DNA指纹技术的发展大体分为三个阶段：第一代的分子标记是以Southern杂交为基础的RFLP，第二代分子标记是以PCR为基础的各种DNA指纹标记，第三代分子标记是以单核苷酸多态性为基础的SNP。本文概述了品种鉴定技术的研究与应用进展，重点介绍了用于棉花品种鉴定的四种主要的分子标记技术：RFLP、RAPD、AFLP和SSR，对每一种分子标记的技术原理、在棉花品种鉴定上的应用研究状况及存在的优缺点进行了具体阐述。通过比较分析，提出了SSR标记适用于棉花品种鉴定的独特优越性。并对基于SSR分子标记技术构建我国棉花品种DNA指纹库的重要意义与必要性进行了分析。

为了全面地了解DNA指纹在品种鉴定上的利用现状，更重要的是促进DNA指纹技术切实有效的应用于植物品种鉴定，本研究归纳了目前开发出的可用于植物品种鉴定的DNA指纹技术，指出已有的DNA指纹品种鉴定技术的优势与不足，总结了DNA指纹应用于品种鉴定的分析措施，并认为受限于缺乏可以将DNA指纹转化为植物鉴定信息的理想措施，所以DNA标记还未真正有效地应用于生产实践中，因此提出一种基于DNA指纹的人工绘制品种鉴定简图(MCID)法是很重要的，本研究也重点阐述了MCID法的实施过程。

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.

利用有代表性的材料进行SNP位点的全基因组扫描分析与综合评估，基于KASP技术开发1套适用于我国棉花杂交种纯度高通量检测的核心SNP组合。从63K的棉花全基因组芯片中筛选获得具有单拷贝特性的SNP标记分别为5474个(中棉所TM-1基因组版本)和1850个(南京农大TM-1基因组版本)。根据芯片扫描分析结果，权衡考虑位点多态性、分型效果、纯合率与杂合率等因素，最终从每条染色体上优选1个杂交种杂合率高且分型效果理想的核心SNP位点，合计26个。采用Kraken^TM软件将SNP位点转化成KASP标记，利用SNPline平台进行SNP分型检测，实现了对大量样品的高通量基因分型，尤其适用于品种纯度快速检测，为SNP标记技术在棉花品种鉴定及指纹数据库构建等方面的应用奠定基础。

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。

目前甘薯中针对SNP位点的分子标记开发及应用的报道较少。为开发甘薯特异SNP分子标记,本研究利用简化基因组测序技术对甘薯种质材料进行测序,筛选稳定的SNP位点,将其开发为基于HRM技术的分子标记,并在甘薯种质材料中进行验证。通过对23个甘薯种质材料简化基因组测序数据的分析,共发现835 756个SNP多态性位点,筛选其中的3 650个含有SNP多态性位点的高质量测序片段,成功设计了134对引物;初步验证发现,22对(16.42%)引物没有扩增产物,15对(11.19%)引物扩增产物2个以上,36对(26.87%)引物的扩增产物没有差异。61对(45.52%)引物在8个样本中的扩增特异性好,而且样本之间有差异。最后筛选34对扩增多态性丰富的引物对52份甘薯种质材料进行扫描,发现材料间多态性介于27.27%~90.91%之间,平均多态性达到59.35%。聚类分析表明,参试52份甘薯种质材料之间的差异较小,多数材料与骨干亲本南瑞苕、徐薯18之间关系较近,国外引进甘薯材料和地方品种差异较大。建议在今后甘薯育种中尽量选用地方品种和国外甘薯品种,从而更好地拓宽甘薯遗传背景。本研究初步建立了基于简化基因组技术和HRM技术开发甘薯SNP分子标记的新思路,为今后甘薯SNP分子标记开发提供了参考。同时本研究开发的甘薯分子标记,丰富了甘薯分子标记类型,为甘薯研究者开展快速的分子标记研究提供了支持。

随着基因测序技术的发展,植物基因组数据越来越丰富,其中的单核苷酸多态性（single nucleotide polymorphism,SNP）数据由于具有高密度、高通量和易于自动化分析等特点而被广泛用于分子标记的开发和应用。竞争性等位基因特异性PCR（kompetitive allele-specific PCR,KASP）技术是近些年来发展起来的一种主要基于SNP的高通量基因分型技术。该技术由于其高通量、低成本和可操作性强等优点而在农作物性状改良等领域具有很大的应用潜力。本文介绍了KASP技术的发展、原理和方法步骤,综述了该技术在主要农作物的种质资源鉴定、分子标记辅助育种、基因定位和种子纯度鉴定等遗传育种中的应用,并讨论了该技术的优缺点,以期为今后农作物育种研究提供参考依据。

Maize lethal necrosis (MLN) occurs when maize chlorotic mottle virus (MCMV) and sugarcane mosaic virus (SCMV) co-infect maize plant. Yield loss of up to 100% can be experienced under severe infections. Identification and validation of genomic regions and their flanking markers can facilitate marker assisted breeding for resistance to MLN. To understand the status of previously identified quantitative trait loci (QTL)in diverse genetic background, F3 progenies derived from seven bi-parental populations were genotyped using 500 selected kompetitive allele specific PCR (KASP) SNPs. The F3 progenies were evaluated under artificial MLN inoculation for three seasons. Phenotypic analyses revealed significant variability (P ≤ 0.01) among genotypes for responses to MLN infections, with high heritability estimates (0.62 to 0.82) for MLN disease severity and AUDPC values. Linkage mapping and joint linkage association mapping revealed at least seven major QTL (qMLN3_130 and qMLN3_142, qMLN5_190 and qMLN5_202, qMLN6_85 and qMLN6_157 qMLN8_10 and qMLN9_142) spread across the 7-biparetal populations, for resistance to MLN infections and were consistent with those reported previously. The seven QTL appeared to be stable across genetic backgrounds and across environments. Therefore, these QTL could be useful for marker assisted breeding for resistance to MLN.

Temperate japonica rice varieties exhibit wide variation in the phenotypes of several important agronomic traits, including disease resistance, pre-harvest sprouting resistance, plant architecture, and grain quality, indicating the presence of genes contributing to favorable agronomic traits. However, gene mapping and molecular breeding has been hampered as a result of the low genetic diversity among cultivars and scarcity of polymorphic DNA markers. Single nucleotide polymorphism (SNP)-based kompetitive allele-specific PCR (KASP) markers allow high-throughput genotyping for marker-assisted selection and quantitative trait loci (QTL) mapping within closely related populations. Previously, we identified 740,566 SNPs and developed 771 KASP markers for Korean temperate japonica rice varieties. However, additional markers were needed to provide sufficient genome coverage to support breeding programs. In this study, the 740,566 SNPs were categorized according to their predicted impacts on gene function. The high-impact, moderate-impact, modifier, and low-impact groups contained 703 (0.1%), 20,179 (2.7%), 699,866 (94.5%), and 19,818 (2.7%) SNPs, respectively. A subset of 357 SNPs from the high-impact group was selected for initial KASP marker development, resulting in 283 polymorphic KASP markers. After incorporation of the 283 markers with the 771 existing markers in a physical map, additional markers were developed to fill genomic regions with large gaps between markers, and 171 polymorphic KASP markers were successfully developed from 284 SNPs. Overall, a set of 1225 KASP markers was produced. The markers were evenly distributed across the rice genome, with average marker density of 3.3 KASP markers per Mbp. The 1225 KASP markers will facilitate QTL/gene mapping and marker-assisted selection in temperate japonica rice breeding programs.

借助于分子标记进行基因型检测的技术在生物遗传改良等领域发挥着重要的作用。国际跨国种业公司凭借其高通量、自动化、大规模的共享检测平台,基因型检测技术得到广泛应用。随着从3G时代的高成本固相芯片和随机测序式基因型检测（genotyping by sequencing,GBS）发展到成本低、对检测平台要求较低、基于靶向测序基因型检测（genotyping by target sequencing,GBTS）的液相芯片,基因型检测技术完成了向4G时代的转变。在本文中首先介绍了两项最新的GBTS技术（基于多重PCR的GenoPlexs和基于液相探针捕获的GenoBaits）及其原理。同时,发展了可以在单个扩增子内检测多个SNP,称之为多聚单核苷酸多态性（multiple single-nucleotide-polymorphism cluster,mSNP或multiple dispersed nucleotide polymorphism,MNP）的技术,极大地提高了目标位点（扩增子）内变异的检测效率。与GBS和固相芯片相比,GBTS技术具有平台广适性、标记灵活性、检测高效性、信息可加性、支撑便捷性和应用广谱性。同一款标记集（例如玉米40K mSNP）,可以获得3种不同的标记形式（40K mSNP、260K SNP和754K单倍型）;并可以根据应用场景的需求,通过控制测序深度获得多种不同的标记密度（1—40K mSNP）。GenoPlexs和GenoBaits 2种技术相结合,可广泛应用于生物进化、遗传图谱构建、基因定位克隆、标记性状关联检测（全基因组关联分析——GWAS和混合样本分析——BSA）、后裔鉴定、基因渐渗、基因累加、品种权保护、品种质量监测、转基因成分/基因编辑/伴生生物检测等领域。目前,已经在20余种主要农作物、蔬菜以及部分动物和微生物中开发了GBTS标记50余套,并已广泛应用于上述领域。最后,展望了与未来GBTS应用相关的几个问题,包括便携式、自动化、高通量、智能化检测平台;根据用户需求定制的可变密度、多功能分子检测;GBTS与其他技术（KASP、高密度芯片、BSA策略等）的整合;基于资源共享的开源育种等。这些将推动GBTS技术在动物、植物和微生物遗传改良等领域的广泛应用。

Large-scale faba bean transcriptome data are available, and the first genotyping platform based on liquid-phase probe targeted capture technology was developed for genetic and molecular breeding studies. Faba bean (Vicia faba L., 2n = 12) is an important food legume crop that is widely grown for multiple uses worldwide. However, no reference genome is currently available due to its very large genome size (approximately 13 Gb) and limited single nucleotide polymorphism (SNP) markers as well as highly efficient genotyping tools have been reported for faba bean. In this study, 16.7 billion clean reads were obtained from transcriptome libraries of flowers and leaves of 102 global faba bean accessions. A total of 243,120 unigenes were de novo assembled and functionally annotated. Moreover, a total of 1,579,411 SNPs were identified and further filtered according to a selection pipeline to develop a high-throughput, flexible, low-cost Faba_bean_130K targeted next-generation sequencing (TNGS) genotyping platform. A set of 69 Chinese faba bean accessions were genotyped with the TNGS genotyping platform, and the average mapping rate of captured reads to reference transcripts was 93.14%, of which 53.23% were located in the targeted regions. The TNGS genotyping results were validated by Sanger sequencing and the average consistency rate reached 93.6%. Comprehensive population genetic analysis was performed on the 69 Chinese faba bean accessions and identified four genetic subgroups correlated with the geographic distribution. This study provides valuable genomic resources and a reliable genotyping tool that could be implemented in genetic and molecular breeding studies to accelerate new cultivar development and improvement in faba bean.

异地加代可以经济有效地加快育种进程。长期以来,海南省作为中国最南端省份,只在冬季用来进行育种材料的扩繁和加代,其周年可以种植农作物的自然气候和环境并未得到充分有效地利用。分子标记辅助育种与其他现代育种技术相融合,将助推南繁种业从单一的繁殖加代向资源引进和评价、育种选择、纯度检测、种质交流和产权保护等在内的全产业链模式转变,实现从海南冬繁到周年育种的转变,将海南的南繁地理和生态优势转化为南繁与育种相整合的全产业链优势,加快育种进展、提高育种效率,促进种业发展。本文讨论了海南地理生态优势与南繁种业现状,南繁种业转型升级的必要性和可能性,以及所面临的挑战和机遇。实现南繁种业的转型升级有赖于异地选择观念的转变、国家相关政策的支持、分子育种平台的支撑、生物安全防控、品种保护制度的建立和完善、资源共享和交流机制的形成。数量和群体遗传、基因型和环境互作、分子设计和大数据构成了南繁种业转型升级所需的育种理论。分子设计包括宏观水平的个体设计、群体设计和物种设计,微观水平的基因设计、代谢设计和网络设计。高通量精准表现型鉴定、环境型鉴定、信息处理和网络技术、决策支撑系统等是南繁种业转型升级所需的育种平台。作为分子育种的核心支撑,现已发展了基于靶向测序-液相芯片的基因型检测（genotyping by target sequencing and liquid chip,GBTS-LC）技术,通过GenoPlexs可以实现高达5 000对标记引物高度均一的多重PCR靶向扩增,而基于液态探针捕获的GenoBaits,可以获取高达40K个目标位点（每个位点包含多个SNP）。该技术具有平台广适性、标记灵活性、检测高效性、信息可加性、支撑便捷性、应用广普性,已成为分子育种中取代固相芯片的重要分子检测技术。要实现“海南育种,全国测试”,需要构建包括高效育种设施、快速育种、转基因和基因编辑技术、双单倍体育种技术、全基因组选择等在内的综合育种体系。为此,要倡导资源共享的开源育种模式,建设横跨动植物的共性方法、技术和平台,开展资源引进、监测和评价,构建种质资源指纹图谱,强化品种权保护、种子质量控制和纯度检测。希望借此推进有关南繁种业转型升级的公众讨论和政府决策,从而推进整个种业的科技进步和现代化。

亚洲栽培稻(Oryza sativa L.)分为籼、粳2个亚种, 随着杂交水稻的发展、种间杂种优势的利用, 籼粳之间的界限变得越来越模糊。本研究利用3000份水稻种质资源信息, 通过计算约2000万个单核苷酸多态性(single nucleotide polymorphism, SNP)位点的SNP-index值, 进行籼粳特异SNP位点筛选, 最终得到4084个籼粳特异SNP位点(4k-SNP); 同时确定以籼粳指数作为水稻品种籼粳鉴定的指标。研究进一步采用大规模简单随机取样等统计分析方法对籼粳特异位点进行数据降维处理, 将4k-SNP精简至40个SNP位点(40-SNP), 用于水稻籼粳鉴定。为了验证40-SNP的籼粳鉴定效果, 本研究一方面利用水稻生产上推广的82份选育品种, 对40-SNP籼粳鉴定结果与4k-SNP鉴定结果进行比较, 结果发现40-SNP与4k-SNP得出的粳型指数非常接近, 相关系数为0.99; 另一方面利用全球6类型(indica、aus、rayada、aromatic、tropical japonica、temperate japonica)水稻品种共49份材料, 对40-SNP籼粳鉴定结果与4k-SNP及程氏指数法籼粳鉴定结果进行比较, 发现40-SNP与4k-SNP及程氏指数法籼粳鉴定结果的相关系数分别在0.98和0.86以上。这些结果证实了40-SNP对水稻品种籼粳鉴定的有效性及准确性。另外发现40-SNP对水稻6种亚群类型也有很好鉴别效果, 其中indica的粳型指数 < 0.20, aus的粳型指数在0.20~0.40, rayada和aromatic的粳型指数在0.60~0.85之间, tropical japonica的粳型指数 > 0.90, temperate japonica粳型指数最高, 基本为1.00。本研究为研究水稻籼粳分化、杂种优势利用以及水稻种子管理条例制定等方面提供了数据支撑及理论基础。

The advances in genotyping technology provide an opportunity to use genomic tools in crop breeding. As compared to field selections performed in conventional breeding programmes, genomics-based genotype screen can potentially reduce number of breeding cycles and more precisely integrate target genes for particular traits into an ideal genetic background. We developed a whole-genome single nucleotide polymorphism (SNP) array, RICE6K, based on Infinium technology, using representative SNPs selected from more than four million SNPs identified from resequencing data of more than 500 rice landraces. RICE6K contains 5102 SNP and insertion-deletion (InDel) markers, about 4500 of which were of high quality in the tested rice lines producing highly repeatable results. Forty-five functional markers that are located inside 28 characterized genes of important traits can be detected using RICE6K. The SNP markers are evenly distributed on the 12 chromosomes of rice with the average density of 12 SNPs per 1 Mb and can provide information for polymorphisms between indica and japonica subspecies as well as varieties within indica and japonica groups. Application tests of RICE6K showed that the array is suitable for rice germplasm fingerprinting, genotyping bulked segregating pools, seed authenticity check and genetic background selection. These results suggest that RICE6K provides an efficient and reliable genotyping tool for rice genomic breeding. © 2013 China National Seed Group Co. Ltd. Plant Biotechnology Journal published by Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

陕西关中蚂蚱麦和山西平遥小白麦是我国北方小麦品种的原始骨干亲本, 解析蚂蚱麦和小白麦及其衍生系的遗传多样性对于小麦品种改良具有重要的参考意义。本研究利用小麦660K SNP芯片对蚂蚱麦、小白麦及其衍生品种(系)进行全基因组扫描, 分析其遗传多样性。结果表明, 小麦3个基因组的多态性SNP标记数为B>A>D, 第4同源群的多态性标记数最少, 149份供试材料基因多样性(H)范围为0.095~0.500, 平均值为0.336; 核苷酸多样性指数(π)范围为0.272~0.435, 平均值为0.340; 而遗传相似系数(GS)变幅为0.335~0.997, 平均值达0.619, 表明蚂蚱麦和小白麦衍生系的遗传多样性较低。聚类分析表明蚂蚱麦和小白麦紧密地聚在亚群I, 其衍生品种(系)分为5个亚群, 其中2000年以前以蚂蚱麦或小白麦的单一衍生系为主, 分在亚群I、II、III, 2000年以后多数品种同时拥有蚂蚱麦和小白麦血缘, 分在亚群IV、V, 遗传多样性较高, 且与大面积推广品种聚为一类。因此, 应加强优异基因资源导入, 拓宽小麦品种的遗传基础, 最终提高育种水平。

Previous molecular characterization studies conducted in Canadian wheat cultivars shed some light on the impact of plant breeding on genetic diversity, but the number of varieties and markers used was small. Here, we used 28,798 markers of the wheat 90K single nucleotide polymorphisms to (a) assess the extent of genetic diversity, relationship, population structure, and divergence among 174 historical and modern Canadian spring wheat varieties registered from 1905 to 2018 and 22 unregistered lines (hereinafter referred to as cultivars), and (b) identify genomic regions that had undergone selection. About 91% of the pairs of cultivars differed by 20-40% of the scored alleles, but only 7% of the pairs had kinship coefficients of < 0.250, suggesting the presence of a high proportion of redundancy in allelic composition. Although the 196 cultivars represented eight wheat classes, our results from phylogenetic, principal component, and the model-based population structure analyses revealed three groups, with no clear structure among most wheat classes, breeding programs, and breeding periods. F statistics computed among different categorical variables showed little genetic differentiation (< 0.05) among breeding periods and breeding programs, but a diverse level of genetic differentiation among wheat classes and predicted groups. Diversity indices were the highest and lowest among cultivars registered from 1970 to 1980 and from 2011 to 2018, respectively. Using two outlier detection methods, we identified from 524 to 2314 SNPs and 41 selective sweeps of which some are close to genes with known phenotype, including plant height, photoperiodism, vernalization, gluten strength, and disease resistance.© 2021. The Author(s).

【目的】利用SNP位点的单拷贝特性，结合陆地棉TM-1参考基因组序列信息，筛选基因组特异的SNP。【方法】以719份遗传背景来源广泛的陆地棉种质资源为材料，采用Illumina公司开发的CottonSNP63K芯片，利用GenomeStudio软件对芯片扫描所获得原始数据进行基因型数据质量控制，获得待测样品SNP位点的基因型数据。根据已公布的陆地棉TM-1基因组的两个版本&mdash;&mdash;中国农业科学院棉花研究所版本Gossypium hirsutum（AD1）genome BGI v1.0与南京农业大学版本G. hirsutum（AD1）genome NBI v1.1为参考序列，对CottonSNP63K芯片（63 058个SNP）各位点的侧翼序列分别进行全基因组Blast比对分析，以筛选具有单拷贝特性的特异SNP位点并用于样品指纹图谱的构建。【结果】利用CottonSNP63K芯片对719份材料进行SNP位点基因分型，主要表现为无检出信号的SNP位点、无多态性的SNP位点、具有多态性的SNP位点，而具有多态性的SNP位点的分型结果又可分为单位点SNP（基因组特异SNP）、双位点SNP和多位点SNP。通过对两个已公布的陆地棉TM-1参考基因组序列Blast比对结果表明，中国农业科学院棉花研究所TM-1基因组版本比对获得基因组特异SNP标记为5 474个，而南京农业大学TM-1基因组版本比对获得基因组特异SNP标记仅为1 850个，两者共有的特异SNP为1 594个，进一步通过分型效果、检出率及多态性3个评价指标，筛选score值&ge;0.7，call frequency值&ge;0.95，且MAF值&ge;0.2的SNP位点，获得471个分型效果理想，检出率高且多态性较高的特异SNP位点。在471个SNP位点中，430个位于染色体上，41个位于scaffold片段上。考虑到标记间的连锁程度，剔除连锁标记37个，最终获得393个核心SNP位点。利用393个核心SNP构建了719份品种资源的特征DNA指纹图谱，除个别材料之间遗传背景高度相似、基因型完全一致外，97%的材料均能实现准确有效的鉴别。【结论】筛选出393个基因组特异的SNP，并利用这些核心SNP构建了719份资源材料的特征DNA指纹图谱，为SNP分子标记应用于棉花重要性状遗传改良提供了参考。

利用全基因组SNP信息, 筛选陆地棉品种特异的核心SNP位点组合, 可为陆地棉品种身份鉴定提供准确高效的检测手段。本研究利用棉花CottonSNP80K芯片对326份不同来源的陆地棉种质进行SNP分型。以南京农业大学陆地棉TM-1基因组Gossypium hirsutum (AD1) genome NBI v1.1版本为参考序列, 对SNP位点进行注释。结果表明, 93.85% (72 990/77 774)的位点检出率超过99%, 61 595 (79.20%)个SNP位点具有多态性, 其中76.32% (47 009)的位点最小等位基因频率(MAF)大于0.1。基于位点检出率大于0.99、位点具多态性、MAF大于0.2、杂合率小于0.05、每条染色体的SNP密度为400 kb/SNP左右等要求, 最终获得4857个覆盖全基因组的高质量核心SNP位点组合。这些核心SNP位点组合平均检出率接近100%; 平均MAF值为0.34; 平均杂合率为0.02; 99%以上的陆地棉材料均能够被准确鉴定。统计分析表明利用核心SNP位点组合与CottonSNP80K的鉴定结果呈极显著相关。本研究提供了包含4857个SNP位点, 适于陆地棉品种指纹图谱绘制的核心SNP位点组合, 可实现陆地棉品种身份鉴定和品种确权。

The increasingly narrow genetic background characteristic of modern crop germplasm presents a challenge for the breeding of cultivars that require adaptation to the anticipated change in climate. Thus, high priority research aims at the identification of relevant allelic variation present both in the crop itself as well as in its progenitors. This study is based on the characterization of genetic variation in barley, with a view to enhancing its response to terminal drought stress.

Single nucleotide polymorphism (SNP) markers have multiple applications in plant breeding of small grains. They are used for the selection of divergent parents, the identification of genetic variants and marker-assisted selection. However, the use of SNPs in varietal purity assessment is under-reported, especially for multi-line varieties from the public sector. In the case of variety evaluation, these genetic markers are tools for maintaining varietal distinctness, uniformity and stability needed for cultivar release of multi-line or pure-line varieties of inbred crops. The objective of this research was to evaluate the purity and relationships of one original (AV-25) and two multi-line sub-populations (AV25-T and AV25-S) of the inbreeding species, oats (Avena sativa L.). Both sub-populations could be useful as forages in the central highland region of Colombia (&gt;2000 masl), such as in the departments of Boyacá and Cundinamarca, even though they were derived from an original composite mixture widely used in the mountainsides of the southern department of Nariño named Avena 25. Representative single plant selections (SPS) from the two sub-populations were grown together with SPS harvests from off-type plants (early and late) and plants from the original AV25 composite mixture, to determine their genetic similarity. Plants were genotyped by DNA extraction of a plateful of 96 individual plant samples and SNPs were detected for an Illumina Infinium 6K Chip assay. The data were used for the analysis of genetic structure and population relationships. The grouping observed based on the genetic data indicated that AV25-T and AV25-S were homogeneous populations and somewhat divergent in their genetic profile compared to the original AV25-C mix. In addition, to the two commercial, certified oat varieties (Cajicá and Cayuse) were different from these. The early and late selections were probable contaminants and could be discarded. We concluded that the use of SNP markers is an appropriate tool for ensuring genetic purity of oat varieties.

探明高粱育种材料的遗传结构和亲缘关系,为今后高粱杂交育种、种质创新及杂种优势群构建提供理论依据。采用简化基因组测序技术（Specific-locus amplified fragment sequencing,SLAF-seq）对37份高粱材料进行测序,以高粱（Sorghum bicolor_v3.1）基因组为参考基因组进行酶切预测,以水稻品种日本晴为对照进行比对分析,开发单核苷酸多态性（Single nucleotide polymorphism,SNP）标记并将其应用于育种材料的遗传结构和亲缘关系分析。结果表明,从37份高粱材料中共获得106.19 Mb的读长数据,不同材料的读长个数在1 461 206-4 628 462;对照数据的双端比对效率为92.15%,酶切效率为89.69%,SLAF建库正常。测序质量值Q30平均为89.60%,所有样品GC含量均值为45.71%,共开发了226 724个SLAF标签,其中多态性SLAF标签有105 053个,通过序列分析共获得185 451个有效标记。群体遗传结构分析和主成分分析都将37份高粱育种材料划分为2个类群,保持系和国外材料聚为一类,恢复系和中国材料聚为一类,分群结果与实际系谱基本相符。根据SNP标记估算材料间的遗传距离,距离值范围为0.0098-0.8841,L2R与L17R遗传距离最小,3765白B与L17R遗传距离最大。本研究明确了部分外引材料的血缘关系,并发现都拉类型、卡佛尔/顶尖类型的不育系与倾中国高粱的恢复系亲缘关系最远,在高粱杂交育种选配亲本上应加以重视。