Rice Genomics and Genetics 2024, Vol.15, No.6, 277-286 http://cropscipublisher.com/index.php/rgg 283 Figure 4 Genetic structure and heterozygosity of rice hybrid varieties. Image caption: (a) Plots of the first two principal components of 1,439 rice hybrid varieties. (b) NJ tree of 1 439 indica hybrids constructed from simple matching distances of whole-genome SNPs. (c) Distribution of whole-genome heterozygosity of all the hybrids. (d) Heterozygosity plots of whole-genome SNPs in indica hybrids. The Ho and the He ( by the Hardy-Weinberg equation) were calculated for each SNP in the rice genome. The thresholds for highly heterozygous SNPs (Ho-He>0.4) and extremely low-heterozygous SNPs (Ho-He<−0.4) are indicated by horizontal lines. S5 (Hybrid sterility-5) locus is indicated (Adopted from Huang et al., 2015) 6.2 Breeding project based on whole genome selection A breeding project based on whole genome selection involves the generation, sequencing, and phenotyping of a large number of hybrid lines. For example, a study involving 10 074 F2 lines from 17 hybrid rice crosses aimed to understand the genetic basis of heterosis for yield traits (Huang et al., 2016). This project classified modern hybrid rice varieties into three groups, each representing different hybrid breeding systems. The technical route for integrating interspecific hybrid vigor and high-yield traits includes the use of marker-assisted selection and the identification of quantitative trait loci (QTLs) for yield traits. In China, the development of super hybrid rice has been achieved by combining the ideotype approach with intersubspecific heterosis, resulting in hybrid varieties that produce significantly higher yields than traditional varieties. The use of wide compatibility genes and thermosensitive genic male sterility (TGMS) genes has further facilitated the breeding of high-yielding hybrids (Azad et al., 2022). The achievements of this breeding project include the identification of key genomic loci that contribute to yield advantages and the development of high-yielding hybrid varieties with superior agronomic traits. The prospects for promotion and application are promising, with the potential for these hybrids to be grown on a large scale, thereby contributing to global food security (Huang et al., 2016). 6.3 Case analysis summary and inspiration The case studies highlight the importance of integrating genetic and genomic tools in hybrid rice breeding. The success of breeding programs that combine intersubspecific heterosis with high-yield traits provides a blueprint for future efforts. The use of wide compatibility systems and marker-assisted selection can significantly enhance breeding efficiency and yield potential (Peng et al., 2008).
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