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Bakala HS, Devi J, Singh G, Singh I. Drought and heat stress: insights into tolerance mechanisms and breeding strategies for pigeonpea improvement. PLANTA 2024; 259:123. [PMID: 38622376 DOI: 10.1007/s00425-024-04401-6] [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: 01/13/2024] [Accepted: 03/29/2024] [Indexed: 04/17/2024]
Abstract
MAIN CONCLUSION Pigeonpea has potential to foster sustainable agriculture and resilience in evolving climate change; understanding bio-physiological and molecular mechanisms of heat and drought stress tolerance is imperative to developing resilience cultivars. Pigeonpea is an important legume crop that has potential resilience in the face of evolving climate scenarios. However, compared to other legumes, there has been limited research on abiotic stress tolerance in pigeonpea, particularly towards drought stress (DS) and heat stress (HS). To address this gap, this review delves into the genetic, physiological, and molecular mechanisms that govern pigeonpea's response to DS and HS. It emphasizes the need to understand how this crop combats these stresses and exhibits different types of tolerance and adaptation mechanisms through component traits. The current article provides a comprehensive overview of the complex interplay of factors contributing to the resilience of pigeonpea under adverse environmental conditions. Furthermore, the review synthesizes information on major breeding techniques, encompassing both conventional methods and modern molecular omics-assisted tools and techniques. It highlights the potential of genomics and phenomics tools and their pivotal role in enhancing adaptability and resilience in pigeonpea. Despite the progress made in genomics, phenomics and big data analytics, the complexity of drought and heat tolerance in pigeonpea necessitate continuous exploration at multi-omic levels. High-throughput phenotyping (HTP) is crucial for gaining insights into perplexed interactions among genotype, environment, and management practices (GxExM). Thus, integration of advanced technologies in breeding programs is critical for developing pigeonpea varieties that can withstand the challenges posed by climate change. This review is expected to serve as a valuable resource for researchers, providing a deeper understanding of the mechanisms underlying abiotic stress tolerance in pigeonpea and offering insights into modern breeding strategies that can contribute to the development of resilient varieties suited for changing environmental conditions.
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Affiliation(s)
- Harmeet Singh Bakala
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Jomika Devi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Gurjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
- Texas A&M University, AgriLife Research Center, Beaumont, TX, 77713, USA.
| | - Inderjit Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
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Dwivedi SL, Heslop-Harrison P, Spillane C, McKeown PC, Edwards D, Goldman I, Ortiz R. Evolutionary dynamics and adaptive benefits of deleterious mutations in crop gene pools. TRENDS IN PLANT SCIENCE 2023; 28:685-697. [PMID: 36764870 DOI: 10.1016/j.tplants.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 12/03/2022] [Accepted: 01/18/2023] [Indexed: 05/13/2023]
Abstract
Mutations with deleterious consequences in nature may be conditionally deleterious in crop plants. That is, while some genetic variants may reduce fitness under wild conditions and be subject to purifying selection, they can be under positive selection in domesticates. Such deleterious alleles can be plant breeding targets, particularly for complex traits. The difficulty of distinguishing favorable from unfavorable variants reduces the power of selection, while favorable trait variation and heterosis may be attributable to deleterious alleles. Here, we review the roles of deleterious mutations in crop breeding and discuss how they can be used as a new avenue for crop improvement with emerging genomic tools, including HapMaps and pangenome analysis, aiding the identification, removal, or exploitation of deleterious mutations.
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Affiliation(s)
| | - Pat Heslop-Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Charles Spillane
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
| | - Peter C McKeown
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
| | - Irwin Goldman
- Department of Horticulture, College of Agricultural and Life Sciences, University of Wisconsin Madison, WI 53706, USA
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, SE 23053, Sweden.
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3
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Salgotra RK, Stewart CN. Genetic Augmentation of Legume Crops Using Genomic Resources and Genotyping Platforms for Nutritional Food Security. PLANTS (BASEL, SWITZERLAND) 2022; 11:1866. [PMID: 35890499 PMCID: PMC9325189 DOI: 10.3390/plants11141866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 11/24/2022]
Abstract
Recent advances in next generation sequencing (NGS) technologies have led the surge of genomic resources for the improvement legume crops. Advances in high throughput genotyping (HTG) and high throughput phenotyping (HTP) enable legume breeders to improve legume crops more precisely and efficiently. Now, the legume breeder can reshuffle the natural gene combinations of their choice to enhance the genetic potential of crops. These genomic resources are efficiently deployed through molecular breeding approaches for genetic augmentation of important legume crops, such as chickpea, cowpea, pigeonpea, groundnut, common bean, lentil, pea, as well as other underutilized legume crops. In the future, advances in NGS, HTG, and HTP technologies will help in the identification and assembly of superior haplotypes to tailor the legume crop varieties through haplotype-based breeding. This review article focuses on the recent development of genomic resource databases and their deployment in legume molecular breeding programmes to secure global food security.
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Affiliation(s)
- Romesh K. Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, Chatha, Jammu 190008, India
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4
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Thudi M, Palakurthi R, Schnable JC, Chitikineni A, Dreisigacker S, Mace E, Srivastava RK, Satyavathi CT, Odeny D, Tiwari VK, Lam HM, Hong YB, Singh VK, Li G, Xu Y, Chen X, Kaila S, Nguyen H, Sivasankar S, Jackson SA, Close TJ, Shubo W, Varshney RK. Genomic resources in plant breeding for sustainable agriculture. JOURNAL OF PLANT PHYSIOLOGY 2021; 257:153351. [PMID: 33412425 PMCID: PMC7903322 DOI: 10.1016/j.jplph.2020.153351] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 05/19/2023]
Abstract
Climate change during the last 40 years has had a serious impact on agriculture and threatens global food and nutritional security. From over half a million plant species, cereals and legumes are the most important for food and nutritional security. Although systematic plant breeding has a relatively short history, conventional breeding coupled with advances in technology and crop management strategies has increased crop yields by 56 % globally between 1965-85, referred to as the Green Revolution. Nevertheless, increased demand for food, feed, fiber, and fuel necessitates the need to break existing yield barriers in many crop plants. In the first decade of the 21st century we witnessed rapid discovery, transformative technological development and declining costs of genomics technologies. In the second decade, the field turned towards making sense of the vast amount of genomic information and subsequently moved towards accurately predicting gene-to-phenotype associations and tailoring plants for climate resilience and global food security. In this review we focus on genomic resources, genome and germplasm sequencing, sequencing-based trait mapping, and genomics-assisted breeding approaches aimed at developing biotic stress resistant, abiotic stress tolerant and high nutrition varieties in six major cereals (rice, maize, wheat, barley, sorghum and pearl millet), and six major legumes (soybean, groundnut, cowpea, common bean, chickpea and pigeonpea). We further provide a perspective and way forward to use genomic breeding approaches including marker-assisted selection, marker-assisted backcrossing, haplotype based breeding and genomic prediction approaches coupled with machine learning and artificial intelligence, to speed breeding approaches. The overall goal is to accelerate genetic gains and deliver climate resilient and high nutrition crop varieties for sustainable agriculture.
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Affiliation(s)
- Mahendar Thudi
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India; University of Southern Queensland, Toowoomba, Australia
| | - Ramesh Palakurthi
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Emma Mace
- Agri-Science Queensland, Department of Agriculture & Fisheries (DAF), Warwick, Australia
| | - Rakesh K Srivastava
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - C Tara Satyavathi
- Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Damaris Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya
| | | | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - Yan Bin Hong
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Vikas K Singh
- South Asia Hub, International Rice Research Institute (IRRI), Hyderabad, India
| | - Guowei Li
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yunbi Xu
- International Maize and Wheat Improvement Center (CYMMIT), Mexico DF, Mexico; Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Sanjay Kaila
- Department of Biotechnology, Ministry of Science and Technology, Government of India, India
| | - Henry Nguyen
- National Centre for Soybean Research, University of Missouri, Columbia, USA
| | - Sobhana Sivasankar
- Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Vienna, Austria
| | | | | | - Wan Shubo
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
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Saxena RK, Hake A, Bohra A, Khan AW, Hingane A, Sultana R, Singh IP, Naik SJS, Varshney RK. A diagnostic marker kit for Fusarium wilt and sterility mosaic diseases resistance in pigeonpea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:367-379. [PMID: 33079215 PMCID: PMC7813729 DOI: 10.1007/s00122-020-03702-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 10/03/2020] [Indexed: 05/29/2023]
Abstract
Fusarium wilt (FW) and sterility mosaic diseases (SMD) are key biotic constraints to pigeonpea production. Occurrence of these two diseases in congenial conditions is reported to cause complete yield loss in susceptible pigeonpea cultivars. Various studies to elucidate genomic architecture of the two traits have revealed significant marker-trait associations for use in breeding programs. However, these DNA markers could not be used effectively in genomics-assisted breeding for developing FW and SMD resistant varieties primarily due to pathogen variability, location or background specificity, lesser phenotypic variance explained by the reported QTL and cost-inefficiency of the genotyping assays. Therefore, in the present study, a novel approach has been used to develop a diagnostic kit for identification of suitable FW and SMD resistant lines. This kit was developed with 10 markers each for FW and SMD resistance. Investigation of the diversity of these loci has shown the role of different alleles in different resistant genotypes. Two genes (C.cajan_03691 and C.cajan_18888) for FW resistance and four genes (C.cajan_07858, C.cajan_20995, C.cajan_21801 and C.cajan_17341) for SMD resistance have been identified. More importantly, we developed a customized and cost-effective Kompetitive allele-specific PCR genotyping assay for the identified genes in order to encourage their downstream applications in pigeonpea breeding programs. The diagnostic marker kit developed here will offer great strength to pigeonpea varietal development program, since the resistance against these two diseases is essentially required for nominating an improved line in varietal release pipeline.
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Affiliation(s)
- Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, India.
| | - Anil Hake
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, India
| | - Abhishek Bohra
- ICAR- Indian Institute of Pulses Research (IIPR), Kanpur, Uttar Pradesh, India
| | - Aamir W Khan
- ICAR- Indian Institute of Pulses Research (IIPR), Kanpur, Uttar Pradesh, India
| | - Anupama Hingane
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, India
| | - Rafat Sultana
- Bihar Agricultural University, Sabour, Bhagalpur, Bihar, India
| | - Indra Prakash Singh
- ICAR- Indian Institute of Pulses Research (IIPR), Kanpur, Uttar Pradesh, India
| | - S J Satheesh Naik
- ICAR- Indian Institute of Pulses Research (IIPR), Kanpur, Uttar Pradesh, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, India.
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Singh N, Rai V, Singh NK. Multi-omics strategies and prospects to enhance seed quality and nutritional traits in pigeonpea. THE NUCLEUS 2020. [DOI: 10.1007/s13237-020-00341-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Bohra A, Saxena KB, Varshney RK, Saxena RK. Genomics-assisted breeding for pigeonpea improvement. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1721-1737. [PMID: 32062675 DOI: 10.1007/s00122-020-03563-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 02/08/2020] [Indexed: 05/25/2023]
Abstract
The review outlines advances in pigeonpea genomics, breeding and seed delivery systems to achieve yield gains at farmers' field. Pigeonpea is a nutritious and stress-tolerant grain legume crop of tropical and subtropical regions. Decades of breeding efforts in pigeonpea have resulted in development of a number of high-yielding cultivars. Of late, the development of CMS-based hybrid technology has allowed the exploitation of heterosis for yield enhancement in this crop. Despite these positive developments, the actual on-farm yield of pigeonpea is still well below its potential productivity. Growing needs for high and sustainable pigeonpea yields motivate scientists to improve the breeding efficiency to deliver a steady stream of cultivars that will provide yield benefits under both ideal and stressed environments. To achieve this objective in the shortest possible time, it is imperative that various crop breeding activities are integrated with appropriate new genomics technologies. In this context, the last decade has seen a remarkable rise in the generation of important genomic resources such as genome-wide markers, high-throughput genotyping assays, saturated genome maps, marker/gene-trait associations, whole-genome sequence and germplasm resequencing data. In some cases, marker/gene-trait associations are being employed in pigeonpea breeding programs to improve the valuable yield and market-preferred traits. Embracing new breeding tools like genomic selection and speed breeding is likely to improve genetic gains. Breeding high-yielding pigeonpea cultivars with key adaptation traits also calls for a renewed focus on systematic selection and utilization of targeted genetic resources. Of equal importance is to overcome the difficulties being faced by seed industry to take the new cultivars to the doorstep of farmers.
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Affiliation(s)
- Abhishek Bohra
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India.
| | - K B Saxena
- , 17, NMC Housing, Al Ain, Abu Dhabi, United Arab Emirates
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India.
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Saxena RK, Kale S, Mir RR, Mallikarjuna N, Yadav P, Das RR, Molla J, Sonnappa M, Ghanta A, Narasimhan Y, Rathore A, Kumar CVS, Varshney RK. Genotyping-by-sequencing and multilocation evaluation of two interspecific backcross populations identify QTLs for yield-related traits in pigeonpea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:737-749. [PMID: 31844966 DOI: 10.1007/s00122-019-03504-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 12/06/2019] [Indexed: 06/10/2023]
Abstract
This study has identified single-nucleotide polymorphism (SNP) markers associated with nine yield-related traits in pigeonpea by using two backcross populations (BP) developed through interspecific crosses and evaluating them at two locations and 3 years. In both the populations, markers have shown strong segregation distortion; therefore, a quantitative trait locus (QTL) mapping mixed model was used. A total of 86 QTLs explaining 12-21% phenotypic variation were detected in BP-1. On the other hand, 107 QTLs explaining 11-29% phenotypic variation were detected in BP-2. Although most QTLs were environment and trait specific, few stable and consistent QTLs were also detected. Interestingly, 11 QTLs in BP-2 were associated with more than one trait. Among these QTLs, eight QTLs associated with days to 50% flowering and days to 75% maturity were located on CcLG07. One SNP "S7_14185076" marker in BP-2 population has been found associated with four traits, namely days to 50% flowering, days to 75% maturity, primary branches per plant and secondary branches per plant with positive additive effect. Hence, the present study has not only identified QTLs for yield-related traits, but also discovered novel alleles from wild species, which can be used for improvement of traits through genomics-assisted breeding.
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Affiliation(s)
- Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRSAT), Patancheru, Telangana, 502324, India
| | - Sandip Kale
- The Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Seeland, OT Gatersleben, Germany
| | - Reyazul Rouf Mir
- Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Wadura Campus, Sopore, Kashmir, 193201, India
| | - Nalini Mallikarjuna
- International Crops Research Institute for the Semi-Arid Tropics (ICRSAT), Patancheru, Telangana, 502324, India
| | - Pooja Yadav
- International Crops Research Institute for the Semi-Arid Tropics (ICRSAT), Patancheru, Telangana, 502324, India
| | - Roma Rani Das
- International Crops Research Institute for the Semi-Arid Tropics (ICRSAT), Patancheru, Telangana, 502324, India
| | - Johiruddin Molla
- International Crops Research Institute for the Semi-Arid Tropics (ICRSAT), Patancheru, Telangana, 502324, India
| | - Muniswamy Sonnappa
- Agricultural Research Station (UAS-Raichur), Gulbarga, Karnataka, 585101, India
| | - Anuradha Ghanta
- Professor Jayashankar Telangana State Agricultural University, Rajendranagar, Hyderabad, Telangana, 500030, India
| | - Yamini Narasimhan
- Professor Jayashankar Telangana State Agricultural University, Rajendranagar, Hyderabad, Telangana, 500030, India
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRSAT), Patancheru, Telangana, 502324, India
| | - C V Sameer Kumar
- Professor Jayashankar Telangana State Agricultural University, Rajendranagar, Hyderabad, Telangana, 500030, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRSAT), Patancheru, Telangana, 502324, India.
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Seed protein content and its relationships with agronomic traits in pigeonpea is controlled by both main and epistatic effects QTLs. Sci Rep 2020; 10:214. [PMID: 31937848 PMCID: PMC6959250 DOI: 10.1038/s41598-019-56903-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/10/2019] [Indexed: 11/08/2022] Open
Abstract
The genetic architecture of seed protein content (SPC) and its relationships to agronomic traits in pigeonpea is poorly understood. Accordingly, five F2 populations segregating for SPC and four agronomic traits (seed weight (SW), seed yield (SY), growth habit (GH) and days to first flowering (DFF)) were phenotyped and genotyped using genotyping-by-sequencing approach. Five high-density population-specific genetic maps were constructed with an average inter-marker distance of 1.6 to 3.5 cM, and subsequently, integrated into a consensus map with average marker spacing of 1.6 cM. Based on analysis of phenotyping data and genotyping data, 192 main effect QTLs (M-QTLs) with phenotypic variation explained (PVE) of 0.7 to 91.3% were detected for the five traits across the five populations. Major effect (PVE ≥ 10%) M-QTLs included 14 M-QTLs for SPC, 16 M-QTLs for SW, 17 M-QTLs for SY, 19 M-QTLs for GH and 24 M-QTLs for DFF. Also, 573 epistatic QTLs (E-QTLs) were detected with PVE ranging from 6.3 to 99.4% across traits and populations. Colocalization of M-QTLs and E-QTLs explained the genetic basis of the significant (P < 0.05) correlations of SPC with SW, SY, DFF and GH. The nature of genetic architecture of SPC and its relationship with agronomic traits suggest that genomics-assisted breeding targeting genome-wide variations would be effective for the simultaneous improvement of SPC and other important traits.
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Yadav P, Saxena KB, Hingane A, Kumar CVS, Kandalkar VS, Varshney RK, Saxena RK. An "Axiom Cajanus SNP Array" based high density genetic map and QTL mapping for high-selfing flower and seed quality traits in pigeonpea. BMC Genomics 2019; 20:235. [PMID: 30898108 PMCID: PMC6429735 DOI: 10.1186/s12864-019-5595-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/11/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pigeonpea has considerable extent of insect-aided natural out-crossing that impedes genetic purity of seeds. Pre-anthesis cleistogamy in pigeonpea promotes self-pollination which helps in maintaining genetic purity. The cleistogamous flowers are linked with shriveled seeds, an undesirable trait from variety adoption point of view, and breeding using genomics tools can help in overcoming this constraint. Therefore, in order to identify genomic regions governing these target traits, one recombinant inbred line (RIL) population was developed using contrasting parents (ICPL 99010 and ICP 5529) for flower shape and shriveled seeds. The RILs were phenotyped for two years and genotyped using the Axiom Cajanus SNP Array. RESULTS Out of the 56,512 unique sequence variations on the array, the mapping population showed 8634 single nucleotide polymorphism (SNPs) segregating across the genome. These data facilitated generation of a high density genetic map covering 6818 SNPs in 974 cM with an average inter-marker distance of 0.1 cM, which is the lowest amongst all pigeonpea genetic maps reported. Quantitative trait loci (QTL) analysis using this genetic map and phenotyping data identified 5 QTLs associated with cleistogamous flower, 3 QTLs for shriveled seed and 1 QTL for seed size. The phenotypic variance explained by these QTLs ranged from 9.1 to 50.6%. A consistent QTL "qCl3.2" was identified for cleistogamous flower on CcLG03 covering a span of 42 kb in the pigeonpea genome. Epistatic QTLs were also identified for cleistogamous flower and shriveled seed traits. CONCLUSION Identified QTLs and genomic interactions for cleistogamous flower, shriveled seed and seed size will help in incorporating the required floral architecture in pigeonpea varieties/lines. Besides, it will also be useful in understanding the molecular mechanisms, and map-based gene cloning for the target traits.
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Affiliation(s)
- Pooja Yadav
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India.,Department of Genetics and Plant Breeding, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya (RVSKVV), Gwalior, 474 002, India
| | - K B Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - Anupama Hingane
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - C V Sameer Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - V S Kandalkar
- Department of Genetics and Plant Breeding, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya (RVSKVV), Gwalior, 474 002, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India.
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11
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Varshney RK, Pandey MK, Bohra A, Singh VK, Thudi M, Saxena RK. Toward the sequence-based breeding in legumes in the post-genome sequencing era. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:797-816. [PMID: 30560464 PMCID: PMC6439141 DOI: 10.1007/s00122-018-3252-x] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/27/2018] [Indexed: 05/19/2023]
Abstract
Efficiency of breeding programs of legume crops such as chickpea, pigeonpea and groundnut has been considerably improved over the past decade through deployment of modern genomic tools and technologies. For instance, next-generation sequencing technologies have facilitated availability of genome sequence assemblies, re-sequencing of several hundred lines, development of HapMaps, high-density genetic maps, a range of marker genotyping platforms and identification of markers associated with a number of agronomic traits in these legume crops. Although marker-assisted backcrossing and marker-assisted selection approaches have been used to develop superior lines in several cases, it is the need of the hour for continuous population improvement after every breeding cycle to accelerate genetic gain in the breeding programs. In this context, we propose a sequence-based breeding approach which includes use of independent or combination of parental selection, enhancing genetic diversity of breeding programs, forward breeding for early generation selection, and genomic selection using sequencing/genotyping technologies. Also, adoption of speed breeding technology by generating 4-6 generations per year will be contributing to accelerate genetic gain. While we see a huge potential of the sequence-based breeding to revolutionize crop improvement programs in these legumes, we anticipate several challenges especially associated with high-quality and precise phenotyping at affordable costs, data analysis and management related to improving breeding operation efficiency. Finally, integration of improved seed systems and better agronomic packages with the development of improved varieties by using sequence-based breeding will ensure higher genetic gains in farmers' fields.
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Affiliation(s)
- Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India.
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Abhishek Bohra
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India
| | - Vikas K Singh
- International Rice Research Institute (IRRI), IRRI South Asia Hub, ICRISAT, Hyderabad, 502324, India
| | - Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
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Chiurugwi T, Kemp S, Powell W, Hickey LT. Speed breeding orphan crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:607-616. [PMID: 30341490 DOI: 10.1007/s00122-018-3202-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/05/2018] [Indexed: 05/18/2023]
Abstract
This review explores how speed breeding protocols that hasten plant growth and development could be applied to shorten breeding cycles and accelerate research activities in orphan crops. There is a growing need for the agri-food sector to sustainably produce larger quantities of higher-quality food, feed and fuel using fewer resources, within the context of changing agroclimatic conditions. Meeting this challenge will require the accelerated development and dissemination of improved plant varieties and substantial improvement of agricultural practices. Speed breeding protocols that shorten plant generation times can hasten breeding and research to help fulfil the ever-increasing demands. Global agri-food systems rely on a relatively small number of plant species; however, there are calls to widen the scope of globally important crops to include orphan crops, which are currently grown and used by the world's poorest people or marketed as niche products for affluent consumers. Orphan crops can supply global diets with key nutrients, support economic development in the world's poorest regions, and bolster the resilience of the global agri-food sector to biotic and abiotic stresses. Little research effort has been invested in orphan crops, with farmers growing landraces that are sourced and traded through poorly structured market systems. Efforts are underway to develop breeding resources and techniques to improve orphan crops. Here, we highlight the current efforts and opportunities to speed breed orphan crops and discuss alternative approaches to deploy speed breeding in the less-resourced regions of the world. Speed breeding is a tool that, when used together with other multidisciplinary R&D approaches, can contribute to the rapid creation of new crop varieties, agricultural practices and products, supporting the production and utilisation of orphan crops at a commercial scale.
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Affiliation(s)
| | - Stuart Kemp
- PastureWise Pty Ltd, Cargerie, VIC, 3334, Australia
| | - Wayne Powell
- SRUC, Peter Wilson Building, King's Buildings, West Mains Road, Edinburgh, EH9 3JG, UK.
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia.
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13
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Saxena RK, Rathore A, Bohra A, Yadav P, Das RR, Khan AW, Singh VK, Chitikineni A, Singh IP, Kumar CVS, Saxena KB, Varshney RK. Development and Application of High-Density Axiom Cajanus SNP Array with 56K SNPs to Understand the Genome Architecture of Released Cultivars and Founder Genotypes. THE PLANT GENOME 2018; 11:180005. [PMID: 30512043 DOI: 10.3835/plantgenome2018.01.0005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
As one of the major outputs of next-generation sequencing (NGS), a large number of genome-wide single-nucleotide polymorphisms (SNPs) have been developed in pigeonpea [ (L.) Huth.]. However, SNPs require a genotyping platform or assay to be used in different evolutionary studies or in crop improvement programs. Therefore, we developed an Axiom SNP array with 56K SNPs uniformly distributed across the genome and assessed its utility in a genetic diversity study. From the whole-genome resequencing (WGRS) data on 104 pigeonpea lines, ∼2 million sequence variations (SNPs and insertion-deletions [InDels]) were identified, from which a subset of 56,512 unique and informative sequence variations were selected to develop the array. The Axiom SNP array developed was used for genotyping 103 pigeonpea lines encompassing 63 cultivars released between 1960 and 2014 and 40 breeding, germplasm, and founder lines. Genotyping data thus generated on 103 pigeonpea lines provided 51,201 polymorphic SNPs and InDels. Genetic diversity analysis provided in-depth insights into the genetic architecture and trends in temporal diversity in pigeonpea cultivars. Therefore, the continuous use of the high-density Axiom SNP array developed will accelerate high-resolution trait mapping, marker-assisted breeding, and genomic selection efforts in pigeonpea.
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14
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Obala J, Saxena RK, Singh VK, Kumar CVS, Saxena KB, Tongoona P, Sibiya J, Varshney RK. Development of sequence-based markers for seed protein content in pigeonpea. Mol Genet Genomics 2018; 294:57-68. [PMID: 30173295 DOI: 10.1007/s00438-018-1484-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 08/22/2018] [Indexed: 12/30/2022]
Abstract
Pigeonpea is an important source of dietary protein to over a billion people globally, but genetic enhancement of seed protein content (SPC) in the crop has received limited attention for a long time. Use of genomics-assisted breeding would facilitate accelerating genetic gain for SPC. However, neither genetic markers nor genes associated with this important trait have been identified in this crop. Therefore, the present study exploited whole genome re-sequencing (WGRS) data of four pigeonpea genotypes (~ 12X coverage) to identify sequence-based markers and associated candidate genes for SPC. By combining a common variant filtering strategy on available WGRS data with knowledge of gene functions in relation to SPC, 108 sequence variants from 57 genes were identified. These genes were assigned to 19 GO molecular function categories with 56% belonging to only two categories. Furthermore, Sanger sequencing confirmed presence of 75.4% of the variants in 37 genes. Out of 30 sequence variants converted into CAPS/dCAPS markers, 17 showed high level of polymorphism between low and high SPC genotypes. Assay of 16 of the polymorphic CAPS/dCAPS markers on an F2 population of the cross ICP 5529 (high SPC) × ICP 11605 (low SPC), resulted in four of the CAPS/dCAPS markers significantly (P < 0.05) co-segregated with SPC. In summary, four markers derived from mutations in four genes will be useful for enhancing/regulating SPC in pigeonpea crop improvement programs.
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Affiliation(s)
- Jimmy Obala
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
- University of KwaZulu-Natal, African Center for Crop Improvement, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Vikas K Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - C V Sameer Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - K B Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Pangirayi Tongoona
- University of KwaZulu-Natal, African Center for Crop Improvement, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Julia Sibiya
- University of KwaZulu-Natal, African Center for Crop Improvement, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India.
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Varshney RK, Thudi M, Pandey MK, Tardieu F, Ojiewo C, Vadez V, Whitbread AM, Siddique KHM, Nguyen HT, Carberry PS, Bergvinson D. Accelerating genetic gains in legumes for the development of prosperous smallholder agriculture: integrating genomics, phenotyping, systems modelling and agronomy. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3293-3312. [PMID: 29514298 DOI: 10.1093/jxb/ery088] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 02/22/2018] [Indexed: 05/23/2023]
Abstract
Grain legumes form an important component of the human diet, provide feed for livestock, and replenish soil fertility through biological nitrogen fixation. Globally, the demand for food legumes is increasing as they complement cereals in protein requirements and possess a high percentage of digestible protein. Climate change has enhanced the frequency and intensity of drought stress, posing serious production constraints, especially in rainfed regions where most legumes are produced. Genetic improvement of legumes, like other crops, is mostly based on pedigree and performance-based selection over the past half century. To achieve faster genetic gains in legumes in rainfed conditions, this review proposes the integration of modern genomics approaches, high throughput phenomics, and simulation modelling in support of crop improvement that leads to improved varieties that perform with appropriate agronomy. Selection intensity, generation interval, and improved operational efficiencies in breeding are expected to further enhance the genetic gain in experimental plots. Improved seed access to farmers, combined with appropriate agronomic packages in farmers' fields, will deliver higher genetic gains. Enhanced genetic gains, including not only productivity but also nutritional and market traits, will increase the profitability of farming and the availability of affordable nutritious food especially in developing countries.
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Affiliation(s)
- Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Francois Tardieu
- French National Institute for Agricultural Research (INRA), Monpellier, France
| | - Chris Ojiewo
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya
| | - Vincent Vadez
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Institut de recherche pour le développement (IRD), Montpellier, France
| | - Anthony M Whitbread
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | | | - Peter S Carberry
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - David Bergvinson
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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16
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Saxena KB, Choudhary AK, Saxena RK, Varshney RK. Breeding pigeonpea cultivars for intercropping: synthesis and strategies. BREEDING SCIENCE 2018; 68:159-167. [PMID: 29875599 PMCID: PMC5982186 DOI: 10.1270/jsbbs.17105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 12/04/2017] [Indexed: 05/05/2023]
Abstract
Pigeonpea [Cajanus cajan (L.) Millsp.] is an ideal pulse crop of rainfed tropics and sub-tropics due to its high nutritive value and ability to survive various biotic and abiotic stresses. Thus it has continued to be cultivated on marginal land mostly under rainfed situation where the risk of crop failure is very high. To have insurance against crop failures and harvest more food in time and space, most farmers grow pigeonpea as an intercrop with short-aged cereals and other crops. Presently, intercropping system accounts for over 70% of the pigeonpea area. However, yield of pigeonpea in this system is very low (400-500 kg/ha). The non-availability of improved cultivars adapted specifically to the intercropping environments is perhaps the major constraint that accounts for low yield. Considering the food and nutritional needs of the ever increasing population, productivity enhancement of this high-protein pulse is highly indispensable. In this review, the authors critically examine the technical difficulties encountered by breeders in developing high yielding cultivars for intercropping systems and discuss the strategies to overcome these constraints.
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Affiliation(s)
- Kul Bhushan Saxena
- International Crops Research Institute for the Semi-arid Tropics,
Patancheru - 502 324, Telangana,
India
| | - Arbind K. Choudhary
- ICAR Research Complex for Eastern Region,
Patna 800 014, Bihar,
India
- Corresponding author (e-mail: )
| | - Rachit K. Saxena
- International Crops Research Institute for the Semi-arid Tropics,
Patancheru - 502 324, Telangana,
India
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-arid Tropics,
Patancheru - 502 324, Telangana,
India
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17
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Saxena RK, Obala J, Sinjushin A, Kumar CVS, Saxena KB, Varshney RK. Characterization and mapping of Dt1 locus which co-segregates with CcTFL1 for growth habit in pigeonpea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1773-1784. [PMID: 28540572 PMCID: PMC5565653 DOI: 10.1007/s00122-017-2924-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/11/2017] [Indexed: 05/13/2023]
Abstract
We report growth habit profiling following SEM, genetic mapping and QTL analysis. Highlighted CcTFL1 , a candidate for determinacy in pigeonpea, since an Indel marker derived from this gene co-segregated with Dt1 locus. Pigeonpea (Cajanus cajan) is one of the most important legume crops grown in arid and semi-arid regions of the world. It is characterized with few unique features compared with other legume species, such as Lotus, Medicago, and Glycine. One of them is growth habit, an important agronomic trait. In the present study, identification of mutations affecting growth habit accompanied by a precise analysis of phenotype has been done which will shed more light upon developmental regulation in pigeonpea. A genetic study was conducted to examine the inheritance of growth habit and a genotyping by sequencing (GBS)-based genetic map constructed using F2 mapping population derived from crossing parents ICP 5529 and ICP 11605. Inheritance studies clearly demonstrated the dominance of indeterminate (IDT) growth habit over determinate (DT) growth habit in F2 and F2:3 progenies. A total of 787 SNP markers were mapped in the genetic map of 1454 cM map length. Growth habit locus (Dt1) was mapped on the CcLG03 contributing more than 61% of total phenotypic variations. Subsequently, QTL analysis highlighted one gene, CcTFL1, as a candidate for determinacy in pigeonpea, since an Indel marker derived from this gene co-segregated with the Dt1 locus. Ability of this Indel-derived marker to differentiate DT/IDT lines was also validated on 262 pigeonpea lines. This study clearly demonstrated that CcTFL1 is a candidate gene for growth habit in pigeonpea and a user-friendly marker was developed in the present study which will allow low-cost genotyping without need of automation.
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Affiliation(s)
- Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India.
| | - Jimmy Obala
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
- University of KwaZulu-Natal, African Center for Crop Improvement, Private Bag X01, Scottsville, 3209, Pietermaritzburg, South Africa
| | - Andrey Sinjushin
- M. V. Lomonosov Moscow State University, Leninskie Gory, Moscow, 119991, Russia
| | - C V Sameer Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - K B Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India.
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Dwivedi SL, Scheben A, Edwards D, Spillane C, Ortiz R. Assessing and Exploiting Functional Diversity in Germplasm Pools to Enhance Abiotic Stress Adaptation and Yield in Cereals and Food Legumes. FRONTIERS IN PLANT SCIENCE 2017; 8:1461. [PMID: 28900432 PMCID: PMC5581882 DOI: 10.3389/fpls.2017.01461] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/07/2017] [Indexed: 05/03/2023]
Abstract
There is a need to accelerate crop improvement by introducing alleles conferring host plant resistance, abiotic stress adaptation, and high yield potential. Elite cultivars, landraces and wild relatives harbor useful genetic variation that needs to be more easily utilized in plant breeding. We review genome-wide approaches for assessing and identifying alleles associated with desirable agronomic traits in diverse germplasm pools of cereals and legumes. Major quantitative trait loci and single nucleotide polymorphisms (SNPs) associated with desirable agronomic traits have been deployed to enhance crop productivity and resilience. These include alleles associated with variation conferring enhanced photoperiod and flowering traits. Genetic variants in the florigen pathway can provide both environmental flexibility and improved yields. SNPs associated with length of growing season and tolerance to abiotic stresses (precipitation, high temperature) are valuable resources for accelerating breeding for drought-prone environments. Both genomic selection and genome editing can also harness allelic diversity and increase productivity by improving multiple traits, including phenology, plant architecture, yield potential and adaptation to abiotic stresses. Discovering rare alleles and useful haplotypes also provides opportunities to enhance abiotic stress adaptation, while epigenetic variation has potential to enhance abiotic stress adaptation and productivity in crops. By reviewing current knowledge on specific traits and their genetic basis, we highlight recent developments in the understanding of crop functional diversity and identify potential candidate genes for future use. The storage and integration of genetic, genomic and phenotypic information will play an important role in ensuring broad and rapid application of novel genetic discoveries by the plant breeding community. Exploiting alleles for yield-related traits would allow improvement of selection efficiency and overall genetic gain of multigenic traits. An integrated approach involving multiple stakeholders specializing in management and utilization of genetic resources, crop breeding, molecular biology and genomics, agronomy, stress tolerance, and reproductive/seed biology will help to address the global challenge of ensuring food security in the face of growing resource demands and climate change induced stresses.
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Affiliation(s)
| | - Armin Scheben
- School of Biological Sciences, Institute of Agriculture, University of Western Australia, PerthWA, Australia
| | - David Edwards
- School of Biological Sciences, Institute of Agriculture, University of Western Australia, PerthWA, Australia
| | - Charles Spillane
- Plant and AgriBiosciences Research Centre, Ryan Institute, National University of Ireland GalwayGalway, Ireland
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural SciencesAlnarp, Sweden
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Singh VK, Khan AW, Saxena RK, Sinha P, Kale SM, Parupalli S, Kumar V, Chitikineni A, Vechalapu S, Sameer Kumar CV, Sharma M, Ghanta A, Yamini KN, Muniswamy S, Varshney RK. Indel-seq: a fast-forward genetics approach for identification of trait-associated putative candidate genomic regions and its application in pigeonpea (Cajanus cajan). PLANT BIOTECHNOLOGY JOURNAL 2017; 15:906-914. [PMID: 28027425 PMCID: PMC5466435 DOI: 10.1111/pbi.12685] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 05/05/2023]
Abstract
Identification of candidate genomic regions associated with target traits using conventional mapping methods is challenging and time-consuming. In recent years, a number of single nucleotide polymorphism (SNP)-based mapping approaches have been developed and used for identification of candidate/putative genomic regions. However, in the majority of these studies, insertion-deletion (Indel) were largely ignored. For efficient use of Indels in mapping target traits, we propose Indel-seq approach, which is a combination of whole-genome resequencing (WGRS) and bulked segregant analysis (BSA) and relies on the Indel frequencies in extreme bulks. Deployment of Indel-seq approach for identification of candidate genomic regions associated with fusarium wilt (FW) and sterility mosaic disease (SMD) resistance in pigeonpea has identified 16 Indels affecting 26 putative candidate genes. Of these 26 affected putative candidate genes, 24 genes showed effect in the upstream/downstream of the genic region and two genes showed effect in the genes. Validation of these 16 candidate Indels in other FW- and SMD-resistant and FW- and SMD-susceptible genotypes revealed a significant association of five Indels (three for FW and two for SMD resistance). Comparative analysis of Indel-seq with other genetic mapping approaches highlighted the importance of the approach in identification of significant genomic regions associated with target traits. Therefore, the Indel-seq approach can be used for quick and precise identification of candidate genomic regions for any target traits in any crop species.
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Affiliation(s)
- Vikas K. Singh
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Aamir W. Khan
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Rachit K. Saxena
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Pallavi Sinha
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Sandip M. Kale
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Swathi Parupalli
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Vinay Kumar
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Annapurna Chitikineni
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Suryanarayana Vechalapu
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | | | - Mamta Sharma
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Anuradha Ghanta
- Agricultural Research Station (ARS)‐TandurProfessor Jayashankar Telangana State Agricultural University (PJTSAU)HyderabadTelangana StateIndia
| | - Kalinati Narasimhan Yamini
- Agricultural Research Station (ARS)‐TandurProfessor Jayashankar Telangana State Agricultural University (PJTSAU)HyderabadTelangana StateIndia
| | - Sonnappa Muniswamy
- Agricultural Research Station (ARS)‐GulbargaUniversity of Agricultural Sciences (UAS)RaichurKarnatakaIndia
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
- School of Plant Biology and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
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20
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Xu Y, Li P, Zou C, Lu Y, Xie C, Zhang X, Prasanna BM, Olsen MS. Enhancing genetic gain in the era of molecular breeding. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2641-2666. [PMID: 28830098 DOI: 10.1093/jxb/erx135] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 04/03/2017] [Indexed: 05/20/2023]
Abstract
As one of the important concepts in conventional quantitative genetics and breeding, genetic gain can be defined as the amount of increase in performance that is achieved annually through artificial selection. To develop pro ducts that meet the increasing demand of mankind, especially for food and feed, in addition to various industrial uses, breeders are challenged to enhance the potential of genetic gain continuously, at ever higher rates, while they close the gaps that remain between the yield potential in breeders' demonstration trials and the actual yield in farmers' fields. Factors affecting genetic gain include genetic variation available in breeding materials, heritability for traits of interest, selection intensity, and the time required to complete a breeding cycle. Genetic gain can be improved through enhancing the potential and closing the gaps, which has been evolving and complemented with modern breeding techniques and platforms, mainly driven by molecular and genomic tools, combined with improved agronomic practice. Several key strategies are reviewed in this article. Favorable genetic variation can be unlocked and created through molecular and genomic approaches including mutation, gene mapping and discovery, and transgene and genome editing. Estimation of heritability can be improved by refining field experiments through well-controlled and precisely assayed environmental factors or envirotyping, particularly for understanding and controlling spatial heterogeneity at the field level. Selection intensity can be significantly heightened through improvements in the scale and precision of genotyping and phenotyping. The breeding cycle time can be shortened by accelerating breeding procedures through integrated breeding approaches such as marker-assisted selection and doubled haploid development. All the strategies can be integrated with other widely used conventional approaches in breeding programs to enhance genetic gain. More transdisciplinary approaches, team breeding, will be required to address the challenge of maintaining a plentiful and safe food supply for future generations. New opportunities for enhancing genetic gain, a high efficiency breeding pipeline, and broad-sense genetic gain are also discussed prospectively.
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Affiliation(s)
- Yunbi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, CP 56130, México
| | - Ping Li
- Nantong Xinhe Bio-Technology, Nantong 226019, PR China
| | - Cheng Zou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Chuanxiao Xie
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xuecai Zhang
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, CP 56130, México
| | - Boddupalli M Prasanna
- CIMMYT (International Maize and Wheat Improvement Center), ICRAF campus, United Nations Avenue, Nairobi, Kenya
| | - Michael S Olsen
- CIMMYT (International Maize and Wheat Improvement Center), ICRAF campus, United Nations Avenue, Nairobi, Kenya
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21
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Construction of genotyping-by-sequencing based high-density genetic maps and QTL mapping for fusarium wilt resistance in pigeonpea. Sci Rep 2017; 7:1911. [PMID: 28507291 PMCID: PMC5432509 DOI: 10.1038/s41598-017-01537-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 03/31/2017] [Indexed: 11/09/2022] Open
Abstract
Fusarium wilt (FW) is one of the most important biotic stresses causing yield losses in pigeonpea. Genetic improvement of pigeonpea through genomics-assisted breeding (GAB) is an economically feasible option for the development of high yielding FW resistant genotypes. In this context, two recombinant inbred lines (RILs) (ICPB 2049 × ICPL 99050 designated as PRIL_A and ICPL 20096 × ICPL 332 designated as PRIL_B) and one F2 (ICPL 85063 × ICPL 87119) populations were used for the development of high density genetic maps. Genotyping-by-sequencing (GBS) approach was used to identify and genotype SNPs in three mapping populations. As a result, three high density genetic maps with 964, 1101 and 557 SNPs with an average marker distance of 1.16, 0.84 and 2.60 cM were developed in PRIL_A, PRIL_B and F2, respectively. Based on the multi-location and multi-year phenotypic data of FW resistance a total of 14 quantitative trait loci (QTLs) including six major QTLs explaining >10% phenotypic variance explained (PVE) were identified. Comparative analysis across the populations has revealed three important QTLs (qFW11.1, qFW11.2 and qFW11.3) with upto 56.45% PVE for FW resistance. This is the first report of QTL mapping for FW resistance in pigeonpea and identified genomic region could be utilized in GAB.
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