Mapping QTL main and interaction influences on milling quality in elite US rice germplasm.

Rice (Oryza sativa L.) head-rice yield (HR) is a key export and domestic quality trait whose genetic control is poorly understood. With the goal of identifying genomic regions influencing HR, quantitative-trait-locus (QTL) mapping was carried out for quality-related traits in recombinant inbred lines (RILs) derived from crosses of common parent Cypress, a high-HR US japonica cultivar, with RT0034, a low-HR indica line (129 RILs) and LaGrue, a low-HR japonica cultivar (298 RILs), grown in two US locations in 2005-2007. Early heading increased HR in the Louisiana (LA) but not the Arkansas (AR) location. Fitting QTL-mapping models to separate QTL main and QTL × environment interaction (QEI) effects and identify epistatic interactions revealed six main-effect HR QTLs in the two crosses, at four of which Cypress contributed the increasing allele. Multi-QTL models accounted for 0.36 of genetic and 0.21 of genetic × environment interaction of HR in MY1, and corresponding proportions of 0.25 and 0.37 in MY2. The greater HR advantage of Cypress in LA than in AR corresponded to a genomewide pattern of opposition of HR-increasing QTL effects by AR-specific effects, suggesting a selection strategy for improving this cultivar for AR. Treating year-location combinations as independent environments resulted in underestimation of QEI effects, evidently owing to lower variation among years within location than between location. Identification of robust HR QTLs in elite long-grain germplasm is suggested to require more detailed attention to the interaction of plant and grain development parameters with environmental conditions than has been given to date.

Walnut (Juglans spp.) genetic diversity determined by restriction fragment length polymorphisms.

The genetic diversity of 13 Juglans species was characterized using nuclear RFLPs. Allelic frequencies among 41 Juglans populations were determined at 19 RFLP loci by hybridizing single locus probes to walnut DNAs digested with the restriction endonuclease EcoRI or HindIII. A 10-fold difference in species heterozygosity levels was seen among species in different sections of the genus. Differentiation among conspecific populations varied over threefold between species. Genetic differentiation among conspecific east Asian populations was larger than that seen among east Asian species, while the opposite trend was seen for Western Hemisphere species. Taxonomic affinities were also indicated by these results, suggesting that J. cinerea should be included as part of section Cardiocaryon rather than as a unique section, Trachycaryon. Juglans hindsii is classified as a distinct species and not a subspecies of J. californica. Strategies for germplasm preservation and species requiring marked collection efforts are given.

RFLP inheritance and linkage in walnut.

Thirty-two low-copy-number genomic DNA clones from a walnut (Juglans sp.) Pst I genomic library were used to establish a molecular-marker linkage map for walnut. The clones were hybridized to restriction-endonuclease-digested DNA from parent walnut trees involved in an interspecific backcross of (J. hindsii x J. regia) x J. regia in order to identify parental polymorphism. Sixty-three backcross progeny were analyzed to determine the inheritance and linkage of 48 RFLP loci. Sixty-six percent of the walnut cloned sequences detected duplicated, but unlinked, loci. Twelve linkage groups were identified by 42 of the RFLP loci. A Poisson probability method for estimating genome size was utilized to calculate the approximate walnut genome length as 1660 cM and to estimate that 138 markers would be needed to cover 95% of the walnut genome within 20 cM of each marker.