Genome-wide microsatellites in amaranth: development, characterization, and cross-species transferability

Tiwari, Kapil K.; Thakkar, Nevya J; Dharajiya, Darshan T.; Bhilocha, Hetal L; Barvaliya, Parita P; Galvadiya, Bhemji P.; Prajapati, N. N.; Patel, M. B.; Solanki, Satyanarayan

doi:10.1007/s13205-021-02930-5

Cited by 9 publications

(6 citation statements)

References 45 publications

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“…In addition, SSRs were identified within Amaranthaceae, as it proved to be a stepping stone for the genetic dissection of complex traits for crop enhancement and varietal development. Genome-wide SSRs were mined as they provide insight into gene regulation and genome organization; these are highly polymorphic, facilitating better map coverage [ 42 , 43 ]. It was observed that intergenic SSRs were more abundant than genic SSRs.…”

Section: Discussionmentioning

confidence: 99%

“…A total of 170,477 protein-coding genes were predicted in five amaranth species. The highest number of genes was present in the A. palmeri genome (48,625), followed by A. cruentus (43,382), A. tuberculatus (30,771), A. hypochondriacus (23,883), and A. hybridus genome (23,820), respectively. The genes were distributed throughout the sixteen scaffolds in A. hypochondriacus, A. tuberculatus, A. hybridus, and A. palmeri, while in A. cruentus, genes were distributed in seventeen chromosomes, as chromosome 2 was disseminated into chromosomes 2A and 2B.…”

Section: Gene Content Distribution and Functional Annotationmentioning

confidence: 99%

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Genome-Wide Comparative Analysis of Five Amaranthaceae Species Reveals a Large Amount of Repeat Content

Singh,

Maurya,

Rajkumar

et al. 2024

Plants

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Amaranthus is a genus of C4 dicotyledonous herbaceous plant species that are widely distributed in Asia, Africa, Australia, and Europe and are used as grain, vegetables, forages, and ornamental plants. Amaranth species have gained significant attention nowadays as potential sources of nutritious food and industrial products. In this study, we performed a comparative genome analysis of five amaranth species, namely, Amaranthus hypochondriacus, Amaranthus tuberculatus, Amaranthus hybridus, Amaranthus palmeri, and Amaranthus cruentus. The estimated repeat content ranged from 54.49% to 63.26% and was not correlated with the genome sizes. Out of the predicted repeat classes, the majority of repetitive sequences were Long Terminal Repeat (LTR) elements, which account for about 13.91% to 24.89% of all amaranth genomes. Phylogenetic analysis based on 406 single-copy orthologous genes revealed that A. hypochondriacus is most closely linked to A. hybridus and distantly related to A. cruentus. However, dioecious amaranth species, such as A. tuberculatus and A. palmeri, which belong to the subgenera Amaranthus Acnida, have formed their distinct clade. The comparative analysis of genomic data of amaranth species will be useful to identify and characterize agronomically important genes and their mechanisms of action. This will facilitate genomics-based, evolutionary studies, and breeding strategies to design faster, more precise, and predictable crop improvement programs.

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Section: Discussionmentioning

confidence: 99%

Section: Gene Content Distribution and Functional Annotationmentioning

confidence: 99%

Genome-Wide Comparative Analysis of Five Amaranthaceae Species Reveals a Large Amount of Repeat Content

Singh,

Maurya,

Rajkumar

et al. 2024

Plants

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“…as molecular markers in species authentication, population genetics, and phylogeny analysis owing to their high substitution rates [74][75][76]. A total of 59, 42, 58, and 56 SSRs were detected in the CP genomes of I. tectorum, I. japonica, I. dichotoma, and I. domestica, respectively (Table 3 and 0 Table S4), including 38, 22, 35, and 33 mononucleotide SSRs; 11, 10, 13, and 12 dinucleotide SSRs; 4, 4, 3, and 3 trinucleotide SSRs; 3, 4, 4, and 4 tetranucleotide SSRs; 3, 1, 2, and 3 pentanucleotide SSRs; and 0, 1, 1, and 1 hexanucleotide SSRs, respectively (Table S4 and Figure 3).…”

Section: Ssr and Long Repeat Sequences Cp Ssrs Have Been Usedmentioning

confidence: 99%

Comparison Analysis Based on Complete Chloroplast Genomes and Insights into Plastid Phylogenomic of Four Iris Species

Feng

Wang

et al. 2022

BioMed Research International

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Iris species, commonly known as rainbow flowers because of their attractive flowers, are extensively grown in landscape gardens. A few species, including Belamcanda chinensis, the synonym of I. domestica and I. tectorum, are known for their medicinal properties. However, research on the genomes and evolutionary relationships of Iris species is scarce. In the current study, the complete chloroplast (CP) genomes of I. tectorum, I. dichotoma, I. japonica, and I. domestica were sequenced and compared for their identification and relationship. The CP genomes of the four Iris species were circular quadripartite with similar lengths, GC contents, and codon usages. A total of 113 specific genes were annotated, including the ycf1 pseudogene in all species and rps19 in I. japonica alone. All the species had mononucleotide (A/T) simple sequence repeats (SSRs) and long forward and palindromic repeats in their genomes. A comparison of the CP genomes based on mVISTA and nucleotide diversity (Pi) identified three highly variable regions (ndhF-rpl32, rps15-ycf1, and rpl16). Phylogenetic analysis based on the complete CP genomes concluded that I. tectorum is a sister of I. japonica, and the subgenus Pardanthopsis with several I. domestica clustered into one branch is a sister of I. dichotoma. These findings confirm the feasibility of superbarcodes (complete CP genomes) for Iris species authentication and could serve as a resource for further research on Iris phylogeny.

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“…Genetic diversity is evaluated by estimating variations in quantitative and qualitative characters, although sometimes it is limited to characterization of quantitative traits affected by environmental situations. Hence, molecular diversity is also utilized for the estimation of variability among genotypes and germplasms (DHARAJIYA et al, 2021). Good amount of diversity has been reported in cowpea for various morphological characters (GHALMI et al, 2010;LAZARIDI et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

“…The advancements of molecular markers technology have broadened the area of genotyping and genetic diversity analysis by potentially revealing a large amount of genetic variation even between closely related taxa (GELOTAR et al, 2019). Molecular markers are quicker and far more precise in the species and genotypes identification (TIWARI et al, 2021). Simple sequence repeat (SSR) or microsatellite markers have proved to be polymorphic robust, multi-allelic in nature, highly reproducible but require nucleotide information for primer design (KALIA et al, 2011;PARITA et al, 2018;KAPURIA et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Morphological and molecular characterization of cowpea (Vigna unguiculata L. Walp.) genotypes

Patel

Dharajiya

et al. 2022

Genetika

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Cowpea [Vigna unguiculata (L.) Walp.], is a legume and one of the most ancient crops known to man and grown in tropical and subtropical regions. Cowpea seeds have a high nutritional value containing high amount of protein (20-25%). Despite of its importance, the utilization of genetic diversity and germplasm characterization in cowpea breeding program has not been fully exploited. Therefore, twelve morphological characters and six polymorphic microsatellite/simple sequence repeat (SSRs) markers were used to analyze genetic diversity in thirty-eight cowpea genotypes. The dendrogram was constructed using UPGMA algorithm and Gower?s dissimilarity values (ranged from 0.0601 to 0.5589) derived from twelve morphological characters. It was grouped in seven clusters showing the most diverse genotypes were CGD 1246 and CGD 1311 (Gower?s distance: 0.5589) and the most similar genotypes were GC 1501 and GC 1601 (Gower?s distance: 0.0601). In molecular characterization, a total of 14 amplicons were detected with a ranged from two to three with an average 2.33 alleles per loci. The mean values of polymorphic information content (PIC) and heterozygosity was 0.319 and 0.399, respectively which are measures of the efficiency of markers for studying polymorphism level available in the cowpea genotypes. Total 224 amplicons were considered for to derive Jaccard?s similarity matrix for the construction of dendrogram (having six clusters) and 2-D PCA (Principal Component Analysis) plot. The morphological characters and SSR markers can be used in diversity analysis and characterization of cowpea genotypes. The per se performing genotypes for individual character can be exploited in population/genotype development of cowpea for the improvement of that particular character. This will provide information to plant breeders for selection of parents to develop populations in cowpea breeding programs.

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Genome-wide microsatellites in amaranth: development, characterization, and cross-species transferability

Cited by 9 publications

References 45 publications

Genome-Wide Comparative Analysis of Five Amaranthaceae Species Reveals a Large Amount of Repeat Content

Genome-Wide Comparative Analysis of Five Amaranthaceae Species Reveals a Large Amount of Repeat Content

Comparison Analysis Based on Complete Chloroplast Genomes and Insights into Plastid Phylogenomic of Four Iris Species

Morphological and molecular characterization of cowpea (Vigna unguiculata L. Walp.) genotypes

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