Latent Space Phenotyping: Automatic Image-Based Phenotyping for Treatment Studies

Association mapping studies have enabled researchers to identify candidate loci for many important environmental tolerance factors, including agronomically relevant tolerance traits in plants. However, traditional genome-by-environment studies such as these require a phenotyping pipeline which is capable of accurately measuring stress responses, typically in an automated high-throughput context using image processing. In this work, we present Latent Space Phenotyping (LSP), a novel phenotyping method which is able to automatically detect and quantify response-to-treatment directly from images. We demonstrate example applications using data from an interspecific cross of the model C4 grass Setaria, a diversity panel of sorghum (S. bicolor), and the founder panel for a nested association mapping population of canola (Brassica napus L.). Using two synthetically generated image datasets, we then show that LSP is able to successfully recover the simulated QTL in both simple and complex synthetic imagery. We propose LSP as an alternative to traditional image analysis methods for phenotyping, enabling the phenotyping of arbitrary and potentially complex response traits without the need for engineering-complicated image-processing pipelines.

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Latent Space Phenotyping: Automatic Image-Based Phenotyping for Treatment Studies

10.1101/557678 ◽

2019 ◽

Cited By ~ 3

Author(s):

Jordan Ubbens ◽

Mikolaj Cieslak ◽

Przemyslaw Prusinkiewicz ◽

Ian Stavness

Keyword(s):

Image Processing ◽

Association Mapping ◽

Stress Responses ◽

Interspecific Cross ◽

Response To Treatment ◽

Resistance Factors ◽

Complex Image ◽

Latent Space ◽

Model C ◽

Candidate Loci

AbstractAssociation mapping studies have enabled researchers to identify candidate loci for many important environmental resistance factors, including agronomically relevant resistance traits in plants. However, traditional genome-by-environment studies such as these require a phenotyping pipeline which is capable of accurately and consistently measuring stress responses, typically in an automated high-throughput context using image processing. In this work, we present Latent Space Phenotyping (LSP), a novel phenotyping method which is able to automatically detect and quantify response to treatment directly from images. Using two synthetically generated image datasets, we first show that LSP is able to successfully recover the simulated QTL in both simple and complex synthetic imagery. We then demonstrate an example application of an interspecific cross of the model C4 grass Setaria. We propose LSP as an alternative to traditional image analysis methods for phenotyping, enabling association mapping studies without the need for engineering complex image processing pipelines.

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Comparison of statistical models for nested association mapping in rapeseed (Brassica napus L.) through computer simulations

BMC Plant Biology ◽

10.1186/s12870-016-0707-6 ◽

2016 ◽

Vol 16 (1) ◽

Cited By ~ 7

Author(s):

Jinquan Li ◽

Anja Bus ◽

Viola Spamer ◽

Benjamin Stich

Keyword(s):

Brassica Napus ◽

Association Mapping ◽

Computer Simulations ◽

Statistical Models ◽

Brassica Napus L ◽

Nested Association Mapping

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Genomic Dissection of Peduncle Morphology in Barley through Nested Association Mapping

Plants ◽

10.3390/plants10010010 ◽

2020 ◽

Vol 10 (1) ◽

pp. 10

Author(s):

Sebastian Zahn ◽

Thomas Schmutzer ◽

Klaus Pillen ◽

Andreas Maurer

Keyword(s):

Quantitative Trait Loci ◽

Association Mapping ◽

Cross Section ◽

Quantitative Trait ◽

Spring Barley ◽

Raw Material ◽

Total Thickness ◽

Nested Association Mapping ◽

Elite Cultivar ◽

Major Qtl

Straw biomass and stability are crucial for stable yields. Moreover, straw harbors the potential to serve as a valuable raw material for bio-economic processes. The peduncle is the top part of the last shoot internode and carries the spike. This study investigates the genetic control of barley peduncle morphology. Therefore, 1411 BC1S3 lines of the nested association mapping (NAM) population “Halle Exotic Barley 25” (HEB-25), generated by crossing the spring barley elite cultivar Barke with an assortment of 25 exotic barley accessions, were used. Applying 50k Illumina Infinium iSelect SNP genotyping yielded new insights and a better understanding of the quantitative trait loci (QTL) involved in controlling the peduncle diameter traits, we found the total thickness of peduncle tissues and the area of the peduncle cross-section. We identified three major QTL regions on chromosomes 2H and 3H mainly impacting the traits. Remarkably, the exotic allele at the QTL on chromosome 3H improved all three traits investigated in this work. Introgressing this QTL in elite cultivars might facilitate to adjust peduncle morphology for improved plant stability or enlarged straw biomass production independent of flowering time and without detrimental effects on grain yield.

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Serum C-reactive protein metabolite (CRPM) is associated with incidence of contralateral knee osteoarthritis

Scientific Reports ◽

10.1038/s41598-021-86064-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Anne-Christine Bay-Jensen ◽

Asger Bihlet ◽

Inger Byrjalsen ◽

Jeppe Ragnar Andersen ◽

Bente Juhl Riis ◽

...

Keyword(s):

Phase Iii ◽

Response To Treatment ◽

C Reactive Protein ◽

Two Phase ◽

Knee Oa ◽

Reactive Protein ◽

Inflammatory Phenotype ◽

The Mean ◽

Using Data

AbstractThe heterogeneous nature of osteoarthritis (OA) and the need to subtype patients is widely accepted in the field. The biomarker CRPM, a metabolite of C-reactive protein (CRP), is released to the circulation during inflammation. Blood CRPM levels have shown to be associated with disease activity and response to treatment in rheumatoid arthritis (RA). We investigated the level of blood CRPM in OA compared to RA using data from two phase III knee OA and two RA studies (N = 1591). Moreover, the association between CRPM levels and radiographic progression was investigated. The mean CRPM levels were significantly lower in OA (8.5 [95% CI 8.3–8.8] ng/mL, n = 781) compared to the RA patients (12.8 [9.5–16.0] ng/mL, n = 60); however, a significant subset of OA patients (31%) had CRPM levels (≥ 9 ng/mL) comparable to RA. Furthermore, OA patients (n = 152) with CRPM levels ≥ 9 ng/mL were more likely to develop contra-lateral knee OA assessed by X-ray over a two-year follow-up period with an odds ratio of 2.2 [1.0–4.7]. These data suggest that CRPM is a blood-based biochemical marker for early identification OA patients with an inflammatory phenotype.

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Design of a Brassica rapa core collection for association mapping studiesThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽

10.1139/g10-082 ◽

2010 ◽

Vol 53 (11) ◽

pp. 884-898 ◽

Cited By ~ 31

Author(s):

Jianjun Zhao ◽

Anna Artemyeva ◽

Dunia Pino Del Carpio ◽

Ram Kumar Basnet ◽

Ningwen Zhang ◽

...

Keyword(s):

Association Mapping ◽

Flowering Time ◽

Brassica Rapa ◽

Core Collection ◽

Field Experiments ◽

Research Centre ◽

Candidate Gene Approach ◽

Core Collections ◽

Genome Wide ◽

Using Data

A Brassica rapa collection of 239 accessions, based on two core collections representing different morphotypes from different geographical origins, is presented and its use for association mapping is illustrated for flowering time. We analyzed phenotypic variation of leaf and seed pod traits, plant architecture, and flowering time using data collected from three field experiments and evaluated the genetic diversity with a set of SSR markers. The Wageningen University and Research Centre (WUR) and the Vavilov Research Institute of Plant Industry (VIR) core collections had similar representations of most morphotypes, as illustrated by the phenotypic and genetic variation within these groups. The analysis of population structure revealed five subgroups in the collection, whereas previous studies of the WUR core collection indicated four subgroups; the fifth group identified consisted mainly of oil accessions from the VIR core collection, winter oils from Pakistan, and a number of other types. A very small group of summer oils is described, that is not related to other oil accessions. A candidate gene approach was chosen for association mapping of flowering time with a BrFLC1 biallelic CAPS marker and a BrFLC2 multiallelic SSR marker. The two markers were significantly associated with flowering time, but their effects were confined to certain morphotypes and (or) alleles. Based on these results, we discuss the optimal design for an association mapping population and the need to fix the heterogeneous accessions to facilitate phenotyping and genotyping.

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Genetic Vulnerability and the Relationship of Commercial Germplasms of Maize in Brazil with the Nested Association Mapping Parents

PLoS ONE ◽

10.1371/journal.pone.0163739 ◽

2016 ◽

Vol 11 (10) ◽

pp. e0163739 ◽

Cited By ~ 2

Author(s):

Luciano Rogério Braatz de Andrade ◽

Roberto Fritsche Neto ◽

Ítalo Stefanine Correia Granato ◽

Gustavo César Sant’Ana ◽

Pedro Patric Pinho Morais ◽

...

Keyword(s):

Association Mapping ◽

Nested Association Mapping ◽

Genetic Vulnerability ◽

Relationship Of ◽

The Relationship

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Metabolomic Assessment of Key Maize Resources: GC-MS and NMR Profiling of Grain from B73 Hybrids of the Nested Association Mapping (NAM) Founders and of Geographically Diverse Landraces

Journal of Agricultural and Food Chemistry ◽

10.1021/acs.jafc.5b04901 ◽

2016 ◽

Vol 64 (10) ◽

pp. 2162-2172 ◽

Cited By ~ 17

Author(s):

Tyamagondlu V. Venkatesh ◽

Alexander W. Chassy ◽

Oliver Fiehn ◽

Sherry Flint-Garcia ◽

Qin Zeng ◽

...

Keyword(s):

Association Mapping ◽

Nested Association Mapping

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Antioxidative and Metabolic Contribution to Salinity Stress Responses in Two Rapeseed Cultivars during the Early Seedling Stage

Antioxidants ◽

10.3390/antiox10081227 ◽

2021 ◽

Vol 10 (8) ◽

pp. 1227

Author(s):

Ali Mahmoud El-Badri ◽

Maria Batool ◽

Ibrahim A. A. Mohamed ◽

Zongkai Wang ◽

Ahmed Khatab ◽

...

Keyword(s):

Salt Stress ◽

Salinity Stress ◽

Stress Responses ◽

Antioxidant Activities ◽

Tricarboxylic Acid Cycle ◽

Seedling Stage ◽

Plant Performance ◽

Salt Tolerant ◽

Brassica Napus L ◽

Early Seedling

Measuring metabolite patterns and antioxidant ability is vital to understanding the physiological and molecular responses of plants under salinity. A morphological analysis of five rapeseed cultivars showed that Yangyou 9 and Zhongshuang 11 were the most salt-tolerant and -sensitive, respectively. In Yangyou 9, the reactive oxygen species (ROS) level and malondialdehyde (MDA) content were minimized by the activation of antioxidant enzymes such as superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) for scavenging of over-accumulated ROS under salinity stress. Furthermore, Yangyou 9 showed a significantly higher positive correlation with photosynthetic pigments, osmolyte accumulation, and an adjusted Na+/K+ ratio to improve salt tolerance compared to Zhongshuang 11. Out of 332 compounds identified in the metabolic profile, 225 metabolites were filtrated according to p < 0.05, and 47 metabolites responded to salt stress within tolerant and sensitive cultivars during the studied time, whereas 16 and 9 metabolic compounds accumulated during 12 and 24 h, respectively, in Yangyou 9 after being sown in salt treatment, including fatty acids, amino acids, and flavonoids. These metabolites are relevant to metabolic pathways (amino acid, sucrose, flavonoid metabolism, and tricarboxylic acid cycle (TCA), which accumulated as a response to salinity stress. Thus, Yangyou 9, as a tolerant cultivar, showed improved antioxidant enzyme activity and higher metabolite accumulation, which enhances its tolerance against salinity. This work aids in elucidating the essential cellular metabolic changes in response to salt stress in rapeseed cultivars during seed germination. Meanwhile, the identified metabolites can act as biomarkers to characterize plant performance in breeding programs under salt stress. This comprehensive study of the metabolomics and antioxidant activities of Brassica napus L. during the early seedling stage is of great reference value for plant breeders to develop salt-tolerant rapeseed cultivars.

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