Recent ipnc items

Structure and sequence evolution in the pennycress (Thlaspi arvense) pangenome

Thu, 14 May 2026 00:00:00 +0000

Eukaryotic genomes harbor many forms of variation, including nucleotide diversity and structural polymorphisms, which experience natural selection and contribute to genome evolution and biodiversity. Harnessing this variation for agriculture hinges on our ability to detect, quantify, catalog, and deploy genetic diversity. Here, we explore seven complete genomes of the emerging biofuel crop pennycress (Thlaspi arvense) drawn from across the species' current genetic diversity to catalog variation in genome structure and content. Across this new pangenome resource, we find contrasting evolutionary modes in different genomic zones. Gene-poor, repeat-rich pericentromeric regions experience frequent rearrangements, including repeated centromere repositioning. By contrast, conserved gene-dense chromosome arms maintain large-scale synteny across accessions even in fast-evolving NOD-like receptor immune genes, where microsynteny breaks down across species, but gene cluster positioning...

Labile carbon dynamics under initial transition to regenerative agriculture

Sun, 26 Apr 2026 00:00:00 +0000

Understanding the dynamics of labile organic carbon (LOC) is critical for evaluating the short-term impacts of regenerative agricultural practices on soil health. We assessed changes in key LOC fractions such as permanganate oxidizable carbon (POXC) measured by 0.01 M, 0.02 M, 0.033 M potassium permanganate, microbial biomass carbon (MBC), and very labile carbon (CVL) across four long-term conservation agriculture (CA) experiment sites located in contrasting agro-ecological zones of South Asia namely Karnal, Patna, Aduthurai, and Gazipur. At each site, four cropping system scenarios (S) were evaluated: S1, current farmers practice; S2, current farmers cropping system with partial CA; S3, current farmers cropping system with full CA; and S4, diversified crop rotation with full CA. Soil samples were collected from 0–15 and 15–30 cm depth after two cropping cycles. Results showed that POXC, MBC, CVL, oxidizable organic carbon (SOC) and total organic carbon (TOC) increased following...

No-till in rice systems: A global meta-analysis of key agronomic practices impacting yields

Fri, 24 Apr 2026 00:00:00 +0000

Context While no-till (NT), one of the pillars of conservation agriculture, is widely practiced in upland crops, considerably less research has been conducted in rice systems. While adoption has been limited, numerous field experiments have evaluated NT rice across diverse regions and management contexts yet reported yield responses to key agronomic practices, soil properties, and climatic conditions remain inconsistent and poorly synthesized at a global scale. Objective Our objective was to conduct a global meta-analysis comparing the effects of NT to conventional tillage (CT) on rice yields and to identify the agronomic practices, soil characteristics, and climate factors most strongly associated with yield changes under NT. Methods We performed a global meta-analysis of 115 studies (579 paired observations) comparing rice yields under NT and CT. Yield response ratios (lnRR) were analyzed using mixed-effects meta-analysis to estimate overall effects. Meta-regression and Random...

Association Between Observed Climate Change and Cardiovascular Disease in the United States

Thu, 23 Apr 2026 00:00:00 +0000

Climate change is affecting nearly all social and environmental determinants of health. However, the extent of resulting cumulative impacts on cardiovascular and other noncommunicable diseases is not known. To address this gap and inform future research, we conducted an ecological evaluation of associations between 14 long-term climate anomaly metrics and prevalence of coronary heart disease (CHD) and stroke in the United States. We calculated long-term anomaly metrics as the difference between their respective 1970-1979 baseline mean and 2013-2022 modern mean values. With fitted random effects regression analysis, we evaluated associations between each anomaly metric, individually and collectively, and census tract-level 2020-2022 mean prevalence of CHD and stroke. In adjusted models with all noncollinear anomaly metrics, we found a net association of all metrics with 0.59% higher CHD prevalence and 0.88% higher stroke prevalence (9.8% and 27.9% relative prevalence, respectively)....

Target-site mechanism confers resistance pattern of ACCase inhibitors in bearded sprangletop (Leptochloa fusca ssp. fascicularis) from California

Wed, 22 Apr 2026 00:00:00 +0000

Abstract Bearded sprangletop is a problematic native grass weed in California’s rice fields. The widespread and extensive use of acetyl-CoA carboxylase (ACCase)–inhibiting herbicides, such as cyhalofop- p -butyl (cyhalofop), has led to speculation that biotypes of bearded sprangletop have developed herbicide resistance to ACCase. The aim of this study was to evaluate suspected resistant bearded sprangletop biotypes, R1, R2, R3, and the susceptible biotype, S1, in terms of their levels of resistance to three ACCase-inhibiting herbicides and to characterize the molecular mechanisms of resistance. Dose–response experiments suggested that the biotype R1, R2, and R3 had high-level resistance to cyhalofop and to quizalofop- p -ethyl (quizalofop), but not clethodim. The study determined that the resistance to ACCase inhibitors was a target-site mechanism resulting from nucleotide substitution. The carboxyl transferase (CT) domain of the ACCase gene’s sequence analysis revealed the substitutions...

DNA methylation is conserved between vegetative propagules in almond (Prunus dulcis Mill DA Webb)

Wed, 22 Apr 2026 00:00:00 +0000

DNA methylation is conserved between vegetative propagules in almond (Prunus dulcis Mill DA Webb)

Multi-environment evaluation and genomic prediction of agronomic traits in the southern US rice genepool.

Wed, 8 Apr 2026 00:00:00 +0000

The southern United States is responsible for 80% of the countrys production of rice, approximately half of which is exported. Understanding genotypic and environmental factors impacting the historical performance of rice (Oryza sativa L.) is important for directing research efforts to optimize production of this globally important crop. A set of 429 rice genotypes including globally diverse historical parents and advanced japonica breeding lines from southern US breeding programs was phenotyped in 2008 for eight agronomic traits in Arkansas, Louisiana, and Mississippi. They were also genotyped using a single-nucleotide polymorphism set optimized for genomic prediction/selection. Genotypic and phenotypic data were analyzed via clustering techniques and principal component analysis. Single-trait and multi-trait genomic prediction were used to predict genetic values on a per-plant basis. We found that contemporary germplasm from the southern state breeding programs was highly interrelated...

Effect of physiological priming on stored coffee seeds

Wed, 25 Mar 2026 00:00:00 +0000

Abstract: The physiological priming has been used to standardize and increase the speed of development of seed lots. The use of this technique is essential in coffee cultivation, as the crop has low longevity associated with slow and uneven germination. The objective was to evaluate the effect of physiological priming on the physiological quality of coffee seeds stored with different water contents. Seeds of two cultivars of Coffea arabica were used: cv. Catuaí Vermelho IAC144 and Topázio MG1190. A portion of the seeds were dried in the shade until reaching 12% moisture, and the other did not undergo drying. The seeds were stored in a cold chamber at 10 °C for nine months. Every three months, the physiological priming technique was performed with subsequent evaluation of the physiological quality by germination tests, root protrusion, normal seedlings at fifteen days, strong normal seedlings, seedlings with expanded cotyledonary leaves and seedling dry weight. Seeds that did not...

Trait‐based approaches to restoration ecology: Synthesizing insights from diverse systems

Wed, 25 Mar 2026 00:00:00 +0000

Under accelerating global change, trait-based approaches are emerging as essential tools in the ecological restoration toolbox. Where restoration has traditionally focused on the recovery of focal species in isolated systems, trait-based methods can provide a common language that extends beyond species- or system-specific contexts, allowing scientists and practitioners to translate insights across organisms and ecosystems and predict functional variation critical to resilience in the face of rapidly changing environmental conditions. Trait-based insights can thus help achieve restoration that is both adaptable and scalable as future climate scenarios unfold. To date, trait-based approaches to restoration have developed and proceeded independently across habitats and ecosystems, limiting information sharing and innovation. Here, we synthesize diverse perspectives and research on trait-informed restoration across ecosystems, distilling our findings into three key insights. First,...

Vigor of maize seeds and its effects on plant stand establishment, crop development and grain yield

Wed, 25 Mar 2026 00:00:00 +0000

Vigor of maize seeds and its effects on plant stand establishment, crop development and grain yield

Lignin content, morphoanatomical traits and antioxidant activity as determinants of soybean seed storage tolerance and quality

Wed, 25 Mar 2026 00:00:00 +0000

The storage of soybean seeds is a critical aspect of the production process, making it essential for genotypes to show tolerance during this phase to maintain seed quality. This study aimed to examine and correlate lignin content in the seed coat, enzyme activity expression, and morphoanatomical characteristics of soybean cultivars with the preservation of physiological quality and storage tolerance. Eight soybean cultivars were selected, produced, and harvested under uniform edaphoclimatic conditions. Physiological quality assessments were conducted at six storage intervals: 0, 60, 120, 180, 240, and 360 days. Evaluations included tests for germination, emergence, accelerated aging, electrical conductivity, and lignin content in the seed coat. Additionally, biochemical and enzymatic analyses of antioxidant metabolism and morphoanatomical examinations were performed using light microscopy on seeds stored for 0 and 360 days. The experiment used an 8 × 6 factorial arrangement, encompassing...

Comparative genomics of six Juglans species reveals disease‐associated gene family contractions