Biology subjects

Flood, P. J.

Publications and source records attributed to Flood, P. J..

5 recordsLinked to original sources

bioRxiv2026

Multi-environment GWAS analysis for photosynthetic light use efficiency in Arabidopsis thaliana

Photosynthesis is acknowledged as a potential target to increase crop yield. Improved photosynthesis may be achieved by conventional breeding, exploiting the available natural genetic variation for photosynthesis traits. This approach is challenging for crops due to limitations in high-throughput photosynthesis phenotyping, the highly polygenic nature of photosynthesis, and its strongly dynamic response to environmental changes. Recent advancements in phenomics make accurate and detailed photosynthesis phenotyping more feasible, with the model species Arabidopsis thaliana paving the way for applications in crops. In this study, we examined photosynthesis parameters over time in the global Arabidopsis HapMap diversity panel exposed to three conditions: optimal nutrient supply, low phosphorus supply and low nitrogen supply. Combined with two previous studies on photosynthesis in response to low temperature, and to a one-step change in irradiance from low light to high light, five high-quality datasets were systematically analysed using the same approach (with one million-maker set, uni- and multi-variate analyses). Our findings emphasize the genetic complexity of photosynthesis, detecting hundreds of significant quantitative trait loci, only a small number of which are robust, and of which most are condition specific. Robust loci, found in multiple conditions, exemplify those suited for conferring higher all-round photosynthesis, and targets for marker-assisted selection, contributing to environmental resilience, while the multitude of small-effect conditional loci suggest that genomic selection approaches may be more suited to improve crop photosynthesis.

genetics↗

bioRxiv2024

Towards an unbiased characterization of genetic polymorphism

Our view of genetic polymorphism is shaped by methods that provide a limited and reference-biased picture. Long-read sequencing technologies, which are starting to provide nearly complete genome sequences for population samples, should solve the problem--except that characterizing and making sense of non-SNP variation is difficult even with perfect sequence data. Here we analyze 27 genomes of Arabidopsis thaliana in an attempt to address these issues, and illustrate what can be learned by analyzing whole-genome polymorphism data in an unbiased manner. Estimated genome sizes range from 135 to 155 Mb, with differences almost entirely due to centromeric and rDNA repeats that are difficult to assemble. The completely assembled chromosome arms comprise roughly 120 Mb in all accessions, but are full of structural variants, largely due to transposable elements. Even with only 27 accessions, a pan-genome coordinate system that includes the resulting variation ends up being [~] 70% larger than the size of any one genome. Our analysis reveals an incompletely annotated mobile-ome: we not only detect several novel TE families, but also find that existing TE annotation is a poor predictor of elements that have recently been active. In contrast to this, the genic portion, or "gene-ome", is highly conserved. By annotating each genome using accession-specific transcriptome data, we find that 13% of all (non-TE) genes are segregating in our 27 accessions, but most of these are transcriptionally silenced. Finally, we show that with short-read data we previously massively underestimated genetic variation of all kinds, including SNPs--mostly in regions where short reads could not be mapped reliably, but also where reads were mapped incorrectly. We demonstrate that SNP-calling errors can be biased by the choice of reference genome, and that RNA-seq and BS-seq results can be strongly affected by mapping reads only to a reference genome rather than to the genome of the assayed individual. In conclusion, while whole-genome polymorphism data pose tremendous analytical challenges, they also have the potential to revolutionize our understanding of genome evolution.

genomics↗

bioRxiv2022

Plethora of QTLs found in Arabidopsis thaliana reveals complexity of genetic variation for photosynthesis in dynamic light conditions

The environments in which plant species evolved are now generally understood to be dynamic rather than static. Photosynthesis has to operate within these dynamic environments, such as sudden changes to light intensities. Plants have evolved photoprotection mechanisms that prevent damage caused by sudden changes to high light intensities. The extent of genetic variation within plants species to deal with these dynamic light conditions remains largely unexplored. Here we show that one accession of A. thaliana has a more efficient photoprotection mechanism in dynamic light conditions, compared to six other accessions. The construction of a doubled haploid population and subsequent phenotyping in a dynamically controlled high-throughput system reveals up to 15 QTLs for photoprotection. Identifying the causal gene underlying one of the major QTLs shows that an allelic variant of cpFtsY results in more efficient photoprotection under high and fluctuating light intensities. Further analyses reveal this allelic variant to be overprotecting, reducing biomass in a range of dynamic environmental conditions. This suggests that within nature, adaptation can occur to more stressful environments and that revealing the causal genes and mechanisms can help improve the general understanding of photosynthetic functioning. The other QTLs possess different photosynthetic properties, and thus together they show how there is ample intraspecific genetic variation for photosynthetic functioning in dynamic environments. With photosynthesis being one of the last unimproved components of crop yield, this amount of genetic variation for photosynthesis forms excellent input for breeding approaches. In these breeding approaches, the interactions with the environmental conditions should however be precisely assessed. Doing so correctly, allows us to tap into natures solution to challenging environmental conditions.

plant biology↗

bioRxiv2018

Linked-read sequencing of gametes allows efficient genome-wide analysis of meiotic recombination

Meiotic crossovers (COs) ensure proper chromosome segregation and redistribute the genetic variation that is transmitted to the next generation. Existing methods for CO identification are challenged by large populations and the demand for genome-wide and fine-scale resolution. Taking advantage of linked-read sequencing, we developed a highly efficient method for genome-wide identification of COs at kilobase resolution in pooled recombinants. We first tested this method using a pool of Arabidopsis F2 recombinants, and obtained results that recapitulated those identified from the same plants using individual whole-genome sequencing. By applying this method to a pool of pollen DNA from a single F1 plant, we established a highly accurate CO landscape without generating or sequencing a single recombinant plant. The simplicity of this approach now enables the simultaneous generation and analysis of multiple CO landscapes and thereby allows for efficient comparison of genotypic and environmental effects on recombination, accelerating the pace at which the mechanisms for the regulation of recombination can be elucidated.

bioinformatics↗

bioRxiv2018

Reciprocal cybrids reveal how organellar genomes affect plant phenotypes

Assessing the impact of variation in chloroplast and mitochondrial DNA (collectively termed the plasmotype) on plant phenotypes is challenging due to the difficulty in separating their effect from nuclear derived variation (the nucleotype). Haploid inducer lines can be used as efficient plasmotype donors to generate new plasmotype-nucleotype combinations (cybrids)(Ravi et al., 2014). We generated a panel comprising all possible cybrids of seven Arabidopsis thaliana accessions and extensively phenotyped these lines for 1859 phenotypes under stable and fluctuating conditions. We show that natural variation in the plasmotype results in additive as well as epistatic effects across all phenotypic categories. Plasmotypes which induce more additive phenotypic changes also cause more significant epistatic effects, suggesting a possible common basis for both additive and epistatic effects. On average epistatic interactions explained twice as much of the variance in phenotypes as additive plasmotype effects. The impact of plasmotypic variation was also more pronounced under fluctuating and stressful environmental conditions. Thus, the phenotypic impact of variation in plasmotypes is the outcome of multilevel Nucleotype X Plasmotype X Environment interactions and, as such, the plasmotype is likely to serve as a reservoir of variation which is only exposed under certain conditions. The production of cybrids using haploid inducers is a quick and precise method for assessing the phenotypic effects of natural variation in organellar genomes. It will facilitate efficient screening of unique nucleotype-plasmotype combinations to both improve our understanding of natural variation in nucleotype plasmotype interactions and identify favourable combinations to improve plant performance.

genetics↗