Target chromosome-segment substitution: A way to breeding by design in rice

Progress in plant breeding depends on the development of genetic resources, genetic knowledge, and breeding techniques. The core of plant breeding is the use of naturally occurring variation. At the beginning of the post-genomic era, a new concept of “breeding by design” was proposed, which aims to control all allelic variation for all genes of agronomic importance. In the past two decades, we have applied a three-step strategy for research on rice breeding by design. In the first step, we constructed a single-segment substitution line (SSSL) library using Huajingxian 74 (HJX74), an elite xian (indica) rice cultivar, as the recipient in which to assemble genes from the rice AA genome. In the second step, we identified a series of desirable genes in the SSSL library. In the third step, we designed new rice lines, and achieved the breeding goals by pyramiding target genes in the HJX74-SSSL library. This review introduces the background, concept, and strategy of breeding by design, as well as our achievements in rice breeding by design using the HJX74-SSSL platform. Our practice shows that target chromosome-segment substitution is a way to breeding by design.