Sparse Phenotyping and Haplotype-Based Models for Genomic Prediction in Rice

Sang He; Shanshan Liang; Lijun Meng; Liyong Cao; Guoyou Ye

doi:10.1186/s12284-023-00643-2

Sparse Phenotyping and Haplotype-Based Models for Genomic Prediction in Rice

Rice (N Y). 2023 Jun 7;16(1):27. doi: 10.1186/s12284-023-00643-2.

Authors

Sang He^{1

2}, Shanshan Liang³, Lijun Meng⁴, Liyong Cao⁵, Guoyou Ye^{6

7}

Affiliations

¹ Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
² CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
³ Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China.
⁴ Kunpeng Institute of Modern Agriculture at Foshan, Foshan, 528200, China.
⁵ Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou, 310006, China. caoliyong@caas.cn.
⁶ CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China. g.ye@irri.org.
⁷ Rice Breeding Innovations Platform, International Rice Research Institute, Metro Manila, Philippines. g.ye@irri.org.

Abstract

The multi-environment genomic selection enables plant breeders to select varieties resilient to diverse environments or particularly adapted to specific environments, which holds a great potential to be used in rice breeding. To realize the multi-environment genomic selection, a robust training set with multi-environment phenotypic data is of necessity. Considering the huge potential of genomic prediction enhanced sparse phenotyping on the cost saving of multi-environment trials (MET), the establishment of a multi-environment training set could also benefit from it. Optimizing the genomic prediction methods is also crucial to enhance the multi-environment genomic selection. Using haplotype-based genomic prediction models is able to capture local epistatic effects which could be conserved and accumulated across generations much like additive effects thereby benefitting breeding. However, previous studies often used fixed length haplotypes composed by a few adjacent molecular markers disregarding the linkage disequilibrium (LD) which is of essential role in determining the haplotype length. In our study, based on three rice populations with different sizes and compositions, we investigated the usefulness and effectiveness of multi-environment training sets with varying phenotyping intensities and different haplotype-based genomic prediction models based on LD-derived haplotype blocks for two agronomic traits, i.e., days to heading (DTH) and plant height (PH). Results showed that phenotyping merely 30% records in multi-environment training set is able to provide a comparable prediction accuracy to high phenotyping intensities; the local epistatic effects are much likely existent in DTH; dividing the LD-derived haplotype blocks into small segments with two or three single nucleotide polymorphisms (SNPs) helps to maintain the predictive ability of haplotype-based models in large populations; modelling the covariances between environments improves genomic prediction accuracy. Our study provides means to improve the efficiency of multi-environment genomic selection in rice.

Keywords: Genomic prediction; Haplotype-based model; Linkage disequilibrium; Rice; Sparse phenotyping; Training set.

Abstract

Grants and funding