Yang XiaoHong

Availability of two-dimensional bulked DNA sampling in uniformity assessment of 8 inbred rice lines.

Poor efficiency of current SSRs on a plant-by-plant basis makes it hesitate to accept SSRs as an alternative for routine DUS test. The present study testified the availability of two-dimensional bulked DNA sampling in uniformity assessment of 8 inbred rice lines with commonly-used SSR markers. Our results showed that, (1) bulked sampling was suggested as 10 individuals, thus in a 10-row × 10-column matrix, the bulked samples could save 80% cost compared with routine SSRs; (2) the way to identifying true off-types from putative ones was modified and optimized as that all the intersections were considered as putative off-types, and further identifications were based on bulked SSR profiles or individual ones; (3) a putative off-type could be detected using 1 markers, or in some cases, 15 markers, and each marker equally detected 12.5 true off-types, ranged from 6 to 20; (4) true off-types were generally detected using 4 or more markers, so the strategy should be based on a group of markers rather than one to reduce the interfere of residual heterozygosity; (5) the very significant correlations (0.553 equally, concluded from the data of off-types) between results of the strategy and traditional morphological test made it prospective to indicate an exclusive acceptable uniformity baseline for SSRs. The reported strategy is available to evaluate uniformity of inbred rice lines with 20% cost of routine SSRs taking advantage of two-dimensional bulked DNA sampling (in a 10-row × 10-column matrix) and 24 commonly-used SSR markers. It could also be interest for the determination of stability and distinctness of inbred rice lines, as well as other non-hybrid plant varieties. However, we found the strategy couldn’t effectively discriminate self-pollinated off-types from those true hybrid individuals.