Rafal Marek Gutaker

Rice (Oryza sativa), one of the key domesticated cereal crops, is comprised of several subspecies or variety groups. A major variety group, O. sativa var. indica, was domesticated in the Indian subcontinent ∼4,500 years ago via introgression of domestication alleles from var. japonica and today represents the predominant rice that is grown worldwide, particularly in tropical and subtropical regions in Asia. Using genome data from 957 indica landraces, including 194 newly re-sequenced cultivars and 38 herbarium specimens collected over the last 167 years, we reconstruct how indica rice moved from the Indian subcontinent to other parts of Asia. Unlike japonica rice, indica rice seems to have dispersed relatively recently (within the last 2,500 years) to China, mainland and island Southeast (SE) Asia. Interestingly, we find that the island SE Asia indica rice landraces show gene flow with island SE Asian japonica landraces. We also find significant gene–environment associations of indica rice with local climatic and edaphic variables that may be linked with local adaptation and possible cultural selection for grain quality traits.

Natural history and agricultural collections contain hundreds of millions of specimens classified in terms of time, space and taxonomy. 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. For herbarium specimens, aDNA is usually extracted from leaf samples and is highly fragmented (typically length of 50–100 bp). 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 from the same specimen. We evaluated endogenous DNA proportion, median fragment length, damage fraction per site ( λ ), decay rates ( k ), 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. 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 herbarium specimens, economic botany and anthropological museum collections.

Understanding crop population history requires genetic material that predates modern breeding. Here, we analysed historical seeds of rice landraces assembled in Southeast Asia during 1957–1958. 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. An 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.

Fonio ( Digitaria exilis (Kippist) Stapf) is an underutilized cereal whose genetic diversity is largely conserved through traditional seed systems managed by smallholder farmers in West Africa. Preserving this diversity is critical for climate adaptation, food security, and future crop improvement, yet empirical evidence on farmer-managed fonio landraces remains limited. This study characterizes farmer-saved fonio landraces and associated seed management practices in Northern Ghana, with emphasis on their role in on-farm conservation of crop genetic resources. Using a stratified random sampling approach, 110 fonio farmers were surveyed across Chereponi, Saboba, Gushegu, Tatale, and Zabzugu districts using structured questionnaires to document identified landraces, seed sources, duration of seed possession, trait preferences, and production practices. The results revealed that fonio cultivation is dominated by farmer-maintained landraces, with Yadema, Kpeintike, Ugabuja, Ipuja and Lipuima being the most cultivated. Most farmers (93%) relied on recycled seed, with some landraces maintained for more than 20 years, indicating strong on-farm conservation. Farmers prioritize traits such as high yield, early maturity, drought tolerance, and ease of dehusking, reflecting both agroecological constraints and post-harvest labour considerations. Fonio production was largely subsistence-oriented, characterized by small farm sizes, with a mean farm size of 1.12 acres (0.453 ha), and low use of external inputs. This study demonstrates that significant fonio genetic resources are conserved through traditional farming practices in Northern Ghana, where there are no formally released commercial cultivars. These findings highlight the need to integrate farmers’ knowledge into participatory breeding and to strengthen community-based seed systems to enhance productivity while safeguarding fonio genetic diversity.

SUMMARY: Understanding crop population history requires genetic material that predates modern breeding. In rice ( Oryza sativa ), extant landraces have revealed a broad regional structure within indica , but the historical depth of these patterns remains uncertain. Here, we analyzed a historical collection of rice landraces assembled in Southeast Asia from 1957 to 1958 (henceforth the Hamada collection). Short-read resequencing yielded 66 high-quality historical samples (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 major regional structure previously described for extant landraces was recovered. Within the Hamada collection, South Vietnamese, Cambodian, and Thai accessions formed a largely continuous mainland Southeast Asian group, whereas North Vietnamese accessions were clearly distinct and comprised two differentiated groups corresponding to two traditional growth seasons (fifth- and tenth-month rice). The fifth-month rice accessions were assigned to the previously reported distinct Vietnam-I5 cluster, showing that this lineage already existed before modern breeding. Admixture graph, f -statistics, and qpWave analyses further indicated that Vietnam-I5 is closely related to a China-associated lineage with a distinct admixture event that cannot be adequately attributed to sampled indica, japonica , or aus groups. Together, these results show that the present-day regional structure of indica was established before modern cultivar replacement, and highlight northern Vietnam as a historical zone of lineage differentiation between Chinese and mainland Southeast Asian rice.

Background and Aims: Seed germination is highly temperature-sensitive, and increasing global temperatures due to climate change are likely to have a strong effect on agriculture. Improved utilisation of indigenous, arid-resilient crops such as fonio (Digitaria exilis) are a commonly proposed solution to improving food security in West Africa. This study develops knowledge of fonio germination requirements and relates them to future predicted climate conditions. Methods: We use an interdisciplinary methodology, integrating extensive laboratory-based seed germination experiments under a range of temperatures, with niche suitability and future climate modelling, to investigate how cultivation of fonio may be impacted by climate change. Key Results: By analysing 37 seed accessions from Guinea, Togo, Mali and Burkina Faso, we estimated the ceiling temperature for germination of this species to be 43 °C (s.d. = ±1.6), with an optimum temperature of 36 °C (s.d. = ±2.2) – as also noted from phenotypic observation of seedlings. There is no obvious difference in response by accessions originating from either hotter or cooler climates. By comparing these temperature thresholds to future climate predictions, tested alongside suitability modelling, we estimate a decline of 7.9–10.45 % in the future suitable area for fonio cultivation, depending on the prediction method, especially affecting Senegal, Mali and Burkina Faso. Newly suitable area is predicted to increase in Guinea, Ghana, Cote d’Ivoire and Nigeria by 5.5 %. Conclusions: Our findings provide valuable insight into the physiology and thermal tolerance of fonio seeds, and identify particularly vulnerable agricultural regions in West Africa which will require additional support. This should include developing future dryland agriculture policies, livelihood projects and resilient crop varieties.

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 ( λ ), 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.

Societal Impact Statement: Promoting agrobiodiversity is a promising strategy for mitigating the negative effects of climate change on global food security. We highlight the central role evolutionary processes play in harnessing the potential of local crops by integrating genomics, archaeology, ethnobotany and traditional ecological knowledge (TEK). Our aim is to empower Indigenous peoples and local communities as key actors in agrobiodiversity and crop innovations, fostering ethical and active collaborations. Local contributions to diversifying the global food system will enhance climate resilience and ensure that the benefits of agricultural innovation are shared more broadly and justly across peoples. Summary: Strengthening diverse agricultural systems can mitigate the effects of accelerated climate change on crop production. Unlocking local crops' potential requires understanding their origins, domestication, fundamental attributes and uses. Here, we review the role of genomics, archaeology and ethnobotany that increased our understanding of crop evolution. We highlight biases in data availability towards globally commercial crops and chart pathways to develop baseline knowledge for local crops. We propose integrating these fields with traditional knowledge to illuminate how cultivation and uses have shaped, and will continue to shape, local crops and promote ethical collaborations. The lessons learnt from the past can help us chart the future of sustainable and climate‐resilient agriculture. Supported with evidence from recent research and traditional knowledge, we propose to orient seed conservation, breeding and accelerated domestication around Indigenous peoples and local communities.

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.

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.