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Local adaptation and genotype by environment (G×E) interactions affect the expression of phenotypes in crop species. An investigation on the interplay between adaptation and G×E on sorghum heterosis phenotypes is lacking. To address this question, a set of 112 diverse grain sorghum hybrids and their 22 inbred parents of local and exotic origins, representing the primary female and male heterotic groups, were tested in five contrasting sorghum growing environments across two years in Queensland, Australia. Plant height, days to flowering, seed yield, grain weight, and grain number were measured and used in the estimation of heterosis. Mid parent heterosis for yield ranged from -25 to 217% and was highly influenced by grain number. In contrast to observations in maize the magnitude of heterosis for yield was not associated with site mean. Striking differences were observed in heterosis in hybrids from locally developed inbred parents compared with hybrids that were developed from exotic inbred parents developed in other countries. Heterosis in the latter combination was higher on average across all the test environments for the majority of traits. We hypothesise maladaptive phenotypic plasticity in the exotic parents contributed to the observed differences in heterosis estimates. These data confirm that heterosis estimates in sorghum must be obtained and interpreted in relevant genetic and environmental contexts. Breeders in developing countries with low sorghum hybrid seed uptake will find these insights useful when selecting hybrids for broader adaptation, improving efficiency of their breeding programs. This article is protected by copyright. All rights reserved

Developing sorghum genotypes adapted to different light environments requires understanding of a plant’s ability to capture light, determined through leaf angle specifically. This study dissected the genetic basis of leaf angle in three-year field trials at two sites, using a sorghum diversity panel (729 accessions). A wide range of variation in leaf angle with medium heritability was observed. Leaf angle explained 36% variation in canopy light extinction coefficient, highlighting the extent to which variation in leaf angle influences light interception at whole canopy level. This study also found the sorghum races of Guinea and Durra consistently having the largest and smallest leaf angle, respectively, highlighting the potential role of leaf angle in adaptation to distinct environments. The genome-wide association study detected 33 QTL associated with leaf angle. Strong synteny was observed with previously detected leaf angle QTL in maize (70%) and rice (40%) within 10 cM, among which the overlap was significantly enriched according to Chi-square tests, suggesting a highly consistent genetic control in grasses. A priori leaf angle candidate genes identified in maize and rice were found to be enriched within a 1-cM window around the sorghum leaf angle QTL. Additionally, protein domain analysis identified the WD40 protein domain as being enriched within a 1-cM window around the QTL. These outcomes show that there is sufficient heritability and natural variation in the angle of upper leaves in sorghum which may be exploited to change light interception and optimise crop canopies for different contexts.

DNA methylation is a chromatin modification that plays an essential role in regulatinggene expression and genome stability and it is typically associated with gene silencingand heterochromatin. Owing to its heritability, alterations in the patterns of DNA methyla-tion have the potential to provide for epigenetic inheritance of traits. Contemporary epige-nomic technologies provide information beyond sequence variation and could supplyalternative sources of trait variation for improvement in crops such as sorghum. Yet, com-pared with other species such as maize and rice, the sorghum DNA methylome is farless well understood. The distribution of CG, CHG, and CHH methylation in the genomeis different compared with other species. CG and CHG methylation levels peak aroundcentromeric segments in the sorghum genome and are far more depleted in the genedense chromosome arms. The genes regulating DNA methylation in sorghum are also yetto be functionally characterised; better understanding of their identity and functional ana-lysis of DNA methylation machinery mutants in diverse genotypes will be important tobetter characterise the sorghum methylome. Here, we catalogue homologous genesencoding methylation regulatory enzymes in sorghum based on genes inArabidopsis,maize, and rice. Discovering variation in the methylome may uncover epialleles thatprovide extra information to explain trait variation and has the potential to be applied inepigenome-wide association studies or genomic prediction. DNA methylation can alsoimprove genome annotations and discover regulatory elements underlying traits. Thus,improving our knowledge of the sorghum methylome can enhance our understanding ofthe molecular basis of traits and may be useful to improve sorghum performance.

The stay-green trait is recognised as a key drought adaptation mechanism in cereals worldwide. Stay-green sorghum plants exhibit delayed senescence of leaves and stems, leading to prolonged growth, a reduced risk of lodging and higher grain yield under end-of-season drought stress. More than 45 quantitative trait loci (QTL) associated with stay-green have been identified, including two major QTL (Stg1 and Stg2). However, none of the contributing genes that regulate functional stay-green are known. Here we show that the PIN FORMED family of auxin efflux carriers induce some of the causal mechanisms driving the stay-green phenotype in sorghum, with SbPIN4 and SbPIN2 located in Stg1 and Stg2, respectively. We found that 9 of 11 sorghum PIN genes aligned with known stay-green QTL. In transgenic studies, we demonstrated that PIN genes located within the Stg1 (SbPIN4), Stg2 (SbPIN2) and Stg3b (SbPIN1) QTL regions acted pleiotropically to modulate canopy development, root architecture and panicle growth in sorghum, with SbPIN1, SbPIN2 and SbPIN4 differentially expressed in various organs relative to the non stay-green control. The emergent consequence of such modifications in canopy and root architecture is a stay-green phenotype. Crop simulation modelling shows that the SbPIN2 phenotype can increase grain yield under drought.

The efficiency with which sorghum crops use intercepted radiation (RUE) affects their maximum productivity. RUE in turn, is affected by crop canopy characteristics, as well as leaf biochemical parameters determining maximum leaf photosynthetic rates. These traits are notoriously slow to measure and have previously not been amenable to selection in breeding programs. We used hyperspectral sensors attached to a tractor to estimate leaf and canopy traits associated with RUE in large sorghum field trials. Using Partial Least Square Regression we developed models to predict leaf biochemical photosynthetic parameters known to limit C4 photosynthesis, such as maximum Rubisco and PEP carboxylation rates (Vcmax and Vpmax, respectively) and maximum electron transport rate (Jmax) from the canopy hyperspectral reflectance. We also used various vegetation indices to predict canopy characteristics such as light interception and biomass which allowed us to calculate canopy radiation use efficiency for each trial plot. This is the first time that parameters related to photosynthetic efficiency in sorghum have been estimated for so many different genotypes, showing that significant and heritable variation exists. The predicted values were also used for Genome Wide Association studies to identify the genomic regions associated with canopy RUE and hence improved productivity. Sorghum being such a great genetic model, this may also help elucidate the genetic mechanisms underpinning photosynthetic efficiency and RUE in other cereals.

Sorghum is primarily grown in hot and dry regions worldwide in large-scale commercial operations and in smallholder farming settings. In these regions, sorghum shows comparative advantages over other summer cereals, including its capacity to fill grain during end-of-season drought. It is also broadly adapted to temperate, subtropical and tropical drylands, and irrigated environments. Worldwide, farmers face the challenge of growing sorghum in highly variable environments. Matching hybrid, agronomy, and environment enables farmers to design more profitable and less risky sorghum production systems. At the crop level, the growth of major organs is predicted based on their potential size, and then the capacity of the crop to capture resources (radiation, water, and nitrogen) to meet the demand is assessed. The extent of resource capture and biomass accumulation and the efficiency with which carbon and nitrogen are partitioned into grain will be discussed, with a focus on productivity under water scarcity. One of the challenges for future sorghum crop improvement will be the capacity to connect across scales from molecular to farm, utilising molecular understanding to develop combinations of plant-level traits that increase productivity at the field level. This will require cross-disciplinary integration to harness ‘big’ data from genotypic and phenotypic studies. Future research in sorghum will need to focus on adaptation mechanisms that manipulate water supply and demand scenarios such as canopy size and root architecture, respectively, and heat adaptation mechanisms. Considerable biological integration will be required to scale-up from the causal polymorphisms at genome level to the phenotype of interest in the field. A new crop modelling frontier is unfolding in plant breeding with the potential to add significant value to the revolution in plant breeding associated with genomic technologies.

The efficient management and distribution of experimental data from pre-breeding projects is important to ensure uptake of valuable germplasm into breeding and research programmes. Being able to access and share this data in standard formats is essential in this process. The adoption of a common informatics platform for crops which may have limited resources brings economies of scale allowing common informatics components to be rolled out across multiple species. The close integration of such a platform with commonly used breeding software, visualization and analysis tools reduces the barrier for entry to researchers working on these data and provides a common framework to facilitate collaborations and data sharing. This work presents significant updates to the Germinate platform and highlights its value in distributing pre-breeding data for 14 crops as part of the project “Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives” (hereafter Crop Trust Crop Wild Relatives project) led by the Crop Trust (https://www.cwrdiversity.org). The addition of data on new crop species compliments data that are already publicly available on the platform. We present a suite of updated Germinate features using examples from these crop species and their wild relatives. The use of Germinate within the Crop Wild Relatives project demonstrates the usefulness of the system and the benefits that a shared informatics platform provides.These data resources provide a foundation on which breeding and research communities can develop additional online resources for their crops, harnessing new data as it becomes available, and benefiting collectively from future developments of the Germinate platform. Through this process Germinate will facilitate the utilization of plant genetic resources, including crop wild relatives. This article is protected by copyright. All rights reserved

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 reserved

A large collection of Ethiopian sorghum landraces, characterized by agro-ecology and racial-group, was found to contain high levels of diversity and admixture, with significant SNP associations identified for environmental adaptation.

Climate change during the last 40 years has had a serious impact on agriculture and threatens global food and nutritional security. From over half a million plant species, cereals and legumes are the most important for food and nutritional security. Although systematic plant breeding has a relatively short history, conventional breeding coupled with advances in technology and crop management strategies has increased crop yields by 56 % globally between 1965-85, referred to as the Green Revolution. Nevertheless, increased demand for food, feed, fiber, and fuel necessitates the need to break existing yield barriers in many crop plants. In the first decade of the 21st century we witnessed rapid discovery, transformative technological development and declining costs of genomics technologies. In the second decade, the field turned towards making sense of the vast amount of genomic information and subsequently moved towards accurately predicting gene-to-phenotype associations and tailoring plants for climate resilience and global food security. In this review we focus on genomic resources, genome and germplasm sequencing, sequencing-based trait mapping, and genomics-assisted breeding approaches aimed at developing biotic stress resistant, abiotic stress tolerant and high nutrition varieties in six major cereals (rice, maize, wheat, barley, sorghum and pearl millet), and six major legumes (soybean, groundnut, cowpea, common bean, chickpea and pigeonpea). We further provide a perspective and way forward to use genomic breeding approaches including marker-assisted selection, marker-assisted backcrossing, haplotype based breeding and genomic prediction approaches coupled with machine learning and artificial intelligence, to speed breeding approaches. The overall goal is to accelerate genetic gains and deliver climate resilient and high nutrition crop varieties for sustainable agriculture.

Societal Impact Statement Sorghum is an important cereal crop that provides calories and nutrients for much of the world's population, and it is often grown with low fertiliser input. Optimising the yield, nutritive content and bioavailability of sorghum grain with minimal input is of importance for human nutrition, and arbuscular mycorrhizal (AM) fungi have previously shown potential to assist in this. Across sorghum genetic diversity, AM fungi improved the yield, nutrition and zinc and iron bioavailability of grain in a low phosphorus soil. Thus, food production systems that effectively manage AM fungi may improve consumer outcomes. Summary Sorghum is a C4 cereal crop that is an important source of calories and nutrition across the world, predominantly cultivated and consumed in low- and middle-income countries. Sorghum can be highly colonised by arbuscular mycorrhizal (AM) fungi, and the plant-fungal association can lead to improvements in biomass and nutrient uptake. High-throughput phenotyping allows us to non-destructively interrogate the ‘hidden’ effects of AM fungi on sorghum growth and phenology. Eight genetically diverse sorghum genotypes were grown in a soil amended with 2 or 20 mg P kg−1 and inoculated with an AM fungal culture of Rhizophagus irregularis. High-throughput phenotyping uncovered the ‘hidden’ effects of AM fungi on growth and phenology, while grain biomass, nutrition, Zn and Fe bioavailability and root AM colonisation was determined after destructive harvest. Sorghum plants colonised by AM fungi generally performed better than non-AM control plants, with greater yield, harvest indices, and grain P, Zn and Fe contents. During the early growth stages, AM colonisation led to temporary growth depressions. There were also AM fungal and P fertilisation effects on sorghum time-of-flowering. The sorghum genotype with the highest AM colonisation could barely produce grain when non-inoculated. The two genotypes that failed to mature had very low AM co

Variation in grain size, a major determinant of grain yield and quality in cereal crops, is determined by both the plant’s genetic potential and the available assimilate to fill the grain in the absence of stress. This study investigated grain size variation in response to variation in assimilate supply in sorghum using a diversity panel (n=837) and a BC-NAM population (n=1,421) across four experiments. To explore the effects of genetic potential and assimilate availability on grain size, the top half of selected panicles was removed at anthesis. Results showed substantial variation in five grain size parameters with high heritability. Artificial reduction in grain number resulted in a general increase in grain weight, with the extent of the increase varying across genotypes. Genome-wide association studies (GWAS) identified 44 grain size QTL that were likely to act on assimilate availability and 50 QTL that were likely to act on genetic potential. This finding was further supported by functional enrichment analysis and co-location analysis with known grain number QTL and candidate genes. RNA interference (RNAi) and overexpression experiments were conducted to validate the function of one of the identified gene, SbDEP1, showing that SbDEP1 positively regulates grain number and negatively regulates grain size by controlling primary branching in sorghum. Haplotype analysis of SbDEP1 suggested a possible role in racial differentiation. The enhanced understanding of grain size variation in relation to assimilate availability presented in this study will benefit sorghum improvement and have implications for other cereal crops.