Genetic diversity and marker-trait associations in a collection of Pak-choi (Brassica rapa L. ssp. chinensis Makino) Accessions

Yu, Shaohua; Zhang, Fenglan; Wang, Xiaoyi; Zhao, Xiuyun; Zhang, Deshuang; Yu, Yangjun; Xu, J. H.

doi:10.1007/s13258-010-0033-6

Cited by 17 publications

(15 citation statements)

References 28 publications

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“…According to Li et al (2011), correction factors concerning population structure and relative kinship are very crucial even though both had relatively small effect on markertrait association. Our findings are consistent with results from other studies on pak-choi (Yu et al, 2010) and Brassica rapa (Pino Del Carpio et al, 2011).…”

Section: Discussionsupporting

confidence: 93%

“…These results indicate that the marker-trait association attained in model GLM without Q was due to population structure. The inclusion of population structure and relative kinship reduce type I error, thus eliminating false positive associations (Yu et al, 2010). According to Li et al (2011), correction factors concerning population structure and relative kinship are very crucial even though both had relatively small effect on markertrait association.…”

Section: Discussionmentioning

confidence: 99%

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Association of SNP Markers With Height Increment in Mpob-Angolan Natural Oil Palm Populations

W¹

2018

JOPR

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Low height increment is one of the desired traits in oil palm breeding and improvement programmes, as dwarf palms facilitate fruit harvesting and extend the economic life of the crop. In this study, 346 natural oil palms collected from Angola and maintained by the Malaysian Palm Oil Board (MPOB) were used. Analysis of variance (ANOVA) for height increment showed a significant difference (P ≤ 0.001) among families in populations, indicating substantial genetic variation for marker-trait association study. We applied nine carefully selected single nucleotide polymorphism (SNP) markers to genotype the oil palms via cleaved amplified polymorphic sequence (CAPS) method. Population structure analysis involving 18 SNP alleles divided the palms into two sub-populations, with no obvious relative kinship (values < 0.3). For association analysis between the SNP markers and height increment, three models were tested. The incorporation of population structure (Q) and relative kinship (K) as correction factors in the model had helped reduce false positive associations. Generally, the mixed linear model (MLM) with Q + K exhibited a more stringent model with less spurious associations detected. Based on this model, one significant marker SNPG00006_FatI corresponding to indole-3-acetic acid (IAA)-amido synthetase gene was identified to be associated with height increment (P ≤ 0.05). The marker, although potentially specific to MPOB-Angolan germplasm, can assist in introgressing the dwarf phenotype into advanced breeding materials through marker-assisted selection (MAS).

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Section: Discussionsupporting

confidence: 93%

Section: Discussionmentioning

confidence: 99%

Association of SNP Markers With Height Increment in Mpob-Angolan Natural Oil Palm Populations

W¹

2018

JOPR

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“…[2][3][4] and G2 (BcL.1-25 vs BcL. [1][2][3][4] groups, a total of 313 common genes were up-regulated and 308 common genes were down-regulated ( Figure 2A and 2B); while between G1 (BcL.1-25 vs BcL. and G3 (BcL.1-4 vs BcL.…”

Section: Quantity Statistics and Veen Diagram Of Differentially Exprementioning

confidence: 99%

“…One of the most common cultivated vegetables in China, non-heading Chinese cabbage (Brassica rapa ssp. chinensis), also known as Pak-choi, while its growth are often affected, from the surroundings by cold even freezing stresses [1,2]. Low temperature, well known, as an important factor, affecting growth and reducing productivity [3][4][5].…”

Section: Introductionmentioning

confidence: 99%

Transcriptome and small RNA combined sequencing analysis of cold tolerance response in non-heading Chinese cabbage

Wang

Zhang

You

et al. 2020

Preprint

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Background: Non-heading Chinese cabbage ( Brassica rapa ssp. chinensis ), as an important leaf vegetable grown worldwide. However, there is currently no enough transcriptome and small RNA combined sequencing analysis of cold tolerance, which hinders further functional genomics research.Results: In this study, 63.43 Gb of clean data was obtained from the transcriptome analysis. The clean data of each sample reached 6.99 Gb, and the basic percentage of Q30 was 93.68% and above. The clean reads of each sample were sequence aligned with the designated reference genome ( Brassica rapa, IVFCAASv1 ), and the efficiency of the alignment varied from 81.54% to 87.24%. According to the comparison results, 1,860 new genes were discovered, of which 1,613 were functionally annotated. Among them, 13 common differentially expressed genes were detected in all materials, including 7 up-regulated and 6 down-regulated. At the same time, we used quantitative real-time PCR to confirm the changes of these gene expression levels. In addition, we sequenced miRNA of the same material. Our findings revealed a total of 34,182,333 small RNA reads, 88,604,604 kinds of small RNA, among which the most common size was 24 nt. In all materials, the number of common differential miRNAs is 8. According to the corresponding relationship between miRNA and its target genes, we carried out Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis on the set of target genes that each group of differentially expressed miRNAs. Through the analysis, it is found that the distribution of candidate target genes in different materials is different. We not only use transcriptome sequencing and small RNA sequencing, but also use experiment to prove that the expression level of differentially expressed genes are obtained by sequencing. Sequencing combined with experiments proved the mechanism of some differential gene expression levels after low temperature treatment.Conclusions: In all, this study provides a resource for genetic and genomic research under abiotic stress in Pak-choi.

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“…SSR markers have been utilized in genetic diversity analysis of Pak-choi. Yu et al (2010) evaluated the genetic diversity of 80 Pak-choi inbred lines using 20 SSR markers. However, to date, no studies related to varietal identification in Pak-choi have been reported.…”

mentioning

confidence: 99%

Validation of a set of informative simple sequence repeats markers for variety identification in Pak‐choi (Brassica rapa L. ssp. chinensis var. communis)

Zhao

Sui

et al. 2017

Plant Breeding

Self Cite

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A core set of 21 simple sequence repeats (SSR) markers was developed for Pak‐choi (Brassica rapa ssp. chinensis var. communis) variety identification. We initially selected 74 SSR markers which exhibited high polymorphism and reproducibility in SSR detection from 2129 SSRs. Using the 74 SSR‐based dendrogram for 45 inbred lines as calibration, 21 core SSRs were selected out. The utility of this core set SSRs was firstly tested in 45 inbred lines and finally verified in 102 commercial varieties. We also constructed a molecular ladder for each core SSR as a reference standard. Diversity analysis of this core SSR panel in 102 varieties demonstrated that each marker generates 2–3 alleles (averaged 2.33), with polymorphism information content values ranging from 0.01 to 0.56 (averaged 0.31). The averaged values of Shannon information index, observed heterozygosity, expected heterozygosity and Wright's fixation index were 0.59, 0.43, 0.38 and −0.09, respectively. Furthermore, the 21 SSR‐based classifications for 102 varieties were consistent with traditional classification based on morphology. This core SSR panel represents an effective tool for genetic variation analysis in Pak‐choi.

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Genetic diversity and marker-trait associations in a collection of Pak-choi (Brassica rapa L. ssp. chinensis Makino) Accessions

Cited by 17 publications

References 28 publications

Association of SNP Markers With Height Increment in Mpob-Angolan Natural Oil Palm Populations

Association of SNP Markers With Height Increment in Mpob-Angolan Natural Oil Palm Populations

Transcriptome and small RNA combined sequencing analysis of cold tolerance response in non-heading Chinese cabbage

Validation of a set of informative simple sequence repeats markers for variety identification in Pak‐choi (Brassica rapa L. ssp. chinensis var. communis)

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