Jacqueline Batley

University of Western Australia | UWA · School of Plant Biology

Crop disease detection is important due to its significant impact on agricultural productivity and global food security. Traditional disease detection methods often rely on labour‐intensive field surveys and manual inspection, which are time‐consuming and prone to human error. In recent years, the advent of imaging technologies coupled with machine...

Plant disease outbreaks continuously challenge food security and sustainability. Traditional chemical methods used to treat diseases have environmental and health concerns, raising the need to enhance inherent plant disease resistance mechanisms. Traits, including disease resistance, can be linked to specific loci in the genome and identifying thes...

Heavy and costly use of phosphorus (P) fertiliser is often needed to achieve high crop yields, but only a small amount of applied P fertiliser is available to most crop plants. Hakea prostrata (Proteaceae) is endemic to the P‐impoverished landscape of southwest Australia and has several P‐saving traits. We identified 16 members of the Phosphate Tra...

In plants, growth and defence are controlled by many molecular pathways that are antagonistic to one another. This results in a ‘growth‐defence trade‐off’, where plants temporarily reduce growth in response to pests or diseases. Due to this antagonism, genetic variants that improve resistance often reduce growth and vice versa. Therefore, in natura...

A pangenome captures the genomic diversity for a species, derived from a collection of genetic sequences of diverse populations. Advances in sequencing technologies have given rise to three primary methods for pangenome construction and analysis: de novo assembly and comparison, reference genome-based iterative assembly and graph-based pangenome co...

A pangenome encompasses the complete genetic diversity of a species, by assembling a range of representative individuals from various populations. This review describes the advances in plant pangenomics, tracing its evolution since the initial plant genome sequencing in 2000, and provides comprehensive best-practice advice to build a linear or grap...

Long non-coding ribonucleic acids (lncRNAs) have been shown to play an important role in plant gene regulation, involving both epigenetic and transcript regulation. LncRNAs are transcripts longer than 200 nucleotides that are not translated into functional proteins but can be translated into small peptides. Machine learning models have predominantl...

Background and aims Hakea prostrata (Proteaceae) is a highly phosphorus-use-efficient plant native to southwest Australia. It maintains a high photosynthetic rate at low leaf phosphorus (P) and exhibits delayed leaf greening, a convergent adaptation that increases nutrient-use efficiency. This study aimed to provide broad physiological and gene exp...

Synthetic Brassica allohexaploids (2n = AABBCC) do not exist naturally but can be produced between six different parent species combinations, and can be used to investigate processes of polyploid formation and genome stabilization. In this study, we investigated hybridization potential, accumulation and frequency of copy number variants (CNVs), fer...

GWAS excels at harnessing dense genomic variant datasets to identify candidate regions responsible for producing a given phenotype. However, GWAS and traditional fine-mapping methods do not provide insight into the complex local landscape of linkage that contains and has been shaped by the causal variant(s). Here, we present 'crosshap', an R packag...

Many genome annotations include false‐positive gene models, leading to errors in phylogenetic and comparative studies. Here, we propose a method to support gene model prediction based on evolutionary conservation and use it to identify potentially erroneous annotations. Using this method, we developed a set of 15,345 representative gene models from...

Interspecific hybridization is widespread in nature and can result in the formation of new hybrid species as well as the transfer of traits between species. However, the fate of newly formed hybrid lineages is relatively understudied. We undertook pairwise crossing between multiple genotypes of three Brassica allotetraploid species Brassica juncea...

Identifying the molecular and genetic basis of resistance to Sclerotinia stem rot (Sclerotinia sclerotiorum) is critical for developing long-term and cost-effective management of this disease in rapeseed/canola (Brassica napus). Current cultural or chemical management options provide, at best, only partial and/or sporadic control. Towards this, a B...

The Brassicaceae family is composed of a broad range of species, including the economically important crops from Brassica , Raphanus , Camelina and Sinapis genera. The production of Brassicaceae species, particularly the crop members, is threatened by major diseases. However, the impact of diseases can be minimized or even negated by improving dise...

Brassica rapa is grown worldwide as economically important vegetable and oilseed crop. However, its production is challenged by yield-limiting pathogens. The sustainable control of these pathogens mainly relies on the deployment of genetic resistance primarily driven by resistance gene analogues (RGAs). While several studies have identified RGAs in...

Established allopolyploids are known to be genomically stable and fertile. However, by contrast, most newly resynthesized allopolyploids are infertile and meiotically unstable. Identifying the genetic factors responsible for genome stability in newly formed allopolyploid is key to understanding how two genomes come together to form a species. One h...

Fusarium wilt of banana is a devastating disease that has decimated banana production worldwide. Host resistance to Fusarium oxysporum f. sp. Cubense (Foc), the causal agent of this disease , is genetically dissected in this study using two Musa acuminata ssp. Malaccensis segregating populations, segregating for Foc Tropical (TR4) and Subtropical (...

The changing climate poses significant threats to agriculture and the ability to ensure sufficient global food production. With the expanding population, there is an urgent demand to increase crop productivity to meet the rising food demand. Producing climate‐smart crop varieties together with developing new agronomic management strategies are stra...

Genome editing is an important strategy to maintain global food security and achieve sustainable agricultural development. Among all genome editing tools, CRISPR-Cas is currently the most prevalent and offers the most promise. In this review, we summarize the development of CRISPR-Cas systems, outline their classification and distinctive features,...

GWAS excels at harnessing dense genomic variant datasets to identify candidate regions responsible for producing a given phenotype. However, GWAS and traditional fine-mapping methods do not provide insight into the complex local landscape of linkage that contains and has been shaped by the causal variant(s). Here, we present ‘crosshap’, an R packag...

Fusarium wilt of banana is a devastating disease that has decimated banana production worldwide. Host resistance to Fusarium oxysporum f. sp. cubense (Foc), the causal agent of this disease, is genetically dissected in this study using two Musa acuminata ssp. malaccensis segregating populations segregating for Foc Tropical (TR4) and Subtropical (ST...

Introduction Wheat is one of the most important staple crops worldwide, and an important source of human protein and mineral element intake. Continuously increasing stable production of wheat is critical for global food security under the challenge of population growth and limited resource input. Objective Spike architecture determines the potenti...

Soybean (Glycine max) is a major crop that contributes more than half of global oilseed production. Much research has been directed towards improvement of the fatty acid profile of soybean seeds through marker assisted breeding. Recently published soybean pangenomes, based on thousands of soybean lines, provide an opportunity to identify new allele...

Narrow-leafed lupin (Lupinus angustifolius) is an important dryland crop, providing a protein source in global grain markets. While agronomic practices have successfully controlled many dicot weeds among narrow-leafed lupins, the closely related sandplain lupin (Lupinus cosentinii) has proven difficult to control, reducing yield and harvest quality...

Pod dehiscence is a major source of yield loss in legumes which is exacerbated by aridity. Disruptive mutations in 'Pod indehiscent 1' (PDH1), a pod sclerenchyma-specific lignin biosynthesis gene, has been linked to significant reductions in dehiscence in several legume species. We compared syntenic PDH1 regions across 12 legumes and two outgroups...

The recent Russia–Ukraine conflict has raised significant concerns about global food security, leaving many countries with restricted access to imported staple food crops, particularly wheat and sunflower oil, sending food prices soaring with other adverse consequences in the food supply chain. This detrimental effect is particularly prominent for...

Utilising resistance (R) genes, such as LepR1, against Leptosphaeria maculans, the causal agent of blackleg in canola (Brassica napus), could help manage the disease in the field and increase crop yield. Here we present a genome wide association study (GWAS) in B. napus to identify LepR1 candidate genes. Disease phenotyping of 104 B. napus genotype...

Citation: Chen, A.; Sun, J.; Martin, G.; Gray, L.-A.; Hřibová, E.; Christelová, P.; Yahiaoui, N.; Rounsley, S.; Lyons, R.; Batley, J.; et al. Identification of a Major QTL-Controlling Resistance to the Subtropical Race 4 of Fusarium oxysporum f. sp. cubense in Musa acuminata ssp. malaccensis. Pathogens 2023, 12, 289. https://doi. Abstract: Vascular...

Over the past decade, advances in plant genotyping have been critical in enabling the identification of genetic diversity, in understanding evolution, and in dissecting important traits in both crops and native plants. The widespread popularity of single-nucleotide polymorphisms (SNPs) has prompted significant improvements to SNP-based genotyping,...

Trunk disease is a major problem on grapevine in Zanjan province, causing serious decline, despite which its aetiology remains unknown. The purpose of this study was to investigate factors involved in grapevine decline in vineyards of Zanjan province. Samples were collected from twigs and branches of grapevines in the region between October and Nov...

Seagrasses are an ecologically important group of plants that have returned to the sea from terrestrial ancestors on at least three occasions (Cymodoceaceae, Posidoniaceae, Zosteraceae). Seagrass-specific genomic adaptations to marine life are known from the Zosteraceae. However, independent lineages may have devised different solutions to life und...

Global agricultural industries are under pressure to meet the future food demand; however, the existing crop genetic diversity might not be sufficient to meet this expectation. Advances in genome sequencing technologies and availability of reference genomes for over 300 plant species reveals the hidden genetic diversity in crop wild relatives (CWRs...

Increasing seed yield, fatty acids, and essential oil content are the main objectives in breeding coriander. However, in order to achieve this, there is a need to understand the nature of gene action and quantify the heterosis and inbreeding depression. Towards this, six genetically diverse parents, their 15 F1 one-way hybrids, and 15 F2 population...

Disease resistance improvement remains a major focus in breeding programs as diseases continue to devastate Brassica production systems due to intensive cultivation and climate change. Genomics has paved the way to understand the complex genomes of Brassicas, which has been pivotal in the dissection of the genetic underpinnings of agronomic traits...

Genetic diversity can influence resilience and adaptative capacity of organisms to environmental change. Genetic diversity within populations is largely structured by reproduction, with the prevalence of asexual versus sexual reproduction often underpinning important diversity metrics that determine selection efficacy. Asexual or clonal reproductio...

The global demand for oilseeds is increasing along with the human population. The family of Brassicaceae crops are no exception, typically harvested as a valuable source of oil, rich in beneficial molecules important for human health. The global capacity for improving Brassica yield has steadily risen over the last 50 years, with the major crop Bra...

Rye (Secale cereale) is a climate-resilient cereal grown extensively as grain or forage crop in Northern and Eastern Europe. In addition to being an important crop, it has been used to improve wheat through introgression of genomic regions for improved yield and disease resistance. Understanding the genomic diversity of rye will assist both the imp...

Rapeseed (Brassica napus, AACC) was formed by hybridization between progenitor species Brassica rapa (AA) and Brassica oleracea (CC). As a result of a limited number of hybridization events between specific progenitor genotypes and strong breeding selection for oil quality traits, rapeseed has limited genetic diversity. The production of resynthesi...

During crop domestication and breeding, wild plant species have been shaped into modern high-yield crops and adapted to the main agro-ecological regions. However, climate change will impact crop productivity in these regions, and agriculture needs to adapt to support future food production. On a global scale, crop wild relatives grow in more divers...

Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world’s most important food crops, efficient exploitation of molecular marker-assisted breedin...

Unlabelled: Brassica juncea (AABB), Indian mustard, is a source of disease resistance genes for a wide range of pathogens. The availability of reference genome sequences for B. juncea has made it possible to characterise the genomic structure and distribution of these disease resistance genes. Potentially functional disease resistance genes can be...

Brassica crop diseases caused by various pathogens, including viruses, bacteria, fungi and oomycetes, have devastating effects on the plants, leading to significant yield loss. This effect is worsened by the impact of climate change and the pressure to increase cultivation worldwide to feed the burgeoning population. As such, managing Brassica dise...

DNA methylation is an epigenetic mark associated with several mechanisms in plants including immunity mechanisms. However, little is known about the regulatory role of DNA methylation in the resistance response of Brassica species against fungal diseases. White rust, caused by the fungus Albugo candida, is one of the most widespread and destructive...

Gene models are regions of the genome that can be transcribed into RNA and translated to proteins, or belong to a class of non-coding RNA genes. The prediction of gene models is a complex process that can be unreliable, leading to false positive annotations. To help support the calling of confident conserved gene models and minimize false positives...

Pimpinella species are annual, biennial, and perennial semibushy aromatic plants cultivated for folk medicine, pharmaceuticals, food, and spices. The karyology and genome size of 17 populations of 16 different Pimpinella species collected from different locations in Iran were analyzed for inter-specific karyotypic and genome size variations. For ka...

Pimpinella species are annual, biennial, and perennial semibushy aromatic plants cultivated for folk medicine, pharmaceuticals, food, and spices. The karyology and genome size of 17 populations of 16 different Pimpinella species collected from different locations in Iran were analyzed for inter-specific karyotypic and genome size variations. For ka...

Polyploidy has the potential to allow organisms to outcompete their diploid progenitor(s) and occupy new environments. Shark Bay, Western Australia, is a World Heritage Area dominated by temperate seagrass meadows including Poseidon's ribbon weed, Posidonia australis. This seagrass is at the northern extent of its natural geographic range and exper...

Blackleg, caused by Leptosphaeria maculans, and L. biglobosa, is a major disease that hinders canola (Brassica napus) production worldwide. In this study, 51 Leptosphaeria isolates, and previously deposited sequences were examined for genetic diversity using ITS, β-tubulin, tef and act gene regions. Phylogenetic analyses showed that the isolates fe...

The use of association studies to identify candidate genes for complex biological traits in plants has been challenging due to a reliance on single reference genomes, leading to missing heritability. Graphical pangenomes and the identification of causal variants help overcome this and provide an important advance for crop breeding.

Bread wheat (Triticum aestivum L.) is one of humanity's most important staple crops, characterized by a large and complex genome with a high level of gene presence–absence variation (PAV) between cultivars, hampering genomic approaches for crop improvement. With the growing global population and the increasing impact of climate change on crop yield...

Various diseases severely affect Brassica crops, leading to significant global yield losses and a reduction in crop quality. In this study, we used the complete protein sequences of 49 cloned resistance genes (R genes) that confer resistance to fungal and bacterial diseases known to impact species in the Brassicaceae family. Homology searches were...

Genomic prediction tools support crop breeding based on statistical methods, such as the genomic best linear unbiased prediction (GBLUP). However, these tools are not designed to capture non-linear relationships within multi-dimensional datasets, or deal with high dimension datasets such as imagery collected by unmanned aerial vehicles. Machine lea...

In the Brassica genus, we find both diploid species (one genome) and allotetraploid species (two different genomes) but no naturally occurring hexaploid species (three different genomes, AABBCC). Although hexaploids can be produced via human intervention, these neo-polyploids have quite unstable genomes and usually suffer from severe genome reshuff...

Rapeseed (Brassica napus L.) is an important oil-producing crop for the world. Its adaptation, yield and quality have been considerably improved in recent decades, but the genomic basis underlying successful breeding selection remains unclear. Hence, we conducted a comprehensive genomic assessment of rapeseed in the breeding process based on the wh...

Soybean (Glycine max) is a legume species of significant economic and nutritional value. The yield of soybean continues to increase with the breeding of improved varieties, and this is likely to continue with the application of advanced genetic and genomic approaches for breeding. Genome technologies continue to advance rapidly, with an increasing...

Climate change and exponential population growth are exposing an immediate need for developing future crops that are highly resilient and adaptable to changing environments to maintain global food security in the next decade. Rigorous selection from long domestication history has rendered cultivated crops genetically disadvantaged, raising concerns...

Blackleg disease, caused by the fungal pathogen Leptosphaeria maculans, is the most devastating disease of canola (Brassica napus, oilseed rape) worldwide. Breeding for genetic resistance is the most widely used tool for controlling this disease and minimizing the impact on yield. To date, five resistance genes (Rlm2, LepR3, Rlm4, Rlm7, Rlm9) have...

Background Yield is the most important and complex trait that is influenced by numerous relevant traits with very complicated interrelations. While there are a large number of studies on the phenotypic relationship and genetic basis of yield traits, systematic studies with further dissection focusing on yield are limited. Therefore, there is still...

Recent growth in crop genomic and trait data have opened opportunities for the application of novel approaches to accelerate crop improvement. Machine learning and deep learning are at the forefront of prediction-based data analysis. However, few approaches for genotype to phenotype prediction compare machine learning with deep learning and further...

Key message The major soy protein QTL, cqProt-003, was analysed for haplotype diversity and global distribution, and results indicate 304 bp deletion and variable tandem repeats in protein coding regions are likely causal candidates. Abstract Here, we present association and linkage analysis of 985 wild, landrace and cultivar soybean accessions in...

Brassica napus (oilseed rape, canola) seedling resistance to Leptosphaeria maculans, the causal agent of blackleg (stem canker) disease, follows a gene-for- gene relationship. The avirulence genes AvrLmS and AvrLep2 were described to be perceived by the re-sistance genes RlmS and LepR2, respectively, present in B. napus ‘Surpass 400’. Here we repor...

Eremophila R.Br. comprises at least 238 species endemic to Australia, with many more having not yet been formally described. Three putative new taxa, namely, E. sp. Hamersley Range (K. Walker KW 136), E. sp. Calvert Range (A. A. Burbidge 738) and E. sp. Rudall River (P. G. Wilson 10512), were segregated from a broadly defined E. tietkensii F.Muell....