Comprehensive Analyses of Simple Sequence Repeat (SSR) in Bamboo Genomes and Development of SSR Markers with Peroxidase Genes

Microsatellites or SSRs are small tandem repeats that are 1–6 bp long. They are usually highly polymorphic and form important portions of genomes. They have been extensively analyzed in humans, animals and model plants; however, information from non-flowering plants is generally lacking. Here, we examined 29 samples of Ophioglossaceae ferns, mainly from the genera Botrychium and Sceptridium. We analyzed the SSR distribution, density and composition in almost 400 nuclear exons and their flanking regions. We detected 45 SSRs in exons and 1475 SSRs in the flanking regions. In the exons, only di-, tri- and tetranucleotides were found, and all of them were 12 bp long. The annotation of the exons containing SSRs showed that they were related to various processes, such as metabolism, catalysis, transportation or plant growth. The flanking regions contained SSRs from all categories, with the most numerous being dinucleotides, followed by tetranucleotides. More than one-third of all the SSRs in the flanking regions were 12 bp long. The SSR densities in the exons were very low, ranging from 0 to 0.07 SSRs/kb, while those in the flanking regions ranged from 0.24 to 0.81 SSRs/kb; and those in the combined dataset ranged from 0.2 to 0.81 SSRs/kb. The majority of the detected SSRs in the flanking regions were polymorphic and present at the same loci across two or more samples but differing in the number of repeats. The SSRs detected here may serve as a basis for further population genetic, phylogenetic or evolutionary genetic studies, as well as for further studies focusing on SSRs in the genomes and their roles in adaptation, evolution and diseases.

Section: Discussioncontrasting

confidence: 58%

Microsatellite Content in 397 Nuclear Exons and Their Flanking Regions in the Fern Family Ophioglossaceae

Koubínová,

Grant

2024

“…SSRs are classified as simple and compound types. The perfect SSRs with a length of 20 bases or above contain continuous repetitions without any interruption, and compound SSRs are interrupted by a non-repetitive nucleotide sequence with a length of 100 bases [ 41 ]. 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.…”

Section: Discussionmentioning

confidence: 99%

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

Singh,

Maurya,

Rajkumar

et al. 2024

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.

“…Although the range is similar, the primers used for these species were different. The fourteen SSR markers detected a lesser total number of alleles (159) and a range of alleles per marker (2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12) among Strychnos spinosa morphotypes (Table 1) compared with the total number (207) and the range of alleles per marker (6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17) detected in Passiflora edulis Sims accessions [21]. A range in major allele frequency from 0.24 to 0.85 with an average of 0.51 in this study (Table 1) was similar to the range (0.17-0.94) and average (0.56) among Psidium genotypes [21].…”

Section: Allelic Profile Of Simple Sequence Repeatsmentioning

confidence: 99%

“…Molecular markers have become an important instrument for characterizing wild and cultivated germplasm during the last decades [11]. Simple sequence repeat (SSR) markers are the most suitable genetic markers due to their multi-allelic nature and co-dominant inheritance, large genome coverage, small amount of starting DNA required, easy detection by polymerase chain reaction, and high polymorphism [5,12]. However, there are no microsatellite (SSR) markers available for Strychnos spinosa, and currently no study has been reported on the molecular diversity of Strychnos spinosa morphotypes.…”

Section: Introductionmentioning

confidence: 99%

Assessing Genetic Variation among Strychnos spinosa Lam. Morphotypes Using Simple Sequence Repeat Markers

Mbhele,

Zharare,

Zimudzi

et al. 2023

Strychnos spinosa Lam., commonly known as green monkey orange, is a highly valued indigenous fruit tree in South Africa with potential for domestication and commercialization. However, no study has reported on the molecular diversity of Strychnos spinosa morphotypes. Therefore, this study aimed to determine genetic variation among 32 Strychnos spinosa morphotypes using simple sequence repeat (SSR) markers. Fourteen amplified SSR markers produced 159 alleles, with a mean of 5.68 per locus. The polymorphic information content (PIC) values ranged from 0.22 (Ssp_1) to 0.84 (Ssp_6). Morphotypes were clustered in a biplot based on their genetic distances. The dendrogram chiefly discriminated morphotypes according to variation of pericarp texture. The population structure had the highest delta value K = 3, thus the 32 morphotypes were divided into three subpopulations based on the Bayesian approach. The affinities produced by the population structure agreed with the genetic distance of closely related morphotypes. This study is the first to report on SSR marker development and their successful use for genetic diversity and population structure studies of Strychnos spinosa. It provides insights into the molecular characterisation of Strychnos spinosa. This can lead to breeding programs and crop improvement programs, particularly in varietal developmental programs, which can contribute to alleviating food security challenges.