Genome-Wide Identification of Sequence Variations and SSR Marker Development in the Munake Grape Cultivar

Zhong, Huan; Zhang, Fuchun; Zhou, Xiaoming; Pan, Mingqi; Xu, Juan; JingZhe, Hao; Han, Seungbaek; Mei, Chuang; He, Xiahong; Wang, Min; Ji, Jiahui; Shi, Wei; Wu, Xinyu

doi:10.3389/fevo.2021.664835

Cited by 9 publications

(4 citation statements)

References 44 publications

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“…Some molecular markers are used within cabbage, like sequence-related amplified polymorphism (SRAP), universal random amplified polymorphic DNA (RAPD), restriction fragment length polymorphism and amplified fragment length polymorphism (AFLP) markers ( Ikten et al, 2019 ). Currently, informative molecular markers have emerged, which offer precious knowledge for genomic and genetic research on cabbage ( Gadaleta et al, 2012 ; Zhong et al, 2017 ). However, regardless of the development of SSR markers, those developed from cabbage reference genome are lacking compared with those in other crops.…”

Section: Introductionmentioning

confidence: 99%

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

Xing

Song

et al. 2021

Front. Plant Sci.

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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.

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Section: Introductionmentioning

confidence: 99%

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

Xing

Song

et al. 2021

Front. Plant Sci.

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“…These results indicated that WRKY gene family was probably high-conserved in different B. striata germplasms. These newly found SSR primers could be used as molecular markers to identify the members of BsWRKY gene families in different germplasm (Zhong et al, 2021).…”

Section: Est-ssr Polymorphism Of Wrky Genes In Different Germplasms O...mentioning

confidence: 99%

Exploring the role and expression pattern of WRKY transcription factor in the growth and development of Bletilla striata based on transcriptome

Huang

Liu

et al. 2023

Gene Reports

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“…Dunlevy [54] analyzed the genotyping and sodium exclusion phenotype of grape hybrid populations ("K51-40 "×" Schwarzmann") based on SSR characteristics in the genome. Zhong [55] identified sequence variation and developed SSR markers across the whole genome of the Munake Grape Cultivar. Although RNA-seq technology has made great progress in recent years, the largescale development of specific SSR markers for miRNA in grapes has not been reported.…”

Section: Development and Application Of Mirna-ssr Markersmentioning

confidence: 99%

Development, Identification and Validation of a Novel SSR Molecular Marker for Heat Resistance of Grapes Based on miRNA

Zhang,

Song,

et al. 2023

Horticulturae

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The adverse effects of high temperatures on fruit quality and yield have been reported in many studies of grapevines. MiRNAs play crucial roles in plant growth and development and also fulfill functions in regulating the high-temperature response. In this research, miRNA-based SSR (simple sequence repeat) polymorphisms were analyzed according to the grape genome sequence and then combined with polymerase chain reaction (PCR) amplification and Sanger sequencing methods to analyze the miRNA-SSR diversity of different heat-resistant grape varieties. A statistical analysis of SSR sequences showed that 391 and 12 SSRs were specific to pri-miRNA and pre-miRNA, respectively. In pri-miRNA containing SSR, hexa-nucleotide repeats were the most abundant (52.69%), followed by tetra-nucleotide (13.04%) and minimum penta-nucleotide (4.09%), which were also observed in pre-miRNA sequences. On the other hand, differences in heat resistance among grape varieties were observed. Based on the results of leaf Fv/Fm images, values and phenotypic changes under high-temperature stress, 20 heat-resistant (e.g., Niagara Rosada and Grand Noir) and 20 heat-sensitive (e.g., Shine Muscat and Jumeigui) grape varieties were identified. Further, PCR-Sanger sequencing was used to screen SSR differences in four thermos-tolerant and four thermos-sensitive grape varieties, and finally, eight SSR differential primers were found to be able to distinguish these varieties. Of these, four pairs of primers were selected for validation in 40 grape germplasm resources (20 thermo-tolerance and 20 thermo-sensitivity). The VMIRSSR167c3 highlights that the ratio of SSR (CT) repeat values greater than 17 in heat-resistant varieties was 90%. In conclusion, the VMIRSSR167c3 marker can accurately distinguish between heat-resistant and heat-sensitive grape varieties. The results provide a novel molecular marker for the genetic improvement of grape germplasm resources and will be beneficial to the breeding of heat-resistant varieties in the future.

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Genome-Wide Identification of Sequence Variations and SSR Marker Development in the Munake Grape Cultivar

Cited by 9 publications

References 44 publications

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

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

Exploring the role and expression pattern of WRKY transcription factor in the growth and development of Bletilla striata based on transcriptome

Development, Identification and Validation of a Novel SSR Molecular Marker for Heat Resistance of Grapes Based on miRNA

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