Pedigree Analysis Reveals Important Genes In Rice

The "Miracle rice" IR8 was a landmark of Green Revolution in 1960s for rice production.While the traits enabling the revolution are well described,the underlying mechanistic and genetic basis is less well resolved.Traditional QTL mapping followed by map based cloning have made tremendous progress in deciphering genes control related genes.However,the genetic bases revealed by QTL mapping are specific to the parental lines.An alternative approach using GWAS solves this limit but suffers from high false positives due to population structure,and both method are highly labor intensive.Since Green Revolution,rice yielding and plant types have been changed significantly,which makes it possible to investigate the responsible gene groups related to these changes.Many widely used cultivars such as IR24 and Minghui63 are derived from IR8 through breeding process,which provides a clear pedigree map to calculate the expected probabilities of inherited proportions from the original parents with classical genetic approaches.It could be proposed that genomic regions enriched through these pedigrees,compared to original parents,are strong candidates for regions responsible for the high yield phenotype.Given an observed proportion(frequency)of any certain genetic fragment as compared to the expected frequency in these cultivars,one can infer the chromosome blocks and genes responsible for high-yielding plant type.Here,we sequenced 21 well-represented cultivars within IR8's pedigree or closely related,along with 9 accessions used in production before Green Revolution as controls.By tracing the pedigree haplotypes in these cultivars and overlapping analyses between parents and offspring,we show the pedigree approach could effectively narrowed down the region and identified a set of candidate target genes for artificial selection on the high-yield phenotype that might have been ignored by commonly used techniques.Through incorporation of the pedigree relationship with high resolution genetic markers,our pedigree analysis identified 28 blocks maintained in all of IR8's descendants that presumably have extremely low probability(<0.34×10-4)of being present without human artificial selection.On these selectively-maintained blocks,99 genes have already been reported in literature which are associated with plant morphological or yielding phenotypes,including the most famous semi-dwarf gene(sdl)during Green Revolution.Additionally,we identified 109 genes on these blocks,expected to be under strong selection,which possess uncharacterized functions.Further,we found clear signatures of recombination dynamics,curving the variation patterns of artificial selection on the recombinational blocks during the breeding of these cultivars.By tracing the changes from generation to generation,we could also clarify the genetic network and position and genotype combination of these important genes.Besides the high-yielding trait,analysis of several cultivars derived from a resistant donor Tetep also confirmed the effectiveness of pedigree approach and provides new way to discovery resistant-related genes.Taken together,we show that pedigree analysis is an effective approach to identify genes under selection during historical breeding processes.Given that many agriculturally important traits have clear pedigrees in various crops,our novel methods can be highly applicable to identify genomic blocks and genes that control relevant traits systematically.