Rahaman Mizanur, Strelkov Stephen E, Hu Hao, Gossen Bruce D, Yu Fengqun
Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, S7N 0X2, Canada.
Dep. of Agricultural, Food and Nutritional Science, Univ. of Alberta, Edmonton, AB, T6G 2P5, Canada.
Plant Genome. 2022 Dec;15(4):e20245. doi: 10.1002/tpg2.20245. Epub 2022 Aug 16.
Clubroot, caused by Plasmodiophora brassicae, is an important disease of brassica crops worldwide. Vegetable turnip (Brassica rapa L.) have proven to be a source of clubroot resistance genes effective against many pathotypes of P. brassicae. The F progeny from the cross B. rapa canola ACDC (susceptible, S) × B. rapa turnip ECD02 (resistant, R) were backcrossed with ACDC, then self-pollinated to produce BC S lines. All the F plants were resistant to four pathotypes (3A, 3D, 3H, and 5X) of P. brassicae. Segregation for R and S in BC to each pathotype was 1:1 and resistance reactions were highly correlated. From whole genome sequencing, 192.1 M sequences with 96% template coverage from ECD02, and 478.9 M sequences with 92% coverage from ACDC, were aligned with the reference genome of B. rapa. Genotyping-by-sequencing was performed on the BC population. The number of aligned short reads per plant in the BC ranged from 1.4 to 8.5 M sequences with 4-8% template coverage. We obtained 1,344 high-quality single-nucleotide polymorphism (SNP) loci with a mean missing rate at 0.27% and distributed them on 10 chromosomes. A single co-localized quantitative trait loci (QTL), designated as Rcr9 on chromosome A08, conferred resistance to the four pathotypes. The QTL explained 68.9-74.4% of phenotypic variation with the logarithm of the odds values of 24.3 to 31.1. Bulked segregant analysis was performed, and 14 SNP markers linked to the gene were developed using the Kompetitive Allele Specific PCR. Rcr9 was mapped into an interval of 2.2 cM, flanked by CF_A08_10664692 and CF_A08_12230973, which spanned 1.51 Mb on the chromosome and included 219 B. rapa genes. Four of these genes (BraA08g012910.3C, BraA08g012920.3C, BraA08g013130.3C, and BraA08g013630.3C) encoded disease resistance proteins.
根肿病由芸薹根肿菌引起，是全球范围内十字花科作物的一种重要病害。蔬菜芜菁（Brassica rapa L.）已被证明是根肿病抗性基因的来源，这些基因对芸薹根肿菌的许多致病型有效。油菜ACDC（感病，S）×芜菁ECD02（抗病，R）杂交产生的F代与ACDC回交，然后自花授粉产生BC1S系。所有F1植株对芸薹根肿菌的四种致病型（3A、3D、3H和5X）均具有抗性。BC1代对每种致病型的抗病（R）和感病（S）分离比例为1:1，抗性反应高度相关。通过全基因组测序，将来自ECD02的1.921亿条序列（模板覆盖率96%）和来自ACDC的4.789亿条序列（覆盖率92%）与芜菁参考基因组进行比对。对BC1群体进行简化基因组测序基因分型。BC1群体中每株植物比对上的短读长序列数量在140万至850万条之间，模板覆盖率为4%-8%。我们获得了1344个高质量单核苷酸多态性（SNP）位点，平均缺失率为0.27%，并将它们分布在10条染色体上。一个共定位的数量性状位点（QTL），命名为A08染色体上的Rcr9，赋予了对这四种致病型的抗性。该QTL解释了68.9%-74.4%的表型变异，对数优势值为24.3至31.1。进行了混合分组分析法，并使用竞争性等位基因特异性PCR开发了14个与该基因连锁的SNP标记。Rcr9被定位到一个2.2厘摩的区间内，两侧分别为CF_A08_10664692和CF_A08_12230973，该区间在染色体上跨度为1.51兆碱基，包含219个芜菁基因。其中四个基因（BraA08g012910.3C、BraA08g012920.3C、BraA08g013130.3C和BraA08g013630.3C）编码抗病蛋白。
