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Mazkirat S, Baitarakova K, Kudaybergenov M, Babissekova D, Bastaubayeva S, Bulatova K, Shavrukov Y. SSR Genotyping and Marker-Trait Association with Yield Components in a Kazakh Germplasm Collection of Chickpea ( Cicer arietinum L.). Biomolecules 2023; 13:1722. [PMID: 38136593 PMCID: PMC10741797 DOI: 10.3390/biom13121722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Genetic diversity and marker-trait association with yield-related components were assessed in 39 chickpea accessions from a germplasm collection with either spring or autumn-sown seeds in South-Eastern Kazakhstan. Chickpea accessions originated from Azerbaijan, Germany, Kazakhstan, Moldova, Russia, Türkiye, Ukraine, Syria, and the International Center for Agricultural Research in the Dry Areas (ICARDA). Eleven SSR markers were used for molecular genotyping. Yield and yield components were evaluated in nine traits in experiments with spring and autumn seed sowing. The number of alleles of polymorphic markers varied from 2 to 11. The greatest polymorphism was found in the studied chickpea genotypes using SSR marker TA22 (11 alleles), while NCPGR6 and NCPGR12 markers were monomorphic. In the studied chickpea accessions, unique alleles of the SSR loci TA14, TA46, TA76s, and TA142 were found that were not previously described by other authors. An analysis of correlation relationships between yield-related traits in chickpea revealed the dependence of yield on plant height, branching, and the setting of a large number of beans. These traits showed maximal values in experiments with chickpea plants from autumn seed sowing. An analysis of the relationship between the SSR markers applied and morphological yield-related traits revealed several informative markers associated with important traits, such as plant height, height to first pod, number of branches, number of productive nodes, number of pods per plant, hundred seed weight, seed weight per plant, and seed yield.
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Affiliation(s)
- Shynar Mazkirat
- Kazakh Research Institute of Agriculture and Plant Growing, Almaty District, Almalybak 040909, Kazakhstan; (K.B.); (M.K.); (D.B.); (S.B.); (K.B.)
| | - Kuralay Baitarakova
- Kazakh Research Institute of Agriculture and Plant Growing, Almaty District, Almalybak 040909, Kazakhstan; (K.B.); (M.K.); (D.B.); (S.B.); (K.B.)
| | - Mukhtar Kudaybergenov
- Kazakh Research Institute of Agriculture and Plant Growing, Almaty District, Almalybak 040909, Kazakhstan; (K.B.); (M.K.); (D.B.); (S.B.); (K.B.)
| | - Dilyara Babissekova
- Kazakh Research Institute of Agriculture and Plant Growing, Almaty District, Almalybak 040909, Kazakhstan; (K.B.); (M.K.); (D.B.); (S.B.); (K.B.)
| | - Sholpan Bastaubayeva
- Kazakh Research Institute of Agriculture and Plant Growing, Almaty District, Almalybak 040909, Kazakhstan; (K.B.); (M.K.); (D.B.); (S.B.); (K.B.)
| | - Kulpash Bulatova
- Kazakh Research Institute of Agriculture and Plant Growing, Almaty District, Almalybak 040909, Kazakhstan; (K.B.); (M.K.); (D.B.); (S.B.); (K.B.)
| | - Yuri Shavrukov
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA 5042, Australia
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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: 5] [Impact Index Per Article: 2.5] [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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Kushwah A, Bhatia D, Singh I, Thudi M, Singh G, Bindra S, Vij S, Gill BS, Bharadwaj C, Singh S, Varshney RK. Identification of stable heat tolerance QTLs using inter-specific recombinant inbred line population derived from GPF 2 and ILWC 292. PLoS One 2021; 16:e0254957. [PMID: 34370732 PMCID: PMC8352073 DOI: 10.1371/journal.pone.0254957] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 07/06/2021] [Indexed: 11/19/2022] Open
Abstract
Heat stress during reproductive stages has been leading to significant yield losses in chickpea (Cicer arietinum L.). With an aim of identifying the genomic regions or QTLs responsible for heat tolerance, 187 F8 recombinant inbred lines (RILs) derived from the cross GPF 2 (heat tolerant) × ILWC 292 (heat sensitive) were evaluated under late-sown irrigated (January-May) and timely-sown irrigated environments (November-April) at Ludhiana and Faridkot in Punjab, India for 13 heat tolerance related traits. The pooled ANOVA for both locations for the traits namely days to germination (DG), days to flowering initiation (DFI), days to 50% flowering (DFF), days to 100% flowering (DHF), plant height (PH), pods per plant (NPP), biomass (BIO), grain yield (YLD), 100-seed weight (HSW), harvest index (HI), membrane permeability index (MPI), relative leaf water content (RLWC) and pollen viability (PV)) showed a highly significant difference in RILs. The phenotyping data coupled with the genetic map comprising of 1365 ddRAD-Seq based SNP markers were used for identifying the QTLs for heat tolerance. Composite interval mapping provided a total of 28 and 23 QTLs, respectively at Ludhiana and Faridkot locations. Of these, 13 consensus QTLs for DG, DFI, DFF, DHF, PH, YLD, and MPI have been identified at both locations. Four QTL clusters containing QTLs for multiple traits were identified on the same genomic region at both locations. Stable QTLs for days to flowering can be one of the major factors for providing heat tolerance as early flowering has an advantage of more seed setting due to a comparatively longer reproductive period. Identified QTLs can be used in genomics-assisted breeding to develop heat stress-tolerant high yielding chickpea cultivars.
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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
| | - Inderjit Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Gurpreet Singh
- Regional Research Station, Faridkot, Punjab Agricultural University, Ludhiana, Punjab, 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
| | - B. S. Gill
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Chellapilla Bharadwaj
- Division of Genetics, ICAR-Indian Institute of Agricultural Research (IARI), New Delhi, India
| | - Sarvjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Rajeev K. Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
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Shin MG, Bulyntsev SV, Chang PL, Korbu LB, Carrasquila-Garcia N, Vishnyakova MA, Samsonova MG, Cook DR, Nuzhdin SV. Multi-trait analysis of domestication genes in Cicer arietinum - Cicer reticulatum hybrids with a multidimensional approach: Modeling wide crosses for crop improvement. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 285:122-131. [PMID: 31203876 DOI: 10.1016/j.plantsci.2019.04.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 04/17/2019] [Accepted: 04/20/2019] [Indexed: 06/09/2023]
Abstract
Domestication and subsequent breeding have eroded genetic diversity in the modern chickpea crop by ˜100-fold. Corresponding reductions to trait variation create the need, and an opportunity, to identify and harness the genetic capacity of wild species for crop improvement. Here we analyze trait segregation in a series of wild x cultivated hybrid populations to delineate the genetic underpinnings of domestication traits. Two species of wild chickpea, C. reticulatum and C. echinospermum, were crossed with the elite, early flowering C. arietinum cultivar ICCV96029. KASP genotyping of F2 parents with an FT-linked molecular marker enabled selection of 284 F3 families with reduced phenological variation: 255 F3 families of C. arietinum x reticulatum (AR) derived from 17 diverse wild parents and 29 F3 families of C. arietinum x echinospermum (AE) from 3 wild parents. The combined 284 lineages were genotyped using a genotyping-by-sequencing strategy and phenotyped for agronomic traits. 50 QTLs in 11 traits were detected from AR and 35 QTLs in 10 traits from the combined data. Using hierarchical clustering to assign traits to six correlated groups and mixed model based multi-trait mapping, four pleiotropic loci were identified. Bayesian analysis further identified four inter-trait relationships controlling the duration of vegetative growth and seed maturation, for which the underlying pleiotropic genes were mapped. A random forest approach was used to explore the most extreme trait differences between AR and AE progenies, identifying traits most characteristic of wild species origin. Knowledge of the genomic basis of traits that segregate in wild-cultivated hybrid populations will facilitate chickpea improvement by linking genetic and phenotypic variation in a quantitative genetic framework.
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Affiliation(s)
- Min-Gyoung Shin
- University of Southern California, Program Quantitative and Computational Biology, Dornsife College of Letters Arts & Science, Los Angeles, CA 90089, USA.
| | - Sergey V Bulyntsev
- Federal Research Center The NI Vavilov All Russian Institute of Plant Genetic Resources, St Petersburg, Russia.
| | - Peter L Chang
- University of Southern California, Program Molecular & Computational Biology, Dornsife College of Letters Arts & Science, Los Angeles, CA 90089, USA; University of California Davis, Department of Plant Pathology, Davis, CA 95616, USA.
| | - Lijalem Balcha Korbu
- University of California Davis, Department of Plant Pathology, Davis, CA 95616, USA; Ethiopian Institute of Agricultural Research, Debre Zeit, Ethiopia.
| | | | - Margarita A Vishnyakova
- Federal Research Center The NI Vavilov All Russian Institute of Plant Genetic Resources, St Petersburg, Russia.
| | - Maria G Samsonova
- Peter the Great St Petersburg Polytechnich University, Department of Applied Mathematics, St Petersburg, Russia.
| | - Douglas R Cook
- University of California Davis, Department of Plant Pathology, Davis, CA 95616, USA.
| | - Sergey V Nuzhdin
- University of Southern California, Program Molecular & Computational Biology, Dornsife College of Letters Arts & Science, Los Angeles, CA 90089, USA; Peter the Great St Petersburg Polytechnich University, Department of Applied Mathematics, St Petersburg, Russia.
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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: 57] [Impact Index Per Article: 11.4] [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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Jha UC. Current advances in chickpea genomics: applications and future perspectives. PLANT CELL REPORTS 2018; 37:947-965. [PMID: 29860584 DOI: 10.1007/s00299-018-2305-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/23/2018] [Indexed: 05/27/2023]
Abstract
Chickpea genomics promises to illuminate our understanding of genome organization, structural variations, evolutionary and domestication-related insights and fundamental biology of legume crops. Unprecedented advancements of next generation sequencing (NGS) technologies have enabled in decoding of multiple chickpea genome sequences and generating huge genomic resources in chickpea both at functional and structural level. This review is aimed to update the current progress of chickpea genomics ranging from high density linkage map development, genome-wide association studies (GWAS), functional genomics resources for various traits, emerging role of abiotic stress responsive coding and non-coding RNAs after the completion of draft chickpea genome sequences. Additionally, the current efforts of whole genome re-sequencing (WGRS) approach of global chickpea germplasm to capture the global genetic diversity existing in the historically released varieties across the world and increasing the resolution of the previously identified candidate gene(s) of breeding importance have been discussed. Thus, the outcomes of these genomics resources will assist in genomics-assisted selection and facilitate breeding of climate-resilient chickpea cultivars for sustainable agriculture.
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Affiliation(s)
- Uday Chand Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India.
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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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Varshney RK, Ribaut JM, Buckler ES, Tuberosa R, Rafalski JA, Langridge P. Can genomics boost productivity of orphan crops? Nat Biotechnol 2012; 30:1172-1176. [PMID: 23222781 DOI: 10.1007/978-3-319-66117-9_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Affiliation(s)
- Rajeev K Varshney
- Center of Excellence in Genomics (CEG), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
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