Trial heterogeneity and variance models in the genetic evaluation of potato tuber yield

Genetic evaluation aims to identify genotypes with high empirical breeding values (EBVs) for selection as parents. In this study, 2157 potato genotypes were evaluated for tuber yield using 8 years of early‐stage trial data collected from a potato breeding programme. Using linear mixed models, spatial parameters to target greater control of localised spatial heterogeneity within trials were estimated and variance models to account for across‐trial genetic heterogeneity were tested. When spatial components improved model fit, correlations of errors were mostly small and negative for marketable tuber yield (MTY) and total tuber yield (TTY), suggesting the presence of interplot competition in some years. For the analysis of multi‐environment trials, a variance model with a simple correlation structure (with heterogeneous variances) was the most favourable variance structure fitted for TTY and PTY (per cent marketable yield). There was very little difference in model fit when comparing a factor analytic structure of order 2 (FA2) with either FA1 or simple correlation structures for MTY, indicating that simple variance models may be preferable for early‐stage genetic evaluation of potato yield.     

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.     

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.     

Components of Visual Selection in Early Clonal Generations of a Potato Breeding Programme

In the first two clonal generations of a potato breeding programme, clones are visually selected for ‘plant appearance’. Selection for plant appearance based on unreplicated small plots is unreliable, due to significant genotype × environment interaction and high error variance. In order to improve the selection efficiency, component traits of plant appearance were identified and the effect of selection for these components was studied. Tuber yield was found to be the principal component of plant appearance while stolon length and tuber appearance contributed significantly, but to a lesser extent. Tuber yield had a higher heritability than plant appearance. Characters determining the appearance of stolons and tubers were found to have equal or lower heritabilities than plant appearance at 80 days after planting and somewhat higher heritabilities than plant appearance at 145 days after planting. Hence, since the expected and observed selection responses of the component characters have been found to be equivalent to that of plant appearance, selection for plant appearance cannot be improved upon by separately selecting for characters like tuber yield and tuber appearance.     

Heritability of Coffea canephora yield estimated from several mating designs

Eleven mating designs, 6 top-crosses and 5 North Carolina II, were used to estimate narrow sense, broad sense and within-cross heritability of Coffea canephora yield in Côte d'Ivoire. The objective was to predict achievable genetic gains according to different breeding strategies. Narrow sense, broad sense, family and within-cross heritabilities were 0.32, 0.43, 0.83 and 0.22, on average respectively. The percentage of additivity was high (81% on average). A degree of variation was nevertheless observed for estimates over trials. This was found to be mainly due to parent sampling in each trial. By theoretical computation, the minimum number of parents required to obtain optimum precision was found to be around 30. Predicted genetic gains for yield through clonal selection at a selection level of 1% ranged from 7 to 28% over the best hybrid in each trial, suggesting thus clones still interesting for breeders. The consequences for coffee breeding are discussed.     

A cassava clonal evaluation trial based on a new cassava breeding scheme

Cassava (Manihot esculenta) breeding at the earlier stages so far has been mainly based on a mass phenotypic recurrent selection, as little data is taken. This has resulted in a long breeding cycle and lack of organised information on the breeding values of parental lines used in the breeding programmes. The International Institute of Tropical Agriculture (CIAT) recently initiated a scheme to try and correct this, by introduction of replication and blocking in the clonal evaluation trial (CET) and collection of data on all genotypes at early stages of breeding. The aim of the study was to evaluate a CET using the new breeding scheme. Replicating and blocking of clones improved the accuracy of the data obtained. High broad-sense heritability values, comparable to those at advanced selection stages, were obtained, as environmental effects were minimised. The highest was for harvest index (HI) (0.80), followed by cassava frogskin disease (CFSD) (0.79), dry matter content (DMC) (0.75) fresh and dry root yields (DRY) (0.73), root weight (RtWt) (0.61), number of commercial roots (0.60) and roots per plant (RtPlt) (0.43). DMC, HI and RtWt were identified as important variables in selection and determination of economic yield at early stages of selection.     

Investigation of long-term field experiments on response of breeding lines to common scab in a potato breeding program

Common scab, caused by Streptomyces scabies, is a disease that produces scab-like surface lesions on potato tubers. Testing for susceptibility/resistance of breeding lines at the Potato Research Centre of Agriculture & Agri-Food Canada (AFC) is carried out in a scab nursery maintained at AFC for the annual scab evaluation field trials. A replicated field trial routinely consists of breeding lines from previous testing season(s) plus newly selected lines. Data of scab scores generated from long-term experiments thus formulate an incomplete 2-way table over combinations of breeding lines (genotypes) and trials (years). This requires an advanced statistical method to estimate genetic parameters for evaluation purposes. A data base with 1,435 scab index scores from 344 breeding lines were extracted from 5 years (1995–1999) of field experiments in the scab nursery maintained at AFC. The statistical method Residual Maximum Likelihood (REML) was employed to estimate variance components of the breeding population and Best Linear Unbiased Predictor (BLUP) was used to predict genetic merit of breeding lines. High heritability was obtained from variance components estimated by REML. The BLUP scores of breeding lines provided reliable evaluation of their responses to common scab. Two data base sub-sets were separately formulated from the original data base for those parents and grandparents of the breeding lines having pedigree records available. They were again subjected to REML and BLUP analyses to compare the responses to common scab and identify sources of resistance at the parental and grandparental levels. Two random data sets with equal sized samples of breeding lines were also generated from the over-all data base. The two sets of BLUP scores between corresponding breeding lines and parents showed high association which provides an assessment of the validity of the evaluation process.     

The modifiability of characters important in potato breeding

About 2,600 potato clones of 29 combinations were repeatedly analyzed for some years at a stretch in order to determine the degree of modifiability of both a large number of separate characters and the general impression of underground plant parts on lifting in an early stage, in the mature condition and on assessing tuber samples.The ultimate aim of these investigations was to find out how far strictness is justified when selection is applied in breeding new potato varieties. Therefore correlations between the clonal generations were calculated from the data obtained for the various characters and the general impression. Only those characters for which these correlations are positive and high, i.e. slightly modifiable characters, can be strictly selected. Flesh colour appeared to be slightly modifiable. This also applies to tuber shape and maturity though these characters are somewhat more modifiable. Considerably to even strongly modifiable are eye depth, stolon length, under water weight and sprout length. Foliage type, stolon number, date of emergence and degree of common scab affection are extremely modifiable. The same is true for the general impression in the three stages mentioned above.As the general impression, in which the various separate characters and such characters as tuber number, size and yield are included, is initially decisive as to retention, it cannot but be concluded on the ground of the results obtained by others and the author that on a strict selection the major part of the most valuable individuals will be lost. This can be avoided if the negative selection takes the place of the positive in the first stages, i.e. instead of retaining only the apparently good ones the very poorest clones should be discarded in every selection stage. Not until the number of tubers suffice to lay out statistically justified tests can a change be made from the negative to the positive selection.     

Genetic variance models for the evaluation of resistance to powdery scab (Spongospora subterranea f. sp. subterranea) from long-term potato breeding trials

Breeding for resistance to soil-borne powdery scab in potato is an important component of the integrated management of this disease. Different genetic variance models within a mixed model framework were applied to data from long-term potato breeding trials, for the genetic evaluation of breeding lines. The multi-environment trial (MET) data came from 12 growing seasons (“years”, synonymous with environments) of New Zealand field trials screening for resistance to powdery scab on potato tubers. Pedigree information on a total of 1,031 genotypes was available. Additive components of the genetic effects were important with narrow-sense heritability estimates (and 95 % confidence intervals) from single-year analyses ranging from 0.26 (0.20, 0.44) to 0.57 (0.53, 0.85). Spatial components estimated from the residual plot effects were not important for most years and even when they were significant, estimates were small. In MET analyses, different variance structures for the genetic effects were tested; a homogeneous correlation model (CORH) gave a better fit to the data than a factor analytic FAk model of order (k), 1 and 2. The year-to-year genetic correlation estimate from CORH was 0.81 and compared with a range of 0.59–0.95 estimated from the FA1 model. There was no strong evidence of non-additive genetic effects with zero or boundary estimates for most years. Models which included the pedigree provided a better fit to the data than models that did not include this relationship information. There was no evidence for genetic improvement in resistance for powdery scab on tubers in the breeding population studied. This suggests that selection pressure for resistance in the past has been weak and greater consideration should be given to selecting parents on empirical breeding values to genetically improve breeding populations for resistance to powdery scab.     

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.     

Field screening of soya bean (Glycine max (L.) Merrill) germplasm for aluminium tolerance by the use of augmented design

Summary Selection for aluminium tolerance is necessary to adapt the soya bean crop to vast areas of acid soil in the tropics such as the Brazilian Savannas (Cerrados). The breeding programmes include field testing of large numbers of varieties. The tests are laborious, time consuming and need to be repeated to minimize effects of uncontrolled environmental factors. The present results show that augmented designs are efficient in the identification of Al-tolerant genotypes. These designs (i) allow elimination of soil differences as common causes for error in comparison of entries, and (ii) can be successfully employed in genetic studies and breeding programmes for crop improvement, being more cost effective than fully replicated trials.     

Path analysis of genotype-environment interactions of potatoes exposed to increasing warm-climate constraints

Summary Twenty potato cultivars were tested in replicated trials in three seasons. The weather gradually changed from relatively high humidity and cold air temperatures in February to dry and hot in July. Fresh and dry weights, sucrose, reducing sugar and starch contents were recorded on tubers sequentially harvested over four stages during the growing period of each of the three trials. The data were analyzed for genotype-environment interactions by a path regression model which is composed of a main effect and four multiplicative effects. The model fitted well to the observed data for all traits but reducing sugar. Results of dry tuber weight were used to calculate a heat susceptibility index for each of the cultivars. Four components of the index were identified based on the path model. Comparison of sizes of the components provided information on the degree of response to the environmental stress of each of the cultivars during successive stages of growth. High yielding and heat tolerant cultivars were identified based on the experimental results.     

Correlations within and between characters between and within generations as a measure for the early generation selection in potato breeding

Summary The main objective was to determine the reliability of selection in early generations of a potato breeding programme. To that end data were recorded in the seedling generation, an early and a late harvested experiment of the first clonal generation and the late harvested second clonal generation on up to 30 genotypes of 55 populations from crosses of three Solanum tuberosum ssp. tuberosum cultivars and seven selected S. tuberosum ssp. andigena clones, adapted to the northern temperate zone. Phenotypic correlations were computed per population in almost all possible combinations within and between characters between and within generations. The mean across 55 comparable correlation coefficients was considered to be the best estimate of the relationship concerned.In all four experiments data were collected on number of tubers, tuber yield and mean tuber weight; in the three experiments of the two clonal generations in addition on date of emergence, number of stems, plant height, haulm type, and general impression of the underground plant parts and in the two late harvested clonal generations on date of maturity and under water weight.The results confirmed that general impression which is largely decisive for the selection in early generations, is a little reliable measure. However, from the magnitude of the mean correlations between experiments within characters it must be concluded that selection for most of these separate characters is hardly more reliable. An exception was date of maturity for which a mean correlation was determined of r=0.78 between the two clonal generations. The second strongest mean correlations, perhaps surprisingly, were for tuber yield, viz. r=0.52 between the seedling generation and the late harvested first as well as the second clonal generation and r=0.63 between the late harvested clonal generations. From the correlations between characters it appeared that for a high tuber yield, besides its components, in particular an early emergence, a large plant height, an attractive haulm type and a late maturity are of importance.The main conclusion is that, as long as not enough seed tubers are available for the layout of statistically sound experiments, a negative instead of a positive selection should be applied to avoid the rejection of most of the valuable genotypes in an early stage. On the basis of the results directives for the application of such a negative selection are given.     

甘薯实生系与其无性系性状相关关系及早期选择利用研究

甘暮实生系是分离世代,其性状的变异与资源品种表现同一趋势,与其无性系在诸多性状上呈强弱不同的正相关关系,这是对实生系进行早期选择利用的基础.根据结薯性可将实生系分为成薯、膨大和直根3个类型,成薯系%因组合而异,受环境影响不明显.5年的研究结果证明:无性系类型间的产量性状有明显差异,从成薯类型选育高产新品系的入选率高.在此问题上和美国Granberry.M.等的认识不同.建议把我国甘薯育种的初选期提早到实生系时期,以缩短育种周期,提高育种效率.笔者认为把甘薯杂交种子培育的株系,定名为实生系,比较确切.     

Realized gains from selection for spring wheat grain yield are different in conventional and organically managed systems

Breeding spring wheat (Triticum aestivum L.) specifically for organic production has been suggested by producers and researchers alike. To investigate the effects of management systems on selected spring wheat breeding line performance in multi-location tests in the northern Great Plains, we used a randomly derived population of 79 F6-derived recombinant inbred lines (RILs) from a cross between the Canadian hard red spring wheat cultivar AC Barrie and the CIMMYT derived cultivar Attila. The population, including the parents, was grown on conventionally and organically managed land in 12 environments over 3 years. Direct selection in each management system (10% selection intensity based on grain yield) resulted in three lines being retained in each management system, over the multi-location testing. Gains from 10% selection for grain yield in a ‘selection’ year were 3.4 times greater in conventional multi-site yield trials than in organically managed trials. Two lines (BA 05 and BA 36) ranked in the top 10% of both the conventional and organic selection trial of 2005, remained ranked 2nd and 1st, respectively, under conventional management in multi-site yield trials. However, these lines ranked 53rd and 21st, respectively, for grain yield in the multi-site organic yield trials. Selected lines were each yield stable within the management system in which they were selected. Following replicated multi-location yield trials, three lines from the population (BA 02, 29 and 58) ranked within the highest 10% yielding lines in both conventional and organic systems. The results of this study suggest that selection differences occur across multi-location tests, and that selection for grain yield in organic systems should be conducted within organic systems. It is evident, however, that data obtained from conventional yield trials also has some relevance towards breeding for organic environments.     

Reciprocal effects in true potato seed breeding in short-day length environments

Reciprocal crosses may have significantly distinct performances regarding tuber characteristics in potato, suggesting the importance of cytoplasmic effects in this crop. The selection of parents for true potato seed breeding therefore needs to consider this potential effect when determining the direction of a cross. The aim of this research was to determine whether a broad‐based true potato seed breeding population, developed at the Centro Internacional de la Papa, could be affected by cytoplasmic effects in the short‐day length environments of the tropics. Two random sets of reciprocal biparental crosses were included in the first set of experiments, which were grown in two contrasting Peruvian locations. Only one out of 14 reciprocal crosses showed significantly distinct performance for tuber yield and tuber set. In the second set, only one of each of the 12 reciprocal crosses had distinct performance for vine earliness, days to flowering and flowering intensity, but four of the reciprocal crosses in the second set showed distinct pollen production. The results suggest that cytoplasmic effects in this breeding population are more important for reproductive characteristics such as pollen production than for tuber yield. This finding is not surprising because male sterility in potato results from the interaction between sensitive cytoplasm and dominant nuclear genes.     

Variance component estimations and allocation of resources for breeding sweetpotato under East African conditions

In Africa, average sweetpotato storage root yields are low and breeding is considered to be an important factor in increasing production. The objectives of this study were to obtain variance component estimations for sweetpotato in this region of the world and then use these to determine the efficiency of variety trials and breeding systems. From an incomplete series of variety trials in Kenya and Uganda (comprising 15 genotypes, three locations, two crop durations and three seasons) variance components were estimated ‐ using the REML method ‐ for the following traits: storage root yield, biomass production, harvest index, storage root dry matter and the Elston index which was used to aggregate all four traits. The storage root yield of clones across all 12 environments ranged from 15.2 to 33.0 t/ha. The variance components were significant for all traits, except the genotype by season interactions for storage root dry matter. The efficiency of selection systems was determined for total test capacities of 450 and 900 plots and using not more than five locations. Two‐stage selection was 17‐81% more efficient than one‐stage selection after two seasons of testing. Two‐stage selection was optimized under the restriction of using at least two locations at step 1. Trials with two locations and one replication at step 1 and five locations and two replications at step 2 were appropriate both for selecting for storage root yield and for simultaneously selecting for storage root yield, biomass production, harvest index and storage root dry matter content by using the Elston index. There are indications that such an allocation of resources for breeding sweetpotato is also appropriate for other regions in Sub‐Saharan Africa.     

The potential for early generation selection to identify potato clones with resistance to Verticillium wilt

Verticillium wilt (VW) of potato, caused primarily by the fungus Verticillium dahliae, results in yield loss and is therefore an important soil-borne disease. Resistance to VW exists in potato germplasm and is used by breeders during cultivar development. Breeders could make more rapid progress toward the development of VW resistant clones if they had an effective early generation selection strategy. The purpose of this study was to determine whether selection for VW resistance could be carried out in the first tuber generation on single hills. One hundred and fifty-two clones from 19 families were planted as single hills on a V. dahliae-infested field. Each plant was scored for vine maturity, VW symptom expression, yield, stem colonization (colony forming units (cfu), in dried basal stem segments) and incidence (percent infected stems). In the second clonal generation, which consisted of replicated four-hill plots, stem colonization scores and incidence values were used to identify clones which were more resistant than a moderately resistant cultivar and others which were more susceptible than a susceptible cultivar. The efficiency and reliability of the single-hill selection strategy, based on symptoms and yield, was then determined by comparison to the four-hill results. We determined that the best single-hill selection strategy was negative selection (discard clones with the lowest performance) with low stringency, based on yield.     

Heritability, and Intra- and Inter-Generation Associations Between Tuber Yield and its Components in Potato (Solanum tuberosum L.)

The relative importance of the components of tuber yield in selection in early generations of a potato-breeding programme was studied. In seedling generation the number of tubers were more important than average tuber weight, whereas in clonal generations the average tuber weight was more important. Correlation coefficients between number of tubers and tuber yield varied from generation to generation whereas those of average tuber weight and tuber yield were more or less constant. Unlike the number of tubers, the average tuber weight of a genotype in a generation influenced its tuber yield in subsequent generations. The average tuber weight had higher heritability than the number of tubers and tuber yield.     

Early generation selection for potato tuber quality in progenies of late blight resistant parents

Developing disease resistant cultivars is one of the major objectives for a potato (Solanum tuberosum L.) breeding program, but many resistant clones have not achieved commercial acceptance because of late maturity and non-marketable tuber characteristics. Selection for tuber quality should have greater emphasis inbreeding disease resistant cultivars. The objectives of this study were 1) to evaluate the ability of late blight (Phytophthora infestans (Mont.) de Bary) resistant parents to transmit chip-processing (tuber appearance, specificgravity, and chip-color) or tablestock (tuber appearance) quality to the offspring and 2) to compare selecting for tuber quality in single-hill versus eight-hill generations. We made crosses among eight unadapted potato cultivars (B0718-3,Bertita, Bzura, Greta, Libertas, Stobrawa, Tollocan, and Zarevo) with reported late blight resistance with adapted susceptible cultivars/breeding clones to generate 95populations (4,750 seedlings). Approximately 10% of the progeny from each cross were selected from single-hill plots based on tuber appearance, number, shape, and internal defects. These selected clones (408) were evaluated for tuber appearance, specific gravity, and chip-color. The same evaluations in the following year were made on tuber samples from eight-hill plots. Libertas and Tollocan were the best parents for transmitting chip-color; B0718-3, Zarevo, and Tollocan for transmitting tuber appearance; and Bzura, Libertas, and Zarevo for transmitting high specific gravity to the highest percentage of the offspring. Overall, 50% and 56% of the clones based on single- and eight-hill generation, respectively, were considered to possess chip-processing quality; over 90% of the clones had acceptable tablestock quality. A total of 71% of the clones possessing acceptable chip-processing and 95% of the clones possessing acceptable tablestock quality selected in both generations were identified in single-hill plots. The evaluation of tuber quality characteristics in single-hill generation not only permitted the identification of clones with acceptable chip-processing and tablestock, but also increased the amount of clonal information for the following generation of selection. In crosses between late blight resistant and susceptible clones, selection for tuber quality traits can be initiated in single-hill generation using a moderate selection intensity and precede late blight testing. This revised version was published online in August 2006 with corrections to the Cover Date.