Comparative transcriptomics analysis uncovers alternative splicing events and molecular markers in cabbage (Brassica oleracea L.)

Xu, Yuanyuan; Zeng, Aisong; Song, Lixiao; Li, Jiaqing; Yan, Jun

doi:10.1007/s00425-019-03108-3

Cited by 13 publications

(5 citation statements)

References 67 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…SSR markers are highly variable, abundant, reproducible, and transferrable, with co-dominant and multi-allelic inheritance; as a result, they are the precious and creditable approaches to carry out gene tapping, genetic mapping, comparative mapping, and genetic diversity analyses on plant species ( Li et al, 2012 ; Silva et al, 2013 ). Generally, SSR markers are developed dependent on SSR motifs as well as the corresponding flanking sequences, and they may be separated from non-coding nt sequences or conserved coding regions in each higher organism ( Sraphet et al, 2011 ; Xu et al, 2019 ). Cross-species amplification has been conducted to discover SSR markers that can be used in plant research, and it is related to the selection of genomic libraries or SSR-abundant cDNA and the search of open databases ( Yang et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

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

Xing

Song

et al. 2021

Front. Plant Sci.

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Section: Introductionmentioning

confidence: 99%

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

Xing

Song

et al. 2021

Front. Plant Sci.

Self Cite

View full text Add to dashboard Cite

show abstract

“…In Arabidopsis , simple IR code: “0, 1ˆ2-” from AStalavista extracted just a little over half of all IR events, yielding a frequency of 24.21% when the total IR frequency is in fact ~40% ( Marquez et al., 2012 ). In cabbage ( Brassica oleracea ), A3SS (10.31%) was the most frequent simple AS event, while complex AS (69.86%) was predominant ( Xu et al., 2019 ). Thus, ES frequencies in plants may have been under-estimated.…”

Section: Discussionmentioning

confidence: 99%

“…By contrast, in animals the most frequent AS event is ES ( Reddy et al., 2013 ; Zhang et al., 2017b ; Wang et al., 2019 ; Jia et al, 2020 ). A handful of reports in plants have identified A3SS ( Tang et al., 2016 ; Shi et al., 2019 ) or ES ( Xu et al., 2019 ; Xia et al., 2020 ) as the most frequent AS event, when considering large datasets comprising over 1000 AS events. Among many software tools exist for AS detection, AStalavista and rMATS are widely accepted in plants ( Song et al., 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Temporal regulation of alternative splicing events in rice memory under drought stress

Yang

Jin

et al. 2022

Plant Diversity

View full text Add to dashboard Cite

“…The transition/transversion (Ti/Tv) ratio in the Raphanus species was 1.47-1. (Hua et al, 2018;S.-G. Park et al, 2021;Xu et al, 2019). The initial variations were further filtered based on stringent criteria for downstream analysis: bi-allelic variation for all genotypes, ≥10 mapped reads per variant locus, a <50% missing rate, and >10% minor allele frequency.…”

Section: Rootmentioning

confidence: 99%

Characterization of agronomic traits and genomic diversity in a newly assembled radish core collection

Huh,

Cho,

Yim

et al. 2023

Crop Science

View full text Add to dashboard Cite

Crop breeding programs are reliant on the genetic diversity of varieties and germplasm collections. Raphanus sativus L. is a root crop species of the Brassicaceae family that accounts for approximately 2% of global vegetable production. We recently reported the assembly of a new radish core collection consisting of 125 accessions obtained from worldwide germplasm banks. To develop a comprehensive plant resource for radish research and breeding, we characterized the agronomic traits of 83 accessions and analyzed their genome‐wide DNA variations along with 17 previously analyzed accessions. A total of 14 agronomically important root, leaf, and flower phenotypic traits were examined according to the guidelines of the International Union for the Protection of New Plant Varieties. Chemical diversity in radish roots was investigated by measuring their sugar, glucosinolate, and anthocyanin contents. Through high‐depth whole‐genome resequencing of 100 accessions and multi‐sample genotyping analysis using the Rs2.0 genome assembly as a reference, we identified a total of 796,294 homozygous high‐quality single‐nucleotide polymorphisms. Genetic structural analysis using a neighbor‐joining algorithm and multi‐dimensional scaling analysis of the variations were applied to classify the accessions into three major groups, including 37 and 55 accessions of European and Asian cultivated radishes, respectively, and 8 wild radish accessions. For each accession, the mitochondria‐encoded Ogura cytoplasmic male‐sterility determinant orf138 and nuclear fertility restorer PPR‐B genes were reconstructed by reference‐guided assembly. It is anticipated that these genetic diversity and agronomic properties of the radish core collection will facilitate breeding programs to develop new radish cultivars with desirable profiles.This article is protected by copyright. All rights reserved

show abstract

Comparative transcriptomics analysis uncovers alternative splicing events and molecular markers in cabbage (Brassica oleracea L.)

Cited by 13 publications

References 67 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.)

Temporal regulation of alternative splicing events in rice memory under drought stress

Characterization of agronomic traits and genomic diversity in a newly assembled radish core collection

Contact Info

Product

Resources

About