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.     

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.     

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.     

牡丹江丘陵区大豆食心虫种群动态及其与气象因子的关系

为了明确牡丹江地区大豆食心虫的种群动态及其与气象因子的关系,试验于2010—2012年利用性诱剂诱捕法在田间进行了系统的调查。结果表明：牡丹江地区大豆食心虫的始见期在7月末,高峰期在8月初至8月中旬,结束于8月末,发生期历时1个月左右;在降水量偏少的年份大豆食心虫的种群动态与日平均温度呈显著正相关,适量的降水会造成空气湿度大,这有利于蛾量的增加,而强降水的出现不利于食心虫的化蛹和成虫出土;在牡丹江地区日平均气温在21~24℃为大豆食心虫的发生适温,而持续的高温、干旱天气不利于成虫的发生。说明温度与降水量均为影响大豆食心虫发生的重要因子。     

榆林市人口系统分析及预测

通过对榆林市人口总量变动,人口分布的分析。并对未来人口发展趋势进行预测,人口总数由 1950年总人口123．51万人到2015年的391．76万人。65年间净增人口268．25万人,增加了 217．19％,平均每年增加人口4．13万人。可见,榆林市的人口发展还是很快,还必须加强计划生育,降 低出生率,控制外来人口。     

Quantitative genetic analysis of erect glandular trichome density in diploid alfalfa

The presence of glandular trichomes may protect alfalfa (Medicago sativa L.) against certain stem-, leaf-, and fruit-eating insect pests. In order to determine appropriate breeding methods to select for this trait, this study characterized quantitative genetic parameters of erect glandular trichome density in `KS94GH6' diploid (2n=2x=16) alfalfa. Eight female and five male plants were crossed in a Design II mating to produce 40 full-sib families. Glandular trichome density was determined on these families under replicated greenhouse conditions in Las Cruces and Los Lunas, New Mexico, U.S.A. The effect of males was significant (p 0.10) across the two environments. Variation among females was not significant within either location or across locations. The dominance genetic variance (<sup>2</sup> <sub>D</sub> = 0.210) was greater than the additive genetic variance (<sup>2</sup> <sub>A</sub> = 0.111). The average degree of dominance exceeded a value of `1' indicating that erect glandular trichome density in KS94GH6 may be influenced by digenic epistasis, and/or repulsion phase linkage disequilibrium. The large contribution of non-additiveeffects was reflected by a low narrow-sense heritability estimate (h ² _n = 0.25). The results indicate that further improvements in erect glandular trichome density in KS94GH6 alfalfa will require replicated progeny testing. Approaches to introgress this trait into cultivated tetraploid alfalfa are discussed.     

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     

带裂缝混凝土氯离子扩散作用试验研究及数值模拟

为了准确评估带裂缝工作混凝土结构的耐久性能,针对氯离子在带裂缝混凝土中的扩散过程进行研究。提出了无损制备裂缝的方法,可高效易行地在混凝土侧面及内部产生裂缝。对带裂缝的水泥砂浆试件进行氯盐溶液浸泡试验,深入研究了单缝和双缝试件中氯离子的扩散作用,修正了氯离子的扩散系数,并对带裂缝混凝土的氯离子扩散过程进行了数值模拟。研究结果表明：氯离子会沿裂缝发展方向及垂直于裂缝发展方向扩散,随着水灰比的减小,砂浆试件的抗氯离子扩散性能明显提高,在一定范围内,当裂缝间距增大,双缝间的氯离子扩散交互影响作用明显减小,ANSYS软件的模拟结果与试验数据吻合良好。     

海岛棉不同果枝品种间杂交纤维品质性状的遗传及F1和F2群体优势分析

以MINQUE（1）统计方法，利用AD模型对9个海岛棉品种（系）及其20个F1组合5个纤维品质性状的3年资料进行遗传分析。结果表明，海岛棉F1代纤维品质性状多以加性效应为主；2.5%跨长、整齐度和比强度还存在极显著的显性效应；5个品质性状的显性效应与环境的互作以及比强度、伸长率和麦克隆值的加性效应与环境的互作均达显著或极     

东北地区小麦赤霉病镰孢菌种群及其致病性测定

为了明确东北地区小麦赤霉病镰孢菌的种群组成及分布,分别从辽宁省沈阳市、黑龙江省哈尔滨市和密山市、内蒙古自治区扎兰屯市、呼伦贝尔市和通辽市等地区采集小麦赤霉病病样,经单孢分离纯化共得到118株镰孢菌,传统形态学鉴定的基础上,采用基因组DNA的EF-1α序列分析技术进行了镰孢菌种类的辅助鉴定,确定属于7个种:禾谷镰孢菌为优势种,分离频率为64.41%,藤仓镰孢菌为次优势种,分离频率为18.64%;燕麦镰孢菌、尖孢镰孢菌、木贼镰孢菌、锐顶镰孢菌和轮枝镰孢菌的分离频率分别为5.08%,3.39%,3.39%,3.39%,1.70%。同时,在玉米成株期进行了致病性测定,结果表明,小麦赤霉病镰孢菌可以侵染玉米,较玉米茎腐镰孢菌的致病力低。     

Quantitative genetic analysis of flowering time in the Davis Population of gerbera

Summary Phenotypic and genetic correlations of flowering time (FT) with cut-flower yield (Y) were estimated from six generations of the Davis Population of gerbera (Gerbera hybrida, Compositae). The phenotypic correlation was –0.34; the genetic correlation was –0.47 when estimated from ANOVA of a NCII design and –0.72 when estimated from parent-offspring analysis. An indirect selection model was constructed to assess the efficiency of indirect selection for Y using FT as a marker. This model includes population size and generation time as variables because they differ for FT and Y. The results indicate that indirect selection will be more efficient than direct selection.Correlations of FT with flower quality traits, including scape length (SL), flower diameter (FD), scape dry weight (SDW) and flower dry weight (FDW), were also estimated. FT was phenotypically independent of these traits. However, statistically significant estimates of genetic correlation indicate that FT may be correlated with flower quality traits. Thus, indirect selection on FT to increase Y may result in undesirable correlated responses for flower quality.     

Application of DNA fingerprints for identification and genetic analysis of Carica papaya and other Carica species

Summary Various DNA fingerprint probes were applied to Carica papaya and other Carica species for both identification and genetic analysis.Each of the Carica papaya cultivars is characterized by a specific DNA fingerprints pattern. Various Carica species also have specific patterns which distinguish them from one another. Band sharing levels were used to estimate the relatedness between the various Carica species.Genetic analysis of 11 progeny from a cross between the Carica papaya cultivars 17/82 and 112 suggests that application of DNA fingerprinting to Carica papaya breeding, could make the process more efficient. Genetic analysis of the DNA fingerprint bands revealed no linkage or allelic relationship among the bands analyzed, indicating that these loci are not clustered in the Carica genome.     

黑线姬鼠种群数量动态及预测预报模型研究

对1987—2005年贵州省余庆县黑线姬鼠种群数量动态及种群数量进行分析预测,结果表明：黑线姬鼠年均捕获率为6.90%±2.57%,一年内在5—6月和10—11月出现2次数量高峰期,最高峰在6月,不同年度、不同月份、不同季节之间种群数量存在显著差异。制定了黑线姬鼠种群数量分级标准。建立了应用早春3 月种群数量基数(X1)、4月种群数量×4月繁殖指数(X2)预测数量高峰期6月种群密度(Y)的2个短期预测预报模型：Y=1.3669X1+5.6175;Y=0.4988X2+7.2940,可提前3个月和2个月预测当年数量峰种群密度和发生程度,经回测验证,数值和数量级预测值与实测值基本相符,数值预测平均吻合率为86.61%和86.11%,数量级预测吻合率均为78.95%,结果比较准确,故该预测预报模型具有一定的实用性和可行性。     

Improvement of spatially and temporally continuous crop leaf area index by integration of CERES-Maize model and MODIS data

The spatially and temporally continuous leaf area index (LAI) mapping is very crucial for many agricultural applications, such as crop yield estimation and growth status monitoring. Data assimilation technology provides an innovational way to improve spatio-temporally continuous crop LAI estimation through integration of remotely sensed observations and crop growth models. In this study, a very fast simulated annealing (VFSA)-based variational assimilation scheme was proposed to integrate the crop growth model (CERES-Maize), MODIS reflectance product (MOD09A1) and a two-layer canopy reflectance model (ACRM) to estimate time-series crop LAI at regional scale. Simultaneously, a new sensitivity analysis method (called “histogram comparison”) was developed to identify sensitive parameters of CERES-Maize and ACRM models. The proposed scheme was applied for continuous crop LAI estimation during the maize growing season in the dominating spring maize planting area of Jilin province, China. Results showed that R² values between LAI estimations from the proposed assimilation scheme (referred to as assimilated LAI) and fine resolution LAI reference maps were 0.24 and 0.63, with RMSE values of 0.21 and 0.54 for Julian day 176, 2010, and Julian day 196, 2010, respectively. The assimilated results were closer to LAI reference maps than the MODIS LAI product and ACRM-based inversion results (referred to as ACRM LAI). Moreover, by introducing the prior information of LAI dynamics depicted by a crop growth model, the assimilated LAI showed better temporal consistency than the MODIS LAI product, LAI profiles simulated by CERES-Maize model (referred to as CERES-Maize LAI), and ACRM LAI. It was found that the accuracies of LAI estimations could be enhanced by assimilating satellite observations into a crop simulation model in the VFSA framework at a regional scale.     

扬糯麦1号8000 kg hm~(–2)以上高产群体质量指标

糯小麦因其独特的品质特性而在食品加工等领域有广泛的用途,但其高产栽培配套技术却鲜有研究,制约了该特种小麦的生产。2010年11月至2013年6月连续3个生长季,以扬糯麦1号为材料,通过密度和氮肥施用量及不同生育期施氮比例处理,构建不同产量水平群体,研究不同群体的产量结构及群体质量特征,以明确高产群体的产量结构及群体质量指标。结果表明,扬糯麦1号≥8000 kg hm–2高产群体的产量构成三要素特点是每公顷520~550万穗、每穗43~46粒、千粒重32~37 g。高产群体拔节期最适茎蘖数为穗数的2.3~2.5倍,茎蘖成穗率为44%~49%,分蘖成穗率为25%~33%,孕穗期和乳熟期的最适叶面积指数(LAI)分别为6.2~6.5和3.2~4.0,开花期干物质积累量为10 000~11 600kg hm–2,花后干物质积累量达5900 kg hm–2以上,适宜粒叶比达0.36粒cm–2叶和12.40 mg cm–2叶以上。高产群体各生育时期LAI值、花后干物质积累量和粒叶比均高于中高产群体(7500~8000 kg hm–2)及中产群体(7500 kg hm–2)。3年中扬糯麦1号均达到高产指标的小区具有以下特征:基本苗为225×104 hm–2,总施氮量为240 kg hm–2,氮肥运筹(基肥∶壮蘖肥∶拔节肥∶孕穗肥)比例为5∶1∶2∶2。     

矮败小麦群体改良的方法与技术

矮败小麦是具有矮秆基因标记的太谷核不育小麦. 根据轮回选择的基本原理和方法, 结合矮败小麦的特点, 我们逐步建立起一套简单易行的群体改良方法. 其主体技术包括组建一个好的基础群体, 利用控制授粉向群体引进优良基因, 通过开花前不良可育株的淘汰提高优良基因的频率, 借助于可育株与不育株的异交使基因重组, 以及正确地选     

氮、钾施用量对中粳稻群体质量和产量的影响

以中粳品种“皖稻68”为材料,研究N、K施用量对单季中稻群体质量和产量的影响。结果表明,在施N量为262.5kg/hm2和施kcl为375.0kg/hm2时产量最高,达11211.1kg/hm2。水稻的总茎蘖数、叶面积指数、干物质积累量、有效穗数和每穗粒数随着施氮量的增加而增高,而分蘖成穗率、有效和高效叶面积率、抽穗后干物质生产积累量和总颖花量以施N量为262.5kg/hm2为最高,进一步增施氮肥则下降,不利于群体质量的提高。钾肥对水稻的有效穗和穗粒数影响不大,但能提高结实率和千粒重,随着施钾量的增加,穗下节间长度占株高的比例增加,有利于提高植株抗倒性,而抽穗后干物质生产积累量也随着施钾量的增加而增加,水稻的群体质量得到优化,产量有增高的趋势,但是不显著。     

稻麦两熟地区不同栽培方式超级稻分蘖特性及其与群体生产力的关系

为探明不同栽培方式水稻在长江下游稻-麦两熟制条件下的分蘖特性及其与群体生产力的关系,以超级稻淮稻9号和徐稻3号为材料,比较研究旱育中苗壮秧精量手栽、小苗机插、直播3种栽培方式水稻分蘖发生与成穗特点及其生产力和对产量的贡献。结果表明,不同栽培方式水稻产量差异极显著,手栽稻最高,直播稻最低。机插稻和直播稻主茎和一次分蘖群对产量贡献大,尤其是直播稻,主茎产量比例达27.5%,二次分蘖群仅5%左右,而手栽稻主茎产量比例小(16.7%),二次分蘖群产量占近20%。一次分蘖群产量比例不同栽培方式间变化幅度较小,都在65.84%~67.09%之间。手栽稻分蘖发生叶位数多,且茎蘖成穗率高,单株成穗数多;一次分蘖群发生在主茎第1至第10叶位,其中第5至第8叶位分蘖发生率与成穗率较高,二次分蘖群以1/5、1/6、1/7发生和成穗为主。机插稻分蘖发生比较集中,一次分蘖群发生在主茎第3叶至第7叶位,第4至第7叶是分蘖发生与成穗的优势叶位,二次分蘖群发生以1/4、2/4、1/5为主,但主要依靠1/4成穗。直播稻一次分蘖群发生在主茎第1至第5叶位,其中第1至第4叶位分蘖发生率与成穗率较高,二次分蘖发生较多,但仅在1/1、2/1、1/2有成穗,且成穗率很低。3种栽培方式均未见三次及三次以上分蘖发生。各栽培方式主茎及优势叶位分蘖群生产力高、穗部性状好,对产量贡献大,产量的85%以上来自这些茎蘖。说明不同栽培方式水稻分蘖发生与成穗规律是不同的,提高茎蘖成穗率,增加单株成穗数,充分发挥分蘖群的调控作用,对提高产量具有重要意义;同时生产中应根据各种栽培方式的实际,应用各自配套的管理技术措施,通过肥水等的精确合理调控,促进优势叶位分蘖早发、多发,抑制无效叶位分蘖发生,提高群体质量,发掘优势叶位的增产潜力,从而实现不同栽培方式水稻的高产高效生产。     

重组自交系群体的检测调整方法及其在大豆NJRIKY群体的应用

重组自交系（RIL）群体是遗传作图和QTL定位研究中常用的群体,构建过程中可能出现的异常偏分离会影响群体的使用。根据理论群体的分析,提出了用均等性、对称性和代表性3类χ2检验评价试验群体;利用代表性测验的家系最大χ2值和家系异常偏分离率调整异常偏分离的群体;并且应用计算机模拟方法编制了确定群体代表性测验参数     

不同寄主对棉铃虫生长发育及种群动态的影响

在恒温（２７℃±１℃）、恒湿（７０±５）％ＲＨ条件下,研究了棉花、玉米、大豆、花生、芝麻５种寄主对棉铃虫生长、发育和繁殖的影响。结果表明,在不同寄主及其不同部位上取食的棉铃虫,其发育历期、蛹重、存活率、成虫的繁殖力和寿命均有显著差异;棉铃虫在玉米、大豆等作物上的密度较高,且不同作物上的幼虫发育参差不齐。作者认为,田间多种作物并存的局面是造成棉铃虫世代混杂、防治困难及猖獗危害的原因之一。