National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.
Life Science and Technology Center, China National Seed Group Co., Ltd., Wuhan 430075, China.
J Genet Genomics. 2013 Dec 20;40(12):629-38. doi: 10.1016/j.jgg.2013.06.009. Epub 2013 Aug 20.
High-throughput SNP genotyping is widely used for plant genetic studies. Recently, a RICE6K SNP array has been developed based on the Illumina Bead Array platform and Infinium SNP assay technology for genome-wide evaluation of allelic variations and breeding applications. In this study, the RICE6K SNP array was used to genotype a recombinant inbred line (RIL) population derived from the cross between the indica variety, Zhenshan 97, and the japonica variety, Xizang 2. A total of 3324 SNP markers of high quality were identified and were grouped into 1495 recombination bins in the RIL population. A high-density linkage map, consisting of the 1495 bins, was developed, covering 1591.2 cM and with average length of 1.1 cM per bin. Segregation distortions were observed in 24 regions of the 11 chromosomes in the RILs. One half of the distorted regions contained fertility genes that had been previously reported. A total of 23 QTLs were identified for yield. Seven QTLs were firstly detected in this study. The positive alleles from about half of the identified QTLs came from Zhenshan 97 and they had lower phenotypic values than Xizang 2. This indicated that favorable alleles for breeding were dispersed in both parents and pyramiding favorable alleles could develop elite lines. The size of the mapping population for QTL analysis using high throughput SNP genotyping platform is also discussed.
高通量 SNP 基因分型广泛应用于植物遗传研究。最近，基于 Illumina BeadArray 平台和 Infinium SNP 分析技术，开发了一种 RICE6K SNP 芯片，用于全基因组评估等位变异和育种应用。在这项研究中，使用 RICE6K SNP 芯片对籼稻品种珍汕 97 和粳稻品种西藏 2 杂交衍生的重组自交系 (RIL) 群体进行了基因分型。共鉴定出 3324 个高质量 SNP 标记，并将其分为 RIL 群体中的 1495 个重组 bin。构建了一个由 1495 个 bin 组成的高密度连锁图谱，覆盖 1591.2 cM，每个 bin 的平均长度为 1.1 cM。在 RILs 的 11 条染色体的 24 个区域观察到分离失真。24 个扭曲区域中有一半包含先前报道的育性基因。共鉴定出 23 个产量相关的 QTL。其中 7 个 QTL 是首次在本研究中检测到的。从约一半鉴定出的 QTL 中，来自珍汕 97 的有利等位基因的表型值低于西藏 2。这表明，有利的等位基因在双亲中分散，并且有利等位基因的聚合可以培育出优良的品系。还讨论了使用高通量 SNP 基因分型平台进行 QTL 分析的作图群体大小。
