Browsing by Author "Lachowiec, Jennifer"

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Adoption of unoccupied aerial systems in agricultural research
(Wiley, 2024-03) Lachowiec, Jennifer; Feldman, Max J.; Inacio Matias, Filipe; LeBauer, David; Gregory, Alexander
A comprehensive survey and subject-expert interviews conducted among agricultural researchers investigated perceived value and barriers to the adoption of unoccupied aerial systems (UASs) in agricultural research. These systems are often referred to colloquially as drones and are composed of unoccupied/uncrewed/unmanned vehicles and incorporated sensors. This study of UASs involved 154 respondents from 21 countries representing various agricultural sectors. The survey identified three key applications considered most promising for UASs in agriculture: precision agriculture, crop phenotyping/plant breeding, and crop modeling. Over 80% of respondents rated UASs for phenotyping as valuable, with 47.6% considering them very valuable. Among the participants, 41% were already using UAS technology in their research, while 49% expressed interest in future adoption. Current users highly valued UASs for phenotyping, with 63.9% considering them very valuable, compared to 39.4% of potential future users. The study also explored barriers to UAS adoption. The most commonly reported barriers were the “High cost of instruments/devices or software” (46.0%) and the “Lack of knowledge or trained personnel to analyze data” (40.9%). These barriers persisted as top concerns for both current and potential future users. Respondents expressed a desire for detailed step-by-step protocols for drone data processing pipelines (34.7%) and in-person training for personnel (16.5%) as valuable resources for UAS adoption. The research sheds light on the prevailing perceptions and challenges associated with UAS usage in agricultural research, emphasizing the potential of UASs in specific applications and identifying crucial barriers to address for wider adoption in the agricultural sector.
Genetic dissection of endosperm hydration in malting barley (Hordeum vulgare)
(Wiley, 2023-08) Jensen, Joseph; Turner, Hannah; Lachowiec, Jennifer; Lutgen, Greg; Yin, Xiang S.; Sherman, Jamie
Hydration of the endosperm is a critical part of the malting process that ensures proper modification of the grain. However, little is known about the genetic controls of endosperm hydration and its relationship to agronomic and malt quality traits. The extent of endosperm hydration is estimated through hydration index (HYI). We measured HYI, agronomic, and malt quality traits on a 169-line subset of the NSGC Barley Core Panel, which includes global malt lines, some dating from the inception of European breeding programmes. Utilizing GWAS, 61 QTLs were identified for HYI, dormancy, agronomic, and malt quality traits. Of these, six were found to be related to HYI and were located on 1H, 2H, 3H, 6H, and 7H. We found HYI QTLs cosegregating with kernel size and hardness (1H and 3H), malting quality (2H and 6H), and dormancy (2H and 6H). These results indicate that endosperm hydration after steeping can be improved by selecting high HYI alleles on 2H, 6H, and 7H, positively impacting malting quality without negatively impacting kernel size or dormancy.
Genetic dissection of natural variation in oilseed traits of camelina by whole-genome resequencing and QTL mapping
(Wiley, 2021-06) Li, Huang; Hu, Xiao; Lovell, John T.; Grabowski, Paul P.; Mamidi, Sujan; Chen, Cindy; Amirebrahimi, Mojgan; Kahanda, Indika; Mumey, Brendan; Barry, Kerrie; Kudrna, David; Schmutz, Jeremy; Lachowiec, Jennifer; Lu, Chaofu
Camelina [Camelina sativa (L.) Crantz] is an oilseed crop in the Brassicaceae family that is currently being developed as a source of bioenergy and healthy fatty acids. To facilitate modern breeding efforts through marker-assisted selection and biotechnology, we evaluated genetic variation among a worldwide collection of 222 camelina accessions. We performed whole-genome resequencing to obtain single nucleotide polymorphism (SNP) markers and to analyze genomic diversity. We also conducted phenotypic field evaluations in two consecutive seasons for variations in key agronomic traits related to oilseed production such as seed size, oil content (OC), fatty acid composition, and flowering time. We determined the population structure of the camelina accessions using 161,301 SNPs. Further, we identified quantitative trait loci (QTL) and candidate genes controlling the above field-evaluated traits by genome-wide association studies (GWAS) complemented with linkage mapping using a recombinant inbred line (RIL) population. Characterization of the natural variation at the genome and phenotypic levels provides valuable resources to camelina genetic studies and crop improvement. The QTL and candidate genes should assist in breeding of advanced camelina varieties that can be integrated into the cropping systems for the production of high yield of oils of desired fatty acid composition.
Hijacking a rapid and scalable metagenomic method reveals subgenome dynamics and evolution in polyploid plants
(Wiley, 2024-04) Reynolds, Gillian; Mumey, Brendan; Strnadova-Neeley, Veronika; Lachowiec, Jennifer
Premise. The genomes of polyploid plants archive the evolutionary events leading to their present forms. However, plant polyploid genomes present numerous hurdles to the genome comparison algorithms for classification of polyploid types and exploring genome dynamics. Methods. Here, the problem of intra- and inter-genome comparison for examining polyploid genomes is reframed as a metagenomic problem, enabling the use of the rapid and scalable MinHashing approach. To determine how types of polyploidy are described by this metagenomic approach, plant genomes were examined from across the polyploid spectrum for both k-mer composition and frequency with a range of k-mer sizes. In this approach, no subgenome-specific k-mers are identified; rather, whole-chromosome k-mer subspaces were utilized. Results. Given chromosome-scale genome assemblies with sufficient subgenome-specific repetitive element content, literature-verified subgenomic and genomic evolutionary relationships were revealed, including distinguishing auto- from allopolyploidy and putative progenitor genome assignment. The sequences responsible were the rapidly evolving landscape of transposable elements. An investigation into the MinHashing parameters revealed that the downsampled k-mer space (genomic signatures) produced excellent approximations of sequence similarity. Furthermore, the clustering approach used for comparison of the genomic signatures is scrutinized to ensure applicability of the metagenomics-based method. Discussion. The easily implementable and highly computationally efficient MinHashing-based sequence comparison strategy enables comparative subgenomics and genomics for large and complex polyploid plant genomes. Such comparisons provide evidence for polyploidy-type subgenomic assignments. In cases where subgenome-specific repeat signal may not be adequate given a chromosomes' global k-mer profile, alternative methods that are more specific but more computationally complex outperform this approach.
Historic trends and sources of year‐over‐year stability in Montana winter wheat yields
(Wiley, 2023-04) Lachowiec, Jennifer; Berg, James E.; Liang, Meng; Correr, Fernando H.
Producers desire cultivars that consistently perform with high yields and end-use qualities. Unlike easily recognized average yield improvements, yield stability over time is less examined, especially when considering the role of breeding relative to other factors like management and changing climatic conditions. Our study system was a 70-year historical dataset from which we estimated the year-over-year stability of winter wheat (Triticum aestivum L.) cultivars released by Montana's Agricultural Experimental Station. We examined yield stability within six locations representing diverse growing conditions across Montana and found no evidence that breeding has improved stability, that stability may be decreasing over time at one location, and that the year-over-year stability of a cultivar is sensitive to location. We examined the role of climatic conditions, including temperature, and rainfall to understand if increased climatic variability was masking improved patterns of stability. However, the lack of impact of breeding remained. These findings suggest that Montana's winter wheat may benefit from selective breeding for increased stability within locations.
Improvement of Endosperm Hydration Counter the Negative Relationship Between Dormancy and Malt Quality in Barley (Hordeum vulgare)
(Wiley, 2024-08) Jensen, Joseph; Uhlmann, Hannah; Lachowiec, Jennifer; Lutgen, Greg; Cook, Jason P.; Yin, Xiang S.; Kephart, Ken; Sherman, Jamie
Dormancy in barley has been thoroughly studied and shown to negatively impact malt quality, resulting in selection against dormancy. However, reduced dormancy coincides with increased preharvest sprout (PHS) risk, thus sparking a new interest in integrating dormancy back into American barley lines if the negative effects of dormancy on malt quality can be overcome. We evaluated the dormancy and hydration index (HYI) in a biparental mapping population to determine the genotypes that would protect against PHS but have good malt quality. We found 4 HYI QTLs and 4 dormancy QTLs, one of which was near the well-described SD2 QTL. The HYI QTLs were pleiotropically related to seed size (1H), dormancy (5H) and malt quality (2H). Lines with dormancy (5H) and increased HYI (2H and 3H) had malt quality similar to nondormant lines while maintaining PHS resistance, suggesting improvements in HYI could be the key to overcoming the negative effects of dormancy in malting.
QTL mapping reveals malt barley quality improvement in two dryland environments associated with extended grain fill and seminal root traits
(Wiley, 2024-05) Williams, Jessica L.; Lamb, Peggy F.; Lutgen, Greg; Lachowiec, Jennifer; Cook, Jason P.; Jensen, Joseph; Bourgault, Maryse; Sherman, Jamie D.
To achieve malt grade and receive full price, barley (Hordeum vulgare L.) crops must meet standards for certain quality traits including percent plump and protein. Terminal drought stress reduces quality and is projected to worsen in barley cultivation areas, underscoring the need for varieties that maintain good malt production with unreliable precipitation. The stay-green trait extends the grain fill phase between heading and maturity and has been linked to stable quality under dry conditions. However, this relationship can be inconsistent and is not well understood. To effectively leverage a longer grain fill phenotype for drought adaptation, a better grasp of its genetics and environmental interaction is needed. Stay-green root system differences have been observed and could be at play. We performed correlation and quantitative trait locus (QTL) analysis on grain fill duration, grain quality, and seminal root traits using a recombinant inbred line (RIL) population segregating for stay-green. Agronomic data were collected in four field trials at two distinct semiarid locations, and roots were measured in a greenhouse assay. Earlier heading and later maturity led to improved quality in both locations and more consistent quality between locations. Earlier heading had a greater influence on quality in the drier environment, while later maturity was more impactful in the less dry environment. We observed co-locations of seminal root trait QTLs with grain fill duration and grain quality. These QTLs lay the groundwork for further investigation into root phenotypes associated with stay-green and the deployment of these traits in breeding for drought adaptation.
Roles of Brassinosteroids in Mitigating Heat Stress Damage in Cereal Crops
(MDPI AG, 2021-03) Kothari, Aishwarya; Lachowiec, Jennifer
Heat stress causes huge losses in the yield of cereal crops. Temperature influences the rate of plant metabolic and developmental processes that ultimately determine the production of grains, with high temperatures causing a reduction in grain yield and quality. To ensure continued food security, the tolerance of high temperature is rapidly becoming necessary. Brassinosteroids (BR) are a class of plant hormones that impact tolerance to various biotic and abiotic stresses and regulate cereal growth and fertility. Fine-tuning the action of BR has the potential to increase cereals’ tolerance and acclimation to heat stress and maintain yields. Mechanistically, exogenous applications of BR protect yields through amplifying responses to heat stress and rescuing the expression of growth promoters. Varied BR compounds and differential signaling mechanisms across cereals point to a diversity of mechanisms that can be leveraged to mitigate heat stress. Further, hormone transport and BR interaction with other molecules in plants may be critical to utilizing BR as protective agrochemicals against heat stress. Understanding the interplay between heat stress responses, growth processes and hormone signaling may lead us to a comprehensive dogma of how to tune BR application for optimizing cereal growth under challenging environments in the field.