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.     

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.     

Breeding objectives and the relative importance of traits in plant and animal breeding: a comparative review

Breeding objectives always involve consideration of multiple traits, even in situations where output of a single trait is dominant. We review literature dealing with formal definition of breeding objectives. Involvement of farmers in the process of setting up breeding objectives is also considered. In the optimal selection index, the relative importance of a trait is scaled by its economic value, derived as marginal profit related to a change in expression of defined size. Normative approaches to derive economic values use partial derivatives of a profit equation with respect to the traits involved or model the bio-economic system with various techniques. The theory is well developed and includes consideration of non-linear profit functions and traits with an intermediate optimum. It is frequently applied in animal breeding. In dairy cattle breeding, a major change of focus from traits related to output (i.e., milk yield) to traits related to cost of input (health, fertility, feed efficiency) has taken place recently. Plant breeders find the concept of deriving relative economic weights of traits difficult to apply and often replace the optimal index by restricted or desired gains indices. A change of paradigms similar to that in cattle breeding seems advisable. Participatory approaches to evaluate the relative importance of traits are more frequently applied in plant breeding than in animal breeding. We review two studies, dealing with methods of acquiring information about selection criteria of farmers planting maize in the Ethiopian highlands and of pastoralists keeping cattle in Uganda, in detail.     

A database management system for information retrieval and documentation of experiments for plant breeders

Summary An existing database system for seed collections has been augmented by programs providing plans for field experiments, record sheets and adhesive labels for seed packets. Information on accession names and parentage is picked up from the database. At the end of the season information on material seleeted in the trials is automatically added to the database.     

Genetic improvement and breeding of tea plant (Camellia sinensis) in China: from individual selection to hybridization and molecular breeding

Tea is an important revenue source for the tea producing countries in the world, including China. China is the place of origin of tea plants, it has the broadest genetic variations in the world. It also has bred more than 200 improved cultivars. The improved cultivars have made important contribution in the tea industry. In this paper the achievements of tea genetic improvement and breeding, the current situation of collection, conservation, appraisal and evaluation of tea germplasms, the establishment and development of tea breeding system were reviewed. The main research emphases for the genetics and breeding of tea plant in the near future in China are proposed.     

Use of genomic and phenotypic selection in lines for prediction of testcrosses in maize II: grain yield and plant traits

Plant breeders have been trying to predict the performance of hybrids based on their parental performance. One application of molecular markers is its use in selection. The objectives were to map quantitative trait loci (QTL) and verify its congruence in maize lines and in their testcrosses and verify the possibility to select testcrosses from the predicted means of the lines by using information from markers. Two-hundred and fifty six lines and the testcrosses of these lines with two testers were evaluated in six environments, considering grain yield, plant lodging, days to anthesis and silking, anthesis-silking interval, plant and ear height and ear placement. QTL were mapped in the lines and in testcrosses and the predicted means of the lines were computed based on QTL effects and in all markers of the genome. The congruence of QTL detected in the lines and testcrosses were small for all traits. The correlations between the predicted means of the lines and the phenotypic means of the testcrosses ranged from low for grain yield to moderate for cycle and stature traits. The highest coincidences of the lines and selected testcrosses were observed for cycle and stature traits and the lowest for grain yield. Even by using molecular markers information, it is only possible to predict the testcrosses performance from the lines information to less complex traits and with reduced dominance effect. For complex traits and with pronounced dominance effect, information of markers must be obtained directly in the testcrosses, so they can be used for selection.     

Manova and discriminant analyses of phenotypic data as a guide for parent selection in kiwifruit (Actinidia deliciosa) breeding

Evaluation of seedling populations assists in identifying those plants most desirable as parents for a breeding programme. A multivariate analysis of variance (Manova) showed that the seedling populations from 6 kiwifruit (Actinidia deliciosa) crosses differed in their overall merit. Discriminant functions were then used to identify the characters most powerful in distinguishing between populations. The populations were placed in order of their function scores which represent overall merit, and the superior populations were determined. The results showed that `Bruno' was a superior female parent for the production of seedlings with high discriminant function scores for floriferousness (male offspring)and productivity and high vitamin C content (female offspring). One male parent D-1-20 was consistently superior to D-1-6 the other male parent. This revised version was published online in July 2006 with corrections to the Cover Date.     

Participatory plant breeding research: Opportunities and challenges for the international crop improvement system

This paper describes the current state of international plant breeding research and explains why the centralized global approach to germplasm improvement that was so successful in the past is today being transformed by the incorporation of decentralized local breeding methods designed to better incorporate the perspective of end users into the varietal development process. It describes international breeding efforts for major crops and identifies factors that have contributed to the success of the international breeding system; discusses shortcomings of the global approach to plant breeding and explains why future successes will depend critically on researchers' ability to incorporate the knowledge and preferences of technology users; reviews a number of farmer participatory research methods that are currently being tested by plant breeding programs throughout the developing world; describes synergies that can potentially be achieved by linking centralized global and decentralized local breeding models; and discusses technical, economic, and institutional challenges that will have to be overcome to integrate end user-based participatory approaches into the international plant breeding system. This revised version was published online in August 2006 with corrections to the Cover Date.     

Kazusa Marker DataBase: a database for genomics,genetics, and molecular breeding in plants

In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops.     

The cell biology of plant transformation: Current state,problems, prospects and the implications for the plant breeding

Summary The DNA delivery systems which are routinely used to introduce genes into crop plants are Agrobacterium tumefaciens, electroporation and particle bombardment. The differences and similarities between these different transformation techniques are outlined. The influence of the cell biological approach, and more specifically the impact of the state of the plant cell at the moment of transformation, on the genotype and phenotype of the regenerated transgenic plant is analysed. In this respect phenomena such as position effects, gene silencing, co-suppression, epistasis, co-transformation and somaclonal variation are discussed. The relevance of these factors for plant breeders is discussed.     

Genotypic differences in susceptibility to wireworm attack in potato: mechanisms and implications for plant breeding

The influence of different tuber compounds on susceptibility to wire-worms (Agriotes obscurus) was studied in experiments with 10–13 potato genotypes. Both greenhouse and field experiments showed that the susceptibility to wireworm attack was negatively correlated with the concentration of glycoalkaloids and positively correlated with the concentration of reducing sugars in the outer 2 mm of the tubers. Varietal differences in chlorogenic acid had no effect on susceptibility. Breeding for high levels of glycoalkaloids in the extreme periphery, but very low levels in the rest of the tuber, will protect the tubers from wireworms and yet result in acceptable glycoalkaloid levels for food safety.     

Organic varieties for cauliflowers and cabbages in Brittany: from genetic resources to participatory plant breeding

Plant breeding for organic agriculture (OA) was stimulated when it came under the European Organic Agriculture Regulation (2092/91) in 2004. In Brittany, the need for specific varieties for organic farming arose early for the Brassica species because of the unsuitability of most of the modern varieties to the principles of OA. Moreover, the private sector of plant breeding finds it economically difficult to satisfy the demands of OA. The aim of the present study is to provide varieties and seed for organic farmers for two vegetable Brassica crops, and to show how genetic resources can contribute to this purpose in the framework of a Participatory Plant Breeding (PPB) programme. The emergence of PPB in Brittany is the result of several concomitant and favourable circumstances: the will of the professionals (represented by IBB, Inter Bio Bretagne), their organization (an experimental station, the PAIS, Plateforme Agrobiologique d’IBB à Suscinio), the research initiative in INRA and the availability of genetic resources. From genetic resource observations, our experience showed several breeding situations: reviving a traditional activity (Roscoff cauliflower and local cabbages), extending tradition (autumn cauliflower), diversifying production by new introductions (coloured cauliflowers), and creating new forms of population varieties (broccoli and coloured cauliflowers). Farmers have taken charge of population breeding by mass selection and the PAIS, with INRA scientific support, has taken up innovative selection and the improvement of varieties completing the farmers’ initiatives. The PAIS remained the central point for information and for providing the seed for trials. Seed production will be managed in a collective way. Until now, the exchange of seed remained an experimental dimension of PPB. French seed legislation represents a limitation on the development of seed exchange by PPB.     

Genetics components of rice root architecture and carbon isotopic fractionation parameters: a tracer for breeding in a water-saving irrigation management

Journal of Crop Science and Biotechnology - Phenotyping is the major bottleneck in the effort to develop varieties of rice (Oryza sativa L.) suitable for growing under a water-saving irrigation...     

Component analysis of plant dry matter production: a basis for selection of breeding parents as illustrated in carnation

Summary Improvement of dry matter production in the vegetative phase is a breeding objective in many crops, especially where whole plants or parts of plants in the vegetative phase constitute the commercial product. Dry matter production is a complex process and plant dry weight, as measured at a given date, is a complex character, of which initial weight of planting material and mean relative growth rate over the period of growth are the major components.The primary objective of the present paper is to demonstrate how a method of component analysis proposed by Sparnaaij and Bos can be used to facilitate breeding for a high rate of vegetative growth. The procedure is illustrated by data from a study of variation in forcing ability among 13 carnation cultivars. It involves a detailed analysis of mean relative growth rate over the period of vegetative growth, including components derived from observations on net rate of photosynthesis and dark respiration.It is shown how component analysis can be used (a) to quantify the relative contribution of initial plant weight and of mean relative growth rate and its components to the genetic variation in plant dry weight, thus allowing a judicious choice of selection criteria for breeding parents, and (b) to predict mean plant dry weight of F₁ hybrids obtained by crossing these parent genotypes, thus facilitating the choice of crosses to be made.     

The use of general and specific combining abilities in a context of gene expression relevant to plant breeding

Many common traits are believed to be a composite reflection of multiple genetic and environmental factors. Recent advances suggest that subtle variations in the regulation of gene expression may contribute to quantitative traits. The nature of sequence variation affecting the regulation of gene expression either in cis (that is, affecting the expression of only one of the two alleles in a heterozygous diploid) or in trans (that is, affecting the expression of both alleles in a heterozygous diploid) is a key and usually unknown feature for the breeders. If the change in expression acts entirely in cis, then the structural gene can be treated as a candidate gene and a potential target for marker-assisted selection. Therefore, gene surveys for cis-regulatory variation are a first step in identifying potential targets for marker-assisted breeding. Here, we discuss in detail the “genome-wide analysis of allele-specific expression differences” (GASED) approach. The GASED approach was developed to screen for cis-regulatory variation on a genome-wide scale. In GASED, mRNA abundance is treated as if it were a quantitative phenotypic response variable, whose genetic between-F₁ hybrid variance is partitioned into additive and non-additive components. In plant breeding, this partitioning of the genetic variance is well known in the context of estimation of general and specific combining abilities for diallel crossing schemes. We demonstrate the GASED method using Arabidopsis thaliana data. The method can be used to screen for cis-regulatory variation in any crop species for which diallel crossing schemes are appropriate and genomic tools are available.     

The impact of participatory plant breeding (PPB) on landrace diversity: A case study for high-altitude rice in Nepal

Participatory plant breeding (PPB) methods were used to develop two farmer-accepted, cold-tolerant rice varieties in Nepal — Machhapuchhre-3 (M-3) and Machhapuchhre-9 (M-9). Both were derived from the cross Fuji 102/Chhomrong Dhan. Following the introduction of these varieties, the changes in the rice landraces and varieties that farmers grew were studied in ten villages. In seven of them for which data were analysed for both 1996 and 1999, adopting farmers grew 18 landraces and four modern varieties of which three, M-3, M-9 and Lumle-2, were the products of PPB. These three varieties covered 10% of the total rice area and 33% of the rice area of the adopting farmers in the seven study villages in the 1999 survey. The adoption of the PPB varieties impacted most on the more commonly grown landraces. With the exception of two villages, the varietal richness among adopting farmers was either static or increased, and there was an overall increase in allelic diversity. However, in future, the increasing adoption of M-3 and M-9 could result in significant reductions in varietal richness, although, allelic diversity may not be greatly reduced. This revised version was published online in July 2006 with corrections to the Cover Date.     

Diagnosis tool for plant and crop N status in vegetative stage: Theory and practices for crop N management

The environmental constraints to agriculture imply that nitrogen (N) fertilizer management should be adjusted to crop N requirements determined by target yields. Nowadays for environmental and economical reasons target yield of farmers can be lower than the potential crop yields as permitted by soil and climatic conditions. So it is important to provide farmers crop N status diagnostic tools in order to decide the rate and the timing of N fertilizer applications. Theory on crop N uptake and allocation allows the determination of a diagnostic tool, the Nitrogen Nutrition Index, based on the determination of the critical N dilution curve for each crop species considered. During the vegetative growth period of all the crop species studied, including C3 and C4 species and monocots and dicots, plant N concentration decreases monotonically as crop grows because of (i) the ontogenetic decline in leaf area per unit of plant mass, and (ii) the remobilisation of N from shaded leaves at the bottom of the canopy to well illuminated leaves at the top. NNI appears then as an indicator well connected with the physiological regulation of N uptake at canopy level. So this indicator can be used as the basis for determination of crop N nutrition status, and then for decision making on the necessity of an N application for achieving target yield. Nevertheless despite its high physiological relevance, NNI cannot be used directly in farm conditions because its determination is very time consuming. So it is necessary to develop indirect methods for NNI estimation through more operational procedures. Several methods have been proposed in literature, such as nitrate concentration in sap or chlorophyll meter. But the calibration or validation of these methods with NNI have not been always made and, when they have been, they did not give univocal relationships, showing a strong dependence of the relationship with cultivar and environment, that limits considerably the relevance of such diagnostic tools in a large range of situations. Easier to use is the indirect estimation of crop NNI by remote sensing measurements. This method allows the estimation of both actual crop mass, through LAI estimation and crop N content, through crop chlorophyll content. The possibility to have repeated estimations of crop NNI during the period of vegetative growth would allow a dynamic diagnostic tool of crop N status. The coupling of indirect measurements of crop N status with dynamic models of crop growth and development should allow a very promising method for crop N diagnostics for decision tools in N fertilization.     

Six years of maize selection in ‘Kitale synthetic II’, ‘Ecuador 573’, and ‘kitale composite a’ using methods of the comprehensive breeding system

Summary Evaluation of the results of six years of selection in the Kitale maize breeding methods study proved reciprocal recurrent selection to be an effective interpopulation improvement method. Ear-to-row selection was effective in improving Kitale Composite A (KCA). Data from a diallel of the cycle-6 ear-to-row substrains showed that where less than 10 lines were selected, inbreeding appeared to depress gain, but differences among the various ear-to-row experiments were not significant. Intererossing the substrains was predicted to reduce the effect of inbreeding. Yield gains in reciprocal recurrent selection and ear-to-row selection were associated with increases in ears per 100 plants. The reciprocal recurrent selection variety cross yield gain was estimated at 3.5% per year (7%/cycle) and that of the best ear-to-row procedure at 2.6% per year. The variety cross syn-2 from reciprocal recurrent selection was predicted to improve at the same rate as the best ear-to-row procedure (E7) with one long growing season per year. Under a cropping system with two similar seasons per year, however, ear-to-row selection should be more effective than reciprocal recurrent selection or its derived syn-2. Mass selection at 10% selection intensity produced significant improvement, but not at 2% selection intensity.S₁ and three half-sib selection methods were ineffective in KCA. Inbreeding and the lack of linkage equilibrium in KCA were discussed as contributing. Theoretical substrain compositing required 30 to 40 lines selected to equal the effectiveness of ear-to-row selection with 10 lines. Full-sib selection was effective in improving yield at 1.2% per year. All the recurrent selection methods showed a significant increase in ears per 100 plants. Population size was shown to be important in reducing losses due to inbreeding.If a hybrid or variety cross is potentially useable, reciprocal recurrent selection provides the best population approach. Initially, the variety cross syn-2 could be released with no additional breeding effort. Transition to variety crosses or traditional hybrids from extracted lines could be done as farmer husbandry improves and seed production facilities develop. Otherwise, open-pollinated varieties superior to existing maizes can be effectively developed using ear-to-row selection. The other methods may be effective in breeding populations when larger effective population sizes are used, but they were not effective in KCA when only 10 lines were recombined each cycle.Contribution from the East African Agriculture and Forestry Research Organization of the East African Community, the U.S. Agency for International Development (Project 618-11-110-657, East African Food Crop Research), the Kenya Ministry of Agriculture, and the Agricultural Research Service of the U.S. Department of Agriculture.