RRC ID 49514
Author Ma X, Fu Y, Zhao X, Jiang L, Zhu Z, Gu P, Xu W, Su Z, Sun C, Tan L.
Title Genomic structure analysis of a set of Oryza nivara introgression lines and identification of yield-associated QTLs using whole-genome resequencing.
Journal Sci Rep
Abstract Oryza nivara, an annual wild AA-genome species of rice, is an important gene pool for broadening the genetic diversity of cultivated rice (O. sativa L.). Towards identifying and utilizing favourable alleles from O. nivara, we developed a set of introgression lines (ILs) by introducing O. nivara segments into the elite indica rice variety 93-11 background through advanced backcrossing and repeated selfing. Using whole-genome resequencing, a high-density genetic map containing 1,070 bin-markers was constructed for the 131 ILs, with an average length of 349 kb per bin. The 131 ILs cover 95% of O. nivara genome, providing a relatively complete genomic library for introgressing O. nivara alleles for trait improvement. Using this high-density bin-map, QTL mapping for 13 yield-related traits was performed and a total of 65 QTLs were detected across two environments. At ~36.9% of detected QTLs, the alleles from O. nivara conferred improving effects on yield-associated traits. Six cloned genes, Sh4/SHA1, Bh4, Sd1, TE/TAD1, GS3 and FZP, colocalised in the peak intervals of 9 QTLs. In conclusion, we developed new genetic materials for exploration and use of beneficial alleles from wild rice and provided a basis for future fine mapping and cloning of the favourable O. nivara-derived QTLs.
Volume 6
Pages 27425
Published 2016-6-2
DOI 10.1038/srep27425
PII srep27425
PMID 27251022
PMC PMC4890301
MeSH Alleles Chromosome Mapping Chromosomes, Plant / genetics Crosses, Genetic Genetic Variation / genetics Genome, Plant / genetics* Genomics / methods Microsatellite Repeats / genetics Oryza / genetics* Phenotype Quantitative Trait Loci / genetics*
IF 4.122
Resource
Rice W2014