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Singh S, Yadav CB, Lubanga N, Hegarty M, Yadav RS. Genome-wide SNPs and candidate genes underlying the genetic variations for protein and amino acids in pearl millet (Pennisetum glaucum) germplasm. PLANTA 2024; 260:63. [PMID: 39068266 PMCID: PMC11283402 DOI: 10.1007/s00425-024-04495-y] [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: 03/19/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
Abstract
MAIN CONCLUSION A total of 544 significant marker-trait associations and 286 candidate genes associated with total protein and 18 amino acids were identified. Thirty-three candidate genes were found near the strong marker trait associations (- log10P ≥ 5.5). Pearl millet (Pennisetum glaucum) is largely grown as a subsistence crop in South Asia and sub-Saharan Africa. It serves as a major source of daily protein intake in these regions. Despite its importance, no systematic effort has been made to study the genetic variations of protein and amino acid content in pearl millet germplasm. The present study was undertaken to dissect the global genetic variations of total protein and 18 essential and non-essential amino acids in pearl millet, using a set of 435 K Single Nucleotide Polymorphisms (SNPs) and 161 genotypes of the Pearl Millet Inbred Germplasm Association Panel (PMiGAP). A total of 544 significant marker-trait associations (at P < 0.0001; - log10P ≥ 4) were detected and 23 strong marker-trait associations were identified using Bonferroni's correction method. Forty-eight pleiotropic loci were found in the genome for the studied traits. In total, 286 candidate genes associated with total protein and 18 amino acids were identified. Thirty-three candidate genes were found near strongly associated SNPs. The associated markers and the candidate genes provide an insight into the genetic architecture of the traits studied and are going to be useful in breeding improved pearl millet varieties in the future. Availabilities of improved pearl millet varieties possessing higher protein and amino acid compositions will help combat the rising malnutrition problem via diet.
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Affiliation(s)
- Satbeer Singh
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3EE, UK
- Division of Agrotechnology, Council of Scientific and Industrial Research (CSIR) - Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176 061, India
| | - Chandra Bhan Yadav
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3EE, UK
- Department of Genetics, Genomics, and Breeding, NIAB-EMR, East Malling, ME19 6BJ, UK
| | - Nelson Lubanga
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3EE, UK
| | - Matthew Hegarty
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3EE, UK
| | - Rattan S Yadav
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3EE, UK.
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Ntakirutimana F, Tranchant-Dubreuil C, Cubry P, Chougule K, Zhang J, Wing RA, Adam H, Lorieux M, Jouannic S. Genome-wide association analysis identifies natural allelic variants associated with panicle architecture variation in African rice, Oryza glaberrima Steud. G3 (BETHESDA, MD.) 2023; 13:jkad174. [PMID: 37535690 PMCID: PMC10542218 DOI: 10.1093/g3journal/jkad174] [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: 06/12/2023] [Revised: 06/12/2023] [Accepted: 07/18/2023] [Indexed: 08/05/2023]
Abstract
African rice (Oryza glaberrima Steud), a short-day cereal crop closely related to Asian rice (Oryza sativa L.), has been cultivated in Sub-Saharan Africa for ∼ 3,000 years. Although less cultivated globally, it is a valuable genetic resource in creating high-yielding cultivars that are better adapted to diverse biotic and abiotic stresses. While inflorescence architecture, a key trait for rice grain yield improvement, has been extensively studied in Asian rice, the morphological and genetic determinants of this complex trait are less understood in African rice. In this study, using a previously developed association panel of 162 O. glaberrima accessions and new SNP variants characterized through mapping to a new version of the O. glaberrima reference genome, we conducted a genome-wide association study of four major morphological panicle traits. We have found a total of 41 stable genomic regions that are significantly associated with these traits, of which 13 co-localized with previously identified QTLs in O. sativa populations and 28 were unique for this association panel. Additionally, we found a genomic region of interest on chromosome 3 that was associated with the number of spikelets and primary and secondary branches. Within this region was localized the O. sativa ortholog of the PHYTOCHROME B gene (Oglab_006903/OgPHYB). Haplotype analysis revealed the occurrence of natural sequence variants at the OgPHYB locus associated with panicle architecture variation through modulation of the flowering time phenotype, whereas no equivalent alleles were found in O. sativa. The identification in this study of genomic regions specific to O. glaberrima indicates panicle-related intra-specific genetic variation in this species, increasing our understanding of the underlying molecular processes governing panicle architecture. Identified candidate genes and major haplotypes may facilitate the breeding of new African rice cultivars with preferred panicle traits.
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Affiliation(s)
| | | | - Philippe Cubry
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jianwei Zhang
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Hélène Adam
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
| | - Mathias Lorieux
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
| | - Stefan Jouannic
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
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Semalaiyappan J, Selvanayagam S, Rathore A, Gupta SK, Chakraborty A, Gujjula KR, Haktan S, Viswanath A, Malipatil R, Shah P, Govindaraj M, Ignacio JC, Reddy S, Singh AK, Thirunavukkarasu N. Development of a new AgriSeq 4K mid-density SNP genotyping panel and its utility in pearl millet breeding. FRONTIERS IN PLANT SCIENCE 2023; 13:1068883. [PMID: 36704175 PMCID: PMC9871632 DOI: 10.3389/fpls.2022.1068883] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/15/2022] [Indexed: 06/18/2023]
Abstract
Pearl millet is a crucial nutrient-rich staple food in Asia and Africa and adapted to the climate of semi-arid topics. Since the genomic resources in pearl millet are very limited, we have developed a brand-new mid-density 4K SNP panel and demonstrated its utility in genetic studies. A set of 4K SNPs were mined from 925 whole-genome sequences through a comprehensive in-silico pipeline. Three hundred and seventy-three genetically diverse pearl millet inbreds were genotyped using the newly-developed 4K SNPs through the AgriSeq Targeted Genotyping by Sequencing technology. The 4K SNPs were uniformly distributed across the pearl millet genome and showed considerable polymorphism information content (0.23), genetic diversity (0.29), expected heterozygosity (0.29), and observed heterozygosity (0.03). The SNP panel successfully differentiated the accessions into two major groups, namely B and R lines, through genetic diversity, PCA, and structure models as per their pedigree. The linkage disequilibrium (LD) analysis showed Chr3 had higher LD regions while Chr1 and Chr2 had more low LD regions. The genetic divergence between the B- and R-line populations was 13%, and within the sub-population variability was 87%. In this experiment, we have mined 4K SNPs and optimized the genotyping protocol through AgriSeq technology for routine use, which is cost-effective, fast, and highly reproducible. The newly developed 4K mid-density SNP panel will be useful in genomics and molecular breeding experiments such as assessing the genetic diversity, trait mapping, backcross breeding, and genomic selection in pearl millet.
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Affiliation(s)
- Janani Semalaiyappan
- Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Rajendranagar, India
| | - Sivasubramani Selvanayagam
- Accelerated Crop Improvement, International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Abhishek Rathore
- Excellence in Breeding (EiB) Platform, The International Maize and Wheat Improvement Center (CIMMYT), El Batán, Mexico
| | - SK. Gupta
- Accelerated Crop Improvement, International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Animikha Chakraborty
- Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Rajendranagar, India
| | | | - Suren Haktan
- Bioinformatics, Thermo Fisher Scientific, Austin, TX, United States
| | - Aswini Viswanath
- Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Rajendranagar, India
| | - Renuka Malipatil
- Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Rajendranagar, India
| | - Priya Shah
- Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Rajendranagar, India
| | | | - John Carlos Ignacio
- Department of Horticulture and Crop Science, The Ohio State University, Wooster, OH, United States
| | - Sanjana Reddy
- Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Rajendranagar, India
| | | | - Nepolean Thirunavukkarasu
- Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Rajendranagar, India
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Faye A, Barnaud A, Kane NA, Cubry P, Mariac C, Burgarella C, Rhoné B, Faye A, Olodo KF, Cisse A, Couderc M, Dequincey A, Zekraouï L, Moussa D, Tidjani M, Vigouroux Y, Berthouly-Salazar C. Genomic footprints of selection in early-and late-flowering pearl millet landraces. FRONTIERS IN PLANT SCIENCE 2022; 13:880631. [PMID: 36311100 PMCID: PMC9597309 DOI: 10.3389/fpls.2022.880631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 08/11/2022] [Indexed: 06/16/2023]
Abstract
Pearl millet is among the top three-cereal production in one of the most climate vulnerable regions, sub-Saharan Africa. Its Sahelian origin makes it adapted to grow in poor sandy soils under low soil water regimes. Pearl millet is thus considered today as one of the most interesting crops to face the global warming. Flowering time, a trait highly correlated with latitude, is one of the key traits that could be modulated to face future global changes. West African pearl millet landraces, can be grouped into early- (EF) and late-flowering (LF) varieties, each flowering group playing a specific role in the functioning and resilience of Sahelian smallholders. The aim of this study was thus to detect genes linked to flowering but also linked to relevant traits within each flowering group. We thus investigated genomic and phenotypic diversity in 109 pearl millet landrace accessions, i.e., 66 early-flowering and 43 late-flowering, grown in the groundnut basin, the first area of rainfed agriculture in Senegal dominated by dry cereals (millet, maize, and sorghum) and legumes (groundnuts, cowpeas). We were able to confirm the role of PhyC gene in pearl millet flowering and identify several other genes that appear to be as much as important, such as FSR12 and HAC1. HAC1 and two other genes appear to be part of QTLs previously identified and deserve further investigation. At the same time, we were able to highlight a several genes and variants that could contribute to the improvement of pearl millet yield, especially since their impact was demonstrated across flowering cycles.
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Affiliation(s)
- Adama Faye
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- LNRPV, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Senegal
- Laboratoire Mixte International LAPSE, Campus de Bel Air, route des Hydrocarbures, Dakar, Senegal
| | - Adeline Barnaud
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- Laboratoire Mixte International LAPSE, Campus de Bel Air, route des Hydrocarbures, Dakar, Senegal
| | - Ndjido Ardo Kane
- LNRPV, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Senegal
- Laboratoire Mixte International LAPSE, Campus de Bel Air, route des Hydrocarbures, Dakar, Senegal
- CERAAS, Institut Sénégalais de Recherches Agricoles, Thiès, Senegal
| | - Philippe Cubry
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Cédric Mariac
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Concetta Burgarella
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Bénédicte Rhoné
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Aliou Faye
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- LNRPV, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Senegal
- Laboratoire Mixte International LAPSE, Campus de Bel Air, route des Hydrocarbures, Dakar, Senegal
| | - Katina Floride Olodo
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- LNRPV, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Senegal
- Laboratoire Mixte International LAPSE, Campus de Bel Air, route des Hydrocarbures, Dakar, Senegal
- CERAAS, Institut Sénégalais de Recherches Agricoles, Thiès, Senegal
| | - Aby Cisse
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- LNRPV, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Senegal
- Laboratoire Mixte International LAPSE, Campus de Bel Air, route des Hydrocarbures, Dakar, Senegal
- CERAAS, Institut Sénégalais de Recherches Agricoles, Thiès, Senegal
| | - Marie Couderc
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Anaïs Dequincey
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Leïla Zekraouï
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Djibo Moussa
- DIADE, Institut de Recherche pour le Développement (IRD), Niamey, Niger
| | - Moussa Tidjani
- DIADE, Institut de Recherche pour le Développement (IRD), Niamey, Niger
| | - Yves Vigouroux
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Cécile Berthouly-Salazar
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- LNRPV, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Senegal
- Laboratoire Mixte International LAPSE, Campus de Bel Air, route des Hydrocarbures, Dakar, Senegal
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Singh M, Nara U. Genetic insights in pearl millet breeding in the genomic era: challenges and prospects. PLANT BIOTECHNOLOGY REPORTS 2022; 17:15-37. [PMID: 35692233 PMCID: PMC9169599 DOI: 10.1007/s11816-022-00767-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 04/30/2022] [Accepted: 05/17/2022] [Indexed: 05/28/2023]
Abstract
Pearl millet, a vital staple food and an important cereal, is emerging as crop having various end-uses as feed, food as well as fodder. Advancement in high-throughput sequencing technology has boosted up pearl millet genomic research in past few years. The available draft genome of pearl millet providing an insight into the advancement of several breeding lines. Comparative and functional genomics have untangled several loci and genes regulating adaptive and agronomic traits in pearl millet. Additionally, the knowledge achieved has far away from being applicable in real breeding practices. We believe that the best path ahead is to adopt genome-based approaches for tailored designing of pearl millet as multi-functional crop with outstanding agronomic traits for various end uses. Presently review highlight several novel concepts and techniques in crop breeding, and summarize the recent advances in pearl millet genomic research, peculiarly genome-wide association dissections of several novel alleles and genes for agronomically important traits.
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Affiliation(s)
- Mandeep Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab 141004 India
| | - Usha Nara
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab 141004 India
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Satyavathi CT, Ambawat S, Khandelwal V, Srivastava RK. Pearl Millet: A Climate-Resilient Nutricereal for Mitigating Hidden Hunger and Provide Nutritional Security. FRONTIERS IN PLANT SCIENCE 2021; 12:659938. [PMID: 34589092 PMCID: PMC8475763 DOI: 10.3389/fpls.2021.659938] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 08/03/2021] [Indexed: 06/03/2023]
Abstract
Pearl millet [Pennisetum glaucum (L.) R. Br.] is the sixth most important cereal crop after rice, wheat, maize, barley and sorghum. It is widely grown on 30 million ha in the arid and semi-arid tropical regions of Asia and Africa, accounting for almost half of the global millet production. Climate change affects crop production by directly influencing biophysical factors such as plant and animal growth along with the various areas associated with food processing and distribution. Assessment of the effects of global climate changes on agriculture can be helpful to anticipate and adapt farming to maximize the agricultural production more effectively. Pearl millet being a climate-resilient crop is important to minimize the adverse effects of climate change and has the potential to increase income and food security of farming communities in arid regions. Pearl millet has a deep root system and can survive in a wide range of ecological conditions under water scarcity. It has high photosynthetic efficiency with an excellent productivity and growth in low nutrient soil conditions and is less reliant on chemical fertilizers. These attributes have made it a crop of choice for cultivation in arid and semi-arid regions of the world; however, fewer efforts have been made to study the climate-resilient features of pearl millet in comparison to the other major cereals. Several hybrids and varieties of pearl millet were developed during the past 50 years in India by both the public and private sectors. Pearl millet is also nutritionally superior and rich in micronutrients such as iron and zinc and can mitigate malnutrition and hidden hunger. Inclusion of minimum standards for micronutrients-grain iron and zinc content in the cultivar release policy-is the first of its kind step taken in pearl millet anywhere in the world, which can lead toward enhanced food and nutritional security. The availability of high-quality whole-genome sequencing and re-sequencing information of several lines may aid genomic dissection of stress tolerance and provide a good opportunity to further exploit the nutritional and climate-resilient attributes of pearl millet. Hence, more efforts should be put into its genetic enhancement and improvement in inheritance to exploit it in a better way. Thus, pearl millet is the next-generation crop holding the potential of nutritional richness and the climate resilience and efforts must be targeted to develop nutritionally dense hybrids/varieties tolerant to drought using different omics approaches.
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Affiliation(s)
- C. Tara Satyavathi
- Indian Council of Agricultural Research - All India Coordinated Research Project on Pearl Millet, Jodhpur, India
| | - Supriya Ambawat
- Indian Council of Agricultural Research - All India Coordinated Research Project on Pearl Millet, Jodhpur, India
| | - Vikas Khandelwal
- Indian Council of Agricultural Research - All India Coordinated Research Project on Pearl Millet, Jodhpur, India
| | - Rakesh K. Srivastava
- Department of Molecular Breeding (Genomics Trait Discovery), International Crops Research Institute for Semi-arid Tropics, Patancheru, India
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Yadav CB, Tokas J, Yadav D, Winters A, Singh RB, Yadav R, Gangashetty PI, Srivastava RK, Yadav RS. Identifying Anti-Oxidant Biosynthesis Genes in Pearl Millet [ Pennisetum glaucum (L.) R. Br.] Using Genome-Wide Association Analysis. FRONTIERS IN PLANT SCIENCE 2021; 12:599649. [PMID: 34122460 PMCID: PMC8194398 DOI: 10.3389/fpls.2021.599649] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 04/19/2021] [Indexed: 05/05/2023]
Abstract
Pearl millet [Pennisetum glaucum (L.) R Br.] is an important staple food crop in the semi-arid tropics of Asia and Africa. It is a cereal grain that has the prospect to be used as a substitute for wheat flour for celiac patients. It is an important antioxidant food resource present with a wide range of phenolic compounds that are good sources of natural antioxidants. The present study aimed to identify the total antioxidant content of pearl millet flour and apply it to evaluate the antioxidant activity of its 222 genotypes drawn randomly from the pearl millet inbred germplasm association panel (PMiGAP), a world diversity panel of this crop. The total phenolic content (TPC) significantly correlated with DPPH (1,1-diphenyl-2-picrylhydrazyl) radical scavenging activity (% inhibition), which ranged from 2.32 to 112.45% and ferric-reducing antioxidant power (FRAP) activity ranging from 21.68 to 179.66 (mg ascorbic acid eq./100 g). Genome-wide association studies (GWAS) were conducted using 222 diverse accessions and 67 K SNPs distributed across all the seven pearl millet chromosomes. Approximately, 218 SNPs were found to be strongly associated with DPPH and FRAP activity at high confidence [-log (p) > 3.0-7.4]. Furthermore, flanking regions of significantly associated SNPs were explored for candidate gene harvesting. This identified 18 candidate genes related to antioxidant pathway genes (flavanone 7-O-beta-glycosyltransferase, GDSL esterase/lipase, glutathione S-transferase) residing within or near the association signal that can be selected for further functional characterization. Patterns of genetic variability and the associated genes reported in this study are useful findings, which would need further validation before their utilization in molecular breeding for high antioxidant-containing pearl millet cultivars.
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Affiliation(s)
- Chandra Bhan Yadav
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Jayanti Tokas
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
- Chaudhary Charan Singh (CCS) Haryana Agricultural University, Hisar, India
| | - Devvart Yadav
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
- Chaudhary Charan Singh (CCS) Haryana Agricultural University, Hisar, India
| | - Ana Winters
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Ram B. Singh
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Rama Yadav
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | | | - Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Rattan S. Yadav
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
- *Correspondence: Rattan S. Yadav
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Srivastava RK, Singh RB, Pujarula VL, Bollam S, Pusuluri M, Chellapilla TS, Yadav RS, Gupta R. Genome-Wide Association Studies and Genomic Selection in Pearl Millet: Advances and Prospects. Front Genet 2020; 10:1389. [PMID: 32180790 PMCID: PMC7059752 DOI: 10.3389/fgene.2019.01389] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/19/2019] [Indexed: 11/13/2022] Open
Abstract
Pearl millet is a climate-resilient, drought-tolerant crop capable of growing in marginal environments of arid and semi-arid regions globally. Pearl millet is a staple food for more than 90 million people living in poverty and can address the triple burden of malnutrition substantially. It remained a neglected crop until the turn of the 21st century, and much emphasis has been placed since then on the development of various genetic and genomic resources for whole-genome scan studies, such as the genome-wide association studies (GWAS) and genomic selection (GS). This was facilitated by the advent of sequencing-based genotyping, such as genotyping-by-sequencing (GBS), RAD-sequencing, and whole-genome re-sequencing (WGRS) in pearl millet. To carry out GWAS and GS, a world association mapping panel called the Pearl Millet inbred Germplasm Association Panel (PMiGAP) was developed at ICRISAT in partnership with Aberystwyth University. This panel consisted of germplasm lines, landraces, and breeding lines from 27 countries and was re-sequenced using the WGRS approach. It has a repository of circa 29 million genome-wide SNPs. PMiGAP has been used to map traits related to drought tolerance, grain Fe and Zn content, nitrogen use efficiency, components of endosperm starch, grain yield, etc. Genomic selection in pearl millet was jump-started recently by WGRS, RAD, and tGBS (tunable genotyping-by-sequencing) approaches for the PMiGAP and hybrid parental lines. Using multi-environment phenotyping of various training populations, initial attempts have been made to develop genomic selection models. This mini review discusses advances and prospects in GWAS and GS for pearl millet.
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Affiliation(s)
- Rakesh K Srivastava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Ram B Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vijaya Lakshmi Pujarula
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Srikanth Bollam
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Madhu Pusuluri
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Tara Satyavathi Chellapilla
- All India Coordinated Research Project on Pearl Millet (AICRP-PM), Indian Council of Agricultural Research (ICAR), Jodhpur, India
| | - Rattan S Yadav
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, United Kingdom
| | - Rajeev Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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9
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Kane NA, Berthouly-Salazar C. Population Genomics of Pearl Millet. POPULATION GENOMICS 2020. [DOI: 10.1007/13836_2020_80] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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10
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Kippes N, Guedira M, Lin L, Alvarez MA, Brown-Guedira GL, Dubcovsky J. Single nucleotide polymorphisms in a regulatory site of VRN-A1 first intron are associated with differences in vernalization requirement in winter wheat. Mol Genet Genomics 2018; 293:1231-1243. [PMID: 29872926 PMCID: PMC6153499 DOI: 10.1007/s00438-018-1455-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 05/31/2018] [Indexed: 02/03/2023]
Abstract
Winter wheats require a long exposure to cold temperatures (vernalization) to accelerate flowering. However, varieties differ in the length of the period of cold required to saturate the vernalization response. Here we show that single nucleotide polymorphisms (SNP) at the binding site of the GRP2 protein in the VRN-A1 first intron (henceforth, RIP3) are associated with significant differences in heading time after a partial vernalization treatment. The ancestral winter VRN-A1 allele in ‘Triple Dirk C’ has one SNP in the RIP3 region (1_SNP) relative to the canonical RIP3 sequence, whereas the derived ‘Jagger’ allele has three SNPs (3_SNPs). Both varieties have a single VRN-A1 copy encoding identical proteins. In an F2 population generated from a cross between these two varieties, plants with the 3_SNPs haplotype headed significantly earlier (P < 0.001) than those with the 1_SNP haplotype, both in the absence of vernalization (17 days difference) and after 3-weeks of vernalization (11 days difference). Plants with the 3_SNPs haplotype showed higher VRN-A1 transcript levels than those with the 1_SNP haplotype. The 3_SNPs haplotype was also associated with early heading in a panel of 127 winter wheat varieties grown in three separate controlled-environment experiments under partial vernalization (36 to 54 days, P < 0.001) and one experiment under field conditions (21 d, P < 0.0001). The RIP3 polymorphisms can be used by wheat breeders to develop winter wheat varieties adapted to regions with different duration or intensity of the cold season.
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Affiliation(s)
- Nestor Kippes
- Department of Plant Sciences, University of California, Davis, CA, 95616-8515, USA.,Department of Plant Biology and Genome Center, University of California, Davis, CA, 95616, USA
| | - Mohammed Guedira
- Department of Crop Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - Lijuan Lin
- Department of Plant Sciences, University of California, Davis, CA, 95616-8515, USA
| | - Maria A Alvarez
- Department of Plant Sciences, University of California, Davis, CA, 95616-8515, USA
| | - Gina L Brown-Guedira
- Department of Crop Science, North Carolina State University, Raleigh, NC, 27695, USA.,USDA-ARS Plant Science Research Unit, Raleigh, NC, 27695, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, 95616-8515, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
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11
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Ousseini IS, Bakasso Y, Kane NA, Couderc M, Zekraoui L, Mariac C, Manicacci D, Rhoné B, Barnaud A, Berthouly-Salazar C, Assoumane A, Moussa D, Moussa T, Vigouroux Y. Myosin XI is associated with fitness and adaptation to aridity in wild pearl millet. Heredity (Edinb) 2017; 119:88-94. [PMID: 28295033 DOI: 10.1038/hdy.2017.13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 01/09/2017] [Accepted: 01/12/2017] [Indexed: 11/09/2022] Open
Abstract
Phenotypic changes in plants can be observed along many environmental gradients and are determined by both environmental and genetic factors. The identification of alleles associated with phenotypic variations is a rapidly developing area of research. We studied the genetic basis of phenotypic variations in 11 populations of wild pearl millet (Pennisetum glaucum) on two North-South aridity gradients, one in Niger and one in Mali. Most of the 11 phenotypic traits assessed in a common garden experiment varied between the populations studied. Moreover, the size of the inflorescence, the number of flowers and aboveground dry mass co-varied positively with a decrease in rainfall. To decipher the genetic basis of these phenotypes, we used an association mapping strategy with a mixed model. We found two SNPs on the same myosin XI contig significantly associated with variations in the average number of flowers. Both the allele frequency of the two SNPs and the average number of flowers co-varied with the rainfall gradient on the two gradients. Interestingly, this gene was also a target of selection during domestication. The Myosin XI gene is thus a good candidate for fitness-related adaptation in wild populations.
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Affiliation(s)
- I S Ousseini
- Institut de Recherche pour le Développement, Montpellier, France.,Université Abdou Moumouni de Niamey, Niamey, Niger.,Université de Montpellier, Montpellier, France.,Institut Sénégalais de la Recherche Agronomique, Campus de Bel Air, Dakar, Sénégal
| | - Y Bakasso
- Université Abdou Moumouni de Niamey, Niamey, Niger
| | - N A Kane
- Institut Sénégalais de la Recherche Agronomique, Campus de Bel Air, Dakar, Sénégal.,Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LMI LAPSE), Centre de Recherche de Bel Air, Dakar, Sénégal
| | - M Couderc
- Institut de Recherche pour le Développement, Montpellier, France
| | - L Zekraoui
- Institut de Recherche pour le Développement, Montpellier, France.,Institut Sénégalais de la Recherche Agronomique, Campus de Bel Air, Dakar, Sénégal.,Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LMI LAPSE), Centre de Recherche de Bel Air, Dakar, Sénégal
| | - C Mariac
- Institut de Recherche pour le Développement, Montpellier, France
| | - D Manicacci
- Université Paris-Sud, UMR 0320 / UMR 8120 Génétique Quantitative et Évolution - Le Moulon, Gif-sur-Yvette, France
| | - B Rhoné
- Institut de Recherche pour le Développement, Montpellier, France.,Centre National de la Recherche Scientifique, Lyon, France
| | - A Barnaud
- Institut de Recherche pour le Développement, Montpellier, France.,Institut Sénégalais de la Recherche Agronomique, Campus de Bel Air, Dakar, Sénégal.,Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LMI LAPSE), Centre de Recherche de Bel Air, Dakar, Sénégal
| | - C Berthouly-Salazar
- Institut de Recherche pour le Développement, Montpellier, France.,Institut Sénégalais de la Recherche Agronomique, Campus de Bel Air, Dakar, Sénégal.,Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LMI LAPSE), Centre de Recherche de Bel Air, Dakar, Sénégal
| | - A Assoumane
- Université Abdou Moumouni de Niamey, Niamey, Niger.,Institut de Recherche pour le Développement, Niamey, Niger
| | - D Moussa
- Institut de Recherche pour le Développement, Niamey, Niger
| | - T Moussa
- Institut de Recherche pour le Développement, Niamey, Niger
| | - Y Vigouroux
- Institut de Recherche pour le Développement, Montpellier, France.,Université de Montpellier, Montpellier, France.,Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LMI LAPSE), Centre de Recherche de Bel Air, Dakar, Sénégal
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12
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Anuradha N, Satyavathi CT, Bharadwaj C, Nepolean T, Sankar SM, Singh SP, Meena MC, Singhal T, Srivastava RK. Deciphering Genomic Regions for High Grain Iron and Zinc Content Using Association Mapping in Pearl Millet. FRONTIERS IN PLANT SCIENCE 2017; 8:412. [PMID: 28507551 PMCID: PMC5410614 DOI: 10.3389/fpls.2017.00412] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 03/10/2017] [Indexed: 05/11/2023]
Abstract
Micronutrient malnutrition, especially deficiency of two mineral elements, iron [Fe] and zinc [Zn] in the developing world needs urgent attention. Pearl millet is one of the best crops with many nutritional properties and is accessible to the poor. We report findings of the first attempt to mine favorable alleles for grain iron and zinc content through association mapping in pearl millet. An association mapping panel of 130 diverse lines was evaluated at Delhi, Jodhpur and Dharwad, representing all the three pearl millet growing agro-climatic zones of India, during 2014 and 2015. Wide range of variation was observed for grain iron (32.3-111.9 ppm) and zinc (26.6-73.7 ppm) content. Genotyping with 114 representative polymorphic SSRs revealed 0.35 mean gene diversity. STRUCTURE analysis revealed presence of three sub-populations which was further supported by Neighbor-Joining method of clustering and principal coordinate analysis (PCoA). Marker-trait associations (MTAs) were analyzed with 267 markers (250 SSRs and 17 genic markers) in both general linear model (GLM) and mixed linear model (MLM), however, MTAs resulting from MLM were considered for more robustness of the associations. After appropriate Bonferroni correction, Xpsmp 2261 (13.34% R2-value), Xipes 0180 (R2-value of 11.40%) and Xipes 0096 (R2-value of 11.38%) were consistently associated with grain iron and zinc content for all the three locations. Favorable alleles and promising lines were identified for across and specific environments. PPMI 1102 had highest number (7) of favorable alleles, followed by four each for PPMFeZMP 199 and PPMI 708 for across the environment performance for both grain Fe and Zn content, while PPMI 1104 had alleles specific to Dharwad for grain Fe and Zn content. When compared with the reference genome Tift 23D2B1-P1-P5, Xpsmp 2261 amplicon was identified in intergenic region on pseudomolecule 5, while the other marker, Xipes 0810 was observed to be overlapping with aspartic proteinase (Asp) gene on pseudomolecule 3. Thus, this study can help in breeding new lines with enhanced micronutrient content using marker-assisted selection (MAS) in pearl millet leading to improved well-being especially for women and children.
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Affiliation(s)
- N. Anuradha
- Division of Genetics, ICAR-Indian Agricultural Research InstituteNew Delhi, India
| | - C. Tara Satyavathi
- Division of Genetics, ICAR-Indian Agricultural Research InstituteNew Delhi, India
- *Correspondence: C. Tara Satyavathi
| | - C. Bharadwaj
- Division of Genetics, ICAR-Indian Agricultural Research InstituteNew Delhi, India
| | - T. Nepolean
- Division of Genetics, ICAR-Indian Agricultural Research InstituteNew Delhi, India
| | - S. Mukesh Sankar
- Division of Genetics, ICAR-Indian Agricultural Research InstituteNew Delhi, India
| | - Sumer P. Singh
- Division of Genetics, ICAR-Indian Agricultural Research InstituteNew Delhi, India
| | - Mahesh C. Meena
- Division of Soil Science and Agricultural Chemistry, ICAR-Indian Agricultural Research InstituteNew Delhi, India
| | - Tripti Singhal
- Division of Genetics, ICAR-Indian Agricultural Research InstituteNew Delhi, India
| | - Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
- Rakesh K. Srivastava
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13
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Mariac C, Ousseini IS, Alio AK, Jugdé H, Pham JL, Bezançon G, Ronfort J, Descroix L, Vigouroux Y. Spatial and Temporal Variation in Selection of Genes Associated with Pearl Millet Varietal Quantitative Traits In situ. Front Genet 2016; 7:130. [PMID: 27507986 PMCID: PMC4960089 DOI: 10.3389/fgene.2016.00130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 07/07/2016] [Indexed: 11/23/2022] Open
Abstract
Ongoing global climate changes imply new challenges for agriculture. Whether plants and crops can adapt to such rapid changes is still a widely debated question. We previously showed adaptation in the form of earlier flowering in pearl millet at the scale of a whole country over three decades. However, this analysis did not deal with variability of year to year selection. To understand and possibly manage plant and crop adaptation, we need more knowledge of how selection acts in situ. Is selection gradual, abrupt, and does it vary in space and over time? In the present study, we tracked the evolution of allele frequency in two genes associated with pearl millet phenotypic variation in situ. We sampled 17 populations of cultivated pearl millet over a period of 2 years. We tracked changes in allele frequencies in these populations by genotyping more than seven thousand individuals. We demonstrate that several allele frequencies changes are compatible with selection, by correcting allele frequency changes associated with genetic drift. We found marked variation in allele frequencies from year to year, suggesting a variable selection effect in space and over time. We estimated the strength of selection associated with variations in allele frequency. Our results suggest that the polymorphism maintained at the genes we studied is partially explained by the spatial and temporal variability of selection. In response to environmental changes, traditional pearl millet varieties could rapidly adapt thanks to this available functional variability.
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Affiliation(s)
- Cédric Mariac
- Institut de Recherche Pour le Développement, UMR DIADE, MontpellierFrance; Institut de Recherche Pour le Développement, NiameyNiger
| | - Issaka S Ousseini
- Institut de Recherche Pour le Développement, UMR DIADE, MontpellierFrance; Institut de Recherche Pour le Développement, NiameyNiger; University Montpellier II, Place Eugène Bataillon, MontpellierFrance; University Montpellier II, Place Eugène Bataillon, MontpellierFrance
| | | | - Hélène Jugdé
- Institut de Recherche Pour le Développement, Niamey Niger
| | - Jean-Louis Pham
- Institut de Recherche Pour le Développement, UMR DIADE, Montpellier France
| | - Gilles Bezançon
- Institut de Recherche Pour le Développement, UMR DIADE, MontpellierFrance; Institut de Recherche Pour le Développement, NiameyNiger
| | - Joelle Ronfort
- Institut National de Recherche Agronomique, INRA, UMR AGAP, Montpellier France
| | - Luc Descroix
- Institut de Recherche Pour le Développement, NiameyNiger; Institut de Recherche Pour le Développement, IRD, UMR LTHE, GrenobleFrance
| | - Yves Vigouroux
- Institut de Recherche Pour le Développement, UMR DIADE, MontpellierFrance; Institut de Recherche Pour le Développement, NiameyNiger; University Montpellier II, Place Eugène Bataillon, MontpellierFrance
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14
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An overview of phytochrome: An important light switch and photo-sensory antenna for regulation of vital functioning of plants. Biologia (Bratisl) 2015. [DOI: 10.1515/biolog-2015-0147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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15
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Dussert Y, Snirc A, Robert T. Inference of domestication history and differentiation between early- and late-flowering varieties in pearl millet. Mol Ecol 2015; 24:1387-402. [PMID: 25705965 DOI: 10.1111/mec.13119] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 02/04/2023]
Abstract
Pearl millet (Pennisetum glaucum) is a staple crop in Sahelian Africa. Farmers usually grow varieties with different cycle lengths and complementary functions in Sahelian agrosystems. Both the level of genetic differentiation of these varieties and the domestication history of pearl millet have been poorly studied. We investigated the neutral genetic diversity and population genetic structure of early- and late-flowering domesticated and wild pearl millet populations using 18 microsatellite loci and 8 nucleotide sequences. Strikingly, early- and late-flowering domesticated varieties were not differentiated over their whole distribution area, despite a clear difference in their isolation-by-distance pattern. Conversely, our data brought evidence for two well-differentiated genetic pools in wild pearl millet, allowing us to test scenarios with different numbers and origins of domestication using approximate Bayesian computation (ABC). The ABC analysis showed the likely existence of asymmetric migration between wild and domesticated populations. The model choice procedure indicated that a single domestication from the eastern wild populations was the more likely scenario to explain the polymorphism patterns observed in cultivated pearl millet.
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Affiliation(s)
- Y Dussert
- Ecologie, Systématique et Evolution, UMR 8079 CNRS, Université Paris-Sud, 91405, Orsay, France; Sorbonne Universités, UPMC Univ Paris06, IFD, 4 Place Jussieu, 75252, Paris Cedex 05, France
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16
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Ogura T, Busch W. From phenotypes to causal sequences: using genome wide association studies to dissect the sequence basis for variation of plant development. CURRENT OPINION IN PLANT BIOLOGY 2015; 23:98-108. [PMID: 25449733 DOI: 10.1016/j.pbi.2014.11.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 11/04/2014] [Accepted: 11/05/2014] [Indexed: 05/20/2023]
Abstract
Tremendous natural variation of growth and development exists within species. Uncovering the molecular mechanisms that tune growth and development promises to shed light on a broad set of biological issues including genotype to phenotype relations, regulatory mechanisms of biological processes and evolutionary questions. Recent progress in sequencing and data processing capabilities has enabled Genome Wide Association Studies (GWASs) to identify DNA sequence polymorphisms that underlie the variation of biological traits. In the last years, GWASs have proven powerful in revealing the complex genetic bases of many phenotypes in various plant species. Here we highlight successful recent GWASs that uncovered mechanistic and sequence bases of trait variation related to plant growth and development and discuss important considerations for conducting successful GWASs.
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Affiliation(s)
- Takehiko Ogura
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Wolfgang Busch
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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17
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Woods DP, Ream TS, Minevich G, Hobert O, Amasino RM. PHYTOCHROME C is an essential light receptor for photoperiodic flowering in the temperate grass, Brachypodium distachyon. Genetics 2014; 198:397-408. [PMID: 25023399 PMCID: PMC4174950 DOI: 10.1534/genetics.114.166785] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 07/03/2014] [Indexed: 12/30/2022] Open
Abstract
We show that in the temperate grass, Brachypodium distachyon, PHYTOCHROME C (PHYC), is necessary for photoperiodic flowering. In loss-of-function phyC mutants, flowering is extremely delayed in inductive photoperiods. PHYC was identified as the causative locus by utilizing a mapping by sequencing pipeline (Cloudmap) optimized for identification of induced mutations in Brachypodium. In phyC mutants the expression of Brachypodium homologs of key flowering time genes in the photoperiod pathway such as GIGANTEA (GI), PHOTOPERIOD 1 (PPD1/PRR37), CONSTANS (CO), and florigen/FT are greatly attenuated. PHYC also controls the day-length dependence of leaf size as the effect of day length on leaf size is abolished in phyC mutants. The control of genes upstream of florigen production by PHYC was likely to have been a key feature of the evolution of a long-day flowering response in temperate pooid grasses.
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Affiliation(s)
- Daniel P Woods
- Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706 United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin 53706 Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Thomas S Ream
- United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin 53706 Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Gregory Minevich
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, New York, New York 10032
| | - Oliver Hobert
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, New York, New York 10032
| | - Richard M Amasino
- Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706 United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin 53706 Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
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18
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Phytochrome C plays a major role in the acceleration of wheat flowering under long-day photoperiod. Proc Natl Acad Sci U S A 2014; 111:10037-44. [PMID: 24961368 DOI: 10.1073/pnas.1409795111] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Phytochromes are dimeric proteins that function as red and far-red light sensors influencing nearly every phase of the plant life cycle. Of the three major phytochrome families found in flowering plants, phytochrome C (PHYC) is the least understood. In Arabidopsis and rice, PHYC is unstable and functionally inactive unless it heterodimerizes with another phytochrome. However, when expressed in an Arabidopsis phy-null mutant, wheat PHYC forms signaling active homodimers that translocate into the nucleus in red light to mediate photomorphogenic responses. Tetraploid wheat plants homozygous for loss-of-function mutations in all PHYC copies (phyC(AB)) flower on average 108 d later than wild-type plants under long days but only 19 d later under short days, indicating a strong interaction between PHYC and photoperiod. This interaction is further supported by the drastic down-regulation in the phyC(AB) mutant of the central photoperiod gene photoperiod 1 (PPD1) and its downstream target flowering locus T1, which are required for the promotion of flowering under long days. These results implicate light-dependent, PHYC-mediated activation of PPD1 expression in the acceleration of wheat flowering under inductive long days. Plants homozygous for the phyC(AB) mutations also show altered profiles of circadian clock and clock-output genes, which may also contribute to the observed differences in heading time. Our results highlight important differences in the photoperiod pathways of the temperate grasses with those of well-studied model plant species.
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