Global Hierarchical Gene Diversity Analysis Suggests the Fertile Crescent Is Not the Center of Origin of the Barley Scald Pathogen Rhynchosporium secalis

A total of 1,366 Rhynchosporium secalis isolates causing scald on barley, rye, and wild barley (Hordeum spontaneum) were assayed for restriction fragment length polymorphism loci, DNA fingerprints, and mating type, to characterize global genetic structure. The isolates originated from 31 field populations on five continents. Hierarchical analysis revealed that more than 70% of the total genetic variation within regions was distributed within a barley field. At the global level, only 58% of the total genetic variation was distributed within fields, while 11% was distributed among fields within regions, and 31% was distributed among regions. A significant correlation was found between genetic and geographic distance. These findings suggest that gene flow is common at the local level while it is low between regions on the same continent, and rare between continents. Analyses of multilocus associations, genotype diversity, and mating type frequencies indicate that sexual recombination is occurring in most of the populations. We found the highest allele richness in Scandinavia followed by Switzerland. This suggests that R. secalis may not have originated at the center of origin of barley, the Fertile Crescent, nor in a secondary center of diversity of barley, Ethiopia.

Multiple Interval Mapping for Quantitative Trait Loci

A new statistical method for mapping quantitative trait loci (QTL), called multiple interval mapping (MIM), is presented. It uses multiple marker intervals simultaneously to fit multiple putative QTL directly in the model for mapping QTL. The MIM model is based on Cockerham's model for interpreting genetic parameters and the method of maximum likelihood for estimating genetic parameters. With the MIM approach, the precision and power of QTL mapping could be improved. Also, epistasis between QTL, genotypic values of individuals, and heritabilities of quantitative traits can be readily estimated and analyzed. Using the MIM model, a stepwise selection procedure with likelihood ratio test statistic as a criterion is proposed to identify QTL. This MIM method was applied to a mapping data set of radiata pine on three traits: brown cone number, tree diameter, and branch quality scores. Based on the MIM result, seven, six, and five QTL were detected for the three traits, respectively. The detected QTL individually contributed from ∼1 to 27% of the total genetic variation. Significant epistasis between four pairs of QTL in two traits was detected, and the four pairs of QTL contributed ∼10.38 and 14.14% of the total genetic variation. The asymptotic variances of QTL positions and effects were also provided to construct the confidence intervals. The estimated heritabilities were 0.5606, 0.5226, and 0.3630 for the three traits, respectively. With the estimated QTL effects and positions, the best strategy of marker-assisted selection for trait improvement for a specific purpose and requirement can be explored. The MIM FORTRAN program is available on the worldwide web (http://www.stat.sinica.edu.tw/~chkao/).

Apportionment of genetic variance in migrating and wintering mallards

Mallards (Anas platyrhynchos, n = 289) wintering in the Southern High Plains of Texas were collected from 15 October 1988 to 7 February 1989 and electrophoretically surveyed for genetic variation at 30 biochemical loci. Genetic data were used to detect mixtures of breeding populations in the wintering aggregation of mallards that migrate into the Southern High Plains and to estimate the proportion of total genetic variation partitioned among breeding populations represented on the study area there. Wintering mallards represented mixtures of genetically heterogeneous breeding populations with a minimum of 10.4 – 11.7% of the genetic variation partitioned among populations represented. Genetic information may be useful in detecting mixtures of breeding populations in specific wintering areas within and among flyways.

Temporal components of genetic variation in migrating and wintering American wigeon

Data from allele frequencies of wintering American wigeon (Anas americana) from the Southern High Plains (SHP) of Texas were used to monitor changes in genetic characteristics of the wintering population through time, and to estimate the average proportion of total genetic variation partitioned among parent breeding populations. Wigeon were surveyed electrophoretically for genetic variation at 25 biochemical loci. Changes in total gene diversity were observed throughout the study period (5 October 1988 to 15 March 1989) at numerous loci. Significant temporal changes in the genetic composition of the wintering population were detected, and a minimum of 7% of the total genetic variation in these wigeon was thought to be partitioned among the breeding populations represented on the SHP. A new influx of migrating wigeon, weather-related movements of wigeon, or spatial subdivision of breeding populations on the SHP may be responsible for shifts observed in the genetic characteristics of the wintering population. Significant heterozygote deficiencies in the sample of wintering wigeon suggest that this species maintains some degree of genetic structure on the breeding grounds. Genetic data collected from wintering waterfowl may provide minimum expectations of the degree of genetic subdivision among breeding populations and may help waterfowl biologists to detect changes in the composition of wintering waterfowl populations through time.