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

Fuquan Ce; Jiaqin Mei; Haiyan He; Yu Zhao; Wenhui Hu; Fengqun Yu; Qinfei Li; Xuesong Ren; Jun Si; Hongyuan Song; Wei Qian

doi:10.3389/fpls.2021.703520

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

Front Plant Sci. 2021 Nov 16:12:703520. doi: 10.3389/fpls.2021.703520. eCollection 2021.

Authors

Fuquan Ce^{1

2

3

4}, Jiaqin Mei^{2

4

5}, Haiyan He^{1

3

6}, Yu Zhao^{1

3}, Wenhui Hu^{1

3

6}, Fengqun Yu⁷, Qinfei Li^{1

3

6}, Xuesong Ren^{1

3

6}, Jun Si^{1

3

6}, Hongyuan Song^{1

3

6}, Wei Qian^{2

4

5}

Affiliations

¹ College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China.
² College of Agronomy and Biotechnology, Southwest University, Chongqing, China.
³ Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing, China.
⁴ Academy of Agricultural Sciences, Southwest University, Chongqing, China.
⁵ State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing, China.
⁶ Chongqing Key Laboratory of Olericulture, Chongqing, China.
⁷ Agriculture and Agri-Food Canada, Saskatoon Research and Development Center, Saskatoon, SK, Canada.

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, 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.

Keywords: Brassica oleracea; Plasmodiophora brassicae; candidate gene; clubroot; functional marker; genomic resequencing.