Fig 2. Genetic linkage and physical maps of the chromosome A9 of Brassica rapa.

(a) A genetic linkage map of a part of A9, carrying the major QTL for seed coat color (SCA9-2), constructed by use of a BC₄S₂ population of B. rapa and genotyping data of six newly-developed SSR markers and one marker used by Kebede et al. [31]; the position of the QTL SCA9-2 is shown. Marker position (cM) indicates the distance from SCA9-2. (b) A physical map of the QTL region SCA9-2 of A9 constructed based on one SSR marker used by Kebede et al. [31] and the six newly-developed markers co-segregating with seed color; the position of the BrTT1 gene is also shown. Different colors indicate different scaffolds (purple = scaffold000059, blue = scaffold000040, green = scaffold000081, yellow = scaffold000084, brown = scaffold000045)(c) A physical map of A9 constructed based on sequence information of the markers from the major and minor QTL regions of the linkage group A9 published by Kebede et al. [31]; the physical map was constructed through aligning the marker sequences to the B. rapa reference genome in BRAD database. (d) The genetic linkage map of A9 published by Kebede et al. [31]; the major seed coat color QTL SCA9-2 and the minor QTL SCA9-1 are shown.