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.     

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.     

Choice of shrinkage parameter and prediction of genomic breeding values in elite maize breeding populations

Genomic selection (GS) is a promising alternative to marker‐assisted selection particularly for quantitative traits. In this study, we examined the prediction accuracy of genomic breeding values by using ridge regression best linear unbiased prediction in combination with fivefold cross‐validation based on empirical data of a commercial maize breeding programme. The empirical data is composed of 930 testcross progenies derived from 11 segregating families evaluated at six environments for grain yield and grain moisture. Accuracy to predict genomic breeding values was affected by the choice of the shrinkage parameter λ², by unbalanced family size, by size of the training population and to a lower extent by the number of markers. Accuracy of genomic breeding values was high suggesting that the selection gain can be improved implementing GS in elite maize breeding programmes.     

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.     

Changes in genetic diversity during seven cycles of recurrent selection for grainyield in oat, Avena sativa L.

Variability for desirable alleles within elite breeding populations is a requirement for long-term genetic improvement. Changes in genetic diversity were evaluated in a recurrent selection programme for enhanced grain yield in oat, Avena sativa L., using coefficient of parentage (r_p) and restriction fragment length polymorphism (RFLP) based genetic similarity (S) estimates. Both r_p and s increased during seven cycles of recurrent selection, indicating a reduction in the level of genetic diversity within the population. The relationship between genetic diversity and agronomic performance was also examined. Genetic similarity measures were poor predictors of the near-homozygous progeny performance and general and specific combining ability effects for three agronomic traits in the recurrent selection programme. In addition, there was no apparent trend for preferential selection of progeny from either more similar or more diverse parents within a given cycle of selection. The overall reduction in genetic diversity in this population has not affected selection response for grain yield. Variability remaining at important loci or de novo variation are possible explanations for the continued selection progress.     

Genetic diversity among populations and breeding lines from recurrent selection in Brassica napus as revealed by RAPD markers

Recurrent selection facilitated by dominant male sterility has been conducted to broaden the genetic basis for cultivar development in Brassica napus. This study aimed to evaluate the genetic variation in four base populations (C0‐C3) and breeding lines from two of the populations produced during recurrent selection by random amplified polymorphic DNA (Rapd) markers. Genetic variation in four populations declined gradually with the advance of selection cycles as measured by expected genetic heterozygosity (from 0.2058 in C0 to 0.1536 in C3) but the decline was not statistically significant. When compared with the average genetic distances for 21 germplasm collections with wide geographical and genetic origins (0.4712) and seven breeding lines from pedigree selection (0.2059), seven breeding lines selected from the C1 population and 11 from the C3 population had a larger average genetic distance (0.5339 and 0.5486, respectively). Clustering analysis indicated that the lines from recurrent selection had a much lower genetic similarity than lines from pedigree selection. Our results suggest that base populations derived from recurrent selection could provide a wider genetic variation for selection of breeding lines with more broad genetic bases.     

Genome-wide association mapping focusing on a rice population derived from rice breeding programs in a region

Plant breeding programs in local regions may generate genetic variations that are desirable to local populations and shape adaptability during the establishment of local populations. To elucidate genetic bases for this process, we proposed a new approach for identifying the genetic bases for the traits improved during rice breeding programs; association mapping focusing on a local population. In the present study, we performed association mapping focusing on a local rice population, consisting of 63 varieties, in Hokkaido, the northernmost region of Japan and one of the northern limits of rice cultivation worldwide. Six and seventeen QTLs were identified for heading date and low temperature germinability, respectively. Of these, 13 were novel QTLs in this population and 10 corresponded to the QTLs previously reported based on QTL mapping. The identification of QTLs for traits in local populations including elite varieties may lead to a better understanding of the genetic bases of elite traits. This is of direct relevance for plant breeding programs in local regions.     

An improved breeding strategy for autotetraploid alfalfa (Medicago sativa L.)

Alfalfa cultivar development will be enhanced by breeding strategies whichutilize the full potential of autotetraploid population genetic structures. Thisstudy evaluates the effectiveness of an allelic selection scheme, which wasdeveloped to overcome limitations of inbreeding depression and to exploitgeneral and specific combining ability effects in autotetraploid populations.Allelic selection entails the minimization of non-additive genetic effects byselecting among full-sib families (F1) which are at uniform levels ofheterozygosity. Such F1 lines are developed by crossing individuals fromtwo unrelated random mating populations. Selected F1 lines wereintercrossed to form an improved population. Eight random matingpopulations of alfalfa were developed to study the effectiveness of allelicselection. Selection for increased dry matter yield resulted in alfalfapopulations with 38 percent greater yield than the parent populations. Twocycles of intercrossing, among selected F1 lines, did not dissipate the gainfrom selection. This result has important implications for synthetic cultivardevelopment in which a major limitation is the decline in productivity withadvancing generations of seed increase. A positively correlated response toselection for dry matter yield was observed for plant height and stemdiameter. The results of this research indicate that continued testing of theallelic selection scheme is warranted and could have a significant impact onthe breeding of autotetraploid alfalfa, particularly for synthetic cultivardevelopment.     

Rye doubled haploids as a research and breeding tool – a practical point of view

Doubled haploid (DH) plants were produced using anther culture from out‐crossing rye, including breeders’ lines, cultivars and F₁ plants with DH parents, to examine the feasibility of using the DH technique for breeding and specifically for developing mapping populations. Only 10–36% of green regenerants produced via anther culture were suitable for research or breeding purposes because of low survival rate or low fertility. Spontaneously arising DH regenerants were more often fertile compared with the colchicine‐treated ones. The fertility of spontaneous DHs varied from sterile to half that found in a normal rye population, which has implications for the design of a crossing scheme and subsequent anther culture. In the reciprocal crosses within one DH population, fertility was the lowest observed, probably because of self‐incompatibility factors, whereas in the DH crosses with normal heterozygous cultivars fertility was the highest. Two mapping populations using DHs were established, the first for out‐crossing rye it would seem. These populations will be used for mapping two important traits, the semi‐dwarf growth habit and preharvest sprouting resistance in rye.     

Outlines of the oil palm breeding programme in Portuguese Guinea

The methods and techniques of oil palm selection and breeding are discussed in relation to the problems of the oil palm industry in Portuguese Guinea.A general survey of the oil palm populations, both cultivated and natural palm groves, was carried out in order to determine existing varieties, their distribution, range of variability, disease incidence and palm oil quality.Yield was established as the major aim in the breeding programme. Short-stem habit and adaptability to different sets of conditions are also considered.Both a long-term and a short-term project are undertaken simultaneously.The long-term programme includes selection of Deli female parents, pollen and seed introductions from pisifera and tenera palms selected in San Thome and single crosses among selected parents. Emphasis is laid on the Deli × pisifera cross to increase oil content, though Deli × tenera and Deli × Deli seed are also produced.The short-term programme involves multiple crosses. A number of mass-selected Deli palms is pollinated using pollen from pisifere or tenera palms selected in San Thome. As a result of the short-term programme over 450,000 hybrid seeds were produced up to the end of 1964.Abbreviations INEAC Institut National pour l'Étude Agronomique du Congo Belge - IRHO Institut de Recherches pour les Huiles et Oléagineux - MEAU Missão de Estudos Agronómicos do Ultramar - WAIFOR West African Institute for Oil Palm Research     

Estimation of genetic parameters and prediction of breeding values in an autotetraploid blueberry breeding population with extensive pedigree data

The strategy for breeding blueberries has been based on phenotypic selection without accounting for pedigree correlation information. A central premise of classical quantitative genetics is that through knowledge of the relationships among individuals in a population, we can make inferences about breeding values (BVs), estimate genetic parameters, and support phenotypic selection. Genetic evaluations using best linear unbiased prediction (BLUP) and restricted maximum likelihood (REML) are founded on pedigree information and have been the standard method used in livestock and forest breeding. Despite theoretical and practical benefits, their application in blueberry breeding programs remains unexploited. The objective of this study was to evaluate the use of REML/BLUP in the University of Florida blueberry breeding program in order to estimate genetic parameters and predict BVs of primary selection traits. To do this, we collected phenotypic data for eight selectable traits (yield, flower bud density, fruit weight, fruit firmness, fruit diameter, fruit soluble solids, fruit pH, and fruit scar diameter) from 1996 individuals. The highest narrow-sense heritabilities were found for fruit weight, scar diameter, and yield. The majority of genetic correlations between traits were under 0.20. The largest genetic gain was achieved when selections from early stages were used as parents and the top 5% of the population was selected. Compared to traditional phenotypic selection, our results are evidencing of the importance of implementing REML/BLUP to estimate genetic parameters that help and support the breeding strategy and maximize genetic gains.     

Heritability of fruit shape in pears

Heritabilities for each of three different height and width ratios describing fruit shape were estimated from measurements on a population of seedlings comprising 17 families of European and Asian pear parentage in the Hort Research pear cultivar breeding programme. In families with European cultivars as parents, the pyriform curvature in the upper, or stem end, half of the fruit was also quantified and heritabilities estimated. Heritabilities were computed using parent-offspring regression and from consideration of the variance components. Heritabilities estimated from parent-offspring regression were generally high and higher than those estimated from variance component analysis, although within the limits of error. Heritability estimates for the height: maximum width ratio were > 0.5 by both methods of estimation indicating that fairly rapid genetic gain could be expected. This revised version was published online in July 2006 with corrections to the Cover Date.     

Adaptation of tropical maize germplasm to temperate environments

Maize (Zea mays L.) is one of few crops that can offer significant genetic gains with the utilization of genetic diversity. Genetically broad-based germplasm has the potential to contribute useful and unique alleles to U.S. Corn Belt breeding programs not present in current U.S. genome sequences (e.g. B73, NAM, etc.). Our objectives were to determine if unique tropical genetic materials have been effectively adapted to temperate environments and how their agronomic performance was relative to adapted populations. An important long-term objective of the Iowa and North Dakota maize breeding programs has been, in addition to the typical elite by elite line pedigree selection cultivar development process, to adapt exotic and unique germplasm, maximize their genetic improvement, and develop unique products for breeding and commercial uses. Stratified mass selection methodology for earliness has been utilized for the adaptation of tropical and temperate populations to Iowa and North Dakota environments. This method has allowed screening of up to 25,000 genotypes per population cycle at a rate of one cycle per year. In addition, the estimated cost per year our programs had for the adaptation of each population was less than $2,000 which could successfully be applied in any breeding program across the globe. This cost has been less than 1 % of the total cost for finding minor genes on the same trait. Our results showed the successful adaptation of exotic populations was independent from genetic background. We can speculate there are a few major genes responsible for most of flowering date expression. We encourage the use of technology to target traits according to their genetic complexity. Stratified mass selection at the phenotypic level has been successful. Each of the populations with either 25 of 100 % tropical germplasm are available for anyone who may desire to expand the germplasm base of their breeding programs with tropical germplasm adapted to temperate mid- and short-season U.S. Corn Belt environments.     

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.     

Combining ability analysis and correlation between breeding values in true potato seed

True potato seed (TPS) requires the selection of appropriate parents for developing hybrid offspring. Parents for routine crossing schemes need to be selected according to their combining ability. Hierarchical and factorial mating designs provide a mean values to assess the general combining ability (GCA) of clones included in crossing schemes. Furthermore, specific combining ability (SCA) may be investigated using the factorial mating design. The aim of this research was to determine the combining ability of clones included in early and intermediate TPS breeding populations developed by the Centro Internacional de la Papa (CIP). Likewise, correlations between breeding values (or additive genetic correlation, p_A) were calculated. Two hierarchical mating designs (in both the early and intermediate populations) and one factorial mating design (in the intermediate population) were evaluated in two contrasting Peruvian locations (La Molina ‐ coastal desert, and San Ramon, warm humid tropics). Plant and tuber characteristics were recorded in these experiments. Significant GCA was observed for tuber yield in all experiments. The male's p_A between plant vigour after transplanting and tuber yield was significant, thereby suggesting that offspring with early vigorous growth are high yielding. Plant vigour was also correlated with tuber set, but only among the breeding value of female parents, which suggests that high tuber yield could be achieved because offspring with early, vigorous growth have many tubers. High tuber yielding hybrids can be obtained by choosing parents with significant GCA, whose tuber yield can also be further enhanced if the crosses have a significant SCA.     

中国野生大豆群体农艺加工性状与SSR关联分析和特异材料的遗传构成

选用204对SSR标记对全国野生大豆群体(174份代表性样本)的基因组扫描,采用TASSEL软件的GLM (general linear model)方法对百粒重、开花期、成熟期、干豆腐得率、干豆乳得率和耐淹性性状值关联分析,解析与性状关联位点的优异等位变异,鉴别出一批与农艺、加工性状关联的优异等位变异及携带优异等位变异的载体材料;进一步分析极值表型材料的遗传构成。结果表明: (1)累计51个位点(次)与性状关联,有些标记同时与2个或多个性状相关联,可能是性状相关的遗传基础;关联位点中累计16位点(次)与连锁分析定位的QTL一致;(2)与地方品种群体和育成品种群体的关联位点比较,发现野生群体关联位点只有少数与之相同,群体间育种性状的遗传结构有明显差异。(3)与多性状关联的位点其等位变异对不同性状的效应方向可相同可不同,如GMES5532a-A332对百粒重和耐淹性的相对死苗率都是增效效应,而GMES5532a-A344对百粒重是减效效应,对相对死苗率是增效效应;(4)极值表型材料间的遗传构成有很大差异。表型值大的材料携带较多增效效应大的位点等位变异,例如N23349的百粒重是9.08 g,含有4个增效效应较大的位点等位变异;表型值小的材料携带较多减效效应大的位点等位变异,如N23387的百粒重是0.75 g,含有4个减效效应较大的位点等位变异。关联作图得到的信息可以弥补连锁定位信息的不足,尤其是全基因组位点上复等位变异的信息为育种提供了亲本选配和后代等位条带辅助选择的依据。     

Screening for Fusarium resistance in seedling populations of Asiatic hybrid lily

A test to select Fusarium resistant seedlings of the Asiatic hybrid lily is described. Young seedlings of 28 populations, obtained from an incomplete diallel between eight parents with different levels of Fusarium resistance, were tested for resistance. Significant differences in Fusarium resistance between and within populations were detected. The average percentage of selected seedlings ranged from 34% in resistant × resistant crosses to 2% in susceptible × susceptible crosses. Although resistant descendants were obtained in susceptible × susceptible crosses, using at least one resistant parent produced higher percentages of resistant seedlings. The resistance level of the parents correlated highly with the general combining ability for Fusarium resistance based on the seedling test. For eight populations, seedlings selected for Fusarium resistance and non-tested (control) seedlings of the same cross were compared, after propagation, in a clonal test. Variation between and within populations, found at seedling level, was confirmed at clonal level. A positive selection response was found for all eight populations. In the seedling test, approximately 18% of the seedlings were selected as resistant of which 15% (2.7% of seedlings tested) appeared to be susceptible escapes. Comparison between selection at seedling level and at clonal level indicated that approximately 25% of the seedlings tested were missed (rejected resistant plants) in the seedling test. The practical use of a seedling test for Fusarium resistance in lily breeding programs is discussed.     

Translation of continuous artificial selection on phenotype into genotype during rice breeding programs

Understanding genetic diversity among local populations is a primary goal of modern crop breeding programs. Here, we demonstrated the genetic relationships of rice varieties in Hokkaido, Japan, one of the northern limits of rice cultivation around the world. Furthermore, artificial selection during rice breeding programs has been characterized using genome sequences. We utilized 8,565 single nucleotide polymorphisms and insertion/deletion markers distributed across the genome in genotype-by-sequencing for genetic diversity analyses. Phylogenetics, genetic population structure, and principal component analysis showed that a total of 110 varieties were classified into four distinct clusters according to different populations geographically and historically. Furthermore, the genome sequences of 19 rice varieties along with historic representations in Hokkaido, nucleotide diversity and F_ST values in each cluster revealed that artificial selection of elite phenotypes focused on chromosomal regions. These results clearly demonstrated the history of the selections on agronomic traits as genome sequences among current rice varieties from Hokkaido.     

Advanced cycle pedigree breeding in sunflower. I: Genetic variability and testcross hybrid performance for seed yield and other agronomic traits

As a plant breeding programme matures there is a general tendency to recycle elite inbred parents, a strategy known as advanced cycle pedigree breeding. The challenge with this approach is not only to maintain genetic variability in the base breeding populations but also their usefulness for further genetic advancement in developing experimental hybrids with better performance than the commercial hybrids on the market. To assess the genetic variability and usefulness of breeding populations in sunflower (Helianthus annuus L.), 109 new inbred lines across four breeding populations Pop1, Pop2, Pop3 and Pop4 in advanced cycle pedigree breeding scheme were testcrossed to two testers to form testcross hybrid (TCH) groups: Pop1_TC, Pop2_TC, Pop3_TC and Pop4_TC. Moderate to high genetic variability along with high heritability were obtained for seed yield and oil yield within and across all TCH groups. Heritability for oil content was low to high ranging from 0.36 (Pop2_TC) to 0.81 (Pop1_TC). Genetic advance (GA%) with a 10 % selection intensity ranged from 36 % (Pop2_TC) to 42 % (Pop1_TC) for seed yield; 38 % (Pop3_TC) to 43 % (Pop1_TC) for oil yield; and 1.3 % (Pop2_TC) to 5.1 % (Pop1_TC) for oil content. To quantify the commercial potential of experimental TCHs, founder parent heterosis (FPH), mid-standard heterosis (MSH) and high standard heterosis (HSH) were calculated. Out of a total of 218 experimental TCHs evaluated, 28 had positive FPH, MPH and HSH values for oil yield representing a 13 % selection intensity as is usually applied in early generation testing.     

Proof of concept to unmask the breeding value of genetic resources of barley (Hordeum vulgare) with a hybrid strategy

Broadening the genetic base of elite breeding programmes is crucial for further breeding success. The absence of major adaption genes, however, often masks the grain yield breeding value of genetic resources. We assessed the ability of a hybrid strategy to provide unbiased performance estimates of 21 barley genetic resources. By crossing them to elite tester lines, 25 three-way hybrids were produced and evaluated together with a part of their parents and eight elite hybrids for important agronomic traits in replicated field trials in four environments. The phenotypic data analyses revealed that the hybrid strategy facilitated to identify promising resources by substantially improving lodging resistance. Combining genotypic data for 5,562 SNPs with the phenotypic data highlighted the potential to boost the diversity of the elite breeding pool via targeted introgression of genetic resources into the male and female heterotic pools. We propose an application of the hybrid strategy for genetic resources of entire genebank collections and to use genome-wide predictions to support a targeted choice of accessions with high value for barley breeding.