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Yadava YK, Chaudhary P, Yadav S, Rizvi AH, Kumar T, Srivastava R, Soren KR, Bharadwaj C, Srinivasan R, Singh NK, Jain PK. Genetic mapping of quantitative trait loci associated with drought tolerance in chickpea (Cicer arietinum L.). Sci Rep 2023; 13:17623. [PMID: 37848483 PMCID: PMC10582051 DOI: 10.1038/s41598-023-44990-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/14/2023] [Indexed: 10/19/2023] Open
Abstract
Elucidation of the genetic basis of drought tolerance is vital for genomics-assisted breeding of drought tolerant crop varieties. Here, we used genotyping-by-sequencing (GBS) to identify single nucleotide polymorphisms (SNPs) in recombinant inbred lines (RILs) derived from a cross between a drought tolerant chickpea variety, Pusa 362 and a drought sensitive variety, SBD 377. The GBS identified a total of 35,502 SNPs and subsequent filtering of these resulted in 3237 high-quality SNPs included in the eight linkage groups. Fifty-one percent of these SNPs were located in the genic regions distributed throughout the genome. The high density linkage map has total map length of 1069 cm with an average marker interval of 0.33 cm. The linkage map was used to identify 9 robust and consistent QTLs for four drought related traits viz. membrane stability index, relative water content, seed weight and yield under drought, with percent variance explained within the range of 6.29%-90.68% and LOD scores of 2.64 to 6.38, which were located on five of the eight linkage groups. A genomic region on LG 7 harbors quantitative trait loci (QTLs) explaining > 90% phenotypic variance for membrane stability index, and > 10% PVE for yield. This study also provides the first report of major QTLs for physiological traits such as membrane stability index and relative water content for drought stress in chickpea. A total of 369 putative candidate genes were identified in the 6.6 Mb genomic region spanning these QTLs. In-silico expression profiling based on the available transcriptome data revealed that 326 of these genes were differentially expressed under drought stress. KEGG analysis resulted in reduction of candidate genes from 369 to 99, revealing enrichment in various signaling pathways. Haplotype analysis confirmed 5 QTLs among the initially identified 9 QTLs. Two QTLs, qRWC1.1 and qYLD7.1, were chosen based on high SNP density. Candidate gene-based analysis revealed distinct haplotypes in qYLD7.1 associated with significant phenotypic differences, potentially linked to pathways for secondary metabolite biosynthesis. These identified candidate genes bolster defenses through flavonoids and phenylalanine-derived compounds, aiding UV protection, pathogen resistance, and plant structure.The study provides novel genomic regions and candidate genes which can be utilized in genomics-assisted breeding of superior drought tolerant chickpea cultivars.
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Affiliation(s)
- Yashwant K Yadava
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India
| | - Pooja Chaudhary
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India
| | - Sheel Yadav
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India
| | - Aqeel Hasan Rizvi
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Tapan Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Rachna Srivastava
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - K R Soren
- ICAR-Indian Institute of Pulses Research, Kanpur, 208024, India
| | - C Bharadwaj
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - R Srinivasan
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India
| | - N K Singh
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India
| | - P K Jain
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India.
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Shehzad M, Ditta A, Cai X, Ur Rahman S, Xu Y, Wang K, Zhou Z, Fang L. Identification of salt stress-tolerant candidate genes in the BC 2F 2 population at the seedling stages of G. hirsutum and G. darwinii using NGS-based bulked segregant analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1125805. [PMID: 37465381 PMCID: PMC10350501 DOI: 10.3389/fpls.2023.1125805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/02/2023] [Indexed: 07/20/2023]
Abstract
Salinity is a major threat to the yield and productivity of cotton seedlings. In the present study, we developed a BC2F2 population of cotton plants from Gossypium darwinii (5-7) and Gossypium hirsutum (CCRI 12-4) salt-susceptible parents to identify salt-resistant candidate genes. The Illumina HiSeq™ strategy was used with bulked segregant analysis. Salt-resistant and salt-susceptible DNA bulks were pooled by using 30 plants from a BC2F2 population. Next-generation sequencing (NGS) technology was used for the sequencing of parents and both bulks. Four significant genomic regions were identified: the first genomic region was located on chromosome 18 (1.86 Mb), the second and third genomic regions were on chromosome 25 (1.06 Mb and 1.94 Mb, respectively), and the fourth was on chromosome 8 (1.41 Mb). The reads of bulk1 and bulk2 were aligned to the G. darwinii and G. hirsutum genomes, respectively, leading to the identification of 20,664,007 single-nucleotide polymorphisms (SNPs) and insertions/deletions (indels). After the screening, 6,573 polymorphic markers were obtained after filtration of the candidate regions. The SNP indices in resistant and susceptible bulks and Δ(SNP-index) values of resistant and susceptible bulks were measured. Based on the higher Δ(SNP-index) value, six effective polymorphic SNPs were selected in a different chromosome. Six effective SNPs were linked to five candidate genes in four genomic regions. Further validation of these five candidate genes was carried out using reverse transcription-quantitative polymerase chain reaction (RT-qPCR), resulting in an expression profile that showed two highly upregulated genes in the salt-tolerant species G. darwinii, i.e., Gohir.D05G367800 and Gohir.D12G239100; however, the opposite was shown in G. hirsutum, for which all genes, except one, showed partial expression. The results indicated that Gohir.D05G367800 and Gohir.D12G239100 may be salt-tolerant genes. We are confident that this study could be helpful for the cloning, transformation, and development of salt-resistant cotton varieties.
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Affiliation(s)
- Muhammad Shehzad
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Allah Ditta
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
- Plant Breeding and Genetics Division, Cotton Group, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Punjab, Pakistan
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
- National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, China
| | - Shafeeq Ur Rahman
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
- National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, China
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Liu Fang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
- National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
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Asati R, Tripathi MK, Tiwari S, Yadav RK, Tripathi N. Molecular Breeding and Drought Tolerance in Chickpea. LIFE (BASEL, SWITZERLAND) 2022; 12:life12111846. [PMID: 36430981 PMCID: PMC9698494 DOI: 10.3390/life12111846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/05/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022]
Abstract
Cicer arietinum L. is the third greatest widely planted imperative pulse crop worldwide, and it belongs to the Leguminosae family. Drought is the utmost common abiotic factor on plants, distressing their water status and limiting their growth and development. Chickpea genotypes have the natural ability to fight drought stress using certain strategies viz., escape, avoidance and tolerance. Assorted breeding methods, including hybridization, mutation, and marker-aided breeding, genome sequencing along with omics approaches, could be used to improve the chickpea germplasm lines(s) against drought stress. Root features, for instance depth and root biomass, have been recognized as the greatest beneficial morphological factors for managing terminal drought tolerance in the chickpea. Marker-aided selection, for example, is a genomics-assisted breeding (GAB) strategy that can considerably increase crop breeding accuracy and competence. These breeding technologies, notably marker-assisted breeding, omics, and plant physiology knowledge, underlined the importance of chickpea breeding and can be used in future crop improvement programmes to generate drought-tolerant cultivars(s).
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Affiliation(s)
- Ruchi Asati
- 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
- Correspondence: (M.K.T.); (N.T.)
| | - 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
| | - Rakesh Kumar Yadav
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Niraj Tripathi
- Directorate of Research Services, Jawaharlal Nehru Agricultural University, Jabalpur 482004, India
- Correspondence: (M.K.T.); (N.T.)
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Kushwah A, Bhatia D, Barmukh R, Singh I, Singh G, Bindra S, Vij S, Chellapilla B, Pratap A, Roorkiwal M, Kumar S, Varshney RK, Singh S. Genetic mapping of QTLs for drought tolerance in chickpea ( Cicer arietinum L.). Front Genet 2022; 13:953898. [PMID: 36061197 PMCID: PMC9437436 DOI: 10.3389/fgene.2022.953898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/05/2022] [Indexed: 01/24/2023] Open
Abstract
Chickpea yield is severely affected by drought stress, which is a complex quantitative trait regulated by multiple small-effect genes. Identifying genomic regions associated with drought tolerance component traits may increase our understanding of drought tolerance mechanisms and assist in the development of drought-tolerant varieties. Here, a total of 187 F8 recombinant inbred lines (RILs) developed from an interspecific cross between drought-tolerant genotype GPF 2 (Cicer arietinum) and drought-sensitive accession ILWC 292 (C. reticulatum) were evaluated to identify quantitative trait loci (QTLs) associated with drought tolerance component traits. A total of 21 traits, including 12 morpho-physiological traits and nine root-related traits, were studied under rainfed and irrigated conditions. Composite interval mapping identified 31 QTLs at Ludhiana and 23 QTLs at Faridkot locations for morphological and physiological traits, and seven QTLs were identified for root-related traits. QTL analysis identified eight consensus QTLs for six traits and five QTL clusters containing QTLs for multiple traits on linkage groups CaLG04 and CaLG06. The identified major QTLs and genomic regions associated with drought tolerance component traits can be introgressed into elite cultivars using genomics-assisted breeding to enhance drought tolerance in chickpea.
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Affiliation(s)
- Ashutosh Kushwah
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Dharminder Bhatia
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Rutwik Barmukh
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Inderjit Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Gurpreet Singh
- Regional Research Station, Punjab Agricultural University, Faridkot, India
| | - Shayla Bindra
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Suruchi Vij
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | | | - Aditya Pratap
- Crop Improvement Division, ICAR- Indian Institute of Pulses Research, Kanpur, India
| | - Manish Roorkiwal
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Shiv Kumar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat Office, Rabat, Morocco
| | - Rajeev K. Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Murdoch’s Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Sarvjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
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Arriagada O, Cacciuttolo F, Cabeza RA, Carrasco B, Schwember AR. A Comprehensive Review on Chickpea ( Cicer arietinum L.) Breeding for Abiotic Stress Tolerance and Climate Change Resilience. Int J Mol Sci 2022; 23:ijms23126794. [PMID: 35743237 PMCID: PMC9223724 DOI: 10.3390/ijms23126794] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 02/05/2023] Open
Abstract
Chickpea is one of the most important pulse crops worldwide, being an excellent source of protein. It is grown under rain-fed conditions averaging yields of 1 t/ha, far from its potential of 6 t/ha under optimum conditions. The combined effects of heat, cold, drought, and salinity affect species productivity. In this regard, several physiological, biochemical, and molecular mechanisms are reviewed to confer tolerance to abiotic stress. A large collection of nearly 100,000 chickpea accessions is the basis of breeding programs, and important advances have been achieved through conventional breeding, such as germplasm introduction, gene/allele introgression, and mutagenesis. In parallel, advances in molecular biology and high-throughput sequencing have allowed the development of specific molecular markers for the genus Cicer, facilitating marker-assisted selection for yield components and abiotic tolerance. Further, transcriptomics, proteomics, and metabolomics have permitted the identification of specific genes, proteins, and metabolites associated with tolerance to abiotic stress of chickpea. Furthermore, some promising results have been obtained in studies with transgenic plants and with the use of gene editing to obtain drought-tolerant chickpea. Finally, we propose some future lines of research that may be useful to obtain chickpea genotypes tolerant to abiotic stress in a scenario of climate change.
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Affiliation(s)
- Osvin Arriagada
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (O.A.); (F.C.)
| | - Felipe Cacciuttolo
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (O.A.); (F.C.)
| | - Ricardo A. Cabeza
- Departamento de Producción Agrícola, Facultad de Ciencias Agrarias, Universidad de Talca, Talca 3460000, Chile;
| | - Basilio Carrasco
- Centro de Estudios en Alimentos Procesados (CEAP), Av. Lircay s/n, Talca 3480094, Chile;
| | - Andrés R. Schwember
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (O.A.); (F.C.)
- Correspondence:
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6
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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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7
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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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Rani A, Devi P, Jha UC, Sharma KD, Siddique KHM, Nayyar H. Developing Climate-Resilient Chickpea Involving Physiological and Molecular Approaches With a Focus on Temperature and Drought Stresses. FRONTIERS IN PLANT SCIENCE 2020; 10:1759. [PMID: 32161601 PMCID: PMC7052492 DOI: 10.3389/fpls.2019.01759] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 12/16/2019] [Indexed: 05/19/2023]
Abstract
Chickpea is one of the most economically important food legumes, and a significant source of proteins. It is cultivated in more than 50 countries across Asia, Africa, Europe, Australia, North America, and South America. Chickpea production is limited by various abiotic stresses (cold, heat, drought, salt, etc.). Being a winter-season crop in northern south Asia and some parts of the Australia, chickpea faces low-temperature stress (0-15°C) during the reproductive stage that causes substantial loss of flowers, and thus pods, to inhibit its yield potential by 30-40%. The winter-sown chickpea in the Mediterranean, however, faces cold stress at vegetative stage. In late-sown environments, chickpea faces high-temperature stress during reproductive and pod filling stages, causing considerable yield losses. Both the low and the high temperatures reduce pollen viability, pollen germination on the stigma, and pollen tube growth resulting in poor pod set. Chickpea also experiences drought stress at various growth stages; terminal drought, along with heat stress at flowering and seed filling can reduce yields by 40-45%. In southern Australia and northern regions of south Asia, lack of chilling tolerance in cultivars delays flowering and pod set, and the crop is usually exposed to terminal drought. The incidences of temperature extremes (cold and heat) as well as inconsistent rainfall patterns are expected to increase in near future owing to climate change thereby necessitating the development of stress-tolerant and climate-resilient chickpea cultivars having region specific traits, which perform well under drought, heat, and/or low-temperature stress. Different approaches, such as genetic variability, genomic selection, molecular markers involving quantitative trait loci (QTLs), whole genome sequencing, and transcriptomics analysis have been exploited to improve chickpea production in extreme environments. Biotechnological tools have broadened our understanding of genetic basis as well as plants' responses to abiotic stresses in chickpea, and have opened opportunities to develop stress tolerant chickpea.
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Affiliation(s)
- Anju Rani
- Department of Botany, Panjab University, Chandigarh, India
| | - Poonam Devi
- Department of Botany, Panjab University, Chandigarh, India
| | - Uday Chand Jha
- Department of Crop Improvement Division, Indian Institute of Pulses Research, Kanpur, India
| | - Kamal Dev Sharma
- Department of Agricultural Biotechnology, Himachal Pradesh Agricultural University, Palampur, India
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, India
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Ortega R, Hecht VFG, Freeman JS, Rubio J, Carrasquilla-Garcia N, Mir RR, Penmetsa RV, Cook DR, Millan T, Weller JL. Altered Expression of an FT Cluster Underlies a Major Locus Controlling Domestication-Related Changes to Chickpea Phenology and Growth Habit. FRONTIERS IN PLANT SCIENCE 2019; 10:824. [PMID: 31333691 PMCID: PMC6616154 DOI: 10.3389/fpls.2019.00824] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 06/07/2019] [Indexed: 05/20/2023]
Abstract
Flowering time is a key trait in breeding and crop evolution, due to its importance for adaptation to different environments and for yield. In the particular case of chickpea, selection for early phenology was essential for the successful transition of this species from a winter to a summer crop. Here, we used genetic and expression analyses in two different inbred populations to examine the genetic control of domestication-related differences in flowering time and growth habit between domesticated chickpea and its wild progenitor Cicer reticulatum. A single major quantitative trait locus for flowering time under short-day conditions [Days To Flower (DTF)3A] was mapped to a 59-gene interval on chromosome three containing a cluster of three FT genes, which collectively showed upregulated expression in domesticated relative to wild parent lines. An equally strong association with growth habit suggests a pleiotropic effect of the region on both traits. These results indicate the likely molecular explanation for the characteristic early flowering of domesticated chickpea, and the previously described growth habit locus Hg. More generally, they point to de-repression of this specific gene cluster as a conserved mechanism for achieving adaptive early phenology in temperate legumes.
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Affiliation(s)
- Raul Ortega
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
| | | | - Jules S. Freeman
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
- Scion, Rotorua, New Zealand
| | - Josefa Rubio
- E. Genomica y Biotecnologia, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), Córdoba, Spain
| | | | - Reyazul Rouf Mir
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - R. Varma Penmetsa
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Douglas R. Cook
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Teresa Millan
- Department of Genetics ETSIAM, University of Córdoba, Córdoba, Spain
| | - James L. Weller
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
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de Camargo AC, Favero BT, Morzelle MC, Franchin M, Alvarez-Parrilla E, de la Rosa LA, Geraldi MV, Maróstica Júnior MR, Shahidi F, Schwember AR. Is Chickpea a Potential Substitute for Soybean? Phenolic Bioactives and Potential Health Benefits. Int J Mol Sci 2019; 20:E2644. [PMID: 31146372 PMCID: PMC6600242 DOI: 10.3390/ijms20112644] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/18/2019] [Accepted: 05/22/2019] [Indexed: 01/07/2023] Open
Abstract
Legume seeds are rich sources of protein, fiber, and minerals. In addition, their phenolic compounds as secondary metabolites render health benefits beyond basic nutrition. Lowering apolipoprotein B secretion from HepG2 cells and decreasing the level of low-density lipoprotein (LDL)-cholesterol oxidation are mechanisms related to the prevention of cardiovascular diseases (CVD). Likewise, low-level chronic inflammation and related disorders of the immune system are clinical predictors of cardiovascular pathology. Furthermore, DNA-damage signaling and repair are crucial pathways to the etiology of human cancers. Along CVD and cancer, the prevalence of obesity and diabetes is constantly increasing. Screening the ability of polyphenols in inactivating digestive enzymes is a good option in pre-clinical studies. In addition, in vivo studies support the role of polyphenols in the prevention and/or management of diabetes and obesity. Soybean, a well-recognized source of phenolic isoflavones, exerts health benefits by decreasing oxidative stress and inflammation related to the above-mentioned chronic ailments. Similar to soybeans, chickpeas are good sources of nutrients and phenolic compounds, especially isoflavones. This review summarizes the potential of chickpea as a substitute for soybean in terms of health beneficial outcomes. Therefore, this contribution may guide the industry in manufacturing functional foods and/or ingredients by using an undervalued feedstock.
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Affiliation(s)
- Adriano Costa de Camargo
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Casilla 306-22, Santiago, Chile.
| | - Bruno Trevenzoli Favero
- University of Copenhagen, Department of Plant and Environmental Sciences, 2630 Taastrup, Denmark.
| | - Maressa Caldeira Morzelle
- Department of Food and Nutrition, Faculty of Nutrition, Federal University of Mato Grosso, Fernando Correa Avenue, P.O. box 2367, Cuiabá, MT 78060-900, Brazil.
| | - Marcelo Franchin
- Department of Physiological Sciences, Piracicaba Dental School, University of Campinas, Piracicaba, SP 13414-903, Brazil.
| | - Emilio Alvarez-Parrilla
- Department of Chemical Biological Sciences, Universidad Autónoma de Ciudad Juárez, Anillo Envolvente del Pronaf y Estocolmo, s/n, Cd, Juárez, Chihuahua 32310, México.
| | - Laura A de la Rosa
- Department of Chemical Biological Sciences, Universidad Autónoma de Ciudad Juárez, Anillo Envolvente del Pronaf y Estocolmo, s/n, Cd, Juárez, Chihuahua 32310, México.
| | - Marina Vilar Geraldi
- Department of Food and Nutrition, University of Campinas-UNICAMP, Campinas, SP 13083-862, Brazil.
| | | | - Fereidoon Shahidi
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada.
| | - Andrés R Schwember
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Casilla 306-22, Santiago, Chile.
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Nadeem M, Li J, Yahya M, Sher A, Ma C, Wang X, Qiu L. Research Progress and Perspective on Drought Stress in Legumes: A Review. Int J Mol Sci 2019; 20:E2541. [PMID: 31126133 PMCID: PMC6567229 DOI: 10.3390/ijms20102541] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/11/2019] [Accepted: 05/22/2019] [Indexed: 12/16/2022] Open
Abstract
Climate change, food shortage, water scarcity, and population growth are some of the threatening challenges being faced in today's world. Drought stress (DS) poses a constant challenge for agricultural crops and has been considered a severe constraint for global agricultural productivity; its intensity and severity are predicted to increase in the near future. Legumes demonstrate high sensitivity to DS, especially at vegetative and reproductive stages. They are mostly grown in the dry areas and are moderately drought tolerant, but severe DS leads to remarkable production losses. The most prominent effects of DS are reduced germination, stunted growth, serious damage to the photosynthetic apparatus, decrease in net photosynthesis, and a reduction in nutrient uptake. To curb the catastrophic effect of DS in legumes, it is imperative to understand its effects, mechanisms, and the agronomic and genetic basis of drought for sustainable management. This review highlights the impact of DS on legumes, mechanisms, and proposes appropriate management approaches to alleviate the severity of water stress. In our discussion, we outline the influence of water stress on physiological aspects (such as germination, photosynthesis, water and nutrient uptake), growth parameters and yield. Additionally, mechanisms, various management strategies, for instance, agronomic practices (planting time and geometry, nutrient management), plant growth-promoting Rhizobacteria and arbuscular mycorrhizal fungal inoculation, quantitative trait loci (QTLs), functional genomics and advanced strategies (CRISPR-Cas9) are also critically discussed. We propose that the integration of several approaches such as agronomic and biotechnological strategies as well as advanced genome editing tools is needed to develop drought-tolerant legume cultivars.
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Affiliation(s)
- Muhammad Nadeem
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.
| | - Jiajia Li
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.
| | - Muhammad Yahya
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Alam Sher
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.
| | - Chuanxi Ma
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.
| | - Xiaobo Wang
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.
| | - Lijuan Qiu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Amalraj A, Taylor J, Bithell S, Li Y, Moore K, Hobson K, Sutton T. Mapping resistance to Phytophthora root rot identifies independent loci from cultivated (Cicer arietinum L.) and wild (Cicer echinospermum P.H. Davis) chickpea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1017-1033. [PMID: 30535647 DOI: 10.1007/s00122-018-3256-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Accepted: 11/30/2018] [Indexed: 05/05/2023]
Abstract
Major QTL for Phytophthora root rot resistance have been identified in three mapping populations with independent sources of resistance contributed by C. echinospermum and C. arietinum. Phytophthora root rot (PRR) caused by the oomycete Phytophthora medicaginis is a major soil-borne disease of chickpea in Australia. With no economic in-crop control of PRR, a genetic approach to improve resistance is the most practical management option. Moderate field resistance has been incorporated in the cultivated C. arietinum variety, Yorker, and a higher level of resistance has been identified in a derivative of wild chickpea (C. echinospermum, interspecific breeding line 04067-81-2-1-1). These genotypes and two other released varieties were used to develop one intra-specific and two interspecific F6-derived recombinant inbred line mapping populations for genetic analysis of resistance. The Yorker × Genesis114 (YG), Rupali × 04067-81-2-1-1 (RB) and Yorker × 04067-81-2-1-1 (YB) populations were genotyped using genotyping-by-sequencing and phenotyped for PRR under three field environments with a mixture of 10 P. medicaginis isolates. Whole-genome QTL analysis identified major QTL QRBprrsi01, QYBprrsi01, QRBprrsi03 and QYBprrsi02 for PRR resistance on chromosomes 3 and 6, in RB and YB populations, respectively, with the resistance source derived from the wild Cicer species. QTL QYGprrsi02 and QYGprrsi03 were also identified on chromosomes 5 and 6 in YG population from C. arietinum. Aligning QTL regions to the corresponding chickpea reference genome suggested that the resistance source from C. arietinum and C. echinospermum may be different. The findings from this study provide tools for marker-assisted selection in chickpea breeding and information to assist the development of populations suitable for fine-mapping of resistance loci to determine the molecular basis for PRR resistance in chickpea.
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Affiliation(s)
- Amritha Amalraj
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA, 5064, Australia
| | - Julian Taylor
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA, 5064, Australia
| | - Sean Bithell
- NSW Department of Primary Industries, 4 Marsden Park Rd, Tamworth, NSW, 2340, Australia
| | - Yongle Li
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA, 5064, Australia
| | - Kevin Moore
- NSW Department of Primary Industries, 4 Marsden Park Rd, Tamworth, NSW, 2340, Australia
| | - Kristy Hobson
- NSW Department of Primary Industries, 4 Marsden Park Rd, Tamworth, NSW, 2340, Australia
| | - Tim Sutton
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA, 5064, Australia.
- South Australian Research and Development Institute, GPO Box 397, Adelaide, SA, 5001, Australia.
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Khan MA, Tong F, Wang W, He J, Zhao T, Gai J. Analysis of QTL-allele system conferring drought tolerance at seedling stage in a nested association mapping population of soybean [Glycine max (L.) Merr.] using a novel GWAS procedure. PLANTA 2018; 248:947-962. [PMID: 29980855 DOI: 10.1007/s00425-018-2952-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/02/2018] [Indexed: 05/20/2023]
Abstract
MAIN CONCLUSION RTM-GWAS identified 111 DT QTLs, 262 alleles with high proportion of QEI and genetic variation accounting for 88.55-95.92% PV in NAM, from which QTL-allele matrices were established and candidate genes annotated. Drought tolerance (DT) is one of the major challenges for world soybean production. A nested association mapping (NAM) population with 403 lines comprising two recombinant inbred line (RIL) populations: M8206 × TongShan and ZhengYang × M8206 was tested for DT using polyethylene-glycol (PEG) treatment under spring and summer environments. The population was sequenced using restriction-site-associated DNA sequencing (RAD-seq) filtered with minor allele frequency (MAF) ≥ 0.01, 55,936 single nucleotide polymorphisms (SNPs) were obtained and organized into 6137 SNP linkage disequilibrium blocks (SNPLDBs). The restricted two-stage multi-locus genome-wide association studies (RTM-GWAS) identified 73 and 38 QTLs with 174 and 88 alleles contributed main effect 40.43 and 26.11% to phenotypic variance (PV) and QTL-environment interaction (QEI) effect 24.64 and 10.35% to PV for relative root length (RRL) and relative shoot length (RSL), respectively. The DT traits were characterized with high proportion of QEI variation (37.52-41.65%), plus genetic variation (46.90-58.40%) in a total of 88.55-95.92% PV. The identified QTLs-alleles were organized into main-effect and QEI-effect QTL-allele matrices, showing the genetic and QEI architecture of the three parents/NAM population. From the matrices, the possible best genotype was predicted to have a weighted average value over two indicators (WAV) of 1.873, while the top ten optimal crosses among RILs with 95th percentile WAV 1.098-1.132, transgressive over the parents (0.651-0.773) but much less than 1.873, implying further pyramiding potential. From the matrices, 134 candidate genes were annotated involved in nine biological processes. The present results provide a novel way for molecular breeding in QTL-allele-based genomic selection for optimal cross selection.
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Affiliation(s)
- Mueen Alam Khan
- Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China
| | - Fei Tong
- Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China
| | - Wubin Wang
- Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China
- Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing, 210095, Jiangsu, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jianbo He
- Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China
- Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing, 210095, Jiangsu, China
| | - Tuanjie Zhao
- Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China
- Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing, 210095, Jiangsu, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Junyi Gai
- Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China.
- Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China.
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing, 210095, Jiangsu, China.
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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Li Y, Ruperao P, Batley J, Edwards D, Khan T, Colmer TD, Pang J, Siddique KHM, Sutton T. Investigating Drought Tolerance in Chickpea Using Genome-Wide Association Mapping and Genomic Selection Based on Whole-Genome Resequencing Data. FRONTIERS IN PLANT SCIENCE 2018; 9:190. [PMID: 29515606 PMCID: PMC5825913 DOI: 10.3389/fpls.2018.00190] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/01/2018] [Indexed: 05/06/2023]
Abstract
Drought tolerance is a complex trait that involves numerous genes. Identifying key causal genes or linked molecular markers can facilitate the fast development of drought tolerant varieties. Using a whole-genome resequencing approach, we sequenced 132 chickpea varieties and advanced breeding lines and found more than 144,000 single nucleotide polymorphisms (SNPs). We measured 13 yield and yield-related traits in three drought-prone environments of Western Australia. The genotypic effects were significant for all traits, and many traits showed highly significant correlations, ranging from 0.83 between grain yield and biomass to -0.67 between seed weight and seed emergence rate. To identify candidate genes, the SNP and trait data were incorporated into the SUPER genome-wide association study (GWAS) model, a modified version of the linear mixed model. We found that several SNPs from auxin-related genes, including auxin efflux carrier protein (PIN3), p-glycoprotein, and nodulin MtN21/EamA-like transporter, were significantly associated with yield and yield-related traits under drought-prone environments. We identified four genetic regions containing SNPs significantly associated with several different traits, which was an indication of pleiotropic effects. We also investigated the possibility of incorporating the GWAS results into a genomic selection (GS) model, which is another approach to deal with complex traits. Compared to using all SNPs, application of the GS model using subsets of SNPs significantly associated with the traits under investigation increased the prediction accuracies of three yield and yield-related traits by more than twofold. This has important implication for implementing GS in plant breeding programs.
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Affiliation(s)
- Yongle Li
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
| | - Pradeep Ruperao
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jacqueline Batley
- School of Biological Sciences, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - David Edwards
- School of Biological Sciences, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Tanveer Khan
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Timothy D. Colmer
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Jiayin Pang
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Tim Sutton
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
- South Australian Research and Development Institute, Adelaide, SA, Australia
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15
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Millán T, Madrid E, Castro P, Gil J, Rubio J. Genetic Mapping and Quantitative Trait Loci. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/978-3-319-66117-9_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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16
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Kaashyap M, Ford R, Bohra A, Kuvalekar A, Mantri N. Improving Salt Tolerance of Chickpea Using Modern Genomics Tools and Molecular Breeding. Curr Genomics 2017; 18:557-567. [PMID: 29204084 PMCID: PMC5684649 DOI: 10.2174/1389202918666170705155252] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 11/28/2016] [Accepted: 12/15/2016] [Indexed: 11/22/2022] Open
Abstract
INTRODUCTION The high protein value, essential minerals, dietary fibre and notable ability to fix atmospheric nitrogen make chickpea a highly remunerative crop, particularly in low-input food production systems. Of the variety of constraints challenging chickpea productivity worldwide, salinity remains of prime concern owing to the intrinsic sensitivity of the crop. In view of the projected expansion of chickpea into arable and salt-stressed land by 2050, increasing attention is being placed on improving the salt tolerance of this crop. Considerable effort is currently underway to address salinity stress and substantial breeding progress is being made despite the seemingly highly-complex and environment-dependent nature of the tolerance trait. CONCLUSION This review aims to provide a holistic view of recent advances in breeding chickpea for salt tolerance. Initially, we focus on the identification of novel genetic resources for salt tolerance via extensive germplasm screening. We then expand on the use of genome-wide and cost-effective techniques to gain new insights into the genetic control of salt tolerance, including the responsive genes/QTL(s), gene(s) networks/cross talk and intricate signalling cascades.
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Affiliation(s)
- Mayank Kaashyap
- School of Science, RMIT University, Melbourne, 3000, Victoria, Australia
| | - Rebecca Ford
- Environmental Futures Research Institute, School of Natural Sciences, Griffith University, Queensland 4111, Australia
| | - Abhishek Bohra
- Crop Improvement Division, Indian Institute of Pulses Research, Kanpur, India
| | - Aniket Kuvalekar
- Interactive Research School for Health Affairs, Bharati Vidyapeeth University, Pune-Satara Road, Pune, Maharashtra, 411043, India
| | - Nitin Mantri
- School of Science, RMIT University, Melbourne, 3000, Victoria, Australia
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Farooq M, Gogoi N, Barthakur S, Baroowa B, Bharadwaj N, Alghamdi SS, Siddique KHM. Drought Stress in Grain Legumes during Reproduction and Grain Filling. JOURNAL OF AGRONOMY AND CROP SCIENCE 2017. [PMID: 0 DOI: 10.1111/jac.12169] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Affiliation(s)
- M. Farooq
- Department of Agronomy; University of Agriculture; Faisalabad Pakistan
- The UWA Institute of Agriculture; The University of Western Australia; Crawley WA Australia
- College of Food and Agricultural Sciences; King Saud University; Riyadh Saudi Arabia
| | - N. Gogoi
- Department of Environmental Science; Tezpur University; Tezpur Assam India
| | - S. Barthakur
- National Research Centre on Plant Biotechnology; Pusa Campus; New Delhi India
| | - B. Baroowa
- Department of Environmental Science; Tezpur University; Tezpur Assam India
| | - N. Bharadwaj
- Department of Environmental Science; Tezpur University; Tezpur Assam India
| | - S. S. Alghamdi
- College of Food and Agricultural Sciences; King Saud University; Riyadh Saudi Arabia
| | - K. H. M. Siddique
- The UWA Institute of Agriculture; The University of Western Australia; Crawley WA Australia
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18
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Singh VK, Khan AW, Jaganathan D, Thudi M, Roorkiwal M, Takagi H, Garg V, Kumar V, Chitikineni A, Gaur PM, Sutton T, Terauchi R, Varshney RK. QTL-seq for rapid identification of candidate genes for 100-seed weight and root/total plant dry weight ratio under rainfed conditions in chickpea. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:2110-2119. [PMID: 27107184 PMCID: PMC5095801 DOI: 10.1111/pbi.12567] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/15/2016] [Accepted: 04/19/2016] [Indexed: 05/18/2023]
Abstract
Terminal drought is a major constraint to chickpea productivity. Two component traits responsible for reduction in yield under drought stress include reduction in seeds size and root length/root density. QTL-seq approach, therefore, was used to identify candidate genomic regions for 100-seed weight (100SDW) and total dry root weight to total plant dry weight ratio (RTR) under rainfed conditions. Genomewide SNP profiling of extreme phenotypic bulks from the ICC 4958 × ICC 1882 population identified two significant genomic regions, one on CaLG01 (1.08 Mb) and another on CaLG04 (2.7 Mb) linkage groups for 100SDW. Similarly, one significant genomic region on CaLG04 (1.10 Mb) was identified for RTR. Comprehensive analysis revealed four and five putative candidate genes associated with 100SDW and RTR, respectively. Subsequently, two genes (Ca_04364 and Ca_04607) for 100SDW and one gene (Ca_04586) for RTR were validated using CAPS/dCAPS markers. Identified candidate genomic regions and genes may be useful for molecular breeding for chickpea improvement.
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Affiliation(s)
- Vikas K Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Aamir W Khan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Deepa Jaganathan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - Mahendar Thudi
- 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
| | - Hiroki Takagi
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Vanika Garg
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - Vinay Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Annapurna Chitikineni
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pooran M Gaur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Tim Sutton
- South Australian Research and Development Institute, Adelaide, Australia
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, Australia
| | | | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- School of Plant Biology and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia.
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19
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Identification of candidate genes and natural allelic variants for QTLs governing plant height in chickpea. Sci Rep 2016; 6:27968. [PMID: 27319304 PMCID: PMC4913251 DOI: 10.1038/srep27968] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 05/25/2016] [Indexed: 01/02/2023] Open
Abstract
In the present study, molecular mapping of high-resolution plant height QTLs was performed by integrating 3625 desi genome-derived GBS (genotyping-by-sequencing)-SNPs on an ultra-high resolution intra-specific chickpea genetic linkage map (dwarf/semi-dwarf desi cv. ICC12299 x tall kabuli cv. ICC8261). The identified six major genomic regions harboring six robust QTLs (11.5-21.3 PVE), associated with plant height, were mapped within <0.5 cM average marker intervals on six chromosomes. Five SNPs-containing genes tightly linked to the five plant height QTLs, were validated based upon their high potential for target trait association (12.9-20.8 PVE) in 65 desi and kabuli chickpea accessions. The vegetative tissue-specific expression, including higher differential up-regulation (>5-fold) of five genes especially in shoot, young leaf, shoot apical meristem of tall mapping parental accession (ICC8261) as compared to that of dwarf/semi-dwarf parent (ICC12299) was apparent. Overall, combining high-resolution QTL mapping with genetic association analysis and differential expression profiling, delineated natural allelic variants in five candidate genes (encoding cytochrome-c-biosynthesis protein, malic oxidoreductase, NADH dehydrogenase iron-sulfur protein, expressed protein and bZIP transcription factor) regulating plant height in chickpea. These molecular tags have potential to dissect complex plant height trait and accelerate marker-assisted genetic enhancement for developing cultivars with desirable plant height ideotypes in chickpea.
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20
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High-density linkage map construction and mapping of seed trait QTLs in chickpea (Cicer arietinum L.) using Genotyping-by-Sequencing (GBS). Sci Rep 2015; 5:17512. [PMID: 26631981 PMCID: PMC4668357 DOI: 10.1038/srep17512] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/30/2015] [Indexed: 12/18/2022] Open
Abstract
This study reports the use of Genotyping-by-Sequencing (GBS) for large-scale SNP discovery and simultaneous genotyping of recombinant inbred lines (RILs) of an intra-specific mapping population of chickpea contrasting for seed traits. A total of 119,672 raw SNPs were discovered, which after stringent filtering revealed 3,977 high quality SNPs of which 39.5% were present in genic regions. Comparative analysis using physically mapped marker loci revealed a higher degree of synteny with Medicago in comparison to soybean. The SNP genotyping data was utilized to construct one of the most saturated intra-specific genetic linkage maps of chickpea having 3,363 mapped positions including 3,228 SNPs on 8 linkage groups spanning 1006.98 cM at an average inter marker distance of 0.33 cM. The map was utilized to identify 20 quantitative trait loci (QTLs) associated with seed traits accounting for phenotypic variations ranging from 9.97% to 29.71%. Analysis of the genomic sequence corresponding to five robust QTLs led to the identification of 684 putative candidate genes whose expression profiling revealed that 101 genes exhibited seed specific expression. The integrated approach utilizing the identified QTLs along with the available genome and transcriptome could serve as a platform for candidate gene identification for molecular breeding of chickpea.
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21
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Kale SM, Jaganathan D, Ruperao P, Chen C, Punna R, Kudapa H, Thudi M, Roorkiwal M, Katta MA, Doddamani D, Garg V, Kishor PBK, Gaur PM, Nguyen HT, Batley J, Edwards D, Sutton T, Varshney RK. Prioritization of candidate genes in "QTL-hotspot" region for drought tolerance in chickpea (Cicer arietinum L.). Sci Rep 2015; 5:15296. [PMID: 26478518 PMCID: PMC4609953 DOI: 10.1038/srep15296] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 09/22/2015] [Indexed: 01/20/2023] Open
Abstract
A combination of two approaches, namely QTL analysis and gene enrichment analysis were used to identify candidate genes in the “QTL-hotspot” region for drought tolerance present on the Ca4 pseudomolecule in chickpea. In the first approach, a high-density bin map was developed using 53,223 single nucleotide polymorphisms (SNPs) identified in the recombinant inbred line (RIL) population of ICC 4958 (drought tolerant) and ICC 1882 (drought sensitive) cross. QTL analysis using recombination bins as markers along with the phenotyping data for 17 drought tolerance related traits obtained over 1–5 seasons and 1–5 locations split the “QTL-hotspot” region into two subregions namely “QTL-hotspot_a” (15 genes) and “QTL-hotspot_b” (11 genes). In the second approach, gene enrichment analysis using significant marker trait associations based on SNPs from the Ca4 pseudomolecule with the above mentioned phenotyping data, and the candidate genes from the refined “QTL-hotspot” region showed enrichment for 23 genes. Twelve genes were found common in both approaches. Functional validation using quantitative real-time PCR (qRT-PCR) indicated four promising candidate genes having functional implications on the effect of “QTL-hotspot” for drought tolerance in chickpea.
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Affiliation(s)
- Sandip M Kale
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India
| | - Deepa Jaganathan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India.,Osmania University, Department of Genetics, Hyderabad, 500007, India
| | - Pradeep Ruperao
- The University of Western Australia, School of Plant Biology and the Institute of Agriculture, Crawley, 6009, Australia.,University of Queensland, School of Agriculture and Food Science, Queensland, 4072, Australia
| | - Charles Chen
- Oklahoma State University, Department of Biochemistry and Molecular Biology, Stillwater, 74074, USA
| | - Ramu Punna
- Cornell University, Biotechnology Building, Ithaca, 14853, USA
| | - Himabindu Kudapa
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India
| | - Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India
| | - Manish Roorkiwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India
| | - Mohan Avsk Katta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India
| | - Dadakhalandar Doddamani
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India
| | - Vanika Garg
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India
| | - P B Kavi Kishor
- Osmania University, Department of Genetics, Hyderabad, 500007, India
| | - Pooran M Gaur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India
| | - Henry T Nguyen
- University of Missouri, National Center for Soybean Biotechnology and Division of Plant Sciences, Columbia, 65211, USA
| | - Jacqueline Batley
- The University of Western Australia, School of Plant Biology and the Institute of Agriculture, Crawley, 6009, Australia
| | - David Edwards
- The University of Western Australia, School of Plant Biology and the Institute of Agriculture, Crawley, 6009, Australia
| | - Tim Sutton
- South Australian Research and Development Institute, Adelaide, 5001, Australia.,University of Adelaide, Australia and School of Agriculture, Adelaide, 5064, Australia
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India.,The University of Western Australia, School of Plant Biology and the Institute of Agriculture, Crawley, 6009, Australia
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22
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Gupta S, Kumar T, Verma S, Bharadwaj C, Bhatia S. Development of gene-based markers for use in construction of the chickpea (Cicer arietinum L.) genetic linkage map and identification of QTLs associated with seed weight and plant height. Mol Biol Rep 2015; 42:1571-80. [PMID: 26446030 DOI: 10.1007/s11033-015-3925-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 10/03/2015] [Indexed: 11/28/2022]
Abstract
Seed weight and plant height are important agronomic traits and contribute to seed yield. The objective of this study was to identify QTLs underlying these traits using an intra-specific mapping population of chickpea. A F11 population of 177 recombinant inbred lines derived from a cross between SBD377 (100-seed weight--48 g and plant height--53 cm) and BGD112 (100-seed weight--15 g and plant height--65 cm) was used. A total of 367 novel EST-derived functional markers were developed which included 187 EST-SSRs, 130 potential intron polymorphisms (PIPs) and 50 expressed sequence tag polymorphisms (ESTPs). Along with these, 590 previously published markers including 385 EST-based markers and 205 genomic SSRs were utilized. Of the 957 markers tested for analysis of parental polymorphism between the two parents of the mapping population, 135 (14.64%) were found to be polymorphic. Of these, 131 polymorphic markers could be mapped to the 8 linkage groups. The linkage map had a total length of 1140.54 cM with an average marker density of 8.7 cM. The map was further used for QTL identification using composite interval mapping method (CIM). Two QTLs each for seed weight, qSW-1 and qSW-2 (explaining 11.54 and 19.24% of phenotypic variance, respectively) and plant height, qPH-1 and qPH-2 (explaining 13.98 and 12.17% of phenotypic variance, respectively) were detected. The novel set of genic markers, the intra-specific linkage map and the QTLs identified in the present study will serve as valuable genomic resources in improving the chickpea seed yield using marker-assisted selection (MAS) strategies.
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Affiliation(s)
- Shefali Gupta
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110067, India
| | - Tapan Kumar
- Indian Agricultural Research Institute, Pusa, New Delhi, 110012, India
| | - Subodh Verma
- 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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23
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Diapari M, Sindhu A, Bett K, Deokar A, Warkentin TD, Tar'an B. Genetic diversity and association mapping of iron and zinc concentrations in chickpea (Cicer arietinum L.). Genome 2015; 57:459-68. [PMID: 25434748 DOI: 10.1139/gen-2014-0108] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chickpea (Cicer arietinum L.) is the world's second most important pulse crop after common bean. Chickpea has historically been an important daily staple in the diet of millions of people, especially in the developing countries. Current chickpea breeding programs have mainly been directed toward high yield, biotic and abiotic stress resilience that has increased global production, but less attention has been directed toward improving micronutrient concentrations in seeds. In an effort to develop micronutrient-dense chickpea lines, a study to examine the variability and to identify SNP alleles associated with seed iron and zinc concentrations was conducted using 94 diverse accessions of chickpea. The results indicated that there is substantial variability present in chickpea germplasm for seed iron and zinc concentrations. In the current set of germplasm, zinc is negatively correlated with grain yield across all locations and years; whereas the negative correlation between iron and grain yield was only significant at the Elrose locality. Eight SNP loci associated with iron and (or) zinc concentrations in chickpea seeds were identified. One SNP located on chromosome 1 (chr1) is associated with both iron and zinc concentrations. On chr4, three SNPs associated with zinc concentration and two SNPs for iron concentration were identified. Two additional SNP loci, one on chr6 and the other on chr7, were also found to be associated with iron and zinc concentrations, respectively. The results show potential opportunity for molecular breeding for improvement of seed iron and zinc concentrations in chickpea.
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Affiliation(s)
- Marwan Diapari
- Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
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24
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Jaganathan D, Thudi M, Kale S, Azam S, Roorkiwal M, Gaur PM, Kishor PBK, Nguyen H, Sutton T, Varshney RK. Genotyping-by-sequencing based intra-specific genetic map refines a ''QTL-hotspot" region for drought tolerance in chickpea. Mol Genet Genomics 2014; 290:559-71. [PMID: 25344290 PMCID: PMC4361754 DOI: 10.1007/s00438-014-0932-3] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 09/23/2014] [Indexed: 11/27/2022]
Abstract
To enhance the marker density in the “QTL-hotspot” region, harboring several QTLs for drought tolerance-related traits identified on linkage group 04 (CaLG04) in chickpea recombinant inbred line (RIL) mapping population ICC 4958 × ICC 1882, a genotyping-by-sequencing approach was adopted. In total, 6.24 Gb data from ICC 4958, 5.65 Gb data from ICC 1882 and 59.03 Gb data from RILs were generated, which identified 828 novel single-nucleotide polymorphisms (SNPs) for genetic mapping. Together with these new markers, a high-density intra-specific genetic map was developed that comprised 1,007 marker loci spanning a distance of 727.29 cM. QTL analysis using the extended genetic map along with precise phenotyping data for 20 traits collected over one to seven seasons identified 49 SNP markers in the “QTL-hotspot” region. These efforts have refined the “QTL-hotspot” region to 14 cM. In total, 164 main-effect QTLs including 24 novel QTLs were identified. In addition, 49 SNPs integrated in the “QTL-hotspot” region were converted into cleaved amplified polymorphic sequence (CAPS) and derived CAPS (dCAPS) markers which can be used in marker-assisted breeding.
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Affiliation(s)
- Deepa Jaganathan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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25
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Thudi M, Gaur PM, Krishnamurthy L, Mir RR, Kudapa H, Fikre A, Kimurto P, Tripathi S, Soren KR, Mulwa R, Bharadwaj C, Datta S, Chaturvedi SK, Varshney RK. Genomics-assisted breeding for drought tolerance in chickpea. FUNCTIONAL PLANT BIOLOGY : FPB 2014; 41:1178-1190. [PMID: 32481067 DOI: 10.1071/fp13318] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 05/23/2014] [Indexed: 06/11/2023]
Abstract
Terminal drought is one of the major constraints in chickpea (Cicer arietinum L.), causing more than 50% production losses. With the objective of accelerating genetic understanding and crop improvement through genomics-assisted breeding, a draft genome sequence has been assembled for the CDC Frontier variety. In this context, 544.73Mb of sequence data were assembled, capturing of 73.8% of the genome in scaffolds. In addition, large-scale genomic resources including several thousand simple sequence repeats and several million single nucleotide polymorphisms, high-density diversity array technology (15360 clones) and Illumina GoldenGate assay genotyping platforms, high-density genetic maps and transcriptome assemblies have been developed. In parallel, by using linkage mapping approach, one genomic region harbouring quantitative trait loci for several drought tolerance traits has been identified and successfully introgressed in three leading chickpea varieties (e.g. JG 11, Chefe, KAK 2) by using a marker-assisted backcrossing approach. A multilocation evaluation of these marker-assisted backcrossing lines provided several lines with 10-24% higher yield than the respective recurrent parents.Modern breeding approaches like marker-assisted recurrent selection and genomic selection are being deployed for enhancing drought tolerance in chickpea. Some novel mapping populations such as multiparent advanced generation intercross and nested association mapping populations are also being developed for trait mapping at higher resolution, as well as for enhancing the genetic base of chickpea. Such advances in genomics and genomics-assisted breeding will accelerate precision and efficiency in breeding for stress tolerance in chickpea.
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Affiliation(s)
- Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India
| | - Pooran M Gaur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India
| | - Lakshmanan Krishnamurthy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India
| | - Reyazul R Mir
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India
| | - Himabindu Kudapa
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India
| | - Asnake Fikre
- Ethiopian Institute of Agricultural Research (EIAR), Debre Zeit, PO Box 2003, Ethiopia
| | | | - Shailesh Tripathi
- Indian Agricultural Research Institute (IARI), New Delhi 110 012, India
| | - Khela R Soren
- Indian Institute of Pulses Research (IIPR), Kanpur 208 024, India
| | | | | | - Subhojit Datta
- Indian Institute of Pulses Research (IIPR), Kanpur 208 024, India
| | | | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India
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26
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Deokar AA, Ramsay L, Sharpe AG, Diapari M, Sindhu A, Bett K, Warkentin TD, Tar'an B. Genome wide SNP identification in chickpea for use in development of a high density genetic map and improvement of chickpea reference genome assembly. BMC Genomics 2014; 15:708. [PMID: 25150411 PMCID: PMC4158123 DOI: 10.1186/1471-2164-15-708] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 07/31/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND In the whole genome sequencing, genetic map provides an essential framework for accurate and efficient genome assembly and validation. The main objectives of this study were to develop a high-density genetic map using RAD-Seq (Restriction-site Associated DNA Sequencing) genotyping-by-sequencing (RAD-Seq GBS) and Illumina GoldenGate assays, and to examine the alignment of the current map with the kabuli chickpea genome assembly. RESULTS Genic single nucleotide polymorphisms (SNPs) totaling 51,632 SNPs were identified by 454 transcriptome sequencing of Cicer arietinum and Cicer reticulatum genotypes. Subsequently, an Illumina GoldenGate assay for 1,536 SNPs was developed. A total of 1,519 SNPs were successfully assayed across 92 recombinant inbred lines (RILs), of which 761 SNPs were polymorphic between the two parents. In addition, the next generation sequencing (NGS)-based GBS was applied to the same population generating 29,464 high quality SNPs. These SNPs were clustered into 626 recombination bins based on common segregation patterns. Data from the two approaches were used for the construction of a genetic map using a population derived from an intraspecific cross. The map consisted of 1,336 SNPs including 604 RAD recombination bins and 732 SNPs from Illumina GoldenGate assay. The map covered 653 cM of the chickpea genome with an average distance between adjacent markers of 0.5 cM. To date, this is the most extensive genetic map of chickpea using an intraspecific population. The alignment of the map with the CDC Frontier genome assembly revealed an overall conserved marker order; however, a few local inconsistencies within the Cicer arietinum pseudochromosome 1 (Ca1), Ca5 and Ca8 were detected. The map enabled the alignment of 215 unplaced scaffolds from the CDC Frontier draft genome assembly. The alignment also revealed varying degrees of recombination rates and hotspots across the chickpea genome. CONCLUSIONS A high-density genetic map using RAD-Seq GBS and Illumina GoldenGate assay was developed and aligned with the existing kabuli chickpea draft genome sequence. The analysis revealed an overall conserved marker order, although some localized inversions between draft genome assembly and the genetic map were detected. The current analysis provides an insight of the recombination rates and hotspots across the chickpea genome.
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Affiliation(s)
| | | | | | | | | | | | | | - Bunyamin Tar'an
- Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr, Saskatoon, SK S7N 5A8, Canada.
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