Publications by authors named "Jacqueline Batley"

156 Publications

Crop breeding for a changing climate: integrating phenomics and genomics with bioinformatics.

Theor Appl Genet 2021 Apr 14. Epub 2021 Apr 14.

School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, 6009, Australia.

Key Message: Safeguarding crop yields in a changing climate requires bioinformatics advances in harnessing data from vast phenomics and genomics datasets to translate research findings into climate smart crops in the field. Climate change and an additional 3 billion mouths to feed by 2050 raise serious concerns over global food security. Crop breeding and land management strategies will need to evolve to maximize the utilization of finite resources in coming years. High-throughput phenotyping and genomics technologies are providing researchers with the information required to guide and inform the breeding of climate smart crops adapted to the environment. Bioinformatics has a fundamental role to play in integrating and exploiting this fast accumulating wealth of data, through association studies to detect genomic targets underlying key adaptive climate-resilient traits. These data provide tools for breeders to tailor crops to their environment and can be introduced using advanced selection or genome editing methods. To effectively translate research into the field, genomic and phenomic information will need to be integrated into comprehensive clade-specific databases and platforms alongside accessible tools that can be used by breeders to inform the selection of climate adaptive traits. Here we discuss the role of bioinformatics in extracting, analysing, integrating and managing genomic and phenomic data to improve climate resilience in crops, including current, emerging and potential approaches, applications and bottlenecks in the research and breeding pipeline.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00122-021-03820-3DOI Listing
April 2021

Candidate Rlm6 resistance genes against Leptosphaeria. maculans identified through a genome-wide association study in Brassica juncea (L.) Czern.

Theor Appl Genet 2021 Mar 25. Epub 2021 Mar 25.

School of Biological Sciences, University of Western Australia, Perth, WA, Australia.

Key Message: One hundred and sixty-seven B. juncea varieties were genotyped on the 90K Brassica assay (42,914 SNPs), which led to the identification of sixteen candidate genes for Rlm6. Brassica species are at high risk of severe crop loss due to pathogens, especially Leptosphaeria maculans (the causal agent of blackleg). Brassica juncea (L.) Czern is an important germplasm resource for canola improvement, due to its good agronomic traits, such as heat and drought tolerance and high blackleg resistance. The present study is the first using genome-wide association studies to identify candidate genes for blackleg resistance in B. juncea based on genome-wide SNPs obtained from the Illumina Infinium 90 K Brassica SNP array. The verification of Rlm6 in B. juncea was performed through a cotyledon infection test. Genotyping 42,914 single nucleotide polymorphisms (SNPs) in a panel of 167 B. juncea lines revealed a total of seven SNPs significantly associated with Rlm6 on chromosomes A07 and B04 in B. juncea. Furthermore, 16 candidate Rlm6 genes were found in these regions, defined as nucleotide binding site leucine-rich-repeat (NLR), leucine-rich repeat RLK (LRR-RLK) and LRR-RLP genes. This study will give insights into the blackleg resistance in B. juncea and facilitate identification of functional blackleg resistance genes which can be used in Brassica breeding.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00122-021-03803-4DOI Listing
March 2021

Genomics Armed With Diversity Leads the Way in Improvement in a Changing Global Environment.

Front Genet 2021 18;12:600789. Epub 2021 Feb 18.

School of Biological Sciences Western Australia and UWA Institute of Agriculture, University of Western Australia, Perth, WA, Australia.

Meeting the needs of a growing world population in the face of imminent climate change is a challenge; breeding of vegetable and oilseed crops is part of the race in meeting these demands. Available genetic diversity constituting the foundation of breeding is essential in plant improvement. Elite varieties, land races, and crop wild species are important resources of useful variation and are available from existing genepools or genebanks. Conservation of diversity in genepools, genebanks, and even the wild is crucial in preventing the loss of variation for future breeding efforts. In addition, the identification of suitable parental lines and alleles is critical in ensuring the development of resilient crops. During the past two decades, an increasing number of high-quality nuclear and organellar genomes have been assembled. Whole-genome re-sequencing and the development of pan-genomes are overcoming the limitations of the single reference genome and provide the basis for further exploration. Genomic and complementary omic tools such as microarrays, transcriptomics, epigenetics, and reverse genetics facilitate the study of crop evolution, breeding histories, and the discovery of loci associated with highly sought-after agronomic traits. Furthermore, in genomic selection, predicted breeding values based on phenotype and genome-wide marker scores allow the preselection of promising genotypes, enhancing genetic gains and substantially quickening the breeding cycle. It is clear that genomics, armed with diversity, is set to lead the way in improvement; however, a multidisciplinary plant breeding approach that includes phenotype = genotype × environment × management interaction will ultimately ensure the selection of resilient varieties ready for climate change.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fgene.2021.600789DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7930750PMC
February 2021

Modeling first order additive × additive epistasis improves accuracy of genomic prediction for sclerotinia stem rot resistance in canola.

Plant Genome 2021 Feb 24:e20088. Epub 2021 Feb 24.

Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia.

The fungus Sclerotinia sclerotiorum infects hundreds of plant species including many crops. Resistance to this pathogen in canola (Brassica napus L. subsp. napus) is controlled by numerous quantitative trait loci (QTL). For such polygenic traits, genomic prediction may be useful for breeding as it can capture many QTL at once while also considering nonadditive genetic effects. Here, we test application of common regression models to genomic prediction of S. sclerotiorum resistance in canola in a diverse panel of 218 plants genotyped at 24,634 loci. Disease resistance was scored by infection with an aggressive isolate and monitoring over 3 wk. We found that including first-order additive × additive epistasis in linear mixed models (LMMs) improved accuracy of breeding value estimation between 3 and 40%, depending on method of assessment, and correlation between phenotypes and predicted total genetic values by 14%. Bayesian models performed similarly to or worse than genomic relationship matrix-based models for estimating breeding values or overall phenotypes from genetic values. Bayesian ridge regression, which is most similar to the genomic relationship matrix-based approach in the amount of shrinkage it applies to marker effects, was the most accurate of this family of models. This confirms several studies indicating the highly polygenic nature of sclerotinia stem rot resistance. Overall, our results highlight the use of simple epistasis terms for prediction of breeding values and total genetic values for a complex disease resistance phenotype in canola.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/tpg2.20088DOI Listing
February 2021

Stable, fertile lines produced by hybridization between allotetraploids Brassica juncea (AABB) and Brassica carinata (BBCC) have merged the A and C genomes.

New Phytol 2021 05 6;230(3):1242-1257. Epub 2021 Mar 6.

Plant Breeding Department, Justus Liebig University, Heinrich-Buff-Ring 26-32, Giessen, 35392, Germany.

Many flowering plant taxa contain allopolyploids that share one or more genomes in common. In the Brassica genus, crop species Brassica juncea and Brassica carinata share the B genome, with 2n = AABB and 2n = BBCC genome complements, respectively. Hybridization results in 2n = BBAC hybrids, but the fate of these hybrids over generations of self-pollination has never been reported. We produced and characterized B. juncea × B. carinata (2n = BBAC) interspecific hybrids over six generations of self-pollination under selection for high fertility using a combination of genotyping, fertility phenotyping, and cytogenetics techniques. Meiotic pairing behaviour improved from 68% bivalents in the F to 98% in the S /S generations, and initially low hybrid fertility also increased to parent species levels. The S /S hybrids contained an intact B genome (16 chromosomes) plus a new, stable A/C genome (18-20 chromosomes) resulting from recombination and restructuring of A and C-genome chromosomes. Our results provide the first experimental evidence that two genomes can come together to form a new, restructured genome in hybridization events between two allotetraploid species that share a common genome. This mechanism should be considered in interpreting phylogenies in taxa with multiple allopolyploid species.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/nph.17225DOI Listing
May 2021

Recent Findings Unravel Genes and Genetic Factors Underlying Resistance in and Its Relatives.

Int J Mol Sci 2020 Dec 30;22(1). Epub 2020 Dec 30.

School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia.

Among the oilseeds, canola () is the most economically significant globally. However, its production can be limited by blackleg disease, caused by the fungal pathogen . The deployment of resistance genes has been implemented as one of the key strategies to manage the disease. Genetic resistance against blackleg comes in two forms: qualitative resistance, controlled by a single, major resistance gene ( gene), and quantitative resistance (QR), controlled by numerous, small effect loci. -gene-mediated blackleg resistance has been extensively studied, wherein several genomic regions harbouring genes against have been identified and three of these genes were cloned. These studies advance our understanding of the mechanism of gene and pathogen avirulence () gene interaction. Notably, these studies revealed a more complex interaction than originally thought. Advances in genomics help unravel these complexities, providing insights into the genes and genetic factors towards improving blackleg resistance. Here, we aim to discuss the existing -gene-mediated resistance, make a summary of candidate genes against the disease, and emphasise the role of players involved in the pathogenicity and resistance. The comprehensive result will allow breeders to improve resistance to thereby increasing yield.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/ijms22010313DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7795555PMC
December 2020

Genome-Wide Identification and Evolution of Receptor-Like Kinases (RLKs) and Receptor like Proteins (RLPs) in .

Biology (Basel) 2020 Dec 30;10(1). Epub 2020 Dec 30.

School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia.

, an allotetraploid species, is an important germplasm resource for canola improvement, due to its many beneficial agronomic traits, such as heat and drought tolerance and blackleg resistance. Receptor-like kinase (RLK) and receptor-like protein (RLP) genes are two types of resistance gene analogues (RGA) that play important roles in plant innate immunity, stress response and various development processes. In this study, genome wide analysis of RLKs and RLPs is performed in . In total, 493 RLKs (LysM-RLKs and LRR-RLKs) and 228 RLPs (LysM-RLPs and LRR-RLPs) are identified in the genome of , using RGAugury. Only 13.54% RLKs and 11.79% RLPs are observed to be grouped within gene clusters. The majority of RLKs (90.17%) and RLPs (52.83%) are identified as duplicates, indicating that gene duplications significantly contribute to the expansion of RLK and RLP families. Comparative analysis between and its progenitor species, and , indicate that 83.62% RLKs and 41.98% RLPs are conserved in , and RLPs are likely to have a faster evolution than RLKs. This study provides a valuable resource for the identification and characterisation of candidate RLK and RLP genes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/biology10010017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7823396PMC
December 2020

Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction in Brassica napus.

BMC Plant Biol 2020 Dec 7;20(1):546. Epub 2020 Dec 7.

School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia.

Background: Brassica napus is an important oilseed crop cultivated worldwide. During domestication and breeding of B. napus, flowering time has been a target of selection because of its substantial impact on yield. Here we use double digest restriction-site associated DNA sequencing (ddRAD) to investigate the genetic basis of flowering in B. napus. An F mapping population was derived from a cross between an early-flowering spring type and a late-flowering winter type.

Results: Flowering time in the mapping population differed by up to 25 days between individuals. High genotype error rates persisted after initial quality controls, as suggested by a genotype discordance of ~ 12% between biological sequencing replicates. After genotype error correction, a linkage map spanning 3981.31 cM and compromising 14,630 single nucleotide polymorphisms (SNPs) was constructed. A quantitative trait locus (QTL) on chromosome C2 was detected, covering eight flowering time genes including FLC.

Conclusions: These findings demonstrate the effectiveness of the ddRAD approach to sample the B. napus genome. Our results also suggest that ddRAD genotype error rates can be higher than expected in F populations. Quality filtering and genotype correction and imputation can substantially reduce these error rates and allow effective linkage mapping and QTL analysis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12870-020-02756-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7720618PMC
December 2020

Frontiers in Dissecting and Managing Diseases: From Reference-Based RGA Candidate Identification to Building Pan-RGAomes.

Int J Mol Sci 2020 Nov 25;21(23). Epub 2020 Nov 25.

School of Biological Sciences, The University of Western Australia, Perth 6009, Australia.

The genus contains abundant economically important vegetable and oilseed crops, which are under threat of diseases caused by fungal, bacterial and viral pathogens. Resistance gene analogues (RGAs) are associated with quantitative and qualitative disease resistance and the identification of candidate RGAs associated with disease resistance is crucial for understanding the mechanism and management of diseases through breeding. The availability of genome assemblies has greatly facilitated reference-based quantitative trait loci (QTL) mapping for disease resistance. In addition, pangenomes, which characterise both core and variable genes, have been constructed for , and . Genome-wide characterisation of RGAs using conserved domains and motifs in reference genomes and pangenomes reveals their clustered arrangements and presence of structural variations. Here, we comprehensively review RGA identification in important genome and pangenome assemblies. Comparison of the RGAs in QTL between resistant and susceptible individuals allows for efficient identification of candidate disease resistance genes. However, the reference-based QTL mapping and RGA candidate identification approach is restricted by the under-represented RGA diversity characterised in the limited number of assemblies. The species-wide repertoire of RGAs make up the pan-resistance gene analogue genome (pan-RGAome). Building a pan-RGAome, through either whole genome resequencing or resistance gene enrichment sequencing, would effectively capture RGA diversity, greatly expanding breeding resources that can be utilised for crop improvement.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/ijms21238964DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7728316PMC
November 2020

Comparison and evolutionary analysis of Brassica nucleotide binding site leucine rich repeat (NLR) genes and importance for disease resistance breeding.

Plant Genome 2021 03 11;14(1):e20060. Epub 2020 Nov 11.

School of Biological Sciences, University of Western Australia, Perth, WA, Australia.

The Brassica genus contains many agriculturally significant oilseed and vegetable crops, however the crop yield is threatened by a range of fungal and bacterial pathogens. Nucleotide Binding Site Leucine Rich Repeat (NLR) genes play important roles in plant innate immunity. The evolution of NLR genes is influenced by genomic processes and pathogen selection. At the whole genome level, whole genome duplications (WGDs) generate abundant gene copies, most of which are lost during genome fractionation. At sub-genomic levels, some retained copies undergo duplication forming clusters which facilitate rapid evolution through recombination. The number, distribution and genetic variations of the NLR genes vary among Brassica species and within populations suggesting differential selection pressure exerted by pathogen populations throughout the evolutionary history. A study of the evolution of disease resistance genes in agriculturally important plants such as Brassicas helps gain insights into their function and inform the identification of resistance genes for breeding of resistant lines.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/tpg2.20060DOI Listing
March 2021

Author Correction: Plant pan-genomes are the new reference.

Nat Plants 2020 Nov;6(11):1389

School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41477-020-00776-yDOI Listing
November 2020

Understanding Host-Pathogen Interactions in in the Omics Era.

Plants (Basel) 2020 Oct 10;9(10). Epub 2020 Oct 10.

School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth 6009, Australia.

(canola/oilseed rape/rapeseed) is an economically important crop, mostly found in temperate and sub-tropical regions, that is cultivated widely for its edible oil. Major diseases of crops such as Blackleg, Clubroot, Sclerotinia Stem Rot, Downy Mildew, Alternaria Leaf Spot and White Rust have caused significant yield and economic losses in rapeseed-producing countries worldwide, exacerbated by global climate change, and, if not remedied effectively, will threaten global food security. To gain further insights into the host-pathogen interactions in relation to diseases, it is critical that we review current knowledge in this area and discuss how omics technologies can offer promising results and help to push boundaries in our understanding of the resistance mechanisms. Omics technologies, such as genomics, proteomics, transcriptomics and metabolomics approaches, allow us to understand the host and pathogen, as well as the interaction between the two species at a deeper level. With these integrated data in multi-omics and systems biology, we are able to breed high-quality disease-resistant crops in a more holistic, targeted and accurate way.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/plants9101336DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7599536PMC
October 2020

The Use of Genetic and Gene Technologies in Shaping Modern Rapeseed Cultivars ( L.).

Genes (Basel) 2020 Sep 30;11(10). Epub 2020 Sep 30.

School of Biological Science, The University of Western Australia, Perth, WA 6009, Australia.

Since their domestication, Brassica oilseed species have undergone progressive transformation allied with the development of breeding and molecular technologies. The canola () crop has rapidly expanded globally in the last 30 years with intensive innovations in canola varieties, providing for a wider range of markets apart from the food industry. The breeding efforts of , the main source of canola oil and canola meal, have been mainly focused on improving seed yield, oil quality, and meal quality along with disease resistance, abiotic stress tolerance, and herbicide resistance. The revolution in genetics and gene technologies, including genetic mapping, molecular markers, genomic tools, and gene technology, especially gene editing tools, has allowed an understanding of the complex genetic makeup and gene functions in the major bioprocesses of the Brassicales, especially Brassica oil crops. Here, we provide an overview on the contributions of these technologies in improving the major traits of and discuss their potential use to accomplish new improvement targets.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/genes11101161DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7600269PMC
September 2020

Resistance Gene Analogs in the Brassicaceae: Identification, Characterization, Distribution, and Evolution.

Plant Physiol 2020 10 12;184(2):909-922. Epub 2020 Aug 12.

School of Biological Sciences, University of Western Australia, Perth, Western Australia WA 6009, Australia

The Brassicaceae consists of a wide range of species, including important crop species and the model plant Arabidopsis (). spp. crop diseases impose significant yield losses annually. A major way to reduce susceptibility to disease is the selection in breeding for resistance gene analogs (RGAs). Nucleotide binding site-leucine rich repeats (NLRs), receptor-like kinases (RLKs), and receptor-like proteins (RLPs) are the main types of RGAs; they contain conserved domains and motifs and play specific roles in resistance to pathogens. Here, all classes of RGAs have been identified using annotation and assembly-based pipelines in all available genome annotations from the Brassicaceae, including multiple genome assemblies of the same species where available (total of 32 genomes). The number of RGAs, based on genome annotations, varies within and between species. In total 34,065 RGAs were identified, with the majority being RLKs (21,691), then NLRs (8,588) and RLPs (3,786). Analysis of the RGA protein sequences revealed a high level of sequence identity, whereby 99.43% of RGAs fell into several orthogroups. This study establishes a resource for the identification and characterization of RGAs in the Brassicaceae and provides a framework for further studies of RGAs for an ultimate goal of assisting breeders in improving resistance to plant disease.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1104/pp.20.00835DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7536671PMC
October 2020

Author Correction: Integration of metabolome and transcriptome reveals flavonoid accumulation in the intergeneric hybrid between Brassica rapa and Raphanus sativus.

Sci Rep 2020 Jul 22;10(1):12520. Epub 2020 Jul 22.

College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-020-69596-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7374088PMC
July 2020

Plant pan-genomes are the new reference.

Nat Plants 2020 08 20;6(8):914-920. Epub 2020 Jul 20.

School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia.

Recent years have seen a surge in plant genome sequencing projects and the comparison of multiple related individuals. The high degree of genomic variation observed led to the realization that single reference genomes do not represent the diversity within a species, and led to the expansion of the pan-genome concept. Pan-genomes represent the genomic diversity of a species and includes core genes, found in all individuals, as well as variable genes, which are absent in some individuals. Variable gene annotations often show similarities across plant species, with genes for biotic and abiotic stress commonly enriched within variable gene groups. Here we review the growth of pan-genomics in plants, explore the origins of gene presence and absence variation, and show how pan-genomes can support plant breeding and evolution studies.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41477-020-0733-0DOI Listing
August 2020

Targeted Knockout of Homologues for Yellow-Seeded with Reduced Flavonoids and Improved Fatty Acid Composition.

J Agric Food Chem 2020 May 12;68(20):5676-5690. Epub 2020 May 12.

Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, Jiangsu 225009, China.

is one of the important oil crops grown worldwide, and oil quality improvement is a major goal in rapeseed breeding. Yellow seed is an excellent trait, which has great potential in improving seed quality and economic value. In this study, we created stable yellow seed mutants using a CRISPR/Cas9 system and obtained the yellow seed phenotype only when the four alleles of two homologues were knocked out, indicating that the two homologues had conserved but redundant functions in regulating seed color. Histochemical staining and flavonoid metabolic analysis proved that the  mutation hindered the synthesis and accumulation of proanthocyanidins. Transcriptome analysis also showed that the mutation inhibited the expression of genes in the phenylpropanoid and flavonoid biosynthetic pathway, which might be regulated by the complex of BnTT2, BnTT8 and BnTTG1. In addition, the homozygous mutants of homologues increased oil content and improved fatty acid composition with higher linoleic acid (C18:2) and linolenic acid (C18:3), which could be used for the genetic improvement of rapeseed. Overall, this research showed that the mutation can be used for yellow seed breeding and oil improvement, which is of great significance in improving the economic value of rapeseeds.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jafc.0c01126DOI Listing
May 2020

Genome-Wide Analysis of the Lateral Organ Boundaries Domain Gene Family in Brassica Napus.

Genes (Basel) 2020 03 6;11(3). Epub 2020 Mar 6.

Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China.

The plant specific LATERAL ORGAN BOUNDARIES (LOB)-domain (LBD) proteins belong to a family of transcription factors that play important roles in plant growth and development, as well as in responses to various stresses. However, a comprehensive study of LBDs in has not yet been reported. In the present study, 126 genes were identified in genome using bioinformatics analyses. The 126 BnLBDs were phylogenetically classified into two groups and nine subgroups. Evolutionary analysis indicated that whole genome duplication (WGD) and segmental duplication played important roles in the expansion of the gene family. On the basis of the RNA-seq analyses, we identified genes with tissue or developmental specific expression patterns. Through -acting element analysis and hormone treatment, we identified 19 genes with putative functions in plant response to abscisic acid (ABA) treatment. This study provides a comprehensive understanding on the origin and evolutionary history of in , and will be helpful in further functional characterisation of .
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/genes11030280DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7140802PMC
March 2020

Exploring the application of wild species for crop improvement in a changing climate.

Curr Opin Plant Biol 2020 08 3;56:218-222. Epub 2020 Feb 3.

School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley 6009, Australia. Electronic address:

Modern agriculture is currently facing challenges from a burgeoning population and changing climate, which requires improved crops with adaptation to climate and elite yield and quality traits. While there is a breeding bottleneck caused by intensive selection, gene banks containing conserved wild relatives and landraces can be used as breeding resources. However, with limited genetic information available on these wild relatives, the application has been hindered. With the development of both genomics and bioinformatics techniques, it is now easier to identify the genetic variation in wild species, which can be utilized for the introgression of elite traits. These wild species can therefore play an important role in food security and breeding sustainability.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.pbi.2019.12.013DOI Listing
August 2020

Trait associations in the pangenome of pigeon pea (Cajanus cajan).

Plant Biotechnol J 2020 09 12;18(9):1946-1954. Epub 2020 Mar 12.

International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.

Pigeon pea (Cajanus cajan) is an important orphan crop mainly grown by smallholder farmers in India and Africa. Here, we present the first pigeon pea pangenome based on 89 accessions mainly from India and the Philippines, showing that there is significant genetic diversity in Philippine individuals that is not present in Indian individuals. Annotation of variable genes suggests that they are associated with self-fertilization and response to disease. We identified 225 SNPs associated with nine agronomically important traits over three locations and two different time points, with SNPs associated with genes for transcription factors and kinases. These results will lead the way to an improved pigeon pea breeding programme.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/pbi.13354DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7415775PMC
September 2020

Genome-Wide Mining of Disease Resistance Gene Analogs Using Conserved Domains.

Methods Mol Biol 2020 ;2107:365-375

School of Biological Sciences, University of Western Australia, Crawley, WA, Australia.

The production of legume crop species is severely affected by disease, imposing a significant yield loss annually worldwide. Plant resistance gene analogs (RGAs) play specific roles in plant resistance responses, and their identification and subsequent application in breeding programs help to reduce this yield loss. RGAs contain conserved domains and motifs, which can be used for their identification and classification. Nucleotide-binding site-leucine-rich repeat (NLR), receptor like kinase (RLK), and receptor like protein (RLP) genes are the main types of RGAs. Computational identification and characterization of RGAs has been performed successfully among different plant species. Here, we explain the computational workflow for genome-wide RGA identification in legumes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-0716-0235-5_20DOI Listing
January 2021

Genotyping for Species Identification and Diversity Assessment Using Double-Digest Restriction Site-Associated DNA Sequencing (ddRAD-Seq).

Methods Mol Biol 2020 ;2107:159-187

School of Biological Sciences, University of Western Australia, Crawley, WA, Australia.

Genotyping-by-sequencing (GBS) is a powerful approach for studying the genetic diversity of legume species. By using restriction enzymes or other methods to generate a reduced representation of the genome for sequencing, GBS can provide genome-wide single nucleotide polymorphisms (SNP) for diversity analysis at high throughput and low cost. Here we describe a novel double-digest restriction site-associated DNA sequencing (ddRAD-seq) approach. We also describe the downstream bioinformatic analysis of the sequencing data, including alignment to a reference genome, de novo assembly, SNP calling, phylogenetic analysis, and structure analysis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-0716-0235-5_8DOI Listing
January 2021

Pangenomics Comes of Age: From Bacteria to Plant and Animal Applications.

Trends Genet 2020 02 24;36(2):132-145. Epub 2019 Dec 24.

School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia. Electronic address:

The pangenome refers to a collection of genomic sequence found in the entire species or population rather than in a single individual; the sequence can be core, present in all individuals, or accessory (variable or dispensable), found in a subset of individuals only. While pangenomic studies were first undertaken in bacterial species, developments in genome sequencing and assembly approaches have allowed construction of pangenomes for eukaryotic organisms, fungi, plants, and animals, including two large-scale human pangenome projects. Analysis of the these pangenomes revealed key differences, most likely stemming from divergent evolutionary histories, but also surprising similarities.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.tig.2019.11.006DOI Listing
February 2020

Integration of metabolome and transcriptome reveals flavonoid accumulation in the intergeneric hybrid between Brassica rapa and Raphanus sativus.

Sci Rep 2019 12 4;9(1):18368. Epub 2019 Dec 4.

College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.

Brassica rapa and Raphanus sativus are two important edible vegetables that contain numerous nutritional ingredients. However, the agronomic traits and nutritional components of the intergeneric hybrid of B. rapa and R. sativus remain poorly understood. In this study, we used a stably inherited intergeneric hybrid of B. rapa and R. sativus as a model to study its metabolome and transcriptome profiles. Morphological and cytological analysis showed the intergeneric hybrid had the expected chromosome number and normal meiosis behavior. Moreover, the metabolome analysis showed multiple important secondary metabolites, including flavonoids and glucosinolates, were significantly upregulated in the hybrid. Furthermore, transcriptome data revealed that the expression level of the important genes involved in phenylpropanoid and flavonoid pathways was significantly upregulated in the hybrid. Ultimately, our data indicate the intergeneric hybrid will be a valuable bioengineering resource and promise to become a new-type hybrid vegetable with great medicinal value in future.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-019-54889-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6893016PMC
December 2019

Identification and QTL mapping of resistance to Turnip yellows virus (TuYV) in oilseed rape, Brassica napus.

Theor Appl Genet 2020 Feb 5;133(2):383-393. Epub 2019 Nov 5.

School of Life Sciences, University of Warwick, Wellesbourne Campus, Warwick, CV35 9EF, UK.

Key Message: Partially dominant resistance to Turnip yellows virus associated with one major QTL was identified in the natural allotetraploid oilseed rape cultivar Yudal. Turnip yellows virus (TuYV) is transmitted by the peach-potato aphid (Myzus persicae) and causes severe yield losses in commercial oilseed rape crops (Brassica napus). There is currently only one genetic resource for resistance to TuYV available in brassica, which was identified in the re-synthesised B. napus line 'R54'. In our study, 27 mostly homozygous B. napus accessions, either doubled-haploid (DH) or inbred lines, representing a diverse subset of the B. napus genepool, were screened for TuYV resistance/susceptibility. Partial resistance to TuYV was identified in the Korean spring oilseed rape, B. napus variety Yudal, whilst the dwarf French winter oilseed rape line Darmor-bzh was susceptible. QTL mapping using the established Darmor-bzh × Yudal DH mapping population (DYDH) revealed one major QTL explaining 36% and 18% of the phenotypic variation in two independent experiments. A DYDH line was crossed to Yudal, and reciprocal backcross (BC) populations from the F with either the susceptible or resistant parent revealed the dominant inheritance of the TuYV resistance. The QTL on ChrA04 was verified in the segregating BC population. A second minor QTL on ChrC05 was identified in one of the two DYDH experiments, and it was not observed in the BC population. The TuYV resistance QTL in 'R54' is within the QTL interval on Chr A04 of Yudal; however, the markers co-segregating with the 'R54' resistance are not conserved in Yudal, suggesting an independent origin of the TuYV resistances. This is the first report of the QTL mapping of TuYV resistance in natural B. napus.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00122-019-03469-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6985063PMC
February 2020

DNA Methylation: Toward Crop Disease Resistance Improvement.

Trends Plant Sci 2019 12 8;24(12):1137-1150. Epub 2019 Oct 8.

School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia. Electronic address:

Crop diseases, in conjunction with climate change, are a major threat to global crop production. DNA methylation is an epigenetic mark and is involved in plants' biological processes, including development, stress adaptation, and genome evolution. By providing a new source of variation, DNA methylation introduces novel direction to both scientists and breeders with its potential in disease resistance enhancement. Here, we discuss the impact of pathogen-induced DNA methylation modifications on a host's transcriptome reprogramming and genome stability, as part of the plant's defense mechanisms. We also highlight the knowledge gaps that need to be investigated for understanding the entire role of DNA methylation in plant pathogen interactions. This will ultimately assist breeders toward improving resistance and decreasing yield losses.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.tplants.2019.08.007DOI Listing
December 2019

Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation.

Plant Biotechnol J 2020 04 10;18(4):969-982. Epub 2019 Oct 10.

UWA School of Biological Sciences and the UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, WA, Australia.

Methods based on single nucleotide polymorphism (SNP), copy number variation (CNV) and presence/absence variation (PAV) discovery provide a valuable resource to study gene structure and evolution. However, as a result of these structural variations, a single reference genome is unable to cover the entire gene content of a species. Therefore, pangenomics analysis is needed to ensure that the genomic diversity within a species is fully represented. Brassica napus is one of the most important oilseed crops in the world and exhibits variability in its resistance genes across different cultivars. Here, we characterized resistance gene distribution across 50 B. napus lines. We identified a total of 1749 resistance gene analogs (RGAs), of which 996 are core and 753 are variable, 368 of which are not present in the reference genome (cv. Darmor-bzh). In addition, a total of 15 318 SNPs were predicted within 1030 of the RGAs. The results showed that core R-genes harbour more SNPs than variable genes. More nucleotide binding site-leucine-rich repeat (NBS-LRR) genes were located in clusters than as singletons, with variable genes more likely to be found in clusters. We identified 106 RGA candidates linked to blackleg resistance quantitative trait locus (QTL). This study provides a better understanding of resistance genes to target for genomics-based improvement and improved disease resistance.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/pbi.13262DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7061875PMC
April 2020

Epigenetics: Potentials and Challenges in Crop Breeding.

Mol Plant 2019 10 18;12(10):1309-1311. Epub 2019 Sep 18.

School of Biological Sciences, University of Western Australia, Perth, WA, Australia. Electronic address:

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.molp.2019.09.006DOI Listing
October 2019

Whole Genome Diversity, Population Structure, and Linkage Disequilibrium Analysis of Chickpea ( L.) Genotypes Using Genome-Wide DArTseq-Based SNP Markers.

Genes (Basel) 2019 09 4;10(9). Epub 2019 Sep 4.

Department of Agronomy & Plant Breeding, College of Agriculture, Sanandaj Branch, Islamic Azad University, Sanandaj, P.O. Box:618, Iran.

Characterization of genetic diversity, population structure, and linkage disequilibrium is a prerequisite for proper management of breeding programs and conservation of genetic resources. In this study, 186 chickpea genotypes, including advanced "" breeding lines and Iranian landrace "" chickpea genotypes, were genotyped using DArTseq-Based single nucleotide polymorphism (SNP) markers. Out of 3339 SNPs, 1152 markers with known chromosomal position were selected for genome diversity analysis. The number of mapped SNP markers varied from 52 (LG8) to 378 (LG4), with an average of 144 SNPs per linkage group. The chromosome size that was covered by SNPs varied from 16,236.36 kbp (LG8) to 67,923.99 kbp (LG5), while LG4 showed a higher number of SNPs, with an average of 6.56 SNPs per Mbp. Polymorphism information content (PIC) value of SNP markers ranged from 0.05 to 0.50, with an average of 0.32, while the markers on LG4, LG6, and LG8 showed higher mean PIC value than average. Unweighted neighbor joining cluster analysis and Bayesian-based model population structure grouped chickpea genotypes into four distinct clusters. Principal component analysis (PCoA) and discriminant analysis of principal component (DAPC) results were consistent with that of the cluster and population structure analysis. Linkage disequilibrium (LD) was extensive and LD decay in chickpea germplasm was relatively low. A few markers showed r ≥ 0.8, while 2961 pairs of markers showed complete LD (r = 1), and a huge LD block was observed on LG4. High genetic diversity and low kinship value between pairs of genotypes suggest the presence of a high genetic diversity among the studied chickpea genotypes. This study also demonstrates the efficiency of DArTseq-based SNP genotyping for large-scale genome analysis in chickpea. The genotypic markers provided in this study are useful for various association mapping studies when combined with phenotypic data of different traits, such as seed yield, abiotic, and biotic stresses, and therefore can be efficiently used in breeding programs to improve chickpea.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/genes10090676DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6770975PMC
September 2019

A reference genome for pea provides insight into legume genome evolution.

Nat Genet 2019 09 2;51(9):1411-1422. Epub 2019 Sep 2.

Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté Bourgogne, Université Bourgogne Franche-Comté, Dijon, France.

We report the first annotated chromosome-level reference genome assembly for pea, Gregor Mendel's original genetic model. Phylogenetics and paleogenomics show genomic rearrangements across legumes and suggest a major role for repetitive elements in pea genome evolution. Compared to other sequenced Leguminosae genomes, the pea genome shows intense gene dynamics, most likely associated with genome size expansion when the Fabeae diverged from its sister tribes. During Pisum evolution, translocation and transposition differentially occurred across lineages. This reference sequence will accelerate our understanding of the molecular basis of agronomically important traits and support crop improvement.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0480-1DOI Listing
September 2019