SoySNP618K array:A high-resolution single nucleotide polymorphism platform as a valuable genomic resource for soybean genetics and breeding

作     者：Yan-Fei Li Ying-Hui Li Shan-Shan Su Jochen CReif Zhao-Ming Qi Xiao-Bo Wang Xing Wang Yu Tian De-Lin Li Ru-Jian Sun Zhang-Xiong Liu Ze-Jun Xu Guang-Hui Fu Ya-Liang Ji Qing-Shan Chen Ji-Qiang Liu Li-Juan Qiu 

作者机构：The National Key Facility for Crop Gene Resources and Genetic Improvement(NFCRI)/Key Laboratory of Crop Gene Resource andGermplasm Enhancement(MOA)/Key Laboratory of Soybean Biology(Beijing)(MOA)Institute of Crop SciencesChinese Academy ofAgricultural SciencesBeijing 100081China Beijing Compass Biotechnology Co.LtdBeijing 102206China Department of Breeding ResearchLeibniz Institute of Plant Genetics and Crop Plant Research(IPK)Gatersleben 06466Germany Key Laboratory of Soybean Biology in Chinese Ministry of Education(Key Laboratory of Soybean Biology and Breeding/Genetics ofChinese Agriculture Ministry)Northeast Agricultural UniversityHarbin 150030China School of AgronomyAnhui Agricultural UniversityHefei 230036China Xuzhou Institute of Agricultural Sciences of Xu-huai Region of JiangsuXuzhou 221131China Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing 100193China Hulun Buir Institution of Agricultural SciencesZhalantunInner Mongolia 021000China Suzhou Academy of Agricultural SciencesSuzhou 234000China 

出 版 物：《Journal of Integrative Plant Biology》 (植物学报（英文版）)

年 卷 期：2022年第64卷第3期

页      面：632-648页

核心收录：

学科分类：09[农学] 0901[农学-作物学] 

基　　金：supported by the Agricultural Science and Technology Innovation Program(ASTIP)of Chinese Academy of Agricultural Sciences(CAAS-ZDRW20210) the National Key Research and Development Program of China(nos.2020YFE0202300 and 2021YFD1201600) the Platform of National Crop Germplasm Resources of China(nos.2016-004 and 2017-004) 

主　　题：functional single nucleotide polymorphism array gene discovery genomic selection genome-wide association studies marker-assisted selection soybean 

摘      要：Innovations in genomics have enabled the development of low-cost,high-resolution,single nucleotide polymorphism(SNP)genotyping arrays that accelerate breeding progress and support basic research in crop ***,we developed and validated the Soy SNP618 K array(618,888 SNPs)for the important crop *** SNPs were selected from whole-genome resequencing data containing 2,214 diverse soybean accessions;29.34%of the SNPs mapped to genic regions representing 86.85%of the 56,044annotated high-confidence ***-by-state analyses of 318 soybeans revealed 17 redundant accessions,highlighting the potential of the Soy SNP618 K array in supporting gene bank *** patterns of population stratification and genomic regions enriched through domestication were highly consistent with previous findings based on resequencing data,suggesting that the ascertainment bias in the Soy SNP618 K array was largely compensated ***-wide association mapping in combination with reported quantitative trait loci enabled fine-mapping of genes known to influence flowering time,E2 and Gm PRR3 b,and of a new candidate gene,Gm ***,genomic prediction of flowering and maturity time in 502 recombinant inbred lines was highly accurate(0.65).Thus,the Soy SNP618 K array is a valuable genomic tool that can be used to address many questions in applied breeding,germplasm management,and basic crop research.