
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Delhi 110012, India;
| | - Sushil K. Chaturvedi
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur 208024, India; (Y.K.); (K.R.S.); (B.M.); (G.P.D.); (S.K.C.)
- College of Agriculture, Rani Lakshmi Bai Central Agricultural University, Jhansi 284003, India
| | - Pooran M. Gaur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India; (R.P.); (A.V.); (A.R.); (S.S.); (P.M.G.); (M.R.)
| | - Manish Roorkiwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India; (R.P.); (A.V.); (A.R.); (S.S.); (P.M.G.); (M.R.)
| | - Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India; (R.P.); (A.V.); (A.R.); (S.S.); (P.M.G.); (M.R.)
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University (RPCAU), Pusa 848125, India
- Correspondence: (M.T.); (N.P.S.); (R.K.V.)
| | - Narendra P. Singh
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur 208024, India; (Y.K.); (K.R.S.); (B.M.); (G.P.D.); (S.K.C.)
- Correspondence: (M.T.); (N.P.S.); (R.K.V.)
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India; (R.P.); (A.V.); (A.R.); (S.S.); (P.M.G.); (M.R.)
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
- Correspondence: (M.T.); (N.P.S.); (R.K.V.)
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Kumari G, Roopa Lavanya G, Shanmugavadivel PS, Singh Y, Singh P, Patidar B, Madhavan L, Gupta S, Singh NP, Pratap A. Genetic diversity and population genetic structure analysis of an extensive collection of wild and cultivated Vigna accessions. Mol Genet Genomics 2021; 296:1337-1353. [PMID: 34611751 DOI: 10.1007/s00438-021-01825-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 09/26/2021] [Indexed: 10/20/2022]
Abstract
Vigna is a large, pan-tropic and highly variable group of the legumes family which is known for its > 10 cultivated species having significant commercial value for their nutritious grains and multifarious uses. The wild vignas are considered a reservoir of numerous useful traits which can be deployed for introgression of resistance to biotic and abiotic stresses, seed quality and enhanced survival capability in extreme environments. Nonetheless, for their effective utilization through introgression breeding information on their genetic diversity, population structure and crossability is imperative. Keeping this in view, the present experiment was undertaken with 119 accessions including 99 wild Vigna accessions belonging to 19 species and 18 cultivated genotypes of Vigna and 2 of Phaseolus. Total 102 polymorphic SSRs were deployed to characterize the material at molecular level which produced 1758 alleles. The genotypes were grouped into four major clusters which were further sub-divided in nine sub-clusters. Interestingly, all cultivated species shared a single cluster while no such similarities were observed for the wild accessions as these were distributed in different groups of sub-clusters. The co-dominant allelic data of 114 accessions were then utilized for obtaining status of the accessions and their hybrid forms. The model-based population structure analysis categorized 114 accessions of Vigna into 6 genetically distinct sub-populations (K = 6) following admixture-model based simulation with varying levels of admixture. 91 (79.82%) accessions resembled their hierarchy and 23 (20.18%) accessions were observed as the admixture forms. Maximum number of accessions (25) were grouped in sub-population (SP) 6 and the least accessions were grouped in SP3 and SP5 (11 each). The population genetic structure, therefore, supported genetic diversity analysis and provided an insight into the genetic lineage of these species which will help in effective use of germplasm for development of cultivars following selective prebreeding activities.
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Affiliation(s)
- Gita Kumari
- ICAR-Indian Institute of Pulses Research, Kalyanpur, Kanpur, 208024, India
| | - G Roopa Lavanya
- Sam Higginbottom University of Agricultural Technology and Sciences, Prayagraj, UP, 211 008, India
| | | | - Yogendra Singh
- ICAR-Indian Institute of Pulses Research, Kalyanpur, Kanpur, 208024, India
| | - Parikshit Singh
- ICAR-Indian Institute of Pulses Research, Kalyanpur, Kanpur, 208024, India
| | - Bharat Patidar
- ICAR-Indian Institute of Pulses Research, Kalyanpur, Kanpur, 208024, India
| | - Latha Madhavan
- ICAR-National Bureau of Plant Genetic Resources, Regional Station, Thrissur, Kerala, 680654, India
| | - Sanjeev Gupta
- ICAR-Indian Institute of Pulses Research, Kalyanpur, Kanpur, 208024, India
| | - N P Singh
- ICAR-Indian Institute of Pulses Research, Kalyanpur, Kanpur, 208024, India
| | - Aditya Pratap
- ICAR-Indian Institute of Pulses Research, Kalyanpur, Kanpur, 208024, India.
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Barmukh R, Soren KR, Madugula P, Gangwar P, Shanmugavadivel PS, Bharadwaj C, Konda AK, Chaturvedi SK, Bhandari A, Rajain K, Singh NP, Roorkiwal M, Varshney RK. Construction of a high-density genetic map and QTL analysis for yield, yield components and agronomic traits in chickpea (Cicer arietinum L.). PLoS One 2021; 16:e0251669. [PMID: 33989359 PMCID: PMC8121343 DOI: 10.1371/journal.pone.0251669] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/30/2021] [Indexed: 12/04/2022] Open
Abstract
Unravelling the genetic architecture underlying yield components and agronomic traits is important for enhancing crop productivity. Here, a recombinant inbred line (RIL) population, developed from ICC 4958 and DCP 92–3 cross, was used for constructing linkage map and QTL mapping analysis. The RIL population was genotyped using a high-throughput Axiom®CicerSNP array, which enabled the development of a high-density genetic map consisting of 3,818 SNP markers and spanning a distance of 1064.14 cM. Analysis of phenotyping data for yield, yield components and agronomic traits measured across three years together with genetic mapping data led to the identification of 10 major-effect QTLs and six minor-effect QTLs explaining up to 59.70% phenotypic variance. The major-effect QTLs identified for 100-seed weight, and plant height possessed key genes, such as C3HC4 RING finger protein, pentatricopeptide repeat (PPR) protein, sugar transporter, leucine zipper protein and NADH dehydrogenase, amongst others. The gene ontology studies highlighted the role of these genes in regulating seed weight and plant height in crop plants. The identified genomic regions for yield, yield components, and agronomic traits, and the closely linked markers will help advance genetics research and breeding programs in chickpea.
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Affiliation(s)
- Rutwik Barmukh
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | | | - Praveen Madugula
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | | | | | | | - Sushil K. Chaturvedi
- ICAR-Indian Institute of Pulses Research, Kanpur, UP, India
- Rani Lakshmi Bai Central Agricultural University, Jhansi, India
| | - Aditi Bhandari
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Kritika Rajain
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Narendra Pratap Singh
- ICAR-Indian Institute of Pulses Research, Kanpur, UP, India
- * E-mail: (RKV); (MR); (NPS)
| | - Manish Roorkiwal
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- * E-mail: (RKV); (MR); (NPS)
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- * E-mail: (RKV); (MR); (NPS)
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12
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Bharadwaj C, Tripathi S, Soren KR, Thudi M, Singh RK, Sheoran S, Roorkiwal M, Patil BS, Chitikineni A, Palakurthi R, Vemula A, Rathore A, Kumar Y, Chaturvedi SK, Mondal B, Shanmugavadivel PS, Srivastava AK, Dixit GP, Singh NP, Varshney RK. Introgression of "QTL-hotspot" region enhances drought tolerance and grain yield in three elite chickpea cultivars. THE PLANT GENOME 2021; 14:e20076. [PMID: 33480153 DOI: 10.1002/tpg2.20076] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/10/2020] [Indexed: 05/27/2023]
Abstract
With an aim of enhancing drought tolerance using a marker-assisted backcrossing (MABC) approach, we introgressed the "QTL-hotspot" region from ICC 4958 accession that harbors quantitative trait loci (QTLs) for several drought-tolerance related traits into three elite Indian chickpea (Cicer arietinum L.) cultivars: Pusa 372, Pusa 362, and DCP 92-3. Of eight simple sequence repeat (SSR) markers in the QTL-hotspot region, two to three polymorphic markers were used for foreground selection with respective cross-combinations. A total of 47, 53, and 46 SSRs were used for background selection in case of introgression lines (ILs) developed in genetic backgrounds of Pusa 372, Pusa 362, and DCP 92-3, respectively. In total, 61 ILs (20 BC3 F3 in Pusa 372; 20 BC2 F3 in Pusa 362, and 21 BC3 F3 in DCP 92-3), with >90% recurrent parent genome recovery were developed. Six improved lines in different genetic backgrounds (e.g. BGM 10216 in Pusa 372; BG 3097 and BG 4005 in Pusa 362; IPC(L4-14), IPC(L4-16), and IPC(L19-1) in DCP 92-3) showed better performance than their respective recurrent parents. BGM 10216, with 16% yield gain over Pusa 372, has been released as Pusa Chickpea 10216 by the Central Sub-Committees on Crop Standards, Notification and Release of Varieties of Agricultural Crops, Ministry of Agriculture and Farmers Welfare, Government of India, for commercial cultivation in India. In summary, this study reports introgression of the QTL-hotspot for enhancing yield under rainfed conditions, development of several introgression lines, and release of Pusa Chickpea 10216 developed through molecular breeding in India.
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Affiliation(s)
- Chellapilla Bharadwaj
- Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, Delhi, 110012, India
| | - Shailesh Tripathi
- Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, Delhi, 110012, India
| | - Khela R Soren
- ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur, Uttar Pradesh, 208024, India
| | - Mahendar Thudi
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Rajesh K Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, Delhi, 110012, India
| | - Seema Sheoran
- Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, Delhi, 110012, India
- Present address: ICAR-Indian Institute of Maize Research (ICAR-IIMR), PAU campus, Ludhiana, Punjab, 141004, India
| | - Manish Roorkiwal
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | | | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Ramesh Palakurthi
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Anilkumar Vemula
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Abhishek Rathore
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Yogesh Kumar
- ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur, Uttar Pradesh, 208024, India
| | - Sushil K Chaturvedi
- ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur, Uttar Pradesh, 208024, India
- Present address: Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh, 284003, India
| | - Biswajit Mondal
- ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur, Uttar Pradesh, 208024, India
| | | | - Avinash K Srivastava
- ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur, Uttar Pradesh, 208024, India
| | - Girish P Dixit
- ICAR-All India Coordinated Research Project on Chickpea (AICRP-Chickpea), ICAR-IIPR, Kanpur, Uttar Pradesh, India
| | - Narendra P Singh
- ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur, Uttar Pradesh, 208024, India
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
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13
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Manchikatla PK, Kalavikatte D, Mallikarjuna BP, Palakurthi R, Khan AW, Jha UC, Bajaj P, Singam P, Chitikineni A, Varshney RK, Thudi M. MutMap Approach Enables Rapid Identification of Candidate Genes and Development of Markers Associated With Early Flowering and Enhanced Seed Size in Chickpea ( Cicer arietinum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:688694. [PMID: 34326857 PMCID: PMC8313520 DOI: 10.3389/fpls.2021.688694] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/02/2021] [Indexed: 05/16/2023]
Abstract
Globally terminal drought is one of the major constraints to chickpea (Cicer arietinum L.) production. Early flowering genotypes escape terminal drought, and the increase in seed size compensates for yield losses arising from terminal drought. A MutMap population for early flowering and large seed size was developed by crossing the mutant line ICC4958-M3-2828 with wild-type ICC 4958. Based on the phenotyping of MutMap population, extreme bulks for days to flowering and 100-seed weight were sequenced using Hi-Seq2500 at 10X coverage. On aligning 47.41 million filtered reads to the CDC Frontier reference genome, 31.41 million reads were mapped and 332,395 single nucleotide polymorphisms (SNPs) were called. A reference genome assembly for ICC 4958 was developed replacing these SNPs in particular positions of the CDC Frontier genome. SNPs specific for each mutant bulk ranged from 3,993 to 5,771. We report a single unique genomic region on Ca6 (between 9.76 and 12.96 Mb) harboring 31, 22, 17, and 32 SNPs with a peak of SNP index = 1 for low bulk for flowering time, high bulk for flowering time, high bulk for 100-seed weight, and low bulk for 100-seed weight, respectively. Among these, 22 SNPs are present in 20 candidate genes and had a moderate allelic impact on the genes. Two markers, Ca6EF10509893 for early flowering and Ca6HSDW10099486 for 100-seed weight, were developed and validated using the candidate SNPs. Thus, the associated genes, candidate SNPs, and markers developed in this study are useful for breeding chickpea varieties that mitigate yield losses under drought stress.
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Affiliation(s)
- Praveen Kumar Manchikatla
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - Danamma Kalavikatte
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Bingi Pujari Mallikarjuna
- Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, Regional Research Centre, Dharwad, India
| | - Ramesh Palakurthi
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Aamir W. Khan
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Uday Chand Jha
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Prasad Bajaj
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Prashant Singam
- Department of Genetics, Osmania University, Hyderabad, India
| | - Annapurna Chitikineni
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev K. Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
- *Correspondence: Rajeev K. Varshney, ;
| | - Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, Australia
- Mahendar Thudi,
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14
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Jha UC, Bohra A, Pandey S, Parida SK. Breeding, Genetics, and Genomics Approaches for Improving Fusarium Wilt Resistance in Major Grain Legumes. Front Genet 2020; 11:1001. [PMID: 33193586 PMCID: PMC7644945 DOI: 10.3389/fgene.2020.01001] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/06/2020] [Indexed: 12/29/2022] Open
Abstract
Fusarium wilt (FW) disease is the key constraint to grain legume production worldwide. The projected climate change is likely to exacerbate the current scenario. Of the various plant protection measures, genetic improvement of the disease resistance of crop cultivars remains the most economic, straightforward and environmental-friendly option to mitigate the risk. We begin with a brief recap of the classical genetic efforts that provided first insights into the genetic determinants controlling plant response to different races of FW pathogen in grain legumes. Subsequent technological breakthroughs like sequencing technologies have enhanced our understanding of the genetic basis of both plant resistance and pathogenicity. We present noteworthy examples of targeted improvement of plant resistance using genomics-assisted approaches. In parallel, modern functional genomic tools like RNA-seq are playing a greater role in illuminating the various aspects of plant-pathogen interaction. Further, proteomics and metabolomics have also been leveraged in recent years to reveal molecular players and various signaling pathways and complex networks participating in host-pathogen interaction. Finally, we present a perspective on the challenges and limitations of high-throughput phenotyping and emerging breeding approaches to expeditiously develop FW-resistant cultivars under the changing climate.
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Affiliation(s)
- Uday Chand Jha
- ICAR-Indian Institute of Pulses Research, Uttar Pradesh, India
| | - Abhishek Bohra
- ICAR-Indian Institute of Pulses Research, Uttar Pradesh, India
| | - Shailesh Pandey
- Forest Protection Division, Forest Research Institute, Dehradun, India
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15
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Sab S, Lokesha R, Mannur DM, Somasekhar, Jadhav K, Mallikarjuna BP, C L, Yeri S, Valluri V, Bajaj P, Chitikineni A, Vemula A, Rathore A, Varshney RK, Shankergoud I, Thudi M. Genome-Wide SNP Discovery and Mapping QTLs for Seed Iron and Zinc Concentrations in Chickpea ( Cicer arietinum L.). Front Nutr 2020; 7:559120. [PMID: 33154975 PMCID: PMC7588353 DOI: 10.3389/fnut.2020.559120] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 08/21/2020] [Indexed: 11/16/2022] Open
Abstract
Biofortification through plant breeding is a cost-effective and sustainable approach towards addressing micronutrient malnutrition prevailing across the globe. Screening cultivars for micronutrient content and identification of quantitative trait loci (QTLs)/genes and markers help in the development of biofortified varieties in chickpea (Cicer arietinum L.). With the aim of identifying the genomic regions controlling seed Fe and Zn concentrations, the F2:3 population derived from a cross between MNK-1 and Annigeri 1 was genotyped using genotyping by sequencing approach and evaluated for Fe and Zn concentration. An intraspecific genetic linkage map comprising 839 single nucleotide polymorphisms (SNPs) spanning a total distance of 1,088.04 cM with an average marker density of 1.30 cM was constructed. By integrating the linkage map data with the phenotypic data of the F2:3 population, a total of 11 QTLs were detected for seed Fe concentration on CaLG03, CaLG04, and CaLG05, with phenotypic variation explained ranging from 7.2% (CaqFe3.4) to 13.4% (CaqFe4.2). For seed Zn concentration, eight QTLs were identified on CaLG04, CaLG05, and CaLG08. The QTLs individually explained phenotypic variations ranging between 5.7% (CaqZn8.1) and 13.7% (CaqZn4.3). Three QTLs for seed Fe and Zn concentrations (CaqFe4.4, CaqFe4.5, and CaqZn4.1) were colocated in the "QTL-hotspot" region on CaLG04 that harbors several drought tolerance-related QTLs. We identified genes in the QTL regions that encode iron-sulfur metabolism and zinc-dependent alcohol dehydrogenase activity on CaLG03, iron ion binding oxidoreductase on CaLG04, and zinc-induced facilitator-like protein and ZIP zinc/iron transport family protein on CaLG05. These genomic regions and the associated markers can be used in marker-assisted selection to increase seed Fe and Zn concentrations in agronomically superior chickpea varieties.
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Affiliation(s)
- Syed Sab
- Department of Genetics and Plant Breeding, University of Agricultural Sciences - Raichur (UAS-R), Raichur, India
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Ramappa Lokesha
- Department of Genetics and Plant Breeding, University of Agricultural Sciences - Raichur (UAS-R), Raichur, India
| | - D. M. Mannur
- Department of Genetics and Plant Breeding, University of Agricultural Sciences - Raichur (UAS-R), Raichur, India
| | - Somasekhar
- Department of Genetics and Plant Breeding, University of Agricultural Sciences - Raichur (UAS-R), Raichur, India
| | - Kisan Jadhav
- Department of Genetics and Plant Breeding, University of Agricultural Sciences - Raichur (UAS-R), Raichur, India
| | - Bingi Pujari Mallikarjuna
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Laxuman C
- Zonal Agricultural Research Station, University of Agricultural Sciences - Raichur, Kalaburagi, India
| | - Sharanbasappa Yeri
- Zonal Agricultural Research Station, University of Agricultural Sciences - Raichur, Kalaburagi, India
| | - Vinod Valluri
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Prasad Bajaj
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Annapurna Chitikineni
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - AnilKumar Vemula
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Abhishek Rathore
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev Kumar Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - I. Shankergoud
- Department of Genetics and Plant Breeding, University of Agricultural Sciences - Raichur (UAS-R), Raichur, India
| | - Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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Gaur R, Verma S, Pradhan S, Ambreen H, Bhatia S. A high-density SNP-based linkage map using genotyping-by-sequencing and its utilization for improved genome assembly of chickpea (Cicer arietinum L.). Funct Integr Genomics 2020; 20:763-773. [PMID: 32856221 DOI: 10.1007/s10142-020-00751-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 08/12/2020] [Accepted: 08/18/2020] [Indexed: 01/06/2023]
Abstract
Genotyping-by-sequencing (GBS) allows rapid identification of markers for use in development of linkage maps, which expedite efficient breeding programs. In the present study, we have utilized GBS approach to identify and genotype single-nucleotide polymorphism (SNP) markers in an inter-specific RIL population of Cicer arietinum L. X C. reticulatum. A total of 141,639 raw SNPs were identified using the TASSEL-GBS pipeline. After stringent filtering, 8208 candidate SNPs were identified of which ~ 37% were localized in the intragenic regions followed by genic regions (~ 30%) and intergenic regions (~ 27%). We then utilized 6920 stringent selected SNPs from present study and 6714 SNPs and microsatellite markers available from previous studies for construction of linkage map. The resulting high-density linkage map comprising of eight linkage groups contained 13,590 markers which spanned 1299.14 cM of map length with an average marker density of 0.095 cM. Further, the derived linkage map was used to improve the available assembly of desi chickpea genome by anchoring 443 previously unplaced scaffolds onto eight linkage groups. The present efforts have refined anchoring of the desi chickpea genome assembly to 55.57% of the ~ 520 Mb of assembled desi genome. To the best of our knowledge, the linkage map generated in the present study represents one of the most dense linkage map developed for the crop till date. It will serve as a valuable resource for fine mapping and positional cloning of important quantitative trait loci (QTLs) associated with agronomical traits and also for anchoring and ordering of future genome sequence assemblies.
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Affiliation(s)
- Rashmi Gaur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110067, India
| | - Subodh Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110067, India
| | - Seema Pradhan
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110067, India
| | - Heena Ambreen
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110067, India
| | - Sabhyata Bhatia
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110067, India.
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Roorkiwal M, Bharadwaj C, Barmukh R, Dixit GP, Thudi M, Gaur PM, Chaturvedi SK, Fikre A, Hamwieh A, Kumar S, Sachdeva S, Ojiewo CO, Tar'an B, Wordofa NG, Singh NP, Siddique KHM, Varshney RK. Integrating genomics for chickpea improvement: achievements and opportunities. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1703-1720. [PMID: 32253478 PMCID: PMC7214385 DOI: 10.1007/s00122-020-03584-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 03/18/2020] [Indexed: 05/19/2023]
Abstract
Integration of genomic technologies with breeding efforts have been used in recent years for chickpea improvement. Modern breeding along with low cost genotyping platforms have potential to further accelerate chickpea improvement efforts. The implementation of novel breeding technologies is expected to contribute substantial improvements in crop productivity. While conventional breeding methods have led to development of more than 200 improved chickpea varieties in the past, still there is ample scope to increase productivity. It is predicted that integration of modern genomic resources with conventional breeding efforts will help in the delivery of climate-resilient chickpea varieties in comparatively less time. Recent advances in genomics tools and technologies have facilitated the generation of large-scale sequencing and genotyping data sets in chickpea. Combined analysis of high-resolution phenotypic and genetic data is paving the way for identifying genes and biological pathways associated with breeding-related traits. Genomics technologies have been used to develop diagnostic markers for use in marker-assisted backcrossing programmes, which have yielded several molecular breeding products in chickpea. We anticipate that a sequence-based holistic breeding approach, including the integration of functional omics, parental selection, forward breeding and genome-wide selection, will bring a paradigm shift in development of superior chickpea varieties. There is a need to integrate the knowledge generated by modern genomics technologies with molecular breeding efforts to bridge the genome-to-phenome gap. Here, we review recent advances that have led to new possibilities for developing and screening breeding populations, and provide strategies for enhancing the selection efficiency and accelerating the rate of genetic gain in chickpea.
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Affiliation(s)
- Manish Roorkiwal
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Australia.
| | | | - Rutwik Barmukh
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - Girish P Dixit
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pooran M Gaur
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Asnake Fikre
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Addis Ababa, Ethiopia
| | - Aladdin Hamwieh
- International Center for Agriculture Research in the Dry Areas (ICARDA), Cairo, Egypt
| | - Shiv Kumar
- International Center for Agriculture Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Supriya Sachdeva
- ICAR-Indian Agricultural Research Institute (IARI), Delhi, India
| | - Chris O Ojiewo
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya
| | - Bunyamin Tar'an
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | | | | | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Australia
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Australia.
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18
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Singh CM, Pratap A, Gupta S, Biradar RS, Singh NP. Association mapping for mungbean yellow mosaic India virus resistance in mungbean ( Vigna radiata L. Wilczek). 3 Biotech 2020; 10:33. [PMID: 31988827 DOI: 10.1007/s13205-019-2035-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 12/23/2019] [Indexed: 01/19/2023] Open
Abstract
The present study aimed to detect the marker-trait association of a selected diverse panel of 127 mungbean genotypes against mungbean yellow mosaic India virus (MYMIV). Virus-specific primers pairs viz., AC-abut/AV-abut and BC-abut/BV-abut confirmed the involvement of MYMIV in yellow mosaic disease development and the same was validated through restriction digestion analysis. 256 genome-wide microsatellite markers were screened on a test panel in which 93 polymorphic markers were used in association studies. Population structure analysis led to formation of six distinct subpopulations. 1097 alleles were detected among 127 test genotypes whereas number of alleles ranged 2-22 and PIC values ranged 0.27-0.92%, indicating ample amount of variation at genome level. 15 microsatellite markers were detected as associated with MYMIV resistance, among them three microsatellites explained 11-14% phenotypic variation. The specific regions close to CEDG293, DMB-SSR008 and DMB-SSR059 associated with MYMIV resistance were detected, located on linkage group 2, 4 and 9 and may prove useful in marker-assisted mungbean improvement programme for enhancing MYMIV resistance.
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19
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Pratap A, Das A, Kumar S, Gupta S. Current Perspectives on Introgression Breeding in Food Legumes. FRONTIERS IN PLANT SCIENCE 2020; 11:589189. [PMID: 33552095 PMCID: PMC7858677 DOI: 10.3389/fpls.2020.589189] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/03/2020] [Indexed: 05/22/2023]
Abstract
Food legumes are important for defeating malnutrition and sustaining agri-food systems globally. Breeding efforts in legume crops have been largely confined to the exploitation of genetic variation available within the primary genepool, resulting in narrow genetic base. Introgression as a breeding scheme has been remarkably successful for an array of inheritance and molecular studies in food legumes. Crop wild relatives (CWRs), landraces, and exotic germplasm offer great potential for introgression of novel variation not only to widen the genetic base of the elite genepool for continuous incremental gains over breeding cycles but also to discover the cryptic genetic variation hitherto unexpressed. CWRs also harbor positive quantitative trait loci (QTLs) for improving agronomic traits. However, for transferring polygenic traits, "specialized population concept" has been advocated for transferring QTLs from CWR into elite backgrounds. Recently, introgression breeding has been successful in developing improved cultivars in chickpea (Cicer arietinum), pigeonpea (Cajanus cajan), peanut (Arachis hypogaea), lentil (Lens culinaris), mungbean (Vigna radiata), urdbean (Vigna mungo), and common bean (Phaseolus vulgaris). Successful examples indicated that the usable genetic variation could be exploited by unleashing new gene recombination and hidden variability even in late filial generations. In mungbean alone, distant hybridization has been deployed to develop seven improved commercial cultivars, whereas in urdbean, three such cultivars have been reported. Similarly, in chickpea, three superior cultivars have been developed from crosses between C. arietinum and Cicer reticulatum. Pigeonpea has benefited the most where different cytoplasmic male sterility genes have been transferred from CWRs, whereas a number of disease-resistant germplasm have also been developed in Phaseolus. As vertical gene transfer has resulted in most of the useful gene introgressions of practical importance in food legumes, the horizontal gene transfer through transgenic technology, somatic hybridization, and, more recently, intragenesis also offer promise. The gains through introgression breeding are significant and underline the need of bringing it in the purview of mainstream breeding while deploying tools and techniques to increase the recombination rate in wide crosses and reduce the linkage drag. The resurgence of interest in introgression breeding needs to be capitalized for development of commercial food legume cultivars.
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Affiliation(s)
- Aditya Pratap
- ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Arpita Das
- Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India
| | - Shiv Kumar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat Office, Rabat, Morocco
- *Correspondence: Sanjeev Gupta,
| | - Sanjeev Gupta
- ICAR-Indian Institute of Pulses Research, Kanpur, India
- Shiv Kumar,
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20
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Integrated and Sustainable Management of Fungal Diseases of Chickpea: Current Status and Challenges. Fungal Biol 2020. [DOI: 10.1007/978-3-030-35947-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Ojiewo C, Monyo E, Desmae H, Boukar O, Mukankusi‐Mugisha C, Thudi M, Pandey MK, Saxena RK, Gaur PM, Chaturvedi SK, Fikre A, Ganga Rao NPVR, SameerKumar CV, Okori P, Janila P, Rubyogo JC, Godfree C, Akpo E, Omoigui L, Nkalubo S, Fenta B, Binagwa P, Kilango M, Williams M, Mponda O, Okello D, Chichaybelu M, Miningou A, Bationo J, Sako D, Diallo S, Echekwu C, Umar ML, Oteng‐Frimpong R, Mohammed H, Varshney RK. Genomics, genetics and breeding of tropical legumes for better livelihoods of smallholder farmers. PLANT BREEDING = ZEITSCHRIFT FUR PFLANZENZUCHTUNG 2019; 138:487-499. [PMID: 31787790 PMCID: PMC6876654 DOI: 10.1111/pbr.12554] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 11/04/2017] [Indexed: 05/04/2023]
Abstract
Legumes are important components of sustainable agricultural production, food, nutrition and income systems of developing countries. In spite of their importance, legume crop production is challenged by a number of biotic (diseases and pests) and abiotic stresses (heat, frost, drought and salinity), edaphic factors (associated with soil nutrient deficits) and policy issues (where less emphasis is put on legumes compared to priority starchy staples). Significant research and development work have been done in the past decade on important grain legumes through collaborative bilateral and multilateral projects as well as the CGIAR Research Program on Grain Legumes (CRP-GL). Through these initiatives, genomic resources and genomic tools such as draft genome sequence, resequencing data, large-scale genomewide markers, dense genetic maps, quantitative trait loci (QTLs) and diagnostic markers have been developed for further use in multiple genetic and breeding applications. Also, these mega-initiatives facilitated release of a number of new varieties and also dissemination of on-the-shelf varieties to the farmers. More efforts are needed to enhance genetic gains by reducing the time required in cultivar development through integration of genomics-assisted breeding approaches and rapid generation advancement.
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Affiliation(s)
- Chris Ojiewo
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)NairobiKenya
| | - Emmanuel Monyo
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)NairobiKenya
| | | | - Ousmane Boukar
- International Institute of Tropical Agriculture (IITA)KanoNigeria
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Stanley Nkalubo
- National Agricultural Research Organization (NARO)NamulongeUganda
| | - Berhanu Fenta
- Ethiopian Institute of Agricultural Research (EIAR)MelkassaEthiopia
| | - Papias Binagwa
- Selian Agricultural Research Institute (SARI)ArushaTanzania
| | | | | | | | - David Okello
- National Semi Arid Resources Research Institute (NaSARRI)SorotiUganda
| | | | - Amos Miningou
- Environmental Institute for Agricultural Research (INERA)OuagadougouBurkina Faso
| | - Joseph Bationo
- Environmental Institute for Agricultural Research (INERA)OuagadougouBurkina Faso
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Varshney RK, Ojiewo C, Monyo E. A decade of Tropical Legumes projects: Development and adoption of improved varieties, creation of market-demand to benefit smallholder farmers and empowerment of national programmes in sub-Saharan Africa and South Asia. PLANT BREEDING = ZEITSCHRIFT FUR PFLANZENZUCHTUNG 2019; 138:379-388. [PMID: 31762525 PMCID: PMC6853253 DOI: 10.1111/pbr.12744] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 05/17/2023]
Abstract
This article highlights 12 years (2007-2019) of research, achievements, lessons learned, challenges and gaps in discovery-to-delivery research in legumes emanating from three projects, collectively called Tropical Legumes (TL) with a total investment of about US$ 67 million funded by the Bill & Melinda Gates Foundation. These projects were implemented by three CGIAR centres (ICRISAT, CIAT and IITA) together with 15 national agricultural research system partners in sub-Saharan Africa and South Asia. The TL projects together with some of their precursors and complementary projects from other agencies, facilitated the development of 266 improved legume varieties and the production of about 497,901 tons of certified seeds of the target legume crops in the focus countries. The certified seeds have been planted on about 5.0 million ha by more than 25 million smallholder farmers in the 15 countries and beyond, producing about 6.1 million tons of grain worth US$ 3.2 billion. Furthermore, the projects also trained 52 next generation scientists that included 10 women, by supporting 34 Masters degrees and 18 PhD degrees.
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Affiliation(s)
- Rajeev K. Varshney
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | - Chris Ojiewo
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)NairobiKenya
| | - Emmanuel Monyo
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)NairobiKenya
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Zwart RS, Thudi M, Channale S, Manchikatla PK, Varshney RK, Thompson JP. Resistance to Plant-Parasitic Nematodes in Chickpea: Current Status and Future Perspectives. FRONTIERS IN PLANT SCIENCE 2019; 10:966. [PMID: 31428112 PMCID: PMC6689962 DOI: 10.3389/fpls.2019.00966] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 07/10/2019] [Indexed: 06/10/2023]
Abstract
Plant-parasitic nematodes constrain chickpea (Cicer arietinum) production, with annual yield losses estimated to be 14% of total global production. Nematode species causing significant economic damage in chickpea include root-knot nematodes (Meloidogyne artiella, M. incognita, and M. javanica), cyst nematode (Heterodera ciceri), and root-lesion nematode (Pratylenchus thornei). Reduced functionality of roots from nematode infestation leads to water stress and nutrient deficiency, which in turn lead to poor plant growth and reduced yield. Integration of resistant crops with appropriate agronomic practices is recognized as the safest and most practical, economic and effective control strategy for plant-parasitic nematodes. However, breeding for resistance to plant-parasitic nematodes has numerous challenges that originate from the narrow genetic diversity of the C. arietinum cultigen. While levels of resistance to M. artiella, H. ciceri, and P. thornei have been identified in wild Cicer species that are superior to resistance levels in the C. arietinum cultigen, barriers to interspecific hybridization restrict the use of these crop wild relatives, as sources of nematode resistance. Wild Cicer species of the primary genepool, C. reticulatum and C. echinospermum, are the only species that have been used to introgress resistance genes into the C. arietinum cultigen. The availability of genomic resources, including genome sequence and re-sequence information, the chickpea reference set and mini-core collections, and new wild Cicer collections, provide unprecedented opportunities for chickpea improvement. This review surveys progress in the identification of novel genetic sources of nematode resistance in international germplasm collections and recommends genome-assisted breeding strategies to accelerate introgression of nematode resistance into elite chickpea cultivars.
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Affiliation(s)
- Rebecca S. Zwart
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, QLD, Australia
| | - Mahendar Thudi
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, QLD, Australia
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Sonal Channale
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, QLD, Australia
| | - Praveen K. Manchikatla
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - Rajeev K. Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - John P. Thompson
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, QLD, Australia
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Jain A, Roorkiwal M, Kale S, Garg V, Yadala R, Varshney RK. InDel markers: An extended marker resource for molecular breeding in chickpea. PLoS One 2019; 14:e0213999. [PMID: 30883592 PMCID: PMC6422259 DOI: 10.1371/journal.pone.0213999] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 03/05/2019] [Indexed: 12/03/2022] Open
Abstract
Chickpea is one of the most important food legumes that holds the key to meet rising global food and nutritional demand. In order to deploy molecular breeding approaches in crop improvement programs, user friendly and cost effective marker resources remain prerequisite. The advent of next generation sequencing (NGS) technology has resulted in the generation of several thousands of markers as part of several large scale genome sequencing and re-sequencing initiatives. Very recently, PCR based Insertion-deletions (InDels) are becoming a popular gel based genotyping solution because of their co-dominant, inexpensive, and highly polymorphic nature. With an objective to expand marker resources for genomics assisted breeding (GAB) in chickpea, whole genome re-sequencing data generated on five parental lines of one interspecific (ICC 4958 × PI 489777) and two intra-specific (ICC 283 × ICC 8261 and ICC 4958 × ICC 1882) mapping populations, were used for identification of InDels. A total of 231,658 InDels were identified using Dindel software with default parameters. Further, a total of 8,307 InDels with ≥20 bp size were selected for development of gel based markers, of which primers could be designed for 7,523 (90.56%) markers. On average, markers appeared at a frequency of 1,038 InDels/LG with a maximum number of markers on CaLG04 (1,952 InDels) and minimum on CaLG08 (360 InDels). In order to validate these InDels, a total of 423 primer pairs were randomly selected and tested on the selected parental lines. A high amplification rate of 80% was observed ranging from 46.06 to 58.01% polymorphism rate across parents on 3% agarose gel. This study clearly reflects the usefulness of available sequence data for the development of genome-wide InDels in chickpea that can further contribute and accelerate a wide range of genetic and molecular breeding activities in chickpea.
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Affiliation(s)
- Ankit Jain
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish Roorkiwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- * E-mail: (RKV); (MR)
| | - Sandip Kale
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Gatersleben, Germany
| | - Vanika Garg
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Ramakrishna Yadala
- 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
- * E-mail: (RKV); (MR)
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Abstract
Agricultural scientists face the dual challenge of breeding input-responsive, widely adoptable and climate-resilient varieties of crop plants and developing such varieties at a faster pace. Integrating the gains of genomics with modern-day phenomics will lead to increased breeding efficiency which in turn offers great promise to develop such varieties rapidly. Plant phenotyping techniques have impressively evolved during the last two decades. The low-cost, automated and semi-automated methods for data acquisition, storage and analysis are now available which allow precise quantitative analysis of plant structure and function; and genetic dissection of complex traits. Appropriate plant types can now be quickly developed that respond favorably to low input and resource-limited environments and address the challenges of subsistence agriculture. The present review focuses on the need of systematic, rapid, minimal invasive and low-cost plant phenotyping. It also discusses its evolution to modern day high throughput phenotyping (HTP), traits amenable to HTP, integration of HTP with genomics and the scope of utilizing these tools for crop improvement.
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Varshney RK, Pandey MK, Bohra A, Singh VK, Thudi M, Saxena RK. Toward the sequence-based breeding in legumes in the post-genome sequencing era. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:797-816. [PMID: 30560464 PMCID: PMC6439141 DOI: 10.1007/s00122-018-3252-x] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/27/2018] [Indexed: 05/19/2023]
Abstract
Efficiency of breeding programs of legume crops such as chickpea, pigeonpea and groundnut has been considerably improved over the past decade through deployment of modern genomic tools and technologies. For instance, next-generation sequencing technologies have facilitated availability of genome sequence assemblies, re-sequencing of several hundred lines, development of HapMaps, high-density genetic maps, a range of marker genotyping platforms and identification of markers associated with a number of agronomic traits in these legume crops. Although marker-assisted backcrossing and marker-assisted selection approaches have been used to develop superior lines in several cases, it is the need of the hour for continuous population improvement after every breeding cycle to accelerate genetic gain in the breeding programs. In this context, we propose a sequence-based breeding approach which includes use of independent or combination of parental selection, enhancing genetic diversity of breeding programs, forward breeding for early generation selection, and genomic selection using sequencing/genotyping technologies. Also, adoption of speed breeding technology by generating 4-6 generations per year will be contributing to accelerate genetic gain. While we see a huge potential of the sequence-based breeding to revolutionize crop improvement programs in these legumes, we anticipate several challenges especially associated with high-quality and precise phenotyping at affordable costs, data analysis and management related to improving breeding operation efficiency. Finally, integration of improved seed systems and better agronomic packages with the development of improved varieties by using sequence-based breeding will ensure higher genetic gains in farmers' fields.
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Affiliation(s)
- Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India.
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Abhishek Bohra
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India
| | - Vikas K Singh
- International Rice Research Institute (IRRI), IRRI South Asia Hub, ICRISAT, Hyderabad, 502324, India
| | - Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
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27
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Mannur DM, Babbar A, Thudi M, Sabbavarapu MM, Roorkiwal M, Yeri SB, Bansal VP, Jayalakshmi SK, Singh Yadav S, Rathore A, Chamarthi SK, Mallikarjuna BP, Gaur PM, Varshney RK. Super Annigeri 1 and improved JG 74: two Fusarium wilt-resistant introgression lines developed using marker-assisted backcrossing approach in chickpea ( Cicer arietinum L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2018; 39:2. [PMID: 30631246 PMCID: PMC6308216 DOI: 10.1007/s11032-018-0908-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 11/27/2018] [Indexed: 05/19/2023]
Abstract
Annigeri 1 and JG 74 are elite high yielding desi cultivars of chickpea with medium maturity duration and extensively cultivated in Karnataka and Madhya Pradesh, respectively. Both cultivars, in recent years, have become susceptible to race 4 of Fusarium wilt (FW). To improve Annigeri 1 and JG 74, we introgressed a genomic region conferring resistance against FW race 4 (foc4) through marker-assisted backcrossing using WR 315 as the donor parent. For foreground selection, TA59, TA96, TR19 and TA27 markers were used at Agricultural Research Station, Kalaburagi, while GA16 and TA96 markers were used at Jawaharlal Nehru Krishi Vishwa Vidyalaya, Jabalpur. Background selection using simple sequence repreats (SSRs) for the cross Annigeri 1 × WR 315 in BC1F1 and BC2F1 lines resulted in 76-87% and 90-95% recurrent parent genome recovery, respectively. On the other hand, 90-97% genome was recovered in BC3F1 lines in the case of cross JG 74 × WR 315. Multilocation evaluation of 10 BC2F5 lines derived from Annigeri 1 provided one superior line referred to as Super Annigeri 1 with 8% increase in yield and enhanced disease resistance over Annigeri 1. JG 74315-14, the superior line in JG 74 background, had a yield advantage of 53.5% and 25.6% over the location trial means in Pantnagar and Durgapura locations, respectively, under Initial Varietal Trial of All India Coordinated Research Project on Chickpea. These lines with enhanced resistance and high yield performance are demonstration of successful deployment of molecular breeding to develop superior lines for FW resistance in chickpea.
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Affiliation(s)
- D. M. Mannur
- Agricultural Research Station, University of Agricultural Sciences (UAS)-Raichur, Kalaburagi, Karnataka 585 101 India
| | - Anita Babbar
- Jawaharlal Nehru Krishi Vishwa Vidyalaya (JNKVV), Jabalpur, Madhya Pradesh 482 004 India
| | - Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502 324 India
| | - Murali Mohan Sabbavarapu
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502 324 India
| | - Manish Roorkiwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502 324 India
| | - Sharanabasappa B. Yeri
- Agricultural Research Station, University of Agricultural Sciences (UAS)-Raichur, Kalaburagi, Karnataka 585 101 India
| | - Vijay Prakash Bansal
- Jawaharlal Nehru Krishi Vishwa Vidyalaya (JNKVV), Jabalpur, Madhya Pradesh 482 004 India
| | - S. K. Jayalakshmi
- Agricultural Research Station, University of Agricultural Sciences (UAS)-Raichur, Kalaburagi, Karnataka 585 101 India
| | - Shailendra Singh Yadav
- Jawaharlal Nehru Krishi Vishwa Vidyalaya (JNKVV), Jabalpur, Madhya Pradesh 482 004 India
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502 324 India
| | - Siva K. Chamarthi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502 324 India
| | - Bingi P. Mallikarjuna
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502 324 India
| | - Pooran M. Gaur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502 324 India
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502 324 India
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28
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Abstract
Chickpea is a highly nutritious grain legume crop, widely appreciated as a health food, especially in the Indian subcontinent. The major constraints on chickpea production are biotic (Helicoverpa, bruchid, aphid, ascochyta) and abiotic (drought, heat, salt, cold) stresses, which reduce the yield by up to 90%. Various strategies like conventional breeding, molecular breeding, and modern plant breeding have been used to overcome these problems. Conventionally, breeding programs aim at development of varieties that combine maximum number of traits through inter-specific hybridization, wide hybridization, and hybridization involving more than two parents. Breeding is difficult in this crop because of its self-pollinating nature and limited genetic variation. Recent advances in in vitro culture and gene technologies offer unique opportunities to realize the full potential of chickpea production. However, as of date, no transgenic chickpea variety has been approved for cultivation in the world. In this review, we provide an update on the development of genetically modified chickpea plants, including those resistant to Helicoverpa armigera, Callosobruchus maculatus, Aphis craccivora, as well as to drought and salt stress. The genes utilized for development of resistance against pod borer, bruchid, aphid, drought, and salt tolerance, namely, Bt, alpha amylase inhibitor, ASAL, P5CSF129A, and P5CS, respectively, are discussed.
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Varshney RK, Thudi M, Pandey MK, Tardieu F, Ojiewo C, Vadez V, Whitbread AM, Siddique KHM, Nguyen HT, Carberry PS, Bergvinson D. Accelerating genetic gains in legumes for the development of prosperous smallholder agriculture: integrating genomics, phenotyping, systems modelling and agronomy. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3293-3312. [PMID: 29514298 DOI: 10.1093/jxb/ery088] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 02/22/2018] [Indexed: 05/23/2023]
Abstract
Grain legumes form an important component of the human diet, provide feed for livestock, and replenish soil fertility through biological nitrogen fixation. Globally, the demand for food legumes is increasing as they complement cereals in protein requirements and possess a high percentage of digestible protein. Climate change has enhanced the frequency and intensity of drought stress, posing serious production constraints, especially in rainfed regions where most legumes are produced. Genetic improvement of legumes, like other crops, is mostly based on pedigree and performance-based selection over the past half century. To achieve faster genetic gains in legumes in rainfed conditions, this review proposes the integration of modern genomics approaches, high throughput phenomics, and simulation modelling in support of crop improvement that leads to improved varieties that perform with appropriate agronomy. Selection intensity, generation interval, and improved operational efficiencies in breeding are expected to further enhance the genetic gain in experimental plots. Improved seed access to farmers, combined with appropriate agronomic packages in farmers' fields, will deliver higher genetic gains. Enhanced genetic gains, including not only productivity but also nutritional and market traits, will increase the profitability of farming and the availability of affordable nutritious food especially in developing countries.
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Affiliation(s)
- Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Francois Tardieu
- French National Institute for Agricultural Research (INRA), Monpellier, France
| | - Chris Ojiewo
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya
| | - Vincent Vadez
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Institut de recherche pour le développement (IRD), Montpellier, France
| | - Anthony M Whitbread
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | | | - Peter S Carberry
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - David Bergvinson
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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