Biology subjects

Pe, M. E.

Publications and source records attributed to Pe, M. E..

3 recordsLinked to original sources

bioRxiv2023

The genetic basis of dynamic non-photochemical quenching and photosystem II efficiency in fluctuating light reveals novel molecular targets for maize (Zea mays) improvement

Maize (Zea mays L.) is a major global crop species which uses C4 photosynthesis. Although C4 is typically considered to be more efficient than C3 photosynthesis, especially under warmer and drier conditions, there is substantial evidence that its efficiency can still be further improved, which may benefit crop performance. Improving photosynthetic efficiency via targeted manipulation of non-photochemical quenching has focused on a limited set of genes that are known to be important determinants of the NPQ response in C3 plants. The C4 pathway may alter NPQ responses but only relatively few studies have explored genetic variation in NPQ kinetics in species that perform C4 photosynthesis. In addition, studies of NPQ responses in field-grown plants of either C3 or C4 species are especially limited. Here we apply high-definition phenotyping of NPQ responses and photosynthetic efficiency and quantitative trait locus (QTL) mapping using a field-grown maize Multi-parent Advanced Generation Inter-Cross (MAGIC) population, which combines the allelic diversity of eight contrasting inbred lines. We find substantial and consistent variation for dynamic NPQ and PSII efficiency for two subsequent field seasons. Further exploration of candidate genes within three major QTL regions identified a strong impact of allelic variation in expression of the minor PSII antenna protein CP24 (LHCB6) on a major QTL for NPQ and efficiency of PSII photochemistry on chromosome 10.

plant biology↗

bioRxiv2022

Genomic and bioclimatic diversity of Ethiopian barley (Hordeum vulgare L.) landraces reveals vulnerability to climate change

The climate crisis is impacting agroecosystems of the global South, threatening the food security of millions of smallholder farmers. Understanding the effect of current and future climates on crop agrobiodiversity may guide breeding efforts and adaptation strategies to sustain the livelihoods of farmers cropping in challenging conditions. Here, we combine a genomic and climatic characterization of a large collection of traditional barley varieties from Ethiopia, key to food security in local smallholder farming systems. We employ data-driven approaches to characterize their local adaptation to current and future climates and identify barley genomic regions with potential for breeding for local adaptation. We used a sequencing approach to genotype at high- density 436 barley varieties, finding that their genetic diversity can be traced back to geography and environmental diversity in Ethiopia. We integrate this information in a genome-wide association study targeting phenology traits measured in common garden experiments as well as climatic features at sampling points of traditional varieties, describing 106 genomic loci associated with local adaptation. We then employ a machine learning approach to link barley genomic diversity with climate variation, estimating barley genomic offset in future climate scenarios. Our data show that the genomic characterization of traditional agrobiodiversity coupled with climate modelling may contribute to the mitigation of the climate crisis effects on smallholder farming systems.

genetics↗

bioRxiv2018

Long non-coding RNAs in wild wheat progenitors

Triticum urartu and Aegilops tauschii are the diploid progenitors of the hexaploid Triticum aestivum (AuAuBBDD), donors of the Au and D genome respectively. In this work we investigate the long noncoding RNAs (lncRNAs) component of the genomes of these two wild wheat relatives. Sixty-eight RNA-seq libraries generated from several organs and conditions were retrieved from public databases. We annotated and characterized 14,515 T. urartu and 20,908 Ae. tauschii bona-fide lncRNA transcripts that show features similar to those of other plant and animal counterparts. Thousands of lncRNAs were found significantly modulated in different organs and exhibited organ specific expression, with a predominant accumulation in the spike, fostering the hypothesis of their crucial role in reproductive organs. Most of the organ-specific lncRNAs were found associated with transposable elements (TEs), indicating the possible role of TEs in lncRNA origin, differentiation and function. The majority of T. urartu and Ae. tauschii lncRNAs appear to be species-specific; nevertheless, we found some lncRNAs conserved between the two wheat progenitors, highlighting the presence and conservation of exonic splicing enhancers sites in multi-exon conserved lncRNAs. In addition, we found cases of lncRNA conservation and their cis regulatory regions spanning the wheat pre-domestication and post-domestication period. Altogether, these results represent the first comprehensive genome-wide encyclopedia of lncRNAs in wild wheat relatives, and they provide clues as to the hidden regulatory pathway mediated by long noncoding RNAs in these largely unexplored wheat progenitors.

plant biology↗