Genome-wide identification of SSR markers in the <i>Brassica</i> A genome and their utility in breeding

Hobson, Neil; Rahman, Habibur

doi:10.1139/cjps-2015-0250

Cited by 12 publications

(12 citation statements)

References 45 publications

(66 reference statements)

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“…SSR markers have been used most commonly due to several advantages, such as high abundance and occurrence throughout the genome, codominant nature, and can be detected through PCR-based assay [79, 80]; therefore, we developed tightly linked SSR markers from the SCA9-2 QTL region by taking the advantage of the B . rapa genome sequence.…”

Section: Discussionmentioning

confidence: 99%

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Fine mapping of the major QTL for seed coat color in Brassica rapa var. Yellow Sarson by use of NIL populations and transcriptome sequencing for identification of the candidate genes

et al. 2019

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Yellow seed is a desirable trait in Brassica oilseed crops. The B. rapa var. Yellow Sarson carry unique yellow seed color genes which are not only important for the development of yellow-seeded oilseed B. rapa cultivars but this variant can also be used to develop yellow-seeded B. napus. In this study, we developed near-isogenic lines (NILs) of Yellow Sarson for the major seed coat color QTL SCA9-2 of the chromosome A9 and used the NILs to fine map this QTL region and to identify the candidate genes through linkage mapping and transcriptome sequencing of the developing seeds. From the 18.4 to 22.79 Mb region of SCA9-2, six SSR markers showing 0.63 to 5.65% recombination were developed through linkage analysis and physical mapping. A total of 55 differentially expressed genes (DEGs) were identified in the SCA9-2 region through transcriptome analysis; these included three transcription factors, Bra028039 (NAC), Bra023223 (C2H2 type zinc finger), Bra032362 (TIFY), and several other genes which encode unknown or nucleic acid binding protein; these genes might be the candidates and involved in the regulation of seed coat color in the materials used in this study. Several biosynthetic pathways, including the flavonoid, phenylpropanoid and suberin biosynthetic pathways were significantly enriched through GO and KEGG enrichment analysis of the DEGs. This is the first comprehensive study to understand the yellow seed trait of Yellow Sarson through employing linkage mapping and global transcriptome analysis approaches.

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Section: Discussionmentioning

confidence: 99%

“…The Yellow Sarson B . rapa used in this study is genetically distinct from the other variants of this species including the Chinese cabbage [80], therefore, slight structural variation between the chromosomes of Yellow Sarson and the reference genome of Chinese cabbage cv. Chiifu was not unexpected.…”

Section: Discussionmentioning

confidence: 99%

Fine mapping of the major QTL for seed coat color in Brassica rapa var. Yellow Sarson by use of NIL populations and transcriptome sequencing for identification of the candidate genes

et al. 2019

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“…(), Li et al. () and Hobson and Rahman (), Suwabe et al. (); the polymorphic markers were used to genotype the inbred lines.…”

Section: Methodsmentioning

confidence: 99%

“…(); the polymorphic markers were used to genotype the inbred lines. Details of the genotyping technique is described elsewhere (Hobson & Rahman, ).…”

Section: Methodsmentioning

confidence: 99%

“…These markers were collected from Agriculture and Agri-Food Canada (http://aafcaac.usask.ca/BrassicaMAST/), Celera AgGen Brassica consortium, Brassica Genome Gateway (https://www.brassica. info/resource/markers/ssr-exchange.php) originally from the BBSRC microsatellite programme and the markers published by Cheng et al (2009), Li et al (2011) and Hobson and Rahman (2016, Suwabe et al (2006); the polymorphic markers were used to genotype the inbred lines. Details of the genotyping technique is described elsewhere (Hobson & Rahman, 2016).…”

Section: Molecular Marker Analysismentioning

confidence: 99%

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Potential of rutabaga (Brassica napus var. napobrassica) gene pool for use in the breeding of B. napus canola

et al. 2020

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The narrow genetic diversity in Brassica napus L. (AACC, 2n = 38) canola is one of the major impediment for continued improvement of this crop. Among the different primary gene pools of B. napus, rutabaga (B. napus var. napobrassica) is genetically distinct from spring canola. The potential value of this gene pool for use in the breeding of B. napus canola was investigated in the present study. For this, 93 advanced generation inbred lines with a spring growth habit were developed from F2 and BC1 populations of rutabaga × spring canola crosses and evaluated in replicated field trials for agronomic and seed quality traits. These inbred lines were also genotyped with SSR markers to assess the extent of allelic diversity introgressed from rutabaga into the inbred lines. Some of the inbred lines gave higher seed yield and had greater oil content than their spring canola parent. Molecular marker analysis showed that genetically distinct B. napus canola lines carrying unique alleles of the A and C genomes of rutabaga could be obtained from both F2– and BC1–derived populations. Thus, the results demonstrate the potential of using the rutabaga gene pool for the improvement of B. napus canola.

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Mapping clubroot resistance of Brassica rapa introgressed into Brassica napus and development of molecular markers for the resistance

et al. 2021

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Genome-wide identification of SSR markers in the Brassica A genome and their utility in breeding

Cited by 12 publications

References 45 publications

Fine mapping of the major QTL for seed coat color in Brassica rapa var. Yellow Sarson by use of NIL populations and transcriptome sequencing for identification of the candidate genes

Fine mapping of the major QTL for seed coat color in Brassica rapa var. Yellow Sarson by use of NIL populations and transcriptome sequencing for identification of the candidate genes

Potential of rutabaga (Brassica napus var. napobrassica) gene pool for use in the breeding of B. napus canola

Mapping clubroot resistance of Brassica rapa introgressed into Brassica napus and development of molecular markers for the resistance

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