Genome-Wide Association Study for Nodule Traits in Guar

Shubham Malani; Waltram Ravelombola; Aurora Manley; Hanh Pham; Madeline Brown; Md Mezanur Rahman

doi:10.3390/cimb47030151

Genome-Wide Association Study for Nodule Traits in Guar

Shubham Malani
, Waltram Ravelombola
, Aurora Manley
, Hanh Pham
, Madeline Brown
, Md Mezanur Rahman

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

Abstract

Guar [Cyamopsis tetragonoloba (L.) Taub] is a diploid legume crop cultivated for galactomannan (guar gum) extracted from the endosperm of the seed. Previous studies have suggested that nodulation of guar can be poor in field conditions; however, solid proof has yet to be provided. The objectives of this study were to conduct a genome-wide association study (GWAS) and to identify single nucleotide polymorphism (SNP) markers associated with nodules in guar. GWAS was performed on a total of 225 guar genotypes using 19,007 filtered SNPs. Tassel 5 was used to run five models: single marker regression (SMR), generalized mixed linear model with PCA as a covariate (GLM_PCA), generalized mixed linear model with Q matrix as a covariate (GLM_Q), mixed linear model with PCA and Kinship (K) as covariates (GLM_PCA + K), and mixed linear model with Q and K as covariates (MLM_Q + K). Across all statistical models, the results showed a total of 3, 2, 25, 7, 2, and 3 SNPs were associated with plant height, nodule number per plant, fresh nodule weight, dry nodule weight, fresh aboveground plant biomass, and dry aboveground plant biomass. These SNPs could be used as a tool to select for better nodule traits in guar.

Original language	English
Article number	151
Journal	Current Issues in Molecular Biology
Volume	47
Issue number	3
DOIs	https://doi.org/10.3390/cimb47030151
State	Published - Mar 2025
Externally published	Yes

Funding

We thank the USDA-ARS Pulse Crop Health Initiative Grant 58-3060-9-042, the USDA National Institute of Food and Agriculture Award No. 2018-67019-27873, the USDA-ARS New and Industrial Crop Evaluation Grant 58-6046-4-008, the USDA Ogallala Aquifer Grant 230, the Texas Department of Agriculture Specialty Block Grant Award No. GSC2024075, the USDA NIFA Multi-State Hatch Project Accession Number 7003209, the Texas A&M Advancing Discovery to Market Grant, and the Texas A&M Institute for Advancing Health through Agriculture Grant for funding.

Keywords

association
genetics
guar
nodule
single nucleotide polymorphism

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10.3390/cimb47030151

Cite this

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title = "Genome-Wide Association Study for Nodule Traits in Guar",

abstract = "Guar [Cyamopsis tetragonoloba (L.) Taub] is a diploid legume crop cultivated for galactomannan (guar gum) extracted from the endosperm of the seed. Previous studies have suggested that nodulation of guar can be poor in field conditions; however, solid proof has yet to be provided. The objectives of this study were to conduct a genome-wide association study (GWAS) and to identify single nucleotide polymorphism (SNP) markers associated with nodules in guar. GWAS was performed on a total of 225 guar genotypes using 19,007 filtered SNPs. Tassel 5 was used to run five models: single marker regression (SMR), generalized mixed linear model with PCA as a covariate (GLM\_PCA), generalized mixed linear model with Q matrix as a covariate (GLM\_Q), mixed linear model with PCA and Kinship (K) as covariates (GLM\_PCA + K), and mixed linear model with Q and K as covariates (MLM\_Q + K). Across all statistical models, the results showed a total of 3, 2, 25, 7, 2, and 3 SNPs were associated with plant height, nodule number per plant, fresh nodule weight, dry nodule weight, fresh aboveground plant biomass, and dry aboveground plant biomass. These SNPs could be used as a tool to select for better nodule traits in guar.",

keywords = "association, genetics, guar, nodule, single nucleotide polymorphism",

author = "Shubham Malani and Waltram Ravelombola and Aurora Manley and Hanh Pham and Madeline Brown and Rahman, \{Md Mezanur\}",

note = "Publisher Copyright: {\textcopyright} 2025 by the authors.",

year = "2025",

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doi = "10.3390/cimb47030151",

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volume = "47",

journal = "Current Issues in Molecular Biology",

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AU - Malani, Shubham

AU - Ravelombola, Waltram

AU - Manley, Aurora

AU - Pham, Hanh

AU - Brown, Madeline

AU - Rahman, Md Mezanur

PY - 2025/3

Y1 - 2025/3

N2 - Guar [Cyamopsis tetragonoloba (L.) Taub] is a diploid legume crop cultivated for galactomannan (guar gum) extracted from the endosperm of the seed. Previous studies have suggested that nodulation of guar can be poor in field conditions; however, solid proof has yet to be provided. The objectives of this study were to conduct a genome-wide association study (GWAS) and to identify single nucleotide polymorphism (SNP) markers associated with nodules in guar. GWAS was performed on a total of 225 guar genotypes using 19,007 filtered SNPs. Tassel 5 was used to run five models: single marker regression (SMR), generalized mixed linear model with PCA as a covariate (GLM_PCA), generalized mixed linear model with Q matrix as a covariate (GLM_Q), mixed linear model with PCA and Kinship (K) as covariates (GLM_PCA + K), and mixed linear model with Q and K as covariates (MLM_Q + K). Across all statistical models, the results showed a total of 3, 2, 25, 7, 2, and 3 SNPs were associated with plant height, nodule number per plant, fresh nodule weight, dry nodule weight, fresh aboveground plant biomass, and dry aboveground plant biomass. These SNPs could be used as a tool to select for better nodule traits in guar.

AB - Guar [Cyamopsis tetragonoloba (L.) Taub] is a diploid legume crop cultivated for galactomannan (guar gum) extracted from the endosperm of the seed. Previous studies have suggested that nodulation of guar can be poor in field conditions; however, solid proof has yet to be provided. The objectives of this study were to conduct a genome-wide association study (GWAS) and to identify single nucleotide polymorphism (SNP) markers associated with nodules in guar. GWAS was performed on a total of 225 guar genotypes using 19,007 filtered SNPs. Tassel 5 was used to run five models: single marker regression (SMR), generalized mixed linear model with PCA as a covariate (GLM_PCA), generalized mixed linear model with Q matrix as a covariate (GLM_Q), mixed linear model with PCA and Kinship (K) as covariates (GLM_PCA + K), and mixed linear model with Q and K as covariates (MLM_Q + K). Across all statistical models, the results showed a total of 3, 2, 25, 7, 2, and 3 SNPs were associated with plant height, nodule number per plant, fresh nodule weight, dry nodule weight, fresh aboveground plant biomass, and dry aboveground plant biomass. These SNPs could be used as a tool to select for better nodule traits in guar.

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KW - genetics

KW - guar

KW - nodule

KW - single nucleotide polymorphism

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JO - Current Issues in Molecular Biology

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ER -

Genome-Wide Association Study for Nodule Traits in Guar

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