Genome-wide pedigree analysis of elite rice Shuhui 527 reveals key regions for breeding

doi:10.1016/S2095-3119(20)63256-7

摘要/Abstract

摘要：

杂交水稻为世界粮食的供应做出了重大贡献，而骨干亲本在杂交水稻品种选育中发挥着重要作用。为明确水稻骨干亲本蜀恢527（SH527，Oryza sativa）在育种过程中所利用的关键基因组区域，本研究对其进行了基于系谱的全基因组分析。利用高密度单核苷酸多态性（SNP）阵列对包括SH527、6个亲本品种及17个衍生恢复系在内的24个品种进行了扫描，分析了上游亲本对SH527基因组的独特贡献，确定了SH527及其衍生品种中保守的关键基因组区域。同时，利用多年的产量性状数据和SNP 芯片结果进行全基因组关联分析，发现了一些可能的已知或新的产量性状的关联位点。这项研究初步揭示了SH527育种的关键区域，将为后续育种提供参考。杂交水稻为世界粮食的供应做出了重大贡献，而骨干亲本在杂交水稻品种选育中发挥着重要作用。为明确水稻骨干亲本蜀恢527（SH527，Oryza sativa）在育种过程中所利用的关键基因组区域，本研究对其进行了基于系谱的全基因组分析。利用高密度单核苷酸多态性（SNP）阵列对包括SH527、6个亲本品种及17个衍生恢复系在内的24个品种进行了扫描，分析了上游亲本对SH527基因组的独特贡献，确定了SH527及其衍生品种中保守的关键基因组区域。同时，利用多年的产量性状数据和SNP 芯片结果进行全基因组关联分析，发现了一些可能的已知或新的产量性状的关联位点。这项研究初步揭示了SH527育种的关键区域，将为后续育种提供参考。

Abstract:

Hybrid rice significantly contributes to the food supply worldwide. Backbone parents play important roles in elite hybrid rice breeding systems. In this study, we performed pedigree-based analysis of the elite backbone parent rice variety, namely, Shuhui 527 (SH527, Oryza sativa), to exploit key genome regions during breeding. Twenty-four cultivars (including SH527, its six progenitors and 17 derived cultivars) were collected and analyzed with high-density single nucleotide polymorphism (SNP) array. Scanning all these cultivars with genome-wide SNP data indicated the unique contributions of progenitors to the SH527 genome and identified the key genomic regions of SH527 conserved within all its derivatives. These findings were further supported by known rice yield-related genes or unknown QTLs identified by genome-wide association study. This study reveals several key regions for SH527 and provides insights into hybrid rice breeding.

Key words: backbone parent , Shuhui 527 , SNPs , genome-wide association study

. [J]. Journal of Integrative Agriculture, 2021, 20(1): 35-45.

REN Yun, CHEN Dan, LI Wen-jie, TAO Luo, YUAN Guo-qiang, CAO Ye, LI Xue-mei, DENG Qi-ming, WANG Shi-quan, ZHENG Ai-ping, ZHU Jun, LIU Huai-nian, WANG Ling-xia, LI Ping, LI Shuang-cheng . Genome-wide pedigree analysis of elite rice Shuhui 527 reveals key regions for breeding[J]. Journal of Integrative Agriculture, 2021, 20(1): 35-45.

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