The Plabsoft database: a comprehensive database management system for integrating phenotypic and genomic data in academic and commercial plant breeding programs

Besides phenotypic data from field trials and molecular data from lab experiments, modern plant breeding programs generate a wide variety of data, for instance pedigree, randomization, geostatistical or climate data. Due to the lack of an integrated database system, breeders generally exploit only part of these data for selection decisions or retrieve only part of the information present in the data. Most approaches in genomics, however, develop their full power only when they are based on analyses of large numbers of genotypes from multiple crosses and current as well as past generations. We have developed a flexible data management and -analyses system for storage and quality control of plant breeding data. It is implemented using the PostgreSQL database management system and linked to the R software environment for integrated statistical analyses of phenotypic and genomic data. The database structure is capable of managing the following types of data observed in breeding programs of all major crops: (a) germplasm data of any species including pedigree data, (b) phenotypic data of any trait and trait complexity, (c) trial management data for any field and trial design, (d) molecular marker data for all common types of markers, as well as (e) project and study management data.     

植物矮生性状的分子遗传研究进展

近年来,随着分子生物学和基因组学的飞速发展,对作物高产性状,高产机理及其相关基因的研究愈加深入,应用基因工程技术对作物进行遗传改良已成为提高作物产量的有效途径,培育理想株型已成为作物育种的重要目标。株高是高等作物的重要农艺性状之一,植株过高容易引起倒伏而减产,而矮生植株抗倒能力强,高产,因而矮化育种对培育理想株型十分重要,矮生基因的发掘研究和利用也越来越受到重视。本文综述了目前高等作物矮生性的分子遗传研究进展,特别是对水稻、小麦、玉米、黄瓜、西瓜和番茄等主要作物矮生性状的遗传特点、分子标记、矮生基因的克隆等方面的研究进展做了较为详细的总结和评价,分析了激素对高等植物矮生突变体的调控,提出了高等植物矮生资源的利用和矮化育种中存在的问题,并探讨了高等植物矮生性状分子遗传学研究和分子育种的发展趋势。     

Population genetic responses of wild forage species to grazing along a rainfall gradient in the Sahel: A study combining phenotypic and molecular analyses

Genetic diversity was studied in wild forage species subjected to grazing along a rainfall gradient in West Niger, within the Sahel with aim of identifying adapted genotypes, which could be used to reclaim degraded land. Two legumes (Alysicarpus ovalifolius and Zornia glochidiata) and two grasses (Brachiaria xantholeuca and Cenchrus biflorus) were selected to relate phenotypic adaptation to genetic diversity in response to grazing and rainfall. Populations of each species were sampled from both heavily grazed and ungrazed sites along a rainfall gradient, approximating 200 mm yr⁻¹ to 800 mm yr⁻¹ rainfall isohyets. The adaptative phenotypic expressions to aridity and grazing of the populations from each of the species were characterised by morphological measures performed on the plants sampled in the field. These analyses were then compared with the results from genetic analyses using the PCR-based techniques of amplified fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD). Analyses of molecular data using cluster analysis (UPGMA), principal co-ordinates analysis (PCO), Mantel tests and an Analysis of Molecular Variance (AMOVA), revealed genotypic distinction between populations subjected to both differing aridity and grazing. The majority of the total genotypic variation sampled in all species occurred among individuals within a population. The significant morphological differentiation found among populations subjected to varying grazing and aridity stresses, determined through linear regression analyses, did not correlate significantly with the genotypic differentiation, as revealed by Mantel tests. The results suggest that grazing does not cause a loss of genetic diversity in the wild forage species studied, although with increasing aridity the impact of grazing on the genetic diversity of populations may increase.R. Jamnadass and A. Muchugi Equal contribution to this work by both authors.     

Conditions under which selection for mean productivity, tolerance to environmental stress, or stability should be used to improve yield across a range of contrasting environments

Computer simulations were conducted to determine whether conclusions obtained for the special case of a single stress and a single non-stress environment apply to the more general situation where a population of testing environments includes a range of stress and non-stress environments. Mean productivity, tolerance to environmental stress, and a regression coefficient stability parameter of genotypes across environments were compared to determine conditions under which these selection criteria should be used to improve yield across a range of contrasting environments. The results obtained from a worked example based on the single crosses from a 7 × 7 diallel cross in maize and the simulation experiment showed that the conclusions of Rosielle & Hamblin (1981) cannot be directly applied to a population of stress and non-stress environments. Selection for mean productivity should increase yield in both stress and non-stress environments unless the genetic variance in stress environments is more than double that in non-stress environments, and the genetic correlation between yields in contrasting environments is highly negative. Mean productivity and tolerance were shown to be positively correlated even if the genetic variance in stress environments is half that in non-stress environments. Genotypes with a high tolerance to stress were found to have low regression coefficient stability parameters, even when a range of stress and non-stress environments was used. This revised version was published online in July 2006 with corrections to the Cover Date.     

中国作物分子设计育种

分子设计育种通过多种技术的集成与整合,对育种程序中的诸多因素进行模拟、筛选和优化,提出最佳的符合育种目标的基因型以及实现目标基因型的亲本选配和后代选择策略,以提高作物育种中的预见性和育种效率,实现从传统的“经验育种”到定向、高效的“精确育种”的转化。分子设计育种主要包含以下3个步骤：(1)研究目标性状基因以及基因间的相互关系,即找基因(或生产品种的原材料),这一步骤包括构建遗传群体、筛选多态性标记、构建遗传连锁图谱、数量性状表型鉴定和遗传分析等内容;(2)根据不同生态环境条件下的育种目标设计目标基因型,即找目标(或设计品种原型),这一步骤利用已经鉴定出的各种重要育种性状的基因信息,包括基因在染色体上的位置、遗传效应、基因到性状的生化网络和表达途径、基因之间的互作、基因与遗传背景和环境之间的互作等,模拟预测各种可能基因型的表现型,从中选择符合特定育种目标的基因型;(3)选育目标基因型的途径分析,即找途径(或制定生产品种的育种方案)。本文评述近几年来我国在遗传研究材料创新、重要性状遗传分析、育种模拟工具开发和应用、设计育种实践、分子设计育种技术体系建设等方面取得的重要进展,结合国内外研究现状对分子设计育种的未来进行展望,最后指出我国近期应加强育种预测方法和工具、基因和环境互作、遗传交配设计、作物功能基因组学、生物信息学方法和工具、设计育种技术体系和决策支持平台等领域的研究,同时重视人才培养和团队建设。     

水稻株型与冠层三维结构计算机模拟初报

利用OpenGL函数库在VC++6.0环境下,采用三角形逼近法,编程实现了对沈农265和秋光两个水稻品种的单株及群体冠层三维结构的可视化模拟。模拟结果较好的反映了植株和群体基本特征,为今后进一步研究水稻群体内光分布奠定了基础。     

河北省穗期麦蚜预测及种群动态模拟

采用聚类代表无法筛选自变量,根据逐步判别分析和逐步回归原理.通过计算机模拟技术,对河北省麦蚜主发生区田间系统调查资料进行了统计分析,组建了麦蚜发生程度4级判别式.应用该式可提前2个月预测穗期蚜量.经对保定、正定的历史数据回判.准确率达100%.对麦蚜种群数量增长研究结果表明,5月份百茎蚜量随时间变化呈“S”型.可用Lgistic曲线方程表述.本研究结果为麦蚜综合防治提供了决策依据.     

旱地棉花产量构成因素的通径分析

研讨了旱地棉花产量与其构成因素间的相互关系及各产量因子对皮棉产量相对重要性和决定作用。结果表明,旱地棉田在干旱和雨涝两种不同条件下,其参数显然不同。一般在干旱条件下,皮棉产量与亩铃数关系密切,在主要产量因素中,亩铃数对皮棉产量的相对重要性最大,决定程序也最高;而在雨涝条件下,皮棉产量与衣分相关关系密切,在主要产量因素中,衣分对皮棉产量的贡献最大,决定程序也最高。通过研究,提出了适应不同条件的棉花育     

农业信息技术在小麦育种中的应用研究

小麦作为我国三大粮食作物之一,其市场需求量不断增加。随着气候等因素变化,小麦产量及品质将受到严峻考验,因此需要更为优良的新品种出现。现阶段我国小麦育种仍主要以传统育种技术为主,而凭借育种家经验,从海量育种群体中筛选获得高产、多抗、优质新品种的难度越来越大。因此,有效提升育种效率变得极为迫切。随着农业信息技术在育种中应用的迅猛发展,无损预测预报与进程信息化管理等高效育种成为可能。本文从育种进程管理、数据采集、综合评判决策、种质资源信息化管理方面介绍国内外信息技术在小麦育种中的研究进展,分析信息化育种的需求和存在的主要问题,并对其应用前景进行展望。     

楸树EST-SSR标记开发及种质资源的遗传多样性分析

利用转录组数据开发SSR标记是一种经济高效的DNA分子标记开发策略。本研究利用高通量测序技术开发楸树(Catalpa bungei)EST-SSR标记,了解其在转录组序列中的分布类型,并利用41对多态性较好的引物对来自安徽(AH)、河南(HN)、湖北(HB)和山东(SD)的4个楸树居群的48个无性系的遗传多样性进行分析。结果表明:在大于1kb的14634条序列中,共鉴定出3999个SSR位点,580条序列包含2个及以上位点;单核苷酸重复(1957,48.94%)是最常见的SSR类型,其次是二核苷酸重复(1164,29.11%),三核苷酸重复(834,20.86%),四核苷酸重复(41,1.03%)和五核苷酸重复(3,0.08%);共扩增出243个等位基因,每个位点的等位基因数为3~13个,平均为4.85个,观测杂合度为0.14?1.00,平均为0.63,期望杂合度为0.42?0.84,平均为0.67,大部分位点偏离哈迪-温伯格平衡;AH和HN居群在有效等位基因数和期望杂合度的数值较高,表明其遗传多样性较丰富;分子方差分析(AMOVA)表明,遗传变异主要发生在居群内。本研究为楸树及同属其他树种种质资源鉴定、遗传多样性提供依据,且在指导楸树良种选育等方面具有重要的意义。     

一种新的符合度算法及其应用

在总结分析了几种常用综合评价方法的基础上, 提出了一种反映观察值与理论值之间相似性的新算法--符合度。该算法就评价信息个体(观察值)与标准值(期望值)的马氏距离, 再由马氏距离转化为评价对象与标准的接近程度, 即符合度(r)。首先进行指标数(p)、相似度(r)与马氏距离(d)的模拟试验, 再通过曲面拟合的方法找出它们之间的关系模型。通过大量抽样试验, 验证符合度的次数分布与原先设定的符合度的良好对应关系, 说明模型的可行性与可靠性。以小麦RVA性状为指标, 利用该算法分析扬麦系统若干品种之间的接近程度, 并评价多变数复杂效应回归分析模拟试验的结果。符合度算法不需要数据标准化处理, 直接利用原始数据, 减少了计算工作量, 降低了因数据标准化处理方法不同而引起的评价结果差异, 同时由于不需要赋权, 排除了主观性的影响, 保证了信息的完整性以及评价结果的可靠性。     

关于糯玉米育种目标和策略的思考

简述了目前中国糯玉米育种的现状,指出存在的问题。结合糯玉米的市场要求,提出糯玉米的育种目标,其顺序为优良品质、高产稳产、抗病抗虫、类型多样。根据玉米育种学和遗传学原理,对糯玉米自交系和杂交种选育的育种策略进行探讨,并提出相应的育种方法。     

植被覆盖度计算机模拟模型与参数敏感性分析

植被覆盖度是重要的生态学参数,对水文、生态、全球变化等研究具有重大意义。目前使用的目测估算法和数码照相法都具有一定的主观性,另外通过自然界中相似样方的大量测量获得稳定的统计规律具有很大的难度,因此建立叶面积指数和植被覆盖度之间的统计模型是估算植被覆盖度的有效方法。本文以大豆为例,利用椭圆来模拟大豆的叶片,选取大豆植株结构的关键参数,通过随机分布函数来模拟植株叶片位置、倾角和大小的分布,获得不同植被结构参数下单位面积上的植被覆盖度,建立植被覆盖度计算机模拟模型。通过实测数据和理论研究结论来验证模拟结果。对模型的参数敏感性进行分析结果表明,叶半短轴是比叶半长轴更为敏感的植被结构参数。该模型为植被覆盖度的研究提供了一种新的思路和方法。     

吉林省花生育种现状及发展方向

为进一步明确吉林省花生育种目标,论述了吉林省花生育种现状、存在的问题及未来发展方向。指出吉林省花生育种近期目标应以高产、早熟、高油和高蛋白为主,中长期目标兼顾抗逆育种、高油酸育种和适宜机械化育种,同时阐明要注重多优良性状的聚合改良。提出将传统育种和现代分子育种技术有机结合,多途径、多手段开展花生新品种选育的育种思路。强调要以市场需求为导向,同时兼顾长期目标与短期效应,满足生产需要。     

优质早籼稻产量性状分析及育种策略探讨

对115份优质早籼稻新品系的产量性状与产量的相关分析和通径分析结果表明：各产量性状均与产量呈正相关,除株高外,其余5个性状与产量的相关均达极显著或显著水平,产量性状之间存在着相互制约和相互依赖的关系;每穴穗数对产量的贡献最大（47.84%）,其次为每穗总粒数（21.86%）,再次为千粒重和结实率（分别为14.47%和9.46%）.根据分析结果,笔者认为优质早籼稻高产育种应主攻分蘖和提高分蘖成穗率,同时注意提高每穗粒数和千粒重.优质早籼稻高产（即产量达500～600kg/667m^2）育种的产量性状模式为单株有效穗8～10穗、每穗总粒数125～150粒、结实率80%以上、千粒重24～27g.     

我国木薯育种研究进展

为了促进中国木薯选育种研究,就中国木薯产业发展需求,育成的主要木薯品种以及国内外木薯育种策略进行了综述,比较了不同育种策略在木薯育种应用上的优缺点,指出了下一阶段中国木薯育种的主要目标,并为中国木薯育种工作的顺利开展提出了几点建议。“十三五”期间,中国木薯产业将围绕“能源化、食用化、特用化、效益化、国际化”的目标进行,全面综合开发利用木薯资源以满足多元化市场的需求。     

Heritability of quantitative traits in segregating common bean families using a Bayesian approach

Genetic parameters for six quantitative traits in the early generation of segregating populations of common beans (Phaseolus vulgaris L.) were evaluated. A Bayesian approach was used for estimating the variance components, breeding values and broad sense heritability of the quantitative traits under analysis. The Markov Chain Monte Carlo method was utilized to analyze the contribution of genes affecting complex traits. Twenty-four F₃ families were evaluated in the field during 2005 in Santa Catarina, southern Brazil. With regard to the grain yield and yield components, the additive variances were relatively similar to the dominance variances. This result is confirmed by the 95% credible set from the posterior distribution. The mean estimates of broad-sense heritability (H²) varied from 11.5% to 64.2%. The heritability estimates of yield and yield components were higher than the estimates for the number of days until flowering and reproductive period. However, for grain yield, the 95% heritability credible set included the heritability estimates from point of crop duration. The predicted genetic gain reached the highest value for the number of pods per plant (10.95%). Days to flowering and reproductive period had the lowest values of genetic advance. One hundred seed-weight, grain yield and seeds per pod exhibited a similar predictable level of genetic gain: GA = 5.73%, 5.81% and 4.77%, respectively. The Bayesian framework provided information that is useful for a breeding program, since it contributes to the understanding of how quantitative traits are genetically controlled.     

水稻光温敏雄性核不育系的系谱分析

近年来, 我国两系杂交水稻快速发展, 截止2010年底, 共有427个两系组合通过审定。两系杂交水稻已经奠定了在我国水稻生产中的重要地位, 而光温敏核不育系是两系杂交水稻的基础。本文从实用性角度研究了1994年以来通过审定和获得新品种保护权的两系组合所涉及的130个光温敏核不育系, 分析了光温敏核不育系的基本来源和其中126个不育系的系谱。以原始光温敏核不育系为起点演绎了不育系之间的衍生关系, 介绍了大面积应用及获得新品种保护权的73个不育系的系谱, 归纳了新光温敏核不育系的育成途径。讨论了不育系育性转换的光温反应类型与其核不育基因来源的关系。提出利用光温敏核不育系开展分子生物学研究过程中, 有必要通过系谱分析不育系之间的衍生关系, 对不育系材料进行有针对性的选择。强调了促进光温敏核不育资源的开放与共享, 对加快实用性光温敏核不育系的选育, 积极应对两系杂交稻制种环境的变化具有重要的意义。     

烟粉虱种群数量消长规律与模型测报技术研究

为了揭示烟粉虱种群数量季节性消长规律,提高其预测预报水平,2006年2月至2007年2月利用塑料黄板涂抹机油在浙江临海城郊蔬菜基地系统诱测烟粉虱成虫消长情况,结果表明烟粉虱种群数量消长呈双峰型曲线变化,并分析了烟粉虱种群消长特性,以及与气象、耕作条件的相关性,建立了8种数学预测模型。应用这些模型可提前反映全年36个旬期的成虫数量变化动态,可进行全年灾变预警以及各旬期的预测预报,经检验预测吻合度达60%。对提高烟粉虱监测预警与综合防治水平具有重要指导意义     

大麦农艺性状与SSR标记的关联分析

为了解大麦亲本材料遗传特性和主要农艺性状特征,采用156份不同来源的大麦材料,在86个多态性SSR位点上检测遗传多样性,同时对7个农艺性状在两试验点作表型鉴定,利用GLM和MLM模型进行分子标记与表型性状的关联分析。结果共检测出392个等位变异,平均每个标记4.6个,PIC值变异范围为0.0612~0.8560。群体遗传结构分析将156份材料分为2个亚群。利用GLM模型分析结果表明,与株高、穗长、芒长、穗粒数和千粒重5个性状相关联的标记有18个,单个标记对表型变异的解释率为4.81%~20.75%;利用MLM模型分析,与株高、穗长、芒长、分蘖数、穗粒数和千粒重6个性状相关联的标记有14个,单个标记对表型变异的解释率范围为6.64%~31.55%。这些关联标记对后续研究有参考价值。