Development of an integrated 200K SNP genotyping array and application for genetic mapping, genome assembly improvement and GWAS in pear (Pyrus)

First author: Xiaolong Li; Affiliations: Nanjing Agricultural University (南京农业大学): Nanjing, China

Corresponding author: Jun Wu

Pear (Pyrus; 2n = 34), the third most important temperate fruit crop, has great nutritional and economic value. Despite the availability of many genomic resources in pear, it is challenging to genotype novel germplasm resources and breeding progeny in a timely and cost‐effective manner. Genotyping arrays can provide fast, efficient, and high‐ hroughput genetic characterization of diverse germplasm, genetic mapping and breeding populations. We present here 200K AXIOM® PyrSNP, a large‐scale single nucleotide polymorphism (SNP) genotyping array to facilitate genotyping of Pyrus species. A diverse panel of 113 re‐sequenced pear genotypes was used to discover SNPs to promote increased adoption of the array. A set of 188 diverse accessions and an F1 population of 98 individuals from ‘Cuiguan’ × ‘Starkrimson’ was genotyped with the array to assess its effectiveness. A large majority of SNPs (166,335 or 83%) are of high quality. The high density and uniform distribution of the array SNPs facilitated prediction of centromeric regions on 17 pear chromosomes, and significantly improved the genome assembly from 75.5% to 81.4% based on genetic mapping. Identification of a gene associated with flowering time and candidate genes linked to size of fruit core via GWAS showed the usefulness of the array in pear genetic research. The newly developed high‐density SNP array presents an important tool for rapid and high‐ hroughput genotyping in pear for genetic map construction, QTL identification and genomic selection.

梨树，二倍体，共34条染色体，是第三个最重要的温带水果作物，具有非常重要的营养和经济价值。虽然梨树研究已经有了许多可以利用的遗传资源，但对梨树新种资资源和育种子代进行即时、有效的基因型分型仍然存在挑战。基因分型芯片可用于种质资源、遗传图谱及育种群体的快速、有效和高通量遗传鉴定。作者构建了大规模单核苷酸多态性基因分型芯片，加速梨树的基因分型。作者基于113个不同梨树基因型的重测序数据用于开发SNP。作者利用新开发的芯片对188个梨树品种及98个F1代群体的个体进行基因型分型，以评估该芯片的效率。高质量的SNP占了所有SNP的83%。芯片SNP的高密度、均质性分布加速了17个梨染色体的着丝粒区预测，并基于遗传图谱将梨基因组组装提升到了81.4%。作者通过GWAS鉴定到了一个开花相关的基因和一个果实大小相关的基因，说明该芯片有助于梨的遗传学研究。本文所报道的高密度SNP芯片作为一个重要的遗传学工具有利于梨的遗传图谱构建、QTL鉴定和基因组选择育种研究。

通讯：吴俊 (http://onlinelibrary.wiley.com/doi/10.1111/tpj.13666/full)

个人简介：1993.9-1997.6，安徽农业大学园艺学院，园艺专业学士；1997.9-2000.6，安徽农业大学园艺学院，果树学专业硕士；2000.9-2003.6，山东农业大学园艺科学与工程学院，果树学专业博士；2003.7-2005.12，南京农业大学园艺学院，讲师；2005.3-2008.9，南京农业大学，果树学博士后；2006.1-2010.12，南京农业大学园艺学院，副教授；2010.2-2011.2，美国伊利诺伊大学香槟校区，访问学者；2011.1-2012.12，南京农业大学，园艺学院/作物遗传与种质创新国家重点实验室，教授四级；2013.1-至今南京农业大学，园艺学院/作物遗传与种质创新国家重点实验室，破格教授三级。

研究方向：果树种质资源与分子育种。主要从事梨的基因组进化、优异资源挖掘与利用、以及分子辅助育种技术等方面的研究。 

doi: https://doi.org/10.1111/pbi.13085

Journal: Plant Biotechnology Journal

First Published: January 28, 2019