Construction of a high-density genetic linkage map and identification of quantitative trait loci associated with clubroot resistance in radish (Raphanus sativus L.)

Construction of high‐density linkage map and identification of QTLs associated with resistance to black rot in radish (Raphanus sativus) by RAD sequencing

“…It is clear that the resolution of these two maps was lower than that of our map, and other maps (spanned distance < 1,200 cM) had lower genome coverage than our map. In this study, the number of markers on Chr.7 was lower than that on other chromosomes, and previous studies also showed similar results (Gan et al, ; Mun et al, ). We inferred that segregation distortion of some exceptional markers, the length of the reference chromosome sequence and the populations resulted in low marker density on Chr.7.…”

“…Generally, our RAD‐seq‐based genetic map has an obvious comparative advantage in terms of marker type, density, genetic distance, etc. The total genetic distance of previous maps ranged from 554.0 to 1,678.2 cM with an average distance of 0.5 to 4.7 cM; most of these maps were constructed with limited markers; and only a few maps were high‐density genetic maps (Bett & Lydiate, ; Budahn et al, ; Gan et al, ; Kamei et al, ; Li et al, ; Mitsui et al, ; Mun et al, ; Shirasawa & Kitashiba, ; Shirasawa et al, ; Tsuro, Suwabe, Kubo, Matsumoto, & Hirai, , ; Xu et al, ; Yu et al, , ). The number of markers in and coverage of most published maps were severely insufficient compared with those in our study, and only two previous maps were longer than our map.…”

“…These maps were mostly used to map genes/QTLs associated with significant agronomic traits, such as taproot shape and pigmentation, disease or pest resistance, 4‐methylthio‐3‐butenyl glucosinolate (4‐MTB‐GSL) content and Cd accumulation (Budahn et al, ; Gan et al, ; Kamei et al, ; Tsuro, Suwabe, Kubo, Matsumoto, & Hirai, ; Xu et al, ; Yu et al, , ); some were used to assist in the genome assembly of radish at the chromosome level (Mitsui et al, ; Mun et al, ; Zhang et al, ). In particular, Gan et al () constructed a 794.3‐cM genetic map based on RAD‐seq, and five QTLs ( RsCr1 , RsCr2 , RsCr3 , RsCr4 and RsCr5 ) associated with resistance to clubroot were detected on two chromosomes (Chr.8 and Chr.9). This finding also proves the feasibility of RAD‐seq in radish linkage map construction and gene/QTL mapping.…”

“…In recent decades, restriction fragment length polymorphism (RFLP), random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) have been the main molecular markers used for construction of genetic maps due to the limitation of sequencing technologies and high costs. In radish, several genetic maps have been reported based on RFLP, RAPD, AFLP, SSR and SNP markers in different populations, and the total coverage of these maps ranges from 554.0 to 1,678.2 cM (Bett & Lydiate, ; Budahn et al, ; Gan et al, ; Kamei et al, ; Kitashiba et al, ; Li et al, ; Mitsui et al, ; Mun et al, ; Shirasawa & Kitashiba, ; Shirasawa et al, ; Tsuro, Suwabe, Kubo, Matsumoto, & Hirai, , ; Xu et al, ; Yu et al, , ; Zhang et al, ; Zou et al, ). Marker density is a key factor affecting the precision of recombinational breakpoint identification and mapping resolution.…”

Quantitative Trait Locus Mapping of Clubroot Resistance and Plasmodiophora brassicae Pathotype Banglim-Specific Marker Development in Brassica rapa

“…For the amphidiploids, B. napus (AC), several results were reported [35][36][37][38]. Additionally, QTLs have been reported in R. sativus [39,40]. This information has been useful for the development of markers for marker-assisted selection [41].…”