Genetic analysis of morphological traits in a new, versatile, rapid-cycling Brassica rapa recombinant inbred line population

Abstract

A recombinant inbred line (RIL) population was produced based on a wide cross between the rapid-cycling and self-compatible genotypes L58, a Caixin vegetable type, and R-o-18, a yellow sarson oil type. A linkage map based on 160 F7 lines was constructed using 100 Single nucleotide polymorphisms (SNPs), 130 AFLP®, 27 InDel, and 13 publicly available SSR markers. The map covers a total length of 1150 centiMorgan (cM) with an average resolution of 4.3 cM/marker. To demonstrate the versatility of this new population, 17 traits, related to plant architecture and seed characteristics, were subjected to quantitative trait loci (QTL) analysis. A total of 47 QTLs were detected, each explaining between 6 and 54% of the total phenotypic variance for the concerned trait. The genetic analysis shows that this population is a useful new tool for analyzing genetic variation for interesting traits in B. rapa, and for further exploitation of the recent availability of the B. rapa whole genome sequence for gene cloning and gene function analysis.

Keywords: Brassica rapa; QTL analysis; plant breeding; recombinant inbred line population.

Figure 1

Phenotyping of RIL population of B. rapa L58 × R-o-18. (A) Seed vivipary; i.e., premature germination of seeds still in the silique, or just after harvesting, (B) silique length (SL) and silique beak length (BL), (C) pod shattering, corresponding to the fraction of opened siliques at harvesting, (D) carpel number, with the left two siliques having two carpels and the two on the right having three.

Figure 2

Genetic linkage map of the B. rapa L58 × R-o-18 RIL population, showing the positions of 270 markers (100 SNP, 130 AFLP, 27 InDel, and 13 SSR markers) distributed over 10 linkage groups corresponding to the 10 chromosomes of the Brassica A genome. Markers labeled with [6 digits|7 digits] are SNPs, markers labeled “E … M..” or “P … M..” are respectively EcoRI/MseI or PstI/MseI generated AFLPs, markers labeled “BrID ….” are InDels and the remaining markers are SSRs.

Figure 3

Frequency distributions of non-normalized data of the reported traits for the L58 × R-o-18 RIL population. The vertical axes indicate the number of lines per trait value class and the horizontal axes indicate the different trait value classes. The parental values (indicated with L and R) are the mean of five replicates.

Figure 4

A clustered heat map showing the LOD profiles of the measured traits. Columns indicate the 10 chromosomes in centimorgans, ascending from the left to right; rows indicate individual trait LOD profiles. A color scale is used to indicate the QTL significance corresponding to the LOD score. Positive values (red and black) represent a positive effect of the trait by the L58 allele, negative values (blue and green) represent a positive effect on the trait by the R-o-18 allele. The width of a bar indicates the significance interval of the QTL that was calculated by rMQM in MAPQTL 6. Hierarchical clustering, shown on the left, reflects the correlation between traits based on the QTL profiles.