Power and false-positive rate in QTL detection with near-isogenic line libraries.

Libraries of near-isogenic lines (NILs) were used for quantitative trait locus (QTL) detection in model species and economically important crops. The experimental design and genetic architecture of the considered traits determine the statistical properties of QTL detection. The objectives of our simulation study were to (i) investigate the population sizes required to develop NIL libraries in barley and maize, (ii) compare NIL libraries with nonoverlapping and overlapping donor segments and (iii) study the number of QTLs and the size of their effects with respect to the power and the false-positive rate of QTL detection. In barley, the development of NIL libraries with target segment lengths of 10 c and marker distances of 5 cM was possible using a BC(3)S(2) backcrossing scheme and population sizes of 140. In maize, population sizes larger than 200 were required. Selection for the recipient parent genome at markers flanking the target segments with distances between 5 and 10 cM was required for an efficient control of the false-positive rate. NIL libraries with nonoverlapping donor chromosome segments had a greater power of QTL detection and a smaller false-positive rate than libraries with overlapping segments. Major genes explaining 30% of the genotypic difference between the donor and recipient were successfully detected even with low heritabilities of 0.5, whereas for minor genes explaining 5 !or 10%, high heritabilities of 0.8 or 0.9 were required. The presented results can assist geneticists and breeders in the efficient development of NIL libraries for QTL detection.

Testcross performance of rye introgression lines developed by marker-assisted backcrossing using an Iranian accession as donor.

Introgression libraries facilitate the identification of favorable exotic alleles or genomic regions, which can be exploited for improving elite breeding material. We evaluated the first two introgression libraries in rye (Secale cereale L.) on the phenotypic and molecular level. Our objectives were to detect candidate introgression lines (pre-ILs) with a better testcross performance than the recurrent parent and identify donor chromosome segments (DCS) responsible for the improved performance. We introduced DCS from the self-incompatible heterozygous exotic Iranian primitive rye accession Altevogt 14160 (donor) into the genetic background of the elite inbred line L2053-N (recurrent parent) by marker-assisted backcrossing and developed 40 BC(2)S(3) lines in each introgression library. Testcross performance for three agronomic and six quality traits was evaluated in replicated field trials across two testers at five locations over 2 years. The phenotypic effect of the DCS was analyzed for all traits. The pre-ILs had on average a testcross performance comparable to that of the recurrent parent. Significant (P < 0.05) differences between individual pre-ILs and the recurrent parent were detected for all traits except for heading date. For more than 60% of the significant (P < 0.05) differences, the pre-ILs were superior to the recurrent parent. For some pre-ILs, specific DCS were identified containing presumably quantitative trait loci responsible for the superior hybrid performance. Consequently, our study revealed that the development and employment of introgression libraries offers the opportunity for a targeted increase of genetic diversity of elite rye material for hybrid performance of agronomically important traits.

Establishment of introgression libraries in hybrid rye (Secale cereale L.) from an Iranian primitive accession as a new tool for rye breeding and genomics.

Genetic diversity of elite breeding material can be increased by introgression of exotic germplasm to ensure long-term selection response. The objective of our study was to develop and characterize the first two rye introgression libraries generated by marker-assisted backcrossing and demonstrate their potential application for improving the baking quality of rye. Starting from a cross between inbred line L2053-N (recurrent parent) and a heterozygous Iranian primitive population Altevogt 14160 (donor) two backcross (BC) and three selfing generations were performed to establish introgression libraries A and B. Amplified fragment length polymorphisms (AFLP markers) and simple sequences repeats (SSRs) were employed to select and characterize candidate introgression lines (pre-ILs) from BC(1) to BC2S3. The two introgression libraries comprise each 40 BC2S3 pre-ILs. For analyzing the phenotypic effects of the exotic donor chromosome segment (DCS) we evaluated the per se performance for pentosan and starch content in replicated field trials at each of four locations in 2005 and 2006. Introgression library A and B cover 74 and 59% of the total donor genome, respectively. The pre-ILs contained mostly two to four homozygous DCS, with a mean length of 12.9 cM (A) and 10.0 cM (B). We detected eight (A) and nine (B) pre-ILs with a significant (P<0.05) higher pentosan content and two pre-ILs (B) with a significant (P<0.05) higher starch content than the elite recurrent parent. Thus, our results indicate that exotic genetic resources in rye carry favorable alleles for baking quality traits, which can be exploited for improving the elite breeding material by marker-assisted selection (MAS). These introgression libraries can substantially foster rye breeding programs and provide a promising opportunity to proceed towards functional genomics.

Linkage disequilibrium in two European F(2) flint maize populations under modified recurrent full-sib selection.

According to quantitative genetic theory, linkage disequilibrium (LD) can hamper the short- and long-term selection response in recurrent selection (RS) programs. We analyzed LD in two European flint maize populations, KW1265 x D146 (A x B) and D145 x KW1292 (C x D), under modified recurrent full-sib selection. Our objectives were to investigate (1) the decay of initial parental LD present in F(2) populations by three generations of intermating, (2) the generation of new LD in four (A x B) and seven (C x D) selection cycles, and (3) the relationship between LD changes and estimates of the additive genetic variance. We analyzed the F(2) and the intermated populations as well as all selection cycles with 104 (A x B) and 101 (C x D) simple sequence repeat (SSR) markers with a uniform coverage of the entire maize genome. The LD coefficient D and the composite LD measure Delta were estimated and significance tests for LD were performed. LD was reduced by intermating as expected from theory. A directional generation of negative LD between favorable alleles could not be observed during the selection cycles. However, considerable undirectional changes in D were observed, which we attributed to genetic sampling due to the finite population size used for recombination. Consequently, a long-term reduction of the additive genetic variance due to negative LD was not observed. Our experimental results support the hypothesis that in practical RS programs with maize, LD generated by selection is not a limiting factor for obtaining a high selection response.

Temporal changes in allele frequencies in two European F(2) flint maize populations under modified recurrent full-sib selection.

Selection and random genetic drift are the two main forces affecting the selection response of recurrent selection (RS) programs by changes in allele frequencies. Therefore, detailed knowledge on allele frequency changes attributable to these forces is of fundamental importance for assessing RS programs. The objectives of our study were to (1) estimate the number, position, and genetic effect of quantitative trait loci (QTL) for selection index and its components in the base populations, (2) determine changes in allele frequencies of QTL regions due to the effects of random genetic drift and selection, and (3) predict allele frequency changes by using QTL results and compare these predictions with observed values. We performed QTL analyses, based on restriction fragment length polymorphisms (RFLPs) and simple sequence repeats (SSRs), in 274 F(2:3) lines of cross KW1265 x D146 (A x B) and 133 F(3:4) lines of cross D145 x KW1292 (C x D) originating from two European flint maize populations. Four (A x B) and seven (C x D) cycles of RS were analyzed with SSRs for significant allele frequency changes due to selection. Several QTL regions for selection index were detected with simple and composite interval mapping. In some of them, flanking markers showed a significant allele frequency change after the first and the final selection cycles. The correlation between observed and predicted allele frequencies was significant only in A x B. We attribute these observations mainly to (1) the high dependence of the power of QTL detection on the population size and (2) the occurrence of undetectable QTL in repulsion phase. Assessment of allele frequency changes in RS programs can be used to detect marker alleles linked to QTL regions under selection pressure.

Genetic drift and selection effects of modified recurrent full-sib selection programs in two F2 populations of European flint maize.

Selection response of a modified recurrent full-sib (FS) selection scheme conducted in two European flint F(2) maize (Zea mays L.) populations was re-evaluated. Our objectives were to (1) determine the selection response for per se and testcross performance in both populations and (2) separate genetic effects due to selection from those due to random genetic drift. Modified recurrent FS selection was conducted at three locations using an effective population size N(e) = 32 and a selection rate of 25% for a selection index, based on grain yield and grain moisture. Recombination was performed according to a pseudo-factorial mating scheme. Selection response was assessed using a population diallel including the source population and advanced selection cycles, as well as testcrosses with unrelated inbred line testers and the parental F(1) generation. Selection response per cycle was significant for grain yield and grain moisture in both populations. Effects of random genetic drift caused only a small reduction in the selection response. No significant selection response was observed for testcrosses, suggesting that for heterotic traits, such as grain yield, a high frequency of favorable alleles in the elite tester masked the effects of genes segregating in the populations. We conclude that our modified recurrent FS selection is an alternative to other commonly applied intrapopulation recurrent selection schemes, and some of its features may also be useful for increasing the efficiency of interpopulation recurrent selection programs.

Comparison of linkage maps from F2 and three times intermated generations in two populations of European flint maize (Zea mays L.).

Intermated mapping populations are expected to result in high mapping resolution for tightly linked loci. The objectives of our study were to (1) investigate the consequences of constructing linkage maps from intermated populations using mapping methods developed for F(2) populations, (2) compare linkage maps constructed from intermated populations (F(2)Syn3) with maps generated from corresponding F(2) and F(3) base populations, and (3) investigate the advantages of intermated mapping populations for applications in plant breeding programs. We constructed linkage maps for two European flint maize populations (A x B, C x D) by mapping 105 SSR markers in generations F(2) and F(2)Syn3 of population A x B, and 102 SSR markers in generations F(3) and F(2)Syn3 of population C x D. Maps for F(2)Syn3 were constructed with mapping methods for F(2) populations (Map A) as well as with those specifically developed for intermated populations (Map B). Both methods relate map distances to recombination frequencies in a single meiosis and, therefore, did not show a map expansion in F(2)Syn3 compared with maps constructed from the respective F(2) or F(3) base populations. Map A and B differed considerably, presumably because of theoretical shortcomings of Map A. Since loosely linked markers could not unambiguously be mapped in the F(2)Syn3 populations, they may hamper the construction of linkage maps from intermated populations.

Trends in population parameters and best linear unbiased prediction of progeny performance in a European F(2) maize population under modified recurrent full-sib selection.

Recurrent selection is a cyclic breeding procedure designed to improve the mean of a population for the trait(s) under selection. Starting from an F(2) population of European flint maize (Zea mays L.) intermated for three generations, we conducted seven cycles of a modified recurrent full-sib (FS) selection scheme. The objectives of our study were to (1) monitor trends across selection cycles in the estimates of the population mean, additive and dominance variances, (2) compare predicted and realized selection responses, and (3) investigate the usefulness of best linear unbiased prediction (BLUP) of progeny performance under the recurrent FS selection scheme applied. Recurrent FS selection was conducted at three locations using a selection rate of 25% for a selection index, based on grain yield and grain moisture. Recombination was performed according to a pseudo-factorial mating scheme, where the selected FS families were divided into an upper-ranking group of parents mated to the lower-ranking group. Variance components were estimated with restricted maximum likelihood. Average grain yield increased 9.1% per cycle, average grain moisture decreased 1.1% per cycle, and the selection index increased 11.2% per cycle. For the three traits we observed, no significant changes in additive and dominance variances occurred, suggesting future selection response at or near current rates of progress. Predictions of FS family performance in Cn+1 based on mean performance of parental FS families in Cn were of equal or higher precision as those based on the mean additive genetic BLUP of their parents, and corresponding correlations were of moderate size only for grain moisture. The significant increase in grain yield combined with the decrease in grain moisture suggest that the F(2) source population with use of a pseudo-factorial mating scheme is an appealing alternative to other types of source materials and random mating schemes commonly used in recurrent selection.