Generating Fo contours from ToBI labels using linear regression

This paper describes a method for generating F0 contours from ToBI labelled utterances. The method uses linear regression to predict F0 target values for the start, mid-vowel and end of every syllable, using features representing the ToBI labels, stress and syllable position. Contours generated by this method for an English database have a correlation of 0.62 and 34.8 Hz RMS error when compared with originals from test data. These results are significant improvements on a previous rule driven method (0.40 and 44.7), and the new method contours are preferred by human listeners. The technique has also been successfully applied to Japanese ToBI with similar improvements

Unit selection in a concatenative speech synthesis system using a large speech database

One approach to the generation of natural-sounding synthesized speech waveforms is to select and concatenate units from a large speech database. Units (in the current work, phonemes) are selected to produce a natural realisation of a target phoneme sequence predicted from text which is annotated with prosodic and phonetic context information. We propose that the units in a synthesis database can be considered as a state transition network in which the state occupancy cost is the distance between a database unit and a target, and the transition cost is an estimate of the quality of concatenation of two consecutive units. This framework has many similarities to HMM-based speech recognition. A pruned Viterbi search is used to select the best units for synthesis from the database. This approach to waveform synthesis permits training from natural speech: two methods for training from speech are presented which provide weights which produce more natural speech than can be obtained by hand-tuning

A global resource for exploring and exploiting genetic variation in sorghum crop wild relatives

One response to mitigate the impact of climate change on agricultural systems is to develop new varieties that are tolerant to the new range of biotic and abiotic challenges this change causes. This requires access to novel variants of genes for complex adaptive traits. Crop wild relatives are a potentially valuable source of these genes however these materials are often difficult to work with and identifying valuable alleles is difficult without substantial investment in pre-breeding. In this study we describe the development of a nested association mapping population for sorghum using two cultivated grain sorghum reference parents and 9 wild and exotic sorghum accessions as donors. The donor parents come from the verticilliflorum, drummondii and margaritiferum taxa and were sampled from a range of environments across Africa. In total the resource of consists of 13 populations and a total of 1,224 lines. The population has been genotyped with DArT markers which produced 42,372 unique SNP markers covering the genome. We determine the utility of the resource for high resolution mapping of complex traits by demonstrating that the exotics contain unique alleles for some example adaptive trait loci and by using the population for GWAS. The resource should provide useful material for plant breeders attempting to deal with the challenges generated by climate change. This article is protected by copyright. All rights reserve

Two distinct classes of QTL determine rust resistance in sorghum

Background: Agriculture is facing enormous challenges to feed a growing population in the face of rapidly evolving pests and pathogens. The rusts, in particular, are a major pathogen of cereal crops with the potential to cause large reductions in yield. Improving stable disease resistance is an on-going major and challenging focus for many plant breeding programs, due to the rapidly evolving nature of the pathogen. Sorghum is a major summer cereal crop that is also a host for a rust pathogen which occurs in almost all sorghum growing areas of the world, causing direct and indirect yield losses in sorghum worldwide, however knowledge about its genetic control is still limited. In order to further investigate this issue, QTL and association mapping methods were implemented to study rust resistance in three bi-parental populations and an association mapping set of elite breeding lines in different environments. Results: In total, 64 significant or highly significant QTL and 21 suggestive rust resistance QTL were identified representing 55 unique genomic regions. Comparisons across populations within the current study and with rust QTL identified previously in both sorghum and maize revealed a high degree of correspondence in QTL location. Negative phenotypic correlations were observed between rust, maturity and height, indicating a trend for both early maturing and shorter genotypes to be more susceptible to rust. Conclusions: The significant amount of QTL co-location across traits, in addition to the consistency in the direction of QTL allele effects, has provided evidence to support pleiotropic QTL action across rust, height, maturity and stay-green, supporting the role of carbon stress in susceptibility to rust. Classical rust resistance QTL regions that did not co-locate with height, maturity or stay-green QTL were found to be significantly enriched for the defence-related NBS-encoding gene family, in contrast to the lack of defence-related gene enrichment in multi-trait effect rust resistance QTL. The distinction of disease resistance QTL hot-spots, enriched with defence-related gene families from QTL which impact on development and partitioning, provides plant breeders with knowledge which will allow for fast-tracking varieties with both durable pathogen resistance and appropriate adaptive traits

A physiological framework to explain genetic and environmental regulation of tillering in sorghum

Tillering determines the plant size of sorghum (Sorghum bicolor) and an understanding of its regulation is important to match genotypes to prevalent growing conditions in target production environments. The aim of this study was to determine the physiological and environmental regulation of variability in tillering among sorghum genotypes, and to develop a framework for this regulation. * Diverse sorghum genotypes were grown in three experiments with contrasting temperature, radiation and plant density to create variation in tillering. Data on phenology, tillering, and leaf and plant size were collected. A carbohydrate supply/demand (S/D) index that incorporated environmental and genotypic parameters was developed to represent the effects of assimilate availability on tillering. Genotypic differences in tillering not explained by this index were defined as propensity to tiller (PTT) and probably represented hormonal effects. * Genotypic variation in tillering was associated with differences in leaf width, stem diameter and PTT. The S/D index captured most of the environmental effects on tillering and PTT most of the genotypic effects. * A framework that captures genetic and environmental regulation of tillering through assimilate availability and PTT was developed, and provides a basis for the development of a model that connects genetic control of tillering to its phenotypic consequences

High resolution wheat yield mapping using Sentinel-2

Accurate crop yield estimates are important for governments, farmers, scientists and agribusiness. This paper provides a novel demonstration of the use of freely available Sentinel-2 data to estimate within-field wheat yield variability in a single year. The impact of data resolution and availability on yield estimation is explored using different combinations of input data. This was achieved by combining Sentinel-2 with environmental data (e.g. meteorological, topographical, soil moisture) for different periods throughout the growing season. Yield was estimated using Random Forest (RF) regression models. They were trained and validated using a dataset containing over 8000 points collected by combine harvester yield monitors from 39 wheat fields in the UK. The results demonstrate that it is possible to produce accurate maps of within-field yield variation at 10 m resolution using Sentinel-2 data (RMSE 0.66 t/ha). When combined with environmental data further improvements in accuracy can be obtained (RMSE 0.61 t/ha). We demonstrate that with knowledge of crop-type distribution it is possible to use these models, trained with data from a few fields, to estimate within-field yield variability on a landscape scale. Applying this method gives us a range of crop yield across the landscape of 4.09 to 12.22 t/ha, with a total crop production of approx. 289,000 t

QTL analysis in multiple sorghum populations facilitates the dissection of the genetic and physiological control of tillering

Tillering in sorghum can be associated with either the carbon supply–demand (S/D) balance of the plant or an intrinsic propensity to tiller (PTT). Knowledge of the genetic control of tillering could assist breeders in selecting germplasm with tillering characteristics appropriate for their target environments. The aims of this study were to identify QTL for tillering and component traits associated with the S/D balance or PTT, to develop a framework model for the genetic control of tillering in sorghum. Four mapping populations were grown in a number of experiments in south east Queensland, Australia. The QTL analysis suggested that the contribution of traits associated with either the S/D balance or PTT to the genotypic differences in tillering differed among populations. Thirty-four tillering QTL were identified across the populations, of which 15 were novel to this study. Additionally, half of the tillering QTL co-located with QTL for component traits. A comparison of tillering QTL and candidate gene locations identified numerous coincident QTL and gene locations across populations, including the identification of common non-synonymous SNPs in the parental genotypes of two mapping populations in a sorghum homologue of MAX1, a gene involved in the control of tiller bud outgrowth through the production of strigolactones. Combined with a framework for crop physiological processes that underpin genotypic differences in tillering, the co-location of QTL for tillering and component traits and candidate genes allowed the development of a framework QTL model for the genetic control of tillering in sorghum