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.

Nitrogen use efficiency in summer sorghum grown on clay soils

Nitrogen fertilizer inputs dominate the fertilizer budget of grain sorghum growers in northern Australia, so optimizing use efficiency and minimizing losses are a primary agronomic objective. We report results from three experiments in southern Queensland sown on contrasting soil types and with contrasting rotation histories in the 2012-2013 summer season. Experiments were designed to quantify the response of grain sorghum to rates of N fertilizer applied as urea. Labelled 15N fertilizer was applied in microplots to determine the fate of applied N, while nitrous oxide (N2O) emissions were continuously monitored at Kingaroy (grass or legume ley histories) and Kingsthorpe (continuous grain cropping). Nitrous oxide is a useful indicator of gaseous N losses. Crops at all sites responded strongly to fertilizer N applications, with yields of unfertilized treatments ranging from 17% to 52% of N-unlimited potential. Maximum yields ranged from 4500 (Kupunn) to 5450 (Kingaroy) and 8010 (Kingsthorpe) kg/ha. Agronomic efficiency (kg additional grain produced/kg fertilizer N applied) at the optimum N rate on the Vertosol sites was 23 (80 N, Kupunn) to 25 (160N, Kingsthorpe), but 40-42 on the Ferrosols at Kingaroy (70-100N). Cumulative N2O emissions ranged from 0.44% (Kingaroy legume) to 0.93% (Kingsthorpe) and 1.15% (Kingaroy grass) of the optimum fertilizer N rate at each site, with greatest emissions from the Vertosol at Kingsthorpe. The similarity in N2O emissions factors between Kingaroy and Kingsthorpe contrasted markedly with the recovery of applied fertilizer N in plant and soil. Apparent losses of fertilizer N ranged from 0-5% (Ferrosols at Kingaroy) to 40-48% (Vertosols at Kupunn and Kingsthorpe). The greater losses on the Vertosols were attributed to denitrification losses and illustrate the greater risks of N losses in these soils in wet seasonal conditions.

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.