Recurrent Selection Program Research Articles

Research Article Genetic diversity as an additional selection criterion in a carioca common bean recurrent selection program for resistance to common bacterial blight

Common beans are a key source of protein and are consumed daily by most of the Brazilian population. More than 70% of what is consumed in this country is classified as carioca beans, based on seed qualities and appearance. We evaluated progenies of carioca common beans of the Brazilian agriculture research agency (Embrapa) recurrent selection program. This recurrent selection program is based on resistance to common bean bacterial blight (CBB), seed yield, and other important agronomic traits. Selection also considers the genetic representativeness of the parents and the genetic diversity among phenotypically selected progenies. Initially, 60 superior progenies were selected based on resistance to CBB and on seed type, in two locations (Santo Antonio de Goias, GO and Ponta Grossa, PR). These progenies were evaluated in the C0S0:2 generation in field trials in six locations during the rainy growing season. A randomized block experimental design was used with two replications, in plots of two 3-m rows spaced at 0.5 m. The most promising C0S0:3 progenies for combined agronomic performance in the different environments were selected and were then evaluated by means of 24 microsatellite molecular markers for the purpose of determining the genetic representativeness of their parents and the genetic diversity among them. The phenotypic data was subjected to analysis of variance for each trait in each of the environments, and then joint analyses were performed. To estimate genetic diversity among the progenies, the Rogers-W genetic distance was used, and a dissimilarity matrix was used to construct a dendrogram of genetic distances through the UPGMA method. Among the 60 C0S0:2 progenies that were evaluated, those that stood out for resistance to CBB also stood out for seed yield and for resistance to other diseases. Various progenies were superior, exhibiting large genetic distances between each other and in relation to the parents. This indicates a possibility of direct and indirect gains from the recurrent selection program. This molecular information will help direct selection of individuals for future recombination cycles.

Assessing Prediction Models for Different Traits in a Rice Population Derived from a Recurrent Selection Program

Genomic selection (GS) is a promising approach to improve rice (Oryza sativa L.) populations by using genome‐wide markers for selection prior to phenotyping to estimate breeding values. In this study, our objectives were to compare certain prediction models with different structures of genetic relationship and statistical approaches for relevant traits in rice and to discuss some implications for integrating GS into a recurrent selection program of irrigated rice. We assessed nine models in terms of predictive potential, using empirical data from S1:3 progenies phenotyped for eight traits with different heritabilities and genotyped with 6174 high‐quality single nucleotide polymorphism markers. For all traits, marker‐based models outperformed prediction based on pedigree records alone. A similar level of accuracy was observed for many models, although the level of prediction stability and prediction bias varied widely. Random forest was slightly superior for less complex traits, although with high prediction bias, whereas the semiparametric RKHS method (reproducing kernel Hilbert spaces) was superior for many traits, showing high stability and low bias. Bayesian variable selection method Bayes Cπ showed acceptable accuracy and stability for several traits and thus could be useful for genomic prediction aiming at persisting accuracy for a long‐term recurrent selection.

Single‐Step Reaction Norm Models for Genomic Prediction in Multienvironment Recurrent Selection Trials

In recurrent selection programs, progeny testing is done in multienvironment trials, which generates genotype × environment interaction (G × E). Therefore, modeling G × E is essential for genomic prediction in the context of recurrent genomic selection (RGS). Developing single‐step, best linear unbiased prediction‐based reaction norm models (termed RN‐HBLUP) using data from nongenotyped and genotyped progenies, can enhance predictive accuracy. Our objectives were to evaluate: (i) a class of RN‐HBLUP models accommodating combined relationship of pedigree and genomic data, environmental covariates, and their interactions for prediction of phenotypic responses; (ii) the predictive accuracy of these models and the relative importance of main effects and interaction components; and (iii) the influence of different grouping strategies of genetic–environmental data (within selection cycles or across cycles) on prediction accuracy of the merit for untested progenies. The genetic material comprised 667 S1:3 progenies of irrigated rice (Oryza sativa L.) and six check cultivars. These materials were evaluated in yield trials conducted in 10 environments during three selection cycles. Genomic information was derived from single‐nucleotide polymorphism markers genotyped on 174 progenies in the third cycle. We evaluated six predictive models. Environmental covariates and G × E interaction explained a significant portion of the phenotypic variance, increasing accuracy and decreasing the bias of phenotypic prediction. Within‐cycle data were sufficient for accurate prediction of untested progenies, even in untested environments. We concluded that the RN‐HBLUP model, with the comprehensive structure, could be useful in improving the prediction accuracy of quantitative traits in RGS programs.

Genetic progress in popcorn recurrent selection by a multivariate mixed-model approach

ABSTRACT Recurrent selection is a viable alternative for popcorn breeding. However, frequent verification of progress attained is required. The aim of this study was to estimate the genetic progress attained for popping expansion (PE) and grain yield (GY) after four cycles of recurrent selection and to compare this progress with the expected progress estimated at the end of each cycle while considering the genetic relationships between the progenies via univariate and multivariate mixed-model approaches. To estimate the genetic parameters and gains from indirect selection, cycles 1, 2, 3, and 4 of a UFLA population were used. To estimate the genetic gains achieved, the following cycles were used: UFLA (original) and cycles 0, 1, 2, 3, and 4, evaluated in three environments. The multivariate approach provided more accurate estimates than did the univariate approach. There was genetic gain for PE in the recurrent selection program. In contrast, gain was not observed for GY using the different estimation strategies.

DIALLEL ANALYSIS OF TOLERANCE TO DROUGHT IN COWPEA GENOTYPES

ABSTRACT The low use of technologies by farmers and the occurrence of biotic and abiotic stresses are limiting factors for cowpea production in the Brazilian Northeast region. The tolerance of genotypes to drought is an alternative to decrease the negative effects of stresses on cowpea production. Thus, the objective of this work was to identify parents and combinations of cowpea genotypes with high probability of generating segregating populations with tolerance to drought. Six cowpea genotypes were crossed in a complete diallel cross design, totaling 30 F2 populations, which were evaluated together with their parents in an experiment under water deficit at the experimental field of the Embrapa Mid-North, Teresina, State of Piauí, Brazil. A triple lattice incomplete block experiment design was used, with three replications, with experimental plot consisting of six 2-m plant rows. Fifteen plants per plot were sampled to evaluate their agronomic characteristics, whose results were subjected to analysis of variance and means were used to estimate the general and specific combining abilities. The genotypes showed significant differences in all characteristics evaluated, denoting the genetic variability of the population. The additive effects were more important than the non-additive effects, and maternal inheritance was detected. The genotypes BRS Xiquexique, Pingo-de-Ouro-1-2 and MNC99-510F-16-1 were the most promising for use in recurrent selection programs for tolerance to water deficit. The hybrid combinations (1) BRS Paraguaçu X (4) CNCx-698-128G, (2) Pingo-de-Ouro-1-2 X (3) BRS Xiquexique, (3) BRS Xiquexique X (5) Santo-Inácio, (4) CNCx-698-128G X (6) MNC99-510F-16-1 and (5) Santo-Inácio X (4) CNCx-698-128G showed potential for generating superior lineages regarding bean production and tolerance to water deficit.

<b>Population structure and impact of recurrent selection on popcorn using EST-SSR markers

The success of any recurrent selection program depends on the genetic variability of the evaluated population, which is used to refer to the diversity of existing alleles at many genetic loci. Thus, the goal of the present study was to investigate the impact of recurrent selection across nine cycles of a UENF-14 popcorn population through the analysis of genetic diversity and structure using microsatellite markers (EST-SSRs). Genomic DNA was extracted from young leaves of 25 individuals from each cycle (C0, C1 C2, C3, C4, C5, C6, C7, and C8), totaling 225 samples from the UENF-14 population. Fifty EST-SSR markers were used for the analysis of genetic diversity across the recurrent selection cycles, 16 of which were polymorphic. Thirty-four alleles were detected, with an average of 2.13 alleles per locus. Throughout all the recurrent selection cycles, there was a reduction in heterozygosity and an increase in inbreeding. The population structure showed a sharing of alleles, inferring that some may be directly related to the main selection characteristics.

Quantitative Trait Loci Mapping of Western Corn Rootworm (Coleoptera: Chrysomelidae) Host Plant Resistance in Two Populations of Doubled Haploid Lines in Maize (Zea mays L.).

Over the last 70 yr, more than 12,000 maize accessions have been screened for their level of resistance to western corn rootworm, Diabrotica virgifera virgifera (LeConte; Coleoptera: Chrysomelidae), larval feeding. Less than 1% of this germplasm was selected for initiating recurrent selection or other breeding programs. Selected genotypes were mostly characterized by large root systems and superior root regrowth after root damage caused by western corn rootworm larvae. However, no hybrids claiming native (i.e., host plant) resistance to western corn rootworm larval feeding are currently commercially available. We investigated the genetic basis of western corn rootworm resistance in maize materials with improved levels of resistance using linkage disequilibrium mapping approaches. Two populations of topcrossed doubled haploid maize lines (DHLs) derived from crosses between resistant and susceptible maize lines were evaluated for their level of resistance in three to four different environments. For each DHL topcross an average root damage score was estimated and used for quantitative trait loci (QTL) analysis. We found genomic regions contributing to western corn rootworm resistance on all maize chromosomes, except for chromosome 4. Models fitting all QTL simultaneously explained about 30 to 50% of the genotypic variance for root damage scores in both mapping populations. Our findings confirm the complex genetic structure of host plant resistance against western corn rootworm larval feeding in maize. Interestingly, three of these QTL regions also carry genes involved in ascorbate biosynthesis, a key compound we hypothesize is involved in the expression of western corn rootworm resistance.

Genetic characterization of the 28 maize landraces in Paraná State

The characterization of maize landraces is extremely important in breeding programs for use of these genotypes as sources of genetic variability. The objective of this study was to quantitatively characterize 28 populations of maize landraces from the state of Paraná using the estimates of the effects of varieties and heterosis parents and the general combining ability, thereby assessing the main agronomic traits. In the crop of 2008/09, 56 inter-varietal hybrids, obtained through a topcross, 28 populations of maize landraces and three check varieties were evaluated for female flowering (FF), plant height (PH), ear height (EH) and grain mass (GY). The treatments were evaluated in a randomized block design, with two replications, at three Paraná State locations: the Experimental Center of the Agronomic Institute of Paraná in Londrina (IAPAR) and the experimental units of Pato Branco and Ponta Grossa. The data were submitted to an analysis of variance, considering a fixed model for genotypes and a random model for environments; the averages grouped by the Scott-Knott test, along with intersections of topcrosses, were analyzed according to a readapted model proposed by Oliveira et al. (1997). According to estimates of the parental effects, the GI 133 population showed the most promising estimates for all characteristics. The GI 088 and GI 173 populations stood out with promising estimates of the effects of heterosis. The conclusion is that the populations GI 133 and GI 173 may be indicated for recurrent selection programs or participation in obtaining composites.

New strategy for evaluating grain cooking quality of progenies in dry bean breeding programs

The methodology available for evaluating the cooking quality of dry beans is impractical for assessing a large number of progenies. The aims of this study were to propose a new strategy for evaluating cooking quality of grains and to estimate genetic and phenotypic parameters using a selection index. A total of 256 progenies of the 13thcycle of a recurrent selection program were evaluated at three locations for yield, grain type, and cooked grains. Samples of grains from each progeny were placing in a cooker and the percentage of cooked grains was assessed. The new strategy for evaluating cooking quality was efficient because it allowed a nine-fold increase in the number of progenies evaluated per unit time in comparison to available methods. The absence of association between grain yield and percentage of cooked grains or grain type indicated that it is possible to select high yielding lines with excellent grain aspect and good cooking properties using a selection index.

Genetic diversity among exotic cotton accessions as for qualitative and quantitative traits.

Studying genetic diversity among a group of genotypes is important in genetic breeding because identifying hybrid combinations of greater heterotic effect also increases the chance of obtaining plants with favorable allele combinations in an intra-population selection program. The objective of this study was to compare different types of long and extra-long staple cotton and their genetic diversity in relation to the fiber traits and some agronomic traits in order to grant breeding programs. Diversity analysis among 29 cotton accessions based on qualitative and quantitative traits and joint including qualitative and quantitative traits was performed. Analysis based on qualitative and quantitative traits and joint met the accessions in three, two, and three groups, respectively. The cross between genotypes Giza 59 and Pima unknown was the most promising to generate segregating populations, comprising simultaneously resistance (based on molecular markers) to blue disease and bacterial blight, partial resistance to root-knot nematode, smaller size, in addition to good fiber characteristics. These populations can be used in recurrent selection programs as donors of alleles for development of long-staple cotton genotypes.

Relevance of Additive and Nonadditive Genetic Relatedness for Genomic Prediction in Rice Population under Recurrent Selection Breeding

In genomic recurrent selection programs of self-pollinated crops, additive genetic effects (breeding values) are effectively relevant for selection of superior progenies as new parents. However, considering additive and nonadditive genetic effects can improve the prediction of genome-enhanced breeding values (GEBV) of progenies, for quantitative traits. In this study, we assessed the magnitude of additive and nonadditive genetic variances for eight key traits in a rice population under recurrent selection, using marker-based relationship matrices. We then assessed the goodness-to-fit, bias, stability and accuracy of prediction for breeding values and total (additive plus nonadditive) genetic values, in five genomic best linear unbiased prediction (GBLUP) models, ignoring or not nonadditive genetic effects. The models were compared using 6174 single nucleotide polymorphisms (SNP) markers from 174 S1:3 progenies evaluated in field yield trial. We found dominance effects accounting for a substantial proportion of the total genetic variance for the key traits in rice, especially for days to flowering. In average of the traits, the component of variance additive, dominance, and epistatic contributed to about 34%, 14% and 9% for phenotypic variance. Additive genomic models, ignoring nonadditive genetic effects, showed better fit to the data and lower bias, in addition to greater stability and accuracy for predict GEBV of progenies. These results improve our understanding of the genetic architecture of the key traits in rice, evaluated in early-generation testing. Clearly, this study highlighted the advantages of additive models using genome-wide information, for genomic prediction applied to recurrent selection in a self-pollinated crop

Selection of cowpea populations tolerant to water deficit by selection index

The objective of this work was to use different selection criteria to identify cowpea genotypes tolerant to water deficit to be used in recurrent selection programs aiming to reduce the cowpea crop cycle and improve its productive components. Six cowpea genotypes were crossed in a complete diallel scheme. The experiment was conducted in an incomplete block experimental design in a triple lattice arrangement, with the 30 F2 populations of cowpea. The genetic variability of 10 traits was verified, and the following selection criteria were used: direct and indirect selection, classical index, index based on desired gains, and index based on sum of ranks. The number of days to flowering (NDF), number of days to maturity (NDMD), pod weight (PW), grain weight per pod (GWP) and 100-grain weight (100GW) were classified as primary traits, and the others as secondary. The direct selection based on the pod weight was the most efficient criterion to reduce the crop cycle and improve productive components of the cowpea genotypes subjected to water deficit conditions. The genotypes Pingo-de-Ouro-1-2 × MNC99-510F-16-1, CNCx698-128G × MNC99-510F-16-1, MNC99-510F-16-1 × Pingo-de-Ouro-1-2, Pingo-de-Ouro-1-2 × BRS Paraguacu, Santo-Inacio × Pingo-de-Ouro-1-2, BRS Xiquexique × Pingo-de-Ouro-1-2 and Pingo-de-Ouro-1-2 × Santo-Inacio were the most suitable to be used in interpopulation recurrent selection programs aiming to reduce the crop cycle and improve productive components of cowpea grown under water deficit conditions.

Effects of Plant Density on Plant Growth before and after Recurrent Selection in Maize

Breeding for higher grain yield in maize (Zea mays L.) using increased selection densities has produced varieties that are adapted to grow at higher population densities. While the effects of density on final grain yield and plant phenotypes are well known, how density affects the early‐season growth of the plant has been less studied. The objective of this experiment was to examine the effects of high planting density on the growth of stalk, tassel, and ear shoots in unselected Iowa Stiff Stalk Synthetic (BSSS) and Iowa Synthetic Corn Borer No. 1 (BSCB1) and in populations that have been selected for high grain yield via a reciprocal recurrent selection program. The selected and unselected populations were planted at four densities ranging from 3.23 to 12.92 plant m−2 in six environments near Ames, IA, over 3 yr. Increased planting density affected plant organ growth timing differently in BSSS and BSCB1. High‐density delayed stalk biomass accumulation in BSCB1 but not BSSS and delayed ear shoot and tassel biomass accumulation in BSSS but not BSCB1. Differences in biomass accumulation and partitioning between unselected populations were generally not observed between selected populations, suggesting that selection caused a convergence in growth patterns between the populations. Increased density lowered maximum growth rates for all plant organs, but reduction in growth rate as a result of density occurred at higher density in selected populations than unselected populations.

Association between Grain Yield, Grain Quality and Morpho-physiological Traits along Ten Cycles of Recurrent Selection in Bread Wheat (Triticum aestivum L.)

The objective of the present investigation was to examine the relationships between agronomical behavior and grain quality along ten cycles of a recurrent selection program performed under rainfed condition. Twenty-four lines, four for each one of the 0, 2, 4, 6, 8 and 10 cycles of recurrent selection, were evaluated for two consecutive years (2011 and 2012). The experimental lines were evaluated under conventional (CT) and no tillage (NT) systems. Grain yield and grain weight were determined and harvest index and grain number estimated. Flour protein content, sodium dodecyl sulphate sedimentation (IS-SDS) and lactic acid SRC (LASRC) were considered as end-use quality predictive tests. The Spearman correlation coefficient was used to measure the relationships among yield, its components and grain quality parameters. Within the context of CT, flour protein content was negatively associated with all the agronomic variables. The IS-SDS has a negative association with the grain weight; meanwhile, LASRC associated positively with all the agronomic variables. When wheat was grown in NT, the relationship between IS-SDS and harvest index, like LASRC with all agronomic traits, was positive. Confining the discussion to the CT results, after ten cycles of recurrent selection the highest grain yield achieved was accompanied by a decrease in protein percentage. However, the decrease in the percentage of protein in more advanced selection cycles was offset by an improvement of its quality.

Genetic variation and combining abilities for vigour and yield in a recurrent selection programme for cacao

SUMMARYThe low genetic diversity of cacao germplasm collections in West Africa is often cited as a limitation to further yield improvement of the crop in its major production countries. Twelve clones obtained from first cycle selection for yield and clones available in international genebanks were tested for their combining ability for key agronomic traits by using these as males in crosses with five female clones available in the Seed Gardens in Ghana. Progenies obtained from a North Carolina II (NC II) mating design and standard varieties were planted at two sites that contrast in terms of soil fertility, rainfall total and distribution. Fifty-eight progenies obtained from the 5 × 12 incomplete NC II mating design and six other progenies, of which two were standard varieties, were evaluated at the more favourable location. At the less favourable location, 44 progenies of the NC II mating design and 20 other progenies, including the two standard varieties, were planted. A randomized complete block design with four replications was used at both locations. Progenies with PA 7 as female parent had better seedling survival at the location with poorer production conditions. Low levels of genetic diversity among female clones at 86 single nucleotide polymorphism loci was reflected in larger standard errors for the additive variance due to female parents relative to that due to male parents. Non-additive genetic effects were much larger than the corresponding additive variance components for all traits at each of the two locations. Average yields over the fourth and fifth years after planting ranged from 0·23 to 1·29 t/ha/year. The standard varieties were not among the best progenies for seedling vigour, yield or yield efficiency (yield per unit trunk cross-sectional area (TCSA) per year). Narrow-sense heritability estimates were higher for three estimates of tree vigour (estimated as increase in TCSA) than for yield traits. Heritability for yield efficiency was a moderate ofh2= 0·5 ± 0·23. The study indicates that further yield increments are attainable by selecting and crossing among the early cacao introductions into West Africa.

Effect of Recurrent Selection on Drought Tolerance and Related Morpho-Physiological Traits in Bread Wheat.

Drought is one of the major abiotic stresses affecting wheat yield. A recurrent selection program was conducted to improve the drought tolerance and yield of bread wheat using drought tolerant advanced breeding lines from a drought tolerant x susceptible cross (HI 1500 x HUW 510). The parental lines were evaluated for yield, biomass and harvest index (HI) in addition to the drought adaptive traits like Canopy Temperature (CT), chlorophyll content and Normalized Difference Vegetative Index (NDVI). After three rounds of recurrent selection, the half sib progenies exhibited a marked reduction in CT, chlorophyll content and biomass; whereas improvement was noted for yield, HI and NDVI. Drought tolerance of the half-sib population appeared enhanced as indicated by drought indices and grain yield. Compared to base population, half-sibs showed better HI, grain filling and a significant (17.1%) increase in grain yield under water stress conditions. Cooler canopies and increased early vigour might have contributed to drought tolerance. A favourable combination of gibberellin sensitive and insensitive Rhtalleles was observed in the recombinant progenies. However, increased yield under water stress had a negative trade off in reduction of biomass. The study also identified potential lines with high yield and drought tolerance for subsequent varietal development for water limited areas.

Heterosis y aptitud combinatoria, para rendimiento y calidad forrajera, en poblaciones de maíz.

Twenty-eight crosses among eight populations of maize forage were evaluated in two environments (Celaya, Gto. y Gómez Palacios, Dgo. México) according with yield and quality forage. This study was carry out to determine the heterotic patterns of the populations and to identify the better populations. Sintético Forrajero and Tuxpeño Bajío populations were the best heterotic pattern, which showed the greater diversity for all traits studied. The highest forage yield was showed for cross between this two populations, 30.85 t/ha and 14.6% of heterosis. In addition, the highest general combining ability effect by forage yield over environments was of the Tuxpeño Bajío population. This suggests that Sintético Forrajero and Tuxpeño Bajío populations are the best option to begin a program of recurrent reciprocal selection. The yield of dry matter and protein was not correlated (0.06); besides, protein had very little variation between maiz forage populations.

Germplasm dynamics: the role of ecotypic diversity in shaping the patterns of genetic variation in Lolium perenne.

Perennial ryegrass (Lolium perenne) is the most widely grown temperate grass species globally. Intensive plant breeding in ryegrass compared to many other crops species is a relatively recent exercise (last 100 years) and provides an interesting experimental system to trace the extent, impact and trajectory of undomesticated ecotypic variation represented in modern ryegrass cultivars. To explore germplasm dynamics in Lolium perenne, 2199 SNPs were genotyped in 716 ecotypes sampled from 90 European locations together with 249 cultivars representing 33 forage/amenity accessions. In addition three pseudo-cross mapping populations (450 individual recombinants) were genotyped to create a consensus genetic linkage map. Multivariate analyses revealed strong differentiation between cultivars with a small proportion of the ecotypic variation captured in improved cultivars. Ryegrass cultivars generated as part of a recurrent selection programme (RSP) are strongly associated with a small number of geographically localised Italian ecotypes which were among the founders of the RSP. Changes in haplotype frequency revealed signatures of selection in genes putatively involved in water-soluble carbohydrate (WSC) accumulation (a trait selected in the RSP). Retrospective analysis of germplasm in breeding programmes (germplasm dynamics) provides an experimental framework for the identification of candidate genes for novel traits such as WSC accumulation in ryegrass.

Selection strategies of full-sib families in two landraces corn populations

The objective of this study were to estimate selection, simultaneous selection of independent characters, and genetics gain, in a recurrent selection program of full-sib families in two corn populations. We evaluated 81 families under irrigation of two native populations of Pinto Amarillo of maize numbers

Combining abilities and inbreeding depression in commercial maize hybrids

<p>The objective of this study was to evaluate the combining ability and inbreeding depression of commercial maize hybrids for agricultural traits. Twenty-two commercial maize hybrids, 96 F1 crosses from a partial diallel scheme, 22 S1 populations and 4 controls were evaluated in a 12x12 simples square lattice experimental setup, totaling 144 treatments, in the municipality of Sabáudia (PR), Brazil, for harvests from 2011/2012 and 2012/2013. Three traits were evaluated: grain yield, plant height and ear height. The Griffing method (1956) was applied for the evaluation of the general combining ability (GCA) and specific combining ability (SCA). The 30B39, 30K64 and 30B30 hybrids showed increased yield, 30F53 and P1630 showed reduced plant height and AG9040 and AG7010 showed reduced ear height. These hybrids can be recommended for the extraction of inbred lines and formation of composites followed by intrapopulation selection. The combinations 30B39 x AG8088, 30B39 x AG9045 and P1630 x AG8021 showed desirable SCA effects for grain yield, plant height and ear height and are recommended for use in reciprocal recurrent selection programs. High magnitudes of inbreeding depression were verified for yield and lower values for inbreeding depression for plant and ear heights. Thus, strategies are recommended for interpopulation breeding accompanied by inbred lines extraction.</p>