Accession PRJCA001768
Title Resequencing of hybrid rice parents: Divergent selection and genetic introgression shaped genome landscape of heterosis in two-line hybrid rice
Relevance Agricultural
Data types Whole genome sequencing
Organisms Oryza sativa
Description The successful application of heterosis in hybrid rice has dramatically improved the rice productivity, but the genetic mechanism for heterosis in the hybrid rice remains unclear. In this study, we generated two populations of rice F1 hybrids with present-day commercial hybrid parents, genotyped the parents with 50 K SNP chip and genome resequencing, and totally recorded the phenotype of the hybrids~43,200 plants at three field trials. By integrating these data with the collected genotypes of ~4,200 rice landraces and improved varieties that were reported previously, we found that the male and female parents have different levels of genome introgressions from other rice sub-populations including indica, aus and japonica, therefore shaping heterotic loci in the hybrids. Among the introgressed exogenous genome, we found that heterotic loci including Ghd8/DTH8, Gn1a and IPA1 existed in wild rice, but were significantly divergently selected among the rice sub-populations, suggesting these loci were subject to environmental adaption. During modern rice hybrid breeding, heterotic loci were further selected by removing loci with negative effect and fixing loci with positive effect and pyramid breeding. Our results provided insight into the genetic basis underlying the heterosis of elite hybrid rice varieties, which would facilitate to better understanding of heterosis and rice hybrid breeding.
Sample scope Monoisolate
Release date 2020-02-07
Grants
Agency program Grant ID Grant title
National Natural Science Foundation of China (NSFC) N/A
Submitter Dechung    Lim  (linzechuan110@163.com)
Organization Peking University
Submission date 2019-09-21

Project Data

Resource name Description
BioSample (115) -
SAMC134271 Genome resequencing of rice hybrid female parent
SAMC134270 Genome resequencing of rice hybrid female parent
SAMC134269 Genome resequencing of rice hybrid female parent
SAMC134268 Genome resequencing of rice hybrid female parent
SAMC134267 Genome resequencing of rice hybrid female parent
SAMC134266 Genome resequencing of rice hybrid female parent
SAMC134265 Genome resequencing of rice hybrid female parent
SAMC134264 Genome resequencing of rice hybrid female parent
SAMC134263 Genome resequencing of rice hybrid female parent
SAMC134262 Genome resequencing of rice hybrid female parent
SAMC134261 Genome resequencing of rice hybrid female parent
SAMC134260 Genome resequencing of rice hybrid female parent
SAMC134259 Genome resequencing of rice hybrid female parent
SAMC134258 Genome resequencing of rice hybrid female parent
SAMC134257 Genome resequencing of rice hybrid female parent
SAMC134256 Genome resequencing of rice hybrid female parent
SAMC134255 Genome resequencing of rice hybrid female parent
SAMC134254 Genome resequencing of rice hybrid female parent
SAMC134253 Genome resequencing of rice hybrid female parent
SAMC134252 Genome resequencing of rice hybrid female parent
SAMC134251 Genome resequencing of rice hybrid female parent
SAMC134250 Genome resequencing of rice hybrid female parent
SAMC134249 Genome resequencing of rice hybrid female parent
SAMC134248 Genome resequencing of rice hybrid female parent
SAMC134247 Genome resequencing of rice hybrid female parent
SAMC134246 Genome resequencing of rice hybrid female parent
SAMC134245 Genome resequencing of rice hybrid female parent
SAMC134244 Genome resequencing of rice hybrid female parent
SAMC134243 Genome resequencing of rice hybrid female parent
SAMC134242 Genome resequencing of rice hybrid female parent
SAMC134241 Genome resequencing of rice hybrid female parent
SAMC134240 Genome resequencing of rice hybrid female parent
SAMC134239 Genome resequencing of rice hybrid female parent
SAMC134238 Genome resequencing of rice hybrid female parent
SAMC134237 Genome resequencing of rice hybrid female parent
SAMC134236 Genome resequencing of rice hybrid female parent
SAMC134235 Genome resequencing of rice hybrid male parent
SAMC134234 Genome resequencing of rice hybrid male parent
SAMC134233 Genome resequencing of rice hybrid male parent
SAMC134232 Genome resequencing of rice hybrid male parent
SAMC134231 Genome resequencing of rice hybrid male parent
SAMC134230 Genome resequencing of rice hybrid male parent
SAMC134229 Genome resequencing of rice hybrid male parent
SAMC134228 Genome resequencing of rice hybrid male parent
SAMC134227 Genome resequencing of rice hybrid male parent
SAMC134226 Genome resequencing of rice hybrid male parent
SAMC134225 Genome resequencing of rice hybrid male parent
SAMC134224 Genome resequencing of rice hybrid male parent
SAMC134223 Genome resequencing of rice hybrid male parent
SAMC134222 Genome resequencing of rice hybrid male parent
SAMC134221 Genome resequencing of rice hybrid male parent
SAMC134220 Genome resequencing of rice hybrid male parent
SAMC134219 Genome resequencing of rice hybrid male parent
SAMC134218 Genome resequencing of rice hybrid male parent
SAMC134217 Genome resequencing of rice hybrid male parent
SAMC134216 Genome resequencing of rice hybrid male parent
SAMC134215 Genome resequencing of rice hybrid male parent
SAMC134214 Genome resequencing of rice hybrid male parent
SAMC134213 Genome resequencing of rice hybrid male parent
SAMC134212 Genome resequencing of rice hybrid male parent
SAMC134211 Genome resequencing of rice hybrid male parent
SAMC134210 Genome resequencing of rice hybrid male parent
SAMC134209 Genome resequencing of rice hybrid male parent
SAMC134208 Genome resequencing of rice hybrid male parent
SAMC134207 Genome resequencing of rice hybrid male parent
SAMC134206 Genome resequencing of rice hybrid male parent
SAMC134205 Genome resequencing of rice hybrid male parent
SAMC134204 Genome resequencing of rice hybrid male parent
SAMC134203 Genome resequencing of rice hybrid male parent
SAMC134202 Genome resequencing of rice hybrid male parent
SAMC134201 Genome resequencing of rice hybrid male parent
SAMC134200 Genome resequencing of rice hybrid male parent
SAMC134199 Genome resequencing of rice hybrid male parent
SAMC134198 Genome resequencing of rice hybrid male parent
SAMC134197 Genome resequencing of rice hybrid male parent
SAMC134196 Genome resequencing of rice hybrid male parent
SAMC134195 Genome resequencing of rice hybrid male parent
SAMC134194 Genome resequencing of rice hybrid male parent
SAMC134193 Genome resequencing of rice hybrid male parent
SAMC134192 Genome resequencing of rice hybrid male parent
SAMC134191 Genome resequencing of rice hybrid male parent
SAMC134190 Genome resequencing of rice hybrid male parent
SAMC134189 Genome resequencing of rice hybrid male parent
SAMC134188 Genome resequencing of rice hybrid male parent
SAMC134187 Genome resequencing of rice hybrid male parent
SAMC134186 Genome resequencing of rice hybrid male parent
SAMC134185 Genome resequencing of rice hybrid male parent
SAMC134184 Genome resequencing of rice hybrid male parent
SAMC134183 Genome resequencing of rice hybrid male parent
SAMC134182 Genome resequencing of rice hybrid male parent
SAMC134181 Genome resequencing of rice hybrid male parent
SAMC134180 Genome resequencing of rice hybrid male parent
SAMC134179 Genome resequencing of rice hybrid male parent
SAMC134178 Genome resequencing of rice hybrid male parent
SAMC134177 Genome resequencing of rice hybrid male parent
SAMC134176 Genome resequencing of rice hybrid male parent
SAMC134175 Genome resequencing of rice hybrid male parent
SAMC134174 Genome resequencing of rice hybrid male parent
SAMC134173 Genome resequencing of rice hybrid male parent
SAMC134172 Genome resequencing of rice hybrid male parent
SAMC134171 Genome resequencing of rice hybrid male parent
SAMC134170 Genome resequencing of rice hybrid male parent
SAMC134169 Genome resequencing of rice hybrid male parent
SAMC134168 Genome resequencing of rice hybrid male parent
SAMC134167 Genome resequencing of rice hybrid male parent
SAMC134166 Genome resequencing of rice hybrid male parent
SAMC134165 Genome resequencing of rice hybrid male parent
SAMC134164 Genome resequencing of rice hybrid male parent
SAMC134163 Genome resequencing of rice hybrid male parent
SAMC134162 Genome resequencing of rice hybrid male parent
SAMC134161 Genome resequencing of rice hybrid male parent
SAMC134160 Genome resequencing of rice hybrid male parent
SAMC134159 Genome resequencing of rice hybrid male parent
SAMC134158 Genome resequencing of rice hybrid male parent
SAMC134157 Genome resequencing of rice hybrid male parent
GSA (1) -
CRA002327 Genome resequencing of two-line hybrid parents