Development of genomic microsatellite markers in cluster bean using next-generation DNA sequencing and their utility in diversity analysis

Kumar, Sushil; Palve, Adinath; Patel, Swati; Selvanayagam, Sivasubramani; Sharma, Ramavtar; Rathore, Abhishek

doi:10.1016/j.cpb.2019.100134

Cited by 18 publications

(10 citation statements)

References 21 publications

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“…On the other hand, sequence-based markers, namely, simple sequence repeats (SSRs), single nucleotide polymorphism (SNPs), and their modifications, being more reliable and reproducible, are employed in linkage mapping, trait mapping, and fine-mapping studies. SSR marker systems are available in pigeon pea [ 58 ], cluster bean [ 59 ], winged bean [ 33 ], and cowpea [ 60 ], whereas inter-species SSRs have been used in dolichos bean [ 61 , 62 ]. SNPs are markers of choice owing to their ubiquitous nature and abundance in the genome.…”

Section: Molecular Markers From Diversity To Qtlsmentioning

confidence: 99%

“…Later on, the same set of EST was utilized to develop SSRs and was used to validate 32 diverse genotypes [ 74 ]. Recently, a total of 73,934 sequences were developed in the GG-4 variety by Mi seq NGS technology [ 59 ]. Later in the process, these sequences were mined for SSRs and resulting in finding 15,399 SSRs [ 59 ].…”

Section: Molecular Markers From Diversity To Qtlsmentioning

confidence: 99%

“…Recently, a total of 73,934 sequences were developed in the GG-4 variety by Mi seq NGS technology [ 59 ]. Later in the process, these sequences were mined for SSRs and resulting in finding 15,399 SSRs [ 59 ]. In future, marker development studies in vegetable legumes would need to be explored to generate genomic resources and genic markers as has been done in other crops.…”

Section: Molecular Markers From Diversity To Qtlsmentioning

confidence: 99%

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Developments and Prospects in Imperative Underexploited Vegetable Legumes Breeding: A Review

Dhaliwal

Talukdar

Gautam

et al. 2020

IJMS

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Vegetable legumes are an essential source of carbohydrates, vitamins, and minerals, along with health-promoting bioactive chemicals. The demand for the use of either fresh or processed vegetable legumes is continually expanding on account of the growing consumer awareness about their well-balanced diet. Therefore, sustaining optimum yields of vegetable legumes is extremely important. Here we seek to present d etails of prospects of underexploited vegetable legumes for food availability, accessibility, and improved livelihood utilization. So far research attention was mainly focused on pulse legumes’ performance as compared to vegetable legumes. Wild and cultivated vegetable legumes vary morphologically across diverse habitats. This could make them less known, underutilized, and underexploited, and make them a promising potential nutritional source in developing nations where malnutrition still exists. Research efforts are required to promote underexploited vegetable legumes, for improving their use to feed the ever-increasing population in the future. In view of all the above points, here we have discussed underexploited vegetable legumes with tremendous potential; namely, vegetable pigeon pea (Cajanus cajan), cluster bean (Cyamopsis tetragonoloba), winged bean (Psophocarpus tetragonolobus), dolichos bean (Lablab purpureus), and cowpea (Vigna unguiculata), thereby covering the progress related to various aspects such as pre-breeding, molecular markers, quantitative trait locus (QTLs), genomics, and genetic engineering. Overall, this review has summarized the information related to advancements in the breeding of vegetable legumes which will ultimately help in ensuring food and nutritional security in developing nations.

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Section: Molecular Markers From Diversity To Qtlsmentioning

confidence: 99%

Section: Molecular Markers From Diversity To Qtlsmentioning

confidence: 99%

Section: Molecular Markers From Diversity To Qtlsmentioning

confidence: 99%

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Developments and Prospects in Imperative Underexploited Vegetable Legumes Breeding: A Review

Dhaliwal

Talukdar

Gautam

et al. 2020

IJMS

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“…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 ).…”

Section: Discussionmentioning

confidence: 99%

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

Chaudhary

Jangra²,

Yadav³

2022

Front. Genet.

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Cluster bean popularly known as “guar” is a drought-tolerant, annual legume that has recently emerged as an economically important crop, owing to its high protein and gum content. The guar gum has wide range of applications in food, pharma, and mining industries. India is the leading exporter of various cluster bean-based products all across the globe. Non-coding RNAs (miRNAs) are involved in regulating the expression of the target genes leading to variations in the associated pathways or final protein concentrations. The understanding of miRNAs and their associated targets in cluster bean is yet to be used to its full potential. In the present study, cluster bean EST (Expressed Sequence Tags) database was exploited to identify the miRNA and their predicted targets associated with metabolic and biological processes especially response to diverse biotic and abiotic stimuli using in silico approach. Computational analysis based on cluster bean ESTs led to the identification of 57 miRNAs along with their targets. To the best of our knowledge, this is the first report on identification of miRNAs and their targets using ESTs in cluster bean. The miRNA related to gum metabolism was also identified. Most abundant miRNA families predicted in our study were miR156, miR172, and miR2606. The length of most of the mature miRNAs was found to be 21nt long and the range of minimal folding energy (MFE) was 5.8–177.3 (−kcal/mol) with an average value of 25.4 (−kcal/mol). The identification of cluster bean miRNAs and their targets is predicted to hasten the miRNA discovery, resulting in better knowledge of the role of miRNAs in cluster bean development, physiology, and stress responses.

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“…Another RNA-Seq-based transcriptome analysis of leaf, shoot, and flower tissues of the ‘RGC-936′ variety identified a different set of 8,687 potential SSRs, which were further embedded into the ‘ClustergeneDB’ database that allows user to retrieve information about cluster bean unigenes [ 5 ]. Yet another large set of 15,399 microsatellite marker-pairs was designed based on the results of next generation DNA sequencing of the ‘GG-4′ guar variety [ 7 ]. Finally, transcriptomes of three guar cultivars (‘M-18′, ‘RGC-1066′, and ‘RGC-936′) were used for short genetic variant discovery [ 8 ] using the unpublished draft genome assembly of the ‘RGC-936′ cultivar [ 9 ].…”

Section: Introductionmentioning

confidence: 99%

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

Grigoreva

Barbitoff

Changalidi

et al. 2021

Plants

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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.

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Development of genomic microsatellite markers in cluster bean using next-generation DNA sequencing and their utility in diversity analysis

Cited by 18 publications

References 21 publications

Developments and Prospects in Imperative Underexploited Vegetable Legumes Breeding: A Review

Developments and Prospects in Imperative Underexploited Vegetable Legumes Breeding: A Review

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

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

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