Identification of QTLs for phenolic compounds in oilseed rape (Brassica napus L.) by association mapping using SSR markers

Rezaeizad, Abbas; Wittkop, Benjamin; Snowdon, Rod J.; Hasan, Maen; Mohammadi, Valiollah; Zali, A.; Friedt, W.

doi:10.1007/s10681-010-0231-y

Cited by 44 publications

(32 citation statements)

References 27 publications

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“…While there is not a clear consensus on what is an appropriate sample size, there seems to be a general agreement that larger samples are better than smaller samples (Hong and Park 2012). Rezaeizad et al (2011) conducted an AM study on seed phenolic compounds using 49 genetically diverse winter-type B. napus germplasm. Honsdorf et al (2010) used 84 canola-quality winter-type B. napus accession for AM study on 14 phenological, morphological and quality traits.…”

Section: Discussionmentioning

confidence: 99%

Association mapping in Brassica napus (L.) accessions identifies a major QTL for blackleg disease resistance on chromosome A01

et al. 2016

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Blackleg disease caused by the fungus Leptosphaeria maculans is one of the most devastating diseases of Brassica napus. Association mapping was used to evaluate the response of 139 B. napus accessions originated from 16 countries with 4 growth habit types to inoculation with L. maculans isolates from pathogenicity group 4. All accessions were inoculated at the seedling stage and 37,346 single nucleotide polymorphism markers based upon genotyping-bysequencing were used for analysis. One major QTL associated with the blackleg disease was identified on chromosome A01 at 9.66 Mbp and explains about 14.7 % of phenotypic variation (p value \2.2E-05).Orthologs of Arabidopsis thaliana hydroxyproline-rich glycoprotein family protein, acyl-CoA oxidase 1 and cysteine-/histidine-rich C1 domain family protein that are involved in plant defense mechanism were identified in this QTL region. At a lower significance (p value \0.00139), thirty-five additional markers were identified which are located on 13 other chromosomes. Stepwise regression identified that these markers belong to ten QTL regions and together explain 51.04 % of phenotypic variations. Additional twenty orthologs of A. thaliana disease resistance genes, transcription factors, genes in phytohormone pathway and signaling in plant defense pathway have been identified to be associated with the blackleg disease. Based on the haplotype at the most significant QTL, a total of 22 genotypes were evaluated in the greenhouse. As expected with the haplotype, we had 100 % success in predicting the phenotype. These markers could further be used for identification of phenotype that can be used in the breeding program.Keywords Brassica napus Á Association mapping Á SNP Á Blackleg IntroductionRapeseed (Brassica napus, 2n = 4x = 38) is one of the most important oilseed crops cultivated in many Electronic supplementary material The online version of this article (

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Section: Discussionmentioning

confidence: 99%

Association mapping in Brassica napus (L.) accessions identifies a major QTL for blackleg disease resistance on chromosome A01

et al. 2016

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“…In the case of cQTL, a set of 100 SNP markers previously developed by resequencing areas of the B. napus genome harboring QTL for seed quality characters (Clarke et al 2013) was used for the analysis. This kind of cQTL approach has been previously reported in B. napus (Rezaeizad et al 2011); however, a bigger population, considerably more markers, additional seed quality traits and more restrictive association mapping models were assessed in the present work. Both mapping approaches were used to analyze seed quality traits obtained in a B. napus winter oilseed rape association panel (89 inbred lines), using seed quality trait data collected during two seasons across two locations in Germany.…”

Section: Introductionmentioning

confidence: 97%

“…Both types of AM approaches have been used in genetic studies in oilseed rape. For instance, GWAS has been used to identify markers associated with phenological and morphological traits ) and seed quality traits (Zou et al 2010;Rezaeizad et al 2011;Harper et al 2012;Li et al 2014). CG has been used to identify polymorphisms in genes involved in glucosinolate biosynthesis (Hasan et al 2008), genes associated with tocopherol content and composition (Fritsche et al 2012) and allelic resistance to Leptosphaeria maculans (Jestin et al 2011) in B. napus. In this study, two different AM approaches, GWAS and candidate QTL (cQTL), were used to identify SNP markers associated with six B. napus seed quality traits.…”

Section: Introductionmentioning

confidence: 99%

Association mapping of seed quality traits in Brassica napus L. using GWAS and candidate QTL approaches

et al. 2015

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Single nucleotide polymorphisms (SNPs) have rapidly become the molecular marker of choice in plant and animal association mapping (AM) studies. In this work, a genome-wide association study (GWAS) and candidate quantitative trait loci (cQTL) approaches were used to identify SNP markers associated with seed quality traits, in a Brassica napus L. association panel composed of 89 adapted winter oilseed rape accessions. Six seed quality traits (oil and protein content, linolenic acid, total glucosinolates, hemicellulose and cellulose content) were evaluated in two different locations for two seasons. For GWAS, 4025 SNP markers evenly distributed along the B. napus genome were genotyped using a 6K Illumina array platform. For cQTL, 100 SNP markers previously discovered in genomic regions underlying seed quality QTL were genotyped using a competitive allele-specific PCR (KASPar). Analysis of the population structure revealed the presence of two weakly differentiated subpopulations (F ST = 0.037), with 82 % of the pairwise kinship comparisons ranging from 0 to 0.1. The GWAS approach resulted in the identification of 17 and 5 significant associations for seed glucosinolate content and seed hemicellulose content, respectively. The cQTL approach identified 4 significant associations for seed glucosinolate content and 6 significant associations for seed hemicellulose content. The associated SNPs were consistently identified across environments and were mapped to previously reported QTL. These results illustrate the suitability of AM to identify SNP markers associated with seed quality traits in B. napus.

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“…In contrast, this method has recently been used to identify traitÁmarker relationships in plants, with most research focusing on the genetics of complex traits in Arabidopsis thaliana (Nordborg et al 2002) and agricultural crops such as rice (Agrama et al 2007), maize (Remington et al 2001;Yan et al 2009aYan et al , 2011 and barley (Kraakman et al 2004). Both genome-wide and candidate gene association mapping techniques have successfully been applied to B. napus L. (Hasan et al 2008;Zou et al 2010;Rezaeizad et al 2011;Delourme et al 2013).…”

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confidence: 99%

Identification of QTL for seed coat colour and oil content inBrassica napusby association mapping using SSR markers

QuCunmin

Hasan

et al. 2015

Can. J. Plant Sci.

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2015. Identification of QTL for seed coat colour and oil content in Brassica napus by association mapping using SSR markers. Can. J. Plant Sci. 95: 387Á395. Association mapping identifies quantitative trait loci (QTL) based on the strength of linkage disequilibrium (LD) between markers and functional polymorphisms across a set of diverse germplasms. In this study, we used association mapping to detect QTL and genome-wide simple sequence repeat (SSR) markers linked to seed coat colour and oil content in a population of 217 oilseed rape (Brassica napus L.) accessions. We corrected for the population structure of B. napus using 389 genome-wide SSR markers. In total, 25 and 11 SSR markers linked to seed coat colour and oil content were detected, respectively, and these two sets of markers were in different linkage groups. Nine of these markers for seed coat colour spanned the major QTL region for seed coat colour, and been mapped to chromosome A9. Six of these markers showed high levels of association with both seed coat colour and oil content, and markers H081N08.8 and KS20291 were mapped to the major QTL region for seed coat colour on chromosome A9. Another marker, CB10364, was in high LD with all determined seed coat colour and oil content traits, and was mapped to the co-localized QTL region for them on chromosome A8. These data indicate that seed coat colour was found to be an important contributor to seed oil content. Further, we show that association mapping using a heterogeneous set of genotypes is a suitable approach for complementing and enhancing previously obtained QTL information for marker-assisted selection.Key words: Brassica napus L., seed coat colour, oil content, quantitative trait loci, association mapping Qu, C., Hasan, M., Lu, K., Liu, L., Zhang, K., Fu, F., Wang, M., Liu, S., Bu, H., Wang, R., Xu, X., Chen, L. et Li, J. 2015. Identification des QTL de la couleur des te´guments et de la teneur en huile des graines de Brassica napus par recoupement cartographique avec les marqueurs SSR. Can. J. Plant Sci. 95: 387Á395. La cartographie par association permet d'identifier les locus quantitatifs (QTL) en fonction du degre´de de´se´quilibre des liaisons ge´ne´tiques entre les marqueurs et les polymorphismes fonctionnels dans une se´rie de germoplasmes varie´s. Les chercheurs ont recouru a`cette technique pour de´tecter les locus quantitatifs et les microsatellites (SSR) du ge´nome relie´s a`la couleur des te´guments de la graine et a`sa teneur en huile chez 217 obtentions de colza (Brassica napus L.). Ils ont rectifie´la structure de la population de B. napus en recourant a`389 marqueurs SSR du ge´nome. En tout, ils ont respectivement de´cele´25 et 11 marqueurs SSR associe´s a`la couleur des te´guments et a`la teneur en huile; ces deux se´ries de marqueurs se trouvent dans des groupes de liaison diffe´rents. Neuf marqueurs de la couleur des te´guments se retrouvent dans l'importante re´gion de QTL associe´e a`ce caracte`re et ont e´te´situe´s sur le chromosome A9. Six marqueurs pre´sentaient une e´tr...

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Identification of QTLs for phenolic compounds in oilseed rape (Brassica napus L.) by association mapping using SSR markers

Cited by 44 publications

References 27 publications

Association mapping in Brassica napus (L.) accessions identifies a major QTL for blackleg disease resistance on chromosome A01

Association mapping in Brassica napus (L.) accessions identifies a major QTL for blackleg disease resistance on chromosome A01

Association mapping of seed quality traits in Brassica napus L. using GWAS and candidate QTL approaches

Identification of QTL for seed coat colour and oil content inBrassica napusby association mapping using SSR markers

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