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.

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.

Effects of corn replacement by sorghum in broiler diets on performance and intestinal mucosa integrity

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Genetic Mapping of Quantitative Trait Loci Associated with Bioenergy Traits, and The Assessment of Genetic Variability in Sweet Sorghum (Sorghum bicolor (L.). Moench)

Sweet sorghum, a botanical variety of sorghum is a potential source of bioenergy because high sugar levels accumulate in its stalks. The objectives of this study were to explore the global diversity of sweet sorghum germplasm, and map the genomic regions that are associated with bioenergy traits. In assessing diversity, 142 sweet sorghum accessions were evaluated with three marker types (SSR, SRAP, and morphological markers) to determine the degree of relatedness among the accessions. The traits measured (anthesis date [AD], plant height [PH], biomass yield [BY], and moisture content [MC]) were all significantly different (P<0.05) among accessions. Morphological marker clustered the accessions into five groups based on PH, MC and AD. The three traits accounted for 92.5% of the variation. There were four and five groups based on SRAP and SSR data respectively classifying accessions mainly on their origin or breeding history. The observed difference between SSR and SRAP based clusters could be attributed to the difference in marker type. SSRs amplify any region of the genome whereas SRAP amplify the open reading frames and promoter regions. Comparing the three marker-type clusters, the markers complimented each other in grouping accessions and would be valuable in assisting breeders to select appropriate lines for crossing. In evaluating QTLs that are associated with bioenergy traits, 165 recombinant inbred lines (RILs) were planted at four environments in Nebraska. A genetic linkage map constructed spanned a length of 1541.3 cM, and generated 18 linkage groups that aligned to the 10 sorghum chromosomes. Fourteen QTLs (6 for brix, 3 for BY, 2 each for AD and MC, and 1 for PH) were mapped. QTLs for the traits that were significantly correlated, colocalized in two clusters on linkage group Sbi01b. Both parents contributed beneficial alleles for most of traits measured, supporting the transgressive segregation in this population. Additional work is needed on exploiting the usefulness of chromosome 1 in breeding sorghum for bioenergy.

Studying the genetic basis of drought tolerance in sorghum by managed stress trials and adjustments for phenological and plant height differences

Managed environments in the form of well watered and water stressed trials were performed to study the genetic basis of grain yield and stay green in sorghum with the objective of validating previously detected QTL. As variations in phenology and plant height may influence QTL detection for the target traits, QTL for flowering time and plant height were introduced as cofactors in QTL analyses for yield and stay green. All but one of the flowering time QTL were detected near yield and stay green QTL. Similar co-localization was observed for two plant height QTL. QTL analysis for yield, using flowering time/plant height cofactors, led to yield QTL on chromosomes 2, 3, 6, 8 and 10. For stay green, QTL on chromosomes 3, 4, 8 and 10 were not related to differences in flowering time/plant height. The physical positions for markers in QTL regions projected on the sorghum genome suggest that the previously detected plant height QTL, Sb-HT9-1, and Dw2, in addition to the maturity gene, Ma5, had a major confounding impact on the expression of yield and stay green QTL. Co-localization between an apparently novel stay green QTL and a yield QTL on chromosome 3 suggests there is potential for indirect selection based on stay green to improve drought tolerance in sorghum. Our QTL study was carried out with a moderately sized population and spanned a limited geographic range, but still the results strongly emphasize the necessity of corrections for phenology in QTL mapping for drought tolerance traits in sorghum.

Functional characterization of sugarcane mustang domesticated transposases and comparative diversity in sugarcane, rice, maize and sorghum

Transposable elements (TEs) account for a large portion of plant genomes, particularly in grasses, in which they correspond to 50%-80% of the genomic content. TEs have recently been shown to be a source of new genes and new regulatory networks. The most striking contribution of TEs is referred as "molecular domestication", by which the element coding sequence loses its movement capacity and acquires cellular function. Recently, domesticated transposases known as mustang and derived from the Mutator element have been described in sugarcane. In order to improve our understanding of the function of these proteins, we identified mustang genes from Sorghum bicolor and Zea mays and performed a phenetic analysis to assess the diversity and evolutionary history of this gene family. This analysis identified orthologous groups and showed that mustang genes are highly conserved in grass genomes. We also explored the transcriptional activity of sugarcane mustang genes in heterologous and homologous systems. These genes were found to be ubiquitously transcribed, with shoot apical meristem having the highest expression levels, and were downregulated by phytohormones. Together, these findings suggest the possible involvement of mustang proteins in the maintenance of hormonal homeostasis.

Comparative mapping of Andropogoneae: Saccharum L. (sugarcane) and its relation to sorghum and maize

Comparative genetic maps of Papuan Saccharum officinarum L. (2n = 80) and S. robustum (2n = 80) were constructed by using single-dose DNA markers (SDMs). SDM-framework maps of S. officinarum and S. robustum were compared with genetic maps of sorghum and maize by way of anchor restriction fragment length polymorphism probes. The resulting comparisons showed striking colinearity between the sorghum and Saccharum genomes. There were no differences in marker order between S. officinarum and sorghum. Furthermore, there were no alterations in SDM order between S. officinarum and S. robustum. The S. officinarum and S. robustum maps also were compared with the map of the polysomic octoploid S. spontaneum ‘SES 208’ (2n = 64, x = 8), thus permitting relations to homology groups (“chromosomes”) of S. spontaneum to be studied. Investigation of transmission genetics in S. officinarum and S. robustum confirmed preliminary results that showed incomplete polysomy in these species. Because of incomplete polysomy, multiple-dose markers could not be mapped for lack of a genetic model for their segregation. To coalesce S. officinarum and S. robustum linkage groups into homology groups (composed of homologous pairing partners), they were compared with sorghum (2n = 20), which functioned as a synthetic diploid. Groupings suggested by comparative mapping were found to be highly concordant with groupings based on highly polymorphic restriction fragment length polymorphism probes detecting multiple SDMs. The resulting comparative maps serve as bridges to allow information from one Andropogoneae to be used by another, for breeding, ecology, evolution, and molecular biology.

Homologues of the maize rust resistance gene Rp1-D are genetically associated with a major rust resistance QTL in sorghum

As part of a comparative mapping study between sugarcane and sorghum, a sugarcane cDNA clone with homology to the maize Rp1-D rust resistance gene was mapped in sorghum. The cDNA probe hybridised to multiple loci, including one on sorghum linkage group (LG) E in a region where a major rust resistance QTL had been previously mapped. Partial sorghum Rp1-D homologues were isolated from genomic DNA of rust-resistant and -susceptible progeny selected from a sorghum mapping population. Sequencing of the Rp1-D homologues revealed five discrete sequence classes: three from resistant progeny and two from susceptible progeny. PCR primers specific to each sequence class were used to amplify products from the progeny and confirmed that the five sequence classes mapped to the same locus on LG E. Cluster analysis of these sorghum sequences and available sugarcane, maize and sorghum Rp1-D homologue sequences showed that the maize Rp1-D sequence and the partial sugarcane Rp1-D homologue were clustered with one of the sorghum resistant progeny sequence classes, while previously published sorghum Rp1-D homologue sequences clustered with the susceptible progeny sequence classes. Full-length sequence information was obtained for one member of a resistant progeny sequence class (Rp1-SO) and compared with the maize Rp1-D sequence and a previously identified sorghum Rp1 homologue (Rph1-2). There was considerable similarity between the two sorghum sequences and less similarity between the sorghum and maize sequences. These results suggest a conservation of function and gene sequence homology at the Rp1 loci of maize and sorghum and provide a basis for convenient PCR-based screening tools for putative rust resistance alleles in sorghum.

Markers associated with stalk number and suckering in sugarcane colocate with tillering and rhizomatousness QTLs in sorghum

Two important factors influencing sugar yield, the primary focus of sugarcane plant breeding programs, are stalk number and suckering. Molecular markers linked to both of these traits are sought to assist in the identification of high sugar yield, high stalk number, low-suckering sugarcane clones. In this preliminary mapping study, 108 progeny from a biparental cross involving two elite Australian sugarcane clones were evaluated at two sites for two years for both stalk number and suckering. A total of 258 DNA markers, including both restriction fragment length polymorphisms (RFLPs) and radio-labelled amplified fragments (RAFs), were scored and evaluated using single-factor analysis. Sixteen (7 RFLPs and 9 RAFs) and 14 (6 RFLPs and 8 RAFs) markers were identified that were significantly associated (P < 0.01) with stalk number and suckering, respectively, across both years and sites. The seven and six RFLP markers associated with stalk number and suckering, respectively, were generated by eight different RFLP probes, of which seven had been mapped in sorghum and (or) sugarcane. Of significant interest was the observation that all seven RFLP probes could be shown to be located within or near QTLs associated with tillering and rhizomatousness in sorghum. This observation highlights the usefulness of comparative mapping between sorghum and sugarcane and suggests that the identification of useful markers for stalk number and suckering in sugarcane would be facilitated by focussing on sorghum QTLs associated with related traits.

Resistance gene analogues in sugarcane and sorghum and their association with quantitative trait loci for rust resistance

Fifty-four different sugarcane resistance gene analogue (RGA) sequences were isolated, characterized, and used to identify molecular markers linked to major disease-resistance loci in sugarcane. Ten RGAs were identified from a sugarcane stem expressed sequence tag (EST) library; the remaining 44 were isolated from sugarcane stem, leaf, and root tissue using primers designed to conserved RGA motifs. The map location of 31 of the RGAs was determined in sugarcane and compared with the location of quantitative trait loci (QTL) for brown rust resistance. After 2 years of phenotyping, 3 RGAs were shown to generate markers that were significantly associated with resistance to this disease. To assist in the understanding of the complex genetic structure of sugarcane, 17 of the 31 RGAs were also mapped in sorghum. Comparative mapping between sugarcane and sorghum revealed syntenic localization of several RGA clusters. The 3 brown rust associated RGAs were shown to map to the same linkage group (LG) in sorghum with 2 mapping to one region and the third to a region previously shown to contain a major rust-resistance QTL in sorghum. These results illustrate the value of using RGAs for the identification of markers linked to disease resistance loci and the value of simultaneous mapping in sugarcane and sorghum.

Domestication and the storage starch biosynthesis pathway: Signatures of selection from a whole sorghum genome sequencing strategy

Next-generation sequencing of complete genomes has given researchers unprecedented levels of information to study the multifaceted evolutionary changes that have shaped elite plant germplasm. In conjunction with population genetic analytical techniques and detailed online databases, we can more accurately capture the effects of domestication on entire biological pathways of agronomic importance. In this study, we explore the genetic diversity and signatures of selection in all predicted gene models of the storage starch synthesis pathway of Sorghum bicolor, utilizing a diversity panel containing lines categorized as either ‘Landraces’ or ‘Wild and Weedy’ genotypes. Amongst a total of 114 genes involved in starch synthesis, 71 had at least a single signal of purifying selection and 62 a signal of balancing selection and others a mix of both. This included key genes such as STARCH PHOSPHORYLASE 2 (SbPHO2, under balancing selection), PULLULANASE (SbPUL, under balancing selection) and ADP-glucose pyrophosphorylases (SHRUNKEN2, SbSH2 under purifying selection). Effectively, many genes within the primary starch synthesis pathway had a clear reduction in nucleotide diversity between the Landraces and wild and weedy lines indicating that the ancestral effects of domestication are still clearly identifiable. There was evidence of the positional rate variation within the well-characterized primary starch synthesis pathway of sorghum, particularly in the Landraces, whereby low evolutionary rates upstream and high rates downstream in the metabolic pathway were expected. This observation did not extend to the wild and weedy lines or the minor starch synthesis pathways.

Stay-green Drought Adaptation Trait Enhances Sorghum Production in Sub-tropical Australia, Central-Western India and Sub-Saharan Africa

Drought during grain filling is a common challenge for sorghum production in north-eastern Australia, central-western India, and sub-Saharan Africa. We show that the stay-green drought adaptation trait enhances sorghum grain yield under post-anthesis drought in these three regions. A positive relationship between stay-green and yield was generally found in breeding trials in north-eastern Australia that sampled 1668 unique hybrid combinations and 23 environments. Physiological studies in Australia also found that introgressing four individual stay-green (Stg1–4) quantitative trait loci (QTLs) into a senescent background reduced water demand before flowering and hence increased water supply during grain filling, resulting in higher grain yield relative to the senescent control. Studies in India found that various Stg QTLs affected both transpiration and transpiration efficiency, although these effects depended on the interaction between genetic background (S35 and R16) and individual QTLs. The yield variation unexplained by harvest index was related to transpiration efficiency in S35 (R2 = 0.29) and R16 (R2 = 0.72), and was related to total water extracted in S35 (R2 = 0.41) but not in R16. Finally, sixty-eight stay-green enriched lines were evaluated in six countries in sub-Saharan Africa during the 2013/14 season. Analysis of the data from Kenya indicates that stay-green and grain size were positively correlated at two sites: Kiboko (high yielding, r2=0.25) and Masongaleni (low yielding, r2=0.37). Together, these studies suggest that stay-green is a beneficial trait for sorghum production in the semi-arid tropics and is a consequence of traits altering the plant water budget.

Domestication and the storage starch biosynthesis pathway: signatures of selection from a whole sorghum genome sequencing strategy

Next-generation sequencing of complete genomes has given researchers unprecedented levels of information to study the multifaceted evolutionary changes that have shaped elite plant germplasm. In conjunction with population genetic analytical techniques and detailed online databases, we can more accurately capture the effects of domestication on entire biological pathways of agronomic importance. In this study, we explore the genetic diversity and signatures of selection in all predicted gene models of the storage starch synthesis pathway of Sorghum bicolor, utilizing a diversity panel containing lines categorized as either ‘Landraces’ or ‘Wild and Weedy’ genotypes. Amongst a total of 114 genes involved in starch synthesis, 71 had at least a single signal of purifying selection and 62 a signal of balancing selection and others a mix of both. This included key genes such as STARCH PHOSPHORYLASE 2 (SbPHO2, under balancing selection), PULLULANASE (SbPUL, under balancing selection) and ADP-glucose pyrophosphorylases (SHRUNKEN2, SbSH2 under purifying selection). Effectively, many genes within the primary starch synthesis pathway had a clear reduction in nucleotide diversity between the Landraces and wild and weedy lines indicating that the ancestral effects of domestication are still clearly identifiable. There was evidence of the positional rate variation within the well-characterized primary starch synthesis pathway of sorghum, particularly in the Landraces, whereby low evolutionary rates upstream and high rates downstream in the metabolic pathway were expected. This observation did not extend to the wild and weedy lines or the minor starch synthesis pathways.