Advances in Modelling the Potato Crop: Sufficiency and Accuracy Considering Uses and Users, Data, and Errors

When we consider complex, multi-step processes such as crop growth or the progress of a disease then simple mathematical functions are inadequate to describe them and we generally use some kind of mathematical model. The commonest form in use is one that we call a simulation model although there are other forms of model such as Rule-based, (e.g. Gu et al. AI Appl 10:13–24, 1996), Bayesian (Gold, Plant Disease Epidemiol 4:84–122, 1989) and ‘fuzzy’ (Burrough, J Soil Sci 40:477–492, 1989), depending upon the application. Models may sometimes be combined into packages that we call decision support systems. This paper will consider simulation modelling and also the combination of complementary models. Mathematical models of the potato crop have been devised, in a range of sophistication, over a long period of years and a quite proper question is: “Where next? What are the developments that are sought or, more importantly, that are needed?”     

青海省几个主要春性甘蓝型油菜杂交种的SSR分析

为了探明青海省主要甘蓝型油菜品种的遗传变异,建立准确高效的种子纯度鉴定方法,本研究选取5个青海省甘蓝型油菜主栽品种,利用140对简单重复序列(Simple sequence repeat,简称SSR)引物对其进行分子标记分析,从中筛选出26对能清晰扩增出多态性主带的引物,进一步对包括这5个品种及其中4个杂交品种的7个亲本系进行扩增后,经6%聚丙烯酰胺凝胶电泳分离和带型分析,成功构建出5个青海省甘蓝型油菜主栽品种及其中4个杂交种亲本系的指纹图谱,并鉴定出了这4个杂交种的共显性标记。这些标记不仅可用于亲本材料和杂交品种真伪的鉴别,还可为杂交种纯度的鉴定提供可靠方法,对亲本知识产权的保护及杂交种推广具有重要的意义。     

SSR标记与田间种植鉴定玉米品种纯度的比较

从行业标准中筛选出8对适用于玉米品种纯度鉴定的引物组合,能区分90％以上的审定品种.96％的审定品种在8个引物组合中有4个以上的杂合位点,具有较高的杂合率和品种区分能力.38份来自全国种子市场的样品同时进行田间种植和SSR纯度鉴定,8对SSR引物组合检测出自交苗平均值为0.6％,异型株为1.8％,纯度为97.7％;田间...     

Potato Ring Rot in Norway: Occurrence and Control

Potato ring rot, caused by the bacterium Clavibacter michiganensis subspecies sepedonicus, is considered to be one of the internationally most important seed potato diseases (Smith et al.; Eur J Plant Pathol 107:739–748, 2001) and has been a problem in Norwegian potato production since its first detection in 1964. Since 1965, Norway has had its own national legislation for the control of the disease. In recent years, this legislation has evolved to be more similar to the EU Commission Directive 2006/56/EC. In 1999, the Norwegian Food Safety Authority initiated an eradication program for potato ring rot with the aim of selling potatoes to other European countries. During the project period (1999–2008), efficient systems for sampling, analysis and eradication measures were built. From 1999 to 2002, the occurrence of potato ring rot in commercial potato production was monitored in all counties. Sampling was carried out according to the instructions of the Norwegian Food Safety Authority, while testing of samples was (from 2000 onwards) carried out by Bioforsk laboratories with modern serological and molecular detection methods. When ring rot was detected in a potato lot, the grower had to implement strict eradication measures. The survey was followed up with two monitoring periods, 2003–2004 and 2005–2008. During the project period, 328 cases of potato ring rot were found. The counties Hedmark, Nordland, Troms, and Tr?ndelag accounted for most of these. The main objectives of this study were to describe the occurrence of potato ring rot in Norwegian potato production and to evaluate the effectiveness of the eradication measures employed for the control of the disease. This survey showed that the overall ring rot situation did improve considerably during the project period (1999–2008), both in relation to prior periods, and when comparing the surveying and monitoring periods. Problem areas where monitoring must be continued remain.     

不同大麦品种特异性SSR分子标记的筛选

为探究鉴别大麦品种特异性所需要SSR标记的数量与鉴别效果,以国内外44个大麦品种为材料,并根据来源不同,将其分为江浙沪组、国内组和国际组;根据SSR标记的多态性及其分布,选取位于大麦7条染色体上的28个SSR标记对参试品种进行遗传多样性分析与特异性鉴定,研究鉴别不同来源组内不同品种所需的最少标记数和最佳标记数.结果 表...     

Genetic Fingerprinting of Potato Varieties from the Northwest Potato Variety Development Program

The Northwest Potato Variety Development (NWPVD) Program has released 45 improved potato varieties since 1985. Thirty-four potato varieties, four breeding clones and two advanced selections from NWPVD Program, and six commonly-grown potato varieties were fingerprinted using 32 simple sequence repeat (SSR) markers and 12,808 single nucleotide polymorphism (SNP) markers. Of 32 SSR markers, 29 exhibited significant polymorphism across all the 46 potato clones studied. A total of 143 alleles were observed with an average of 4.6 alleles per SSR marker. These markers span all 12 chromosomes of potato, with a maximum of five markers from chromosome VIII and minimum of one marker from chromosome VI. The polymorphic information content (PIC) and expected heterozygosity (H_e) of the SSR markers ranges between 0.18 to 0.75 and 0.20 to 0.78, respectively. Based on PIC, H_e, and ease of scoring, we recommend a set of eight SSR markers: STG0016, STI0004, STI0012, STI0023, STI0030, STI0033, STM1016 and STM1104 for fingerprinting NWPVD varieties. Out of 12,808 SNPs, 88.8% resulted in reliable three cluster diploid calling of which 87.8% were polymorphic. Tetraploid calling resulted in 44.2% of SNPs of which 94.5% were polymorphic. Our study provided fingerprinting resources for the NWPVD varieties and can be used in issues related to intellectual property rights, ownership, trademark and diversity analysis.     

马铃薯脱毒种薯质量追溯体系建设的探析

马铃薯脱毒种薯生产是解决马铃薯因病毒感染引起品种退化的最有效途径。马铃薯品种资源丰富,种薯质量要求高,生产环节多,级别多元化,但目前在国内尚无专一机构作种薯质量认定,种薯生产一旦出现问题将无从可追。本文借鉴农产品质量追溯系统的做法,以本单位种薯生产为依托,从标准体系、质量认证、编码规则、数据采集与档案管理等方面,探讨马铃薯质量追溯系统的建设。     

Molecular Analysis of Potatoes from the Pacific Northwest Tri-State Variety Development Program and Selection of Markers for Practical DNA Fingerprinting Applications

DNA fingerprinting is a valuable tool for plant cultivar discrimination and identification. Simple Sequence Repeat (SSR) markers represent an excellent option for obtaining DNA fingerprints of potatoes in an easy, fast, and reliable fashion. The highly polymorphic and co-dominant nature of SSRs gives them good discrimination power to declare the distinctiveness of new potato clones for Plant Variety Protection (PVP) and to properly identify existing cultivars. They are also useful for confirming origin and avoiding duplications and mixtures in breeding, foundation and certification programs, and also during growing and marketing stages. A total of 54 (50 tetraploid and 4 diploid) potato clones, including new cultivars released by the Pacific Northwest Tri-State Potato Variety Development Program and a set of common commercial cultivars, were analyzed using 25 SSR markers. Marketing classes (French fry processing, fresh market, and chip processing) were clearly separated using those markers. We have empirically selected a subset of six SSRs that differentiate all the potato varieties and clones present in the study. This subset of six SSR markers could be used for practical DNA fingerprinting. In order to declare distinctiveness, we recommend that common reference varieties always be genotyped together with the newly tested potato clones and that focus be placed on the relative allelic differences between the new clones and the reference varieties.     

SSR分子标记技术在杂交水稻种子纯度鉴定中的应用

SSR标记由于具有数量丰富、多态性高、遗传上呈共显性、实验操作简单、结果稳定可靠、引物序列易交流等优点，已成为杂交水稻种子纯度鉴定的一种理想分子标记。概述了SSR分子标记技术应用于杂交水稻种子纯度鉴定的原理、技术要点及其研究进展，并就该技术产业化应重点考虑的问题进行了讨论。     

基于NYT 1433-2014中48对SSR引物的94份杂交稻亲本DNA分子数字指纹库研究

建立方法简便、分辨率高的水稻品种遗传多态性和真实性鉴定的分子指纹技术对于指导水稻育种和规范种子市场都具有重要意义。农业部颁布的水稻品种鉴定技术规程行业新标准是基于35个不同遗传特点的代表性水稻品种建立的SSR分子标记技术规程。本研究根据该标准方法,对94份杂交水稻亲本材料的遗传多态性和特异性进行了比较分析,结果表明,供试品种间至少具有3对以上引物扩增的DNA片段差异,即利用该标准能很好地区分供试杂交水稻亲本的遗传差异。对新标准中48对推荐引物的比较与分析表明,46对引物扩增的DNA片段多态性较高,而RM176和RM551两对引物扩增带多态性较低,因此在其染色体的其他位点可进一步研究多态性更高的分子标记。与标准中35个水稻品种的指纹库进行比较,发现了16个新的等位变异,这些位点可作为标准指纹库的信息补充,丰富标准库中的遗传信息。对94个杂交水稻亲本的分子指纹比较分析,发现23个亲本材料具有特异性分子标记,这些特异分子标记可应用于杂交组合的真实性以及杂交种子纯度的分子鉴定。根据供试亲本的数字分子指纹,构建了87个不育系与7个父本杂交的虚拟组合数字分子指纹库以及虚拟组合的真实性和纯度快速鉴定的特异数字分子标记。     

两系杂交稻亲本SSR指纹图谱的建立及其在种子纯度鉴定中的应用

利用筛选到的20对SSR引物建立了两系杂交稻32个亲本(24个光温敏不育系和8个恢复系)的DNA指纹图谱,针对所涉及的9个杂交稻组合,获得能在父、母本间表现出多态性的特异SSR标记48个.以杂交稻组合两优932为例,在实验室用一个特异SSR标记(RM302)对200粒种子样本进行了纯度鉴定,结果鉴定纯度为90.50%,与田间种植鉴定结果90.60%(海南鉴定)和91.57%(武汉鉴定)基本一致,表明SSR标记技术适用于构建DNA指纹图谱和种子纯度鉴定.     

利用SSR标记构建湖南省审杂交水稻品种DNA指纹图谱

筛选出48对SSR引物对湖南省审定的77个杂交水稻品种进行了DNA分子指纹图谱构建和品种鉴定,成功建立了品种指纹图谱数据库,可有效进行杂交水稻品种鉴定.     

Development of a Potato Cultivar (<Emphasis Type="Italic">Solanum tuberosum</Emphasis> L.) Core Collection,a Valuable Tool to Prospect Genetic Variation for Novel Traits

This study presents the development of a core collection capturing the genetic diversity of a collection of 350 tetraploid cultivated potato varieties (Solanum tuberosum L.). The core collection was established by using simple sequence repeats (SSR) data and the M strategy, which aims at maximizing the allelic diversity. A 48-core collection was defined which captured 99.5% of the SSR alleles used to establish it, and 96.9% of the SSR alleles which belonged to an independent set of markers. The defined core collection was further validated by analysing 35 agro-morphological traits. The class coverage value and the estimates of the Shannon-Weaver diversity index indicated a good representation of the phenotypic diversity in the core collection. Furthermore, the core set included accessions having the most desirable status for several agronomic traits. A linkage disequilibrium (LD) analysis, using data obtained with the SolCAP SNP array on the defined core collection, was performed. The population structure analysis showed that the core collection did not present a clear genetic structure. The linkage disequilibrium analysis carried out between markers located on the same pseudomolecule within 10,000 bp concluded that 41.3% of these pairs of SNP markers have a significant LD. We conclude that this core collection, representative of the genetic diversity of cultivated potato varieties, is a relevant tool for a first screening for genetic variation regarding novel traits of interest.     

SSR荧光标记毛细管电泳法与国家冬油菜区试指纹鉴定平台的构建

为了提高油菜品种指纹检测的精确性及未来构建大规模油菜新品种指纹数据库的需求,应用SSR荧光标记毛细管电泳检测法构建国家冬油菜区试指纹鉴定平台。以40对荧光引物对2012-2013年度163份国家冬油菜区试参试品种（系）进行分析。结果共检测到42个等位位点和131个等位变异。其中A基因组（n1～n10）检测位点25个,C基因组(n11～n19)检测位点17个。每个位点等位变异数从2到6不等,平均为3.02。42个检测位点的PIC值变化范围在0.10～0.69之间,平均值为0.36。其中引物BRGMS171的杂合度、PIC值分别高达0.67、0.70,可考虑作为以后区试杂交种纯度鉴定的核心标记。SSR位点的纯合度分析得出本年度18份常规种平均纯合度为81.9%,145份杂交种为57.9%。以131个等位变异计算品种（系）间DICE相似系数,163份品种（系）间平均遗传相似系数变幅为0.607～0.765,变幅最大的为品种（系）FC03（0.438～0.879）,变幅最小为品种（系）宜油21（0.611～0.806）。     

60Co-γ和EMS诱变“天隆一号”突变体库变异特征的初步分析

为培育新的适应长江流域气候类型的大豆品种,利用60Co-γ射线和EMS分别对大豆天隆一号的种子进行诱变处理,构建大豆突变体库。对350份有表型变异的株系进行连续两年田间鉴定,运用60对SSR标记进行分子检测,并对籽粒表型变化明显的突变株进行苯基丙酸类代谢主要酶qPCR分析。结果表明:350份材料中有145份在株高、叶形、花色、种皮色、结荚习性等方面有稳定可见的表型变异,101份材料中检测到与野生型天隆一号存在至少1个SSR位点差异,其中M3-SD-1与M3-SD-2有超过10个标记的差异。SSR分析表明,表型发生变异的突变体主要是由DNA变化引起的,且突变体发生了多位点变异,突变位点也彼此不同。qPCR检测结果显示,种皮色、脐色等发生突变的3个材料苯基丙酸类代谢途径中关键基因的表达量发生显著变化。研究结果既可以为大豆品种改良提供新的种质资源,也有助于大豆功能基因组的研究。     

我国主要杂交水稻组合及其亲本SSR标记和纯度鉴定

选用分布于水稻12条染色体上的26对SSR引物对我国9个主要的杂交水稻组合及其亲本进行了SSR标记分析,21对多态性引物共扩增出62条条带,平均2.95条,能够有效地区分所有恢复系和大部分不育系。杂交种条带均为父母本的互补型,很适合做杂交种纯度鉴定。用引物RM17对杂交稻组合汕优63和两优培九进行了100粒单种子SSR鉴定,所测纯度分别为96.0%和98.0%,与田间纯度96.2%和97.7%非常接近,显示出SSR技术在品种认证和纯度鉴定中有广阔的前景。     

应用形态、等位酶和SSR标记研究水稻矮仔占衍生品种的遗传差异

选取我国水稻矮仔占衍生品种24份,应用形态学、等位酶和微卫星(SSR)标记,分析矮仔占衍生品种的遗传差异。聚类分析表明3种方法在鉴别品种的遗传差异上存在较大差异。形态性状和SSR标记均能有效地鉴别24份衍生品种,而等位酶仅能鉴别其中17份。从形态学性状看,以香药糯与其他品种的遗传差异最大,SSR分析以香药糯、珍珠矮11和辐陆选与其他品种的遗传差异较大,而等位酶分析,则以团结1号与其他品种的差异最大。三类标记的遗传距离间虽存在有一定的相关性,但相关系数较小（0.217~0.494）,其中,形态学性状与SSR标记间相关极显著（r= 0.494,P= 0.002）,等位酶与其他两类标记的相关性均不显著。研究结果还表明,系统选育和辐射选育的品种与亲本间有可能存在较大的遗传差异。     

An applied fingerprinting system for cultivated potato using simple sequence repeats

The ability to quickly and accurately identify potato (Solanum tuberosum L.) clones is important to potato-breeding programs, seed and commercial potato growers, and marketing and utilization of potato cultivars. Since 1990, the Michigan State University Potato Breeding and Genetics Program has used an isozyme-based fingerprinting system to identify potato cultivars. Isozyme analysis is an economical and effective means of discriminating potato clones; however, isozyme analysis requires fresh, healthy tuber or leaf tissue. DNA-based fingerprinting using simple sequence repeats (SSRs or microsatellites) has been shown to discriminate between potato clones. The objective of this study was to identify the most useful SSR primer pairs that accurately and efficiently distinguish clones for an applied fingerprinting system of cultivated potato. SSR primer pairs with high polymorphism were selected from previous tetraploid potato studies. DNA isolated from 17 potato clones representing round-white, russet, and red market classes were visualized on both polyacrylamide (PAGE) and agarose gel systems. Polymorphism was observed in all 18 primer combinations on PAGE and 14 using agarose gel electrophoresis. All 17 cultivars were discriminated on PAGE with various combinations of two primer pairs: STIIKA using STACCAS3, STIN-HWI, or STM0031; and STACCAS3 using STGBSS1, POTM1-2, STM1104, or STM0031. The combination of STM0019, STM0031, STGBSS1, and POTM1-2 was able to differentiate all 17 clones using agarose gel electrophoresis. PAGE was determined to be the preferred system for variety identification, but agarose gel electrophoresis can be used to differentiate lines when specific varietal comparisons are needed. In addition, five different DNA source tissue types were evaluated (fresh foliar, freeze-dried foliar, fresh tuber, freeze-dried tuber epidermis, and freeze-dried tuber tissue). Amplification products were similar for all five tissue sources used for DNA isolation. This ability to isolate DNA from freeze-dried tissue will allow cultivar identification when fresh tissue is not available. The SSR primer pairs presented here can be used as a practical fingerprinting system for cultivated potato identification.