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Mohanty JK, Thakro V, Yadav A, Nayyar H, Dixit GP, Agarwal P, Parida SK, Jha UC. Delineation of genes for a major QTL governing heat stress tolerance in chickpea. PLANT MOLECULAR BIOLOGY 2024; 114:19. [PMID: 38363401 DOI: 10.1007/s11103-024-01421-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 12/08/2023] [Indexed: 02/17/2024]
Abstract
Chickpea (Cicer arietinum) is a cool season grain legume experiencing severe yield loss during heat stress due to the intensifying climate changes and its associated gradual increase of mean temperature. Hence, understanding the genetic architecture regulating heat stress tolerance has emerged as an important trait to be addressed for enhancing yield and productivity of chickpea under heat stress. The present study is intended to identify the major genomic region(s) governing heat stress tolerance in chickpea. For this, an integrated genomics-assisted breeding strategy involving NGS-based high-resolution QTL-seq assay, QTL region-specific association analysis and molecular haplotyping was deployed in a population of 206 mapping individuals and a diversity panel of 217 germplasm accessions of chickpea. This combinatorial strategy delineated a major 156.8 kb QTL genomic region, which was subsequently narrowed-down to a functional candidate gene CaHSFA5 and its natural alleles associated strongly with heat stress tolerance in chickpea. Superior natural alleles and haplotypes delineated from the CaHSFA5 gene have functional significance in regulating heat stress tolerance in chickpea. Histochemical staining, interaction studies along with differential expression profiling of CaHSFA5 and ROS scavenging genes suggest a cross talk between CaHSFA5 with ROS homeostasis pertaining to heat stress tolerance in chickpea. Heterologous gene expression followed by heat stress screening further validated the functional significance of CaHSFA5 for heat stress tolerance. The salient outcomes obtained here can have potential to accelerate multiple translational genomic analysis including marker-assisted breeding and gene editing in order to develop high-yielding heat stress tolerant chickpea varieties.
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Affiliation(s)
- Jitendra K Mohanty
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Virevol Thakro
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Antima Yadav
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, 160014, India
| | - Girish P Dixit
- Indian Institute of Pulses Research (IIPR), Uttar Pradesh, Kanpur, 208024, India
| | - Pinky Agarwal
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Uday Chand Jha
- Indian Institute of Pulses Research (IIPR), Uttar Pradesh, Kanpur, 208024, India.
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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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Basu U, Parida SK. The developmental dynamics in cool season legumes with focus on chickpea. PLANT MOLECULAR BIOLOGY 2023; 111:473-491. [PMID: 37016106 DOI: 10.1007/s11103-023-01340-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/09/2023] [Indexed: 06/19/2023]
Abstract
Chickpea is one of the most widely consumed grain legume world-wide. Advances in next-generation sequencing and genomics tools have led to genetic dissection and identification of potential candidate genes regulating agronomic traits in chickpea. However, the developmental particularities and its potential in reforming the yield and nutritional value remain largely unexplored. Studies in crops such as rice, maize, tomato and pea have highlighted the contribution of key regulator of developmental events in yield related traits. A comprehensive knowledge on the development aspects of a crop can pave way for new vistas to explore. Pea and Medicago are the close relatives of genus Cicer and the basic developmental events in these legumes are similar. However, there are some distinct developmental features in chickpea which hold potential for future crop improvement endeavours. The global chickpea germplasm encompasses wide range of diversities in terms of morphology at both vegetative and reproductive stages. There is an immediate need for understanding the genetic and molecular basis of this diversity and utilizing them for the yield contributing trait improvement. The review discusses some of the key developmental events which have potential in yield enhancement and the lessons which can be learnt from model legumes in this regard.
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Affiliation(s)
- Udita Basu
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, P.O. Box: 10531, New Delhi, 110067, India
| | - Swarup K Parida
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, P.O. Box: 10531, New Delhi, 110067, India.
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4
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Thakro V, Malik N, Basu U, Srivastava R, Narnoliya L, Daware A, Varshney N, Mohanty JK, Bajaj D, Dwivedi V, Tripathi S, Jha UC, Dixit GP, Singh AK, Tyagi AK, Upadhyaya HD, Parida SK. A superior gene allele involved in abscisic acid signaling enhances drought tolerance and yield in chickpea. PLANT PHYSIOLOGY 2023; 191:1884-1912. [PMID: 36477336 PMCID: PMC10022645 DOI: 10.1093/plphys/kiac550] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 10/15/2022] [Indexed: 06/17/2023]
Abstract
Identifying potential molecular tags for drought tolerance is essential for achieving higher crop productivity under drought stress. We employed an integrated genomics-assisted breeding and functional genomics strategy involving association mapping, fine mapping, map-based cloning, molecular haplotyping and transcript profiling in the introgression lines (ILs)- and near isogenic lines (NILs)-based association panel and mapping population of chickpea (Cicer arietinum). This combinatorial approach delineated a bHLH (basic helix-loop-helix) transcription factor, CabHLH10 (Cicer arietinum bHLH10) underlying a major QTL, along with its derived natural alleles/haplotypes governing yield traits under drought stress in chickpea. CabHLH10 binds to a cis-regulatory G-box promoter element to modulate the expression of RD22 (responsive to desiccation 22), a drought/abscisic acid (ABA)-responsive gene (via a trans-expression QTL), and two strong yield-enhancement photosynthetic efficiency (PE) genes. This, in turn, upregulates other downstream drought-responsive and ABA signaling genes, as well as yield-enhancing PE genes, thus increasing plant adaptation to drought with reduced yield penalty. We showed that a superior allele of CabHLH10 introgressed into the NILs improved root and shoot biomass and PE, thereby enhancing yield and productivity during drought without compromising agronomic performance. Furthermore, overexpression of CabHLH10 in chickpea and Arabidopsis (Arabidopsis thaliana) conferred enhanced drought tolerance by improving root and shoot agro-morphological traits. These findings facilitate translational genomics for crop improvement and the development of genetically tailored, climate-resilient, high-yielding chickpea cultivars.
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Affiliation(s)
- Virevol Thakro
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - 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
| | - Laxmi Narnoliya
- 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
| | - Nidhi Varshney
- 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
| | - Deepak Bajaj
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Vikas Dwivedi
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi 110012, India
| | - Uday Chand Jha
- Crop Improvement Division, Indian Institute of Pulses Research (IIPR), Kanpur 208024, India
| | - Girish Prasad Dixit
- Crop Improvement Division, Indian Institute of Pulses Research (IIPR), Kanpur 208024, India
| | - Ashok K Singh
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi 110012, India
| | - Akhilesh K Tyagi
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi 110021, India
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Singh RK, Singh C, Chandana BS, Mahto RK, Patial R, Gupta A, Gahlaut V, Hamwieh A, Upadhyaya HD, Kumar R. Exploring Chickpea Germplasm Diversity for Broadening the Genetic Base Utilizing Genomic Resourses. Front Genet 2022; 13:905771. [PMID: 36035111 PMCID: PMC9416867 DOI: 10.3389/fgene.2022.905771] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 06/24/2022] [Indexed: 12/01/2022] Open
Abstract
Legume crops provide significant nutrition to humans as a source of protein, omega-3 fatty acids as well as specific macro and micronutrients. Additionally, legumes improve the cropping environment by replenishing the soil nitrogen content. Chickpeas are the second most significant staple legume food crop worldwide behind dry bean which contains 17%–24% protein, 41%–51% carbohydrate, and other important essential minerals, vitamins, dietary fiber, folate, β-carotene, anti-oxidants, micronutrients (phosphorus, calcium, magnesium, iron, and zinc) as well as linoleic and oleic unsaturated fatty acids. Despite these advantages, legumes are far behind cereals in terms of genetic improvement mainly due to far less effort, the bottlenecks of the narrow genetic base, and several biotic and abiotic factors in the scenario of changing climatic conditions. Measures are now called for beyond conventional breeding practices to strategically broadening of narrow genetic base utilizing chickpea wild relatives and improvement of cultivars through advanced breeding approaches with a focus on high yield productivity, biotic and abiotic stresses including climate resilience, and enhanced nutritional values. Desirable donors having such multiple traits have been identified using core and mini core collections from the cultivated gene pool and wild relatives of Chickpea. Several methods have been developed to address cross-species fertilization obstacles and to aid in inter-specific hybridization and introgression of the target gene sequences from wild Cicer species. Additionally, recent advances in “Omics” sciences along with high-throughput and precise phenotyping tools have made it easier to identify genes that regulate traits of interest. Next-generation sequencing technologies, whole-genome sequencing, transcriptomics, and differential genes expression profiling along with a plethora of novel techniques like single nucleotide polymorphism exploiting high-density genotyping by sequencing assays, simple sequence repeat markers, diversity array technology platform, and whole-genome re-sequencing technique led to the identification and development of QTLs and high-density trait mapping of the global chickpea germplasm. These altogether have helped in broadening the narrow genetic base of chickpeas.
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Affiliation(s)
| | - Charul Singh
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - B S Chandana
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | - Rohit K Mahto
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | - Ranjana Patial
- Department of Agricultural Sciences, Chandigarh University, Mohali, India
| | - Astha Gupta
- School of Agricultural Sciences, Sharda University, Greater Noida, India
| | - Vijay Gahlaut
- Institute of Himalayan Bioresource Technology (CSIR), Pālampur, India
| | - Aladdin Hamwieh
- International Center for Agriculture Research in the Dry Areas (ICARDA), Giza, Egypt
| | - H D Upadhyaya
- Department of Entomology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, United States
| | - Rajendra Kumar
- Indian Agricultural Research Institute (ICAR), New Delhi, India
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An empirical analysis of mtSSRs: could microsatellite distribution patterns explain the evolution of mitogenomes in plants? Funct Integr Genomics 2021; 22:35-53. [PMID: 34751851 DOI: 10.1007/s10142-021-00815-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 10/19/2022]
Abstract
Microsatellites (SSRs) are tandem repeat sequences in eukaryote genomes, including plant cytoplasmic genomes. The mitochondrial genome (mtDNA) has been shown to vary in size, number, and distribution of SSRs among different plant groups. Thus, SSRs contribute with genomic diversity in mtDNAs. However, the abundance, distribution, and evolutionary significance of SSRs in mtDNA from a wide range of algae and plants have not been explored. In this study, the mtDNAs of 204 plant and algal species were investigated related to the presence of SSRs. The number of SSRs was positively correlated with genome size. Its distribution is dependent on plant and algal groups analyzed, although the cluster analysis indicates the conservation of some common motifs in algal and terrestrial plants that reflect common ancestry of groups. Many SSRs in coding and non-coding regions can be useful for molecular markers. Moreover, mitochondrial SSRs are highly abundant, representing an important source for natural or induced genetic variation, i.e., for biotechnological approaches that can modulate mtDNA gene regulation. Thus, this comparative study increases the understanding of the plant and algal SSR evolution and brings perspectives for further studies.
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Jha UC, Nayyar H, Palakurthi R, Jha R, Valluri V, Bajaj P, Chitikineni A, Singh NP, Varshney RK, Thudi M. Major QTLs and Potential Candidate Genes for Heat Stress Tolerance Identified in Chickpea ( Cicer arietinum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:655103. [PMID: 34381469 PMCID: PMC8350164 DOI: 10.3389/fpls.2021.655103] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/31/2021] [Indexed: 05/15/2023]
Abstract
In the context of climate change, heat stress during the reproductive stages of chickpea (Cicer arietinum L.) leads to significant yield losses. In order to identify the genomic regions responsible for heat stress tolerance, a recombinant inbred line population derived from DCP 92-3 (heat sensitive) and ICCV 92944 (heat tolerant) was genotyped using the genotyping-by-sequencing approach and evaluated for two consecutive years (2017 and 2018) under normal and late sown or heat stress environments. A high-density genetic map comprising 788 single-nucleotide polymorphism markers spanning 1,125 cM was constructed. Using composite interval mapping, a total of 77 QTLs (37 major and 40 minor) were identified for 12 of 13 traits. A genomic region on CaLG07 harbors quantitative trait loci (QTLs) explaining >30% phenotypic variation for days to pod initiation, 100 seed weight, and for nitrogen balance index explaining >10% PVE. In addition, we also reported for the first time major QTLs for proxy traits (physiological traits such as chlorophyll content, nitrogen balance index, normalized difference vegetative index, and cell membrane stability). Furthermore, 32 candidate genes in the QTL regions that encode the heat shock protein genes, heat shock transcription factors, are involved in flowering time regulation as well as pollen-specific genes. The major QTLs reported in this study, after validation, may be useful in molecular breeding for developing heat-tolerant superior lines or varieties.
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Affiliation(s)
- Uday Chand Jha
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, India
| | - Ramesh Palakurthi
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rintu Jha
- Institute of Crop Science, Chinese Academy of Agricultural Science (CAAS), Beijing, China
| | - Vinod Valluri
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Prasad Bajaj
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Annapurna Chitikineni
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Narendra P. Singh
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Rajeev K. Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- University of Southern Queensland, Toowoomba, QLD, Australia
- *Correspondence: Mahendar Thudi
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Basu U, Narnoliya L, Srivastava R, Sharma A, Bajaj D, Daware A, Thakro V, Malik N, Upadhyaya HD, Tripathi S, Hegde VS, Tyagi AK, Parida SK. CLAVATA signaling pathway genes modulating flowering time and flower number in chickpea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2017-2038. [PMID: 30929032 DOI: 10.1007/s00122-019-03335-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 03/20/2019] [Indexed: 05/26/2023]
Abstract
A combinatorial genomic strategy delineated functionally relevant natural allele of a CLAVATA gene and its marker (haplotype)-assisted introgression led to development of the early-flowering chickpea cultivars with high flower number and enhanced yield/productivity. Unraveling the genetic components involved in CLAVATA (CLV) signaling is crucial for modulating important shoot apical meristem (SAM) characteristics and ultimately regulating diverse SAM-regulated agromorphological traits in crop plants. A genome-wide scan identified 142 CLV1-, 28 CLV2- and 6 CLV3-like genes, and their comprehensive genomic constitution and phylogenetic relationships were deciphered in chickpea. The QTL/fine mapping and map-based cloning integrated with high-resolution association analysis identified SNP loci from CaCLV3_01 gene within a major CaqDTF1.1/CaqFN1.1 QTL associated with DTF (days to 50% flowering) and FN (flower number) traits in chickpea, which was further ascertained by quantitative expression profiling. Molecular haplotyping of CaCLV3_01 gene, expressed specifically in SAM, constituted two major haplotypes that differentiated the early-DTF and high-FN chickpea accessions from late-DTF and low-FN. Enhanced accumulation of transcripts of superior CaCLV3_01 gene haplotype and known flowering promoting genes was observed in the corresponding haplotype-introgressed early-DTF and high-FN near-isogenic lines (NILs) with narrow SAM width. The superior haplotype-introgressed NILs exhibited early-flowering, high-FN and enhanced seed yield/productivity without compromising agronomic performance. These delineated molecular signatures can regulate DTF and FN traits through SAM proliferation and differentiation and thereby will be useful for translational genomic study to develop early-flowering cultivars with enhanced yield/productivity.
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Affiliation(s)
- Udita Basu
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Laxmi Narnoliya
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rishi Srivastava
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Akash Sharma
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Anurag Daware
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Virevol Thakro
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Naveen Malik
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - V S Hegde
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Kumar J, Choudhary AK, Gupta DS, Kumar S. Towards Exploitation of Adaptive Traits for Climate-Resilient Smart Pulses. Int J Mol Sci 2019; 20:E2971. [PMID: 31216660 PMCID: PMC6627977 DOI: 10.3390/ijms20122971] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/18/2019] [Accepted: 05/28/2019] [Indexed: 12/20/2022] Open
Abstract
Pulses are the main source of protein and minerals in the vegetarian diet. These are primarily cultivated on marginal lands with few inputs in several resource-poor countries of the world, including several in South Asia. Their cultivation in resource-scarce conditions exposes them to various abiotic and biotic stresses, leading to significant yield losses. Furthermore, climate change due to global warming has increased their vulnerability to emerging new insect pests and abiotic stresses that can become even more serious in the coming years. The changing climate scenario has made it more challenging to breed and develop climate-resilient smart pulses. Although pulses are climate smart, as they simultaneously adapt to and mitigate the effects of climate change, their narrow genetic diversity has always been a major constraint to their improvement for adaptability. However, existing genetic diversity still provides opportunities to exploit novel attributes for developing climate-resilient cultivars. The mining and exploitation of adaptive traits imparting tolerance/resistance to climate-smart pulses can be accelerated further by using cutting-edge approaches of biotechnology such as transgenics, genome editing, and epigenetics. This review discusses various classical and molecular approaches and strategies to exploit adaptive traits for breeding climate-smart pulses.
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Affiliation(s)
- Jitendra Kumar
- Indian Institute of Pulses Research, Kalyanpur, Kanpur 208 024, Uttar Pradesh, India.
| | | | - Debjyoti Sen Gupta
- Indian Institute of Pulses Research, Kalyanpur, Kanpur 208 024, Uttar Pradesh, India.
| | - Shiv Kumar
- Biodiversity and Integrated Gene Management Program, International Centre for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 6299, Rabat-Institute, Rabat, Morocco.
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Sharma A, Basu U, Malik N, Daware A, Thakro V, Narnoliya L, Bajaj D, Tripathi S, Hegde VS, Upadhyaya HD, Tyagi AK, Parida SK. Genome-wide cis-regulatory signatures for modulation of agronomic traits as exemplified by drought yield index (DYI) in chickpea. Funct Integr Genomics 2019; 19:973-992. [PMID: 31177403 DOI: 10.1007/s10142-019-00691-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 05/07/2019] [Accepted: 05/10/2019] [Indexed: 12/26/2022]
Abstract
Developing functional molecular tags from the cis-regulatory sequence components of genes is vital for their deployment in efficient genetic dissection of complex quantitative traits in crop plants including chickpea. The current study identified 431,194 conserved non-coding SNP (CNSNP) from the cis-regulatory element regions of genes which were annotated on a chickpea genome. These genome-wide CNSNP marker resources are made publicly accessible through a user-friendly web-database ( http://www.cnsnpcicarbase.com ). The CNSNP-based quantitative trait loci (QTL) and expression QTL (eQTL) mapping and genome-wide association study (GWAS) were further integrated with global gene expression landscapes, molecular haplotyping, and DNA-protein interaction study in the association panel and recombinant inbred lines (RIL) mapping population to decode complex genetic architecture of one of the vital seed yield trait under drought stress, drought yield index (DYI), in chickpea. This delineated two constituted natural haplotypes and alleles from a histone H3 protein-coding gene and its transcriptional regulator NAC transcription factor (TF) harboring the major QTLs and trans-acting eQTL governing DYI in chickpea. The effect of CNSNPs in TF-binding cis-element of a histone H3 gene in altering the binding affinity and transcriptional activity of NAC TF based on chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) assay was evident. The CNSNP-led promising molecular tags scanned will essentially have functional significance to decode transcriptional gene regulatory function and thus can drive translational genomic analysis in chickpea.
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Affiliation(s)
- Akash Sharma
- Genomics-Assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, 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
| | - Naveen Malik
- 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
| | - Virevol Thakro
- Genomics-Assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Laxmi Narnoliya
- Genomics-Assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Deepak Bajaj
- Genomics-Assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - V S Hegde
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Akhilesh K Tyagi
- Genomics-Assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.,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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11
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Narnoliya L, Basu U, Bajaj D, Malik N, Thakro V, Daware A, Sharma A, Tripathi S, Hegde VS, Upadhyaya HD, Singh AK, Tyagi AK, Parida SK. Transcriptional signatures modulating shoot apical meristem morphometric and plant architectural traits enhance yield and productivity in chickpea. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:864-883. [PMID: 30758092 DOI: 10.1111/tpj.14284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 01/31/2019] [Accepted: 02/07/2019] [Indexed: 06/09/2023]
Abstract
Plant height (PH) and plant width (PW), two of the major plant architectural traits determining the yield and productivity of a crop, are defined by diverse morphometric characteristics of the shoot apical meristem (SAM). The identification of potential molecular tags from a single gene that simultaneously modulates these plant/SAM architectural traits is therefore prerequisite to achieve enhanced yield and productivity in crop plants, including chickpea. Large-scale multienvironment phenotyping of the association panel and mapping population have ascertained the efficacy of three vital SAM morphometric trait parameters, SAM width, SAM height and SAM area, as key indicators to unravel the genetic basis of the wide PW and PH trait variations observed in desi chickpea. This study integrated a genome-wide association study (GWAS); quantitative trait locus (QTL)/fine-mapping and map-based cloning with molecular haplotyping; transcript profiling; and protein-DNA interaction assays for the dissection of plant architectural traits in chickpea. These exertions delineated natural alleles and superior haplotypes from a CabHLH121 transcription factor (TF) gene within the major QTL governing PW, PH and SAM morphometric traits. A genome-wide protein-DNA interaction assay assured the direct binding of a known stem cell master regulator, CaWUS, to the WOX-homeodomain TF binding sites of a CabHLH121 gene and its constituted haplotypes. The differential expression of CaWUS and transcriptional regulation of its target CabHLH121 gene/haplotypes were apparent, suggesting their collective role in altering SAM morphometric characteristics and plant architectural traits in the contrasting near isogenic lines (NILs). The NILs introgressed with a superior haplotype of a CabHLH121 exhibited optimal PW and desirable PH as well as enhanced yield and productivity without compromising any component of agronomic performance. These molecular signatures of the CabHLH121 TF gene have the potential to regulate both PW and PH traits through the modulation of proliferation, differentiation and maintenance of the meristematic stem cell population in the SAM; therefore, these signatures will be useful in the translational genomic study of chickpea genetic enhancement. The restructured cultivars with desirable PH (semidwarf) and PW will ensure maximal planting density in a specified cultivable field area, thereby enhancing the overall yield and productivity of chickpea. This can essentially facilitate the achievement of better remunerative outputs by farmers with rational land use, therefore ensuring global food security in the present scenario of an increasing population density and shrinking per capita land area.
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Affiliation(s)
- Laxmi Narnoliya
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, 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
| | - Deepak Bajaj
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Naveen Malik
- 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
| | - Anurag Daware
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, 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
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Venkatraman S Hegde
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Hari D Upadhyaya
- International Crops Research Institute for the SemiArid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Ashok K Singh
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Akhilesh K Tyagi
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
- 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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12
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Basu U, Upadhyaya HD, Srivastava R, Daware A, Malik N, Sharma A, Bajaj D, Narnoliya L, Thakro V, Kujur A, Tripathi S, Bharadwaj C, Hegde VS, Pandey AK, Singh AK, Tyagi AK, Parida SK. ABC Transporter-Mediated Transport of Glutathione Conjugates Enhances Seed Yield and Quality in Chickpea. PLANT PHYSIOLOGY 2019; 180:253-275. [PMID: 30737266 PMCID: PMC6501113 DOI: 10.1104/pp.18.00934] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 12/12/2018] [Indexed: 05/28/2023]
Abstract
The identification of functionally relevant molecular tags is vital for genomics-assisted crop improvement and enhancement of seed yield, quality, and productivity in chickpea (Cicer arietinum). The simultaneous improvement of yield/productivity as well as quality traits often requires pyramiding of multiple genes, which remains a major hurdle given various associated epistatic and pleotropic effects. Unfortunately, no single gene that can improve yield/productivity along with quality and other desirable agromorphological traits is known, hampering the genetic enhancement of chickpea. Using a combinatorial genomics-assisted breeding and functional genomics strategy, this study identified natural alleles and haplotypes of an ABCC3-type transporter gene that regulates seed weight, an important domestication trait, by transcriptional regulation and modulation of the transport of glutathione conjugates in seeds of desi and kabuli chickpea. The superior allele/haplotype of this gene introgressed in desi and kabuli near-isogenic lines enhances the seed weight, yield, productivity, and multiple desirable plant architecture and seed-quality traits without compromising agronomic performance. These salient findings can expedite crop improvement endeavors and the development of nutritionally enriched high-yielding cultivars in chickpea.
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Affiliation(s)
- Udita Basu
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, Telangana, India
| | - Rishi Srivastava
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Anurag Daware
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Naveen Malik
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Akash Sharma
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Deepak Bajaj
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Laxmi Narnoliya
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Virevol Thakro
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Alice Kujur
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Chellapilla Bharadwaj
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India
| | - V S Hegde
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Ajay K Pandey
- National Agri-Food Biotechnology Institute, Mohali 140306, Punjab, India
| | - Ashok K Singh
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Akhilesh K Tyagi
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
- 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, Aruna Asaf Ali Marg, New Delhi 110067, India
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13
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Basu U, Bajaj D, Sharma A, Malik N, Daware A, Narnoliya L, Thakro V, Upadhyaya HD, Kumar R, Tripathi S, Bharadwaj C, Tyagi AK, Parida SK. Genetic dissection of photosynthetic efficiency traits for enhancing seed yield in chickpea. PLANT, CELL & ENVIRONMENT 2019; 42:158-173. [PMID: 29676051 DOI: 10.1111/pce.13319] [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: 09/18/2017] [Accepted: 04/03/2018] [Indexed: 06/08/2023]
Abstract
Understanding the genetic basis of photosynthetic efficiency (PE) contributing to enhanced seed yield per plant (SYP) is vital for genomics-assisted crop improvement of chickpea. The current study employed an integrated genomic strategy involving photosynthesis pathway gene-based association mapping, genome-wide association study, quantitative trait loci (QTL) mapping, and expression profiling. This identified 16 potential single nucleotide polymorphism loci linked to major QTLs underlying 16 candidate genes significantly associated with PE and SYP traits in chickpea. The allelic variants were tightly linked to positively interacting QTLs regulating both enhanced PE and SYP traits as exemplified by a chlorophyll A-B binding protein-coding gene. The leaf tissue-specific pronounced up-regulated expression of 16 associated genes in germplasm accessions and homozygous individuals of mapping population was evident. Such combinatorial genomic strategy coupled with gene haplotype-specific association and in silico protein-protein interaction study delineated natural alleles and superior haplotypes from a chlorophyll A-B binding (CAB) protein-coding gene and its interacting gene, Timing of CAB Expression 1 (TOC1), which appear to be most promising candidates in modulating chickpea PE and SYP traits. These functionally pertinent molecular signatures identified have efficacy to drive marker-assisted selection for developing PE-enriched cultivars with high seed yield in chickpea.
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Affiliation(s)
- Udita Basu
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Akash Sharma
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Naveen Malik
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Anurag Daware
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Laxmi Narnoliya
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Virevol Thakro
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - Rajendra Kumar
- U.P. Council of Agricultural Research, Gomati Nagar, Lucknow, 226010, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Chellapilla Bharadwaj
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
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15
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Basu U, Srivastava R, Bajaj D, Thakro V, Daware A, Malik N, Upadhyaya HD, Parida SK. Genome-wide generation and genotyping of informative SNPs to scan molecular signatures for seed yield in chickpea. Sci Rep 2018; 8:13240. [PMID: 30185866 PMCID: PMC6125345 DOI: 10.1038/s41598-018-29926-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 06/18/2018] [Indexed: 01/21/2023] Open
Abstract
We discovered 2150 desi and 2199 kabuli accessions-derived SNPs by cultivar-wise individual assembling of sequence-reads generated through genotyping-by-sequencing of 92 chickpea accessions. Subsequent large-scale validation and genotyping of these SNPs discovered 619 desi accessions-derived (DAD) SNPs, 531 kabuli accessions-derived (KAD) SNPs, 884 multiple accessions-derived (MAD) SNPs and 1083 two accessions (desi ICC 4958 and kabuli CDC Frontier)-derived (TAD) SNPs that were mapped on eight chromosomes. These informative SNPs were annotated in coding/non-coding regulatory sequence components of genes. The MAD-SNPs were efficient to detect high intra-specific polymorphic potential and wide natural allelic diversity level including high-resolution admixed-population genetic structure and precise phylogenetic relationship among 291 desi and kabuli accessions. This signifies their effectiveness in introgression breeding and varietal improvement studies targeting useful agronomic traits of chickpea. Six trait-associated genes with SNPs including quantitative trait nucleotides (QTNs) in combination explained 27.5% phenotypic variation for seed yield per plant (SYP). A pentatricopeptide repeat (PPR) gene with a synonymous-coding SNP/QTN significantly associated with SYP trait was found most-promising in chickpea. The essential information delineated can be of immense utility in genomics-assisted breeding applications to develop high-yielding chickpea cultivars.
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Affiliation(s)
- Udita Basu
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rishi Srivastava
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Virevol Thakro
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Anurag Daware
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Naveen Malik
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, Telangana, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
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16
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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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Pavan S, Lotti C, Marcotrigiano AR, Mazzeo R, Bardaro N, Bracuto V, Ricciardi F, Taranto F, D'Agostino N, Schiavulli A, De Giovanni C, Montemurro C, Sonnante G, Ricciardi L. A Distinct Genetic Cluster in Cultivated Chickpea as Revealed by Genome-wide Marker Discovery and Genotyping. THE PLANT GENOME 2017; 10. [PMID: 28724069 DOI: 10.3835/plantgenome2016.11.0115] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The accurate description of plant biodiversity is of utmost importance to efficiently address efforts in conservation genetics and breeding. Herein, we report the successful application of a genotyping-by-sequencing (GBS) approach in chickpea ( L.), resulting in the characterization of a cultivated germplasm collection with 3187 high-quality single nucleotide polymorphism (SNP) markers. Genetic structure inference, principal component analysis, and hierarchical clustering all indicated the identification of a genetic cluster corresponding to black-seeded genotypes traditionally cultivated in Southern Italy. Remarkably, this cluster was clearly distinct at both genetic and phenotypic levels from germplasm groups reflecting commercial chickpea classification into and seed types. Fixation index estimates for individual polymorphisms pointed out loci and genomic regions that might be of significance for the diversification of agronomic and commercial traits. Overall, our findings provide information on genetic relationships within cultivated chickpea and highlight a gene pool of great interest for the scientific community and chickpea breeding, which is limited by the low genetic diversity available in the primary gene pool.
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Genetic dissection of plant growth habit in chickpea. Funct Integr Genomics 2017; 17:711-723. [PMID: 28600722 DOI: 10.1007/s10142-017-0566-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/01/2017] [Accepted: 05/26/2017] [Indexed: 12/17/2022]
Abstract
A combinatorial genomics-assisted breeding strategy encompassing association analysis, genetic mapping and expression profiling is found most promising for quantitative dissection of complex traits in crop plants. The present study employed GWAS (genome-wide association study) using 24,405 SNPs (single nucleotide polymorphisms) obtained with genotyping-by-sequencing (GBS) of 92 sequenced desi and kabuli accessions of chickpea. This identified eight significant genomic loci associated with erect (E)/semi-erect (SE) vs. spreading (S)/semi-spreading (SS)/prostrate (P) plant growth habit (PGH) trait differentiation regardless of diverse desi and kabuli genetic backgrounds of chickpea. These associated SNPs in combination explained 23.8% phenotypic variation for PGH in chickpea. Five PGH-associated genes were validated successfully in E/SE and SS/S/P PGH-bearing parental accessions and homozygous individuals of three intra- and interspecific RIL (recombinant inbred line) mapping populations as well as 12 contrasting desi and kabuli chickpea germplasm accessions by selective genotyping through Sequenom MassARRAY. The shoot apical, inflorescence and floral meristems-specific expression, including upregulation (seven-fold) of five PGH-associated genes especially in germplasm accessions and homozygous RIL mapping individuals contrasting with E/SE PGH traits was apparent. Collectively, this integrated genomic strategy delineated diverse non-synonymous SNPs from five candidate genes with strong allelic effects on PGH trait variation in chickpea. Of these, two vernalization-responsive non-synonymous SNP alleles carrying SNF2 protein-coding gene and B3 transcription factor associated with PGH traits were found to be the most promising in chickpea. The SNP allelic variants associated with E/SE/SS/S PGH trait differentiation were exclusively present in all cultivated desi and kabuli chickpea accessions while wild species/accessions belonging to primary, secondary and tertiary gene pools mostly contained prostrate PGH-associated SNP alleles. This indicates strong adaptive natural/artificial selection pressure (Tajima's D 3.15 to 4.57) on PGH-associated target genomic loci during chickpea domestication. These vital leads thus have potential to decipher complex transcriptional regulatory gene function of PGH trait differentiation and for understanding the selective sweep-based PGH trait evolution and domestication pattern in cultivated and wild chickpea accessions adapted to diverse agroclimatic conditions. Collectively, the essential inputs generated will be of profound use in marker-assisted genetic enhancement to develop cultivars with desirable plant architecture of erect growth habit types in chickpea.
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Saeed A, Darvishzadeh R. Association analysis of biotic and abiotic stresses resistance in chickpea ( Cicer spp.) using AFLP markers. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1333455] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Ali Saeed
- Department of Seed and Plant Improvement, West Azerbaijan Agricultural and Natural Resources Research & Education Centre, Agricultural Research, Education and Extension Organization (AREEO), Urmia, Iran
| | - Reza Darvishzadeh
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Urmia University, Urmia, Iran
- Department of Agricultural Biotechnology, Institue of Biotechnology, Urmia University, Urmia, Iran
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20
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Srivastava R, Bajaj D, Sayal YK, Meher PK, Upadhyaya HD, Kumar R, Tripathi S, Bharadwaj C, Rao AR, Parida SK. Genome-wide development and deployment of informative intron-spanning and intron-length polymorphism markers for genomics-assisted breeding applications in chickpea. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 252:374-387. [PMID: 27717474 DOI: 10.1016/j.plantsci.2016.08.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 08/03/2016] [Accepted: 08/24/2016] [Indexed: 06/06/2023]
Abstract
The discovery and large-scale genotyping of informative gene-based markers is essential for rapid delineation of genes/QTLs governing stress tolerance and yield component traits in order to drive genetic enhancement in chickpea. A genome-wide 119169 and 110491 ISM (intron-spanning markers) from 23129 desi and 20386 kabuli protein-coding genes and 7454 in silico InDel (insertion-deletion) (1-45-bp)-based ILP (intron-length polymorphism) markers from 3283 genes were developed that were structurally and functionally annotated on eight chromosomes and unanchored scaffolds of chickpea. A much higher amplification efficiency (83%) and intra-specific polymorphic potential (86%) detected by these markers than that of other sequence-based genetic markers among desi and kabuli chickpea accessions was apparent even by a cost-effective agarose gel-based assay. The genome-wide physically mapped 1718 ILP markers assayed a wider level of functional genetic diversity (19-81%) and well-defined phylogenetics among domesticated chickpea accessions. The gene-derived 1424 ILP markers were anchored on a high-density (inter-marker distance: 0.65cM) desi intra-specific genetic linkage map/functional transcript map (ICC 4958×ICC 2263) of chickpea. This reference genetic map identified six major genomic regions harbouring six robust QTLs mapped on five chromosomes, which explained 11-23% seed weight trait variation (7.6-10.5 LOD) in chickpea. The integration of high-resolution QTL mapping with differential expression profiling detected six including one potential serine carboxypeptidase gene with ILP markers (linked tightly to the major seed weight QTLs) exhibiting seed-specific expression as well as pronounced up-regulation especially in seeds of high (ICC 4958) as compared to low (ICC 2263) seed weight mapping parental accessions. The marker information generated in the present study was made publicly accessible through a user-friendly web-resource, "Chickpea ISM-ILP Marker Database". The designing of multiple ISM and ILP markers (2-5 markers/gene) from an individual gene (transcription factor) with numerous aforementioned desirable genetic attributes can widen the user-preference to select suitable primer combination for simultaneous large-scale assaying of functional allelic variation, natural allelic diversity, molecular mapping and expression profiling of genes among chickpea accessions. This will essentially accelerate the identification of functionally relevant molecular tags regulating vital agronomic traits for genomics-assisted crop improvement by optimal resource expenses in chickpea.
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Affiliation(s)
- Rishi Srivastava
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Yogesh K Sayal
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Prabina K Meher
- Division of Statistical Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Rajendra Kumar
- U.P. Council of Agricultural Research, Gomati Nagar, Lucknow 226010, Uttar Pradesh, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi 110012, India
| | - Chellapilla Bharadwaj
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi 110012, India
| | - Atmakuri R Rao
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
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Srivastava R, Bajaj D, Malik A, Singh M, Parida SK. Transcriptome landscape of perennial wild Cicer microphyllum uncovers functionally relevant molecular tags regulating agronomic traits in chickpea. Sci Rep 2016; 6:33616. [PMID: 27680662 PMCID: PMC5041113 DOI: 10.1038/srep33616] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 08/26/2016] [Indexed: 01/03/2023] Open
Abstract
The RNA-sequencing followed by de-novo transcriptome assembly identified 11621 genes differentially xpressed in roots vs. shoots of a wild perennial Cicer microphyllum. Comparative analysis of transcriptomes between microphyllum and cultivated desi cv. ICC4958 detected 12772 including 3242 root- and 1639 shoot-specific microphyllum genes with 85% expression validation success rate. Transcriptional reprogramming of microphyllum root-specific genes implicates their possible role in regulating differential natural adaptive characteristics between wild and cultivated chickpea. The transcript-derived 5698 including 282 in-silico polymorphic SSR and 127038 SNP markers annotated at a genome-wide scale exhibited high amplification and polymorphic potential among cultivated (desi and kabuli) and wild accessions suggesting their utility in chickpea genomics-assisted breeding applications. The functional significance of markers was assessed based on their localization in non-synonymous coding and regulatory regions of microphyllum root-specific genes differentially expressed predominantly in ICC 4958 roots under drought stress. A high-density 490 genic SSR- and SNP markers-anchored genetic linkage map identified six major QTLs regulating drought tolerance-related traits, yield per plant and harvest-index in chickpea. The integration of high-resolution QTL mapping with comparative transcriptome profiling delineated five microphyllum root-specific genes with non-synonymous and regulatory SNPs governing drought-responsive yield traits. Multiple potential key regulators and functionally relevant molecular tags delineated can drive translational research and drought tolerance-mediated chickpea genetic enhancement.
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Affiliation(s)
- Rishi Srivastava
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Ayushi Malik
- Faculty of Science, Jamia Hamdard University, Hamdard Nagar, New Delhi 110062, India
| | - Mohar Singh
- National Bureau of Plant Genetic Resources Regional Station, Shimla, Himachal Pradesh 171004, India
| | - Swarup K. Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
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Parida SK, Kalia S, Pandit A, Nayak P, Singh RK, Gaikwad K, Srivastava PS, Singh NK, Mohapatra T. Single nucleotide polymorphism in sugar pathway and disease resistance genes in sugarcane. PLANT CELL REPORTS 2016; 35:1629-1653. [PMID: 27289592 DOI: 10.1007/s00299-016-1978-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 03/21/2016] [Indexed: 06/06/2023]
Abstract
Single nucleotide polymorphism in sugar pathway and disease resistance genes showing genetic association with sugar content and red rot resistance would be useful in marker-assisted genetic improvement of sugarcane. Validation and genotyping of potential sequence variants in candidate genes are necessary to understand their functional significance and trait association potential. We discovered, characterized, validated and genotyped SNPs and InDels in sugar pathway and disease resistance genes of Saccharum complex and sugarcane varieties using amplicon sequencing and CAPS assays. The SNPs were abundant in the non-coding 3'UTRs than 5'UTRs and coding sequences depicting a strong bias toward C to T transition substitutions than transversions. Sequencing of cloned amplicons validated 61.6 and 45.2 % SNPs detected in silico in 21 sugar pathway and 16 disease resistance genes, respectively. Sixteen SNPs in four sugar pathway genes and 10 SNPs in nine disease resistance genes were validated through cost-effective CAPS assay. Functional and adaptive significance of SNP and protein haplotypes identified in sugar pathway and disease resistance genes was assessed by correlating their allelic variation with missense amino acid substitutions in the functional domains, alteration in protein structure models and possible modulation of catalytic enzyme activity in contrasting high and low sugar and moderately red rot resistant and highly susceptible sugarcane genotypes. A strong genetic association of five SNPs in the sugar pathway and disease resistance genes, and an InDel marker in the promoter sequence of sucrose synthase-2 gene, with sugar content and red rot resistance, was evident. The functionally relevant SNPs and InDels, detected and validated in sugar pathway and disease resistance genes, and genic CAPS markers designed, would be of immense use in marker-assisted genetic improvement of sugarcane for sugar content and disease resistance.
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Affiliation(s)
- Swarup K Parida
- National Research Centre on Plant Biotechnology, New Delhi, 110012, India
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Sanjay Kalia
- National Research Centre on Plant Biotechnology, New Delhi, 110012, India
- Department of Biotechnology, CGO Complex, Lodhi Road, New Delhi, 110003, India
| | - Awadhesh Pandit
- National Research Centre on Plant Biotechnology, New Delhi, 110012, India
- National Centre for Biological Sciences, Bengaluru, 560065, Karnataka , India
| | - Preetam Nayak
- Utkal University, Vanivihar, Bhubaneswar, Odisha, 751004, India
| | - Ram Kushal Singh
- U.P. Council of Sugarcane Research, Shahjahanpur, Uttar Pradesh, 242001, India
| | - Kishor Gaikwad
- National Research Centre on Plant Biotechnology, New Delhi, 110012, India
| | | | - Nagendra K Singh
- National Research Centre on Plant Biotechnology, New Delhi, 110012, India
| | - Trilochan Mohapatra
- National Research Centre on Plant Biotechnology, New Delhi, 110012, India.
- Indian Council of Agricultural Research, Krishi Bhavan, New Delhi, 110001, India.
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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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Bajaj D, Srivastava R, Nath M, Tripathi S, Bharadwaj C, Upadhyaya HD, Tyagi AK, Parida SK. EcoTILLING-Based Association Mapping Efficiently Delineates Functionally Relevant Natural Allelic Variants of Candidate Genes Governing Agronomic Traits in Chickpea. FRONTIERS IN PLANT SCIENCE 2016; 7:450. [PMID: 27148286 PMCID: PMC4835497 DOI: 10.3389/fpls.2016.00450] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 03/22/2016] [Indexed: 05/22/2023]
Abstract
The large-scale mining and high-throughput genotyping of novel gene-based allelic variants in natural mapping population are essential for association mapping to identify functionally relevant molecular tags governing useful agronomic traits in chickpea. The present study employs an alternative time-saving, non-laborious and economical pool-based EcoTILLING approach coupled with agarose gel detection assay to discover 1133 novel SNP allelic variants from diverse coding and regulatory sequence components of 1133 transcription factor (TF) genes by genotyping in 192 diverse desi and kabuli chickpea accessions constituting a seed weight association panel. Integrating these SNP genotyping data with seed weight field phenotypic information of 192 structured association panel identified eight SNP alleles in the eight TF genes regulating seed weight of chickpea. The associated individual and combination of all SNPs explained 10-15 and 31% phenotypic variation for seed weight, respectively. The EcoTILLING-based large-scale allele mining and genotyping strategy implemented for association mapping is found much effective for a diploid genome crop species like chickpea with narrow genetic base and low genetic polymorphism. This optimized approach thus can be deployed for various genomics-assisted breeding applications with optimal expense of resources in domesticated chickpea. The seed weight-associated natural allelic variants and candidate TF genes delineated have potential to accelerate marker-assisted genetic improvement of chickpea.
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Affiliation(s)
- Deepak Bajaj
- Govt. of India, Plant Genomics and Molecular Breeding Lab, Department of Biotechnology, National Institute of Plant Genome ResearchNew Delhi, India
| | - Rishi Srivastava
- Govt. of India, Plant Genomics and Molecular Breeding Lab, Department of Biotechnology, National Institute of Plant Genome ResearchNew Delhi, India
| | - Manoj Nath
- National Research Centre on Plant BiotechnologyNew Delhi, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research InstituteNew Delhi, India
| | | | - Hari D. Upadhyaya
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Akhilesh K. Tyagi
- Govt. of India, Plant Genomics and Molecular Breeding Lab, Department of Biotechnology, National Institute of Plant Genome ResearchNew Delhi, India
| | - Swarup K. Parida
- Govt. of India, Plant Genomics and Molecular Breeding Lab, Department of Biotechnology, National Institute of Plant Genome ResearchNew Delhi, India
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Bajaj D, Upadhyaya HD, Das S, Kumar V, Gowda CLL, Sharma S, Tyagi AK, Parida SK. Identification of candidate genes for dissecting complex branch number trait in chickpea. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 245:61-70. [PMID: 26940492 DOI: 10.1016/j.plantsci.2016.01.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 01/15/2016] [Indexed: 06/05/2023]
Abstract
The present study exploited integrated genomics-assisted breeding strategy for genetic dissection of complex branch number quantitative trait in chickpea. Candidate gene-based association analysis in a branch number association panel was performed by utilizing the genotyping data of 401 SNP allelic variants mined from 27 known cloned branch number gene orthologs of chickpea. The genome-wide association study (GWAS) integrating both genome-wide GBS- (4556 SNPs) and candidate gene-based genotyping information of 4957 SNPs in a structured population of 60 sequenced desi and kabuli accessions (with 350-400 kb LD decay), detected 11 significant genomic loci (genes) associated (41% combined PVE) with branch number in chickpea. Of these, seven branch number-associated genes were further validated successfully in two inter (ICC 4958 × ICC 17160)- and intra (ICC 12299 × ICC 8261)-specific mapping populations. The axillary meristem and shoot apical meristem-specific expression, including differential up- and down-regulation (4-5 fold) of the validated seven branch number-associated genes especially in high branch number as compared to the low branch number-containing parental accessions and homozygous individuals of two aforesaid mapping populations was apparent. Collectively, this combinatorial genomic approach delineated diverse naturally occurring novel functional SNP allelic variants in seven potential known/candidate genes [PIN1 (PIN-FORMED protein 1), TB1 (teosinte branched 1), BA1/LAX1 (BARREN STALK1/LIKE AUXIN1), GRAS8 (gibberellic acid insensitive/GAI, Repressor of ga13/RGA and Scarecrow8/SCR8), ERF (ethylene-responsive element-binding factor), MAX2 (more axillary growth 2) and lipase] governing chickpea branch number. The useful information generated from this study have potential to expedite marker-assisted genetic enhancement by developing high-yielding cultivars with more number of productive (pods and seeds) branches in chickpea.
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Affiliation(s)
- Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Shouvik Das
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Vinod Kumar
- National Research Centre on Plant Biotechnology (NRCPB), New Delhi 110012, India
| | - C L L Gowda
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Shivali Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
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Malik N, Dwivedi N, Singh AK, Parida SK, Agarwal P, Thakur JK, Tyagi AK. An Integrated Genomic Strategy Delineates Candidate Mediator Genes Regulating Grain Size and Weight in Rice. Sci Rep 2016; 6:23253. [PMID: 27000976 PMCID: PMC4802383 DOI: 10.1038/srep23253] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 03/02/2016] [Indexed: 12/31/2022] Open
Abstract
The present study deployed a Mediator (MED) genes-mediated integrated genomic strategy for understanding the complex genetic architecture of grain size/weight quantitative trait in rice. The targeted multiplex amplicon resequencing of 55 MED genes annotated from whole rice genome in 384 accessions discovered 3971 SNPs, which were structurally and functionally annotated in diverse coding and non-coding sequence-components of genes. Association analysis, using the genotyping information of 3971 SNPs in a structured population of 384 accessions (with 50–100 kb linkage disequilibrium decay), detected 10 MED gene-derived SNPs significantly associated (46% combined phenotypic variation explained) with grain length, width and weight in rice. Of these, one strong grain weight-associated non-synonymous SNP (G/A)-carrying OsMED4_2 gene was validated successfully in low- and high-grain weight parental accessions and homozygous individuals of a rice mapping population. The seed-specific expression, including differential up/down-regulation of three grain size/weight-associated MED genes (including OsMED4_2) in six low and high-grain weight rice accessions was evident. Altogether, combinatorial genomic approach involving haplotype-based association analysis delineated diverse functionally relevant natural SNP-allelic variants in 10 MED genes, including three potential novel SNP haplotypes in an OsMED4_2 gene governing grain size/weight differentiation in rice. These molecular tags have potential to accelerate genomics-assisted crop improvement in rice.
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Affiliation(s)
- Naveen Malik
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Nidhi Dwivedi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Ashok K Singh
- Division of Genetics, Rice Section, Indian Agricultural Research Institute (IARI), New Delhi 110012, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Pinky Agarwal
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Jitendra K Thakur
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
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Daware A, Das S, Srivastava R, Badoni S, Singh AK, Agarwal P, Parida SK, Tyagi AK. An Efficient Strategy Combining SSR Markers- and Advanced QTL-seq-driven QTL Mapping Unravels Candidate Genes Regulating Grain Weight in Rice. FRONTIERS IN PLANT SCIENCE 2016; 7:1535. [PMID: 27833617 PMCID: PMC5080349 DOI: 10.3389/fpls.2016.01535] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 09/29/2016] [Indexed: 05/05/2023]
Abstract
Development and use of genome-wide informative simple sequence repeat (SSR) markers and novel integrated genomic strategies are vital to drive genomics-assisted breeding applications and for efficient dissection of quantitative trait loci (QTLs) underlying complex traits in rice. The present study developed 6244 genome-wide informative SSR markers exhibiting in silico fragment length polymorphism based on repeat-unit variations among genomic sequences of 11 indica, japonica, aus, and wild rice accessions. These markers were mapped on diverse coding and non-coding sequence components of known cloned/candidate genes annotated from 12 chromosomes and revealed a much higher amplification (97%) and polymorphic potential (88%) along with wider genetic/functional diversity level (16-74% with a mean 53%) especially among accessions belonging to indica cultivar group, suggesting their utility in large-scale genomics-assisted breeding applications in rice. A high-density 3791 SSR markers-anchored genetic linkage map (IR 64 × Sonasal) spanning 2060 cM total map-length with an average inter-marker distance of 0.54 cM was generated. This reference genetic map identified six major genomic regions harboring robust QTLs (31% combined phenotypic variation explained with a 5.7-8.7 LOD) governing grain weight on six rice chromosomes. One strong grain weight major QTL region (OsqGW5.1) was narrowed-down by integrating traditional QTL mapping with high-resolution QTL region-specific integrated SSR and single nucleotide polymorphism markers-based QTL-seq analysis and differential expression profiling. This led us to delineate two natural allelic variants in two known cis-regulatory elements (RAV1AAT and CARGCW8GAT) of glycosyl hydrolase and serine carboxypeptidase genes exhibiting pronounced seed-specific differential regulation in low (Sonasal) and high (IR 64) grain weight mapping parental accessions. Our genome-wide SSR marker resource (polymorphic within/between diverse cultivar groups) and integrated genomic strategy can efficiently scan functionally relevant potential molecular tags (markers, candidate genes and alleles) regulating complex agronomic traits (grain weight) and expedite marker-assisted genetic enhancement in rice.
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Affiliation(s)
- Anurag Daware
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
| | - Sweta Das
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
| | - Rishi Srivastava
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
| | - Saurabh Badoni
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
| | - Ashok K. Singh
- Rice Section, Division of Genetics, Indian Agricultural Research Institute (IARI)New Delhi, India
| | - Pinky Agarwal
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
| | - Swarup K. Parida
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
- *Correspondence: Akhilesh K. Tyagi, Swarup K. Parida, ;
| | - Akhilesh K. Tyagi
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
- *Correspondence: Akhilesh K. Tyagi, Swarup K. Parida, ;
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Upadhyaya HD, Bajaj D, Narnoliya L, Das S, Kumar V, Gowda CLL, Sharma S, Tyagi AK, Parida SK. Genome-Wide Scans for Delineation of Candidate Genes Regulating Seed-Protein Content in Chickpea. FRONTIERS IN PLANT SCIENCE 2016; 7:302. [PMID: 27047499 PMCID: PMC4803732 DOI: 10.3389/fpls.2016.00302] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 02/25/2016] [Indexed: 05/17/2023]
Abstract
Identification of potential genes/alleles governing complex seed-protein content (SPC) is essential in marker-assisted breeding for quality trait improvement of chickpea. Henceforth, the present study utilized an integrated genomics-assisted breeding strategy encompassing trait association analysis, selective genotyping in traditional bi-parental mapping population and differential expression profiling for the first-time to understand the complex genetic architecture of quantitative SPC trait in chickpea. For GWAS (genome-wide association study), high-throughput genotyping information of 16376 genome-based SNPs (single nucleotide polymorphism) discovered from a structured population of 336 sequenced desi and kabuli accessions [with 150-200 kb LD (linkage disequilibrium) decay] was utilized. This led to identification of seven most effective genomic loci (genes) associated [10-20% with 41% combined PVE (phenotypic variation explained)] with SPC trait in chickpea. Regardless of the diverse desi and kabuli genetic backgrounds, a comparable level of association potential of the identified seven genomic loci with SPC trait was observed. Five SPC-associated genes were validated successfully in parental accessions and homozygous individuals of an intra-specific desi RIL (recombinant inbred line) mapping population (ICC 12299 × ICC 4958) by selective genotyping. The seed-specific expression, including differential up-regulation (>four fold) of six SPC-associated genes particularly in accessions, parents and homozygous individuals of the aforementioned mapping population with a high level of contrasting SPC (21-22%) was evident. Collectively, the integrated genomic approach delineated diverse naturally occurring novel functional SNP allelic variants in six potential candidate genes regulating SPC trait in chickpea. Of these, a non-synonymous SNP allele-carrying zinc finger transcription factor gene exhibiting strong association with SPC trait was found to be the most promising in chickpea. The informative functionally relevant molecular tags scaled-down essentially have potential to accelerate marker-assisted genetic improvement by developing nutritionally rich chickpea cultivars with enhanced SPC.
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Affiliation(s)
- Hari D. Upadhyaya
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Deepak Bajaj
- National Institute of Plant Genome ResearchNew Delhi, India
| | | | - Shouvik Das
- National Institute of Plant Genome ResearchNew Delhi, India
| | - Vinod Kumar
- National Research Centre on Plant BiotechnologyNew Delhi, India
| | - C. L. L. Gowda
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Shivali Sharma
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | | | - Swarup K. Parida
- National Institute of Plant Genome ResearchNew Delhi, India
- *Correspondence: Swarup K. Parida, ;
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Srivastava R, Singh M, Bajaj D, Parida SK. A High-Resolution InDel (Insertion-Deletion) Markers-Anchored Consensus Genetic Map Identifies Major QTLs Governing Pod Number and Seed Yield in Chickpea. FRONTIERS IN PLANT SCIENCE 2016; 7:1362. [PMID: 27695461 PMCID: PMC5025440 DOI: 10.3389/fpls.2016.01362] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 08/29/2016] [Indexed: 05/12/2023]
Abstract
Development and large-scale genotyping of user-friendly informative genome/gene-derived InDel markers in natural and mapping populations is vital for accelerating genomics-assisted breeding applications of chickpea with minimal resource expenses. The present investigation employed a high-throughput whole genome next-generation resequencing strategy in low and high pod number parental accessions and homozygous individuals constituting the bulks from each of two inter-specific mapping populations [(Pusa 1103 × ILWC 46) and (Pusa 256 × ILWC 46)] to develop non-erroneous InDel markers at a genome-wide scale. Comparing these high-quality genomic sequences, 82,360 InDel markers with reference to kabuli genome and 13,891 InDel markers exhibiting differentiation between low and high pod number parental accessions and bulks of aforementioned mapping populations were developed. These informative markers were structurally and functionally annotated in diverse coding and non-coding sequence components of genome/genes of kabuli chickpea. The functional significance of regulatory and coding (frameshift and large-effect mutations) InDel markers for establishing marker-trait linkages through association/genetic mapping was apparent. The markers detected a greater amplification (97%) and intra-specific polymorphic potential (58-87%) among a diverse panel of cultivated desi, kabuli, and wild accessions even by using a simpler cost-efficient agarose gel-based assay implicating their utility in large-scale genetic analysis especially in domesticated chickpea with narrow genetic base. Two high-density inter-specific genetic linkage maps generated using aforesaid mapping populations were integrated to construct a consensus 1479 InDel markers-anchored high-resolution (inter-marker distance: 0.66 cM) genetic map for efficient molecular mapping of major QTLs governing pod number and seed yield per plant in chickpea. Utilizing these high-density genetic maps as anchors, three major genomic regions harboring each of pod number and seed yield robust QTLs (15-28% phenotypic variation explained) were identified on chromosomes 2, 4, and 6. The integration of genetic and physical maps at these QTLs mapped on chromosomes scaled-down the long major QTL intervals into high-resolution short pod number and seed yield robust QTL physical intervals (0.89-2.94 Mb) which were essentially got validated in multiple genetic backgrounds of two chickpea mapping populations. The genome-wide InDel markers including natural allelic variants and genomic loci/genes delineated at major six especially in one colocalized novel congruent robust pod number and seed yield robust QTLs mapped on a high-density consensus genetic map were found most promising in chickpea. These functionally relevant molecular tags can drive marker-assisted genetic enhancement to develop high-yielding cultivars with increased seed/pod number and yield in chickpea.
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Affiliation(s)
| | - Mohar Singh
- National Bureau of Plant Genetic Resources Regional StationShimla, India
| | - Deepak Bajaj
- National Institute of Plant Genome ResearchNew Delhi, India
| | - Swarup K. Parida
- National Institute of Plant Genome ResearchNew Delhi, India
- *Correspondence: Swarup K. Parida ;
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Das S, Singh M, Srivastava R, Bajaj D, Saxena MS, Rana JC, Bansal KC, Tyagi AK, Parida SK. mQTL-seq delineates functionally relevant candidate gene harbouring a major QTL regulating pod number in chickpea. DNA Res 2015; 23:53-65. [PMID: 26685680 PMCID: PMC4755527 DOI: 10.1093/dnares/dsv036] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 11/09/2015] [Indexed: 11/23/2022] Open
Abstract
The present study used a whole-genome, NGS resequencing-based mQTL-seq (multiple QTL-seq) strategy in two inter-specific mapping populations (Pusa 1103 × ILWC 46 and Pusa 256 × ILWC 46) to scan the major genomic region(s) underlying QTL(s) governing pod number trait in chickpea. Essentially, the whole-genome resequencing of low and high pod number-containing parental accessions and homozygous individuals (constituting bulks) from each of these two mapping populations discovered >8 million high-quality homozygous SNPs with respect to the reference kabuli chickpea. The functional significance of the physically mapped SNPs was apparent from the identified 2,264 non-synonymous and 23,550 regulatory SNPs, with 8–10% of these SNPs-carrying genes corresponding to transcription factors and disease resistance-related proteins. The utilization of these mined SNPs in Δ (SNP index)-led QTL-seq analysis and their correlation between two mapping populations based on mQTL-seq, narrowed down two (CaqaPN4.1: 867.8 kb and CaqaPN4.2: 1.8 Mb) major genomic regions harbouring robust pod number QTLs into the high-resolution short QTL intervals (CaqbPN4.1: 637.5 kb and CaqbPN4.2: 1.28 Mb) on chickpea chromosome 4. The integration of mQTL-seq-derived one novel robust QTL with QTL region-specific association analysis delineated the regulatory (C/T) and coding (C/A) SNPs-containing one pentatricopeptide repeat (PPR) gene at a major QTL region regulating pod number in chickpea. This target gene exhibited anther, mature pollen and pod-specific expression, including pronounced higher up-regulated (∼3.5-folds) transcript expression in high pod number-containing parental accessions and homozygous individuals of two mapping populations especially during pollen and pod development. The proposed mQTL-seq-driven combinatorial strategy has profound efficacy in rapid genome-wide scanning of potential candidate gene(s) underlying trait-associated high-resolution robust QTL(s), thereby expediting genomics-assisted breeding and genetic enhancement of crop plants, including chickpea.
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Affiliation(s)
- Shouvik Das
- National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Mohar Singh
- National Bureau of Plant Genetic Resources Regional Station, Shimla, Himachal Pradesh 171004, India
| | - Rishi Srivastava
- National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Maneesha S Saxena
- National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Jai C Rana
- National Bureau of Plant Genetic Resources (NBPGR), New Delhi 110012, India
| | - Kailash C Bansal
- National Bureau of Plant Genetic Resources (NBPGR), New Delhi 110012, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
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Bajaj D, Das S, Upadhyaya HD, Ranjan R, Badoni S, Kumar V, Tripathi S, Gowda CLL, Sharma S, Singh S, Tyagi AK, Parida SK. A Genome-wide Combinatorial Strategy Dissects Complex Genetic Architecture of Seed Coat Color in Chickpea. FRONTIERS IN PLANT SCIENCE 2015; 6:979. [PMID: 26635822 PMCID: PMC4647070 DOI: 10.3389/fpls.2015.00979] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 10/26/2015] [Indexed: 05/29/2023]
Abstract
The study identified 9045 high-quality SNPs employing both genome-wide GBS- and candidate gene-based SNP genotyping assays in 172, including 93 cultivated (desi and kabuli) and 79 wild chickpea accessions. The GWAS in a structured population of 93 sequenced accessions detected 15 major genomic loci exhibiting significant association with seed coat color. Five seed color-associated major genomic loci underlying robust QTLs mapped on a high-density intra-specific genetic linkage map were validated by QTL mapping. The integration of association and QTL mapping with gene haplotype-specific LD mapping and transcript profiling identified novel allelic variants (non-synonymous SNPs) and haplotypes in a MATE secondary transporter gene regulating light/yellow brown and beige seed coat color differentiation in chickpea. The down-regulation and decreased transcript expression of beige seed coat color-associated MATE gene haplotype was correlated with reduced proanthocyanidins accumulation in the mature seed coats of beige than light/yellow brown seed colored desi and kabuli accessions for their coloration/pigmentation. This seed color-regulating MATE gene revealed strong purifying selection pressure primarily in LB/YB seed colored desi and wild Cicer reticulatum accessions compared with the BE seed colored kabuli accessions. The functionally relevant molecular tags identified have potential to decipher the complex transcriptional regulatory gene function of seed coat coloration and for understanding the selective sweep-based seed color trait evolutionary pattern in cultivated and wild accessions during chickpea domestication. The genome-wide integrated approach employed will expedite marker-assisted genetic enhancement for developing cultivars with desirable seed coat color types in chickpea.
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Affiliation(s)
- Deepak Bajaj
- National Institute of Plant Genome ResearchNew Delhi, India
| | - Shouvik Das
- National Institute of Plant Genome ResearchNew Delhi, India
| | - Hari D. Upadhyaya
- International Crops Research Institute for the Semi-Arid TropicsTelangana, India
| | - Rajeev Ranjan
- National Institute of Plant Genome ResearchNew Delhi, India
| | - Saurabh Badoni
- National Institute of Plant Genome ResearchNew Delhi, India
| | - Vinod Kumar
- National Research Centre on Plant BiotechnologyNew Delhi, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research InstituteNew Delhi, India
| | | | - Shivali Sharma
- International Crops Research Institute for the Semi-Arid TropicsTelangana, India
| | - Sube Singh
- International Crops Research Institute for the Semi-Arid TropicsTelangana, India
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Upadhyaya HD, Bajaj D, Das S, Saxena MS, Badoni S, Kumar V, Tripathi S, Gowda CLL, Sharma S, Tyagi AK, Parida SK. A genome-scale integrated approach aids in genetic dissection of complex flowering time trait in chickpea. PLANT MOLECULAR BIOLOGY 2015; 89:403-20. [PMID: 26394865 DOI: 10.1007/s11103-015-0377-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 09/02/2015] [Indexed: 05/08/2023]
Abstract
A combinatorial approach of candidate gene-based association analysis and genome-wide association study (GWAS) integrated with QTL mapping, differential gene expression profiling and molecular haplotyping was deployed in the present study for quantitative dissection of complex flowering time trait in chickpea. Candidate gene-based association mapping in a flowering time association panel (92 diverse desi and kabuli accessions) was performed by employing the genotyping information of 5724 SNPs discovered from 82 known flowering chickpea gene orthologs of Arabidopsis and legumes as well as 832 gene-encoding transcripts that are differentially expressed during flower development in chickpea. GWAS using both genome-wide GBS- and candidate gene-based genotyping data of 30,129 SNPs in a structured population of 92 sequenced accessions (with 200-250 kb LD decay) detected eight maximum effect genomic SNP loci (genes) associated (34% combined PVE) with flowering time. Six flowering time-associated major genomic loci harbouring five robust QTLs mapped on a high-resolution intra-specific genetic linkage map were validated (11.6-27.3% PVE at 5.4-11.7 LOD) further by traditional QTL mapping. The flower-specific expression, including differential up- and down-regulation (>three folds) of eight flowering time-associated genes (including six genes validated by QTL mapping) especially in early flowering than late flowering contrasting chickpea accessions/mapping individuals during flower development was evident. The gene haplotype-based LD mapping discovered diverse novel natural allelic variants and haplotypes in eight genes with high trait association potential (41% combined PVE) for flowering time differentiation in cultivated and wild chickpea. Taken together, eight potential known/candidate flowering time-regulating genes [efl1 (early flowering 1), FLD (Flowering locus D), GI (GIGANTEA), Myb (Myeloblastosis), SFH3 (SEC14-like 3), bZIP (basic-leucine zipper), bHLH (basic helix-loop-helix) and SBP (SQUAMOSA promoter binding protein)], including novel markers, QTLs, alleles and haplotypes delineated by aforesaid genome-wide integrated approach have potential for marker-assisted genetic improvement and unravelling the domestication pattern of flowering time in chickpea.
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Affiliation(s)
- Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Shouvik Das
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Maneesha S Saxena
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Saurabh Badoni
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Vinod Kumar
- National Research Centre on Plant Biotechnology (NRCPB), New Delhi, 110012, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - C L L Gowda
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Shivali Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
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CNMS: The preferred genic markers for comparative genomic, molecular phylogenetic, functional genetic diversity and differential gene regulatory expression analyses in chickpea. J Biosci 2015; 40:579-92. [PMID: 26333404 DOI: 10.1007/s12038-015-9545-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The intra/inter-genomic comparative mapping-based phylogenetic footprinting identified 5 paralogous and 656 orthologous genome-wide CNMS markers in the upstream sequences of chickpea genes. These CNMS markers revealed a high-degree of gene-based syntenic relationship between chickpea and Medicago genomes while minimum between chickpea and Vitis genomes. The time of divergence and duplication estimated using CNMS markers highlight the expected phylogenetic relationships between chickpea and six dicot (legume) species as well as occurrence of ancient genome (approximately 53 Mya) with small-scale recent segmental (approximately 10 Mya) duplication events in chickpea. A wider level of functional molecular diversity (14 to 88 percent) and admixed population genetic structure was detected among desi, kabuli and wild genotypes by genic CNMS markers at a genome-wide scale suggesting their utility in large-scale genetic analysis in chickpea. The subfunctionalization at the cis-regulatory element region and TFBS (transcription factor binding site) motif levels in the upstream sequences of CNMS marker-associated orthologous genes than the paralogues was predominant. Functional constraint might have considerable effect on these CNMScontaining regulatory elements controlling consistent orthologous gene expression in dicots. A rapid subfunctionalization based on diverge differential expression of paralogous CNMS marker-associated genes particularly those that underwent recent small-scale segmental duplication events in chickpea was apparent. The differential regulation of expression and subfunctionalization potential of Ultra CNMS marker-associated genes suggest their utility in deciphering the complex gene regulatory function as well as identification and targeted mapping of potential genes/QTLs governing vital agronomic traits in chickpea. The gene-based CNMS markers with desirable inherent genetic attributes like higher degree of comparative genome mapping, functional genetic diversity and differential gene regulatory expression potential can significantly propel the genomics-assisted chickpea crop improvement.
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Kole C, Muthamilarasan M, Henry R, Edwards D, Sharma R, Abberton M, Batley J, Bentley A, Blakeney M, Bryant J, Cai H, Cakir M, Cseke LJ, Cockram J, de Oliveira AC, De Pace C, Dempewolf H, Ellison S, Gepts P, Greenland A, Hall A, Hori K, Hughes S, Humphreys MW, Iorizzo M, Ismail AM, Marshall A, Mayes S, Nguyen HT, Ogbonnaya FC, Ortiz R, Paterson AH, Simon PW, Tohme J, Tuberosa R, Valliyodan B, Varshney RK, Wullschleger SD, Yano M, Prasad M. Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects. FRONTIERS IN PLANT SCIENCE 2015; 6:563. [PMID: 26322050 PMCID: PMC4531421 DOI: 10.3389/fpls.2015.00563] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 07/08/2015] [Indexed: 05/19/2023]
Abstract
Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops, which can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful in enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.
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Affiliation(s)
| | - Mehanathan Muthamilarasan
- Department of Plant Molecular Genetics and Genomics, National Institute of Plant Genome ResearchNew Delhi, India
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of QueenslandSt Lucia, QLD, Australia
| | - David Edwards
- School of Agriculture and Food Sciences, University of QueenslandBrisbane, QLD, Australia
| | - Rishu Sharma
- Department of Plant Pathology, Faculty of Agriculture, Bidhan Chandra Krishi ViswavidyalayaMohanpur, India
| | - Michael Abberton
- Genetic Resources Centre, International Institute of Tropical AgricultureIbadan, Nigeria
| | - Jacqueline Batley
- Centre for Integrated Legume Research, University of QueenslandBrisbane, QLD, Australia
| | - Alison Bentley
- The John Bingham Laboratory, National Institute of Agricultural BotanyCambridge, UK
| | | | - John Bryant
- CLES, Hatherly Laboratories, University of ExeterExeter, UK
| | - Hongwei Cai
- Forage Crop Research Institute, Japan Grassland Agriculture and Forage Seed AssociationNasushiobara, Japan
- Department of Plant Genetics and Breeding, College of Agronomy and Biotechnology, China Agricultural UniversityBeijing, China
| | - Mehmet Cakir
- Faculty of Science and Engineering, School of Biological Sciences and Biotechnology, Murdoch UniversityMurdoch, WA, Australia
| | - Leland J. Cseke
- Department of Biological Sciences, The University of Alabama in HuntsvilleHuntsville, AL, USA
| | - James Cockram
- The John Bingham Laboratory, National Institute of Agricultural BotanyCambridge, UK
| | | | - Ciro De Pace
- Department of Agriculture, Forests, Nature and Energy, University of TusciaViterbo, Italy
| | - Hannes Dempewolf
- Global Crop Diversity Trust, Platz der Vereinten NationenBonn, Germany
| | - Shelby Ellison
- Department of Horticulture, University of WisconsinMadison, WI, USA
| | - Paul Gepts
- Section of Crop and Ecosystem Sciences, Department of Plant Sciences, University of California, DavisDavis, CA, USA
| | - Andy Greenland
- The John Bingham Laboratory, National Institute of Agricultural BotanyCambridge, UK
| | - Anthony Hall
- Department of Botany and Plant Sciences, University of CaliforniaRiverside, Riverside, USA
| | - Kiyosumi Hori
- Agrogenomics Research Center, National Institute of Agrobiological SciencesTsukuba, Japan
| | | | - Mike W. Humphreys
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityWales, UK
| | - Massimo Iorizzo
- Department of Horticulture, University of WisconsinMadison, WI, USA
| | | | - Athole Marshall
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityWales, UK
| | - Sean Mayes
- Biotechnology and Crop Genetics, Crops for the FutureSemenyih, Malaysia
| | - Henry T. Nguyen
- National Center for Soybean Biotechnology and Division of Plant Science, University of MissouriColumbia, MO, USA
| | | | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural SciencesSundvagen, Sweden
| | | | - Philipp W. Simon
- Department of Horticulture, USDA-ARS, University of WisconsinMadison, WI, USA
| | - Joe Tohme
- Agrobiodiversity and Biotechnology Project, Centro International de Agricultura TropicalCali, Columbia
| | | | - Babu Valliyodan
- National Center for Soybean Biotechnology and Division of Plant Science, University of MissouriColumbia, MO, USA
| | - Rajeev K. Varshney
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Stan D. Wullschleger
- Oak Ridge National Laboratory, Environmental Sciences Division, Climate Change Science InstituteOak Ridge, TN, USA
| | - Masahiro Yano
- National Agriculture and Food Research Organization, Institute of Crop ScienceTsukuba, Japan
| | - Manoj Prasad
- Department of Plant Molecular Genetics and Genomics, National Institute of Plant Genome ResearchNew Delhi, India
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Kujur A, Upadhyaya HD, Shree T, Bajaj D, Das S, Saxena MS, Badoni S, Kumar V, Tripathi S, Gowda CLL, Sharma S, Singh S, Tyagi AK, Parida SK. Ultra-high density intra-specific genetic linkage maps accelerate identification of functionally relevant molecular tags governing important agronomic traits in chickpea. Sci Rep 2015; 5:9468. [PMID: 25942004 PMCID: PMC5386344 DOI: 10.1038/srep09468] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 03/04/2015] [Indexed: 12/28/2022] Open
Abstract
We discovered 26785 and 16573 high-quality SNPs differentiating two parental genotypes of a RIL mapping population using reference desi and kabuli genome-based GBS assay. Of these, 3625 and 2177 SNPs have been integrated into eight desi and kabuli chromosomes, respectively in order to construct ultra-high density (0.20-0.37 cM) intra-specific chickpea genetic linkage maps. One of these constructed high-resolution genetic map has potential to identify 33 major genomic regions harbouring 35 robust QTLs (PVE: 17.9-39.7%) associated with three agronomic traits, which were mapped within <1 cM mean marker intervals on desi chromosomes. The extended LD (linkage disequilibrium) decay (~15 cM) in chromosomes of genetic maps have encouraged us to use a rapid integrated approach (comparative QTL mapping, QTL-region specific haplotype/LD-based trait association analysis, expression profiling and gene haplotype-based association mapping) rather than a traditional QTL map-based cloning method to narrow-down one major seed weight (SW) robust QTL region. It delineated favourable natural allelic variants and superior haplotype-containing one seed-specific candidate embryo defective gene regulating SW in chickpea. The ultra-high-resolution genetic maps, QTLs/genes and alleles/haplotypes-related genomic information generated and integrated strategy for rapid QTL/gene identification developed have potential to expedite genomics-assisted breeding applications in crop plants, including chickpea for their genetic enhancement.
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Affiliation(s)
- Alice Kujur
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Hari D. Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Tanima Shree
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shouvik Das
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Maneesha S. Saxena
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Saurabh Badoni
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Vinod Kumar
- National Research Centre on Plant Biotechnology (NRCPB), New Delhi 110012, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi 110012, India
| | - C. L. L. Gowda
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Shivali Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Sube Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Akhilesh K. Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Swarup K. Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
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Das S, Upadhyaya HD, Bajaj D, Kujur A, Badoni S, Laxmi, Kumar V, Tripathi S, Gowda CLL, Sharma S, Singh S, Tyagi AK, Parida SK. Deploying QTL-seq for rapid delineation of a potential candidate gene underlying major trait-associated QTL in chickpea. DNA Res 2015; 22:193-203. [PMID: 25922536 PMCID: PMC4463844 DOI: 10.1093/dnares/dsv004] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/20/2015] [Indexed: 11/24/2022] Open
Abstract
A rapid high-resolution genome-wide strategy for molecular mapping of major QTL(s)/gene(s) regulating important agronomic traits is vital for in-depth dissection of complex quantitative traits and genetic enhancement in chickpea. The present study for the first time employed a NGS-based whole-genome QTL-seq strategy to identify one major genomic region harbouring a robust 100-seed weight QTL using an intra-specific 221 chickpea mapping population (desi cv. ICC 7184 × desi cv. ICC 15061). The QTL-seq-derived major SW QTL (CaqSW1.1) was further validated by single-nucleotide polymorphism (SNP) and simple sequence repeat (SSR) marker-based traditional QTL mapping (47.6% R2 at higher LOD >19). This reflects the reliability and efficacy of QTL-seq as a strategy for rapid genome-wide scanning and fine mapping of major trait regulatory QTLs in chickpea. The use of QTL-seq and classical QTL mapping in combination narrowed down the 1.37 Mb (comprising 177 genes) major SW QTL (CaqSW1.1) region into a 35 kb genomic interval on desi chickpea chromosome 1 containing six genes. One coding SNP (G/A)-carrying constitutive photomorphogenic9 (COP9) signalosome complex subunit 8 (CSN8) gene of these exhibited seed-specific expression, including pronounced differential up-/down-regulation in low and high seed weight mapping parents and homozygous individuals during seed development. The coding SNP mined in this potential seed weight-governing candidate CSN8 gene was found to be present exclusively in all cultivated species/genotypes, but not in any wild species/genotypes of primary, secondary and tertiary gene pools. This indicates the effect of strong artificial and/or natural selection pressure on target SW locus during chickpea domestication. The proposed QTL-seq-driven integrated genome-wide strategy has potential to delineate major candidate gene(s) harbouring a robust trait regulatory QTL rapidly with optimal use of resources. This will further assist us to extrapolate the molecular mechanism underlying complex quantitative traits at a genome-wide scale leading to fast-paced marker-assisted genetic improvement in diverse crop plants, including chickpea.
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Affiliation(s)
- Shouvik Das
- National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502324, India
| | - Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Alice Kujur
- National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Saurabh Badoni
- National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Laxmi
- National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Vinod Kumar
- National Research Centre on Plant Biotechnology (NRCPB), New Delhi 110012, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi 110012, India
| | - C L Laxmipathi Gowda
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502324, India
| | - Shivali Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502324, India
| | - Sube Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502324, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
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