A database for a more efficient perennial ryegrass breeding programme

Summary The development and use of a computer database specifically designed to be used to store data from a plant breeding programme on perennial ryegrass (Lolium perenne) is described. Setting up a database requires data analysis in order to establish a conceptual dat model and a conceptual processing data. Every model has been written with MERISE method. With the models, a database has been built using ORACLE relational database management system. It is tailored to meet our own requirements which may be common to other database users.     

4M-software package for modelling cropping systems

4M is an easy-to-handle software that has been designed for both educational and scientific purposes. Our main goal in developing 4M was to preserve the features of CERES in a user-friendly software that can be easily extended with additional modules. The package has several characteristics that make it more than a simple crop model. 4M offers optional routines for several processes of the described soil-plant-atmosphere system. The users can build different system models, according to specific purposes. 4M includes input data generators for estimating soil and weather input data that are difficult to measure. 4M is able to simulate crop rotations by using the final conditions of the system after crop harvest as initial conditions for the following crop.     

The choice of locality for plant breeding when selecting for high yield and general adaptation

Summary The choice of localities for initial yield testing of selections in a plant breeding programme is often arbitary. We describe a method that allows a more objective approach based on the correlation between the performance of varieties in a locality and their performance over a large area. The method was checked using data from the Western Australian Department of Agriculture regional wheat variety testing programme, and it was found possible to identify combinations of localities which produced significant predictions over both years and genotypes.     

Characterisation of Cannabis accessions with regard to cannabinoid content in relation to other plant characters

Summary Ninety seven Cannabis accessions were evaluated for cannabinoid content and non-chemical plant characters. Variation within populations for cannabinoid content, and consistency of chemical characters at the population level were investigated. The relationship between chemical and other plant characters was very limited. Leaflet width and phenological data can be used for a rough prediction of the chemical phenotype on a population level. Various combinations of cannabinoid content and other economic plant characters were observed, thus a breeding programme will not be hampered by strict linkage. For a selection programme a direct analysis of cannabinoids will be inevitable.     

Genetic analysis without replications: model evaluation and application in spring wheat

Genetic data collected from various plant breeding and genetic studies may not be replicated in field designs although field variation is always present. In this study, we addressed this problem using spring wheat (Triticum aestivum L.) trial data collected from two locations. There were no intralocation replications and an extended additive-dominance (AD) model was used to account for field variation. We numerically evaluated the data from simulations and estimated the variance components. For demonstration purposes we also analyzed three agronomic traits from the actual spring wheat data set. Results showed that these data could be effectively analyzed using an extended AD model, which was more comparable to a conventional AD model. Actual data analysis revealed that grain yield was significantly influenced by systematic field variation. Additive effects were significant for all traits and dominance effects were significant for plant height and time-to-flowering. Genetic effects were predicted and used to demonstrate that most spring wheat lines developed by the South Dakota State University breeding program (SD lines) exhibited good general combining ability effects for yield improvement. Thus, this study provides a general framework to appropriately analyze data in situations where field crop data are collected from non-replicated designs.     

Participatory plant breeding in maize: A case study from Gujarat, India

This paper describes how plant breeders and farmers worked together to produce improved varieties of maize for the low-resource farmers of the Panchmahals district of Gujarat, India. Initially, farmers tested a range of maize varieties in a participatory varietal selection (PVS) programme. However, none of these proved to be very popular with farmers, although farmers who had more fertile fields adopted the variety Shweta from Uttar Pradesh. Hence, in 1994 a participatory plant breeding (PPB)programme was begun to generate new, more appropriate varieties. Yellow- and white-endospermed maize varieties were crossed that had been either adopted to some extent following PVS or had attributes, such as very early maturity,that farmers had said were desirable. In subsequent generations, the population was improved by mass selection for traits identified by farmers. In some generations,farmers did this in populations which were grown by breeders on land rented from a farmer. Soil fertility management was lower than that normally used on the research-station. The breeding programme produced several varieties that have performed well in research-station and on-farm trials. One of them, GDRM-187, has been officially released as GM-6 for cultivation in hill areas of Gujarat state,India. It yielded 18% more than the local control in research-station trials, while being seven days earlier to silk. In farmers' fields, where average yields were lower, the yield advantage was 28% and farmers perceived GDRM-187 to have better grain quality than local landraces. PPB produced a variety that was earlier to mature than any of those produced by conventional maize breeding, and took fewer years to do so. The returns from PPB,compared to conventional breeding, are higher because it is cheaper and benefits to farmers are realised earlier. This revised version was published online in August 2006 with corrections to the Cover Date.     

Bayesian analysis of complex traits in pedigreed plant populations

A Bayesian approach to analyze complex traits is presented that can help plant eneticists and breeders in exploiting the marker and phenotypic data on pedigreed populations as available from ongoing breeding programs. The statistical model for the quantitative trait may include non-genetic and genetic components. The latter component can be divided into QTL on known marker linkage groups, major genes and a polygenic component. The full probability model, prior assumptions on model variables are presented and criterion for model selection and posterior inferences are given. Simulated data on a known pedigreed population structure of the EU project HiDRAS was used to illustrate the use of the Bayesian approach to analyze complex traits. It was shown that estimates for QTL parameters were more accurate when non-genetic factors were included in the model and when a polygenic component was included when not all linkage groups were analyzed simultaneously. The Bayesian approach has been implemented into the software package FlexQTL and allows plant breeders explore their pedigreed populations for segregating QTL alleles that are relevant in their breeding program.     

Number of crosses and population size for participatory and classical plant breeding

In the breeding of self-pollinating crops, crossing creates variation upon which selection is exerted. If the value of crosses cannot be predicted then this uncertainty means that many crosses need to be made. However, since there is a limit to the capacity of a breeding programme, more numerous crosses result in each cross having a small population size, fewer progenies in later generations and a lower probability of recovering good genotypes from each cross. Published theory on the optimum number of crosses in a plant breeding programme, for a predominantly self-pollinating crop, usually assumes that all crosses are equal value. This overestimates the number of crosses required. When the optimum size of a population in a favourable cross is considered, theory predicts that very large populations are desirable. The required population size is even larger if linkage of loci controlling different traits is also considered. Hence, in an inbreeding crop, one possible strategy is to select a small number of crosses that are considered favourable and produce large populations from them to increase the probability of recovering superior genotypes. In an out breeding crop, the analogy is a few composites with large population sizes. This low-cross-number strategy is ideally suited to the particular constraints and advantages of participatory plant breeding. Such an approach, although not essential, may still be advantageous in classical breeding. When a breeding programme is based on few crosses, which parents are chosen is crucial and farmer participatory methods are highly effective in narrowing the choice. Modified bulk population breeding methods, and recurrent selection are desirable strategies in the participatory plant breeding of self-pollinating crops when combined with a low-cross-number approach. This revised version was published online in August 2006 with corrections to the Cover Date.     

A high-throughput DNA extraction method for barley seed

A non-destructive, quick DNA extraction method for barley seed is described. The method is simple and consists of drilling out a sample from the seed, adding sodium hydroxide, heating in a microwave oven and neutralizing with Tris-HCl. The seed DNA extract can be used directly for PCR with extra cycles added to the PCR programme compared to PCR programmes used for leaf extracts. This protocol was developed in particular for a micro satellite marker genetically linked to barley yellow mosaic virus resistance, but it can be applied toother markers of interest for barley breeding. The quick seed extraction protocol makes it possible to handle thousands of samples per day. Extraction of DNA from seed also facilitates transfer of plant material compared to the long-distance transfer of leaf samples. This revised version was published online in July 2006 with corrections to the Cover Date.     

Evaluation of strategies to optimize training populations for genomic prediction in oat (Avena sativa)

Genomic selection is a promising breeding methodology that could increase selection accuracy and intensity and reduce generation interval. As the cost of genotyping decreases, it will be important to optimize training populations for costly phenotypic experiments for many complex traits. The aim of this research was to evaluate different optimization strategies, by using historical data from the Norwegian oat breeding programme at Graminor. In this paper, we focus on the optimization criteria: genetic diversity, phenotypic variance and genetic similarity between the training and testing populations. The four training population strategies—prediction core, diversity core, phenotypic selection and random selection—were applied to an oat candidate population of 1124 lines. An independent testing population was used to calculate the mean prediction abilities for the traits days to heading and plant height. Moreover, the strategies were tested in three independent wheat populations. The results showed that prediction core was the most promising strategy to select training populations with high genetic similarity to the testing set, high genetic diversity, and high phenotypic variance, which resulted in higher prediction ability across population sizes and traits.     

Optimisation of breeding for agronomic traits in fibre hemp (Cannabis sativa L.) by study of parent-offspring relationships

Summary In the framework of a comprehensive Dutch research project the feasibility of hemp cultivation for paper pulp production is being investigated. This project also includes a hemp breeding programme which was initiated at CPRO-DLO in 1990. Hemp breeding is primarily aimed at improving bast fibre production since bast fibre is qualitatively superior to woody core fibre for paper pulp production. The progress of the ongoing breeding programme is hampered by the lack of knowledge on the inheritance of agronomic traits.The following traits were examined on 252 parental plants in 1991 and subsequently on their progenies in 1992: fibre content, plant height, date of flowering, stem diameter and cannabinoid contents. For each trait heritabilities were estimated and direct and indirect effects of artificial selection were studied.The heritability of bast fibre content was high and mass selection proved to be an efficient method causing no undesirable influence on other characters. Characters not directly related to bast fibre yield such as date of flowering, plant height and stem diameter were shown to have disadvantages as selection criteria for the improvement of bast fibre yield.The cannabinoids THC and CBD were studied, as the acceptance of hemp cultivation requires a low level. The content of THC, the psychoactive component can be successfully reduced by mass selection, but it is not certain that mass selection is the most efficient method.     

Sustainable plant breeding

Plant breeders disrupt Hardy–Weinberg equilibrium through selection, non‐random mating, drift, migration and mutation. Sustainable plant breeding can be defined as productive and competitive breeding that is achieved without loss of genetic diversity in the elite breeding population during the professional career of the breeder. Breeding is often productive but not sustainable. From 1974 to 2000, the animal breeding programme Meatlinc in the United Kingdom had effective population size of 95, population inbreeding of 0.19% per year and generation interval of 2.15 years. Genetic progress in Meatlinc tripled in the 8 years following introduction of best linear unbiased prediction (BLUP) selection (based on the information from relatives) in 1992. Canola breeding in Australia from 1970 to 2000 had longer generation interval (6 years), smaller effective population size (<11) and higher rates of inbreeding (>0.7% per year). BLUP selection in canola was first reported in 2010. Neither programme replaced genetic diversity lost through selection and drift. Most breeding programmes violate conditions of the infinitesimal model, thereby reducing predictability of selection, but breeders can minimize these limitations to sustainable plant breeding.     

BLUP for phenotypic selection in plant breeding and variety testing

Best linear unbiased prediction (BLUP) is a standard method for estimating random effects of a mixed model. This method was originally developed in animal breeding for estimation of breeding values and is now widely used in many areas of research. It does not, however, seem to have gained the same popularity in plant breeding and variety testing as it has in animal breeding. In plants, application of mixed models with random genetic effects has up until recently been mainly restricted to the estimation of genetic and non-genetic components of variance, whereas estimation of genotypic values is mostly based on a model with fixed effects. This paper reviews recent developments in the application of BLUP in plant breeding and variety testing. These include the use of pedigree information to model and exploit genetic correlation among relatives and the use of flexible variance–covariance structures for genotype-by-environment interaction. We demonstrate that BLUP has good predictive accuracy compared to other procedures. While pedigree information is often included via the so-called numerator relationship matrix $({\user2{A}})Best linear unbiased prediction (BLUP) is a standard method for estimating random effects of a mixed model. This method was originally developed in animal breeding for estimation of breeding values and is now widely used in many areas of research. It does not, however, seem to have gained the same popularity in plant breeding and variety testing as it has in animal breeding. In plants, application of mixed models with random genetic effects has up until recently been mainly restricted to the estimation of genetic and non-genetic components of variance, whereas estimation of genotypic values is mostly based on a model with fixed effects. This paper reviews recent developments in the application of BLUP in plant breeding and variety testing. These include the use of pedigree information to model and exploit genetic correlation among relatives and the use of flexible variance–covariance structures for genotype-by-environment interaction. We demonstrate that BLUP has good predictive accuracy compared to other procedures. While pedigree information is often included via the so-called numerator relationship matrix , we stress that it is frequently straightforward to exploit the same information by a simple mixed model without explicit reference to the -matrix. This paper is dedicated to Prof. Dr. Wolfgang K?hler (University of Giessen, Germany) on the occasion of his 65th birthday.     

Variation in photosynthetic activity in cereals and its implications in a plant breeding programme I. Variation in seedling leaves and flag leaves

Summary The extent of variation in photosynthetic activity in the seedling and flag leaves of fourteen oat varieties, and in the seedling leaves of three varieties each of wheat and barley has been investigated. The suitability of NaH¹⁴CO₃ and Warburg manometric techniques for handling the attribute of photosynthetic efficiency in a plant breeding programme is assessed.Results obtained are considered in comparison with estimates of net assimilation rate (E), relative growth rate (R) and leaf area ratio (F) derived from growth analysis data. The relationships with yield and implications for a plant improvement programme are discussed.     

棉花抗黄萎病生理与生化机制研究

本文概述了棉花抗黄萎病的特点与规律,指出棉花植株是通过自身组织结构的强化、植物抗毒素的合成以及微生物之间的互作三方面应对黄萎病菌的侵染。认为棉花植株主要通过促进木质素生成和增加积累量以强化组织结构。在棉花抗病反应中以植物抗毒素的合成为主要途径,包括萜类、酶类和激素类3类化学物质,其中酶类物质如几丁质酶已经在很多植物中被证明具有抗病作用,但是其具体作用途径仍不清楚。土壤中某些微生物也可以对黄萎病菌产生作用。重点讨论了在棉花抗黄萎病信号通路中重要分子磷酸激酶和磷酸酯酶在植株抗性防卫中起着级联调控开关的作用,在现有信号调控研究基础上其在抗病机制中可能的参与途径。对目前棉花抗黄萎病分子育种研究中存在的主要问题和可能的解决途径进行了探讨,展望了其发展的方向。     

Single seed descent as a breeding method for swedes (<Emphasis Type="Italic">Brassica napus</Emphasis> L. var. <Emphasis Type="Italic">napobrassica</Emphasis> Peterm)

The results are presented of two single seed descent (SSD) breeding programmes for swedes (Brassica napus L. var. napobrassica Peterm). The first programme produced cultivar Virtue and was done as part of a research programme on heterosis. It involved the production and trialling in 1991 of 95 F₆ families from a single cross made in 1985 between lines derived from cultivars Criffel and Marian. Six F₆ families were mass multiplied in polythene tunnels in 1992, using blowflies as pollinators, and trialled in 1993 and 1994 before Virtue was entered into National List (NL) trials in 1995. The second programme was done as a commercially funded breeding programme and involved the production and trialling in 1999 of 1,037 F₆ families from 15 crosses made in 1993. Fifty F₆ families were advanced to F₇ in a glasshouse in 2000 and assessed in 2001. Six F₇ families were mass multiplied in polythene tunnels in 2002 and trialled in 2003. Two cultivars, Gowrie and Lomond, from the cross between Airlie and Invitation, were produced from the programme and entered NL trials in 2004. The SSD was traditional in the sense that each advanced family was descended from a different F₂ plant without selection and a glasshouse was used for the selfing generations. However, it differed from the schemes that have been operated for soybean and spring cereals in that it was not possible to grow two or three generations a year because of the vernalization requirements of swedes, and it was not possible to grow a large number of plants at really high density because the inflorescences needed to be covered with Glassine bags to prevent cross pollination. In yield trials over 4 years, Gowrie had the highest dry-matter yield (12.59 t/ha) of the three new cultivars, out yielded Magres (11.28 t/ha) and other shopping swedes, but was not as high yielding as cultivar Kenmore (13.44 t/ha) which had been produced by pedigree inbreeding with selection. A modified SSD breeding scheme is recommended in which family selection is practised at F₃.     

Genetic interpretations of the effects of bulk breeding on four populations of beans (Phaseolus vulgaris L.)

Summary The effects of bulk breeding on yield and its components in two high-yeilding and two low-yielding bean populations when grown at crop densities are interpreted in terms of gene action and selection. There was considerable additive variation in the crosses, dominance effects were variable but tended to be negative. The results were compared with results obtained at low density by another worker with the same populations, and this showed that interpretations of gene action in hybrid vigour depend on the test environment used. The interpretations were also compared with plant breeding interpretations made on the same material (Hamblin, 1977), and it was found that a single pattern of response to natural selection, in plant breeding terms, may be explained by more than one genetic interpretation and, conversely, a single genetic interpretation may result in different patterns of response in plant breeding terms. The value of composite crosses in plant breeding are discussed and it is concluded that there is a greater chance of producing improved lines from a large number of simple crosses than from a smaller number of composite crosses.     

Collaborative and consultative participatory plant breeding of rice for the rainfed uplands of eastern India

We describe a participatory plant breeding (PPB) programme in rice for the rainfed uplands of eastern India. Collaborative participation (farmers grew and selected in segregating materials in their fields) and consultative participation (farmers selected among progenies in researchers' plots) were used. The PPB was started with only two crosses and, of these, Kalinga III/IR64 was the most successful and produced two released varieties: Ashoka 200F from collaborative breeding and Ashoka 228 from consultative breeding. Both yielded significantly more than control varieties, including Kalinga III, in research trials and in participatory trials in farmers' fields. Qualitative data from participatory trials was highly informative, statistically analysable, and cheaper to obtain than quantitative data. In low-yielding research-station and on-farm trials the two new upland varieties showed no significant genotype × environment interaction with the check varieties. However, in higher-yielding All India Coordinated Rice Improvement Project trials, both varieties were more adapted to low yielding environments than the national check variety. Farmers liked the varieties for their early maturity, improved lodging resistance, higher fodder and grain yield, long-slender grains and excellent cooking quality. Before certified seed production, farmer groups have produced large quantities of seed that have spread widely through informal channels. The returns from PPB, compared to conventional breeding, were higher because it cost less, the genetic gains per year were higher, and the benefits to farmers were realised earlier. This revised version was published online in August 2006 with corrections to the Cover Date.     

昆明市居住小区植物群落蚊虫滋生现状研究

为研究居住小区不同植物群落类型造成蚊虫滋生引发的蚊患问题，对昆明市10个小区植物种植群落及常用植物的蚊虫滋生现状进行分析。采用典型样地调查样方法于四季雨后每日17:00—20:00直接采集小区植物空间的蚊虫量，调查人工植物群落乔灌草各层蚊虫滋生量的基本现状，运用SPSS统计分析蚊虫滋生受植物群落和季节影响的差异性。结果表明，10个居住小区的植物群落主要为乔灌草类、乔灌/乔草类、灌草类和单层类；4种群落类型的蚊虫滋生量冬春两季差异不显著，夏秋两季灌草类和单层类差异显著；单层类蚊虫滋生量最少，灌草类蚊虫滋生量最多；结合昆明市居住小区植物现状，植物景观配植最优可为玉兰、吊兰和樱花。     

Agronomic diversity of naked barley (<Emphasis Type="Italic">Hordeum vulgare</Emphasis> L.): a potential resource for breeding new food barley for Europe

Naked (hulless) barley was neglected by plant breeders in Europe during the period of intensive crop improvement in the 20th Century, but it is now receiving renewed interest due to the potential health benefits it can convey. Very few naked barley cultivars have been developed for modern UK or European agricultural systems, in contrast to the wide diversity of naked barley in Asia. Prior to initiating any breeding programme, phenotyping in UK field conditions is needed to assess the value of existing exotic landraces. This article reports such a programme where naked barley landrace lines were grown alongside modern cultivars and unimproved UK hulled landrace lines over 4 years at a research station in North Wales and assessed for yield and agronomic traits. Multivariate analysis of the traits suggested that accessions clustered by region of origin. Himalayan landrace lines formed Eastern and Western clusters while Japanese and Korean landrace lines were distinct from these. European naked barleys were found to be closest to European hulled barleys, suggesting that the distinctiveness of the Asian naked barley landrace lines was due to origin rather than the naked grain trait per se. The only agronomic trait that could be attributed to naked grain was poorer crop establishment, but some Himalayan landrace lines showed vigorous seedling growth. Modern lines of naked barley from Syria gave superior yields to old UK hulled barleys, indicating that there is potential for breeding modern UK cultivars of naked barley.