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Maybery-Reupert K, Isenegger D, Hayden M, Cogan N. Development of genomic resources for Rhodes grass ( Chloris gayana), draft genome and annotated variant discovery. Front Plant Sci 2023; 14:1239290. [PMID: 37731974 PMCID: PMC10507473 DOI: 10.3389/fpls.2023.1239290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/18/2023] [Indexed: 09/22/2023]
Abstract
Genomic resources for grasses, especially warm-season grasses are limited despite their commercial and environmental importance. Here, we report the first annotated draft whole genome sequence for diploid Rhodes grass (Chloris gayana), a tropical C4 species. Generated using long read nanopore sequencing and assembled using the Flye software package, the assembled genome is 603 Mbp in size and comprises 5,233 fragments that were annotated using the GenSas pipeline. The annotated genome has 46,087 predicted genes corresponding to 92.0% of the expected genomic content present via BUSCO analysis. Gene ontology terms and repetitive elements are identified and discussed. An additional 94 individual plant genotypes originating from three diploid and two tetraploid Rhodes grass cultivars were short-read whole genome resequenced (WGR) to generate a single nucleotide polymorphism (SNP) resource for the species that can be used to elucidate inter- and intra-cultivar relationships across both ploidy levels. A total of 75,777 high quality SNPs were used to generate a phylogenetic tree, highlighting the diversity present within the cultivars which agreed with the known breeding history. Differentiation was observed between diploid and tetraploid cultivars. The WGR data were also used to provide insights into the nature and evolution of the tetraploid status of the species, with results largely agreeing with the published literature that the tetraploids are autotetraploid.
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Affiliation(s)
- Kellie Maybery-Reupert
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Daniel Isenegger
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Matthew Hayden
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Noel Cogan
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
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Mollard FPO, Di Bella CE, Loguzzo MB, Grimoldi AA, Striker GG. High Recovery from Either Waterlogging or Drought Overrides Any Beneficial Acclimation of Chloris gayana Facing a Subsequent Round of Stress. Plants (Basel) 2022; 11:2699. [PMID: 36297722 PMCID: PMC9610420 DOI: 10.3390/plants11202699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/15/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Climate models predict that plants will face extreme fluctuations in water availability in future global change scenarios. Then, forage production will be more frequently subjected to the destabilizing pressure of sequentially occurring waterlogging and drought events. While the isolated effects of drought (D) and waterlogging (WL) are well characterized, little is known about the consequences when both stresses occur sequentially. We hypothesized that plants sequentially subjected to opposite water scenarios (D followed by WL or vice versa) are less stress tolerant than plants experiencing repetitions of the same type of water stress (i.e., D + D or WL + WL) due to contrasting acclimation and allocation to either shoots (WL) or roots (D). Chloris gayana (a tropical forage grass capable of tolerating either D and WL) plants were randomly assigned to nine treatments (a sequence of two stress rounds-WL or D-each followed by a recovery phase at field capacity). Relative growth rates and allometric responses were measured after each stress round and recovery period. In the first round of stress, both WL and D reduced plant RGR similarly, despite their allocation being opposite-prioritizing shoots or roots under WL and D, respectively. The high recovery displayed after either WL or D overrode any possible acclimation of the plants facing a second round of water stress. We conclude that the tolerance of C. gayana to sequential water stress (either for WL or D) is likely to depend more heavily on its recovery ability than on its previous adjustment to any stress scenario that may evoke memory responses. Knowledge like this could help improve forage grass breeding and the selection of cultivars for poorly drained soils subject to sequential stress events.
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Affiliation(s)
- Federico P. O. Mollard
- IFEVA, CONICET, Cátedra de Fisiología Vegetal, Departamento de Biología Aplicada y Alimentos, Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453, Buenos Aires C1417DSE, Argentina
| | - Carla E. Di Bella
- IFEVA, CONICET, Cátedra de Forrajicultura, Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453, Buenos Aires C1417DSE, Argentina
| | - María B. Loguzzo
- Cátedra de Fisiología Vegetal, Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453, Buenos Aires C1417DSE, Argentina
| | - Agustín A. Grimoldi
- IFEVA, CONICET, Cátedra de Forrajicultura, Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453, Buenos Aires C1417DSE, Argentina
| | - Gustavo G. Striker
- IFEVA, CONICET, Cátedra de Fisiología Vegetal, Departamento de Biología Aplicada y Alimentos, Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453, Buenos Aires C1417DSE, Argentina
- UWA School of Agriculture and Environment, Faculty of Science, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
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Tola E, Al-Gaadi KA, Madugundu R, Zeyada AM, Kayad AG, Biradar CM. Characterization of spatial variability of soil physicochemical properties and its impact on Rhodes grass productivity. Saudi J Biol Sci 2016; 24:421-429. [PMID: 28149182 PMCID: PMC5272951 DOI: 10.1016/j.sjbs.2016.04.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/31/2016] [Accepted: 04/19/2016] [Indexed: 11/30/2022] Open
Abstract
Characterization of soil properties is a key step in understanding the source of spatial variability in the productivity across agricultural fields. A study on a 16 ha field located in the eastern region of Saudi Arabia was undertaken to investigate the spatial variability of selected soil properties, such as soil compaction ‘SC’, electrical conductivity ‘EC’, pH (acidity or alkalinity of soil) and soil texture and its impact on the productivity of Rhodes grass (Chloris gayana L.). The productivity of Rhodes grass was investigated using the Cumulative Normalized Difference Vegetation Index (CNDVI), which was determined from Landsat-8 (OLI) images. The statistical analysis showed high spatial variability across the experimental field based on SC, clay and silt; indicated by values of the coefficient of variation (CV) of 22.08%, 21.89% and 21.02%, respectively. However, low to very low variability was observed for soil EC, sand and pH; with CV values of 13.94%, 7.20% and 0.53%, respectively. Results of the CNDVI of two successive harvests showed a relatively similar trend of Rhodes grass productivity across the experimental area (r = 0.74, p = 0.0001). Soil physicochemical layers of a considerable spatial variability (SC, clay, silt and EC) were utilized to delineate the experimental field into three management zones (MZ-1, MZ-2 and MZ-3); which covered 30.23%, 33.85% and 35.92% of the total area, respectively. The results of CNDVI indicated that the MZ-1 was the most productive zone, as its major areas of 50.28% and 45.09% were occupied by the highest CNDVI classes of 0.97–1.08 and 4.26–4.72, for the first and second harvests, respectively.
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Affiliation(s)
- E Tola
- Precision Agriculture Research Chair, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - K A Al-Gaadi
- Precision Agriculture Research Chair, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia; Department of Agricultural Engineering, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - R Madugundu
- Precision Agriculture Research Chair, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - A M Zeyada
- Precision Agriculture Research Chair, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - A G Kayad
- Department of Agricultural Engineering, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - C M Biradar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Bldg no. 15, Khalid Abu Dalbouh St. Abdoun, P.O. Box 950764, Code No. 11195 Amman, Jordan
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Tefera G, Tegegne F, Mekuriaw Y, Melaku S, Tsunekawa A. Effects of different forms of white lupin (Lupinus albus) grain supplementation on feed intake, digestibility, growth performance and carcass characteristics of Washera sheep fed Rhodes grass (Chloris gayana) hay-based diets. Trop Anim Health Prod 2015; 47:1581-90. [PMID: 26250152 DOI: 10.1007/s11250-015-0901-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/31/2015] [Indexed: 11/30/2022]
Abstract
Protein is the major limiting nutrient in feeding ruminants especially in dryland areas. Thus, looking for locally available protein sources such as white lupin (Lupinus albus) grain is commendable. The objective of this experiment was to determine effects of supplementation of different forms of white lupin grain (WLG) on feed and nutrient intake, digestibility, growth and carcass characteristics. Twenty-five yearling male Washera sheep with initial body weight (BW) of 16.26 ± 1.41 kg (mean ± SD) were used. Animals were blocked into five based on their initial BW and were randomly assigned to one of the following five dietary treatments: Rhodes grass (Chloris gayana) hay (RGH) alone (T1) or supplemented with 300 g (on dry matter (DM) basis) raw WLG (T2) or raw soaked and dehulled WLG (T3) or roasted WLG (T4) or raw soaked WLG (T5). Supplementation with WLG significantly improved total DM and nutrient intake (P < 0.001), nutrient digestibility (P < 0.01), and average daily gain (ADG) and feed conversion efficiency (FCE) (P < 0.001). Carcass quality parameters were significantly (P < 0.001) higher for supplemented sheep. However, the difference in carcass quality parameters among supplemented groups was not significant (P > 0.05). It is concluded that roasting white lupin grain can lead to a better feed and nutrient intake and consequently better carcass quality. White lupin grain can be recommended not only for maintenance but also for optimum performance of ruminants.
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Affiliation(s)
- Gebru Tefera
- Koga irrigation and watershed management project, Bahir Dar, Ethiopia
| | - Firew Tegegne
- Department of Animal Production and Technology, Bahir Dar University, P.O. Box 79, Bahir Dar, Ethiopia.
- Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori, 680-0001, Japan.
| | - Yeshambel Mekuriaw
- Department of Animal Production and Technology, Bahir Dar University, P.O. Box 79, Bahir Dar, Ethiopia
| | - Solomon Melaku
- Haramaya University, School of Animal and Range Sciences, P.O.Box 138, Dire Dawa, Ethiopia
| | - Atsushi Tsunekawa
- Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori, 680-0001, Japan
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Scholz LM, Kopittke PM, Menzies NW, Dalzell SA, Macfarlane DC, Wehr JB. Use of fluoride-containing water for the irrigation of soil-plant systems. J Agric Food Chem 2015; 63:4737-4745. [PMID: 25925108 DOI: 10.1021/acs.jafc.5b01001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Many groundwaters used for irrigation contain elevated concentrations of F, but much remains unknown regarding how this F behaves within soils and plants. The present study investigated the adsorption and desorption of F from several soils in short- to medium-term irrigation systems and related foliar F concentrations in three forage plant species to the maximum tolerable level (MTL) in the diets of grazing animals (being 1.8 μmol/g for young cattle, for example). Although adsorption isotherms could be successfully used to predict the behavior (adsorption and desorption) of F within the soil, this was not related to the subsequent accumulation of F in plant foliage. In addition, the extent to which F accumulated in the foliage depended on the plant species. Regardless, F generally did not accumulate in plant foliage to levels exceeding the MTL when used at rates equivalent to irrigation for 25 years. In addition to uptake by roots, F may accumulate in foliar tissues directly due to retention from overhead irrigation. The data presented here regarding the behavior of F in soils and plants will assist in the rigorous regulation of F-containing irrigation water to ensure maximum plant growth while simultaneously minimizing potential harm.
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Affiliation(s)
- Lisa M Scholz
- †The University of Queensland, School of Agriculture and Food Sciences, St Lucia, Queensland 4072, Australia
| | - Peter M Kopittke
- †The University of Queensland, School of Agriculture and Food Sciences, St Lucia, Queensland 4072, Australia
| | - Neal W Menzies
- †The University of Queensland, School of Agriculture and Food Sciences, St Lucia, Queensland 4072, Australia
| | - Scott A Dalzell
- ‡Santos, Queensland Business Unit Environment, Brisbane, Queensland 4000, Australia
| | - David C Macfarlane
- ‡Santos, Queensland Business Unit Environment, Brisbane, Queensland 4000, Australia
| | - J Bernhard Wehr
- †The University of Queensland, School of Agriculture and Food Sciences, St Lucia, Queensland 4072, Australia
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