Next generation DNA sequencing technology delivers valuable genetic markers for the genomic orphan legume species, Bituminaria bituminosa

Background: Bituminaria bituminosa is a perennial legume species from the Canary Islands and Mediterranean region that has potential as a drought-tolerant pasture species and as a source of pharmaceutical compounds. Three botanical varieties have previously been identified in this species: albomarginata, bituminosa and crassiuscula. B. bituminosa can be considered a genomic 'orphan' species with very few genomic resources available. New DNA sequencing technologies provide an opportunity to develop high quality molecular markers for such orphan species.Results: 432,306 mRNA molecules were sampled from a leaf transcriptome of a single B. bituminosa plant using Roche 454 pyrosequencing, resulting in an average read length of 345 bp (149.1 Mbp in total). Sequences were assembled into 3,838 isotigs/contigs representing putatively unique gene transcripts. Gene ontology descriptors were identified for 3,419 sequences. Raw sequence reads containing simple sequence repeat (SSR) motifs were identified, and 240 primer pairs flanking these motifs were designed. Of 87 primer pairs developed this way, 75 (86.2%) successfully amplified primarily single fragments by PCR. Fragment analysis using 20 primer pairs in 79 accessions of B. bituminosa detected 130 alleles at 21 SSR loci. Genetic diversity analyses confirmed that variation at these SSR loci accurately reflected known taxonomic relationships in original collections of B. bituminosa and provided additional evidence that a division of the botanical variety bituminosa into two according to geographical origin (Mediterranean region and Canary Islands) may be appropriate. Evidence of cross-pollination was also found between botanical varieties within a B. bituminosa breeding programme.Conclusions: B. bituminosa can no longer be considered a genomic orphan species, having now a large (albeit incomplete) repertoire of expressed gene sequences that can serve as a resource for future genetic studies. This experimental approach was effective in developing codominant and polymorphic SSR markers for application in diverse genetic studies. These markers have already given new insight into genetic variation in B. bituminosa, providing evidence that a division of the botanical variety bituminosa may be appropriate. This approach is commended to those seeking to develop useful markers for genomic orphan species

Messina (\u3cem\u3eMelilotus siculus\u3c/em\u3e)–A New Pasture Legume for Saltland

Messina (Melilotus siculus ((Turra) Vitman ex B.D. Jacks)) is a new annual pasture legume for saltland in temperate Australia and regions of the world that experience Mediterranean climates. Messina has greater tolerance to the combined stresses of salinity and water-logging than existing commercial pasture legumes. Coupled with desirable agronomic traits these characteristics give messina the capacity to rehabilitate saltland and increase productivity on land where existing legumes fail. This paper reviews the agronomic perform-ance of messina in relation to top soil salinity levels

Root aeration via aerenchymatous phellem:three-dimensional micro-imaging and radial O₂ profiles in <em>Melilotus siculus</em>

micro-CT, multiscale model, oxygen

Waterlogging tolerance is associated with root porosity in barley (Hordeum vulgare L.)

Tolerance to waterlogging is an important breeding objective for barley (Hordeum vulgare L.); however, it is a complex quantitative trait. It is difficult to screen large numbers of lines in the field due to environmental variability, and it is also challenging to screen large numbers in controlled conditions if yield data are to be collected. The direct measurement of traits that contribute to waterlogging tolerance, such as aerenchyma development in roots, may offer advantages especially if molecular markers can be developed to screen breeding populations. A doubled haploid population from a cross between Franklin and YuYaoXiangTian Erleng was screened for adventitious root porosity (gas-filled volume per unit root volume) as an indicator of aerenchyma formation. A single QTL for root porosity was identified on chromosome 4H which explained 35.7 and 39.0 % of phenotypic variation in aerated and oxygen-deficient conditions, respectively. The nearest marker was EBmac0701. This QTL is located in the same chromosomal region that contributed to tolerance when the same population was screened in an earlier independent soil waterlogging experiment. Comparative mapping revealed that this QTL is syntenic with the Qaer1.02-3 QTL in maize and the Sub1A-1 gene in rice, which are associated with aerenchyma formation (maize) and submergence tolerance (rice), respectively. This is the first report of a QTL for root porosity in barley which elucidates a major mechanism of waterlogging tolerance

Evaluation and breeding of tedera for Mediterranean climates in southern Australia

Tedera (Bituminaria bituminosa C.H. Stirton var. albomarginata and var. crassiuscula) has been identified as one of the most productive and drought-tolerant species of herbaceous perennial legumes based on 6 years of field evaluation in Western Australia in areas with Mediterranean climate and annual rainfall ranging from 200 to 600mm. Importantly, tedera demonstrated broad adaptation to diverse soils, and some accessions have shown moderate levels of tolerance to waterlogging and salinity. Tedera exhibits minimal leaf shedding during summer and autumn. Economic modelling strongly suggests that giving livestock access to green tedera in summer and autumn will dramatically increase farm profit by reducing supplementary feeding. The breeding program (2006-12) evaluated the available genetic diversity of tedera for its field performance in seven nurseries with 6498 spaced plants in total covering a wide variation in rainfall, soils and seasons. Best overall plants were selected using a multivariate selection index generated with best linear unbiased predictors (BLUPs) of dry matter cuts and leaf retention traits. The breeding program also evaluated tedera for grazing tolerance, grazing preference by livestock, waterlogging tolerance, seed production, cold tolerance, disease susceptibility and presence of secondary compounds. Tedera is a diploid, self-pollinated species. Therefore, 28 elite parents were hand-crossed in several combinations to combine outstanding attributes of parents; F1 hybrids were confirmed with the aid of highly polymorphic, simple sequence repeat markers. The F1s were progressed to F4s by single-seed descent breeding. Elite parent plants were selfed for two generations to be progressed in the breeding program without hybridisation. Over time, selections from the crossing and selfing program will deliver cultivars of three ideotypes: (i) drought-tolerant, (ii) cold- and drought-tolerant, (iii) waterlogging- and drought-tolerant

Nurture Early for Optimal Nutrition (NEON) participatory learning and action women’s groups to improve infant feeding and practices in South Asian infants: pilot randomised trial study protocol

Introduction Feeding practices developed in early life can impact a child’s nutrition, growth, dental health, cognitive development and lifetime risk of chronic diseases. Substantial evidence suggests ethnic health inequalities, and non-recommended complementary infant feeding practices among UK’s South Asian (SA) population. Nurture Early for Optimal Nutrition aims to use women’s group participatory learning and action (PLA) cycles to optimise infant feeding, care and dental hygiene practices in SA infants &lt;2 years in East London.Methods and analysis A three-arm pilot feasibility cluster randomised controlled trial will assess feasibility, acceptability, costs and explore preliminary effectiveness for proposed primary outcome (ie, reporting on body mass index (BMI) z-score). Multilingual SA community facilitators will deliver the intervention, group PLA Cycle, to mothers/carers in respective ethnic/language groups. 12 wards are randomised to face-to-face PLA, online PLA and usual care arms in 1:1:1 ratio. Primary outcomes are feasibility and process measures (ie, BMI z-score, study records, feedback questionnaires, direct observation of intervention and sustainability) for assessment against Go/Stop criteria. Secondary outcomes are cluster-level and economic outcomes (ie, eating behaviour, parental feeding practices, network diffusion, children development performance, level of dental caries, general practitioner utilisation, costs, staff time). Outcomes are measured at baseline, every 2 weeks during intervention, 14 weeks and at 6 months by blinded outcome assessors where possible. This study will use concurrent mixed-methods evaluation. Quantitative analyses include descriptive summary with 95% CI and sample size calculation for the definitive trial. The intervention effect with CI will be estimated for child BMI z-score. Implementation will be evaluated qualitatively using thematic framework analysis.Ethics and dissemination Ethics approval was obtained from University College London (UCL), National Health Service (Health Research Authority (HRA) and Health and Care Research Wales (HRCW)). Results will be published in peer-reviewed journals, presented at scientific conferences/workshops with commissioners, partners and participating communities. Plain language summaries will be disseminated through community groups, websites and social media.Trial registration number IRAS-ID-296259 (ISRCTN10234623)