scholarly journals Hi-C yields chromosome-length scaffolds for a legume genome, Trifolium subterraneum

2018 ◽  
Author(s):  
Olga Dudchenko ◽  
Melanie Pham ◽  
Christopher Lui ◽  
Sanjit S. Batra ◽  
Marie Hoeger ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Subterranean Clover ◽  
Trifolium Subterraneum ◽  
Chromosome Length ◽  
Pasture Legume

AbstractWe present a chromosome-length assembly of the genome of subterranean clover, Trifolium subterraneum, a key Australian pasture legume. Specifically, in situ Hi-C data (48X) was used to correct misjoins and anchor, order, and orient scaffolds in a previously published genome assembly (TSUd_r1.1; scaffold N50: 287kb). This resulted in an improved genome assembly (TrSub3; scaffold N50: 56Mb) containing eight chromosome-length scaffolds that span 95% of the sequenced bases in the input assembly.

scholarly journals Harvesting subterranean clover seed – current practices, technology and issues

2021 ◽  
Vol 72 (3) ◽  
pp. 223
Author(s):  
Wesley M. Moss ◽  
Andrew L. Guzzomi ◽  
Kevin J. Foster ◽  
Megan H. Ryan ◽  
Phillip G. H. Nichols
Keyword(s):  
Soil Erosion ◽  
Case Studies ◽  
Seed Production ◽  
Subterranean Clover ◽  
Trifolium Subterraneum ◽  
Root Cause ◽  
Pasture Plant ◽  
Clover Seed ◽  
Production Industry ◽  
Pasture Legume

Subterranean clover (Trifolium subterraneum L.) is Australia’s most widely sown annual pasture legume. Its widespread use as a pasture plant requires a well-functioning seed production industry, and Australia is the only significant producer of subterranean clover seed globally. However, the sustainability of this industry is under threat due to its reliance on ageing harvest equipment and the resultant environmental impacts. In order to evaluate seed harvesting practices, technology, and issues, we report on case studies, workshops, and a survey of seed producers across southern Australia. The Horwood Bagshaw Clover Harvester, designed in the 1950s, remains the most popular subterranean clover seed harvester. We discuss its use and modifications, and document several contemporary issues facing the seed production industry. Issues are primarily soil erosion and degradation; the expensive, slow and labour-intensive harvest process; and poor reliability and maintainability of harvesters that are now at least 30 years old. We conclude the root cause of these issues is the suction harvest technology utilised by the Horwood Bagshaw Clover Harvester. Analysis of the current harvest system is provided to support the development of new approaches to harvest subterranean clover seeds.

Pasture legume species differ in their capacity to acidify soil

1998 ◽  
Vol 49 (1) ◽  
pp. 53 ◽  
Author(s):  
C. Tang ◽  
L. Barton ◽  
C. Raphael
Keyword(s):  
Acid Production ◽  
Dry Matter ◽  
Subterranean Clover ◽  
Trifolium Subterraneum ◽  
Growth Stages ◽  
Total Acid ◽  
Ash Alkalinity ◽  
Ornithopus Sativus ◽  
Excess Cations ◽  
Pasture Legume

The capacity of subterranean clover (Trifolium subterraneum L. cv. Clare), medic (Medicago murex Willd. cv. Zodiac), serradella (Ornithopus sativus Brot. line SP1/13), biserrula (Biserrula pelecinus L. line Mor99), and woolly clover (Trifolium tomentosum L.) to acidify soil under N2 fixation was compared in a pot experiment using a poorly buffered sandy soil. The amount of acid produced per kg shoot dry matter (specific acid production) varied betweefin species and with growth stages, ranging from 44 to 128 cmol/kg shoot. Subterranean clover and serradella acidied soil to a greater extent than woolly clover and medic, whereas biserrula acidified soil least. Irrespective of pasture species and growth stage, specific acid production correlated well with concentrations of excess cations and calcium in shoots. Furthermore, total excess cation, ash alkalinity, and calcium in shoots were all good indicators of total acid production across all of the species.

scholarly journals Exogenous ACC Deaminase Is Key to Improving the Performance of Pasture Legume-Rhizobial Symbioses in the Presence of a High Manganese Concentration

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1630
Author(s):  
Ana Paço ◽  
José Rodrigo da-Silva ◽  
Denise Pereira Torres ◽  
Bernard R. Glick ◽  
Clarisse Brígido
Keyword(s):  
Rhizobium Leguminosarum ◽  
Subterranean Clover ◽  
Acc Deaminase ◽  
Trifolium Subterraneum ◽  
Endophytic Bacterium ◽  
Manganese Concentration ◽  
Soil Conditions ◽  
Knockout Mutant ◽  
Mn Toxicity ◽  
Pasture Legume

Manganese (Mn) toxicity is a very common soil stress around the world, which is responsible for low soil fertility. This manuscript evaluates the effect of the endophytic bacterium Pseudomonas sp. Q1 on different rhizobial-legume symbioses in the absence and presence of Mn toxicity. Three legume species, Cicer arietinum (chickpea), Trifolium subterraneum (subterranean clover), and Medicago polymorpha (burr medic) were used. To evaluate the role of 1-aminocyclopropane-1-carboxylate (ACC) deaminase produced by strain Q1 in these interactions, an ACC deaminase knockout mutant of this strain was constructed and used in those trials. The Q1 strain only promoted the symbiotic performance of Rhizobium leguminosarum bv. trifolii ATCC 14480T and Ensifer meliloti ATCC 9930T, leading to an increase of the growth of their hosts in both conditions. Notably, the acdS gene disruption of strain Q1 abolished the beneficial effect of this bacterium as well as causing this mutant strain to act deleteriously in those specific symbioses. This study suggests that the addition of non-rhizobia with functional ACC deaminase may be a strategy to improve the pasture legume–rhizobial symbioses, particularly when the use of rhizobial strains alone does not yield the expected results due to their difficulty in competing with native strains or in adapting to inhibitory soil conditions.

Izmir subterranean clover (Trifolium subterraneum L. var. subterraneum)

2007 ◽  
Vol 47 (2) ◽  
pp. 226 ◽  
Author(s):  
P. G. H. Nichols ◽  
G. A. Sandral ◽  
B. S. Dear ◽  
C. T. de Koning ◽  
D. L. Lloyd ◽  
...  
Keyword(s):  
Seed Production ◽  
Seed Set ◽  
New South ◽  
South Australia ◽  
Subterranean Clover ◽  
Trifolium Subterraneum ◽  
Good Seed ◽  
Improvement Program ◽  
South Wales ◽  
Pasture Legume

Izmir is a hardseeded, early flowering, subterranean clover of var. subterraneum (Katz. et Morley) Zohary and Heller collected from Turkey and developed by the collaborating organisations of the National Annual Pasture Legume Improvement Program. It is a more hardseeded replacement for Nungarin and best suited to well-drained, moderately acidic soils in areas with a growing season of less than 4.5 months. Izmir seed production and regeneration densities in 3-year pasture phases were similar to Nungarin in 21 trials across southern Australia, but markedly greater in years following a crop or no seed set. Over all measurements, Izmir produced 10% more winter herbage and 7% more spring herbage than Nungarin. Its greater hardseededness and good seed production, makes it better suited to cropping rotations than Nungarin. Softening of Izmir hard seeds occurs later in the summer–autumn period than Nungarin, giving it slightly greater protection from seed losses following false breaks to the season. Izmir is recommended for sowing in Western Australia, New South Wales, Victoria, South Australia and Queensland. Izmir has been granted Plant Breeders Rights in Australia.

Biserrula and subterranean clover can co-exist during the vegetative phase but are out-competed by capeweed

2011 ◽  
Vol 62 (3) ◽  
pp. 236 ◽  
Author(s):  
S. A. Conning ◽  
M. Renton ◽  
M. H. Ryan ◽  
P. G. H. Nichols
Keyword(s):  
Subterranean Clover ◽  
Trifolium Subterraneum ◽  
Farming Systems ◽  
Exponential Model ◽  
Pasture Management ◽  
Relative Growth ◽  
Broad Leaf ◽  
Ley Farming ◽  
The Common ◽  
Pasture Legume

Biserrula (Biserrula pelecinus L.) is a recently domesticated annual pasture legume developed for ley farming systems that have traditionally relied upon subterranean clover (Trifolium subterraneum L.). This study examined competitive interactions between biserrula and subterranean clover and the common broad-leaf weed capeweed (Arctotheca calendula L.) during seedling establishment and vegetative growth, in order to develop guidelines for successful legume pasture management. Two glasshouse experiments were conducted to investigate the allocation of biomass to roots and shoots in biserrula, capeweed, and subterranean clover and its relationship with competitive ability in the first 100 days after sowing. In Experiment 1, capeweed had a higher relative growth rate of shoots and roots than the two legumes and developed a more extensive root system. Experiment 2 consisted of growing binary mixtures of the three species at different densities. The effect of competition on the biomass of biserrula, capeweed, and subterranean clover was best modelled by a power–exponential model. Increasing capeweed densities suppressed the biomass production of both biserrula and subterranean clover, whereas capeweed biomass increased with increasing densities of subterranean clover. This study suggests that the competitive advantage of capeweed is mainly conferred during the seedling stage. It also suggests that biserrula and subterranean clover germinating at the same time can co-exist as a mixed sward, at least up until flowering, if biserrula density is high relative to subterranean clover.

Studies on nodulation responses to pelleting of subterranean clover seed.

1961 ◽  
Vol 12 (4) ◽  
pp. 578 ◽  
Author(s):  
JA Thompson
Keyword(s):  
Seed Coat ◽  
Field Experiments ◽  
Chemical Constituents ◽  
Chemical Properties ◽  
Subterranean Clover ◽  
Trifolium Subterraneum ◽  
Coating Materials ◽  
Physical Separation ◽  
Clover Seed

In a series of field experiments on seven soils of pH 6.0 or higher, nodulation of subterranean clover (Trifolium subterraneum L. var. Tallarook) was improved by pelleting the seed with various glues and coating materials, prior to inoculation with dry peat inoculum. On these soils the responses were not related to the chemical properties of the pellet materials. The beneficial effect was apparently the result of physical separation of the seed coat and inoculum. It is postulated that pelleting of seed protects the inoculum from an antibiotic, whlch has been found in subterranean clover seed coats, and which is active against Rhizobium in culture. On a soil of pH 5.1 a nodulation response to two types of pelleting materials was apparently related to the chemical constituents of the coating materials. In this soil there was less evidence of the importance of physical separation of the inoculum from the seed coat. It seems likely that soils may differ considerably in their ability to inactivate the antibiotic. Nodulation was not improved by in situ fumigation, prior to sowing, of two soils of pH 6.0 and 6.6, which indicated that antagonism by soil microorganisms was not the cause of poor nodulation in these soils. Significant nodulation responses to pelleting were obtained in sowings in these fumigated soils.

scholarly journals Delineating the Tnt1 Insertion Landscape of the Model Legume Medicago truncatula cv. R108 at the Hi-C Resolution Using a Chromosome-Length Genome Assembly

2021 ◽  
Vol 22 (9) ◽  
pp. 4326
Author(s):  
Parwinder Kaur ◽  
Christopher Lui ◽  
Olga Dudchenko ◽  
Raja Sekhar Nandety ◽  
Bhavna Hurgobin ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Medicago Truncatula ◽  
Genome Assembly ◽  
Mutant Gene ◽  
Chromosome Length ◽  
Model Legume ◽  
Physical Information ◽  
High Transformation ◽  
Genome Scale

Legumes are of great interest for sustainable agricultural production as they fix atmospheric nitrogen to improve the soil. Medicago truncatula is a well-established model legume, and extensive studies in fundamental molecular, physiological, and developmental biology have been undertaken to translate into trait improvements in economically important legume crops worldwide. However, M. truncatula reference genome was generated in the accession Jemalong A17, which is highly recalcitrant to transformation. M. truncatula R108 is more attractive for genetic studies due to its high transformation efficiency and Tnt1-insertion population resource for functional genomics. The need to perform accurate synteny analysis and comprehensive genome-scale comparisons necessitates a chromosome-length genome assembly for M. truncatula cv. R108. Here, we performed in situ Hi-C (48×) to anchor, order, orient scaffolds, and correct misjoins of contigs in a previously published genome assembly (R108 v1.0), resulting in an improved genome assembly containing eight chromosome-length scaffolds that span 97.62% of the sequenced bases in the input assembly. The long-range physical information data generated using Hi-C allowed us to obtain a chromosome-length ordering of the genome assembly, better validate previous draft misjoins, and provide further insights accurately predicting synteny between A17 and R108 regions corresponding to the known chromosome 4/8 translocation. Furthermore, mapping the Tnt1 insertion landscape on this reference assembly presents an important resource for M. truncatula functional genomics by supporting efficient mutant gene identification in Tnt1 insertion lines. Our data provide a much-needed foundational resource that supports functional and molecular research into the Leguminosae for sustainable agriculture and feeding the future.

scholarly journals Urana subterranean clover (Trifolium subterraneum L. var. subterraneum)

2006 ◽  
Vol 46 (8) ◽  
pp. 1105 ◽  
Author(s):  
P. G. H. Nichols ◽  
M. J. Barbetti ◽  
G. A. Sandral ◽  
B. S. Dear ◽  
C. T. de Koning ◽  
...  
Keyword(s):  
New South ◽  
South Australia ◽  
Field Performance ◽  
Subterranean Clover ◽  
Trifolium Subterraneum ◽  
Growing Season ◽  
Crop Rotations ◽  
Improvement Program ◽  
South Wales ◽  
Pasture Legume

Urana is a hardseeded, moderately early flowering F5-derived crossbred subterranean clover of var. subterraneum [(Katz. et Morley) Zohary and Heller] developed by the collaborating organisations of the National Annual Pasture Legume Improvement Program. It has been selected for release as a new cultivar on the basis of its high winter and spring herbage production and overall field performance relative to other subterranean clovers of similar maturity. Urana is recommended for sowing in Western Australia, New South Wales, Victoria, South Australia and Queensland. It is best suited to well-drained, moderately acidic soils in areas with a growing season of 5–7 months, which extends into mid-October. Urana is suited to phase farming and crop rotations. It has been granted Plant Breeders Rights in Australia.

Coolamon subterranean clover (Trifolium subterraneum L. var. subterraneum)

2007 ◽  
Vol 47 (2) ◽  
pp. 223 ◽  
Author(s):  
P. G. H. Nichols ◽  
M. J. Barbetti ◽  
G. A. Sandral ◽  
B. S. Dear ◽  
C. T. de Koning ◽  
...  
Keyword(s):  
New South ◽  
South Australia ◽  
Subterranean Clover ◽  
Trifolium Subterraneum ◽  
Growing Season ◽  
Improvement Program ◽  
Permanent Pasture ◽  
South Wales ◽  
Clover Scorch ◽  
Pasture Legume

Coolamon is a mid-season to late-season flowering F4-derived crossbred subterranean clover of var. subterraneum, developed by the collaborating organisations of the National Annual Pasture Legume Improvement Program. It is a replacement for Junee and has been selected for release on the basis of its greater herbage production and persistence, and its resistance to both known races of clover scorch. Coolamon is recommended for sowing in Western Australia, New South Wales, Victoria, South Australia and Queensland. It is best suited to well-drained, moderately acidic soils in areas with a growing season of 6.5–8 months that extends into November. Coolamon is best suited to phase farming and permanent pasture systems. It can also be used in cropping rotations, but at least 2 years of pasture are required between crops. Coolamon has been granted Plant Breeders Rights in Australia.

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