[Show abstract][Hide abstract] ABSTRACT: Sorghum is a staple food for half a billion people and, through growth on marginal land with minimal inputs, is an important source of feed, forage and increasingly, biofuel feedstock. Here we present information about non-cellulosic cell wall polysaccharides in a diverse set of cultivated and wild Sorghum bicolor grains. Sorghum grain contains predominantly starch (64–76%) but is relatively deficient in other polysaccharides present in wheat, oats and barley. Despite overall low quantities, sorghum germplasm exhibited a remarkable range in polysaccharide amount and structure. Total (1,3;1,4)-β-glucan ranged from 0.06–0.43% (w/w) whilst internal cellotriose:cellotetraose ratios ranged from 1.8–2.9:1. Arabinoxylan amounts fell between 1.5–3.6% (w/w) and the arabinose:xylose ratio, denoting arabinoxylan structure, ranged from 0.95–1.35. The distribution of these and other cell wall polysaccharides varied across grain tissues as assessed by electron microscopy. When ten genotypes were tested across five environmental sites, genotype (G) was the dominant source of variation for both (1,3;1,4)-β-glucan and arabinoxylan content (69–74%), with environment (E) responsible for 5–14%. There was a small G×E effect for both polysaccharides. This study defines the amount and spatial distribution of polysaccharides and reveals a significant genetic influence on cell wall composition in sorghum grain.
[Show abstract][Hide abstract] ABSTRACT: 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 Puccinia purpurea, 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.ResultsIn 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.
[Show abstract][Hide abstract] ABSTRACT: Increased disease resistance is a key target of cereal breeding programs, with disease outbreaks continuing to threaten global food production, particularly in Africa. Of the disease resistance gene families, the nucleotide-binding site plus leucine-rich repeat (NBS-LRR) family is the most prevalent and ancient and is also one of the largest gene families known in plants. The sequence diversity in NBS-encoding genes was explored in sorghum, a critical food staple in Africa, with comparisons to rice and maize and with comparisons to fungal pathogen resistance QTL.
In sorghum, NBS-encoding genes had significantly higher diversity in comparison to non NBS-encoding genes and were significantly enriched in regions of the genome under purifying and balancing selection, both through domestication and improvement. Ancestral genes, pre-dating species divergence, were more abundant in regions with signatures of selection than in regions not under selection. Sorghum NBS-encoding genes were also significantly enriched in the regions of the genome containing fungal pathogen disease resistance QTL; with the diversity of the NBS-encoding genes influenced by the type of co-locating biotic stress resistance QTL.
NBS-encoding genes are under strong selection pressure in sorghum, through the contrasting evolutionary processes of purifying and balancing selection. Such contrasting evolutionary processes have impacted ancestral genes more than species-specific genes. Fungal disease resistance hot-spots in the genome, with resistance against multiple pathogens, provides further insight into the mechanisms that cereals use in the "arms race" with rapidly evolving pathogens in addition to providing plant breeders with selection targets for fast-tracking the development of high performing varieties with more durable pathogen resistance.
[Show abstract][Hide abstract] ABSTRACT: A QTL model for the genetic control of tillering in sorghum is proposed, presenting new opportunities for sorghum breeders to select germplasm with tillering characteristics appropriate for their target environments. 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.
[Show abstract][Hide abstract] ABSTRACT: 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.
New Phytologist 03/2014; 203(1). DOI:10.1111/nph.12767 · 6.55 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Sorghum is a food and feed cereal crop adapted to heat and drought and a staple for 500 million of the world's poorest people. Its small diploid genome and phenotypic diversity make it an ideal C4 grass model as a complement to C3 rice. Here we present high coverage (16-45 × ) resequenced genomes of 44 sorghum lines representing the primary gene pool and spanning dimensions of geographic origin, end-use and taxonomic group. We also report the first resequenced genome of S. propinquum, identifying 8 M high-quality SNPs, 1.9 M indels and specific gene loss and gain events in S. bicolor. We observe strong racial structure and a complex domestication history involving at least two distinct domestication events. These assembled genomes enable the leveraging of existing cereal functional genomics data against the novel diversity available in sorghum, providing an unmatched resource for the genetic improvement of sorghum and other grass species.
[Show abstract][Hide abstract] ABSTRACT: The production of adequate agricultural outputs to support the growing human population places great demands on agriculture, especially in light of ever-greater restrictions on input resources. Sorghum is a drought-adapted cereal capable of reliable production where other cereals fail, and thus represents a good candidate to address food security as agricultural inputs of water and arable land grow scarce. A long-standing issue with sorghum grain is that it has an inherently lower digestibility. Here we show that a low-frequency allele type in the starch metabolic gene, pullulanase, is associated with increased digestibility, regardless of genotypic background. We also provide evidence that the beneficial allele type is not associated with deleterious pleiotropic effects in the modern field environment. We argue that increasing the digestibility of an adapted crop is a viable way forward towards addressing food security while maximizing water and land-use efficiency.
[Show abstract][Hide abstract] ABSTRACT: The stay-green drought adaptation mechanism has been widely promoted as a way of improving grain yield and lodging resistance in sorghum [Sorghum bicolor (L.) Moench] and as a result has been the subject of many physiological and genetic studies. The relevance of these studies to elite sorghum hybrids is not clear given that they sample a limited number of environments and were conducted using inbred lines or relatively small numbers of experimental F-1 hybrids. In this study we investigated the relationship between stay-green and yield using data from breeding trials that sampled 1668 unique hybrid combinations and 23 environments whose mean yields varied from 2.3 to 10.5 t ha(-1). The strength and direction of the association between stay-green and grain yield varied with both environment and genetic background (male tester). The majority of associations were positive, particularly in environments with yields below 6 t ha(-1). As trial mean yield increased above 6 t ha(-1) there was a trend toward an increased number of negative associations; however, the number and magnitude of the positive associations were larger. Given that post-flowering drought is very commonly experienced by sorghum crops world wide and average yields are 1.2 and 2.5 t ha(-1) for the world and Australia, respectively, our results indicate that selection for stay-green in elite sorghum hybrids may be broadly beneficial for increasing yield in a wide range of environments.
[Show abstract][Hide abstract] ABSTRACT: The stay-green drought adaptation mechanism
has been widely promoted as a way of improving
grain yield and lodging resistance in sorghum
[Sorghum bicolor (L.) Moench] and as a result
has been the subject of many physiological
and genetic studies. The relevance of these
studies to elite sorghum hybrids is not clear
given that they sample a limited number of
environments and were conducted using inbred
lines or relatively small numbers of experimental
F1 hybrids. In this study we investigated the
relationship between stay-green and yield
using data from breeding trials that sampled
1668 unique hybrid combinations and 23
environments whose mean yields varied from
2.3 to 10.5 t ha–1. The strength and direction
of the association between stay-green and
grain yield varied with both environment and
genetic background (male tester). The majority
of associations were positive, particularly in
environments with yields below 6 t ha–1. As
trial mean yield increased above 6 t ha–1 there
was a trend toward an increased number of
negative associations; however, the number
and magnitude of the positive associations
were larger. Given that post-fl owering drought is
very commonly experienced by sorghum crops
world wide and average yields are 1.2 and 2.5
t ha–1 for the world and Australia, respectively,
our results indicate that selection for staygreen
in elite sorghum hybrids may be broadly
benefi cial for increasing yield in a wide range of
[Show abstract][Hide abstract] ABSTRACT: Detecting artificial selection in the genome of domesticated species can not only shed light on human history but can also be beneficial to future breeding strategies. Evidence for selection has been documented in domesticated species including maize and rice, but few studies have to date detected signals of artificial selection in the Sorghum bicolor genome. Based on evidence that domesticated S. bicolor and its wild relatives show significant differences in endosperm structure and quality, we sequenced three candidate seed storage protein (kafirin) loci and three candidate starch biosynthesis loci to test whether these genes show non-neutral evolution resulting from the domestication process. We found strong evidence of non-neutral selection at the starch synthase IIa gene, while both starch branching enzyme I and the beta kafirin gene showed weaker evidence of non-neutral selection. We argue that the power to detect consistent signals of non-neutral selection in our dataset is confounded by the absence of low frequency variants at four of the six candidate genes. A future challenge in the detection of positive selection associated with domestication in sorghum is to develop models that can accommodate for skewed frequency spectrums.
PLoS ONE 08/2011; 6(8):e23041. DOI:10.1371/journal.pone.0023041 · 3.53 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Loss of genetic diversity in elite breeding populations is often identified as a potential impediment to future genetic gain. The use of diverse unadapted germplasm in breeding has been suggested as one way of combating this problem but often proves impractical, due to the poor performance of progeny produced by crosses between adapted and unadapted parent lines. This study evaluates the effectiveness of a breeding method aimed at utilizing unadapted sorghum [Sorghum bicolor (L.) Moench] germplasm. The method involves producing large BC 1 F 1 populations, using a single elite line as the recurrent parent, and then selecting the resulting progeny for key adaptive traits (e.g., height and flowering time). Populations of 30 to 90 BC 1 F 4 lines derived from 56 unadapted parents were then evaluated in hybrid combination in 21 trials over a 4-yr period. The unadapted sources included lines with geographic or racial diversity, phenotypic diversity for key traits, elite lines from breeding programs in other countries, and cross-compatible wild species. Despite strong selection for acceptable height and maturity, considerable genetic variation for grain yield was retained in the populations, with molecular marker analysis indicating an average of 22% of the genome being retained in each line as compared with a theoretical 25% in the absence of selection. In all cases progeny were identified in each population that performed significantly better than the recurrent parent hybrid for grain yield, and in some cases specific adaptation of particular populations was observed. The method we used proved to be an effective way to introduce new alleles from unadapted sorghum germplasm into elite breeding material. The potential of the populations as a resource for nested association mapping to elucidate the architecture of complex traits is discussed.
[Show abstract][Hide abstract] ABSTRACT: Loss of genetic diversity in elite breeding populations is often identified as a potential impediment to future genetic gain and the use of diverse unadapted germplasm in breeding has been suggested as one way of combating this problem but is often impractical due to the poor performance of progeny from crosses between adapted and unadapted parent lines. This study describes the development of a large sorghum nested association mapping (NAM) population based around a reference parent design specifically developed to solve these problems. Each subpopulation was derived from a large Bc1F1 population using a single elite line as the recurrent parent. Inbred lines were then derived by selection for key agronomic characteristics. To date more than 4000 lines from 100 subpopulations have been developed sampling the entire diversity of sorghum including wild relatives. The resulting populations can be evaluated for quantitative traits in field conditions without the confounding effects of major adaptation genes. Multi-environment phenotypic data is available for many of the populations and a subset of the populations have been subjected to whole genome scans with DArT markers and subsequently used for QTL analysis. In addition 28 of the exotic lines and the elite parent have been resequenced providing a direct link to the genotyped and phenotyped NAM populations. Combined with accurate environmental characterisation using simulation modelling the resulting resource is providing a unique opportunity to not only fast-track gene discovery through the identification of functional sequence polymorphisms but also to contribute to genetic progress in elite breeding programs.
International Plant and Animal Genome Conference XX 2012;