Genetic issues and pitfalls in transgenic plant breeding

Transgene technology provides a powerful tool for developing traits that are otherwise difficult to achieve through conventional breeding. In order to effectively apply the technology to breeding, we need to understand how transgenes behave in plants. Transgenes may or may not follow Mendelian segregation; their expression can be significantly affected by integration positions and structures of the transgenic DNA in host genomes; transgenes may become unstable over generations, genetic background sand environmental conditions; and they may have significantly negative impact on expression of endogenous genes. If not well understood, the sehurdles could become significant barriers in transgenic breeding. This paper reviews some genetic issues and pitfalls that are often encountered in transgenic breeding. Because of the necessity of being brief, transgene expression, silencing, and breeding are the three areas of focuses in this discussion. While molecular mechanisms underlying many of the transgenic phenomena have not been completely understood, some practical ‘rules’ are now available for creating, evaluating and selecting desirable transgenic transformants. It can be certain that with more transgenic plants generated and characterized our knowledge of transgene genetics at both molecular and plant levels will continue to accumulate. This revised version was published online in July 2006 with corrections to the Cover Date.     

Impact of plant genetic resources on wheat breeding

This article describes the impact of plant genetic resources on wheat breeding. It defines the important contribution of N.I. Vavilov Institute (St. Petersburg, Russia) to broadening the genetic diversity of new wheat cultivars. Special attention is given to conducting a comprehensive evaluation of intraspecific variability for valuable characters, including: 1) formation of special subcollections, consisting of accessions with useful characters and accessions representing intraspecies diversity for a given character; 2) revealing genetic differences among phenotypically superior accessions; 3) determining a genetic system of intraspecific variability for a given character; 4) formation of a genetic collection; 5) revealing and developing the donors of useful characters. An example using plant height shows that the proposed research approach adequately determines the genetic potential of species and reveals the most effective genes for practical uses. It is assumed that the main sources of genes for breeding Triticum aestivum L. in order of importance will remain: 1) intraspecific diversity of T. aestivum itself; 2) other Triticum species; 3) other genera of the Triticeae Dum. tribe (particularly Aegilops L.); 4) more remote genera of the Poaceae Barnh. botanical family. It is stressed that existing diversity of T. aestivum has been poorly investigated genetically and only partially used by breeders. Properly evaluated, it can provide multiple solutions for traditional and new problems of wheat improvement. This revised version was published online in August 2006 with corrections to the Cover Date.     

Estimation of parental value for varieties used in plant breeding

A method to estimate variety value directly in a plant breeding process is proposed. The approach is based on frequencies of variety progenies succeeding in breeding trials. The number of crossing combinations is demonstrated to estimate parental breeding values (PBV) more effectively than the number of lines. Because of the possibility of significant sexual effects the parental breeding value is estimated by the square mean of the female and male variety breeding values. For adequate PBV estimation, all the varieties tested should involve an equal number of crossing combinations as male and female parents. The Latin square principle can be used for planning such crosses. The results of barley breeding programmes are used as an example for the application of the proposed method. It is shown that the PBV estimates obtained in a current breeding cycle allow the effectiveness of the following cycles to be increased by better planning of the subsequent crosses.     

Heterosis: its genetic basis and its utilisation in plant breeding

Summary To discuss the utilisation of heterosis in plant breeding it is necessary to consider its genetic basis. In cross fertilized plants in which the phenomenon of heterosis is very important, such as maize, it appears that a great part can be explained by the mutation load. However in both autogamous or allogamous plants it is difficult to exclude a role of marginal overdominance which could justify hybrid variety production.To know in a relatively short time whether it will be better to develop lines or hybrids it is necessary to know the parameters (mean and variance) of the distribution of all varieties of a given type which can be derived from the breeding population. A numerical application allows the determination of the situations where the best single crosses will be better than the best lines. With some approximate values of the necessary parameters, the case of grain yield in maize and in wheat is briefly discussed.To develop lines or hybrids, a general strategy is given. Its main axis is population improvement which has to be adapted to the type of varieties to develop. It is shown that according to the situation the type of varieties to develop can change with time: single crosses can be more justified at the beginning and lines can be justified later if all heterosis were fixable. To develop hybrids the best scheme is reciprocal recurrent selection with half-sib or full-sib progenies followed by pedigree reciprocal selection initiated by full-sib progeny tests. With this strategy there is no problem of the prediction of hybrid performances. However it seems possible to develop some predictors of heterosis or of specific combining ability between two lines using some criteria of genetic distances. Preliminary results with distances computed from the behaviour of lines in a two-tester top cross design appears very stimulating.Communication given at the206th meeting of teh Genetical Society of Grain Britain     

Combining ability and patterns of inheritance for plant and fruit traits in Japanese quince (Chaenomeles japonica)

Phenotypic variation and pattern ofinheritance was investigated for plant andfruit traits in Japanese quince (Chaenomeles japonica, Maloideae). Japanesequince is a minor fruit crop in Latvia andLithuania, and is presently being developedfor production of juice, aroma and fruitfibre in Sweden and Finland. General andspecific combining ability was estimatedfor five plant vegetative traits, eightfruit yield and morphology traits, and fivefruit biochemistry traits in a studypopulation consisting of 14 hybridfamilies. Thorniness seems to be controlledprimarily by a single locus. All othertraits studied appear to be governedprimarily by additive genes, as judged fromgeneral combining ability estimates.Significant specific combining ability(SCA) was detected for yield, plant heightand some fruit traits. However, therelative contribution of SCA to the overallgenetic variance was in general low. Anefficient breeding strategy for Japanesequince could therefore be based onrecurrent selection.     

Component analysis of complex characters in plant breeding

Summary A method is described by which the contribution of individual components to the variation of a complex character is quantified. The method is adapted for use in plant breeding from the sequential component analysis, developed for agronomic experiments by Eaton & Kyte (1978). It applies to a situation in which the complex character y is the product of n components (x₁,...x_n). The components are ratios of observed primary characters, introduced in a logical sequence. The proposed method differs from that of Eaton & Kyte in that: (1) the data are not log-transformed, and (2) the complementary determinations of y by its components are obtained directly from differences between the coefficients of determination of y by the successive primary characters rather than from a stepwise multiple regression of ln y on its log-transformed components.A comparison of the two methods suggests that the differences in results are caused mainly by the logtransformation which Eaton & Kyte apply to transform the relationship between y and its components into a linear one. The proposed alternative procedure avoids the transformation of the data; the multiplicative relationship between y and its components is retained and so is the assumed additive inheritance of the components. These two features of component analysis allow an active exploitation of specific combining ability based on recombinative heterosis.Present address: Giltaylaan 12, 6703 GB Wageningen, The Netherlands.     

Family selection in plant breeding

Summary Plant breeding programmes rarely take explicit practical account of the two sources of genetic variance, namely between and within full-sib families, even though existence of these two sources of variation has long been recognised. This paper refers to inbred and clonal crops, not to outbred, seed-propagated species. Theory suggests that the two variances should be of similar size, sometimes very similar. Good comparisons have never been made because variance within families is laborious to estimate. It is proposed that sets of families be assayed as to means in formal trials and only the best few, judged against standards as having potential for superior segregates, should be exploited thoroughly. The calculation as to approximate equality of genetic variances between and within families is important. The vast majority of families should probably be discarded without further ado, and at considerable economy. Sensible decision-making requires an economic component in order to exploit the trade-off between the cost of the initial trial and families discarded without further cost. The object of this paper is a critical review of practical principles, not a general review of a large and diffuse literature.     

Secondary somatic embryogenesis and applications in plant breeding

Summary Secondary somatic embryogenesis is the phenomenon whereby new somatic embryos are initiated from somatic embryos. Such cultures have been described in at least 80 Gymnosperm and Angiosperm species. In the initial step (primary somatic embryogenesis) such cultures have to be started from plant explants. In general, primary somatic embryogenesis from vegetative plant explants is, indirect and mostly driven by auxin (AUX) or auxin and cytokinin (AUX/CYT) supplemented media, whereas, from zygotic embryos it is direct and driven, to a larger extent, by CYT or growth regulator free media. Primary somatic embryogenesis from floral plant explants is between these two extremes. Indirect and direct somatic embryogenesis should be seen as two extremes of one continuum: in indirect somatic embryogenesis the embryos develop up to the (pre)-globular stage and in direct somatic embryogenesis to mature stages before they are subjected to secondary embryogenesis. In general, secondary embryogenesis requires no growth regulators in species with CYT driven primary embryogenesis. Whereas, continuous exposure to growth regulators is needed in species with CYT/AUX or AUX driven primary embryogenesis.In most species somatic embryos can be converted into shoots, although the frequencies are mostly low. In general, somatic embryos induced by growth regulator free or CYT supplemented media meet more difficulties in shoot development than embryos induced by AUX supplemented media. Applications of secondary somatic embryogenesis for plant breeding are discussed.     

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.     

Heritability, variance components and correlation of morphological and phenological traits in hazelnut

Most traits of interest in hazelnut are quantitative, yet there is little information available on heritability, variance components, or correlations. In this study, 13 morphological and four phenological traits were observed for 3 years on 41 parental genotypes, and for 2 years on seed‐lings representing 35 progenies. Narrow‐sense heritability estimates obtained by regression of offspring means on midparent values were all high, ranging from 0.56 for amount of kernel fibre to 0.89 for nut depth. Data on the parent genotypes was used to analyse variance components and showed that genotypic variance accounted for most of the phenotypic variance for all traits, and there was very little variation among trees within genotypes. Genotype‐year interaction accounted for only a very small part of the phenotypic variance for most traits, and changes in genotype rank were few and minor. Thus, selection based on genotype means is appropriate. The largest genotype‐year interaction components were observed for time of nut maturity, time of stigma exsertion, time of catkin elongation, number of nuts per cluster and amount of kernel fibre. For these five traits, evaluation over a period of years is advised. Correlation coefficients were large and positive for four nut size traits, indicating some redundancy in these measurements. Three of the phenological traits (time of stigma exsertion, time of catkin elongation, and time of leaf budbreak) were also highly and positively correlated. A large genetic correlation (0.44 < r < 0.73) was noted between good blanching and early phenology (catkin elongation, stigma exsertion and leaf budbreak), although plots of individual seedling values showed a large degree of scattering. Genetic correlations also indicated that seedlings with small nuts also tend to have compressed nuts, short husks and catkins that elongate later, but plots of individual seedling values showed large scattering. Correlations among the six traits directly related to the objectives of the Oregon State University hazelnut breeding programme (kernel weight, per cent kernel, nut shape index, blanching ability, relative husk length and nut maturity) were very low, indicating that they can be handled as independent traits.     

Molecular markers and doubled haploids in European plant breeding programmes

The breeding companies and laboratories involved in this article cover a wide range of crops grown in the temperate climate zone: small grain cereals, oilseed crops, forage crops, turf, vegetables and potato. Speed and efficiency are becoming increasingly important in variety breeding and doubled haploids (DH) and genetic markers are important biotechnological tools to accelerate materials to market. Collaborative research between universities, research institutions and breeding companies has resulted in the routine use of DH technology and molecular markers in practical breeding of barley, wheat and rapeseed. DH populations have been established not only for barley, wheat and rapeseed, but for rye, oat and triticale, where DH technology is less developed. A driver here is the value of the crop e.g. although wheat is less responsive to DH production the value of the end product makes the effort worthwhile. Simple and rapid DNA extraction methods used in high-throughput marker assisted selection (MAS) systems are essential for routine use of markers. MAS is used both to monitor the presence of genes of interest and also to monitor the genetic background. DH technology in forage, turf and vegetables is still in progress and the practical use of markers in all crops is limited by access to trait linked markers. Collaboration and technology transfer with universities, research institutions and breeding companies is essential for the improvement of both DH protocols in recalcitrant crops and marker technology in all crops.     

Combining ability and correlations for yield components in early generations of potato breeding

A partial diallel set of crosses was made between 14 potato cultivars chosen for their fertility, from those included in a potato breeding programme at the NEIKER – Basque Institute for Agricultural Research. The progeny were grown in completely randomized trials from 1997 to 1999. Performance for yield, tuber number and average tuber weight was analysed in seedling and two clonal generations. Variance estimates due to both general combining ability (GCA) and specific combining ability (SCA) were significant in all generations for all traits under study. However, SCA was more important than GCA in almost all cases. Correlation coefficients among characters, generations, GCA and SCA effects were examined. For tuber yield no relation was obtained between generations; however, average tuber weight and yield were positively associated in all generations. The results indicate that appropriate selection criteria depend strongly on the particular cross. The implication for a breeding strategy are discussed.     

Achievements and limitations of contemporary common bean breeding using conventional and molecular approaches

Common bean (Phaseolus vulgaris L.) improvement programs have been successful using conventional breeding methods to accomplish a wide array of important objectives. Specific achievements include the extension of range of adaptation of the crop, the development of cultivars with enhanced levels of disease and pest resistance and breeding lines that possess greater tolerance to drought. The most effective breeding method depends on the expression and inheritance of the trait to be selected and the target environment. Many bean improvement programs use molecular markers to facilitate cultivar development. In fact, several recent germplasm releases have used molecular markers to introgress and or pyramid major genes and QTL for disease resistance. Related species (P. coccineus and P. acultifolius) via interspecific hybridizations remain an important albeit long-term source for resistance to economically important diseases. Slow progress has been made in the improvement of traits such as adaptation to low soil fertility and tolerance to high levels of soluble Al in the soil using conventional breeding methods. The inability to directly measure root traits and the importance of genotype × environment interaction complicate the selection of these traits. In addition, symbiotic relationships with Rhizobium and mycorrhiza need to be taken into consideration when selecting for enhanced biological N fixation and greater or more efficient acquisition of soil P. Genomic examination of complex traits such as these should help bean breeders devise more effective selection strategies. As integration of genomics in plant breeding advances, the challenge will be to develop molecular tools that also benefit breeding programs in developing countries. Transgenic breeding methods for bean improvement are not well defined, nor efficient, as beans are recalcitrant to regeneration from cell cultures. Moreover, if issues related to consumer acceptance of GMOs cannot be resolved, traits such as herbicide tolerance in transgenic bean cultivars which would help farmers reduce production costs and decrease soil erosion will remain unrealized.     

Conventional and contemporary approaches for drought tolerance rice breeding: Progress and prospects

Drought is becoming a major threat to rice farming across the globe owing to the depletion of water tables in rice-growing belts. Drought affects rice plants at multiple stages, causing damage at morphological and physio-biochemical levels, leading to severe losses that exceed losses from all other stresses. The amalgamation of conventional breeding methods with modern molecular biology tools and biometrical methods could help accelerate the genetic gain for drought tolerance in rice. Many drought-tolerance traits with genetic determinants have been identified and exploited for tolerance rice variety breeding. The integration of genome-wide association study and genomic selection tools with speed breeding shortened the breeding cycle and aided in rapid improvement of genetic gain. In this review, we emphasized the progress made through classical breeding as well as the limitations and usefulness of current genomic methods in improving drought tolerance. We briefly addressed methods for identifying genetic determinants for drought tolerance and deploying them through genomics-assisted breeding programmes to develop high-yielding drought-tolerant rice cultivars.     

Genomics-assisted breeding: The next-generation wheat breeding era

Common wheat provides approximately 20% of the total dietary calorie intake of human beings. Recent technological advances in whole-genome sequencing and their application in wheat and its progenitor species provide new opportunities to uncover the genetic variation of wheat traits and to accelerate the traditional breeding (TB) strategies in the context of genomics-assisted breeding (GAB). Integration of TB, marker-assisted selection (MAS) and genomic selection (GS) with high-density SNP markers is expected to accelerate the breeding process and to further enhance genetic gain. With the assistance of the next- or third-generation sequencing technologies and high-throughput phenotyping platforms, GAB can now realistically be considered in the following area: (i) genome sequencing and high-quality assembly to uncover new variations, (ii) whole-genome sequence-based association studies, (iii) gene function (or functional gene) identification and (iv) integration of whole genomic breeding information, utilizing multi-omics data and different breeding strategies. We argue that GAB is becoming the preferred strategy in pursuit of new wheat cultivars with superior traits on high yielding, high nutritional quality, climate-resilience and so on.     

Combining ability for yield and plant phenology in plantain-derived populations

Genetic enhancement of Musa spp. has aimed at producing hybrids with high yield, short stature, fast crop cycling, and disease resistance through interspecific and interploidy crosses. Progeny testing for parental selection has seldom been carried out in Musa and little is known on combining ability and heterosis in this species. A 5 × 5 factorial mating design was used to estimate components of phenotypic variance in 4 x-2 x hybrid populations and to determine the combining ability of their progenitors for yield and associated traits. General combining ability was much greater than specific combining ability for these traits, and, therefore, only little recombinative heterosis could be expected upon crossing. Thus, the 4 x-2 x breeding scheme should aim to accumulate favourable alleles in 4 x and 2 x clones through recurrent selection. Such clones could be used per se or in crosses aimed at restoring the seedlessness character in the progeny due to female sterility in a triploid background. This revised version was published online in August 2006 with corrections to the Cover Date.     

Farmer and formal breeding of sorghum (Sorghum bicolor (L.) Moench) and the implications for integrated plant breeding

Sorghum (Sorghum bicolor (L.) Moench) is the fifth most important cereal crop worldwide and it is the fourth most important crop in Ethiopia. The national average yield amounts 1302 kg/ha. In order to assess the achievement in farmer breeding various types of research were undertaken. These include survey research to quantify the trend in productivity, the level of and reasons for adoption of improved varieties, yield performance and preference evaluation of farmers’ varieties (FVs) and improved varieties (IVs). As per the trend analysis over the last four decades, total production and yield per hectare has increased by 11.63 and 14.2%, respectively. However, area allocated to sorghum has decreased over years by −2.93%. The lack of consistent productivity is attributed to the fluctuation of environmental factors. Sorghum production in Ethiopia is predominantly based on varieties developed by farmers. The share of IVs is very low. FVs and IVs are adopted by 87.3 and 12.7% of the farmers, respectively. Besides, the adoption of IVs is limited to the lowland crop ecology. The comparative yield of FVs is higher than IVs by 132%. On top of yield, farmers do prefer their varieties for other multipurpose values namely feed, fuel wood and construction material. FVs under production are identified in each wereda. Farmer breeding has been successful compared to four decades of formal breeding. On the other hand, both farmer and formal breeding are not without weaknesses; a comparative balance sheet is outlined for both. Ideotypes for the three major crop ecologies are suggested and integrated plant breeding is anticipated to develop the proposed ideotypes thereby increase sorghum productivity in the region.     

中国花生育种的发展历程与展望

花生是重要的油料作物和经济作物。几十年来,中国花生生产迅速发展,花生良种的培育和推广在其中的贡献巨大。为了阐明花生育种在中国的发展历程以及今后的发展方向,本研究介绍了中国花生品种的更替历程,综述了除引种和传统的杂交育种技术之外,新技术在花生育种中的应用,归纳了中国花生育种的目标。指出综合利用花生育种新技术并结合常规育种技术,培育高产、早熟、优质、多抗、适于出口以及适于机械化栽培和加工的花生新品种将是今后中国花生育种的发展方向。     

How narrowly adapted are the products of decentralised breeding? The spread of rice varieties from a participatory plant breeding programme in Nepal

Acceptable rice varieties for high-altitude areas of Nepal were bred by participatory plant breeding (PPB). One of the most adopted varieties, Machhapuchhre-3 (M-3), performed much better in the formal trials system than the products from centralised breeding and was released in 1996. From 1996 to 1999, the spread of M-3 was monitored in high-altitude villages along with unreleased variety Machhapuchhre-9 (M-9), derived from the same cross. The study was done by interviewing individual households, groups, and field verification. Both M-3 and M-9 spread from farmer-to-farmer and through interventions by Non-Government Organisations (NGOs) and Government Organisations (GOs). Their adoption had steadily increased and their spread commenced five to six years earlier than would have been the case in a conventional system. The PPB programme was decentralised – all selection was in only two villages in the same valley – but this did not result in specific adaptation. The varieties were adopted in distant villages situated at much lower altitudes to the original PPB sites and the greatest yield advantage of the varieties over the local landraces was also at these lower altitudes. This revised version was published online in August 2006 with corrections to the Cover Date.