Single-cross maize hybrids display superior heterosis and are produced from crossing two parental inbred lines belonging to genetically different heterotic groups. Here we assembled 1,604 historically utilized maize inbred lines belonging to various female heterotic groups (FHGs) and male heterotic groups (MHGs), and conducted phenotyping and genomic sequencing analyses. We found that the FHGs and MHGs have undergone both convergent and divergent changes for different sets of agronomic traits. Using genome-wide selection scans and association analyses, we identified a large number of candidate genes that contributed to the improvement of agronomic traits of the FHGs and MHGs. Moreover, we observed increased genetic differentiation between the FHGs and MHGs across the breeding eras, and we found a positive correlation between increasing heterozygosity levels in the differentiated genes and heterosis in hybrids. Furthermore, we validated the function of two selected genes and a differentiated gene. This study provides insights into the genomic basis of modern hybrid maize breeding.© 2022. The Author(s), under exclusive licence to Springer Nature Limited.

Hybrid maize displays superior heterosis and contributes over 30% of total worldwide cereal production. However, the molecular mechanisms of heterosis remain obscure. Here we show that structural variants (SVs) between the parental lines have a predominant role underpinning maize heterosis. De novo assembly and analyses of 12 maize founder inbred lines (FILs) reveal abundant genetic variations among these FILs and, through expression quantitative trait loci and association analyses, we identify several SVs contributing to genomic and phenotypic differentiations of various heterotic groups. Using a set of 91 diallel-cross F hybrids, we found strong positive correlations between better-parent heterosis of the F hybrids and the numbers of SVs between the parental lines, providing concrete genomic support for a prevalent role of genetic complementation underlying heterosis. Further, we document evidence that SVs in both ZAR1 and ZmACO2 contribute to yield heterosis in an overdominance fashion. Our results should promote genomics-based breeding of hybrid maize.© 2023. The Author(s), under exclusive licence to Springer Nature America, Inc.

中国已经成为全球鲜食玉米最主要生产和消费国家之一, 解析我国鲜食玉米品种之间的遗传多样性和亲缘关系, 对品种鉴定和品种培育具有重要的指导意义。本研究利用Illumina Maize 6K芯片对全国范围内的385个鲜食玉米品种进行全基因组扫描, 了解群体结构, 划分种质类群, 估算品种间的遗传距离, 揭示其遗传多样性。结果表明, 5067个SNP标记在385个鲜食玉米品种中基因多样性平均0.406, 变幅为0.097~0.500; 多态信息含量(polymorphism information content, PIC)平均0.319, 变幅为0.092~0.375。通过PCA分析和群体遗传结构分析一致表明, 本研究所收集的品种主要划分为3个类群, 分别为糯玉米类群(糯玉米和甜糯玉米, 共185个品种)、温带甜玉米类群(123个品种)和热带甜玉米类群(77个品种)。两两品种间的遗传距离在0.132~0.472之间, 平均值为0.37。通过F_ST分析检测到不同类群间有160个区域受到强烈选择, 其中包括4个玉米籽粒淀粉合成途径的关键基因(sh2、su1、su2和wx1), 进一步利用分子标记验证了sh2和DGAT1-2两个位点在鲜食玉米群体不同选择模式。本研究为我国鲜食玉米品种选育和改良提供了重要的理论指导。

单核苷酸多态性（SNP）作为最新一代遗传分子标记，已广泛应用于生物各研究领域。本文围绕SNP 分子标记的开发和检测以及在作物品种鉴定中的应用展开阐述。目前SNP 的开发主要有基于公共数据库和测序两种途径，检测方法从以凝胶电泳为基础的传统检测向高通量自动化的新检测技术发展。在品种鉴定中，对于大样本群体和多SNP 检测位点的作物，建议使用基因芯片或基因测序分型（GBS）技术；对于小样本群体和少SNP 检测1 位点的作物，则通过竞争性等位基因特异性PCR（KASP）和高分辨率熔解曲线（HRM）分型技术实现更加灵活高效低成本的检测。

The rapid development and application of molecular marker assays have facilitated genomic selection and genome-wide linkage and association studies in wheat breeding. Although PCR-based markers (e.g. simple sequence repeats and functional markers) and genotyping by sequencing have contributed greatly to gene discovery and marker-assisted selection, the release of a more accurate and complete bread wheat reference genome has resulted in the design of single-nucleotide polymorphism (SNP) arrays based on different densities or application targets. Here, we evaluated seven types of wheat SNP arrays in terms of their SNP number, distribution, density, associated genes, heterozygosity and application. The results suggested that the Wheat 660K SNP array contained the highest percentage (99.05%) of genome-specific SNPs with reliable physical positions. SNP density analysis indicated that the SNPs were almost evenly distributed across the whole genome. In addition, 229 266 SNPs in the Wheat 660K SNP array were located in 66 834 annotated gene or promoter intervals. The annotated genes revealed by the Wheat 660K SNP array almost covered all genes revealed by the Wheat 35K (97.44%), 55K (99.73%), 90K (86.9%) and 820K (85.3%) SNP arrays. Therefore, the Wheat 660K SNP array could act as a substitute for other 6 arrays and shows promise for a wide range of possible applications. In summary, the Wheat 660K SNP array is reliable and cost-effective and may be the best choice for targeted genotyping and marker-assisted selection in wheat genetic improvement.© 2020 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

为揭示糯玉米种质的遗传多样性,利用新一代分子标记技术-SNPs(Single nucleotide polymorphisms)对39份不同基因型的糯玉米自交系进行了基因型分析。结果表明,1 059个SNP标记在39份自交系中的多态性信息含量(PIC)为0.05~0.38,平均含量为0.31;最小等位基因频率(MAF)为0.03~0.50,平均值为0.29;期望杂合度变化范围为0.05~0.50,平均期望杂合度为0.39。39份自交系之间的亲缘关系(Kinship)系数为0.00~0.91,京6与京糯6之间亲缘关系最近。通过Neighbor-joining(NJ)聚类分析,将39份自交系划分为5大类群,其中系谱来源不清晰的糯玉米自交系均被划分至不同类群中,明确了其亲缘关系。因此,SNP标记适用于糯玉米自交系的遗传多样性分析及亲缘关系研究,可为糯玉米种质资源利用及品种选育提供参考。

There is a rapidly rising trend in the development and application of molecular marker assays for gene mapping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of genotyping-by-sequencing (GBS) platforms have been developed in over 25 crop species and perennial trees. However, much less effort has been made on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. In this review, we discuss the scientific bottlenecks in existing SNP arrays and GBS technologies and the strategies to develop targeted platforms for crop molecular breeding. We propose that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops. The development of such platforms faces serious challenges at both the technological level due to cost ineffectiveness, and the knowledge level due to large genotype-phenotype gaps in crop plants. It is expected that such genotyping platforms will be achieved in the next ten years in major crops in consideration of (a) rapid development in gene discovery of important traits, (b) deepened understanding of quantitative traits through new analytical models and population designs, (c) integration of multi-layer -omics data leading to identification of genes and pathways responsible for important breeding traits, and (d) improvement in cost effectiveness of large-scale genotyping. Crop breeding chips and genotyping platforms will provide unprecedented opportunities to accelerate the development of cultivars with desired yield potential, quality, and enhanced adaptation to mitigate the effects of climate change.Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.