期刊
PLANT BIOTECHNOLOGY JOURNAL
卷 17, 期 8, 页码 1582-1594出版社
WILEY
DOI: 10.1111/pbi.13085
关键词
Pyrus; SNP array; genotyping; genetic map; genome assembly improvement; genome wide association studies
资金
- National Science Fund for Distinguished Young Scholars of China [31725024]
- Earmarked Fund for the China Agriculture Research System [CARS-28]
- 333 High Level Talents Project of Jiangsu Province [BRA2016367]
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-throughput genetic characterization of diverse germplasm, genetic mapping and breeding populations. We present here 200K AXIOM (R) 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 F-1 population of 98 individuals from 'Cuiguan' x '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 genome wide association studies 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-throughput genotyping in pear for genetic map construction, QTL identification and genomic selection.
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