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New resources for genetic studies in maize (Zea mays L.): a genome-wide Maize6H-60K single nucleotide polymorphism array and its application

文献类型： 外文期刊

作者： Tian, Hongli 1 ; Yang, Yang 1 ; Yi, Hongmei 1 ; Xu, Liwen 1 ; He, Hang 2 ; Fan, Yaming 1 ; Wang, Lu 1 ; Ge, Jianrong 1 ; Liu 1 ;

作者机构： 1.Beijing Acad Agr & Forestry Sci, Maize Res Ctr, Beijing Key Lab Maize DNA Fingerprinting & Mol Br, Beijing 100097, Peoples R China

2.Peking Univ, Sch Adv Agr Sci, State Key Lab Prot & Plant Gene Res, Beijing 100871, Peoples R China

3.Peking Univ, Sch Life Sci, State Key Lab Prot & Plant Gene Res, Beijing 100871, Peoples R China

关键词： genotyping; germplasm resource evaluation; maize (Zea mays L; ); molecular breeding; SNP array; variety identification

期刊名称：PLANT JOURNAL （ 影响因子：6.417； 五年影响因子：7.627 ）

ISSN： 0960-7412

年卷期： 2021 年 105 卷 4 期

页码：

收录情况： SCI

摘要： Despite the availability of numerous molecular markers in maize, effective evaluation of all types of germplasm resources, accurate identification of varieties and analysis of a large number of materials in a timely, low-cost manner is challenging. Here, we present Maize6H-60K, a genome-wide single nucleotide polymorphism (SNP) array to facilitate maize genotyping. We first identified 160 million variants by sequencing data of 388 representative inbreds and then tiled 200 000 high-quality variants on a screening array. These variants were further narrowed down to 61 282 using stringent filtering criteria. Among the 60 000 markers, 21 460 SNPs (35%) were within genic regions and 12 835 (21%) were located in coding regions. To assess their effectiveness, 329 inbreds, 221 hybrids, 34 parent-offspring sets and six breeding samples were genotyped. Overall, 48 972 SNPs (80%) were categorized into the highest quality class, that of 'poly high resolution'. A total of 54 658 (89.29%) and 53 091 (86.73%) SNPs had minor allele frequency values >= 0.20 in inbreds and hybrids respectively. A linkage disequilibrium (LD) analysis revealed that LD decline was in equilibrium when r(2) was between 0.10 and 0.15, which corresponds to a physical distance of 400-600 kb. UPGMA clustering analysis divided the 329 inbred lines into nine groups that were consistent with known pedigrees. A background analysis of breeding materials indicated that the 60 000 markers were suitable for evaluation of breeding populations constructed by materials between or within heterotic groups. The developed Maize6H-60K array should be an important tool in maize genetic studies, variety identification and molecular breeding.

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