Open AccessPedigree-based genome re-sequencing reveals genetic variation patterns of elite backbone varieties during modern rice improvement
Author(s) -
Xianwei Zheng,
Lanzhi Li,
Fan Liang,
Chang-Jun Tan,
Shuzhu Tang,
Sibin Yu,
Ying Diao,
Shuangcheng Li,
Zhongli Hu
Publication year - 2017
Publication title -
scientific reports
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.24
H-Index - 213
ISSN - 2045-2322
DOI - 10.1038/s41598-017-00415-1
Subject(s) - pedigree chart , biology , genetic diversity , single nucleotide polymorphism , genome , genetic variation , genetics , snp , gene , microbiology and biotechnology , genotype , population , sociology , demography
Rice breeding has achieved great productivity improvements by semi-dwarf varieties and hybrid vigour. Due to poor understanding of genetic basis of elite backbone varieties, the continuous increasing in rice yield still faces great challenges. Here, 52 elite rice varieties from three historical representative pedigrees were re-sequenced with 10.1× depth on average, and ~6.5 million single nucleotide polymorphisms (SNPs) were obtained. We identified thousands of low-diversity genomic regions and 0-diversity genes during breeding. Using pedigree information, we also traced SNP transmission patterns and observed breeding signatures in pedigree. These regions included the larger number of key well-known functional genes. Besides, 35 regions spanning 0.16% of the rice gnome had been differentially selected between conventional and restorer pedigrees. These genes identified here will be useful to the further pedigree breeding. Our study provides insights into the genetic basis of backbone varieties and will have immediate implications for performing genome-wide breeding by design.