Context. Preharvest granulation of Imperial mandarins is a significant problem for the Australian market. Causes of, and solutions for, this physiological disorder are poorly understood despite decades of research worldwide.

Aims. This research aimed to find management practices for growers to reduce granulation.

Methods. A 5-year on-farm trial in central Queensland, Australia, compared standard versus deficit irrigation and five rates of winter nitrogen application.

Key results. Reducing water (irrigation plus rainfall) in the 16–18 weeks following flowering reduced granulation in 3 of 5 years. Granulation increases with ratio of total water received to evapotranspiration, particularly in low crop load years. Higher nitrogen applications reduced granulation in 4 of 5 years, although treatment means were only significantly different at α = 0.05 in 1 year. Granulation increased with stronger early spring flush growth in a low crop load year and with later spring flush growth in one of two high crop load years. The deficit irrigation treatment had less spring flush growth and higher fruit set than the control in all years. Higher nitrogen treatments had more flush growth in high crop load years and less in low crop load years. Our data suggests competition between flush growth and fruit development for mineral resources and/or carbohydrates is a factor in the variability of granulation from fruit to fruit, but crop load is more important.

Conclusions. The three key strategies to minimise granulation are to maintain high crop loads, reduce irrigation after flowering, and apply sufficient nitrogen in winter.

Implications. This research will improve fruit quality for the consumer and financial returns to growers.

Context. Wheat (Triticum aestivum L.) is an important crop that provides food to millions of people all over the world. Currently, wheat production is limited due to various biotic and abiotic stresses resulting from uneven patterns of climate change. Therefore, it is very important to develop climate-resilient wheat cultivars. Crop genetic diversity allows the scientific community to identify genetic variations that can be utilised in the development of improved cultivars.

Aims. This study planned to characterise the wheat germplasm with the iPBS-retrotransposons marker system.

Methods. A total of 30 iPBS-retrotransposons markers were screened and among these, the 12 most polymorphic markers were selected for further analysis.

Key results. Molecular characterisation yielded a total of 170 bands, of which 143 were polymorphic. A substantial level of genetic diversity was observed (mean effective number of alleles: 1.37, Shannon’s information index: 0.23, gene diversity: 0.35). Maximum genetic distance was observed in G9 and G60 genotypes. Analysis of molecular variance revealed that most genetic variation (95%) occurred within the populations. The model-based structure algorithm divided the studied germplasm into three populations based on their collection regions. Similarly, the neighbour-joining analysis also divided 70 tested wheat genotypes into three populations, whereas principal coordinate analysis divided the evaluated germplasm into four populations.

Conclusions. This study confirms the iPBS-retrotransposons as an ideal marker for the genetic diversity assessment studies for any crop, especially for wheat.

Implications. The results presented here will be helpful for the scientific community in the marker-assisted breeding of wheat.

Context. Alpine pastures are seminatural grasslands which play a crucial role in biodiversity conservation, service provisioning, and mountain livestock systems. The soil microbial communities of pasture are fundamental in ecosystem nutrient cycles, but they are relatively underexplored in European Alpine pastures.

Aims. We explored the many soil microbial genes encoding key functions in the nitrogen cycle in three historical alpine pastures grazed by dairy cattle, considering different soils, temporal dynamics, and exclusion of cattle grazing for one summer.

Methods. 216 samples were collected across four sampling times. The abundance of genetic determinants involved in nitrogen fixation (nifH), nitrification (amoA bacterial and archaeal), and denitrification (nirK and nosZ) were quantified using real-time polymerase chain reaction.

Key results. The terminal denitrification nosZ gene was the most sensitive indicator and responded significantly to soil chemical composition and animal grazing. Sampling time affected nitrogen fixation nifH and intermediate denitrification nirK in relation to rainfall cumulation dynamics. The amoA nitrification genes showed high variability but no significant effects from the tested factors.

Conclusions. In spite of a general homeostatic trend occurring in these habitats and of the short term analysis, some genes acted as sensitive reporters of soil compositional differences, intraseasonal climatic variations, and grazing disturbance.

Implications. A stocking rate of >0.6 livestock units per hectare can be recommended, to combine animal production with conditions that favour complete denitrification, thus potentially reducing the nitrous oxide greenhouse gas emissions. Higher livestock grazing intensity can be withstood by the ecosystem without denitrification-related drawbacks when the preceding 10 days display a cumulated rainfall lower than 22 mm.

Context. Brassica juncea germplasm exhibits significant variations in flowering timing and vernalisation requirements. However, knowledge gaps exist with respect to variations in expression and the divergent evolution of flowering genes in B. juncea subgenomes.

Aims. This study aims to examine the role of flowering genes in defining trait variation and to identify indications of directional selection on these genes.

Methods. Employing a combination of genome-wide association studies, functional genomics and population genetic assays, we explored the genetic architecture underlying flowering time variation within expansive germplasm collections of this allopolyploid and its progenitor species.

Key results. Genome-wide association studies aided in predicting 17 and 34 candidate genes in B. rapa and B. juncea, respectively. Seven of these (FT, FLC, BAG4, ELF4-L2, EFM, SEP4, and LSH6) were predicted in both B. juncea and B. rapa. Some genes, GA20OX3, NF-YA1, PI, MMP, RPS10B, CRY2, AGL72, LFY, TOC1, ELF5, EFM, FLC and TFL1 exhibited directional selection as inferred from negative Tajima’s D and Fu’s Fs statistics.

Conclusions. Common predicted genes are known influencers of flowering time and phenological changes between species as well as across zones of adaptation. An analysis of gene expression patterns indicates that the gene expression bias in resynthesised B. juncea could be influenced by the cytoplasmic background. Most expression variants are found in B genome copies. Some genes lacked expression variation in their diploid progenitors, whereas these genes exhibit expression variation in polyploid species.

Implications. This study highlights that integrating genome-wide association studies with molecular signals of natural selection can effectively contribute to our understanding of the ecological genetics of adaptive evolution.

Context. Development of high-yielding potato cultivars represents the most efficient and sustainable strategy to secure global food and nutrition. In the past decades, numerous quantitative trait loci (QTL) mapping studies have identified various QTLs associated with morphological traits in potato. However, the varying genetic backgrounds of germplasm and the diverse QTL analysis algorithms restrict the utility of identified QTLs for research.

Aims. One of the primary objectives of breeders is to identify consistent chromosomal regions linked to economically significant quantitative traits associated with yield through QTL analysis. To achieve this, an investigation was conducted to pinpoint the most stable QTLs for traits such as maturity, harvest index, plant height, stem diameter, tuber starch content, sprouting, and flesh colour.

Methods. In order to detect stable QTLs for major agronomic traits, metaQTL analysis was performed using 294 QTLs from 14 publications.

Key results. A total of 10 metaQTLs were found to be associated with seven morphological traits. Meta-analysis was considerably refined as compared to the initial QTLs and provided the closest flanking markers for investigated traits and reduce confidence interval mainly to five folds as compared to the mean confidence interval of initial QTLs. The metaQTLs of morphological traits juxtaposed along Chromosomes II, III, IV, and V from independent studies were considered the most stable QTLs over different field trails and genetic background.

Conclusions. Ten metaQTLs were identified that contain major consensus QTLs for various morphological traits in potato.

Implications. This study will enable the integration of QTLs to create new cultivars with targeted quantitative traits, thereby accelerating breeding initiatives.

Context. Soil acidity constrains crop production in Australia. The practice of liming can reduce soil acidity but produces greenhouse gas emissions.

Aims. By examining land use sequences over three decades at a range of locations in Western Australia, this study aims to identify firstly where and when liming might boost farm profits and secondly, what emissions and land use management flexibilities are generated by liming.

Methods. Bioeconomic simulation modelling is used to identify the gross margins and emissions associated with liming in land use sequences at 14 locations in Western Australia. Three intensities of cropping and three different rotational sequences are considered. The simulations account for price and weather–year variations across a 30-year period of analysis.

Key results. Liming is profitable at almost all locations and across all rotation sequences examined. Where problematic soil acidity is a feature or is poised to soon become a problem at a location, liming is a profitable ameliorative practice that enables greater diversity in land use. For most situations assessed, liming increases emissions. The exceptions are at locations where liming prevents a switch away from a crop-dominant system, due to soil acidity reducing crop yields, into additional sheep production that increases emissions.

Conclusions. Liming is profitable in most acidic soil situations and preserves land use flexibility, although additional greenhouse gas emissions are often generated.

Implications. Liming acidic soils bolsters land use profitability and helps sustain biologically diverse land use sequences, despite often increasing greenhouse gas emissions.