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

Abstract

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.

In silico Identification of miRNAs and Their Targets in Cluster Bean for Their Role in Development and Physiological Responses

“…Despite, high industrial importance of the guar gum this crop is considered as orphan as little progress has been made and availability of genetic and genomic resources is very limited in this crop ( Ravelombola et al, 2021 ). Recently, advanced molecular and genomic approaches have been utilized in this orphan crop to combat the yield losses and elucidate the function of galactomannan related genes ( Al-Qurainy et al, 2019 ; Kumar et al, 2020 ; Rajaprakasam et al, 2021 ; Grigoreva et al, 2021a ; Grigoreva et al, 2021b ; Acharya et al, 2022 ). Attempts have also been made to sequence cluster bean genome ( Grigoreva et al, 2019 ); however, this first sequencing attempt has a gap of 50% ( Grigoreva et al, 2019 ).…”

Dissection of figured wood trait in curly birch (Betula pendula var. carelica) using high-throughput genotyping

“…A detailed protocol has been previously described and validated by our research group for the genotyping of various plant species, e.g. aspen 16 , guar 17 and grapevine 18 . Total DNA was isolated by a modified CTAB method according to the protocol 19 and stored at -20 °C until needed.…”

“…A detailed protocol has been previously described and validated by our research group for the genotyping of various plant species, e.g. aspen 16 , guar 17 and grapevine 18 .…”

СЕЛЕКЦИЯ ГУАРА В РОССИЙСКОЙ ФЕДЕРАЦИИ В СВЯЗИ С ПЕРСПЕКТИВОЙ ПРОИЗВОДСТВА ОТЕЧЕСТВЕННОЙ КАМЕДИ (Обзор)

“…SSR использовали для изучения генетического разнообразия (49). Выделены SNP, которые могут быть эффективны в отношении признака, определяющего высокую семенную продуктивность гуара, -числа вызревших бобов на растении (50). Однако число полученных маркеров для генома гуара все еще значительно меньше, чем у других бобовых с секвенированными геномами, и пока недостаточно для селекционных программ нового поколения.…”