F 1 crosses; variation among populations is partitioned into populations and midparent heterosis (Gardner and Diallel mating designs provide to breeders useful genetic information, Eberhart, 1966;Hallauer and Miranda, 1988; Murray et such as general combining ability (GCA) and specific combining ability (SCA), to help them devise appropriate breeding and selection strategies. al., 2003). Heterosis is further partitioned into average, Here we report a much-improved version of DIALLEL-SAS that was variety, and specific heterosis, but additive and domioriginally released in 1997. The new program, DIALLEL-SAS05, has a nance parameters cannot be determined in Analysis II clear and user-friendly interface that was designed to meet users' because they are confounded with the source of varianeeds for various diallel-cross design experiments. DIALLEL-SAS05 tion labeled "variety" (Murray et al., 2003). The GEAN has major advantages over DIALLEL-SAS in that: (i) it analyzes III provides estimates of variety and GCA effects from not only all four Griffing's diallel methods (both fixed and random an analysis that contains the following sources of variamodels), but it also computes Gardner-Eberhart's Analyses II and tion: parents, parents vs. F 1 crosses, and F 1 crosses; GCA III; (ii) it provides desired results from diallel experiments with parent effects are estimated in a manner similar to Griffing's number from 4 to 12, (iii) it can analyze diallel data from any number Method 4, Model 1 (Murray et al., 2003). Both GEAN of environments, and (iv) for a random-effects model, it provides estimates of GCA ( 2 g ) and SCA ( 2 s ) variances, which can be used II and GEAN III provide estimates of average heterosis to estimate additive ( 2 A ) and dominance ( 2 D ) variances, and ulti-and SCA (Gardner and Eberhart, 1966; Murray et al., mately narrow-sense heritability (h 2 ). DIALLEL-SAS05 also provides 2003). Many researchers have fruitfully used GEAN for information on GCA ϫ ENV, SCA ϫ ENV, reciprocal ϫ ENV, studying heterosis and estimating GCA and SCA in maternal ϫ ENV, and nonmaternal ϫ ENV interactions, when applivariety diallels (Crossa et al., 1987; Ali et al., 2001; Lee cable. DIALLEL-SAS05 should greatly improve researchers' effiet al., 2003). ciency in analyzing and interpreting diallel-cross data. The program Murray et al. (2003) pointed out that formulas for code is available on a CD from the corresponding author. the effects for GEAN II and GEAN III were nonintuitive both biologically and genetically and incorporated the number of parents as multipliers. They further 2002; Hakizimana et al., 2004), durum wheat (Triticum

SummaryThe rth3 (roothairless 3) mutant is specifically affected in root hair elongation. We report here the cloning of the rth3 gene via a PCR-based strategy (amplification of insertion mutagenized sites) and demonstrate that it encodes a COBRA-like protein that displays all the structural features of a glycosylphosphatidylinositol anchor. Genes of the COBRA family are involved in various types of cell expansion and cell wall biosynthesis. The rth3 gene belongs to a monocot-specific clade of the COBRA gene family comprising two maize and two rice genes. While the rice (Oryza sativa) gene OsBC1L1 appears to be orthologous to rth3 based on sequence similarity (86% identity at the protein level) and maize/rice synteny, the maize (Zea mays L.) rth3-like gene does not appear to be a functional homolog of rth3 based on their distinct expression profiles. Massively parallel signature sequencing analysis detected rth3 expression in all analyzed tissues, but at relatively low levels, with the most abundant expression in primary roots where the root hair phenotype is manifested. In situ hybridization experiments confine rth3 expression to root hair-forming epidermal cells and lateral root primordia. Remarkably, in replicated field trials involving near-isogenic lines, the rth3 mutant conferred significant losses in grain yield.

Improvement of germplasm as a parental source for developing inbreds has been an important part of most maize (Zea mays L.) breeding programs. Reciprocal recurrent selection is a cyclical breeding procedure designed to improve the interpopulation cross of two base populations. The objective of this study was to evaluate the direct and indirect responses of 11 cycles of reciprocal recurrent selection in the BSSS(R) (Iowa Stiff Stalk Synthetic) and BSCB1(R) (Iowa Corn Borer Synthethic no. 1) maize populations. The populations per se, populations per se selfed, interpopulation crosses, and interpopulation crosses selfed corresponding to C0, C4, C7, C8, C9, C10, and C11 of the populations were evaluated. Testcrosses of the original and advanced cycles of the populations per se with inbreds B73 and Mo17 and with BSSS(R)C0 and BSCB1(R)C0 also were evaluated in the study. Response in grain yield of the BSSS(R) × BSCB1(R) interpopulation cross was 6.95% (or 0.28 Mg ha-1) cycle-1. Grain yield of BSCB1(R) increased 1.94% (or 0.06 Mg ha-1) cycle-1 , but grain yield of BSSS(R) did not change significantly. Midparent heterosis of the interpopulation cross increased from 25.44 to 76.04% from C0 to C11. Inbreeding depression in the population crosses increased from 1.01 to 2.32 Mg ha-1 after 11 cycles of selection. The frequency of heterozygotes for grain yield in the population crosses seems to have increased with cycles of selection. Testcrosses to the C0 populations and the inbreds showed linear increases in grain yield, indicating that selection Improved general and specific combining ability of the populations. Selection was effective in reducing root and stalk lodging. No changes in grain moisture were observed. changes in other agronomic traits were in the desired direction. Disciplines

Restriction fragment length polymorphisms (RFLPs) have been suggested as molecular markers to facilitate improvement of agronomic traits in maize (Zea mays L.). The objective of this study was to evaluate the utility of RFLP data in elucidating heterotic patterns among maize lines. Eight maize inbred lines and their 28 singlecross hybrids werevaluated for grain yield at two Iowa locations in each of 2 yr in a randomizedcomplete block design. The diallel mating design permitted estimation of general and specific combining ability effects. Restriction fragment length polymorphism analysis of inbred lines included five restriction enzymes and five eDNA and 28 genomic clones distributed over the maize genome. Restriction fragment length polymorphism patterns of crosses were predicted from analysis of the inbred parents. Genetic distances between inbred lines were estimated as modified Rogers' distance (MRD). Grain yield and specific combining ability were significantly correlated with MRD for six of the 10 chromosomes. Dispersion of inbred lines and hybrids for RFLP allele frequencies was generally consistent with expectations based on known pedigrees. Results from this study suggest RFLP analysis as a potential alternative to field testing when attempting to assign maize inbred lines to heterotic groups. Disciplines

Restriction fragment length polymorphisms (RFLPs) have been proposed as molecular markers for characterizing the genetic diversity in maize (Zea mays L.). The objectives of this study were to evaluate the usefulness of RFLP data for (i) elucidating heterotic patterns among maize inbreds and (ii) assessing genetic similarity among related and unrelated lines. Thirty-two maize inbreds from the U.S. Corn Belt were analyzed for RFLPs with two restriction enzymes and 83 DNA probes distributed over the maize genome. Eighty-two probes detected polymorphisms with at least one enzyme. On average, 4.3 variants were found per probeenzyme combination across all 32 inbreds. Genetic distances among lines, estimated from RFLP data as Rogers' distance (RD), revealed considerable diversity among lines from Iowa Stiff Stalk Synthetic (BSSS), Reid Yellow Dent (RYD), and Lancaster Sure Crop (LSC). Lines from different heterotic groups had a slightly greater RD mean than unrelated lines from the same heterotic group, yet differences were small when compared with the wide range of RDs for individual lines combinations within each group. RDs between related lines agreed well with expectations based on coancestry coefficients determined from pedigree data with few exceptions. Principal component analyses of RFLP data resulted in a separate grouping of lines from BSSS/RYD and LSC. Dispersion of lines of miscellaneous origins was generally consistent with expectations based on known breeding behavior and pedigrees. Results from this study suggest that RFLP data can be used for assigning inbreds into heterotic groups and quantifying genetic similarity between related lines, but it seems that a large number of probe-enzyme combinations are required to obtain reliable estimates of genetic distance.

Second cycle breeding, utilizing backcross and F 2 generations, has become the predominant type of line development program in the U.S. maize (Zea mays L.) industry. Epistasis and linkage have been identified as possible limits to progress from selection in F 2 and backcross populations. Objectives of this study were to determine the importance of epistasis in an elite maize hybrid and to determine the appropriate generation for initiation of inbred line development. Six generations of progeny were developed from B73 and B84: the two parental generations, Pl (B73) and P2 (B84); the F 2 generation [(B73 × B84) F 2 ]; the BCP 1 generation [(B73 × B84) × B73]; the BCP 2 generation [(B73 × B84) × B84]; and the F 2-Syn 8 generation (the F 2 generation random mated for eight generations). Testcross progeny were produced by crossing random S 9 plants from each of the six generations onto the inbred tester Mo17. One-hundred progeny of F 2 × Mo17 and F 2-Syn 8 × Mo17 and 50 progeny of BCP 1 × Mo17 and BCP 2 × Mo17, as well as the parental testcrosses, were harvested. The experiment was evaluated at four locations in 1990 and three locations in 1991. Epistatic effects were significant for grain yield and grain moisture, and accounted for 21 and 18% of the variation among generation means, respectively. The genetic variance and heritability for grain yield ranked F 2-Syn 8 > F 2 > BCP 1 > BCP 2 , but differences among generations were not significant. The predicted gains for each generation ranked in agreement with the heritability. Under low selection intensities (a = 20%), the predicted mean (usefulness) ranked the generations BCP2 2 > F 2 >> F 2-Syn 8 > BCPI. Under high selection intensity (a = 1%), usefulness ranked the generations F 2 > F 2-Syn 8 > BCP 2 > BCP 1. The choice between F 2 and backcrosses as source populations is primarily a function of selection intensity. Our results suggest little to no advantage of random mating the F 2 before initiating selection and inbreeding.

Restriction fragment length polymorphisms (RFLPs) have been proposed for investigating relationships among inbred lines and predicting heterosis and performance of single-cross hybrids in maize (Zea mays L.). Such use was evaluated in 20 maize inbreds classified as first-cycle, second-cycle, good, and poor lines, and in diallel crosses within types. Eight generations (parents, F 1 , F 2 , F 3 , backcrosses, and backcrosses selfed) from 67 crosses were evaluated for grain yield in five Iowa environments. Genetic effects were estimated from generation means by ordinary diallel analyses and the Eberhart-Gardner genetic model. Poor inbreds showed significantly greater average heterosis than did good lines. Estimates of additive ✕ additive epistatic effects were negative and highly significant in all except first-cycle lines. Using two restriction enzymes and 82 genomic) DNA probes distributed throughout the maize genome, all but one probe revealed polymorphisms with at least one enzyme (~4.5 variants per RFLP locus). Genetic distances between lines within types were estimated as Rogers' distances (RD). Within diallel sets, RD values were partitioned into general (GRD)and specific (SRD). All four types of lines showed similar means and substantial variation for RD; GRD explained 40% of the variation among RD values. Cluster analyses revealed associations among lines generally consistent with expectations based on known pedigrees. Correlations of RD and SRD with F 1 yield heterosis, specific heterosis, and specific combining ability were positive but small (r = ≤ 0.50) when combined for all crosses. Results indicated that RFLPs can be used to investigate pedigree relationships among maize inbreds, but also suggest that RFLP-based genetic distance measures are of limited use in predicting heterotic performance of single crosses between unrelated lines. Disciplines

The effects of breeding on allele frequency changes at 82 restriction fragment length polymorphism (RFLP) loci were examined in two maize (Zea mays L.) populations undergoing reciprocal recurrent selection, Iowa Stiff Stalk Synthetic and Iowa Corn Borer Synthetic #1. After 12 cycles of selection, approximately 30% of the alleles were extinct and 10% near fixation in each population. A test of selective neutrality identified several loci in each population whose allele frequency changes cannot be explained by genetic drift; interpopulation mean expected heterozygosity increased for that subset of 28 loci but not for the remaining 54 loci. Mean expected heterozygosity within the two subpopulations decreased 39%, while the between-population component of genetic variation increased from 0.5% to 33.4% of the total. Effective population size is a key parameter for discerning allele frequency changes due to genetic drift versus those resulting from selection and genetic hitchhiking. Empirical estimates of effective population size for each population were within the range predicted by the breeding method. KeywordsEffective population size, Selection, Genetic drift, Diversity, Restriction fragment length polymorphism Abstract The effects of breeding on allele frequency changes at 82 restriction fragment length polymorphism (RFLP) loci were examined in two maize (Zea mays L.) populations undergoing reciprocal recurrent selection, Iowa Stiff Stalk Synthetic and Iowa Corn Borer Synthetic #1. After 12 cycles of selection, approximately 30% of the alleles were extinct and 10% near fixation in each population. A test of selective neutrality identified several loci in each population whose allele frequency changes cannot be explained by genetic drift; interpopulation mean expected heterozygosity increased for that subset of 28 loci but not for the remaining 54 loci. Mean expected heterozygosity within the two subpopulations decreased 39%, while the between-population component of genetic variation increased from 0.5% to 33.4% of the total. Effective population size is a key parameter for discerning allele frequency changes due to genetic drift versus those resulting from selection and genetic hitchhiking. Empirical estimates of effective population size for each population were within the range predicted by the breeding method.