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In recurrent selection programs, progeny testing is done in multienvironment trials, which generates genotype x environment interaction (G x E). Therefore, modeling G x 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 singlenucleotide polymorphism markers genotyped on 174 progenies in the third cycle. We evaluated six predictive models. Environmental covariates and G x 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. [ABSTRACT FROM AUTHOR]

One of the greatest challenges in plant breeding is the selection of parental combinations that will produce progeny that are superior to either parent. The objective of this research was to determine if yield heterosis in the F2 bulk of a soybean [Glycine max (L.) Merr.] single cross is a predictor of significant genetic variance for yield and superior line yields among random inbred lines derived from the F2 generation. In one experiment, thirty-seven F6:7 inbred lines from each of five bi-parental populations along with parents and the bulk F2 generation were yield tested at three locations. Of the five populations, three had significant genotypic variance for yield. The only two transgressive segregating lines came from the population with the greatest genotypic variation for yield and the only one with midparent F2 yield heterosis (15% at P > 0.06). In another experiment, random inbred lines were derived from four single crosses chosen from a seven parent half diallel cross with similar midparent yields. Two exhibited F2 yield heterosis and two did not. Derived F5:6 lines were yield tested in three environments. After adjustment for maturity, both populations derived from the non-heterotic crosses had zero genetic variation. Genetic variance estimates for the two populations derived from heterotic crosses were larger than their standard errors and significant at P > Z = 0.07 and P > Z = 0.05. These experiments provide evidence that F2 bulk heterosis can be a predictor of significant genetic variation among inbred soybean lines derived from a single cross. [ABSTRACT FROM AUTHOR]

Autogamous plant breeders obtain numerous populations annually, and in the progeny selection process, the merit of the population is not considered. Thus, it would be important to have a progeny selection index that includes not only the effects of progenies in the different generations but also the effects of populations in all the generations and the data from parents and the F1 and F2 generations simultaneously. The main objective of this paper was to develop a selection method that encompasses the entire structure of an autogamous plant breeding program including all the data as of the parents, the F1 and F2 generations, and also both the progeny and population effects in the F3 to F6 generations. To do so, a selection index (called selection index with parents, populations, progenies, and generations [SIPPPG]), which includes all these effects, was proposed. Estimators were also derived for computation of the contribution (through indirect heritabilities and selective accuracies) of each source of information for predicting the additive genetic value of the lines to be obtained at the end of the selection process. The new approach was assessed through numerical evaluation and a total index was also obtained using field data derived from a breeding program with the common bean crop. This new index yields gains in selection efficiency ranging from 5 to 28% depending on the relative magnitude of the genetic variation among populations. [ABSTRACT FROM AUTHOR]

Predicting genetic variances of biparental populations has been a long-standing goal for plant breeders. The ability to discriminate among crosses with similarly predicted high means but different levels of genetic variance (VG) should improve the effectiveness of breeding. We developed a procedure that uses established progeny simulation and genomic prediction strategies to predict the population mean (μ) and VG, the mean of the desired 10% of the progeny (superior progeny mean [μsp]), and correlated responses of multiple traits for biparental populations. The proposed procedure, PopVar, is herein demonstrated using a training population (TP) composed of 383 breeding lines that have been genotyped and phenotyped for yield and deoxynivalenol (DON). Marker effects estimated from the TP were used to calculate genotypic estimated breeding values (GEBVs) of 200 simulated recombinant inbred lines (RILs) per cross. Values of μ, VG, and μsp were then calculated directly from the RIL GEBVs. We found that μ explained 82 and 88% of variation in μsp for yield and DON, respectively, and adding VG to the regression model increased those respective R2 values to 99.5 and 99.6%. The results of correlated response revealed that although yield and DON are unfavorably correlated, the correlation was near zero or slightly negative in some simulated crosses, indicating the potential to increase yield while decreasing DON. This work extends the current benefits of genomic selection to include the ability to design crosses that maximize genetic variance with more favorable correlations among traits. PopVar is available as an R package that researchers and breeders are encouraged to use for empirical evaluation of the methodology. [ABSTRACT FROM AUTHOR]

A potential strategy to address the lack of success of North American orchardgrass (Dactylis glomerata L.) breeding programs to increase forage yield and other agronomic traits is the incorporation of novel sources of germplasm. In an attempt to identify novel orchardgrass germplasm sources with agronomic potential, the study described herein characterized 162 half-sib families (HSFs) from six orchardgrass germplasm populations and three orchardgrass cultivars. Study conditions were Millville, UT, and Rexburg, ID, field sites with data collection from 2008 to 2010. The genotype × location interaction variance differed from zero for dry matter yield, crude protein, in vitro true digestibility (IVTD), neutral detergent fiber, and seed weight. Within location broad-sense heritability differed for all traits at both locations (0.36 ± 0.10 to 0.77 ± 0.03) except IVTD at Rexburg. For each trait there were HSFs that possessed values similar to or better than the included check cultivars (CCs). Additionally, in several instances the mean phenotype of the HSFs from a specific family was better than the phenotype of the corresponding parental population and/or the mean phenotype of the CCs. Overall, for each trait there existed sufficient genetic variation to develop an elite orchardgrass breeding program for irrigated conditions. [ABSTRACT FROM AUTHOR]

Hagberg falling number (FN) is an important quality trait used for grain grading. The FN test can only be measured in the late stages of variety development when progeny are homogeneous and sufficient grain is available for testing. The FN is strongly influenced by environmental conditions during reproductive growth stages, including excess moisture, extreme temperature, and biotic and abiotic stresses. The objective of this study was to identify potential genomic regions that influence FN in a subset of 110 hard white spring (HWS) wheat (Triticum aestivum L.) accessions from the National Small Grain Collection (NSGC) using genomewide association mapping. The FN tests were conducted using grain flour samples of these accessions grown in five environments. A total of 1740 single nucleotide polymorphism (SNP) markers were used to detect SNP-FN associations using both the general linear model (GLM) and the mixed linear model (MLM). Thirteen quantitative trait loci (QTL) located in nine chromosomal regions were identified in both GLM and MLM approaches. Pyramiding these QTL could explain up to 45% of the phenotypic variation of FN. The present study identified several potential markers for use in marker-assisted selection for high FN lines in wheat breeding. [ABSTRACT FROM AUTHOR]

Studies in the northeastern United States have shown that the improved cultivars of narrowleaf plantain (Plantago lanceolata L.) do not have sufficient winter hardiness to persist under wintertime conditions typical of that region. However, an experimental line, PG700, developed from productive plants collected from the southern, mid-Atlantic, and midwestern United States had significantly greater survival after freezing than the commercially available cultivars. A field study was initiated in 2006 to select for additional freezing tolerance in PG700. Superior materials collected after twoyears of selection pressure were evaluated in growth chambers for survival after exposure to -11 and -14°C or after exposure to drought that was severe enough to kill all visible leaves. The cultivar Tonic was included as a freezingsusceptible control. Survival of spaced plants of PG700 in the field was high, with mortality rates of 9% following the first winter after transplanting, 26% of the remaining plants after the following summer, and 11% after the second winter. Even with the low selection pressure, progeny of plants selected after the first winter had more than twice the survival rate of the original population when exposed to -14°C. No Tonic plants survived at -14°C. PG700 did not have greater drought resistance than Tonic, nor was its drought resistance improved by the selection process. Increased freezing tolerance will increase the suitability of plantain as a component of perennial pasture mixtures in temperate regions of the United States. [ABSTRACT FROM AUTHOR]

Genomewide selection within an A/B biparental cross is most advantageous if it could be effectively done before the cross is phenotyped. Our objectives were to determine if a general combining ability (GCA) model is useful for genomewide selection in an A/B cross, and to assess the influence of training population size (NGCA), number of crosses pooled into the training population (N×), linkage disequilibrium (r²), and heritability (h²) on the prediction accuracy with the GCA model. The GCA model involved pooling 4 to 38 maize crosses with A and B as one of the parents into the training population for an A/B cross, whereas the same background (SB) model involved pooling crosses between random inbreds. Across 30 A/B test populations, the mean response to selection (R) with the GCA model was 0.19 Mg ha-1 for testcross grain yield, -6 g kg-1 for moisture, and 0.38 kg hL-1 for test weight. These R values with the GCA model were 68 to 76% of the corresponding R values with phenotypic selection (PS). The R values with the SB model were only 15 to 28% of the R values with PS. Increasing the size of the training population with random crosses from the same heterotic group was less important than including crosses with A and B as one of the parents. Prediction accuracy was most highly correlated with h²r²√NGCA and h²r²√N×. Our results indicated that the GCA model is routinely effective for genomewide selection within A/B crosses, before phenotyping the progeny in the cross. [ABSTRACT FROM AUTHOR]

The establishment of a solid heterotic pattern has been beneficial to maize (Zea mays L.) breeding in North America. It has been shown that genetic divergence between heterotic groups has increased over time, but the relative importance of drift versus selection for hybrid performance on the increased divergence is not known. Reciprocal recurrent selection is a systematic method of selection on hybrid performance, where two populations are selected and improved on the basis of the population-cross performance. The University of Nebraska performed a replicated recurrent selection program (UNL-RpRS) for eight cycles of selection. Three replicate programs were conducted in parallel for both reciprocal full-sib selection (RFS) and S1-progeny selection. The objective of this study was to evaluate the effect of selection for hybrid performance on population divergence using the UNL-RpRS as a model system. Genome-wide divergence among the base populations increased over eight cycles of selection. Divergence was not, however, greater among base populations subjected to RFS compared with S1-progeny selection. Moreover, Wright's fixation index (Fst) values among replicate populations within a base population and selection method were as large as Fst values between complementary populations selected for population cross performance using RFS. A small increase in divergence through RFS relative to S1-progeny selection was observed when markers were filtered for high levels of adjacent linkage disequilibrium (LD), but the effect was consistent across replicates. We did not consistently detect effects of selection for hybrid performance on genome-wide divergence between populations, suggesting selection was not a strong force in diverging populations in the UNL-RpRS. [ABSTRACT FROM AUTHOR]

Most research in maize (Zea mays L.) parent- progeny relationships has focused on heterosis for plant grain yield (PGY) determination, whereas nonheterotic effects for traits other than PGY has remained less explored. Our objectives were to analyze (i) frequency distribution and phenotypic plasticity for 29 eco-physiological traits in different genotypic groups (6 inbreds and 12 hybrids) and environments, (ii) parent- progeny relationships for these traits as well as variations in these relationships caused by contrasting growing conditions, and (iii) direct and indirect effects of traits measured in inbreds on hybrid PGY determination. Genotypes were cropped in the field at two contrasting N levels during three growing seasons. Range in phenotypic plasticity was (i) similar for inbreds and hybrids, (ii) largest for traits such as PGY and nitrogen use efficiency (NUE), and (iii) smallest for traits such as time to flowering and kernel weight. Inbred phenotype was usually (26 traits) a good predictor of hybrid phenotype, but analysis of standardized data demonstrated that (i) for nine traits (e.g., PGY, kernel numbers) this relationship was exclusively driven by environmental effects, and (ii) for the other traits there was a true genetic control. A high correlation (r > 0.26; P = 0.024) was established between hybrids PGY and 12 traits measured in inbreds, among which we distinguished NUE and ear growth rate for their high direct effect and participation in the indirect effect of other traits. [ABSTRACT FROM AUTHOR]

To overcome the severe limitation of crop yield that may result from drought, specific plant traits are being explored. Soybean [Glycine max (L.) Merr.] genotypes that express a "slow-wilting" phenotype have been evaluated as sources of useful drought traits. However, the unique physiological characteristic of PI 471938 resulting in slow-wilting progeny and in high-yielding progeny has not been resolved. This study was undertaken to explore the possibility that it may have especially tolerant N fixation activity as soil dries. In fact, greenhouse experiments confirmed this possibility with its N fixation tolerance being among the greatest reported for soybean genotypes. Like other genotypes with N fixation drought tolerance, the accumulation of ureides in its leaves is low compared to a fast-wilting cultivar. Measurements of water status of PI 471938 as compared to the fast-wilting cultivar Benning showed that PI 471938 is able to maintain a greater leaf turgor pressure during soil drying as a result of a lower osmotic potential. [ABSTRACT FROM AUTHOR]

Forage breeding can be extraordinarily complex because of the number of species, perenniality, mode of reproduction, mating system, and a variable genetic correlation between spaced plants and sward plots. Aiming to compare eight forage breeding methods for direct selection gain and correlated response, different scenarios of trait heritability and genetic correlation have been evaluated based on deterministic equations of expected (theoretical) breeding accuracy applied to half-sib progenies evaluated in spaced-plant trails, sward-plot trials, or both. Relative efficiency for each method is given in relation to individual selection. Methods differ most when heritability is lower than 0.3, which coincides with the majority of the situations met by forage breeders. Genetic gain of best linear unbiased prediction (BLUP)-based methods is superior to all other methods for trait heritability lower than 0.3, independent of field-trail plot methods, except for parental selection. Methods based on BLUP have also shown higher efficiency when the genetic correlation between spaced-plant and sward-plot trials evaluations of a trait is lower than 0.7 and indirect-trait heritability is lower than 0.3. The choice of forage breeding method should include consideration of the mode of reproduction and the target-trait heritability. The benefits of BLUP-based selection methods should receive more serious consideration by forage breeders. [ABSTRACT FROM AUTHOR]

Cultivated sorghum [Sorghum bicolor (L.) Moench subsp. bicolor] can interbreed with a feral weedy relative shattercane [S. bicolor nothosubsp. drummondii (Steud.) de Wet ex Davidse]. Traits introduced from cultivated sorghum could contribute to the invasiveness of a shattercane population. An experiment was conducted to determine the potential for pollenmediated gene flow from grain sorghum to shattercane. Shattercane with juicy midrib (dd) was planted in soybean [Glycine max (L.) Merr.] fields during 2 yr in concentric arcs at varying distances from a 0.39 ha sorghum pollen source with dry midrib (DD). The arcs were placed so that prevailing winds would carry sorghum pollen to the shattercane. Seven hundred twenty seeds from each of over 300 shattercane panicles in anthesis during sorghum pollen shed each year were collected. Progeny were evaluated by phenotype to determine rate of hybridization. Hybridization averaged 3.6% within the source in 2008 and 16.0% in 2009 and declined as distance increased. Hybridization as high as 2.6% for an individual panicle was measured at the farthest distance evaluated (200 m). Wind direction and speed were also measured and their product affected hybridization rate for all pollination periods. Results indicate that genes from cultivated sorghum will likely be introduced into shattercane populations at distances of at least 200 m and that rate of hybridization is dependent on weather factors such as wind. Source size is also important in determining hybridization rate but was not studied here. [ABSTRACT FROM AUTHOR]

Cytoplasmic-genic male sterility systems (CMS) help control pollination in carrot and table beet breeding programs and hybrid seed production. A challenge common to these breeding programs is identification of F1 hybrid progeny in crosses where both parents carry normal (N) cytoplasm. Such fertile × fertile crosses often produce both F1 and selfed progeny, making identification of F1 hybrids difficult. Such identification has traditionally been accomplished in carrot and table beet by visually scoring roots using heterosis for size. However, if heterosis is lacking, misidentification can result in systematic errors in the breeding process. We sought to determine how effective visual selection of hybrid progeny is in the context of table beet and carrot breeding programs. We used amplified fragment length polymorphisms (AFLP) markers to genotype parents and progeny in a variety of fertile × fertile crosses. Progeny were also grown in the field and evaluated for hybridity based on visual selection using the phenotype of heterosis for size. Two of five fertile × fertile table beet crosses and three of five fertile × fertile carrot crosses showed highly significant differences between visual selection for hybridity and AFLP marker analysis (p < 0.01). Misidentification of roots as F1 hybrids when they were actually selfpollinated occurred in some crosses as much as 75% of the time. Both type I, a hybrid root scored as an inbred, and type II, an inbred root scored as a hybrid, errors were committed. Across all matings, type I errors occurred on average 40.9% of the time and type II errors occurred on average 8.5% of the time. Type II errors have important consequences because both parents are not represented and recombined in the progeny resulting in further inbreeding. The results of this study indicate that using heterosis for size as a hybrid selection method can be inaccurate for identification of hybrids in certain crosses and may introduce error into breeding programs. [ABSTRACT FROM AUTHOR]

The coefficient of parentage among 121 cultivars of Coffea arabica L. in Brazil released from 1939 to 2009 was estimated and used to study the genetic diversity and the breeding pattern of the breeding programs. A low genetic diversity was observed within the C. arabica cultivars of Brazil. The genetic base of 121 cultivars released in Brazil between 1939 and 2009 was defined by 13 ancestors. Seven ancestors contribute with 97.55% of the genetic base of C. arabica cultivars. Bourbon Vermelho contributed with 52.76% for the genetic pool of the C. arabica cultivars of Brazil followed by Sumatra (19.05%) and Híbrido de Timor (11.59%). Mundo Novo and Icatu Vermelho contributed with 87.65% for the genetic base of the C. arabica cultivars. It was calculated that 97.55% of the genetic base of the Brazilian C. arabica cultivars is derived from seven ancestors, indicating a narrow genetic base. Among the first progenies, Mundo Novo contributed with 69.39% of the genetic base of C. arabica cultivars in Brazil. The increase in the genetic diversity among C. arabica cultivars observed in recent decades is due to the introduction of parental lines with diverse genetic base. High genetic diversity was observed among cultivars released by Empresa de Pesquisa Agropecuária de Minas Gerais/Universidade Federal de Viçosa, Fundação Procafé, and Instituto Agronômico do Paraná. The 121 Brazilian cultivars were clustered into four groups based on coefficient of parentage. The distributions of genotypes over the cluster groups showed the effect of parental line contribution. [ABSTRACT FROM AUTHOR]

Cultivated soybean [Glycine max (L.) Merr.] is a major source of oil and protein in global food production. As demand for soy-based products increases, it is essential for breeders to find ways to increase yield beyond conventional methods. Alternative methods of cultivar development and improvement must be identified. Our objectives were to determine if the ms9 locus conferring male sterility in soybean was environmentally sensitive and, if it were, to determine which environments could be used in hybrid seed production. This was accomplished through characterization of pollen phenotypes and selfed seed set among progeny of soybean genotype T359H (Genetic Type Collection number T359H), a heterozygous maintainer line for the ms9 locus. T359H was evaluated in seven environmental regimens in growth chamber experiments. We used a split-plot design to test the effect of temperature regimens and male-sterile phenotypic classifications within chambers. As day temperature increased from 30 to 35°C, selfed seed set on male-sterile, female-fertile plants decreased. Conversely, night temperature affected neither fertile nor male-sterile, female-fertile selfed seed set. This suggests that ms9 can be used in hybrid seed production in controlled environments where day temperature is 35°C during the flowering. These temperature conditions and their effect on ms9 may provide an alternative method to produce hybrid seed in soybean cultivar development programs. [ABSTRACT FROM AUTHOR]

The value of milled rice (Oryza sativa L) depends on the percent whole versus broken kernels after milling. Kernel fissures caused by pre- or postharvest stresses are the leading cause of breakage on milling. 'Cypress' is known to be more fissure resistant (FR) than most cultivars, but breeding success has been limited by a lack of ability to identify FR among F2 and F3 progeny. An induced-fissuring method wherein small samples of seed are evaluated for fissure rates after controlled exposure to humid laboratory conditions can distinguish FR among purebreeding rice cultivars. To measure the efficacy of the induced-fissuring system for evaluating FR among segregating breeding progeny, we applied divergent selection for FR and fissure susceptibility (FS) on seed harvested from -300 Cypress (FR) x 'LaGrue' (FS) F2 plants and evaluated selection success using seed from F2:3 plants grown in Arkansas and Texas. A second round of divergent selection was made among F3 progeny followed by F3:4 progeny testing. Fissure susceptible F2:3 progeny fissured twice as much as FR progeny, with an average response to selection of 13.5%. Response to F3 selection was smaller (averaging 2.6%), suggesting some fixation of alleles due to the F2 selections. Narrow-sense heritabilities (h2) were 0.54 and 0.73 for the FR and FS F2 selections, respectively. This study documented successful early-generation selection for FR, opening new opportunity for breeders to develop rice cultivars improved for this important trait. [ABSTRACT FROM AUTHOR]

Demand for high-quality cotton (Gossypium hirsutum L.) in international markets has increased the demand for improved fiber quality in U.S.-grown cultivars. In an effort to meet this demand, cotton plant breeders seek alleles related to improved fiber quality. This study was conducted to evaluate fiber quality traits in a diallel analysis of eight cotton genotypes to determine genotypes with the greatest potential for improvement of fiber quality. Genotypes included four experimental extra -long staple (ELS) lines, A-106-8 ELS, B-147-21 ELS, B-182-39 ELS, and C-155-22 ELS, and four cultivars, 'Deltapine 491' (PI 618609), 'Deltapine 50' (PI 529566), 'FiberMax 832' (PI 603955; Constable et al., 2001), and 'Tamcot CAMD-E' (PI 529633; Bird, 1979). Parents and F1 progeny were grown in replicated trials at the Texas AgriLife Research Farm near College Station, TX, in 2007 and 2008. Significant (p < 0.05) genotype × year (G×Y) interactions were observed for all traits. Significant (p < 0.05) general combining ability (GCA) effects and specific combining ability (SCA) effects were found for most fiber quality traits measured as well as lint percent. Combining ability effects varied by year, which is reflected in significant general combining ability × year (GCA×Y) and specific combining ability × year (SCA×Y) interctions. Extra-long staple experimental lines from the Texas A&M University breeding program had the greatest potential for improving fiber length and strength as indicated by GCA. [ABSTRACT FROM AUTHOR]

Pollination bags for making controlled crosses between switchgrass (Panicum virgatum L.) plants were made from a polyester micromesh fabric with a mesh size of 41 μm, which is smaller than the mean reported 43 µm diameter of switchgrass pollen. When used in paired-plant crosses between switchgrass plants, the mean amount of seed produced per plant was about 1 g, or approximately 800 seeds, which was significantly greater than the 10 to 250 seeds produced previously in paired-plant crosses of switchgrass using paper pollination bags. The four- to tenfold increase in seed produced per cross enables the progeny of the crosses to be evaluated in larger numbers in genetic studies and in replicated space-transplanted or seeded sward evaluation trials. The micromesh pollination bags cost about $15 each because of fabric costs but could be reused for 10 or more pollination seasons at an annual cost per cross of about $1.50 or less. [ABSTRACT FROM AUTHOR]