The genetic basis of 11 yield-related traits in parents of hybrid rice

Hybrid rice exhibits both great heterosis (hybrid vigour) and yield potential compared with either inbred parentvariety. Gains in the yield from breeding hybrid rice first requires selection of optimal mating parents that when crossed will produce a rice hybrid with desired traits including high yield performance. Yet whilst this is the most critical stage in the hybrid breeding pipeline it is also the most time consuming. Over the decades, plant breeders have developed general combining ability (GCA), a measure used for the selection of elite inbred lines that make the highest contributions to hybrid performance. It is however important to initially recognize the genomic locus that is strongly associated with the GCA of parental traits. With this in mind a recent study by Zaid et al., and published in AoBP, used a novel association analysis approach to link GCA of parental lines to key genomic regions.

Performance of hybrid rice F1 plant population at milling stage in paddy field. Image credit: Delin Hong.

The authors calculated the GCA values of 33 parents of hybrid rice and genetically sequenced them to identify single nucleotide polymorphisms (SNPs). Identified SNPs were merged and optimized for the construction of single nucleotide polymorphism linkage disequilibrium block (SNPLDB) markers. A single-factor analysis of variance-based association method between the constructed SNPLDB markers and GCA effects values detected 99 significant SNPLDBs for GCA of 11 yield-related traits.The authors mined 50 favourable GCA alleles at the associated SNPLDBs regions, distributed across the 33 parental genomes. The parental genomes possessed a small number of favourable GCA alleles for studied traits, with the exception of days to heading and plant height. These results suggest that the identified GCA alleles could be used to improve the GCA performance of parents of hybrid rice through optimal crossing design. Moreover, favourable GCA alleles could be incorporated in the parental genomes through marker-assisted selection experiments, and the parental lines carrying more alleles could be utilized in breeding as superior parents to develop rice hybrids with desirable characteristics.

Researcher highlight

Delin Hong

Delin Hong obtained PhD in crop genetics and breeding in 1988 under the supervision of late Professor Yuhua Ma at Nanjing Agricultural University (NAU), China. Hong currently holds a professor position in the College of Agriculture, NAU.

Hong has been lecturing two courses (Principles and Methods of Crop Breeding, Principles and Methods of Seed Production) for undergraduate students, and two courses (Molecular Plant Breeding, Theory and Technology of Seed Industrialization) for graduate students. As a hybrid rice (Oryza sativa L.) breeder, he is interested in identifying superior genotypic loci of combing ability trait that could be useful for further enhance heterosis level and in discovering elite alleles for outcrossing traits (for example, stigma length) that could be useful for reducing hybrid seed cost by increasing F1 seed yield.

Further reading

Ullah Zaid, I., Tang, W., He, J., Ullah Khan, S., & Hong, D. (2018). Association analysis uncovers the genetic basis of general combining ability of 11 yield-related traits in parents of hybrid rice. AoB PLANTS, 11(1). https://doi.org/10.1093/aobpla/ply077