Genome-Wide Analysis of Simple Sequence Repeats in Cabbage (Brassica oleracea L.)

Abstract

Cabbage (Brassica oleracea L. var. capitata) accounts for a critical vegetable crop belonging to Brassicaceae family, and it has been extensively planted worldwide. Simple sequence repeats (SSRs), the markers with high polymorphism and co-dominance degrees, offer a crucial genetic research resource. The current work identified totally 64,546 perfect and 93,724 imperfect SSR motifs in the genome of the cabbage ‘TO1000.’ Then, we divided SSRs based on the respective overall length and repeat number into different linkage groups. Later, we characterized cabbage genomes from the perspectives of motif length, motif-type classified and SSR level, and compared them across cruciferous genomes. Furthermore, a large set of 64,546 primer pairs were successfully identified, which generated altogether 1,113 SSR primers, including 916 (82.3%) exhibiting repeated and stable amplification. In addition, there were 32 informative SSR markers screened, which might decide 32 cabbage genotypes for their genetic diversity, with level of polymorphism information of 0.14–0.88. Cultivars were efficiently identified by the new strategy designating manual diagram for identifying cultivars. Lastly, 32 cabbage accessions were clearly separately by five Bol-SSR markers. Besides, we verified whether such SSRs were available and transferable in 10 Brassicaceae relatives. Based on the above findings, those genomic SSR markers identified in the present work may facilitate cabbage research, which lay a certain foundation for further gene tagging and genetic linkage analyses, like marker-assisted selection, genetic mapping, as well as comparative genomic analysis.

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

“…In this study, SSR markers extracted from peroxidase genes of P. edulis were highly conservative and transferable from P. edulis to some related species in Bambusoideae. The results were consistent with the research on cabbage and popular [ 6 , 17 ]. Meanwhile, a total of 89 alleles with a range of 2 to 16 loci were detected ( Table 2 ), indicating the wide range of diversity among the bamboo accessions.…”

“…SSR identification is mainly relied on in the construction and screening of SSR-enriched libraries in earlier studies [ 4 , 5 ]. In recent years, with the rapid development of next-generation sequencing technology, genome-wide SSR identification has been conducted in plants such as Brassica oleracea [ 6 ], Psidium guajava [ 7 ] and Camellia sinensis [ 8 ], which have been considered as a more effective and comprehensive method [ 3 ]. Moreover, many studies suggest that SSRs in genic regions might affect gene regulation, translation, gene silencing, messenger RNA splicing, and metabolic activities [ 9 , 10 , 11 ].…”

First Report on Development of Genome-Wide Microsatellite Markers for Stock (Matthiola incana L.)

“…Simple sequence repeats (SSRs), also known as microsatellites, are tandemly repeated DNA motifs occurring in both coding and noncoding regions [ 17 , 18 ]. It has been discovered that SSRs are ubiquitous in genomes, with repeat units of 1–6 nt.…”

“…It has been discovered that SSRs are ubiquitous in genomes, with repeat units of 1–6 nt. As the most useful DNA marker system for variety identification and germplasm management, SSR molecular markers have several advantages due to their abundance, high polymorphism, multiple alleles, co-dominance, low-cost, and the ease of assay by PCR [ 17 , 18 ], which have been applied extensively in genetic analysis, such as the analysis of population structure and genetic diversity [ 19 , 20 ], QTL mapping [ 21 , 22 , 23 ], marker-assisted selection breeding [ 24 , 25 , 26 ], and DNA fingerprinting [ 27 , 28 ], etc. SSR molecular markers are rarely used in M. incana [ 11 , 14 ], which is largely due to the fact that SSR molecular markers have not been developed in M. incana .…”

Genome-Wide Survey and Analysis of Microsatellites in Waterlily, and Potential for Polymorphic Marker Development

“…Among them, SSR markers have the advantages of high polymorphism, genome richness and co-dominance in genetic diversity and phylogenetic analysis. Meanwhile, genome-wide microsatellite mining has been carried out on many species, such as Brassica napus [ 8 ], Punica granatum [ 9 ], Brassica oleracea [ 10 ], Fagopyrum tataricum [ 11 ] and Anemone coronaria [ 12 ], which offered novel molecular markers for their genetic improvement and genetic diversity studies. Moreover, in aquatic plants, genome-wide SSR markers of N. nucifera [ 6 ] were mined and polymorphic primers were successfully developed to analyze the inner-species difference and genetic similarities between cultivated and wild lotus.…”