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Chamorro LL, Brugnoli EA, Zilli AL, Schulz RR, Marcón F, Acuña CA. Flowering Periods, Seed Yield Components, Seed Quality, and Patterns of Seed Shattering in Paspalum: Effect of Taxonomy and Nitrogen Fertilization. PLANTS (BASEL, SWITZERLAND) 2024; 13:2411. [PMID: 39273895 PMCID: PMC11397397 DOI: 10.3390/plants13172411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 08/12/2024] [Accepted: 08/21/2024] [Indexed: 09/15/2024]
Abstract
Perennial warm-season grasses typically have reduced seed yield, making it essential to identify the critical seed yield components. An induced increase in nitrogen could help determine which components are most limiting. This research aimed to estimate seed yield components in Paspalum; evaluate N fertilization effects on the reproductive phase, seed yield components, and seed quality; and establish the pattern of seed shattering over time. Nine genotypes covering different reproductive periods were used. The experimental design was a randomized complete block design in a split-plot arrangement with three replications. The main plots had two nitrogen levels (0 and 150 Kg N ha-1), and the sub-plots contained different genotypes. Seed yield variation was mainly related to reproductive tiller density among germplasm with different flowering periods. Early-flowering germplasm showed an extended flowering period (159%), greater tiller density (27.7%), greater reproductive tiller density (157%), and higher yield (302%) in response to nitrogen fertilization. Seed-quality traits and seed retention were not affected by nitrogen fertilization. Seed retention over time followed an inverted sigmoid pattern, though there was considerable variation among taxonomic groups. Early-flowering germplasm exhibited superior seed retention. Seed yield in Paspalum is mainly influenced by the density of reproductive tillers and seed retention.
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Affiliation(s)
- Luis Leandro Chamorro
- Instituto de Botánica del Nordeste, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste, Sargento Cabral 2131, Corrientes P.C. 3400, Argentina
| | - Elsa Andrea Brugnoli
- Instituto de Botánica del Nordeste, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste, Sargento Cabral 2131, Corrientes P.C. 3400, Argentina
| | - Alex Leonel Zilli
- Instituto de Botánica del Nordeste, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste, Sargento Cabral 2131, Corrientes P.C. 3400, Argentina
| | - Roberto Ramón Schulz
- Instituto de Botánica del Nordeste, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste, Sargento Cabral 2131, Corrientes P.C. 3400, Argentina
| | - Florencia Marcón
- Instituto de Botánica del Nordeste, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste, Sargento Cabral 2131, Corrientes P.C. 3400, Argentina
| | - Carlos Alberto Acuña
- Instituto de Botánica del Nordeste, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste, Sargento Cabral 2131, Corrientes P.C. 3400, Argentina
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2
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Vega JM, Podio M, Orjuela J, Siena LA, Pessino SC, Combes MC, Mariac C, Albertini E, Pupilli F, Ortiz JPA, Leblanc O. Chromosome-scale genome assembly and annotation of Paspalum notatum Flüggé var. saurae. Sci Data 2024; 11:891. [PMID: 39152143 PMCID: PMC11329641 DOI: 10.1038/s41597-024-03731-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 08/02/2024] [Indexed: 08/19/2024] Open
Abstract
Paspalum notatum Flüggé is an economically important subtropical fodder grass that is widely used in the Americas. Here, we report a new chromosome-scale genome assembly and annotation of a diploid biotype collected in the center of origin of the species. Using Oxford Nanopore long reads, we generated a 557.81 Mb genome assembly (N50 = 56.1 Mb) with high gene completeness (BUSCO = 98.73%). Genome annotation identified 320 Mb (57.86%) of repetitive elements and 45,074 gene models, of which 36,079 have a high level of confidence. Further characterisation included the identification of 59 miRNA precursors together with their putative targets. The present work provides a comprehensive genomic resource for P. notatum improvement and a reference frame for functional and evolutionary research within the genus.
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Grants
- PUE 22920160100043CO Consejo Nacional de Investigaciones Científicas y Técnicas (National Scientific and Technical Research Council)
- PIP 11220200101680CO Consejo Nacional de Investigaciones Científicas y Técnicas (National Scientific and Technical Research Council)
- PICT 2019 3414 Ministry of Science, Technology and Productive Innovation, Argentina | Agencia Nacional de Promoción Científica y Tecnológica (National Agency for Science and Technology, Argentina)
- PICT 2019-02153 Ministry of Science, Technology and Productive Innovation, Argentina | Agencia Nacional de Promoción Científica y Tecnológica (National Agency for Science and Technology, Argentina)
- PICT-2017-1956 Ministry of Science, Technology and Productive Innovation, Argentina | Agencia Nacional de Promoción Científica y Tecnológica (National Agency for Science and Technology, Argentina)
- PIP 80020190300021UR Universidad Nacional de Rosario (National University of Rosario)
- 101007438 EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)
- 872417 EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)
- PRIN 2022Z4HLLJ Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
- P2022KFJB5 Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
- Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
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Affiliation(s)
- Juan Manuel Vega
- Laboratorio de Biología Molecular, Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR) CONICET-UNR, Facultad de Ciencias Agrarias, Campo Experimental Villarino, Universidad Nacional de Rosario, Zavalla (S2125ZAA), Santa Fe, Argentina
| | - Maricel Podio
- Laboratorio de Biología Molecular, Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR) CONICET-UNR, Facultad de Ciencias Agrarias, Campo Experimental Villarino, Universidad Nacional de Rosario, Zavalla (S2125ZAA), Santa Fe, Argentina
| | - Julie Orjuela
- DIADE, Univ. Montpellier, CIRAD, IRD, Montpellier, France
| | - Lorena A Siena
- Laboratorio de Biología Molecular, Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR) CONICET-UNR, Facultad de Ciencias Agrarias, Campo Experimental Villarino, Universidad Nacional de Rosario, Zavalla (S2125ZAA), Santa Fe, Argentina
| | - Silvina C Pessino
- Laboratorio de Biología Molecular, Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR) CONICET-UNR, Facultad de Ciencias Agrarias, Campo Experimental Villarino, Universidad Nacional de Rosario, Zavalla (S2125ZAA), Santa Fe, Argentina
| | | | - Cedric Mariac
- DIADE, Univ. Montpellier, CIRAD, IRD, Montpellier, France
| | - Emidio Albertini
- Department of Agricultural, Food and Environmental Science, University of Perugia, 06121, Perugia, Italy
| | - Fulvio Pupilli
- Institute of Biosciences and Bioresources (IBBR), National Research Council (CNR), 06128, Perugia, Italy
| | - Juan Pablo A Ortiz
- Laboratorio de Biología Molecular, Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR) CONICET-UNR, Facultad de Ciencias Agrarias, Campo Experimental Villarino, Universidad Nacional de Rosario, Zavalla (S2125ZAA), Santa Fe, Argentina.
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3
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Glison N, Gaiero P, Monteverde E, Speranza PR. Breeding for reduced seed dormancy to domesticate new grass species. Genet Mol Biol 2024; 47Suppl 1:e20230262. [PMID: 38666746 PMCID: PMC11046443 DOI: 10.1590/1678-4685-gmb-2023-0262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 03/01/2024] [Indexed: 04/29/2024] Open
Abstract
Introducing new grass species into cultivation has long been proposed as beneficial to increase the sustainability and diversity of productive systems. However, wild species with potential tend to show high seed dormancy, causing slow, poor, and unsynchronized seedling emergence. Meanwhile, domesticated species, such as cereals, show lower seed dormancy, facilitating their successful establishment. In this work, we conduct a review of phenotypic variation on seed dormancy and its genetic and molecular basis. This quantitative and highly heritable trait shows phenotype plasticity which is modulated by environmental factors. The level of dormancy depends on the expression of genes associated with the metabolism and sensitivity to the hormones abscisic acid (ABA) and gibberellins (GA), along with other dormancy-specific genes. The genetic regulation of these traits is highly conserved across species. The low seed dormancy observed in cereals and some temperate forages was mostly unconsciously selected during various domestication processes. Emphasis is placed on selecting materials with low seed dormancy for warm-season forage grasses to improve their establishment and adoption. Finally, we review advances in the domestication of dallisgrass, where seed dormancy was considered a focus trait throughout the process.
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Affiliation(s)
- Nicolás Glison
- Universidad de la República, Facultad de Agronomía, Departamento de Biología Vegetal, Montevideo, Uruguay
| | - Paola Gaiero
- Universidad de la República, Facultad de Agronomía, Departamento de Biología Vegetal, Montevideo, Uruguay
| | - Eliana Monteverde
- Universidad de la República, Facultad de Agronomía, Departamento de Biología Vegetal, Montevideo, Uruguay
- University of Illinois, Department of Crop Sciences, Urbana, IL, USA
| | - Pablo R. Speranza
- Universidad de la República, Facultad de Agronomía, Departamento de Biología Vegetal, Montevideo, Uruguay
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Reproductive and Agronomic Characterization of Novel Apomictic Hybrids of Paspalum (Poaceae). Genes (Basel) 2023; 14:genes14030631. [PMID: 36980903 PMCID: PMC10047980 DOI: 10.3390/genes14030631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/18/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
The tetraploid germplasm of Paspalum contains a large diversity that can be used to generate better forages. The objective was to evaluate a group of Paspalum notatum and Paspalum simplex apomictic hybrids for a set of agronomic traits and apomixis expressivity. Forage yield, cold tolerance, winter regrowth, and seed yield were evaluated. The expressivity of apomixis was evaluated in P. simplex hybrids by flow cytometry. Progeny testing with molecular markers was used to determine the genotypic variability in the progeny. Differences within P. notatum and P. simplex hybrids were observed for all traits, and some of them were superior in comparison with the controls. The accumulated forage yield during three years was 988 g m−2 in the P. notatum hybrids, whereas, in P. simplex, the average forage yield per harvest (40 days of regrowth) was 180 g m−2. In P. simplex, the apomixis expressivity varied between 0 and 100%, and 65% of the hybrids showed high apomixis expressivity (superior to 70%). The genotypic mean homogeneity in the progeny was 76% and 85% in P. notatum and P. simplex, respectively. The generation of hybrids with high apomixis expressivity that combine good agronomic performance and homogeneity in the offspring is possible in tetraploid P. notatum and P. simplex.
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Jiang K, Yang Z, Sun J, Liu H, Chen S, Zhao Y, Xiong W, Lu W, Wang ZY, Wu X. Evaluation of the tolerance and forage quality of different ecotypes of seashore paspalum. FRONTIERS IN PLANT SCIENCE 2022; 13:944894. [PMID: 36247632 PMCID: PMC9559843 DOI: 10.3389/fpls.2022.944894] [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: 05/16/2022] [Accepted: 09/06/2022] [Indexed: 06/16/2023]
Abstract
Seashore paspalum is a halophytic, warm-season grass with wide applications. It is noted for its superior salt tolerance in saline environments; however, the nutritive value of seashore paspalum and the effect of salinity remains to be determined. Therefore, this study aimed to evaluate the relationship between agronomic traits and forage quality and identified the effects of short-term high-salt stress (1 week, 700 mM NaCl) on the growth and forage nutritive value of 16 ecotypes of seashore paspalum. The salt and cold tolerances of the seashore paspalum ecotypes were assessed based on the survival rate following long-term high-salt stress (7 weeks, 700 mM NaCl) and exposure to natural low temperature stress. There were significant genetic (ecotype-specific) effects on plant height, leaf-stem ratio, and survival rate of seashore paspalum following salt or low temperature stress. Plant height was significantly negatively correlated with the leaf-stem ratio (r = -0.63, P<0.01), but the heights and leaf-stem ratios were not significantly correlated with the fresh weight (FW) and dry weight (DW) of the shoots. High salinity decreased the FW and DW of the shoots by 50.6% and 23.6%, respectively, on average. Seashore paspalum exhibited outstanding salt tolerance and forage quality at high salinity. The survival rate of the different ecotypes of seashore paspalum varied from 6.5% to 49.0% following treatment with 700 mM NaCl for 7 weeks. The crude protein (CP) content of the control and treatment groups (700 mM NaCl) was 17.4% and 19.3%, respectively, of the DW on average, and the CP content of most ecotypes was not significantly influenced by high salinity. The average ether extract (EE) content ranged from 4.6% to 4.4% of the DW under control and saline conditions, respectively, indicating that the influence was not significant. The neutral detergent fiber (NDF) and acid detergent fiber (ADF) contents of the control group were 57.4% and 29.8%, respectively, of the DW on average. Salt stress reduced the content of NDF and ADF to 50.2% and 25.9%, respectively, of the DW on average. Altogether, the results demonstrated that stress did not have any significant effects on the CP and EE content of most ecotypes, but reduced the NDF and ADF content and improved relative feed value (RFV). The results obtained herein support the notion that seashore paspalum is a good candidate for improving the forage potential of saline soils and can provide useful guidelines for livestock producers.
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Affiliation(s)
- Kai Jiang
- College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Zhimin Yang
- College of Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Juan Sun
- College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Huancheng Liu
- College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Shenmiao Chen
- College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Yongzhuo Zhao
- College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Wangdan Xiong
- College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Wenjie Lu
- College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Zeng-Yu Wang
- College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Xueli Wu
- College of Grassland Science, Qingdao Agricultural University, Qingdao, China
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6
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Spotting the Targets of the Apospory Controller TGS1 in Paspalum notatum. PLANTS 2022; 11:plants11151929. [PMID: 35893633 PMCID: PMC9332697 DOI: 10.3390/plants11151929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/27/2022] [Accepted: 06/30/2022] [Indexed: 11/17/2022]
Abstract
Sexuality and apomixis are interconnected plant reproductive routes possibly behaving as polyphenic traits under the influence of the environment. In the subtropical grass Paspalum notatum, one of the controllers of apospory, a main component of gametophytic apomixis reproduction, is TRIMETHYLGUANOSINE SYNTHASE 1 (TGS1), a multifunctional gene previously associated with RNA cleavage regulation (including mRNA splicing as well as rRNA and miRNA processing), transcriptional modulation and the establishment of heterochromatin. In particular, the downregulation of TGS1 induces a sexuality decline and the emergence of aposporous-like embryo sacs. The present work was aimed at identifying TGS1 target RNAs expressed during reproductive development of Paspalum notatum. First, we mined available RNA databases originated from spikelets of sexual and apomictic plants, which naturally display a contrasting TGS1 representation, to identify differentially expressed mRNA splice variants and miRNAs. Then, the role of TGS1 in the generation of these particular molecules was investigated in antisense tgs1 sexual lines. We found that CHLOROPHYLL A-B BINDING PROTEIN 1B-21 (LHC Ib-21, a component of the chloroplast light harvesting complex), QUI-GON JINN (QGJ, encoding a MAP3K previously associated with apomixis) and miR2275 (a meiotic 24-nt phasi-RNAs producer) are directly or indirectly targeted by TGS1. Our results point to a coordinated control exercised by signal transduction and siRNA machineries to induce the transition from sexuality to apomixis.
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Roy AK, Chakraborti M, Radhakrishna A, Dwivedi KK, Srivastava MK, Saxena S, Paul S, Khare A, Malaviya DR, Kaushal P. Alien genome mobilization and fixation utilizing an apomixis mediated genome addition (AMGA) strategy in Pennisetum to improve domestication traits of P. squamulatum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2555-2575. [PMID: 35726065 DOI: 10.1007/s00122-022-04138-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
An approach to release 'frozen' variability in apomictic species using sexuality of another species, eventually its utilization in crop improvement and de-novo domestication of crop wild relatives is presented. Pennisetum squamulatum, a secondary gene pool species of pearl millet (P. glaucum), harbours many desirable traits. However, it was neither utilized to improve pearl millet fodder traits nor improvement of its own domestication traits was attempted, due to the complexities of genomes and apomictic reproduction. To overcome this, we followed an Apomixis Mediated Genome Addition (AMGA) strategy and utilized the contrasting reproductive capacities (sexuality and apomixis) of both the species to access the otherwise un-available variability embedded in P. squamulatum. Segregating population of interspecific hybrids exhibited significant variability and heterosis for desired morphological, agronomical, and nutritional traits. Elite apomictic and perennial hybrids were evaluated in breeding trials, and eventually a novel grass cultivar was released for commercial cultivation in India. The performance of newly developed cultivar was superior to other adapted perennial grasses of arid and semi-arid rangelands. Through AMGA, the sexuality of one species was successfully utilized to 'release' the 'frozen' variability embedded in another species. Subsequently, the hybrids representing desirable trait combinations were again 'fixed' utilizing the apomixis alleles from the male parent in a back-and-forth apomixis-sexual-apomixis selection cycle. This study also demonstrated the potential of AMGA to improve crop relatives through genomes introgression as well as de novo domestication of new crops from wild species.
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Affiliation(s)
- A K Roy
- ICAR - Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - M Chakraborti
- ICAR - National Rice Research Institute, Cuttack, 753006, India
| | - A Radhakrishna
- ICAR - Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - K K Dwivedi
- ICAR - Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - M K Srivastava
- ICAR - Indian Institute of Soybean Research, Indore, 452001, India
| | - S Saxena
- ICAR - Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - S Paul
- ICAR - Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - Aarti Khare
- ICAR - Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - D R Malaviya
- ICAR - Indian Institute of Sugarcane Research, Lucknow, 226002, India
| | - P Kaushal
- ICAR - National Institute of Biotic Stress Management, Raipur, 493225, India.
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Muguerza MB, Gondo T, Ishigaki G, Shimamoto Y, Umami N, Nitthaisong P, Rahman MM, Akashi R. Tissue Culture and Somatic Embryogenesis in Warm-Season Grasses—Current Status and Its Applications: A Review. PLANTS 2022; 11:plants11091263. [PMID: 35567264 PMCID: PMC9101205 DOI: 10.3390/plants11091263] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 11/16/2022]
Abstract
Warm-season grasses are C4 plants and have a high capacity for biomass productivity. These grasses are utilized in many agricultural production systems with their greatest value as feeds for livestock, bioethanol, and turf. However, many important warm-season perennial grasses multiply either by vegetative propagation or form their seeds by an asexual mode of reproduction called apomixis. Therefore, the improvement of these grasses by conventional breeding is difficult and is dependent on the availability of natural genetic variation and its manipulation through breeding and selection. Recent studies have indicated that plant tissue culture system through somatic embryogenesis complements and could further develop conventional breeding programs by micropropagation, somaclonal variation, somatic hybridization, genetic transformation, and genome editing. This review summarizes the tissue culture and somatic embryogenesis in warm-season grasses and focus on current status and above applications including the author’s progress.
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Affiliation(s)
- Melody Ballitoc Muguerza
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-Nishi, Miyazaki 889-2192, Japan; (M.B.M.); (G.I.); (Y.S.); (R.A.)
| | - Takahiro Gondo
- Frontier Science Research Center, University of Miyazaki, 1-1 Gakuenkibanadai-Nishi, Miyazaki 889-2192, Japan
- Correspondence:
| | - Genki Ishigaki
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-Nishi, Miyazaki 889-2192, Japan; (M.B.M.); (G.I.); (Y.S.); (R.A.)
| | - Yasuyo Shimamoto
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-Nishi, Miyazaki 889-2192, Japan; (M.B.M.); (G.I.); (Y.S.); (R.A.)
| | - Nafiatul Umami
- Faculty of Animal Science, Universitas Gadjah Mada, Jl Fauna 3, Yogyakarta 55281, Indonesia;
| | - Pattama Nitthaisong
- Faculty of Agricultural Technology, King Mongkut’s Institute of Technology Ladkrabang, Bangkok 10520, Thailand;
| | - Mohammad Mijanur Rahman
- Faculty of Agro-Based Industry, Jeli Campus, Universiti Malaysia Kelantan, Jeli 17600, Kelantan, Malaysia;
| | - Ryo Akashi
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-Nishi, Miyazaki 889-2192, Japan; (M.B.M.); (G.I.); (Y.S.); (R.A.)
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9
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Oberti H, Spangenberg G, Cogan N, Reyno R, Feijoo M, Murchio S, Dalla-Rizza M. Genome-wide analysis of Claviceps paspali: insights into the secretome of the main species causing ergot disease in Paspalum spp. BMC Genomics 2021; 22:766. [PMID: 34702162 PMCID: PMC8549174 DOI: 10.1186/s12864-021-08077-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 10/11/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The phytopatogen Claviceps paspali is the causal agent of Ergot disease in Paspalum spp., which includes highly productive forage grasses such as P. dilatatum. This disease impacts dairy and beef production by affecting seed quality and producing mycotoxins that can affect performance in feeding animals. The molecular basis of pathogenicity of C. paspali remains unknown, which makes it more difficult to find solutions for this problem. Secreted proteins are related to fungi virulence and can manipulate plant immunity acting on different subcellular localizations. Therefore, identifying and characterizing secreted proteins in phytopathogenic fungi will provide a better understanding of how they overcome host defense and cause disease. The aim of this work is to analyze the whole genome sequences of three C. paspali isolates to obtain a comparative genome characterization based on possible secreted proteins and pathogenicity factors present in their genome. In planta RNA-seq analysis at an early stage of the interaction of C. paspali with P. dilatatum stigmas was also conducted in order to determine possible secreted proteins expressed in the infection process. RESULTS C. paspali isolates had compact genomes and secretome which accounted for 4.6-4.9% of the predicted proteomes. More than 50% of the predicted secretome had no homology to known proteins. RNA-Seq revealed that three protein-coding genes predicted as secreted have mayor expression changes during 1 dpi vs 4 dpi. Also, three of the first 10 highly expressed genes in both time points were predicted as effector-like. CAZyme-like proteins were found in the predicted secretome and the most abundant family could be associated to pectine degradation. Based on this, pectine could be a main component affected by the cell wall degrading enzymes of C. paspali. CONCLUSIONS Based on predictions from DNA sequence and RNA-seq, unique probable secreted proteins and probable pathogenicity factors were identified in C. paspali isolates. This information opens new avenues in the study of the biology of this fungus and how it modulates the interaction with its host. Knowledge of the diversity of the secretome and putative pathogenicity genes should facilitate future research in disease management of Claviceps spp.
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Affiliation(s)
- H Oberti
- Instituto Nacional de Investigación Agropecuaria (INIA). Unidad de Biotecnología. Estación Experimental INIA Las Brujas, Ruta 48 km, 10, Canelones, Uruguay
| | - G Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, 5 Ring Road, Bundoora, VIC, 3083, Australia
| | - N Cogan
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, 5 Ring Road, Bundoora, VIC, 3083, Australia
| | - R Reyno
- Instituto Nacional de Investigación Agropecuaria (INIA). Programa Pasturas y Forrajes. Estación Experimental INIA Tacuarembó, Ruta 5 km, 386, Tacuarembó, Uruguay
| | - M Feijoo
- Centro Universitario Regional del Este (CURE), Polo de Desarrollo Universitario: Patogenicidad, toxicidad y genética en los ecosistemas pastoriles de la región Este de Uruguay, Ruta 8 km, 281, Treinta y Tres, Uruguay
| | - S Murchio
- Instituto Nacional de Investigación Agropecuaria (INIA). Unidad de Biotecnología. Estación Experimental INIA Las Brujas, Ruta 48 km, 10, Canelones, Uruguay
| | - M Dalla-Rizza
- Instituto Nacional de Investigación Agropecuaria (INIA). Unidad de Biotecnología. Estación Experimental INIA Las Brujas, Ruta 48 km, 10, Canelones, Uruguay.
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10
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Martins FB, Moraes ACL, Aono AH, Ferreira RCU, Chiari L, Simeão RM, Barrios SCL, Santos MF, Jank L, do Valle CB, Vigna BBZ, de Souza AP. A Semi-Automated SNP-Based Approach for Contaminant Identification in Biparental Polyploid Populations of Tropical Forage Grasses. FRONTIERS IN PLANT SCIENCE 2021; 12:737919. [PMID: 34745171 PMCID: PMC8569613 DOI: 10.3389/fpls.2021.737919] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Artificial hybridization plays a fundamental role in plant breeding programs since it generates new genotypic combinations that can result in desirable phenotypes. Depending on the species and mode of reproduction, controlled crosses may be challenging, and contaminating individuals can be introduced accidentally. In this context, the identification of such contaminants is important to avoid compromising further selection cycles, as well as genetic and genomic studies. The main objective of this work was to propose an automated multivariate methodology for the detection and classification of putative contaminants, including apomictic clones (ACs), self-fertilized individuals, half-siblings (HSs), and full contaminants (FCs), in biparental polyploid progenies of tropical forage grasses. We established a pipeline to identify contaminants in genotyping-by-sequencing (GBS) data encoded as allele dosages of single nucleotide polymorphism (SNP) markers by integrating principal component analysis (PCA), genotypic analysis (GA) measures based on Mendelian segregation, and clustering analysis (CA). The combination of these methods allowed for the correct identification of all contaminants in all simulated progenies and the detection of putative contaminants in three real progenies of tropical forage grasses, providing an easy and promising methodology for the identification of contaminants in biparental progenies of tetraploid and hexaploid species. The proposed pipeline was made available through the polyCID Shiny app and can be easily coupled with traditional genetic approaches, such as linkage map construction, thereby increasing the efficiency of breeding programs.
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Affiliation(s)
- Felipe Bitencourt Martins
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), São Paulo, Brazil
| | - Aline Costa Lima Moraes
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), São Paulo, Brazil
| | - Alexandre Hild Aono
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), São Paulo, Brazil
| | | | - Lucimara Chiari
- Embrapa Gado de Corte, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | - Rosangela Maria Simeão
- Embrapa Gado de Corte, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | | | | | - Liana Jank
- Embrapa Gado de Corte, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | | | | | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), São Paulo, Brazil
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), São Paulo, Brazil
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11
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Soliman M, Bocchini M, Stein J, Ortiz JPA, Albertini E, Delgado L. Environmental and Genetic Factors Affecting Apospory Expressivity in Diploid Paspalum rufum. PLANTS 2021; 10:plants10102100. [PMID: 34685909 PMCID: PMC8537111 DOI: 10.3390/plants10102100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/22/2021] [Accepted: 09/27/2021] [Indexed: 11/30/2022]
Abstract
In angiosperms, gametophytic apomixis (clonal reproduction through seeds) is strongly associated with polyploidy and hybridization. The trait is facultative and its expressivity is highly variable between genotypes. Here, we used an F1 progeny derived from diploid apomictic (aposporic) genotypes of Paspalum rufum and two F2 families, derived from F1 hybrids with different apospory expressivity (%AES), to analyze the influence of the environment and the transgenerational transmission of the trait. In addition, AFLP markers were developed in the F1 population to identify genomic regions associated with the %AES. Cytoembryological analyses showed that the %AES was significantly influenced by different environments, but remained stable across the years. F1 and F2 progenies showed a wide range of %AES variation, but most hybrids were not significantly different from the parental genotypes. Maternal and paternal genetic linkage maps were built covering the ten expected linkage groups (LG). A single-marker analysis detected at least one region of 5.7 cM on LG3 that was significantly associated with apospory expressivity. Our results underline the importance of environmental influence in modulating apospory expressivity and identified a genomic region associated with apospory expressivity at the diploid level.
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Affiliation(s)
- Mariano Soliman
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR), CONICET, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Rosario S2125ZAA, Zavalla, Argentina; (M.S.); (J.S.); (J.P.A.O.)
| | - Marika Bocchini
- Department Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy; (M.B.); (E.A.)
| | - Juliana Stein
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR), CONICET, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Rosario S2125ZAA, Zavalla, Argentina; (M.S.); (J.S.); (J.P.A.O.)
| | - Juan Pablo A. Ortiz
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR), CONICET, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Rosario S2125ZAA, Zavalla, Argentina; (M.S.); (J.S.); (J.P.A.O.)
| | - Emidio Albertini
- Department Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy; (M.B.); (E.A.)
| | - Luciana Delgado
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR), CONICET, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Rosario S2125ZAA, Zavalla, Argentina; (M.S.); (J.S.); (J.P.A.O.)
- Correspondence:
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12
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Germplasm Conservation: Instrumental in Agricultural Biodiversity—A Review. SUSTAINABILITY 2021. [DOI: 10.3390/su13126743] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Germplasm is a valuable natural resource that provides knowledge about the genetic composition of a species and is crucial for conserving plant diversity. Germplasm protection strategies not only involve rescuing plant species threatened with extinction, but also help preserve all essential plants, on which rests the survival of all organisms. The successful use of genetic resources necessitates their diligent collection, storage, analysis, documentation, and exchange. Slow growth cultures, cryopreservation, pollen and DNA banks, botanical gardens, genetic reserves, and farmers’ fields are a few germplasm conservation techniques being employed. However, the adoption of in-vitro techniques with any chance of genetic instability could lead to the destruction of the entire substance, but the improved understanding of basic regeneration biology would, in turn, undoubtedly increase the capacity to regenerate new plants, thus expanding selection possibilities. Germplasm conservation seeks to conserve endangered and vulnerable plant species worldwide for future proliferation and development; it is also the bedrock of agricultural production.
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13
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Ortiz JPA, Pupilli F, Acuña CA, Leblanc O, Pessino SC. How to Become an Apomixis Model: The Multifaceted Case of Paspalum. Genes (Basel) 2020; 11:E974. [PMID: 32839398 PMCID: PMC7564465 DOI: 10.3390/genes11090974] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 12/12/2022] Open
Abstract
In the past decades, the grasses of the Paspalum genus have emerged as a versatile model allowing evolutionary, genetic, molecular, and developmental studies on apomixis as well as successful breeding applications. The rise of such an archetypal system progressed through integrative phases, which were essential to draw conclusions based on solid standards. Here, we review the steps adopted in Paspalum to establish the current body of knowledge on apomixis and provide model breeding programs for other agronomically important apomictic crops. In particular, we discuss the need for previous detailed cytoembryological and cytogenetic germplasm characterization; the establishment of sexual and apomictic materials of identical ploidy level; the development of segregating populations useful for inheritance analysis, positional mapping, and epigenetic control studies; the development of omics data resources; the identification of key molecular pathways via comparative gene expression studies; the accurate molecular characterization of genomic loci governing apomixis; the in-depth functional analysis of selected candidate genes in apomictic and model species; the successful building of a sexual/apomictic combined breeding scheme.
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Affiliation(s)
- Juan Pablo A. Ortiz
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR), CONICET, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, S2125ZAA Zavalla, Argentina;
| | - Fulvio Pupilli
- Institute of Biosciences and Bioresources (IBBR-CNR), 06128 Perugia, Italy;
| | - Carlos A. Acuña
- Instituto de Botánica del Nordeste (IBONE), CONICET, Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste, 3400 Corrientes, Argentina;
| | - Olivier Leblanc
- UMR DIADE, IRD, Univ. Montpellier, 34090 Montpellier, France;
| | - Silvina C. Pessino
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR), CONICET, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, S2125ZAA Zavalla, Argentina;
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