Targeted Genomic Mapping of a Red Seed Color Gene ( R‐A1 ) in Wheat

Seed color is an important trait affecting flour yield and quality in wheat. Seed color also is either tightly linked to or pleiotropically controls seed dormancy in wheat, because most of the red‐seeded wheats are tolerant to preharvest sprouting in comparison to white‐seeded wheats. Seed color in hexaploid wheat is controlled by the dominant red seed color genes R‐A1 , R‐B1 , and R‐D1 located in orthologous positions on chromosome arms 3AL, 3BL, and 3DL, respectively. By using wheat ESTs and synteny with rice, we identified one STS marker and one EST marker flanking R‐A1 in a 4.4‐cM interval by using an RIL and F 2 populations of Langdon (LDN)/LDN‐DIC3A (disomic substitution of T. turgidum subsp. dicoccoides chromosome 3A for 3A of LDN). Physical mapping of the R‐A1 gene using tightly linked markers on a set of deletion lines specific to the long arms of group‐3 chromosomes indicated that the red seed color genes are located in the distal region (less than 10% of the chromosome arm 3L), which is a high‐recombination, gene‐rich region in wheat. Comparative genomic analysis indicated that, except for a very minor rearrangement of gene sequences in wheat relative to rice, macrocolinearity is well conserved between the consensus distal deletion bin of wheat 3L‐0.80–1.00 and rice chromosome arm 1L. The R‐A1 gene of wheat was targeted into a single PAC of rice using colinear flanking markers.