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Article: Root Pulling Force Across Drought in Maize Reveals Genotype by Environment Interactions and Candidate Genes.

Woods, Patrick / Lehner, Kevin R / Hein, Kirsten / Mullen, Jack L / McKay, John K

2022 Volume 13, Page(s) 883209

Abstract: High-throughput, field-based characterization of root systems for hundreds of genotypes in thousands of plots is necessary for breeding and identifying loci underlying variation in root traits and their plasticity. We designed a large-scale sampling of ... ...

Abstract	High-throughput, field-based characterization of root systems for hundreds of genotypes in thousands of plots is necessary for breeding and identifying loci underlying variation in root traits and their plasticity. We designed a large-scale sampling of root pulling force, the vertical force required to extract the root system from the soil, in a maize diversity panel under differing irrigation levels for two growing seasons. We then characterized the root system architecture of the extracted root crowns. We found consistent patterns of phenotypic plasticity for root pulling force for a subset of genotypes under differential irrigation, suggesting that root plasticity is predictable. Using genome-wide association analysis, we identified 54 SNPs as statistically significant for six independent root pulling force measurements across two irrigation levels and four developmental timepoints. For every significant GWAS SNP for any trait in any treatment and timepoint we conducted
Language	English
Publishing date	2022-04-15
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2613694-6
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2022.883209
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Article: Quantitative trait locus mapping for carbon isotope ratio and root pulling force in canola

Mekonnen, Melaku D. / Mullen, Jack L. / Arathi, H.S. / Assefa, Yared / McKay, John K. / Byrne, Patrick F.

Agrosystems, geosciences & environment. 2020, v. 3, no. 1

2020

Abstract: Carbon isotope ratio (δ¹³C) and root pulling force (RPF) are associated with dehydration avoidance in plants. The δ¹³C measures the efficiency of C gain relative to water loss, whereas RPF, the vertical force required to pull plants from the ground, ... ...

Abstract	Carbon isotope ratio (δ¹³C) and root pulling force (RPF) are associated with dehydration avoidance in plants. The δ¹³C measures the efficiency of C gain relative to water loss, whereas RPF, the vertical force required to pull plants from the ground, indirectly estimates root‐related dehydration avoidance capacity. To determine quantitative trait loci (QTL) controlling these traits in canola (Brassica napus L.), a mapping population was evaluated in 2011 and 2012 in Fort Collins, CO. The split‐plot experiment had two moisture regimes (main plot) and 148 doubled haploid lines (subplot), replicated three times. Analysis of variance indicated highly significant (P < .01) variation among genotypes for δ¹³C, RPF, days to flowering, and several other agronomic traits. In 2011, δ¹³C was correlated (P < .01) with days to flowering in both moisture treatments (r = .41 dry, 0.31 wet) and with fresh biomass in the dry treatment (r = .64). The RPF was consistently correlated with plant height (r = .32–.54, P < .01) and fresh biomass (r = .17–.58, P < .05) in all environments. In 2011, QTL were detected on chromosomes A09 and C08 for δ¹³C and on chromosomes A05, C01, C04, and C08 for RPF. The QTL for δ¹³C, RPF, and plant height co‐localized on C08. In 2012, QTL were detected on A02 for δ¹³C and on C01 and C08 for RPF. Moderate heritability and low QTL × environment interaction for δ¹³C and RPF suggest that if validated, markers for these traits could be used in marker‐assisted selection.
Keywords	Brassica napus ; analysis of variance ; biomass ; canola ; carbon ; environment ; haploidy ; heritability ; isotopes ; marker-assisted selection ; plant height ; quantitative trait loci ; quantitative traits
Language	English
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ISSN	2639-6696
DOI	10.1002/agg2.20095
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Quantitative trait loci controlling agronomic and biochemical traits in Cannabis sativa.

Woods, Patrick / Campbell, Brian J / Nicodemus, Timothy J / Cahoon, Edgar B / Mullen, Jack L / McKay, John K

Genetics

2021 Volume 219, Issue 2

Abstract: Understanding the genetic basis of complex traits is a fundamental goal of evolutionary genetics. Yet, the genetics controlling complex traits in many important species such as hemp (Cannabis sativa) remain poorly investigated. Because hemp's change in ... ...

Abstract	Understanding the genetic basis of complex traits is a fundamental goal of evolutionary genetics. Yet, the genetics controlling complex traits in many important species such as hemp (Cannabis sativa) remain poorly investigated. Because hemp's change in legal status with the 2014 and 2018 U.S. Federal Farm Bills, interest in the genetics controlling its numerous agriculturally important traits has steadily increased. To better understand the genetics of agriculturally important traits in hemp, we developed an F2 population by crossing two phenotypically distinct hemp cultivars (Carmagnola and USO31). Using whole-genome sequencing, we mapped quantitative trait loci (QTL) associated with variation in numerous agronomic and biochemical traits. A total of 69 loci associated with agronomic (34) and biochemical (35) trait variation were identified. We found that most QTL co-localized, suggesting that the phenotypic distinctions between Carmagnola and USO31 are largely controlled by a small number of loci. We identified TINY and olivetol synthase as candidate genes underlying co-localized QTL clusters for agronomic and biochemical traits, respectively. We functionally validated the olivetol synthase candidate by expressing the alleles in yeast. Gas chromatography-mass spectrometry assays of extracts from these yeast colonies suggest that the USO31 olivetol synthase is functionally less active and potentially explains why USO31 produces lower cannabinoids compared to Carmagnola. Overall, our results help modernize the genomic understanding of complex traits in hemp.
MeSH term(s)	Cannabis/genetics ; Cannabis/growth & development ; Cannabis/metabolism ; Intramolecular Transferases/genetics ; Plant Proteins/genetics ; Quantitative Trait Loci ; Quantitative Trait, Heritable
Chemical Substances	Plant Proteins ; Intramolecular Transferases (EC 5.4.-) ; olivetolic acid cyclase, Cannabis sativa (EC 5.4.-)
Language	English
Publishing date	2021-06-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1093/genetics/iyab099
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Article ; Online: Screening for Natural Variation in Water Use Efficiency Traits in a Diversity Set of Brassica napus L. Identifies Candidate Variants in Photosynthetic Assimilation.

Pater, Dianne / Mullen, Jack L / McKay, John K / Schroeder, Julian I

Plant & cell physiology

2017 Volume 58, Issue 10, Page(s) 1700–1709

Abstract: Seed yield and quality of crop species are significantly reduced by water deficit. Stable isotope screening (δ13C) of a diversity set of 147 accessions of Brassica napus grown in the field identified several accessions with extremes in water use ... ...

Abstract	Seed yield and quality of crop species are significantly reduced by water deficit. Stable isotope screening (δ13C) of a diversity set of 147 accessions of Brassica napus grown in the field identified several accessions with extremes in water use efficiency (WUE). We next conducted an investigation of the physiological characteristics of selected natural variants with high and low WUE to understand how these characteristics translate to differences in WUE. We identified an interesting Spring accession, G302 (Mozart), that exhibited the highest WUE in the field and high CO2 assimilation rates coupled with an increased electron transport capacity (Jmax) under the imposed conditions. Differences in stomatal density and stomatal index did not translate to differences in stomatal conductance in the investigated accessions. Stomatal conductance response to exogenous ABA was analyzed in selected high and low WUE accessions. Spring lines showed little variation in response to exogenous ABA, while one Semi-Winter line (SW047) showed a significantly more rapid response to exogenous ABA, that corresponded to the high WUE indicated by δ13C measurements. This research illustrates the importance of examining natural variation at a physiological level for investigation of the underlying mechanisms influencing the diversity of carbon isotope discrimination values in the field and identifies natural variants in B. napus with improved WUE and potential relevant traits.
MeSH term(s)	Abscisic Acid/pharmacology ; Biodiversity ; Brassica napus/drug effects ; Brassica napus/growth & development ; Brassica napus/metabolism ; Brassica napus/physiology ; Carbon Dioxide/metabolism ; Carbon Isotopes ; Ecotype ; Electron Transport/drug effects ; Gases/metabolism ; Photosynthesis/drug effects ; Plant Leaves/drug effects ; Plant Leaves/metabolism ; Plant Stomata/drug effects ; Plant Stomata/physiology ; Plant Transpiration/drug effects ; Plant Transpiration/physiology ; Ribulose-Bisphosphate Carboxylase/metabolism ; Water/metabolism
Chemical Substances	Carbon Isotopes ; Gases ; Water (059QF0KO0R) ; Carbon Dioxide (142M471B3J) ; Abscisic Acid (72S9A8J5GW) ; Ribulose-Bisphosphate Carboxylase (EC 4.1.1.39)
Language	English
Publishing date	2017-10-19
Publishing country	Japan
Document type	Journal Article
ZDB-ID	208907-5
ISSN	1471-9053 ; 0032-0781
ISSN (online)	1471-9053
ISSN	0032-0781
DOI	10.1093/pcp/pcx108
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Article: Combining quantitative trait loci analysis with physiological models to predict genotype‐specific transpiration rates

REUNING, GRETCHEN A / BAUERLE, WILLIAM L / MCKAY, JOHN K / MULLEN, JACK L

Plant, cell and environment. 2015 Apr., v. 38, no. 4

2015

Abstract: Transpiration is controlled by evaporative demand and stomatal conductance (gs), and there can be substantial genetic variation in gs. A key parameter in empirical models of transpiration is minimum stomatal conductance (g0), a trait that can be measured ...

Abstract	Transpiration is controlled by evaporative demand and stomatal conductance (gs), and there can be substantial genetic variation in gs. A key parameter in empirical models of transpiration is minimum stomatal conductance (g0), a trait that can be measured and has a large effect on gsand transpiration. In Arabidopsis thaliana, g0exhibits both environmental and genetic variation, and quantitative trait loci (QTL) have been mapped. We used this information to create a genetically parameterized empirical model to predict transpiration of genotypes. For the parental lines, this worked well. However, in a recombinant inbred population, the predictions proved less accurate. When based only upon their genotype at a single g0QTL, genotypes were less distinct than our model predicted. Follow‐up experiments indicated that both genotype by environment interaction and a polygenic inheritance complicate the application of genetic effects into physiological models. The use of ecophysiological or ‘crop’ models for predicting transpiration of novel genetic lines will benefit from incorporating further knowledge of the genetic control and degree of independence of core traits/parameters underlying gsvariation.
Keywords	Arabidopsis thaliana ; ecophysiology ; genetic lines ; genetic variation ; genotype ; genotype-environment interaction ; models ; polygenic inheritance ; prediction ; quantitative trait loci ; stomatal conductance
Language	English
Dates of publication	2015-04
Size	p. 710-717.
Publishing place	Blackwell Scientific Publications
Document type	Article
ZDB-ID	391893-2
ISSN	1365-3040 ; 0140-7791
ISSN (online)	1365-3040
ISSN	0140-7791
DOI	10.1111/pce.12429
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Drought adaptation in

Monroe, J Grey / Powell, Tyler / Price, Nicholas / Mullen, Jack L / Howard, Anne / Evans, Kyle / Lovell, John T / McKay, John K

eLife

2018 Volume 7

Abstract: Interdisciplinary syntheses are needed to scale up discovery of the environmental drivers and molecular basis of adaptation in nature. Here we integrated novel approaches using whole genome sequences, satellite remote sensing, and transgenic experiments ... ...

Abstract	Interdisciplinary syntheses are needed to scale up discovery of the environmental drivers and molecular basis of adaptation in nature. Here we integrated novel approaches using whole genome sequences, satellite remote sensing, and transgenic experiments to study natural loss-of-function alleles associated with drought histories in wild
MeSH term(s)	Adaptation, Physiological/genetics ; Arabidopsis/genetics ; Droughts ; Flowers/genetics ; Gene Expression Profiling ; Loss of Function Mutation ; Phenotype ; Plants, Genetically Modified ; Stress, Physiological ; Time Factors
Language	English
Publishing date	2018-12-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.41038
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Article ; Online: Combining quantitative trait loci analysis with physiological models to predict genotype-specific transpiration rates.

Reuning, Gretchen A / Bauerle, William L / Mullen, Jack L / McKay, John K

Plant, cell & environment

2015 Volume 38, Issue 4, Page(s) 710–717

Abstract: Transpiration is controlled by evaporative demand and stomatal conductance (gs ), and there can be substantial genetic variation in gs . A key parameter in empirical models of transpiration is minimum stomatal conductance (g0 ), a trait that can be ... ...

Abstract	Transpiration is controlled by evaporative demand and stomatal conductance (gs ), and there can be substantial genetic variation in gs . A key parameter in empirical models of transpiration is minimum stomatal conductance (g0 ), a trait that can be measured and has a large effect on gs and transpiration. In Arabidopsis thaliana, g0 exhibits both environmental and genetic variation, and quantitative trait loci (QTL) have been mapped. We used this information to create a genetically parameterized empirical model to predict transpiration of genotypes. For the parental lines, this worked well. However, in a recombinant inbred population, the predictions proved less accurate. When based only upon their genotype at a single g0 QTL, genotypes were less distinct than our model predicted. Follow-up experiments indicated that both genotype by environment interaction and a polygenic inheritance complicate the application of genetic effects into physiological models. The use of ecophysiological or 'crop' models for predicting transpiration of novel genetic lines will benefit from incorporating further knowledge of the genetic control and degree of independence of core traits/parameters underlying gs variation.
MeSH term(s)	Arabidopsis/genetics ; Arabidopsis/physiology ; Droughts ; Environment ; Genetic Variation ; Genotype ; Phenotype ; Plant Leaves/genetics ; Plant Leaves/physiology ; Plant Stomata/genetics ; Plant Stomata/physiology ; Plant Transpiration/physiology ; Quantitative Trait Loci/genetics ; Species Specificity ; Water/physiology
Chemical Substances	Water (059QF0KO0R)
Language	English
Publishing date	2015-04
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	391893-2
ISSN	1365-3040 ; 0140-7791
ISSN (online)	1365-3040
ISSN	0140-7791
DOI	10.1111/pce.12429
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Article: TSPmap

Monroe, J Grey / Allen, Zachariah A / Tanger, Paul / Mullen, Jack L / Lovell, John T / Moyers, Brook T / Whitley, Darrell / McKay, John K

BioData mining

2017 Volume 10, Page(s) 38

Abstract: Background: Recent advances in nucleic acid sequencing technologies have led to a dramatic increase in the number of markers available to generate genetic linkage maps. This increased marker density can be used to improve genome assemblies as well as ... ...

Abstract	Background: Recent advances in nucleic acid sequencing technologies have led to a dramatic increase in the number of markers available to generate genetic linkage maps. This increased marker density can be used to improve genome assemblies as well as add much needed resolution for loci controlling variation in ecologically and agriculturally important traits. However, traditional genetic map construction methods from these large marker datasets can be computationally prohibitive and highly error prone. Results: We present Conclusions: With the advancement of low cost sequencing technologies, the number of markers used in the generation of genetic maps is expected to continue to rise.
Language	English
Publishing date	2017-12-19
Publishing country	England
Document type	Journal Article
ZDB-ID	2438773-3
ISSN	1756-0381
ISSN	1756-0381
DOI	10.1186/s13040-017-0158-0
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Article ; Online: QTL analysis of root morphology, flowering time, and yield reveals trade-offs in response to drought in Brassica napus.

Fletcher, Richard S / Mullen, Jack L / Heiliger, Annie / McKay, John K

Journal of experimental botany

2014 Volume 66, Issue 1, Page(s) 245–256

Abstract: Drought escape and dehydration avoidance represent alternative strategies for drought adaptation in annual crops. The mechanisms underlying these two strategies are reported to have a negative correlation, suggesting a trade-off. We conducted a ... ...

Abstract	Drought escape and dehydration avoidance represent alternative strategies for drought adaptation in annual crops. The mechanisms underlying these two strategies are reported to have a negative correlation, suggesting a trade-off. We conducted a quantitative trait locus (QTL) analysis of flowering time and root mass, traits representing each strategy, in Brassica napus to understand if a trade-off exists and what the genetic basis might be. Our field experiment used a genotyped population of doubled haploid lines and included both irrigated and rainfed treatments, allowing analysis of plasticity in each trait. We found strong genetic correlations among all traits, suggesting a trade-off among traits may exist. Summing across traits and treatments we found 20 QTLs, but many of these co-localized to two major QTLs, providing evidence that the trade-off is genetically constrained. To understand the mechanistic relationship between root mass, flowering time, and QTLs, we analysed the data by conditioning upon correlated traits. Our results suggest a causal model where such QTLs affect root mass directly as well as through their impacts on flowering time. Additionally, we used draft Brassica genomes to identify orthologues of well characterized Arabidopsis thaliana flowering time genes as candidate genes. This research provides valuable clues to breeding for drought adaptation as it is the first to analyse the inheritance of the root system in B. napus in relation to drought.
MeSH term(s)	Adaptation, Biological ; Brassica napus/anatomy & histology ; Brassica napus/genetics ; Brassica napus/growth & development ; Brassica napus/metabolism ; Droughts ; Flowers/genetics ; Flowers/growth & development ; Genetic Variation ; Genotype ; Haploidy ; Plant Roots/anatomy & histology ; Plant Roots/genetics ; Quantitative Trait Loci ; Reproduction/genetics
Language	English
Publishing date	2014-11-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2976-2
ISSN	1460-2431 ; 0022-0957
ISSN (online)	1460-2431
ISSN	0022-0957
DOI	10.1093/jxb/eru423
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Article ; Online: Deployment of Lidar from a Ground Platform: Customizing a Low-Cost, Information-Rich and User-Friendly Application for Field Phenomics Research.

Heun, John T / Attalah, Said / French, Andrew N / Lehner, Kevin R / McKay, John K / Mullen, Jack L / Ottman, Michael J / Andrade-Sanchez, Pedro

Sensors (Basel, Switzerland)

2019 Volume 19, Issue 24

Abstract: Using sensors and electronic systems for characterization of plant traits provides valuable digital inputs to support complex analytical modeling in genetics research. In field applications, frequent sensor deployment enables the study of the dynamics of ...

Abstract	Using sensors and electronic systems for characterization of plant traits provides valuable digital inputs to support complex analytical modeling in genetics research. In field applications, frequent sensor deployment enables the study of the dynamics of these traits and their interaction with the environment. This study focused on implementing lidar (light detection and ranging) technology to generate 2D displacement data at high spatial resolution and extract plant architectural parameters, namely canopy height and cover, in a diverse population of 252 maize (
Language	English
Publishing date	2019-12-05
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2052857-7
ISSN	1424-8220 ; 1424-8220
ISSN (online)	1424-8220
ISSN	1424-8220
DOI	10.3390/s19245358
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