title: Genomic structure analysis of a set of Oryza nivara introgression lines and identification of yield-associated QTLs using whole-genome resequencing.
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.
authors.affiliation: National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, MOE, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Ma
authors.affiliation: National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, MOE, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China.
authors.forename: Yongcai
authors.initials: Y
authors.lastname: Fu
authors.affiliation: National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, MOE, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China.|State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China.
authors.forename: Xinhui
authors.initials: X
authors.lastname: Zhao
authors.affiliation: National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, MOE, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China.
authors.forename: Liyun
authors.initials: L
authors.lastname: Jiang
authors.affiliation: National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, MOE, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China.
authors.forename: Zuofeng
authors.initials: Z
authors.lastname: Zhu
authors.affiliation: National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, MOE, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China.
authors.forename: Ping
authors.initials: P
authors.lastname: Gu
authors.affiliation: State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China.
authors.forename: Wenying
authors.initials: W
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Su
authors.affiliation: National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, MOE, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China.|State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China.
authors.forename: Chuanqing
authors.initials: C
authors.lastname: Sun
authors.affiliation: National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, MOE, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China.
authors.forename: Lubin
authors.initials: L
authors.lastname: Tan
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D003433:Crosses, Genetic; D014644:Genetic Variation / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics / Q000379:methods; D018895:Microsatellite Repeats / Q000235:genetics; D012275:Oryza / Q000235:genetics*; D010641:Phenotype; D040641:Quantitative Trait Loci / Q000235:genetics*