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Bithell SL, Asif MA, Backhouse D, Drenth A, Harden S, Hobson K. Selection for Phytophthora Root Rot Resistance in Chickpea Crosses Affects Yield Potential of Chickpea × Cicer echinospermum Backcross Derivatives. PLANTS (BASEL, SWITZERLAND) 2024; 13:1432. [PMID: 38891240 PMCID: PMC11174912 DOI: 10.3390/plants13111432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 06/21/2024]
Abstract
Phytophthora root rot (PRR) of chickpea (Cicer arietinum) caused by Phytophthora medicaginis is an important disease. Partial resistance to PRR is sourced from Cicer echinospermum. In this study, we evaluated if lines with low levels of PRR foliage symptoms in two contrasting recombinant inbred line (RIL) populations parented by chickpea cultivars (Yorker and Rupali) and 04067-81-2-1-1 (C. echinospermum, interspecific breeding line) had a significant drag on yield parameters. For the Yorker × 04067-81-2-1-1 population with the highest level of PRR resistance, in the absence of PRR, low foliage symptom RIL had significantly later flowering and podding, lower grain yields, and lighter seed and shorter plant phenotypes than high foliage symptom RIL. A quantitative trait locus analysis identified significant QTL for flowering, height, 100-seed weight, and yield, and there was a significantly higher frequency of alleles for the negative agronomic traits (i.e., drag) from the 04067-81-2-1-1 parent in low foliage symptom RIL than in high foliage symptom RIL. For the Rupali × 04067-81-2-1-1 population with lower levels of PRR resistance, in the absence of PRR, low foliage symptom RIL had significantly lighter seed and shorter plants than high foliage symptom RIL. Significant QTL were detected, the majority were for the timing of flowering and podding (n = 18), others were for plant height, yield, and 100-seed weight. For this second population, the frequency of alleles for the negative agronomic traits from the 04067-81-2-1-1 parent did not differ between low and high foliage symptom RIL. The 100 seed weight of RIL under moderate PRR disease pressure showed some promise as a yield component trait to identify phenotypes with both high levels of PRR resistance and grain yield potential for further seed number evaluations. We identified that large population sizes are required to enable selection among chickpea × C. echinospermum crosses for high levels of PRR resistance without a significant drag on yield.
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Affiliation(s)
- Sean L. Bithell
- New South Wales Department of Primary Industries, Tamworth, NSW 2340, Australia
| | - Muhammd A. Asif
- Chickpea Breeding Australia, New South Wales Department of Primary Industries, Tamworth Agricultural Institute, Tamworth, NSW 2340, Australia; (M.A.A.)
| | - David Backhouse
- School of Environmental and Rural Sciences, University of New England, Armidale, NSW 2350, Australia;
| | - Andre Drenth
- Centre for Horticultural Science, University of Queensland, Brisbane, QLD 4072, Australia;
| | - Steve Harden
- New South Wales Department of Primary Industries, Tamworth, NSW 2340, Australia
| | - Kristy Hobson
- Chickpea Breeding Australia, New South Wales Department of Primary Industries, Tamworth Agricultural Institute, Tamworth, NSW 2340, Australia; (M.A.A.)
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Malik N, Basu U, Srivastava R, Daware A, Ranjan R, Sharma A, Thakro V, Mohanty JK, Jha UC, Tripathi S, Tyagi AK, Parida SK. Natural alleles of Mediator subunit genes modulate plant height in chickpea. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1271-1292. [PMID: 37671896 DOI: 10.1111/tpj.16423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/04/2023] [Indexed: 09/07/2023]
Abstract
SUMMARYPlant height (PH) is an important plant architectural trait targeted during Green Revolution to enhance crop yields. Identification of genes and natural alleles governing plant height without compromising agronomic performance can fill the lacuna of knowledge connecting ideal plant architecture with maximum achievable yield in chickpea. Through coherent strategy involving genome‐wide association study, QTL/fine mapping, map‐based cloning, molecular haplotyping, and downstream functional genomics, the current study identified two Mediator subunit genes namely, CaMED23 and CaMED5b and their derived natural alleles/haplotypes underlying the major QTLs and trans‐acting eQTLs regulating plant height in chickpea. Differential accumulation of haplotype‐specific transcripts of these two Mediator genes in corresponding haplotype‐introgressed near‐isogenic lines (NILs) correlates negatively with the plant height trait. Quantitative as well as qualitative estimation based on histology, scanning electron microscopy, and histochemical assay unraveled the reduced lengths and cell sizes of internodes along with compromised lignin levels in dwarf/semi‐dwarf chickpea NILs introgressed with superior CaMED23 and CaMED5b gene haplotypes. This observation, supported by global transcriptome profiling‐based diminished expression of various phenylpropanoid pathway genes upstream of lignin biosynthesis in dwarf/semi‐dwarf NILs, essentially links plant height with lignin accumulation. The identified molecular signatures in the Mediator subunit genes can be efficiently utilized to develop desirable dwarf/semi‐dwarf‐type chickpea cultivars without affecting their yield per plant via modulating lignin/phenylpropanoid biosynthesis.
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Affiliation(s)
- Naveen Malik
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, 303002, India
| | - Udita Basu
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rishi Srivastava
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Anurag Daware
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rajeev Ranjan
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Akash Sharma
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Virevol Thakro
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Jitendra K Mohanty
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Uday Chand Jha
- Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India
| | | | - Akhilesh K Tyagi
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Swarup K Parida
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
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Susmitha P, Kumar P, Yadav P, Sahoo S, Kaur G, Pandey MK, Singh V, Tseng TM, Gangurde SS. Genome-wide association study as a powerful tool for dissecting competitive traits in legumes. FRONTIERS IN PLANT SCIENCE 2023; 14:1123631. [PMID: 37645459 PMCID: PMC10461012 DOI: 10.3389/fpls.2023.1123631] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/08/2023] [Indexed: 08/31/2023]
Abstract
Legumes are extremely valuable because of their high protein content and several other nutritional components. The major challenge lies in maintaining the quantity and quality of protein and other nutritional compounds in view of climate change conditions. The global need for plant-based proteins has increased the demand for seeds with a high protein content that includes essential amino acids. Genome-wide association studies (GWAS) have evolved as a standard approach in agricultural genetics for examining such intricate characters. Recent development in machine learning methods shows promising applications for dimensionality reduction, which is a major challenge in GWAS. With the advancement in biotechnology, sequencing, and bioinformatics tools, estimation of linkage disequilibrium (LD) based associations between a genome-wide collection of single-nucleotide polymorphisms (SNPs) and desired phenotypic traits has become accessible. The markers from GWAS could be utilized for genomic selection (GS) to predict superior lines by calculating genomic estimated breeding values (GEBVs). For prediction accuracy, an assortment of statistical models could be utilized, such as ridge regression best linear unbiased prediction (rrBLUP), genomic best linear unbiased predictor (gBLUP), Bayesian, and random forest (RF). Both naturally diverse germplasm panels and family-based breeding populations can be used for association mapping based on the nature of the breeding system (inbred or outbred) in the plant species. MAGIC, MCILs, RIAILs, NAM, and ROAM are being used for association mapping in several crops. Several modifications of NAM, such as doubled haploid NAM (DH-NAM), backcross NAM (BC-NAM), and advanced backcross NAM (AB-NAM), have also been used in crops like rice, wheat, maize, barley mustard, etc. for reliable marker-trait associations (MTAs), phenotyping accuracy is equally important as genotyping. Highthroughput genotyping, phenomics, and computational techniques have advanced during the past few years, making it possible to explore such enormous datasets. Each population has unique virtues and flaws at the genomics and phenomics levels, which will be covered in more detail in this review study. The current investigation includes utilizing elite breeding lines as association mapping population, optimizing the choice of GWAS selection, population size, and hurdles in phenotyping, and statistical methods which will analyze competitive traits in legume breeding.
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Affiliation(s)
- Pusarla Susmitha
- Regional Agricultural Research Station, Acharya N.G. Ranga Agricultural University, Andhra Pradesh, India
| | - Pawan Kumar
- Department of Genetics and Plant Breeding, College of Agriculture, Chaudhary Charan Singh (CCS) Haryana Agricultural University, Hisar, India
| | - Pankaj Yadav
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Rajasthan, India
| | - Smrutishree Sahoo
- Department of Genetics and Plant Breeding, School of Agriculture, Gandhi Institute of Engineering and Technology (GIET) University, Odisha, India
| | - Gurleen Kaur
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Manish K. Pandey
- Department of Genomics, Prebreeding and Bioinformatics, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Varsha Singh
- Department of Plant and Soil Sciences, Mississippi State University, Starkville, MS, United States
| | - Te Ming Tseng
- Department of Plant and Soil Sciences, Mississippi State University, Starkville, MS, United States
| | - Sunil S. Gangurde
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
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Basu U, Parida SK. Restructuring plant types for developing tailor-made crops. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1106-1122. [PMID: 34260135 DOI: 10.1111/pbi.13666] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 05/27/2023]
Abstract
Plants have adapted to different environmental niches by fine-tuning the developmental factors working together to regulate traits. Variations in the developmental factors result in a wide range of quantitative variations in these traits that helped plants survive better. The major developmental pathways affecting plant architecture are also under the control of such pathways. Most notable are the CLAVATA-WUSCHEL pathway regulating shoot apical meristem fate, GID1-DELLA module influencing plant height and tillering, LAZY1-TAC1 module controlling branch/tiller angle and the TFL1-FT determining the floral fate in plants. Allelic variants of these key regulators selected during domestication shaped the crops the way we know them today. There is immense yield potential in the 'ideal plant architecture' of a crop. With the available genome-editing techniques, possibilities are not restricted to naturally occurring variations. Using a transient reprogramming system, one can screen the effect of several developmental gene expressions in novel ecosystems to identify the best targets. We can use the plant's fine-tuning mechanism for customizing crops to specific environments. The process of crop domestication can be accelerated with a proper understanding of these developmental pathways. It is time to step forward towards the next-generation molecular breeding for restructuring plant types in crops ensuring yield stability.
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Affiliation(s)
- Udita Basu
- Genomics-Assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Swarup K Parida
- Genomics-Assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
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Gayacharan, Parida SK, Mondal N, Yadav R, Vishwakarma H, Rana JC. Mining legume germplasm for genetic gains: An Indian perspective. Front Genet 2023; 14:996828. [PMID: 36816034 PMCID: PMC9933516 DOI: 10.3389/fgene.2023.996828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 01/05/2023] [Indexed: 01/24/2023] Open
Abstract
Legumes play a significant role in food and nutritional security and contribute to environmental sustainability. Although legumes are highly beneficial crops, it has not yet been possible to enhance their yield and production to a satisfactory level. Amid a rising population and low yield levels, per capita average legume consumption in India has fallen by 71% over the last 50 years, and this has led to protein-related malnutrition in a large segment of the Indian population, especially women and children. Several factors have hindered attempts to achieve yield enhancement in grain legumes, including biotic and abiotic pressures, a lack of good ideotypes, less amenability to mechanization, poorer responsiveness to fertilizer input, and a poor genetic base. Therefore, there is a need to mine the approximately 0.4 million ex situ collections of legumes that are being conserved in gene banks globally for identification of ideal donors for various traits. The Indian National Gene Bank conserves over 63,000 accessions of legumes belonging to 61 species. Recent initiatives have been undertaken in consortia mode with the aim of unlocking the genetic potential of ex situ collections and conducting large-scale germplasm characterization and evaluation analyses. We assume that large-scale phenotyping integrated with omics-based science will aid the identification of target traits and their use to enhance genetic gains. Additionally, in cases where the genetic base of major legumes is narrow, wild relatives have been evaluated, and these are being exploited through pre-breeding. Thus far, >200 accessions of various legumes have been registered as unique donors for various traits of interest.
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Affiliation(s)
- Gayacharan
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Swarup K. Parida
- DBT-National Institute of Plant Genome Research, New Delhi, India
| | - Nupur Mondal
- Shivaji College, University of Delhi, New Delhi, India
| | - Rashmi Yadav
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | | | - Jai C. Rana
- Alliance of Bioversity International and CIAT, India Office, National Agricultural Science Complex, New Delhi, India
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6
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Kuzbakova M, Khassanova G, Oshergina I, Ten E, Jatayev S, Yerzhebayeva R, Bulatova K, Khalbayeva S, Schramm C, Anderson P, Sweetman C, Jenkins CLD, Soole KL, Shavrukov Y. Height to first pod: A review of genetic and breeding approaches to improve combine harvesting in legume crops. FRONTIERS IN PLANT SCIENCE 2022; 13:948099. [PMID: 36186054 PMCID: PMC9523450 DOI: 10.3389/fpls.2022.948099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/17/2022] [Indexed: 06/16/2023]
Abstract
Height from soil at the base of plant to the first pod (HFP) is an important trait for mechanical harvesting of legume crops. To minimise the loss of pods, the HFP must be higher than that of the blades of most combine harvesters. Here, we review the genetic control, morphology, and variability of HFP in legumes and attempt to unravel the diverse terminology for this trait in the literature. HFP is directly related to node number and internode length but through different mechanisms. The phenotypic diversity and heritability of HFP and their correlations with plant height are very high among studied legumes. Only a few publications describe a QTL analysis where candidate genes for HFP with confirmed gene expression have been mapped. They include major QTLs with eight candidate genes for HFP, which are involved in auxin transport and signal transduction in soybean [Glycine max (L.) Merr.] as well as MADS box gene SOC1 in Medicago trancatula, and BEBT or WD40 genes located nearby in the mapped QTL in common bean (Phaseolus vulgaris L.). There is no information available about simple and efficient markers associated with HFP, which can be used for marker-assisted selection for this trait in practical breeding, which is still required in the nearest future. To our best knowledge, this is the first review to focus on this significant challenge in legume-based cropping systems.
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Affiliation(s)
- Marzhan Kuzbakova
- Faculty of Agronomy, S. Seifullin Kazakh Agro Technical University, Nur-Sultan, Kazakhstan
| | - Gulmira Khassanova
- Faculty of Agronomy, S. Seifullin Kazakh Agro Technical University, Nur-Sultan, Kazakhstan
| | - Irina Oshergina
- A.I. Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan
| | - Evgeniy Ten
- A.I. Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan
| | - Satyvaldy Jatayev
- Faculty of Agronomy, S. Seifullin Kazakh Agro Technical University, Nur-Sultan, Kazakhstan
| | - Raushan Yerzhebayeva
- Kazakh Research Institute of Agriculture and Plant Growing, Almalybak, Kazakhstan
| | - Kulpash Bulatova
- Kazakh Research Institute of Agriculture and Plant Growing, Almalybak, Kazakhstan
| | - Sholpan Khalbayeva
- Kazakh Research Institute of Agriculture and Plant Growing, Almalybak, Kazakhstan
| | - Carly Schramm
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Peter Anderson
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Crystal Sweetman
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Colin L. D. Jenkins
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Kathleen L. Soole
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Yuri Shavrukov
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
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7
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Srungarapu R, Mahendrakar MD, Mohammad LA, Chand U, Jagarlamudi VR, Kondamudi KP, Kudapa H, Samineni S. Genome-Wide Association Analysis Reveals Trait-Linked Markers for Grain Nutrient and Agronomic Traits in Diverse Set of Chickpea Germplasm. Cells 2022; 11:cells11152457. [PMID: 35954301 PMCID: PMC9367858 DOI: 10.3390/cells11152457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/22/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Chickpea is an inexpensive source of protein, minerals, and vitamins to the poor people living in arid and semi-arid regions of Southern Asia and Sub-Saharan Africa. New chickpea cultivars with enhanced levels of protein, Fe and Zn content are a medium-term strategy for supplying essential nutrients for human health and reducing malnutrition. In the current study, a chickpea reference set of 280 accessions, including landraces, breeding lines, and advanced cultivars, was evaluated for grain protein, Fe, Zn content and agronomic traits over two seasons. Using a mid-density 5k SNP array, 4603 highly informative SNPs distributed across the chickpea genome were used for GWAS analysis. Population structure analysis revealed three subpopulations (K = 3). Linkage disequilibrium (LD) was extensive, and LD decay was relatively low. A total of 20 and 46 marker-trait associations (MTAs) were identified for grain nutrient and agronomic traits, respectively, using FarmCPU and BLINK models. Of which seven SNPs for grain protein, twelve for Fe, and one for Zn content were distributed on chromosomes 1, 4, 6, and 7. The marker S4_4477846 on chr4 was found to be co-associated with grain protein over seasons. The markers S1_11613376 and S1_2772537 co-associated with grain Fe content under NSII and pooled seasons and S7_9379786 marker under NSI and pooled seasons. The markers S4_31996956 co-associated with grain Fe and days to maturity. SNP annotation of associated markers were found to be related to gene functions of metal ion binding, transporters, protein kinases, transcription factors, and many more functions involved in plant metabolism along with Fe and protein homeostasis. The identified significant MTAs has potential use in marker-assisted selection for developing nutrient-rich chickpea cultivars after validation in the breeding populations.
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Affiliation(s)
- Rajasekhar Srungarapu
- Accelerated Crop Improvement, Chickpea Breeding, International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
- Department of Molecular Biology and Biotechnology, Acharya N.G. Ranga Agricultural University, Guntur 522034, India
| | - Mahesh Damodhar Mahendrakar
- Accelerated Crop Improvement, Chickpea Breeding, International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
| | - Lal Ahamed Mohammad
- Department of Genetics and Plant Breeding, Acharya N.G. Ranga Agricultural University, Guntur 522034, India
| | - Uttam Chand
- Accelerated Crop Improvement, Chickpea Breeding, International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
| | - Venkata Ramana Jagarlamudi
- Department of Genetics and Plant Breeding, Acharya N.G. Ranga Agricultural University, Guntur 522034, India
| | - Kiran Prakash Kondamudi
- Department of Statistics and Computer Applications, Acharya N.G. Ranga Agricultural University, Guntur 522034, India
| | - Himabindu Kudapa
- Genomics, Pre-Breeding and Bioinformatics, International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
| | - Srinivasan Samineni
- Accelerated Crop Improvement, Chickpea Breeding, International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
- Correspondence:
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Bindra S, Singh I, Gill BS, Grewal SK, Kaur J, Kaur L, Salaria S, Kaur A, Kushwah A, Srinivasan S, Singh S. Inheritance and biochemical basis of yellowing of apical leaves: a unique trait in chickpea (Cicer arietinum L.). J Genet 2021. [DOI: 10.1007/s12041-021-01302-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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9
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Reddy VRP, Das S, Dikshit HK, Mishra GP, Aski M, Meena SK, Singh A, Pandey R, Singh MP, Tripathi K, Gore PG, Priti, Bhagat TK, Kumar S, Nair R, Sharma TR. Genome-Wide Association Analysis for Phosphorus Use Efficiency Traits in Mungbean ( Vigna radiata L. Wilczek) Using Genotyping by Sequencing Approach. FRONTIERS IN PLANT SCIENCE 2020; 11:537766. [PMID: 33193476 PMCID: PMC7658405 DOI: 10.3389/fpls.2020.537766] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 09/18/2020] [Indexed: 10/10/2023]
Abstract
Mungbean (Vigna radiata L. Wilczek) is an annual grain legume crop affected by low availability of phosphorus. Phosphorus deficiency mainly affects the growth and development of plants along with changes in root morphology and increase in root-to-shoot ratio. Deciphering the genetic basis of phosphorus use efficiency (PUE) traits can benefit our understanding of mungbean tolerance to low-phosphorus condition. To address this issue, 144 diverse mungbean genotypes were evaluated for 12 PUE traits under hydroponics with optimum- and low-phosphorus levels. The broad sense heritability of traits ranged from 0.63 to 0.92 and 0.58 to 0.92 under optimum- and low-phosphorus conditions, respectively. This study, reports for the first time such a large number of genome wide Single nucleotide polymorphisms (SNPs) (76,160) in mungbean. Further, genome wide association study was conducted using 55,634 SNPs obtained by genotyping-by-sequencing method. The results indicated that total 136 SNPs shared by both GLM and MLM models were associated with tested PUE traits under different phosphorus regimes. We have identified SNPs with highest p value (-log10(p)) for some traits like, TLA and RDW with p value (-log10(p)) of more than 6.0 at LP/OP and OP condition. We have identified nine SNPs (three for TLA and six for RDW trait) which was found to be present in chromosomes 8, 4, and 7. One SNP present in Vradi07g06230 gene contains zinc finger CCCH domain. In total, 71 protein coding genes were identified, of which 13 genes were found to be putative candidate genes controlling PUE by regulating nutrient uptake and root architectural development pathways in mungbean. Moreover, we identified three potential candidate genes VRADI11G08340, VRADI01G05520, and VRADI04G10750 with missense SNPs in coding sequence region, which results in significant variation in protein structure at tertiary level. The identified SNPs and candidate genes provide the essential information for genetic studies and marker-assisted breeding program for improving low-phosphorus tolerance in mungbean.
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Affiliation(s)
| | - Shouvik Das
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Harsh Kumar Dikshit
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Gyan Prakash Mishra
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Muraleedhar Aski
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Surendra Kumar Meena
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
- Division of Basic Science, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Akanksha Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
- Amity Institute of Organic Agriculture, Amity University, Noida, India
| | - Renu Pandey
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Madan Pal Singh
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Kuldeep Tripathi
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Padmavati Ganpat Gore
- Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Priti
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Shiv Kumar
- Biodiversity and Integrated Gene Management Program, International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
| | | | - Tilak Raj Sharma
- Division of Crop Science, Indian Council of Agricultural Research, New Delhi, India
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Marone D, Rodriguez M, Saia S, Papa R, Rau D, Pecorella I, Laidò G, Pecchioni N, Lafferty J, Rapp M, Longin FH, De Vita P. Genome-Wide Association Mapping of Prostrate/Erect Growth Habit in Winter Durum Wheat. Int J Mol Sci 2020; 21:ijms21020394. [PMID: 31936286 PMCID: PMC7014441 DOI: 10.3390/ijms21020394] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/28/2019] [Accepted: 01/06/2020] [Indexed: 02/08/2023] Open
Abstract
By selecting for prostrate growth habit of the juvenile phase of the cycle, durum wheat cultivars could be developed with improved competitive ability against weeds, and better soil coverage to reduce the soil water lost by evaporation. A panel of 184 durum wheat (Triticum turgidum subsp. durum) genotypes, previously genotyped with DArT-seq markers, was used to perform association mapping analysis of prostrate/erect growth habit trait and to identify candidate genes. Phenotypic data of plant growth habit were recorded during three consecutive growing seasons (2014–2016), two different growth conditions (field trial and greenhouse) and two sowing periods (autumn and spring). Genome-wide association study revealed significant marker-trait associations, twelve of which were specific for a single environment/year, 4 consistent in two environments, and two MTAs for the LSmeans were identified across all environments, on chromosomes 2B and 5A. The co-localization of some MTAs identified in this study with known vernalization and photoperiod genes demonstrated that the sensitivity to vernalization and photoperiod response are actually not only key components of spring/winter growth habit, but they play also an important role in defining the magnitude of the tiller angle during the tillering stage. Many zinc-finger transcription factors, such as C2H2 or CCCH-domain zinc finger proteins, known to be involved in plant growth habit and in leaf angle regulation were found as among the most likely candidate genes. The highest numbers of candidate genes putatively related to the trait were found on chromosomes 3A, 4B, 5A and 6A. Moreover, a bioinformatic approach has been considered to search for functional ortholog genes in wheat by using the sequence of rice and barley tiller angle-related genes. The information generated could be used to improve the understanding of the mechanisms that regulate the prostrate/erect growth habit in wheat and the adaptive potential of durum wheat under resource-limited environmental conditions.
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Affiliation(s)
- Daniela Marone
- Research Centre for Cereal and Industrial Crops, CREA, SS 673, km 25.200, 71122 Foggia, Italy; (D.M.); (S.S.); (I.P.); (G.L.); (N.P.)
| | - Monica Rodriguez
- Department of Agriculture, University of Sassari, Via E. de Nicola, 14, 07100 Sassari, Italy; (M.R.); (D.R.)
- Centro per la Conservazione e Valorizzazione della Biodiversità Vegetale, Università degli Studi di Sassari, SS 127bis, km 28.500 Surigheddu, 07041 Alghero, Italy
| | - Sergio Saia
- Research Centre for Cereal and Industrial Crops, CREA, SS 673, km 25.200, 71122 Foggia, Italy; (D.M.); (S.S.); (I.P.); (G.L.); (N.P.)
- Research Centre for Cereal and Industrial Crops, CREA, SS 11, km 2.500, 13100 Vercelli, Italy
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy;
| | - Domenico Rau
- Department of Agriculture, University of Sassari, Via E. de Nicola, 14, 07100 Sassari, Italy; (M.R.); (D.R.)
| | - Ivano Pecorella
- Research Centre for Cereal and Industrial Crops, CREA, SS 673, km 25.200, 71122 Foggia, Italy; (D.M.); (S.S.); (I.P.); (G.L.); (N.P.)
| | - Giovanni Laidò
- Research Centre for Cereal and Industrial Crops, CREA, SS 673, km 25.200, 71122 Foggia, Italy; (D.M.); (S.S.); (I.P.); (G.L.); (N.P.)
| | - Nicola Pecchioni
- Research Centre for Cereal and Industrial Crops, CREA, SS 673, km 25.200, 71122 Foggia, Italy; (D.M.); (S.S.); (I.P.); (G.L.); (N.P.)
| | - Julia Lafferty
- Saatzucht Donau GesmbH & CoKG, Saatzuchtstrasse 11, A-2301 Probstdorf, Austria;
| | - Matthias Rapp
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstraße 21, 70593 Stuttgart, Germany; (M.R.); (F.H.L.)
| | - Friedrich H. Longin
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstraße 21, 70593 Stuttgart, Germany; (M.R.); (F.H.L.)
| | - Pasquale De Vita
- Research Centre for Cereal and Industrial Crops, CREA, SS 673, km 25.200, 71122 Foggia, Italy; (D.M.); (S.S.); (I.P.); (G.L.); (N.P.)
- Correspondence: ; Tel.: +39-0881-714911
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11
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Ma L, Yi D, Gong W, Gong P, Wang Z. De novo transcriptome characterisation of two auxin-related genes associated with plant growth habit in Astragalus adsurgens Pall. PLANT BIOLOGY (STUTTGART, GERMANY) 2020; 22:3-12. [PMID: 31571396 DOI: 10.1111/plb.13052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/25/2019] [Indexed: 06/10/2023]
Abstract
Astragalus adsurgens Pall., a perennial legume native to China, is commonly used as a forage crop. And it has great value for sustainable development of grasslands in arid and semi arid regions. However, to date, little is known regarding the A. adsurgens genome, and no studies have determined whether it would be possible to improve the germplasm of A. adsurgens through genetic modification. In this study, we used an RNA-seq protocol to generate a de novo transcriptome including 151,516 unigenes of A. adsurgens. We compared the transcriptomes of A. adsurgens having different growth habits (prostrate/erect) and identified 14,133 single nucleotide polymorphism sites (SNP) in 8,139 unigenes. Differential expression gene (DEG) analysis suggested that 10,982 unigenes were up-regulated in the prostrate plant relative to the erect plant, while 10,607 unigenes were down-regulated. Of the 21,589 DEG, Unigene72782_All (LAX4) and CL12494.Contig3_All (TIR1), an auxin transporter gene and an auxin transport inhibitor gene, respectively, were predicted to influence the growth habit of A. adsurgens, which were verified by qRT-PCR in these phenotypes. These results suggest that auxin transport was more active in the prostrate plant than in the erect plant, resulting in asymmetric distribution of auxin that affects the growth habit of A. adsurgens. Overall, this study may provide a basis for future research on key genes in A. adsurgens and may deepen our understanding of the molecular mechanisms regulating plant growth habit.
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Affiliation(s)
- L Ma
- Institute of Animal Sciences, Chinese Academy of Agriculture Sciences, Beijing, China
| | - D Yi
- Institute of Animal Sciences, Chinese Academy of Agriculture Sciences, Beijing, China
| | - W Gong
- Institute of Animal Sciences, Chinese Academy of Agriculture Sciences, Beijing, China
- College of Pratacultural Science, Gansu Agricultural University, Lanzhou, China
| | - P Gong
- Institute of Animal Sciences, Chinese Academy of Agriculture Sciences, Beijing, China
- Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Z Wang
- Institute of Animal Sciences, Chinese Academy of Agriculture Sciences, Beijing, China
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12
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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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13
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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: 7] [Impact Index Per Article: 1.2] [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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