Genome-Wide Microsatellite Characterization and Marker Development in the Sequenced Brassica Crop Species

Shi, J.; Huang, S.; Zhan, Jinyi; Yu, J.; Wang, X.; Hua, W.; Liu, S.; Liu, G.; Wang, H.

doi:10.1093/dnares/dsu011

Cited by 9 publications

(13 citation statements)

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“…Tri-and hexanucleotide SSRs were generally found to have the highest GC contents. The results also suggested that (A/T) n motifs are the most predominant in each genome, consistent with findings in previous reports (Sharma et al 2007;Shi et al 2013;Li et al 2016). This can be interpreted as confirming high AT content in the majority of the analyzed SSRs.…”

Section: Discussionsupporting

confidence: 91%

“…Among trinucleotide SSRs, the (AAT) n motif was the most predominant in C. nucifera, C. simplicifolius, and E. guineensis, and consistent with reports from garden asparagus (Li et al 2016), cucumber (Cavagnaro et al 2010), pineapple (Fang et al 2016), and Medicago truncatula and Populus trichocarpa (Sonah et al 2011). The (AAG) n was the dominant trinucleotide motif in P. dactylifera and E. oleifera, similar to previous reports in Arabidopsis thaliana (Sonah et al 2011) and Brassica species (Shi et al 2013). The AT-rich motifs (AAAT) n , (AAAG) n , (AATT) n , (AAAAT) n , (AAAAG) n , (AATAT) n , (AAATT) n , (AAAAAT) n , (ACATAT) n , and (AAAAAG) n were the most abundant tetra-, penta-and hexanucleotide SSRs in the five palm genomes.…”

Section: Discussionsupporting

confidence: 91%

“…Previously, microsatellite abundances were found to be similar in species of the same genus (Shi et al 2014). Here, only E. oleifera and E. guineensis are classified into the same genus, and these species did not have similar profiles overall.…”

Section: Discussionmentioning

confidence: 56%

“…Overall, the overrepresentation of (AT) n motifs in palm genomes can be explained by the fact that strand separation is easier for AT-rich than for GC-rich sequences, raising the possibility of slipped strand mispairing (Zhao et al 2011). A previous study revealed that the (AAAT) n , (AAAAT) n , (AAAAT) n , and (AAAAAT) n motifs also predominated in Brassica species (Shi et al 2013).…”

Section: Discussionmentioning

confidence: 95%

“…The high mutation rates of SSRs make them highly informative and useful for a wide range of applications such as evolutionary research, population genotyping, and markerassisted breeding. Recent studies have utilized genomewide approaches for the development of SSR markers in plants (Shi et al 2014;Deng et al 2016;Kumari et al 2019). Perhaps the main advantage of this strategy is to produce a large number of SSR markers distributed evenly throughout the genome.…”

Section: Discussionmentioning

confidence: 99%

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Genome-wide characterization of simple sequence repeats in Palmae genomes

2020

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Background Microsatellites or simple sequence repeats (SSRs) have become the most significant DNA marker technology used in genetic research. The availability of complete draft genomes for a number of Palmae species has made it possible to perform genome-wide analysis of SSRs in these species. Palm trees are tropical and subtropical plants with agricultural and economic importance due to the nutritional value of their fruit cultivars. Objective This is the first comprehensive study examining and comparing microsatellites in completely-sequenced draft genomes of Palmae species. Methods We identified and compared perfect SSRs with 1-6 bp nucleotide motifs to characterize microsatellites in Palmae species using PERF v0.2.5. We analyzed their relative abundance, relative density, and GC content in five palm species:

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Section: Discussionsupporting

confidence: 91%

Section: Discussionsupporting

confidence: 91%

Section: Discussionmentioning

confidence: 56%

Section: Discussionmentioning

confidence: 95%

Section: Discussionmentioning

confidence: 99%

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Genome-wide characterization of simple sequence repeats in Palmae genomes

2020

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Genome wide simple sequence repeats development and their application in genetic diversity analysis in wax gourd (Benincasa hispida)

Wang

Jiang

et al. 2022

Plant Breeding

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Wax gourd is one of the most important winter vegetables of the Cucurbitaceae family. There are only limited markers available for this crop and the draft genome of wax gourd provides a powerful tool for simple sequence repeats (SSR) marker development. In this study, we developed genome‐wide SSR markers from wax gourd genome and characterized their distribution and frequency of different motifs and repeats. A total of 52,431 microsatellites from wax gourd genome were identified, of which 39,319 SSR markers were developed. The 1152 non‐wax gourd SSR markers were selected from cucumber, melon, watermelon and pumpkin to test their transferability in wax gourd. The 580 SSR markers could be transferable in wax gourd, and 42 of them were detected with polymorphic in 11 tested accessions of wax gourd. In addition, 11 good polymorphic transferrable SSR markers and 21 SSR markers of wax gourd were selected to investigate the genetic diversity and population structure of 129 wax gourd accessions. One hundred twelve alleles were detected by these 32 SSR markers. The result of population structure showed that the 129 wax gourd accessions were divided into two main populations, and the genetic diversity analysis separated them into two clusters. The large number of wax gourd SSR markers developed in this study provides a valuable resource for genetic linkage map construction, molecular mapping, and marker‐assisted selection (MAS) in wax gourd.

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Development of novel SSR molecular markers using a Next-Generation Sequencing approach (ddRADseq) in Stetsonia coryne (Cactaceae)

Gutiérrez

Filippi

Aguirre

et al. 2021

An. Acad. Bras. Ciênc.

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The Cactaceae family is native to the American continent with several centers of diversity. In South America, one of these centers is the Central Andes and many species are considered to be threatened or vulnerable according to the International Union for Conservation of Nature (IUCN). Stetsonia coryne is an emblematic giant columnar cacti of the Chaco phytogeographic province. It has an extensive geographical distribution in many countries of the continent. However, to date there are no specifi c molecular markers for this species, neither reports of population genetic variability studies, such as for many cactus species. The lack of information is fundamentally due to the lack of molecular markers that allow these studies. In this work, by applying a Genotyping by Sequencing (GBS) technique, we developed polymorphic SSR markers for the Stetsonia coryne and evaluated their transferability to phylogenetically close species, in order to account for a robust panel of molecular markers for multispecies-studies within Cactaceae.

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Genome-Wide Microsatellite Characterization and Marker Development in the Sequenced Brassica Crop Species

Cited by 9 publications

References 0 publications

Genome-wide characterization of simple sequence repeats in Palmae genomes

Genome-wide characterization of simple sequence repeats in Palmae genomes

Genome wide simple sequence repeats development and their application in genetic diversity analysis in wax gourd (Benincasa hispida)

Development of novel SSR molecular markers using a Next-Generation Sequencing approach (ddRADseq) in Stetsonia coryne (Cactaceae)

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