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The demographic history, genomic variation, and transcontinental genotype-phenotype-environment map of mungbean
No full textThe breeding of mungbean, a crucial Asian legume, has been hampered by the lack of genomic resources. The International Mungbean Improvement Network (IMIN) aims to ensure global access to diverse germplasms and genomic resources. Using 780 worldwide wild and cultivated accessions, we report this species' most comprehensive (pan)genomic variation, demographic history, and genotype-phenotype-environment map. Despite archaeological evidence of the earliest cultivation in South Asia, present-day wild populations only possess relict traces of shared polymorphisms with cultivars. We showed that parallel losses of black seed coats in two Vigna species were caused by the same mutational mechanism in the same gene. In large-scale cross-continent field trials, we found accessions from distant environments from the trial sites have lower performance, especially in high-heritability and high-yield sites, suggesting future breeding priority in benign conditions on accessions from similar environments. Our comprehensive genomic and trial resources facilitate future breeding success of this essential crop
Early-season floral bud loss has little impact on the maturity, yield, and lint quality of high-yielding Bt cotton crops
No full textProtecting floral buds (squares) from insect damage in cotton during early growth is a priority for crop managers despite unclear implications for yield potential and increased system risks from early-season insecticide use. This study was conducted to determine the compensatory responses of high-yielding Bacillus thuringiensis (Bt) cotton, Gossypium hirsutum L. cultivars, following manual square damage across 30 experiments, spanning different seasons and environments under commercial production conditions. Square removal from the first five sympodia (fruiting branches) before flowering reduced yield by 9% in one experiment, increased yield by 9%–12% in three experiments and had no effect in the remaining experiments. The most damaging treatment, with squares removed twice across 10 sympodia, reduced yield in just nine experiments by 10%–23%. Lint strength and length remained high, exceeding Australian market preferences. Micronaire decreased with later or more severe square loss particularly in shorter season environments, but economic impact varied. Compensatory growth following pre-flowering square loss increased fruiting site production without raising total biomass or boll proportion commensurately and caused only minor boll opening delay (<4 days). Yield compensation occurred through increased boll retention at the first position on upper canopy sympodia and more distal positions on remaining sympodia and was un-reliant on growth of additional mainstem sympodia. Square loss impacts were greater after commencement of flowering or when pre-flowering losses continued during the early-flowering period. Crop managers can have confidence to reduce pre-flowering pesticide use without jeopardizing high yields, which may produce additional systems benefits
Genomic regions associated with spot blotch resistance in elite barley breeding populations
No full textSpot blotch (SB), a prevalent foliar disease of barley, is caused by the hemibiotrophic fungal pathogen Bipolaris sorokiniana. Predominately occurring in humid growing regions worldwide, SB can result in yield losses of up to 30%. Genetic resistance remains the most effective strategy for disease management; however, most Australian barley cultivars exhibit susceptibility despite the previous identification of major resistance loci. This study investigates the genetic architecture underlying spot blotch resistance within an Australian barley breeding program. Resistance was assessed at both the seedling and adult growth stages using a single conidial isolate (SB61) across two consecutive years. A total of 337 barley lines were genotyped with 16,824 polymorphic DArT-seq™ markers. Two mapping approaches were employed: a single-marker genome-wide association study (GWAS) and a haplotype-based local genomic estimated breeding values (Local GEBV) approach. Both methodologies identified two major resistance-associated regions on chromosomes 3H and 7H, effective across growth stages. Additionally, the haplotype-based Local GEBV approach revealed resistance-associated regions on 1H, 3H, and 6H that were not detected by GWAS. Haplotype stacking analysis underscored the critical role of the 7H region for adult-plant resistance when combined with other resistance haplotypes, suggesting significant gene-by-gene interactions and highlighting the complex, quantitative nature of spot blotch resistance. This research confirms the presence of key resistance loci within Australian barley breeding populations, provides novel insight into the genetic architecture of spot blotch resistance, and emphasises the potential to enhance resistance through haplotype stacking and whole-genome prediction approaches
De novo long-read assembly and annotation for genomes of two cotton-associated Fusarium oxysporum isolates
No full textFusarium wilt of cotton is a major production constraint worldwide caused by Fusarium oxysporum f. sp. vasinfectum. Strain variations contribute to differences in disease expression across different geographic locations. Genomes for two Australian isolates of F. oxysporum isolated from cotton are presented. The strains differ in their symptomatology on cotton plants and group in distinct lineages, different to those cotton infecting strains found overseas
Progress of the National Tropical Weeds Eradication Program
No full textThe nationally cost-shared National Tropical Weeds Eradication Program (NTWEP) targets infestations of Miconia calvescens DC., Limnocharis flava (L.) Buchenau, Mikania micrantha Kunth, Miconia racemosa (Aubl.) DC. and Miconia nervosa (SM.) Triana. All target weeds are native to tropical and subtropical areas of Central and South America, and the Caribbean. The program commenced in late 2003 and recently received endorsement for a national Response Plan from 2024 to 2028.
Survey and control operations for NTWEP are predominantly on-ground and conducted by NTWEP field crews in Queensland and Rous County Council in New South Wales. The New South Wales and Northern Territory governments also assist with coordinating and conducting various NTWEP related activities in their respective jurisdictions. Queensland Parks and Wildlife Service and several local governments also provide on ground support to the Program.
As a long running program, the NTWEP has developed various sources of field data to measure the progress towards eradication and reporting progress as indicators to nationally cost-sharing partners. This eradication data, progress and issues differ for each target weed and are discussed below
Developing next generation beef leaders to impact and influence within the rangelands
No full textThe Australian northern beef industry faces significant challenges in environmental stewardship, economic sustainability, and human resilience. The next generation of industry leaders must understand, develop, advocate for, and implement solutions to these issues. To support this process, Advancing Beef Leaders (ABL) was launched in 2020, as a joint initiative led by the Queensland Department of Primary Industries (DPI), and supported by private sector collaborators. A capacity building program, ABL aims to develop groups of emerging producer and community leaders who are skilled and enthused to pursue positive change in their industry, regions, and personal businesses. The focus of the program is to overlay relevant beef industry technical content with appropriate personal development, governance, and communication skills; encouraging participants to build stronger peer and mentor networks and spark the confidence needed to influence effectively in their businesses, community, and industry. By mid-2023, from 53 past participants there were 22 appointments to community and industry committees within two years of finishing their ABL programs. Also from the 53 participants were 45 examples of leadership progress such as applying for a higher-level leadership program, progressing careers, and getting directly involved as a co-operator in industry RD&E. Graduates have reported applying ABL learnings to their beef businesses, including adoption of on-property improved practices, better financial literacy, focus on drought resilience and business planning, earlier attention to family succession, and improved communications. Recently, another 22 new participants were selected for the 2024/2025 cohort. Advancing Beef Leaders has proved to be a program that opens pathways to leadership, enhances industry impact and adoption, and develops influence for graduates. With a growing interest from across Australia, the ABL program is excited to begin expansion nationally
Rangeland monitoring can engage graziers
No full textLong-term monitoring is critically important in understanding how rangelands change across time in response to climate and management. In Queensland, the state-wide monitoring system called QGraze was established to monitor long-term pasture condition. The system has not only provided an opportunity to detect change in rangeland condition, but also engage with and build capacity with land managers in the livestock industry.
Beginning in 1991, the Queensland state Department of Primary Industries (DPI) in collaboration with land managers, installed nearly 450 sites on grazing lands across the state. Since then, these sites have been used by several projects to help inform the current state of rangeland condition and trends, such as monitoring the spread of the exotic grass Bothriochloa pertusa in the Burdekin district in North Queensland.
Just as importantly, enhanced engagement with graziers occurs as a result of surveying QGraze sites on their properties. This allows for the collaborative sharing of information and knowledge between DPI staff and the local grazing community. Graziers are interested to learn about their pasture and land condition in finer detail and the changes over time. The subsequent discussion regarding the contributing factors is valuable to inform their management decisions. Given the long timeframe over which monitoring has occurred, these conversations often span multiple generations, managers, and seasonal conditions. In turn, DPI staff are provided with perspective and context around the factors contributing to rangeland condition.
Due to the dedicated maintenance and monitoring of the sites by staff, QGraze provides a valuable resource for a combined understanding of the natural resource base underpinning Queensland’s grazing lands
The value proposition for systematic long-term vegetation studies
No full textLong-term vegetation observations are rare but essential for the effective management of our natural assets. Studies of 3-4 years allow us to discern short-term variability, but long-term trends are only detectable over multiple decades. Through a meta-analysis of several medium to long-term studies in Australia—Kidman Springs, 30 and 50 years; Koonamore, 90+ years; the Brigalow Catchment study, 60 years; the Wambiana grazing trial, 26 years; several Australian Wildlife Conservancy sites across northern Australia, 19+ years; and one site in the USA, Jornada, 105 years—we discuss their benefits, the challenges, the management of the resulting data and information, and their future. We will argue that such sites are vital for the determination of the effects of perturbations caused by fire, thinning, grazing, water diversion, soil erosion, pollution, pathogens, weeds, insect pests and feral animals. They provide points of validation for a variety of types of models, help us better understand the systems involved, and inform management. Quite often these benefits are unpredictable and depend on multi-disciplinary synthesis. The interpretation of the data from such sites can be enhanced by integration with longer term remote sensed data. Ongoing measurement, management and custodianship is, however, often fraught. Measurements that were designed, for example, in 1920, are not always seen as relevant today, a disincentive for participating researchers. Support from the institutions managing the sites has proved variable. Sites can be attractive for a sponsoring body for their sheer age, but usually there is little understanding of the discipline involved, or what is required for their continuation. The expectation for data and information from such sites has changed profoundly with time. Repositories and observatories like the Environmental Data Initiative in the USA and TERN in Australia provide data from several long-term sites. We can expect changes and expectations to evolve into the future
Factors influencing pasture utilisation in northern Australian rangelands
No full textAnnual pasture growth and utilisation were retrospectively modelled using the biophysical GRASP model for 20 pre-existing breeder herd datasets from across northern Australia as part of a broader study to quantify the effect of pasture utilisation rates on the reproductive performance of extensive beef breeding females. Annual pasture utilisation was more influenced by variation in stocking rate in the central and northern Northern Territory (NT) regions, while variation in pasture growth explained more of the variability in pasture utilisation in the Southern NT and north eastern (NE) Queensland regions. In the Alice Springs region, median pasture utilisation was 1.8 x higher than recommended levels on commercial stations compared to the utilisation rate on the research station where it was 0.7 x recommended levels, despite higher relative rainfall for the commercial herd studies. In contrast, in the Barkly the median utilisation on commercial stations was lower than recommended levels (0.7 x recommended) possibly reflecting the high relative rainfall during those studies. On commercial stations in northern NT and NE Queensland regions, median utilisation was 1.2 and 1.3 respectively x recommended levels, but this was for years with rainfall 1.6 and 1.7 times the long-term median respectively
Integrating multiomics and modern breeding tools for accelerating genetic improvement in Annonas
No full textCustard apples ( Annona spp.) are among the most important horticultural crops in the world, including Australia. The genus Annona comprises several economically and nutritionally significant species, including atemoya, cherimoya, sugar apple, ilama, soursop, bullock’s heart, and bibra. These fruits are valued for their exotic taste and are popular backyard fruit crops in many countries. While some species are commercially cultivated and exported, the broader potential of these crops remains largely untapped. Despite their historical significance, these Annona species remain neglected or underutilised, with breeding efforts restricted to only a few countries. Extensive genetic resources, including germplasm collections, candidate genotypes, and mapping populations, are available for crop improvement. Traditional breeding methods - such as selection, crossbreeding, and mutation breeding – have been widely applied alongside modern breeding approaches like marker-assisted selection (MAS). However, several challenges, such as a lack of information regarding the crop and a long juvenile period, hinder crop improvement in custard apples. Recent advancements and affordability of sequencing technologies have enabled an increase in the number of multiomics studies, especially genomics and transcriptomics within Annona species. Integrating these data with proteomics, metabolomics, and phenomics will facilitate the genetic dissection of important traits in Annona . This review provides a comprehensive overview of the current advancements and future prospects of multiomics tools and technologies developed and their potential to accelerate custard apple breeding programs