Genome-Wide Association Study for Nodule Traits in Guar
Guar [<i>Cyamopsis tetragonoloba</i> (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....
Saved in:
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2025-02-01
|
| Series: | Current Issues in Molecular Biology |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1467-3045/47/3/151 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850089424713416704 |
|---|---|
| author | Shubham Malani Waltram Ravelombola Aurora Manley Hanh Pham Madeline Brown Md. Mezanur Rahman |
| author_facet | Shubham Malani Waltram Ravelombola Aurora Manley Hanh Pham Madeline Brown Md. Mezanur Rahman |
| author_sort | Shubham Malani |
| collection | DOAJ |
| description | Guar [<i>Cyamopsis tetragonoloba</i> (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. |
| format | Article |
| id | doaj-art-30665e30342b402c8151f94d792b96eb |
| institution | DOAJ |
| issn | 1467-3037 1467-3045 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Current Issues in Molecular Biology |
| spelling | doaj-art-30665e30342b402c8151f94d792b96eb2025-08-20T02:42:46ZengMDPI AGCurrent Issues in Molecular Biology1467-30371467-30452025-02-0147315110.3390/cimb47030151Genome-Wide Association Study for Nodule Traits in GuarShubham Malani0Waltram Ravelombola1Aurora Manley2Hanh Pham3Madeline Brown4Md. Mezanur Rahman5Texas A&M AgriLife Research, 11708 Highway 70 South, Vernon, TX 76384, USATexas A&M AgriLife Research, 11708 Highway 70 South, Vernon, TX 76384, USATexas A&M AgriLife Research, 11708 Highway 70 South, Vernon, TX 76384, USATexas A&M AgriLife Research, 1102 East Drew Street, Lubbock, TX 79403, USATexas A&M AgriLife Research, 11708 Highway 70 South, Vernon, TX 76384, USADepartment of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX 79409, USAGuar [<i>Cyamopsis tetragonoloba</i> (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.https://www.mdpi.com/1467-3045/47/3/151guarnodulesingle nucleotide polymorphismassociationgenetics |
| spellingShingle | Shubham Malani Waltram Ravelombola Aurora Manley Hanh Pham Madeline Brown Md. Mezanur Rahman Genome-Wide Association Study for Nodule Traits in Guar Current Issues in Molecular Biology guar nodule single nucleotide polymorphism association genetics |
| title | Genome-Wide Association Study for Nodule Traits in Guar |
| title_full | Genome-Wide Association Study for Nodule Traits in Guar |
| title_fullStr | Genome-Wide Association Study for Nodule Traits in Guar |
| title_full_unstemmed | Genome-Wide Association Study for Nodule Traits in Guar |
| title_short | Genome-Wide Association Study for Nodule Traits in Guar |
| title_sort | genome wide association study for nodule traits in guar |
| topic | guar nodule single nucleotide polymorphism association genetics |
| url | https://www.mdpi.com/1467-3045/47/3/151 |
| work_keys_str_mv | AT shubhammalani genomewideassociationstudyfornoduletraitsinguar AT waltramravelombola genomewideassociationstudyfornoduletraitsinguar AT auroramanley genomewideassociationstudyfornoduletraitsinguar AT hanhpham genomewideassociationstudyfornoduletraitsinguar AT madelinebrown genomewideassociationstudyfornoduletraitsinguar AT mdmezanurrahman genomewideassociationstudyfornoduletraitsinguar |