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HTPdb and HTPtools:Exploiting maize haplotypetag polymorphisms for germplasm resource analyses and genomics-informed breeding

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Plant Communications 2022年第4期3卷 54-63页

作者： Yikun Zhao Hongli Tian Chunhui Li Hongmei Yi Yunlong Zhang Xiaohui Li Han Zhao Yongxue Huo Rui Wang Dingming Kang Yuncai Lu Zhihao Liu Ziyue Liang Liwen Xu Yang Yang Ling Zhou Tianyu Wang Jiuran Zhao Fengge Wang Maize Research Center Beijing Academy of Agriculture&Forestry Sciences(BAAFS)Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular BreedingShuguang Garden Middle Road No.9Beijing 100097China Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China Jilin Academy of Agricultural Sciences Maize Research InstituteGongzhuling 136100China Provincial Key Laboratory of Agrobiology Institute of Crop Germplasm and BiotechnologyJiangsu Academy of Agricultural SciencesNanjing 210014China College of Agronomy and Biotechnology China Agricultural UniversityBeijing 100193China College of Advanced Agriculture and Ecological Environment Heilongjiang UniversityHarbin 150080China

Along with rapid advances in high-throughput-sequencing technology,the development and application of molecular markers has been critical for the progress that has been made in crop breeding and genetic *** molecular markers should be able to rapidly genotype tens of thousands of breeding accessions with tens to hundreds of *** this study,we developed a multiplex molecular marker,the haplotype-tag polymorphism(HTP),that integrates Maize6H-60K array data from 3,587 maize inbred lines with 6,375 blocks from the recombination block *** applying strict filtering criteria,we obtained 6,163 highly polymorphic HTPs,which were evenly distributed in the ***,we developed a genome-wide HTP analysis toolkit,HTPtools,which we used to establish an HTP database(HTPdb)covering the whole genomes of 3,587 maize inbred lines commonly used in breeding.A total of 172,921 non-redundant HTP allelic variations were *** major HTPtools modules combine seven algorithms(e.g.,chain Bayes probability and the heterotic-pattern prediction algorithm)and a new plotting engine named“BCplot”that enables rapid visualization of the background information of multiple backcross *** was designed for big-data analyses such as complex pedigree reconstruction and maize heterotic-pattern *** HTP-based analytical strategy and the toolkit developed in this study are applicable for high-throughput genotyping and for genetic mapping,germplasm resource analyses,and genomics-informed breeding in maize.

关键词： haplotype tag database maize pedigree reconstruction heterotic-pattern prediction genomicsinformed breeding

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