Simple sequence repeat (SSR) and other DNA sequence-tagged site markers can be genotyped more rapidly and cost efficiently by simultaneously amplifying multiple loci (multiplex PCR). The development of PCR-multiplexes for a nearly genome-wide framework of 78 SSR marker loci in cultivated sunflower ( Helianthus annuus L.) is described herein. The most outstanding single-locus SSR markers in the public collection (300 out of 1,089) were identified and screened for polymorphisms among 24 elite inbred lines, preparatory to selecting SSR markers for testing in multiplex PCRs. The selected SSR markers produced robust PCR products, amplified a single locus each, were polymorphic among elite inbred lines (minimum, mean and maximum heterozygosities were 0.08, 0.53 and 0.85, respectively), and supply a dense genome-wide framework of predominantly or completely codominant, single-locus DNA markers for molecular breeding and genomics research in sunflower. Thirteen six-locus multiplex PCRs were developed for 78 SSR marker loci strategically positioned throughout the sunflower genome (three to five per linkage group) by identifying compatible SSR primer combinations and optimizing multiplex PCR protocols. The multiplexed SSR markers, when coupled with 17 complementary SSR marker loci, create a 'standard genotyping' set ideal for first-pass scans of the genome, as are often needed when screening bulked-segregant DNA samples or mapping phenotypic trait loci. The minimum, mean and maximum heterozygosities of the multiplexed SSR markers were 0.38, 0.62 and 0.83, respectively. The PCR-multiplexes increase genotyping throughput, reduce reagent costs, and are ideal for repetitive genotyping applications where common sets of SSR marker loci are required or advantageous.

In comparison to conventional marker-assisted selection (MAS), which utilizes only a subset of genetic markers associated with a trait to predict breeding values (BVs), genome-wide selection (GWS) improves prediction accuracies by incorporating all markers into a model simultaneously. This strategy avoids risks of missing quantitative trait loci (QTL) with small effects. Here, we evaluated the accuracy of prediction for three corn flowering traits days to silking, days to anthesis, and anthesis-silking interval with GWS based on cross-validation experiments using a large data set of 25 nested association mapping populations in maize (Zea mays). We found that GWS via ridge regression-best linear unbiased prediction (RR-BLUP) gave significantly higher predictions compared to MAS utilizing composite interval mapping (CIM). The CIM method may be selected over multiple linear regression to decrease over-estimations of the efficiency of GWS over a MAS strategy. The RR-BLUP method was the preferred method for estimating marker effects in GWS with prediction accuracies comparable to or greater than BayesA and BayesB. The accuracy with RR-BLUP increased with training sample proportion, marker density, and heritability until it reached a plateau. In general, gains in accuracy with RR-BLUP over CIM increased with decreases of these factors. Compared to training sample proportion, the accuracy of prediction with RR-BLUP was relatively insensitive to marker density.

Simple sequence repeats (SSRs) are abundant and frequently highly polymorphic in transcribed sequences and widely targeted for marker development in eukaryotes. Sunflower (Helianthus annuus) transcript assemblies were built and mined to identify SSRs and insertions-deletions (INDELs) for marker development, comparative mapping, and other genomics applications in sunflower. We describe the spectrum and frequency of SSRs identified in the sunflower EST database, a catalog of 16,643 EST-SSRs, a collection of 484 EST-SSR and 43 EST-INDEL markers developed from common sunflower ESTs, polymorphisms of the markers among the parents of several intraspecific and interspecific mapping populations, and the transferability of the markers to closely and distantly related species in the Compositae. Of 17,904 unigenes in the transcript assembly, 1,956 (10.9%) harbored one or more SSRs with repeat counts of n > or = 5. EST-SSR markers were 1.6-fold more polymorphic among exotic than elite genotypes and 0.7-fold less polymorphic than non-genic SSR markers. Of 466 EST-SSR or INDEL markers screened for cross-species amplification and polymorphisms, 413 (88.6%) amplified alleles from one or more wild species (H. argophyllus, H. tuberosus, H. anomalus, H. paradoxus, and H. deserticola), whereas 69 (14.8%) amplified alleles from safflower (Carthamus tinctorius) and 67 (14.4%) amplified alleles from lettuce (Lactuca sativa); hence, only a fraction were transferable to distantly related genera in the Compositae, whereas most were transferable to wild relatives of H. annuus. Several thousand additional SSRs were identified in the EST database and supply a wealth of templates for EST-SSR marker development in sunflower.

and widely used are single dominant genes (Burlov and Kostyuk, 1976; Pogorletsky and Geshele, 1976; Vran-Orobanche cumana Wallr. (ϭ O. cernua Loefl., broomrape), a ceanu et al., 1980;Burlov and Artemenko, 1983; Ishweedy parasitic plant, is a serious pest of cultivated sunflower (Helianthus annuus L.). Breeding for resistance has been crucial for protecting Shalom-Gordon et al., 1993;Sukno et al., 1998Sukno et al., , 1999; Lu sunflowers from broomrape damage, a challenging task because new et al., 2000). The development of Orobanche-resistant races of the pathogen continually emerge and ultimately defeat known inbred lines is complicated by the weedy and noxious resistance genes. Despite several attempts to identify DNA markers characteristics of the parasite, the need for geographic tightly linked to Orobanche resistance genes, the closest reported thus containment, susceptible escapes and other screening far is 5.6 centimorgans (cM) downstream of Or 5 , a gene for resistance variability, the genetic complexity of physiological races to Race E. The Or 5 locus was placed on the simple sequence repeat of the pathogen, genetic background effects, and geno-(SSR) map of sunflower by genotyping and phenotyping 262 recomtype ϫ environment interactions; hence, Orobanche rebinant inbred lines (RILs) from a cross between elite inbred lines (PHC ϫ sistance is an ideal target for molecular breeding. De-PHD) segregating for resistance to Orobanche Race E. Polymerase spite the complexities underlying Orobanche resistance chain reaction (PCR) multiplexes were used to screen 78 SSR marker loci, strategically positioned throughout the genome, for polymor-breeding in sunflower, race-specific dominant genes seem phisms between resistant and susceptible bulks of PHC ϫ PHD RILs. to protect the crop and are ideal sources of resistance The bulks were polymorphic for three of five Linkage Group 3 (LG3) for single-cross hybrid breeding because they only need SSR marker loci amplified by the PCR multiplexes. The RILs were be incorporated into one parent or the other. Moreover, phenotyped for resistance to Race E and genotyped for 13 SSR markallelic and nonallelic resistance genes can be pyramided ers from the upper end of LG3. The Or 5 locus mapped to the end of by working opposite sides of a hybrid pedigree.LG3 distal to the SSR marker loci (the closest SSR marker locusThe first Orobanche-resistant sunflowers were develwas 6.2 cM downstream of Or 5 . The terminal and perhaps telomeric oped by introgressing resistance genes from Jerusalem location of Or 5 on LG3 sheds light on difficulties, past and present, artichoke (H. tuberosus L.) to cultivated sunflower (Vranof identifying flanking DNA markers tightly linked to Or 5 . ceanu et al., 1980). The first (Race A) resistant cultivars (Kruglik A-41 and Saratovsky 169) were developed by 1916 (Pustovoit, 1976Parker and Riches, 1993). Resis-

Glucosinolates in the new oilseed crop meadowfoam: natural variation in Section Inflexae of Limnanthes, a new glucosinolate in L. floccosa, and QTL analysis in L. alba Abstract Meadowfoam, an oilseed crop grown in the Willamette Valley of Oregon, was developed from Limnanthes alba (Benth.), an herbaceous winter annual native to the west coast of North America. Meadowfoam oil is valued for unique properties attributed to the predominance of very long-chain fatty acids and desaturation at the D5 position. Seed meal remaining after commercial oil extraction contains intact glucosinolates and has potential pesticidal properties owing to isothiocyanate and nitrile glucosinolate derivatives. We identified and quantitated seed glucosinolates in four species of Section Inflexae of Limnanthes to assess variation for this trait in primary and secondary gene pools of cultivated meadowfoam. Glucosinolate content in seeds ranged from 30 to 204 lmol/g dry weight. Only glucolimnanthin (3-methoxybenzyl glucosinolate) was detected in L. alba, L. montana and L. gracilis, but L. floccosa contained glucolepigramin (3-hydroxybenzyl glucosinolate) as well as glucolimnanthin. Two QTL affecting seed glucosinolate content were identified in an inter-subspecific BC 1 population derived from a cross between L. alba subsp. alba and L. alba subsp. versicolor.