Abstract
Aneuploidy, the presence of an abnormal number of chromosomes in a cell, occurs spontaneously in tetraploid rice and can cause phenotypic abnormalities. Therefore, the reliable identification and exclusion of aneuploid plants is important in polyploid crop breeding. However, conventional cytological detection is labor-intensive and poorly suited to large-scale screening in the breeding process. In this study, we developed a simple next-generation sequencing (NGS)-based pipeline to estimate chromosomal dosage from relative read counts and efficiently detect spontaneous aneuploidy. Applying this approach to selfed progeny of interspecific hybrid tetraploid rice, we found that approximately 30% of the progeny derived from a single eutetraploid plant were aneuploid, although the frequency varied among lineages. Aneuploidy frequency also differed among chromosomes, occurring rarely for chromosomes 1 and 3 and more frequently for chromosome 9. Gain-type aneuploidies, including pentasomy and hexasomy, were more frequent than loss-type aneuploidy, such as trisomy. Aneuploidy was associated with variation in six of the 12 agronomic traits examined: awn length, culm length, panicle length, spikelet number per panicle, seed fertility, and total grain number. These results support a substantial contribution of aneuploidy to phenotypic variation in interspecific hybrid tetraploid rice, while population-dependent differences in aneuploid frequency suggest a possible contribution of genetic background.
