Biology subjects

Gutaker, R. M.

Publications and source records attributed to Gutaker, R. M..

7 recordsLinked to original sources

bioRxiv2026

Historical rice samples from the 1950s reveal pre-modern-breeding population structure in indica landraces of mainland Southeast Asia

Understanding crop population history requires genetic material that predates modern breeding. Here, we analyzed historical seeds of rice landraces assembled in Southeast Asia from 1957 to 1958. Target capture resequencing of coding regions yielded high-quality genomic data from 66 historical accessions (seven from North Vietnam, 30 from South Vietnam, 13 from Cambodia, two from Laos, and 14 from Thailand). When integrated with published rice panels, all historical accessions were assigned to indica, and the previously described major regional structure was recovered. Within the historical collection, South Vietnamese, Cambodian, and Thai accessions formed a largely continuous group, whereas North Vietnamese accessions were clearly distinct and comprised two differentiated groups corresponding to the traditional growth seasons (fifth- and tenth-month rice). Notably, the fifth-month rice accessions were assigned to the recently reported Vietnam-I5 cluster. Admixture graph, f-statistics, and qpAdm analyses further indicated that Vietnam-I5 is closely related to a China-associated lineage; however, this relationship was not fully explained by sampled indica, japonica, or aus proxies. Together, these results show that major components of the present-day indica regional structure were already present before modern cultivar replacement, and highlight northern Vietnam as a historical zone of lineage differentiation between Chinese and mainland Southeast Asian rice. HighlightGenomic analyses of historical indica rice seeds reveal that a distinctive northern Vietnamese lineage and a genetic continuum across southern Vietnam, Cambodia, and Thailand predated modern cultivar replacement.

plant biology↗

bioRxiv2026

Historical plant embryos as alternative sources of ancient DNA for whole genome sequencing

Natural history and agricultural collections, which contain hundreds of millions of specimens classified in terms of time, space, and taxonomy, are valuable resources for diverse fields of research. Since the first success of ancient DNA (aDNA) isolation in the 1980s, these repositories, including herbaria for plants, have been intensively used to support studies in taxonomy, macroevolution, and genetic responses to anthropogenic activities over the past centuries. Two major challenges of aDNA research are environmental contamination and DNA degradation. For herbarium specimens, aDNA is usually extracted from leaf samples. It is highly fragmented (typically length of 50 to 100 bp) with a higher breakdown rate than that in most bone remains. To optimise the amount of data retrieved and minimise destructive sampling, we isolated DNA from an unconventional plant tissue type - seed embryos. We carried out whole-genome sequencing and compared sequenced DNA quality between embryo and leaf tissue. We evaluated endogenous DNA proportion, median fragment length, damage fraction per site ({lambda}), decay rates, nucleotide misincorporations, and library complexity for three species: cultivated rice Oryza sativa, wild rice O. rufipogon, and wild barley Hordeum spontaneum. In O. sativa, embryos exhibited significantly higher endogenous content and median fragment length than leaves, while in O. rufipogon only median fragment length was higher. The superior DNA preservation was likely due to the protective role of the seed husk, which might play an important role in DNA preservation in plants collected in the tropics. By contrast, in temperate H. spontaneum, tissue type had minimal impact on DNA quality. Despite the minuscule size of the embryos, all derived genomic libraries were highly complex, sufficient for deep whole genome sequencing. These results highlight seed embryos as a promising alternative aDNA source for millions of herbarium specimens, and enable effective genomic analyses of other historical plant collections, such as economic botany and anthropological museum collections.

genomics↗

bioRxiv2025

Patterns of aDNA Damage Through Time end Environments, lessons from herbarium specimens

Herbarium collections are a vast but underutilized resource for ancient DNA research, containing over 400 million specimens with detailed metadata and spanning centuries of global biodiversity. Understanding patterns of DNA preservation in natural collections is crucial for optimizing ancient DNA studies and informing future curation practices. We analysed genomic data for 573 herbarium specimens from six plant species from the genera Hordeum and Oryza collected from the Americas and Eurasia over 220 years. Using standardized laboratory protocols and shotgun sequencing, we quantified DNA degradation and elucidated factors that accelerate it. We find significant age-dependent DNA fragmentation rates, indicating temporal degradation processes not detected in prehistoric samples. In our analysis, DNA decay rates in herbarium specimens were almost eight times faster than in moa bones, reflecting fundamental differences in tissue composition and preservation environments. Environmental conditions at the time of specimen collection emerged as the major determinants of post-mortem damage rates, with the interaction term between temperature and genus being the dominant driver of cytosine deamination. We find no effect of sample storage on DNA damage and degradation. These findings provide insights into how climatic origin, preservation environment, taxonomic identity and age influence DNA preservation while highlighting opportunities for improving institutional preservation practices. Due to standardised preservation conditions, museum collections can provide better insights into DNA damage and degradation over time than archaeological and paleontological samples.

molecular biology↗

bioRxiv2025

Impacts of climate change on fonio millet: in-vitro seed germination and suitability modelling of an important indigenous West African crop

Seed germination is highly temperature sensitive. Climate change factors such as increasing temperatures are likely to have a harmful effect on agriculture, particularly after crop sowing. Better utilisation of indigenous, arid-resilient crops like fonio (Digitaria exilis) are a commonly proposed solution to improving food security. This study develops knowledge of fonio germination requirements and how these correspond to future climate conditions across West Africa. We use a combined approach; integrating seed germination experiments under a range of temperatures, and niche suitability modelling to investigate how cultivation of fonio will be impacted by climate change. We find that from 37 seed accessions collected across Guinea, Togo, Mali, and Burkina Faso, the ceiling temperature for germination is around 42{degrees}C, with an optimum temperature of 30-35{degrees}C - also noted from phenotypic observations. Drought trials show successful germination to beyond -1MPa. There is no obvious difference in response by accessions originating from either hotter or cooler climates. By comparing these temperature thresholds with future climate predictions, alongside a suitability modelling approach, we predict an average decline of 10% in the suitable area for fonio cultivation, especially affecting Senegal, Mali, and Burkina Faso. Newly suitable area is predicted to increase in Guinea, Ghana, Cote dIvoire, and Nigeria by around 5%. These findings provide valuable insight for developing future dryland agriculture policies and prioritisation of resilient crops.

plant biology↗

bioRxiv2020

Archaeogenomics of a ~2,100-year-old Egyptian leaf provides a new timestamp on date palm domestication

O_LIThe date palm (Phoenix dactylifera) has been a cornerstone of Middle Eastern and North African agriculture for millennia. It is presumed that date palms were first domesticated in the Persian Gulf and subsequently introduced into North Africa, where their evolution in the latter region appears to have been influenced by gene flow from the wild relative P. theophrasti, which is restricted to Crete and Turkey. However, the timing of gene flow from P. theophrasti to P. dactylifera remains unknown due to the limited archaeobotanical evidence of P. theophrasti and their exclusion from population genomic studies. C_LIO_LIWe addressed this issue by investigating the relatedness and ancestry of a ~2,100-year-old P. dactylifera leaf from Saqqara (Egypt), combining genome sequencing of this ancient specimen with a broad sample of date palm cultivars and closely related species. C_LIO_LIThe ancient Saqqara date palm shares close genetic ancestry with North African date palm populations. We find clear genomic admixture between the Saqqara date palm, P. theophrasti and the closest known relative P. sylvestris. C_LIO_LIOur study highlights that gene flow from P. theophrasti and P. sylvestris to North African date palms had already occurred at least ~2,100 years ago, providing a minimum timestamp for hybridisation between species. C_LI

evolutionary biology↗

bioRxiv2019

Genomic history and ecology of the geographic spread of rice

Rice (Oryza sativa) is one of the worlds most important food crops. We reconstruct the history of rice dispersal in Asia using whole-genome sequences of >1,400 landraces, coupled with geographic, environmental, archaeobotanical and paleoclimate data. We also identify extrinsic factors that impact genome diversity, with temperature a leading abiotic factor. Originating [~]9,000 years ago in the Yangtze Valley, rice diversified into temperate and tropical japonica during a global cooling event [~]4,200 years ago. Soon after, tropical rice reached Southeast Asia, where it rapidly diversified starting [~]2,500 yBP. The history of indica rice dispersal appears more complicated, moving into China [~]2,000 yBP. Reconstructing the dispersal history of rice and its climatic correlates may help identify genetic adaptation associated with the spread of a key domesticated species.\n\nOne sentence summaryWe reconstructed the ancient dispersal of rice in Asia and identified extrinsic factors that impact its genomic diversity.

evolutionary biology↗

bioRxiv2018

Modulation of ACD6 dependent hyperimmunity by natural alleles of an Arabidopsis thaliana NLR resistance gene

Plants defend themselves against pathogens by activating an array of immune responses. Unfortunately, immunity programs may also cause unintended collateral damage to the plant itself. The quantitative disease resistance gene ACCELERATED CELL DEATH 6 (ACD6) serves as a nexus for the trade-off between growth and pathogen resistance in wild populations of Arabidopsis thaliana. An autoimmune allele, ACD6-Est, first identified in the natural accession Est-1, is found in over 10% of wild strains, even though it causes a clear fitness penalty under optimal growth conditions. There is, however, extensive variation in the strength of the autoimmune phenotype expressed by strains with an ACD6-Est allele, indicative of genetic modifiers. Quantitative genetic analysis suggests that the population genetic basis of ACD6 modulation is complex, with different strains often carrying different large-effect modifiers. One modifier is SUPPRESSOR OF NPR1-1, CONSTITUTIVE 1 (SNC1), located in a highly polymorphic cluster of nucleotide-binding domain and leucine-rich repeat (NLR) immune receptor genes, which are prototypes for qualitative disease resistance genes. Allelic variation at SNC1 correlates with ACD6-Est activity in multiple accessions, and a common structural variant affecting the NL linker sequence can explain differences in SNC1 activity. Taken together, we find that an NLR gene can mask the activity of an ACD6 autoimmune allele in natural A. thaliana populations, thereby linking different arms of the plant immune system.\n\nAuthor summaryPlants defend themselves against pathogens by activating immune responses. Unfortunately, these can cause unintended collateral damage to the plant itself. Nevertheless, some wild plants have genetic variants that confer a low threshold for the activation of immunity. While these enable a plant to respond particularly quickly to pathogen attack, such variants might be potentially dangerous. We are investigating one such variant of the immune gene ACCELERATED CELL DEATH 6 (ACD6) in the plant Arabidopsis thaliana. We discovered that there are variants at other genetic loci that can mask the effects of an overly active ACD6 gene. One of these genes, SUPPRESSOR OF NPR1-1, CONSTITUTIVE 1 (SNC1), codes for a known immune receptor. The SNC1 variant that attenuates ACD6 activity is rather common in A. thaliana populations, suggesting that new combinations of the hyperactive ACD6 variant and this antagonistic SNC1 variant will often arise by natural crosses. Similarly, because the two genes are unlinked, outcrossing will often lead to the hyperactive ACD6 variants being unmasked again. We propose that allelic diversity at SNC1 contributes to the maintenance of the hyperactive ACD6 variant in natural A. thaliana populations.

plant biology↗