Genome wide polymorphisms and yield heterosis in rice (Oryza sativa subsp. indica)

The linear relationship between genetic distance and heterosis within maize heterotic groups has inspired efforts to predict heterosis using molecular markers in other species. In this study, three cytoplasmic male sterile and three restorer lines from a hybrid rice breeding program were crossed in all possible (9) combinations and the F1 offspring grown in replicated trials in three locations. Whole genome sequence analyses were used to identify hybrid pair genome-wide polymorphisms and the extent to which these polymorphisms were associated with heterosis estimated. The number of total hybrid pair SNP ranged from 150,823 to 331,876 and mid-parent heterosis from −13.6 % to 18.6 %. Hybrid pair total SNP, total INDEL, gene SNP and gene INDEL counts were generally correlated at the whole genome and chromosome level. There was a close correlation between chromosome SNP and INDEL frequencies while gene presence-absence analysis found little difference between cross combinations. The relationship between whole genome SNP and heterosis was best explained by a second order polynomial of negative sign, suggesting a positive heterotic response may be achieved by maintaining a balance between inbreeding and outbreeding depression, and that genome wide polymorphisms may have a role in predicting heterosis in rice

Genome-wide DNA polymorphisms in elite indica rice inbreds discovered by whole-genome sequencing

Advances in next-generation sequencing technologies have aided discovery of millions of genome-wide DNA polymorphisms, single nucleotide polymorphisms (SNPs) and insertions-deletions (InDels), which are an invaluable resource for marker-assisted breeding. Whole-genome resequencing of six elite indica rice inbreds (three cytoplasmic male sterile and three restorer lines) resulted in the generation of 338million 75-bp paired-end reads, which provided 85.4% coverage of the Nipponbare genome. A total of 2819086 nonredundant DNA polymorphisms including 2495052 SNPs, 160478 insertions and 163556 deletions were discovered between the inbreds and Nipponbare, providing an average of 6.8 SNPs/kb across the genome. Distribution of SNPs and InDels in the chromosome was nonrandom with SNP-rich and SNP-poor regions being evident across the genome. A contiguous 4.3-Mb region on chromosome 5 with extremely low SNP density was identified. Overall, 83262 nonsynonymous SNPs spanning 16379 genes and 3620 nonsynonymous InDels in 2625 genes have been discovered which provide valuable insights into the basis underlying performance of the inbreds and the hybrids between these inbred combinations. SNPs and InDels discovered from this diverse set of indica rice inbreds not only enrich SNP resources for molecular breeding but also enable the study of genome-wide variations on hybrid performance