scholarly journals Identification of Candidate Genes for Clubroot-Resistance in Brassica oleracea Using Quantitative Trait Loci-Sequencing

2021 ◽  
Vol 12 ◽  
Author(s):  
Fuquan Ce ◽  
Jiaqin Mei ◽  
Haiyan He ◽  
Yu Zhao ◽  
Wenhui Hu ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Brassica Oleracea ◽  
Candidate Genes ◽  
Quantitative Trait ◽  
Plasmodiophora Brassicae ◽  
Potential Candidate ◽  
Clubroot Resistance ◽  
Group I ◽  
Trait Loci ◽  
Group Ii

Clubroot caused by Plasmodiophora brassicae is a devastating disease of cabbage (Brassica oleracea). To identify quantitative trait loci (QTLs) for clubroot resistance (CR) in B. oleracea, genomic resequencing was carried out in two sets of extreme pools, group I and group II, which were constructed separately from 110 and 74 F2 cloned lines derived from the cross between clubroot-resistant (R) cabbage “GZ87” (against race 4) and susceptible (S) cabbage “263.” Based on the QTL-sequencing (QTL-Seq) analysis of group I and group II, three QTLs (i.e., qCRc7-2, qCRc7-3, and qCRc7-4) were determined on the C07 chromosome. RNA-Seq and qRT-PCR were conducted in the extreme pools of group II before and after inoculation, and two potential candidate genes (i.e., Bol037115 and Bol042270), which exhibiting upregulation after inoculation in the R pool but downregulation in the S pool, were identified from the three QTLs on C07. A functional marker “SWU-OA” was developed from qCRc7-4 on C07, exhibiting ∼95% accuracy in identifying CR in 56 F2 lines. Our study will provide valuable information on resistance genes against P. brassicae and may accelerate the breeding process of B. oleracea with CR.

scholarly journals Identification of Candidate Genes for Clubroot-Resistance in Brassica oleracea using QTL-Seq

2021 ◽  
Author(s):  
Fuquan Ce ◽  
Jiaqin Mei ◽  
Haiyan He ◽  
Yu Zhao ◽  
Wenhui Hu ◽  
...  
Keyword(s):  
Brassica Oleracea ◽  
Candidate Genes ◽  
Plasmodiophora Brassicae ◽  
Potential Candidate ◽  
Clubroot Resistance ◽  
Group I ◽  
Before And After ◽  
Group Ii ◽  
The One ◽  
Race 4

Abstract Clubroot caused by Plasmodiophora brassicae is a devastating disease of cabbage (Brassica oleracea). To identify quantitative trait loci (QTLs) for clubroot resistance (CR) in B. oleracea, genomic resequencing was carried out in two sets of extreme pools that constructed from 184 F2 cloned-lines derived from cross between clubroot-resistant cabbage ‘GZ87’ (against race 4) and susceptible cabbage ‘263’. QTL-seq analyses identified one CR QTL from group I on chromosome C07 and four QTLs from group II on C04 and C07, among which three QTLs of C07 that found from group II were located within the one detected from group I. RNA-Seq and qRT-PCR were conducted in the extreme pools of group II before and after inoculation identified two potential candidate genes (Bol037115 and Bol042270) from the three QTLs interval on C07, which exhibiting up-regulation after inoculation in the resistant pool but down-regulation in the susceptible pool. A functional marker ‘SWU-OA’ was developed from one QTL on C07, exhibiting ~95% accuracy in identifying CR in 56 F2 lines. Our study will provide valuable information on digging resistance genes against P. brassicae and may accelerate breeding process of B. oleracea with CR.Key Message QTLs and potential candidate genes for clubroot resistance were identified in Brassica oleracea

Accumulation of quantitative trait loci conferring broad-spectrum clubroot resistance in Brassica oleracea

2013 ◽  
Vol 32 (4) ◽  
pp. 889-900 ◽  
Author(s):  
Hiroya Tomita ◽  
Motoki Shimizu ◽  
Md. Asad-ud Doullah ◽  
Ryo Fujimoto ◽  
Keiichi Okazaki
Keyword(s):  
Quantitative Trait Loci ◽  
Brassica Oleracea ◽  
Broad Spectrum ◽  
Quantitative Trait ◽  
Clubroot Resistance ◽  
Trait Loci

scholarly journals A Fine mapping quantitative trait loci that underlie resistance to soybean sudden death syndrome using NILs and SNPs.

2018 ◽  
pp. 583-591
Author(s):  
Yi Chen Lee ◽  
M Javed Iqbal ◽  
Victor N Njiti ◽  
Stella Kantartzi ◽  
David A. Lightfoot
Keyword(s):  
Quantitative Trait Loci ◽  
Sudden Death ◽  
Candidate Genes ◽  
Quantitative Trait ◽  
Soybean Cyst Nematode ◽  
Snp Markers ◽  
Sudden Death Syndrome ◽  
Isogenic Line ◽  
Trait Loci ◽  
Glycine Max L

Soybean (Glycine max (L.) Merr.) cultivars differ in their resistance to sudden death syndrome (SDS), caused by Fusarium virguliforme. Breeding for improving SDS response has been challenging, due to interactions among the 18-42 known resistance loci. Four quantitative trait loci (QTL) for resistance to SDS (cqRfs–cqRfs3) were clustered within 20 cM of the rhg1 locus underlying resistance to soybean cyst nematode (SCN) on Chromosome (Chr.) 18. Another locus on Chr. 20 (cqRfs5) was reported to interact with this cluster. The aims here were to compare the inheritance of resistance to SDS in a near isogenic line (NIL) population that was fixed for resistance to SCN but segregated at two of the four loci (cqRfs1 and cqRfs) for SDS resistance; to examine the interaction with the locus on Chr. 20; and to identify candidate genes underlying QTL. Used were; a NIL population derived from residual heterozygosity in an F5:7 recombinant inbred line EF60 (lines 1-38); SDS response data from two locations and years; four segregating microsatellite and 1,500 SNP markers. Polymorphic regions were found from 2,788 Kbp to 8,938 Kbp on Chr. 18 and 33,100 Kbp to 34,943 Kbp on Chr. 20 that were significantly (0.005 < P > 0.0001) associated with resistance to SDS. The QTL fine maps suggested that the two loci on Chr. 18 were three loci (cqRfs1, cqRfs, and cqRfs19). Candidate genes were inferred.  An epistatic interaction was inferred between Chr. 18 and Chr. 20 loci. Therefore, SDS resistance QTL were both complex and interacting.

scholarly journals Meta-Analysis of Quantitative Trait Loci Associated with Seedling-Stage Salt Tolerance in Rice (Oryza sativa L.)

Plants ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 33 ◽  
Author(s):  
Md. Islam ◽  
John Ontoy ◽  
Prasanta Subudhi
Keyword(s):  
Quantitative Trait Loci ◽  
Salt Tolerance ◽  
Candidate Genes ◽  
Quantitative Trait ◽  
Oryza Sativa L ◽  
Meta Analysis ◽  
Seedling Stage ◽  
Phenotypic Variance ◽  
A Genome ◽  
Trait Loci

Soil and water salinity is one of the major abiotic stresses that reduce growth and productivity in major food crops including rice. The lack of congruence of salt tolerance quantitative trait loci (QTLs) in multiple genetic backgrounds and multiple environments is a major hindrance for undertaking marker-assisted selection (MAS). A genome-wide meta-analysis of QTLs controlling seedling-stage salt tolerance was conducted in rice using QTL information from 12 studies. Using a consensus map, 11 meta-QTLs for three traits with smaller confidence intervals were localized on chromosomes 1 and 2. The phenotypic variance of 3 meta-QTLs was ≥20%. Based on phenotyping of 56 diverse genotypes and breeding lines, six salt-tolerant genotypes (Bharathy, I Kung Ban 4-2 Mutant, Langmanbi, Fatehpur 3, CT-329, and IARI 5823) were identified. The perusal of the meta-QTL regions revealed several candidate genes associated with salt-tolerance attributes. The lack of association between meta-QTL linked markers and the level of salt tolerance could be due to the low resolution of meta-QTL regions and the genetic complexity of salt tolerance. The meta-QTLs identified in this study will be useful not only for MAS and pyramiding, but will also accelerate the fine mapping and cloning of candidate genes associated with salt-tolerance mechanisms in rice.

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