TY - JOUR

T1 - Development of SNP set for the marker-assisted selection of guar (Cyamopsis tetragonoloba (L.) Taub.) based on a custom reference genome assembly

AU - Grigoreva, Elizaveta

AU - Barbitoff, Yury

AU - Changalidi, Anton

AU - Karzhaev, Dmitry

AU - Volkov, Vladimir

AU - Shadrina, Veronika

AU - Safronycheva, Elizaveta

AU - Ben, Cécile

AU - Gentzbittel, Laurent

AU - Potokina, Elena

N1 - Publisher Copyright: © 2021 by the author. Licensee MDPI, Basel, Switzerland.

PY - 2021/10

Y1 - 2021/10

N2 - 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 In-dia, 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.

AB - 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 In-dia, 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.

KW - Guar

KW - GWAS

KW - Myo-inositol phosphate metabolism

KW - Population structure

KW - RADseq

KW - SNPs

UR - http://www.scopus.com/inward/record.url?scp=85116056079&partnerID=8YFLogxK

U2 - 10.3390/plants10102063

DO - 10.3390/plants10102063

M3 - Article

AN - SCOPUS:85116056079

VL - 10

JO - Plants

JF - Plants

SN - 2223-7747

IS - 10

M1 - 2063

ER -