6 Research Papers Published by Savanna Institute Scientists in 2023

1. The first two chromosome-scale genome assemblies of American hazelnut enable comparative genomic analysis of the genus Corylus 

Published in: Plant Biotechnology Journal https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.14199

Written by: Brainard SH, Sanders DM, Bruna T, Shengqiang S, Dawson JC  (2023)

Summary by Authors:

The native, perennial shrub American hazelnut (Corylus americana) is cultivated in the Midwestern United States for its significant ecological benefits, as well as its high-value nut crop. Implementation of modern breeding methods and quantitative genetic analyses of C. americana requires high-quality reference genomes, a resource that is currently lacking. We therefore developed the first chromosome-scale assemblies for this species using the accessions ‘Rush’ and ‘Winkler’. Genomes were assembled using HiFi PacBio reads and Arima Hi-C data, and Oxford Nanopore reads and a high-density genetic map were used to perform error correction. N50 scores are 31.9 Mb and 35.3 Mb, with 90.2% and 97.1% of the total genome assembled into the 11 pseudomolecules, for ‘Rush’ and ‘Winkler’, respectively. Gene prediction was performed using custom RNAseq libraries and protein homology data. ‘Rush’ has a BUSCO score of 99.0 for its assembly and 99.0 for its annotation, while ‘Winkler’ had corresponding scores of 96.9 and 96.5, indicating high-quality assemblies. These two independent assemblies enable unbiased assessment of structural variation within C. americana, as well as patterns of syntenic relationships across the Corylus genus. Furthermore, we identified high-density SNP marker sets from genotyping-by-sequencing data using 1343 C. americana, C. avellana and C. americana × C. avellana hybrids, in order to assess population structure in natural and breeding populations. Finally, the transcriptomes of these assemblies, as well as several other recently published Corylus genomes, were utilized to perform phylogenetic analysis of sporophytic self-incompatibility (SSI) in hazelnut, providing evidence of unique molecular pathways governing self-incompatibility in Corylus.

2. Improving selection efficiency in C. americana × C. avellana interspecific hybrids through the development of an indel-based genetic map

Published in: Acta Hort  https://www.biorxiv.org/content/10.1101/2023.02.05.527175v2

Written by: Brainard SH, Fischbach JA, Braun LC, Dawson JC (2023)

Abstract by Authors:

This study reports a genetic map created using a progeny family descended from the interspecific hazelnut cross Corylus avellana × Corylus americana. This research represents a critical step in the development of genomic tools that enable the deployment of next-generation sequencing methods in the breeding of hazelnut, specifically the improvement of well-adapted Midwestern hazelnut varieties. To produce this map, we first developed high-density molecular markers using short-read Illumina sequencing of genotype-by-sequencing libraries. By aligning reads to a newly assembled reference genome for C. americana, we were able to identify over 75,000 high-quality indel-based polymorphisms across an F1 experimental population. These markers exhibited both high allele depth coverage, and low linkage disequilibrium, making them well-suited to genetic map development. We constructed such a map using 95 individuals from a single F1 family, demonstrating the utility of next-generation sequencing to efficiently and accurately generate high-density genetic maps. This research will improve the efficiency of breeding efforts, both through the validation of specific molecular markers that are associated with agronomically-relevant traits in breeding populations of interest.

4. Poorly drained depressions can be hotspots of nutrient leaching from agricultural soils

Published in: Journal of Environmental Quality 52:678-690. https://acsess.onlinelibrary.wiley.com/doi/full/10.1002/jeq2.20461 

Written by: Hall SJ, Tenesaca CG, Lawrence NC, Green DIS, Helmers MJ, Crumpton WG, Heaton EA, VanLoocke A (2023)

Abstract by Authors:

Much of the US Corn Belt has been drained with subsurface tile to improve crop production, yet poorly drained depressions often still flood intermittently, suppressing crop growth. Impacts of depressions on field-scale nutrient leaching are unclear. Poor drainage might promote denitrification and physicochemical retention of phosphorus (P), but ample availability of water and nutrients might exacerbate nutrient leaching from cropped depressions. We monitored nitrate, ammonium, and reactive P leaching across multiple depression-to-upland transects in north-central Iowa, using resin lysimeters buried and retrieved on an annual basis. Crops included conventional corn/soybean (Zea mays/Glycine max) rotations measured at fields with and without a winter rye (Secale cereale) cover crop, as well as juvenile miscanthus (Miscanthus × giganteus), a perennial grass. Leaching of nitrogen (N) and P was greater in depressions than in uplands for most transects and years. The median difference in nutrient leaching between paired depressions and uplands was 56 kg N ha−1 year−1 for nitrate (p = 0.0008), 0.6 kg N ha−1 year−1 for ammonium (p = 0.03), and 2.4 kg P ha−1 year−1 for reactive P (p = 0.006). Transects managed with a cover crop or miscanthus tended to have a smaller median difference in nitrate (but not ammonium or P) leaching between depressions and uplands. Cropped depressions may be disproportionate sources of N and P to downstream waters despite their generally poor drainage characteristics, and targeted management with cover crops or perennials might partially mitigate these impacts for N, but not necessarily for P.

5. Controls on organic and inorganic soil carbon distribution in a poorly drained agroecosystem with subsurface drainage

Published in: Biogeochemistry 163:121–137 https://link.springer.com/article/10.1007/s10533-023-01026-x; https://dr.lib.iastate.edu/entities/publication/96d3cde4-886c-4584-8f13-10757d3f5680 

Written by: Huang W, Mirabito A, Tenesaca CG, Mejia-Garcia WF, Lawrence N, Kaleita AL, VanLoocke A, Hall SJ (2023)

Abstract by Authors:

Many productive agricultural soils have naturally poor drainage characteristics and may intermittently pond water even where artificial drainage infrastructure is present, especially in topographic depressions. Soil organic carbon (SOC) is often higher in depressions than uplands, but whether temporary ponding increases SOC by suppressing decomposition remains an important knowledge gap. We measured SOC and inorganic C (carbonate) along topographic gradients from tile-drained depressions to adjacent uplands and tested their relationships with hydrological and biogeochemical properties in corn/soybean fields in Iowa, USA, and examined soil respiration and its stable C isotopes (δ13C) by lab incubation. The 0–30 cm SOC concentration was greatest at depression bottoms, as expected, while carbonate C was highest at boundaries between depressions and uplands. However, only carbonate C, not SOC, increased in depressions with increasingly poor drainage (greater ponding duration). Silt + clay content was the strongest positive predictor of SOC, while ponding duration and oxalate-extractable iron were negatively related to SOC in a statistical model (R2 = 0.83). These negative relationships are consistent with suppression of crop biomass production and iron-mediated decomposition in periodically anoxic soil. Soil C/N ratios were similar in depressions and uplands, indicating that plant detritus did not accumulate with ponding. Stable C isotopes of respiration from incubated soils indicated a similar C3/C4 plant mixture in depressions and uplands, consistent with decomposing soybean and corn residues. In contrast, depression soil organic matter had lower δ13C and δ15N values than uplands, more consistent with pre-agricultural prairie plants than crop residues. Accumulation of SOC in these agricultural depressions is more likely explained by erosion than by suppression of decomposition due to temporary ponding. Gaining additional SOC may require fundamental changes in management, or wetland restoration.

6.Evolving conceptions of silvopasture among farmers and natural resource professionals in Wisconsin, USA

Published in: Frontiers in Sustainable Food Systems, Vol. 7. https://doi.org/10.3389/fsufs.2023.983376

Written by: Mayerfeld D, Keeley K, Rickenback M, Rissman A, Ventura S (2023)

Abstract by Authors:

Silvopasture has gained attention as an agroecological practice that may simultaneously meet farmer goals and provide environmental benefits, including climate change mitigation. At the same time there are significant concerns about the potential for livestock to damage trees and forest soils. Like other innovative agroecological systems, silvopasture combines management complexity with limited research knowledge. Unlike annual crops, the effects of silvopasture management can take decades to assess and require forestry as well as agronomic expertise. We conducted mixed-methods research on silvopasture attitudes and knowledge among farmers, agricultural advisors, and foresters in Wisconsin between 2014 and 2019. We asked: (1) How do farmers who practice grazing, agricultural advisors, and foresters perceive silvopasture? and (2) How did coverage of silvopasture change between 2009 and 2019 in a popular grazing publication? Perceptions of silvopasture were influenced by recent weather history, markets for forest and agricultural products, existing land uses, and other contextual factors. Some farmers and agricultural advisors were committed to silvopasture despite significant obstacles to implementing the practice. Over the course of the study period agricultural advisors increased their willingness to provide silvopasture advice to farmers and professional colleagues, and coverage of silvopasture increased in a popular grazing publication. Finally, a multi-county supportive community of practice was associated with greater enthusiasm for the practice. The greater acceptance of silvopasture among resource professionals follows an increase in silvopasture research and outreach in the region. This interest in silvopasture suggests both a need for, and openness to, greater collaboration among forestry and agricultural professionals and farmers to develop sustainable silvopasture standards.

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