Biology subjects

Lage, J.

Publications and source records attributed to Lage, J..

5 recordsLinked to original sources

bioRxiv2026

Extending the seasons at both ends? Understanding the physiological and genetic context required for stay green mediated yield increase in wheat (Triticum aestivum)

Flowering time and monocarpic senescence are tightly environmentally and genetically controlled. Typically, early flowering and staygreen traits are associated with opposing life-history strategies; stress avoidance versus adaptation; with flowering time an overarching regulator of crop cycle length. We developed RIL populations segregating for Ppd-1 and NAM-1 variation, which are otherwise isogenic. Multi-year field experiments enabled exploration and uncoupling of the relationship between heading and staygreen traits. Heading date manipulation enabled introduction of staygreen traits to their target breeding environments, characterised by a hot-finish. Under moderate stress, we report a 2.9% and 1.9% increase in grain width (P<0.0001), and 5.8% and 3.7% increase in TGW (P<0.0001), plus significantly greater yield (P<0.1) for late heading staygreen RILs homozygous for NAM-A1, and NAM-D1 missense variants, respectively. Grain yield increases were proportionate to the delay in senescence, being greater for the NAM-A1 than the NAM-D1 variant. For RIL populations segregating for both traits, senescence variation was observed relative to heading-date. Regarding grain yield, the staygreen trait-associated increase in source size could not compensate for the Ppd-1a associated pleiotropic reduction in sink size, even under hypothesised continental target breeding environments, with trait competition identified. Therefore, to maximise the benefits associated with staygreen traits, especially in early-heading favouring environments required targeted manipulation of source-sink dynamics, and we propose multiple strategies. HighlightStaygreen traits were associated with extending grain fill duration, increasing grain width, TGW and grain yield. There appears an antagonist relationship between earlier heading and staygreen traits.

plant biology↗

bioRxiv2020

Capturing and Selecting Senescence Variation in Wheat

Senescence is a highly quantitative trait, but in wheat the genetics underpinning senescence regulation remain relatively unknown. To select senescence variation, and ultimately identify novel genetic regulators, accurate characterisation of senescence phenotypes is essential. When investigating senescence, phenotyping efforts often focus on, or are limited to, visual assessment of the flag leaves. However, senescence is a whole plant process, involving remobilisation and translocation of resources into the developing grain. Furthermore, the temporal progression of senescence poses challenges regarding trait quantification and description, whereupon the different models and approaches applied result in varying definitions of apparently similar metrics. To gain a holistic understanding of senescence we phenotyped flag leaf and peduncle senescence progression, alongside grain maturation. Reviewing the literature, we identified techniques commonly applied in quantification of senescence variation and developed simple methods to calculate descriptive and discriminatory metrics. To capture senescence dynamism, we developed the idea of calculating thermal time to different flag leaf senescence scores, for which between year Spearmans rank correlations of r [≥] 0.59, P < 4.7 x 10-5(TT70), identify as an accurate phenotyping method. Following our experience of senescence trait genetic mapping, we recognised the need for singular metrics capable of discriminating senescence variation, identifying Thermal Time to Flag Leaf Senescence score of 70 (TT70) and Mean Peduncle senescence (MeanPed) scores as most informative. Moreover, grain maturity assessments confirmed a previous association between our staygreen traits and grain fill extension, illustrating trait functionality. Here we review different senescence phenotyping approaches and share our experiences of phenotyping two independent RIL populations segregating for staygreen traits. Together, we direct readers towards senescence phenotyping methods we found most effective, encouraging their use when investigating and discriminating senescence variation of differing genetic bases, and to aid trait selection and weighting in breeding and research programs alike.

plant biology↗

bioRxiv2020

Delaying or Delivering: Identification of novel NAM-1 alleles which delay senescence to extend grain fill duration of wheat

Senescence is a complex quantitative trait under genetic and environmental control, involving the remobilisation of resources from vegetative tissue into grain. Delayed senescence, or staygreen traits, are associated with conferring stress tolerance, with extended photosynthetic activity hypothesised to sustain grain filling. The genetics of senescence regulation are largely unknown, with senescence variation often correlated with phenological traits. Here, we confirm staygreen phenotypes of two Triticum aestivum cv. Paragon EMS mutants previously identified during a forward genetic screen and selected for their agronomic performance, similar phenology and differential senescence phenotypes. Through grain filling experiments, we confirm a positive relationship between onset of senescence and grain fill duration, reporting an associated [~]14 % increase in final dry grain weight for one mutant, P < 0.05. Recombinant Inbred Line (RIL) populations segregating for senescence were developed for trait mapping purposes, and phenotyped over multiple years under field conditions. Staygreen traits were mapped using exome-capture enabled bulk segregant analysis (BSA), whereupon senescence was quantified, and metrics compared to qualify senescence traits and aid RIL selection. Using BSA we mapped our two staygreen traits to two independent, dominant, loci of 4.8 and 16.7 Mb in size encompassing 56 and 142 genes. Combining single marker association analysis with variant effect prediction, we identified SNPs encoding self-validating mutations located in NAM-1 homoeologues and propose these as gene candidates. SummaryApplying an exome-capture enabled Bulk Segregant Analysis, we identified novel NAM-1 alleles underpinning two staygreen traits associated with enhancing grain fill duration and grain weight

plant biology↗

bioRxiv2019

Allele-specific miRNA-binding analysis identifies candidate target genes for breast cancer risk

Most breast cancer (BC) risk-associated variants (raSNPs) identified in genome-wide association studies (GWAS) are believed to cis-regulate the expression of genes. We hypothesise that cis-regulatory variants contributing to disease risk may be affecting miRNA genes and/or miRNA-binding. To test this we adapted two miRNA-binding prediction algorithms -- TargetScan and miRanda -- to perform allele-specific queries, and integrated differential allelic expression (DAE) and expression quantitative trait loci (eQTL) data, to query 150 genome-wide significant (P [≤] 5 x 10-8) raSNPs, plus proxies. We found that no raSNP mapped to a miRNA gene, suggesting that altered miRNA targeting is an unlikely mechanism involved in BC risk. Also, 11.5% (6 out of 52) raSNPs located in 3UTRs of putative miRNA target genes were predicted to alter miRNA::mRNA pair binding stability in five candidate target genes. Of these, we propose RNF115, at locus 1q21.1, as a strong novel target gene associated with BC risk, and re-inforce the role of miRNA mediated cis-regulation at locus 19p13.11. We believe that integrating allele-specific querying in miRNA-binding prediction, and data supporting cis-regulation of expression, improves the identification of candidate target genes in BC risk, as well as in other common cancers and complex diseases.

cancer biology↗

bioRxiv2018

The effects of training population design on genomic prediction accuracy in wheat

Genomic selection offers several routes for increasing genetic gain or efficiency of plant breeding programs. In various species of livestock there is empirical evidence of increased rates of genetic gain from the use of genomic selection to target different aspects of the breeders equation. Accurate predictions of genomic breeding value are central to this and the design of training sets is in turn central to achieving sufficient levels of accuracy. In summary, small numbers of close relatives and very large numbers of distant relatives are expected to enable accurate predictions.\n\nTo quantify the effect of some of the properties of training sets on the accuracy of genomic selection in crops we performed an extensive field-based winter wheat trial. In summary, this trial involved the construction of 44 F2:4 bi- and triparental populations, from which 2992 lines were grown on four field locations and yield was measured. For each line, genotype data were generated for 25,000 segregating single nucleotide polymorphism markers. The overall heritability of yield was estimated to 0.65, and estimates within individual families ranged between 0.10 and 0.85. Within cross genomic prediction accuracies of yield BLUEs were 0.125 - 0.127 using two different cross-validation approaches, and generally increased with training set size. Using related crosses in training and validation sets generally resulted in higher prediction accuracies than using unrelated crosses. The results of this study emphasize the importance of the training set design in relation to the genetic material to which the resulting prediction model is to be applied.

genetics↗