Association mapping is a method for detection of gene effects based on linkage disequilibrium (LD) that complements QTL analysis in the development of tools for molecular plant breeding. In this study, association mapping was performed on a selected sample of 95 cultivars of soft winter wheat. Population structure was estimated on the basis of 36 unlinked simple-sequence repeat (SSR) markers. The extent of LD was estimated on chromosomes 2D and part of 5A, relative to the LD observed among unlinked markers. Consistent LD on chromosome 2D was ,1 cM, whereas in the centromeric region of 5A, LD extended for 5 cM. Association of 62 SSR loci on chromosomes 2D, 5A, and 5B with kernel morphology and milling quality was analyzed through a mixed-effects model, where subpopulation was considered as a random factor and the marker tested was considered as a fixed factor. Permutations were used to adjust the threshold of significance for multiple testing within chromosomes. In agreement with previous QTL analysis, significant markers for kernel size were detected on the three chromosomes tested, and alleles potentially useful for selection were identified. Our results demonstrated that association mapping could complement and enhance previous QTL information for marker-assisted selection. T HE basic objective of association mapping (AM)studies is to detect correlations between genotypes and phenotypes in a sample of individuals on the basis of linkage disequilibrium (LD) (Zondervan and Cardon 2004). In the study of genetics of complex diseases in humans, AM offers the important advantage of sampling unrelated individuals in the population, as compared to other experimental designs that require sampling within families (Risch 2000). In contrast to humans, plants can be manipulated to develop large experimental populations with desirable characteristics for genetic mapping, so in principle use of the association approach might not seem as appealing as it is in humans.However, sampling unrelated genotypes presents a number of advantages for the development of tools for marker-assisted selection in plant breeding ( Jannink et al. 2001). First, the experimental population can be a representative sample of the population to which inference is desired. Examples are a core collection from a gene bank, varieties representing the elite germplasm of a breeding program or inbred lines representing a synthetic outcrossing population. In this way, information derived from the experiments should be readily applicable to crop improvement. Second, AM can be more efficient in the use of resources. A group of unrelated individuals normally presents variation for many phenotypic aspects; thus several traits can be studied in the same population using the same genotypic data. A higher proportion of molecular markers are likely to be polymorphic, providing better genome coverage than any biparental map. Furthermore, if elite lines are used for study, multi-year and multi-location phenotypic data may be available at no additional cost (Ra...

Association analysis is a method potentially useful for detection of marker-trait associations based on linkage disequilibrium, but little information is available on the application of this technique to plant breeding populations. With appropriate statistical methods, valid association analysis can be done in plant breeding populations; however, the most significant marker may not be closest to the functional gene. Bias can arise from (i) covariance among markers and QTL, frequently related to population structure or intense selection and (ii) differences in initial frequencies of marker alleles in the population, such that exclusive alleles tend to be in higher association. The potentials and limitations of germplasm bank collections, synthetic populations, and elite germplasm are compared, as experimental materials for association analysis integrated with plant breeding practice. Synthetics offer a favorable balance of power and precision for association analysis and would allow mapping of quantitative traits with increasing resolution through cycles of intermating. A model to describe the association between markers and genes as conditional probabilities in synthetic populations under recurrent selection is proposed, which can be computed on the basis of assumptions related to the history of the population. This model is useful for predicting the potential of different populations for association analysis and forecasting the response to marker-assisted selection.

Plant breeding can be broadly defined as alterations caused in plants as a result of their use by humans, ranging from unintentional changes resulting from the advent of agriculture to the application of molecular tools for precision breeding. The vast diversity of breeding methods can be simplified into three categories: (i) plant breeding based on observed variation by selection of plants based on natural variants appearing in nature or within traditional varieties; (ii) plant breeding based on controlled mating by selection of plants presenting recombination of desirable genes from different parents; and (iii) plant breeding based on monitored recombination by selection of specific genes or marker profiles, using molecular tools for tracking within-genome variation. The continuous application of traditional breeding methods in a given species could lead to the narrowing of the gene pool from which cultivars are drawn, rendering crops vulnerable to biotic and abiotic stresses and hampering future progress. Several methods have been devised for introducing exotic variation into elite germplasm without undesirable effects. Cases in rice are given to illustrate the potential and limitations of different breeding approaches.

No abstract

The objective of this study was to estimate the results ofthe upland rice {Oryza sativa L.) breeding program conducted by the Brazilian Agricultural Research Corporation (Embrapa) and collaborators over the period of 1984 to 2009 covering 25 annual steps of improvement. The best lines generated by this program are evaluated in "value for cultivation and use (VCU) trials." This study used data from 603 VCU trials conducted in seven Brazilian States. The group of lines entering VCU in each year was faken as a sample of the elife program in that year. Best linear unbiased estimates (BLUEs) of the means of groups were computed, and the regression of the BLUEs on years was taken as an estimate of the efficiency of the breeding program.

Milling and baking quality traits in wheat (Triticum aestivum L.) were studied by QTL analysis in the ITMI population, a set of 114 recombinant inbred lines (RILs) generated from a synthetic-hexaploid (W7985) x bread-wheat (Opata 85) cross. Grain from RILs grown in U.S., French, and Mexican wheat-growing regions was assayed for kernel-texture traits, protein concentration and quality, and dough strength and mixing traits. Only kernel-texture traits showed similar genetic control in all environments, with Opata ha alleles at the hardness locus Ha on chromosome arm 5DS increasing grain hardness, alkaline water retention capacity, and flour yield. Dough strength was most strongly influenced by Opata alleles at 5DS loci near or identical to Ha. Grain protein concentration was associated not with high-molecular-weight glutenin loci but most consistently with the Gli-D2 gliadin locus on chromosome arm 6DS. In Mexican-grown material, a 2DS locus near photoperiod-sensitivity gene Ppd1 accounted for 25% of variation in protein, with the ppd1-coupled allele associated with higher (1.1%) protein concentration. Mixogram traits showed most influence from chromosomal regions containing gliadin or low-molecular-weight glutenin loci on chromosome arms 1AS, 1BS, and 6DS, with the synthetic hexaploid contributing favorable alleles. Some RI lines showed quality values consistently superior to those of the parental material, suggesting the potential of further evaluating new combinations of alleles from diploid and tetraploid relatives, especially alleles of known storage proteins, for improvement of quality traits in wheat cultivars

Association analysis was applied to a panel of accessions of Embrapa Rice Core Collection (ERiCC) with 86 SSR and field data from two experiments. A clear subdivision between lowland and upland accessions was apparent, thereby indicating the presence of population structure. Thirty-two accessions with admixed ancestry were identified through structure analysis, these being discarded from association analysis, thus leaving 210 accessions subdivided into two panels. The association of yield and grain-quality traits with SSR was undertaken with a mixed linear model, with markers and subpopulation as fixed factors, and kinship matrix as a random factor. Eight markers from the two appraised panels showed significant association with four different traits, although only one (RM190) maintained the marker-trait association across years and cultivation. The significant association detected between amylose content and RM190 was in agreement with previous QTL analyses in the literature. Herein, the feasibility of undertaking association analysis in conjunction with germplasm characterization was demonstrated, even when considering low marker density. The high linkage disequilibrium expected in rice lines and cultivars facilitates the detection of marker-trait associations for implementing marker assisted selection, and the mining of alleles related to important traits in germplasm.

Os ganhos genéticos para produtividade obtidos pelo programa de melhoramento do arroz irrigado por inundação na Região Nordeste do Brasil no período de 1984 a 1993 foram estimados visando avaliar a eficiência do programa e traçar novas estratégias. Esta estimativa foi feita a partir dos dados de 59 ensaios regionais de rendimento conduzidos pelas empresas de pesquisa agropecuária do Nordeste, em cooperação com a Embrapa-Centro Nacional de Pesquisa de Arroz e Feijão (CNPAF), Goiânia, GO. O método estatístico utilizado baseia-se em médias ajustadas por modelo linear generalizado. O ganho genético médio estimado foi de 54,9 ± 14,4 kg/ha/ano (0,8%). Nos últimos três anos houve uma tendência de interrupção dos ganhos. A pequena magnitude dos ganhos para produção nesta região podem ser atribuídos ao direcionamento do programa de geração de linhagens da Embrapa para qualidade de grãos e resistência a doenças, às diferenças ambientais existentes entre Goiânia e a Região Nordeste e ao pequeno número de ensaios conduzidos. A genealogia das linhagens foi traçada e verificou-se que os principais ancestrais são os mesmos das cultivares recomendadas. A base genética das linhagens é estreita, o que também pode estar contribuindo para a obtenção de pequenos ganhos genéticos para produtividade.