Next Article in Journal
Biochemical and Molecular Characterization of the Rice Chalcone Isomerase Family
Next Article in Special Issue
Targeting the B1 Gene and Analysis of Its Polymorphism Associated with Awned/Awnless Trait in Russian Germplasm Collections of Common Wheat
Previous Article in Journal
Genetic Mapping of the HLA1 Locus Causing Hybrid Lethality in Nicotiana Interspecific Hybrids
Previous Article in Special Issue
Introgression of Bacterial Blight Resistance Genes in the Rice Cultivar Ciherang: Response against Xanthomonas oryzae pv. oryzae in the F6 Generation
 
 
Article

Development of SNP Set for the Marker-Assisted Selection of Guar (Cyamopsis tetragonoloba (L.) Taub.) Based on a Custom Reference Genome Assembly

1
Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg 194021, Russia
2
Sirius University of Science and Technology, Sochi 354340, Russia
3
Department of Cytology and Histology, Saint Petersburg State University, St. Petersburg 199034, Russia
4
Department of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg 199034, Russia
5
Bioinformatics Institute, St. Petersburg 197342, Russia
6
Faculty of Software Engineering and Computer Systems, ITMO University, St. Petersburg 197101, Russia
7
Skolkovo Institute of Science and Technology, Moscow 121205, Russia
*
Author to whom correspondence should be addressed.
Co-first authors, these authors contributed equally to this work.
Academic Editors: Irina N. Leonova and Yuri Shavrukov
Plants 2021, 10(10), 2063; https://doi.org/10.3390/plants10102063
Received: 24 August 2021 / Revised: 20 September 2021 / Accepted: 27 September 2021 / Published: 30 September 2021
Guar gum, a polysaccharide derived from guar seeds, is widely used in a variety of industrial applications, including oil and gas production. Although guar is mostly propagated in India, interest in guar as a new industrial legume crop is increasing worldwide, demanding the development of effective tools for marker-assisted selection. In this paper, we report a wide-ranging set of 4907 common SNPs and 327 InDels generated from RADseq genotyping data of 166 guar plants of different geographical origin. A custom guar reference genome was assembled and used for variant calling. A consensus set of variants was built using three bioinformatic pipelines for short variant discovery. The developed molecular markers were used for genome-wide association study, resulting in the discovery of six markers linked to the variation of an important agronomic trait—percentage of pods matured to the harvest date under long light day conditions. One of the associated variants was found inside the putative transcript sequence homologous to an ABC transporter in Arabidopsis, which has been shown to play an important role in D-myo-inositol phosphates metabolism. Earlier, we suggested that genes involved in myo-inositol phosphate metabolism have significant impact on the early flowering of guar plants. Hence, we believe that the developed SNP set allows for the identification of confident molecular markers of important agrobiological traits. View Full-Text
Keywords: guar; RADseq; SNPs; population structure; GWAS; myo-inositol phosphate metabolism guar; RADseq; SNPs; population structure; GWAS; myo-inositol phosphate metabolism
Show Figures

Figure 1

MDPI and ACS Style

Grigoreva, E.; Barbitoff, Y.; Changalidi, A.; Karzhaev, D.; Volkov, V.; Shadrina, V.; Safronycheva, E.; Ben, C.; Gentzbittel, L.; Potokina, E. Development of SNP Set for the Marker-Assisted Selection of Guar (Cyamopsis tetragonoloba (L.) Taub.) Based on a Custom Reference Genome Assembly. Plants 2021, 10, 2063. https://doi.org/10.3390/plants10102063

AMA Style

Grigoreva E, Barbitoff Y, Changalidi A, Karzhaev D, Volkov V, Shadrina V, Safronycheva E, Ben C, Gentzbittel L, Potokina E. Development of SNP Set for the Marker-Assisted Selection of Guar (Cyamopsis tetragonoloba (L.) Taub.) Based on a Custom Reference Genome Assembly. Plants. 2021; 10(10):2063. https://doi.org/10.3390/plants10102063

Chicago/Turabian Style

Grigoreva, Elizaveta, Yury Barbitoff, Anton Changalidi, Dmitry Karzhaev, Vladimir Volkov, Veronika Shadrina, Elizaveta Safronycheva, Cécile Ben, Laurent Gentzbittel, and Elena Potokina. 2021. "Development of SNP Set for the Marker-Assisted Selection of Guar (Cyamopsis tetragonoloba (L.) Taub.) Based on a Custom Reference Genome Assembly" Plants 10, no. 10: 2063. https://doi.org/10.3390/plants10102063

Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop