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.

Identification of pathotypes of the sorghum rust pathogen, Puccinia purpurea, in Australia

This study aimed to determine if pathotypic diversity of the sorghum rust pathogen, P. purpurea, exists in eastern Australia. A differential set of 10 Sorghum bicolor genotypes was used to identify four putative pathotypes from the 28 P. purpurea isolates that were tested. Pathotypes 1 and 3 were the most common, together comprising 85.7 % of the isolates tested, while pathotype 2 comprised 10.7 % of isolates, and pathotype 4 the remainder. Based on the limited number of isolates that were tested, there was evidence of geographic specialization amongst the pathotypes, with pathotype 1 not being found in north Queensland. This work has provided conclusive evidence that pathotypes of P. purpurea exist in the sorghum growing regions of Australia and has resulted in the development of a protocol for identifying pathotypes and screening breeding and experimental lines for resistance to these pathotypes. However, further investigations on the pathotypic diversity of P. purpurea and on the temporal and geographic distribution of these four as well as any additional undiscovered pathotypes are needed.

Identifying the Function of Sorghum's Drought Tolerance Stay-Green QTL

The goal of this research is to understand the function of allelic variation of genes underpinning the stay-green drought adaptation trait in sorghum in order to enhance yield in water-limited environments. Stay-green, a delayed leaf senescence phenotype in sorghum, is primarily an emergent consequence of the improved balance between the supply and demand of water. Positional and functional fine-mapping of candidate genes associated with stay-green in sorghum is the focus of an international research partnership between Australian (UQ/DAFFQ) and US (Texas A&M University) scientists. Stay-green was initially mapped to four chromosomal regions (Stg1, Stg2, Stg3, and Stg4) by a number of research groups in the US and Australia. Physiological dissection of near-isolines containing single introgressions of Stg QTL (Stg1-4) indicate that these QTL reduce water demand before flowering by constricting the size of the canopy, thereby increasing water availability during grain filling and, ultimately, grain yield. Stg and root angle QTL are also co-located and, together with crop water use data, suggest the role of roots in the stay-green phenomenon. Candidate genes have been identified in Stg1-4, including genes from the PIN family of auxin efflux carriers in Stg1 and Stg2, with 10 of 11 PIN genes in sorghum co-locating with Stg QTL. Modified gene expression in some of these PIN candidates in the stay-green compared with the senescent types has been found in preliminary RNA expression profiling studies. Further proof-of-function studies are underway, including comparative genomics, SNP analysis to assess diversity at candidate genes, reverse genetics and transformation.

Fine mapping of qGW1, a major QTL for grain weight in sorghum

Key message We detected seven QTLs for 100-grain weight in sorghum using an F 2 population, and delimited qGW1 to a 101-kb region on the short arm of chromosome 1, which contained 13 putative genes. Abstract Sorghum is one of the most important cereal crops. Breeding high-yielding sorghum varieties will have a profound impact on global food security. Grain weight is an important component of grain yield. It is a quantitative trait controlled by multiple quantitative trait loci (QTLs); however, the genetic basis of grain weight in sorghum is not well understood. In the present study, using an F2 population derived from a cross between the grain sorghum variety SA2313 (Sorghum bicolor) and the Sudan-grass variety Hiro-1 (S. bicolor), we detected seven QTLs for 100-grain weight. One of them, qGW1, was detected consistently over 2 years and contributed between 20 and 40 % of the phenotypic variation across multiple genetic backgrounds. Using extreme recombinants from a fine-mapping F3 population, we delimited qGW1 to a 101-kb region on the short arm of chromosome 1, containing 13 predicted gene models, one of which was found to be under purifying selection during domestication. However, none of the grain size candidate genes shared sequence similarity with previously cloned grain weight-related genes from rice. This study will facilitate isolation of the gene underlying qGW1 and advance our understanding of the regulatory mechanisms of grain weight. SSR markers linked to the qGW1 locus can be used for improving sorghum grain yield through marker-assisted selection.

Genetic differentiation analysis for the identification of complementary parental pools for sorghum hybrid breeding in Ethiopia

Key message The potential for exploiting heterosis for sorghum hybrid production in Ethiopia with improved local adaptation and farmers preferences has been investigated and populations suitable for initial hybrid development have been identified. Abstract Hybrids in sorghum have demonstrated increased productivity and stability of performance in the developed world. In Ethiopia, the uptake of hybrid sorghum has been limited to date, primarily due to poor adaptation and absence of farmer’s preferred traits in existing hybrids. This study aimed to identify complementary parental pools to develop locally adapted hybrids, through an analysis of whole genome variability of 184 locally adapted genotypes and introduced hybrid parents (R and B). Genetic variability was assessed using genetic distance, model-based STRUCTURE analysis and pair-wise comparison of groups. We observed a high degree of genetic similarity between the Ethiopian improved inbred genotypes and a subset of landraces adapted to lowland agro-ecology with the introduced R lines. This coupled with the genetic differentiation from existing B lines, indicated that these locally adapted genotype groups are expected to have similar patterns of heterotic expression as observed between introduced R and B line pools. Additionally, the hybrids derived from these locally adapted genotypes will have the benefit of containing farmers preferred traits. The groups most divergent from introduced B lines were the Ethiopian landraces adapted to highland and intermediate agro-ecologies and a subset of lowland-adapted genotypes, indicating the potential for increased heterotic response of their hybrids. However, these groups were also differentiated from the R lines, and hence are different from the existing complementary heterotic pools. This suggests that although these groups could provide highly divergent parental pools, further research is required to investigate the extent of heterosis and their hybrid performance.

Non-cellulosic cell wall polysaccharides are subject to genotype × environment effects in sorghum (Sorghum bicolor) grain

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 to 0.43 (w/w) whilst internal cellotriose:cellotetraose ratios ranged from 1.8 to 2.9:1. Arabinoxylan amounts fell between 1.5 and 3.6 (w/w) and the arabinose:xylose ratio, denoting arabinoxylan structure, ranged from 0.95 to 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.

Heat stress effects on grain sorghum productivity-biology and modelling

Heat stress can cause sterility in sorghum and the anticipated increased frequency of high temperature events implies increasing risk to sorghum productivity in Australia. Here we summarise our research on specific varietal attributes associated with heat stress tolerance in sorghum and evaluate how they might affect yield outcomes in production environments by a crop simulation analysis. We have recently conducted a range of controlled environment and field experiments to study the physiology and genetics of high temperature effects on growth and development of sorghum. Sorghum seed set was reduced by high temperature effects (>36-38oC) on pollen germination around flowering, but genotypes differed in their tolerance to high temperature stress. Effects were quantified in a manner that enabled their incorporation into the APSIM sorghum crop model. Simulation analysis indicated that risk of high temperature damage and yield loss depended on sowing date, and variety. While climate trends will exacerbate high temperature effects, avoidance by crop management and genetic tolerance seems possible.

SorGSD: a sorghum genome SNP database

Sorghum (Sorghum bicolor) is one of the most important cereal crops globally and a potential energy plant for biofuel production. In order to explore genetic gain for a range of important quantitative traits, such as drought and heat tolerance, grain yield, stem sugar accumulation, and biomass production, via the use of molecular breeding and genomic selection strategies, knowledge of the available genetic variation and the underlying sequence polymorphisms, is required.

Genomic regions influencing seminal root traits in barley

Water availability is a major limiting factor for crop production, making drought adaptation and its many component traits a desirable attribute of plant cultivars. Previous studies in cereal crops indicate that root traits expressed at early plant developmental stages, such as seminal root angle and root number, are associated with water extraction at different depths. Here, we conducted the first study to map seminal root traits in barley (Hordeum vulgare L.). Using a recently developed high-throughput phenotyping method, a panel of 30 barley genotypes and a doubled-haploid (DH) population (ND24260 × 'Flagship') comprising 330 lines genotyped with diversity array technology (DArT) markers were evaluated for seminal root angle (deviation from vertical) and root number under controlled environmental conditions. A high degree of phenotypic variation was observed in the panel of 30 genotypes: 13.5 to 82.2 and 3.6 to 6.9° for root angle and root number, respectively. A similar range was observed in the DH population: 16.4 to 70.5 and 3.6 to 6.5° for root angle and number, respectively. Seven quantitative trait loci (QTL) for seminal root traits (root angle, two QTL; root number, five QTL) were detected in the DH population. A major QTL influencing both root angle and root number (RAQ2/RNQ4) was positioned on chromosome 5HL. Across-species analysis identified 10 common genes underlying root trait QTL in barley, wheat (Triticum aestivum L.), and sorghum [Sorghum bicolor (L.) Moench]. Here, we provide insight into seminal root phenotypes and provide a first look at the genetics controlling these traits in barley.

Fine Mapping of qDor7, a Major QTL Affecting Seed Dormancy in Sorghum (Sorghum bicolor (L.) Moench)

Seed dormancy is a key domestication trait for major crops, which is acquired in long-term systems development processes and enables the survival of plants in adverse natural conditions. It is a complex trait under polygenic control and is affected by endogenous and environmental factors. In the present study, a major seed dormancy QTL in sorghum (Sorghum bicolor (L.) Moench), qDor7, detected previously, was fine mapped using a large, multi-generational population. The qDor7 locus was delimited to a 96-kb region which contains 16 predicted gene models. These results lay a solid foundation for cloning qDor7. In addition, the functional markers tightly linked to the seed dormancy QTL may be used in marker-assisted selection for seed dormancy in sorghum.

Protein content and amino acid composition of some varieties of grain sorghum

Determination of the protein content and lysine levels of a number of nonhybrid varieties of grain sorghum indicates large variations in the protein content. Statistical analysis of data on amounts of lysine shows that a negative correlation exists between per cent lysine in the protein and per cent protein in the seed. The proportion of various protein fractions in endosperm of five varieties of grain sorghum of both low- and high-protein type has been determined. Results show that prolamine and glutelin are the principal protein fractions, and increased protein levels in sorghum varieties are correlated with an increase mainly in the prolamine fraction. Nine high- and low-protein varieties of grain sorghum have been analyzed for their amino acid composition by ion exchange procedures. One of the high-protein genetic varieties of sorghum has a high concentration of lysine in the seed. Amino acid composition of the protein fractions of two varieties is also reported. These data permit an evaluation of the nutritional quality of sorghum protein and factors that influence the quality of the protein.

Disc electrophoresis of sorghum seed proteins in polyacrylamide gels

Electrophoretic analyses of sorghum flour protein by disc electrophoresis in polyacrylamide gels containing urea have been described. The albumin, globulin, and prolamin fractions of sorghum endosperm meal have been investigated, using pH 9.5 and 4.3 gel systems with four different buffers. Highly complex patterns were observed for all three protein fractions. It has been suggested that this method can provide a convenient tool for the analyses of seed proteins which are relatively insoluble in aqueous buffers.

Sorghum proteinase inhibitors: purification and some biochemical properties

An investigation has been carried out on the proteinase inhibitors of grain sorghum (Sorghum bicolor (L.) Moench). One of the inhibitors has been isolated in a pure form and characterized. The proteinase inhibitor was extracted from the acetone-defatted sorghum meal and purified by selective thermal denaturation, ammonium sulfate fractionation, Sephadex gel filtration and DEAE-cellulose chromatography (DEAE-preparation II). This preparation was demonstrated to be a mixture of three inhibitor components by polyacrylamide disc gel electrophoresis. Further resolution of this mixture into Inhibitors I to III was achieved by QAE-Sephadex chromatography. Sorghum Inhibitor III was homogeneous by the criteria of disc gel electrophoresis and has been more fully characterized. A molecular weight of 25,000 was obtained for Inhibitor III by gel filtration and was in agreement with the value calculated from the amino acid composition of the inhibitor. The N-terminal amino acid residue of Inhibitor III, a single chain protein, was isoleucine. Sorghum proteinase inhibitors inhibit specifically the serine proteinases and are inactive towards the other classes of proteinases. Inhibitor III is primarily a chymotrypsin inhibitor, whereas Inhibitors I and II inhibit both trypsin and chymotrypsin.