A population of 96 doubled haploid lines (DHLs) was prepared from F1 plants of the hexaploid wheat cross Chinese Spring x SQ1 (a high abscisic acid-expressing breeding line) and was mapped with 567 RFLP, AFLP, SSR, morphological and biochemical markers covering all 21 chromosomes, with a total map length of 3,522 cM. Although the map lengths for each genome were very similar, the D genome had only half the markers of the other two genomes. The map was used to identify quantitative trait loci (QTLs) for yield and yield components from a combination of 24 site x treatment x year combinations, including nutrient stress, drought stress and salt stress treatments. Although yield QTLs were widely distributed around the genome, 17 clusters of yield QTLs from five or more trials were identified: two on group 1 chromosomes, one each on group 2 and group 3, five on group 4, four on group 5, one on group 6 and three on group 7. The strongest yield QTL effects were on chromosomes 7AL and 7BL, due mainly to variation in grain numbers per ear. Three of the yield QTL clusters were largely site-specific, while four clusters were largely associated with one or other of the stress treatments. Three of the yield QTL clusters were coincident with the dwarfing gene Rht-B1 on 4BS and with the vernalisation genes Vrn-A1 on 5AL and Vrn-D1 on 5DL. Yields of each DHL were calculated for trial mean yields of 6 g plant(-1) and 2 g plant(-1) (equivalent to about 8 t ha(-1) and 2.5 t ha(-1), respectively), representing optimum and moderately stressed conditions. Analyses of these yield estimates using interval mapping confirmed the group-7 effects on yield and, at 2 g plant(-1), identified two additional major yield QTLs on chromosomes 1D and 5A. Many of the yield QTL clusters corresponded with QTLs already reported in wheat and, on the basis of comparative genetics, also in rice. The implications of these results for improving wheat yield stability are discussed.

Information about the genetic diversity and population structure in elite breeding material is of fundamental importance for the improvement of crops. The objectives of our study were to (a) examine the population structure and the genetic diversity in elite maize germplasm based on simple sequence repeat (SSR) markers, (b) compare these results with those obtained from single nucleotide polymorphism (SNP) markers, and (c) compare the coancestry coefficient calculated from pedigree records with genetic distance estimates calculated from SSR and SNP markers. Our study was based on 1,537 elite maize inbred lines genotyped with 359 SSR and 8,244 SNP markers. The average number of alleles per locus, of group specific alleles, and the gene diversity (D) were higher for SSRs than for SNPs. Modified Roger’s distance (MRD) estimates and membership probabilities of the STRUCTURE matrices were higher for SSR than for SNP markers but the germplasm organization in four heterotic pools was consistent with STRUCTURE results based on SSRs and SNPs. MRD estimates calculated for the two marker systems were highly correlated (0.87). Our results suggested that the same conclusions regarding the structure and the diversity of heterotic pools could be drawn from both markers types. Furthermore, although our results suggested that the ratio of the number of SSRs and SNPs required to obtain MRD or D estimates with similar precision is not constant across the various precision levels, we propose that between 7 and 11 times more SNPs than SSRs should be used for analyzing population structure and genetic diversity.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-009-1256-2) contains supplementary material, which is available to authorized users.

No abstract

No abstract

Mapping quantitative trait loci (QTL) in plants is usually conducted using a population derived from a cross between two inbred lines. The power of such QTL detection and the estimation of the effects highly depend on the choice of the two parental lines. Thus, the QTL found represent only a small part of the genetic architecture and can be of limited economical interest in marker-assisted selection. On the other hand, applied breeding programmes evaluate large numbers of progeny derived from multiple-related crosses for a wide range of agronomic traits. It is assumed that the development of statistical techniques to deal with pedigrees in existing plant populations would increase the relevance and cost effectiveness of QTL mapping in a breeding context. In this study, we applied a two-step IBD-based-variance component method to a real wheat breeding population, composed of 374 F6 lines derived from 80 different parents. Two bread wheat quality related traits were analysed by the method. Results obtained show very close agreement with major genes and QTL already known for those two traits. With this new QTL mapping strategy, inferences about QTL can be drawn across the breeding programme rather than being limited to the sample of progeny from a single cross and thus the use of the detected QTL in assisting breeding would be facilitated.

Plants accumulate abscisic acid (ABA) under droughted conditions. Genetic variation in the accumulation of ABA in deteched and partially dehydrated leaves of rice has previously been reported, and this was found to be associated with variation in leaf size (smaller leaves made more ABA). Correlation analysis failed to distinguish clearly between a causal relationship between the two traits and close genetic between loci controlling the traits. Here we present a detailed genetic analysis of ABA accumulation in detached and partially dehydrated rice leaves. using a population of F2 plants generated from the lowland x upland cross IR20 (high-ABA) x 63-83 (low-ABA) which was mapped with RFLP and AFLP markers. Several highly significant quantitative trait loci (QTLs) for ABA accumulation and leaf weight were identified. Only one of the minor QTLs for ABA accumulation (accounting for only 4% of the phenotypic variance) was coincident with any QTLs for leaf size such that the high-ABA allele was associated with smaller leaves. This analysis, therefore, showed that the association previously found between ABA accumulation and leaf size was probably largely due to genetic linkage and not to a direct effect of leaf size on ABA accumulation or vice versa. Because of the importance of ABA accumulation in regulating responses of plants to drought stress and the effects of plant size on the rate of development of stress, QTLs for drought-induced ABA accumulation, leaf size and tiller number were compared between rice and wheat. In particular, a possible location in rice was sought for a homoeologue of the major wheat vernalization responsive gene, Vrn1, as this gene is also associated with major effects on leaf size, tiller number and ABA accumulation in wheat. The likelihood of homoeologous loci regulating ABA accumulation, leaf size and tiller number in the two crops is discussed.

Mapping quantitative trait loci in plants is usually conducted using a population derived from a cross between two inbred lines. The power of such QTL detection and the parameter estimates depend largely on the choice of the two parental lines. Thus, the QTL detected in such populations represent only a small part of the genetic architecture of the trait. In addition, the effects of only two alleles are characterized, which is of limited interest to the breeder, while common pedigree breeding material remains unexploited for QTL mapping. In this study, we extend QTL mapping methodology to a generalized framework, based on a two-step IBD variance component approach, applicable to any type of breeding population obtained from inbred parents. We then investigate with simulated data mimicking conventional breeding programs the influence of different estimates of the IBD values on the power of QTL detection. The proposed method would provide an alternative to the development of specifically designed recombinant populations, by utilizing the genetic variation actually managed by plant breeders. The use of these detected QTL in assisting breeding would thus be facilitated. T HE availability of molecular markers in the 1980scalled the fixed-model approach (Xu and Atchley 1995) since it considers a fixed number of distinct alleles opened a new scope for quantitative genetics and breeding. It was anticipated that the manipulation of (most often two) at each putative QTL. Statistical methods for the QTL analysis of biparental populations unloci underlying quantitative traits (QTL) would be as easily feasible as with Mendelian factors. This, however, derwent successive improvements through the advent of interval mapping (Lander and Botstein 1989) and has generally not been the case, despite the large corpus of theoretical studies on marker-assisted selection (MAS;

No abstract