Genetic analysis of gene expression for pigmentation in Chinese cabbage (Brassica rapa)

Kim, Chang-Kug; Park, Sung-Han; Kikuchi, Shoshi; Kwon, Soo-Jin; Park, Suhyoung; Yoon, Ung-Han; Park, DongSuk; Seol, Young-Joo; Hahn, Jang-Ho; Park, Soochul; Kim, Donghern

doi:10.1007/s13206-010-4206-9

Cited by 14 publications

(17 citation statements)

References 34 publications

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“…The polygenic effect agrees with Kim et al. () who conducted a microarray study on pigmentation of Chinese cabbage ( B. rapa ) where 38 unknown genes were identified that potentially play a role in anthocyanin biosynthesis. A blast analysis conducted with seedling anthocyanin DArT markers sequences had hit on both chromosome A7 of consensus map and B. rapa genome sequences.…”

Section: Discussionsupporting

confidence: 88%

Quantitative trait loci mapping of seed colour, hairy leaf, seedling anthocyanin, leaf chlorosis and days to flowering in F₂ population of Brassica rapa L.

2014

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A diversity arrays technology (DArT) map was constructed to identify quantitative trait loci (QTL) affecting seed colour, hairy leaf, seedling anthocyanin, leaf chlorosis and days to flowering in Brassica rapa using a F 2 population from a cross between two parents with contrasting traits. Two genes with dominant epistatic interaction were responsible for seed colour. One major dominant gene controls the hairy leaf trait. Seedling anthocyanin was controlled by a major single dominant gene. The parents did not exhibit leaf chlorosis; however, 32% F 2 plants showed leaf chlorosis in the population. A distorted segregation was observed for days to flowering in the F 2 population. A linkage map was constructed with 376 DArT markers distributed over 12 linkage groups covering 579.7 cM. The DArT markers were assigned on different chromosomes of B. rapa using B. rapa genome sequences and DArT consensus map of B. napus. Two QTL (RSC1-2 and RSC12-56) located on chromosome A8 and chromosome A9 were identified for seed colour, which explained 19.4% and 18.2% of the phenotypic variation, respectively. The seed colour marker located in the ortholog to Arabidopsis thaliana Transparent Testa2 (AtTT2). Two QTL RLH6-0 and RLH9-16 were identified for hairy leaf, which explained 31.6% and 20.7% phenotypic variation, respectively. A single QTL (RSAn-12-157) on chromosome A7, which explained 12.8% of phenotypic variation was detected for seedling anthocyanin. The seedling anthocyanin marker is found within the A. thaliana Transparent Testa12 (AtTT12) ortholog. A QTL (RLC6-04) for leaf chlorosis was identified, which explained 55.3% of phenotypic variation. QTL for hairy leaf and leaf chlorosis were located 0-4 cM apart on the same chromosome A1. A single QTL (RDF-10-0) for days to flowering was identified, which explained 21.4% phenotypic variation.Key words: quantitative trait loci -seed colour -hairy leafseedling anthocyanin -leaf chlorosis -days to floweringBrassica rapa Brassica rapa (AA, 2n = 20) is a major oilseed crop in Indian subcontinent and important vegetable in China and many other countries. It is one of the parent species of rapeseed or canola (Brassica napus, AACC, 2n = 38) and is an excellent model system to study polyploidy-related genome evolution with Arabidopsis thaliana and other Brassica species with larger

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Section: Discussionsupporting

confidence: 88%

Quantitative trait loci mapping of seed colour, hairy leaf, seedling anthocyanin, leaf chlorosis and days to flowering in F₂ population of Brassica rapa L.

2014

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“…This microarray is a powerful tool for studying the complex biological responses involved in anthocyanin pigmentation biosynthesis in Chinese cabbage 43 . We performed a five-stage analysis to evaluate gene expression profiles during anthocyanin biosynthesis.…”

Section: Discussionmentioning

confidence: 99%

“…In this study, we used 300K Brassica rapa (version 2.0) microarrays 43 . These microarrays were designed such that seven probes could cover a 150-bp region at the 3′ end of genes.…”

Section: Microarray Experimentsmentioning

confidence: 99%

Computational identification of Chinese cabbage anthocyaninspecific genes

Kim

Kikuchi

et al. 2011

BioChip J

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Therefore, 3,895 candidate genes related to anthocyanin biosynthesis in Chinese cabbage were identified using a 300K Brassica rapa microarray analysis. Gene expression during six stages of leaf developmental stages were examined in FC (green leaf) and FA (red leaf) Chinese cabbage cultivars. The 317 transcription factor genes found to be associated with anthocyanin were classified into 11 functional groups. The ratio of expression levels of each transcription factor between the two cultivars was examined during the six leaf developmental stages. A total of 14 genes were found to be expressed in all developmental stages commonly. Among these genes, 10 unknown and hypothetical genes were differentially revealed to be expressed between the two cultivars at each developmental stage, as determined by microarray analysis, and were verified by RT-PCR validation. These genes most likely play regulatory roles in either anthocyanin production or metabolism during flavonoid biosynthesis. While these genes require further validation and characterization, our results illustrate the potential usefulness of this multi-layered screening method using Chinese cabbage (Brassica rapa) microarrays.

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“…Microarray can be used to elucidate relationships between genes and enables genome-wide analyses under numerous conditions 21 . Several studies have demonstrated the successful use of microarray to analyze gene expression changes in a number of crop species, including black rice 22,23 . Using Ds insertion lines is one of the most important methods in rice breeding and in understanding the function of the genome, including studying gene functions in plants with the Activator/Dissociation (Ac/Ds) transposon 24 .…”

Section: Original Researchmentioning

confidence: 99%

Computational identification of seed-specific transcription factors involved in anthocyanin production in black rice

et al. 2010

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To better understand the functional characterization of anthocyanin gene expression in black rice, we performed a detailed computational examination. The experiment was performed using the newly designed 135K Oryza sativa microarray to assess gene expression at three time points after the heading stage in Ds insertion lines. Transcription factors related to anthocyanin pigmentation biosynthesis were clustered. A total of 8,517 genes exhibited greater than 2.5-fold up-or downregulation in each comparison between three rice groups and three seed developmental stages. The resultant 82 transcription factor genes found to be associated with anthocyanin were classified into 12 groups. In addition, 12 unknown and hypothetical genes were identified from comparisons between the white cultivar and two black Ds insertion mutants tested. We identified 12 unknown and hypothetical genes involved in anthocyanin biosynthesis. These genes likely play either a regulatory role in the anthocyanin production process or are related to anthocyanin metabolism during flavonoid biosynthesis. While these genes require further characterization and validation, the results here underline the potential use of the newly designed microarray.

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Genetic analysis of gene expression for pigmentation in Chinese cabbage (Brassica rapa)

Cited by 14 publications

References 34 publications

Quantitative trait loci mapping of seed colour, hairy leaf, seedling anthocyanin, leaf chlorosis and days to flowering in F₂ population of Brassica rapa L.

Quantitative trait loci mapping of seed colour, hairy leaf, seedling anthocyanin, leaf chlorosis and days to flowering in F₂ population of Brassica rapa L.

Computational identification of Chinese cabbage anthocyaninspecific genes

Computational identification of seed-specific transcription factors involved in anthocyanin production in black rice

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Genetic analysis of gene expression for pigmentation in Chinese cabbage (Brassica rapa)

Cited by 14 publications

References 34 publications

Quantitative trait loci mapping of seed colour, hairy leaf, seedling anthocyanin, leaf chlorosis and days to flowering in F2 population of Brassica rapa L.

Quantitative trait loci mapping of seed colour, hairy leaf, seedling anthocyanin, leaf chlorosis and days to flowering in F2 population of Brassica rapa L.

Computational identification of Chinese cabbage anthocyaninspecific genes

Computational identification of seed-specific transcription factors involved in anthocyanin production in black rice

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Quantitative trait loci mapping of seed colour, hairy leaf, seedling anthocyanin, leaf chlorosis and days to flowering in F₂ population of Brassica rapa L.

Quantitative trait loci mapping of seed colour, hairy leaf, seedling anthocyanin, leaf chlorosis and days to flowering in F₂ population of Brassica rapa L.