Seed weight and oil content are important properties of cultivated sunflower under complex genetic and environmental control, and associated with morphological and developmental characteristics such as plant height or flowering dates. Using a genetic map with 290 markers for a cross between two inbred sunflower lines and 2 years of observations on F3 families, QTL controlling seed weight, oil content, plant height, plant lodging, flowering dates, maturity dates and delay from flowering to maturity were detected. QTL detected were compared between the F2 and F3 generations and between the 2 years of testing for the F3 families in 1997 and 1999. Some of the QTL controlling seed weight overlapped with those controlling oil content. Several other co-localisations of QTL controlling developmental or morphological characteristics were observed and the relationships between the traits were also shown by correlation analyses. The relationships between all these traits and with resistance to Sclerotinia sclerotiorum and Diaporthe helianthi are discussed.

With the development of genetic maps and the identification of the most-likely positions of quantitative trait loci (QTLs) on these maps, molecular markers for lodging resistance can be identified. Consequently, marker-assisted selection (MAS) has the potential to improve the efficiency of selection for lodging resistance in a breeding program. This study was conducted to identify genetic loci associated with lodging resistance, plant height and reaction to mycosphaerella blight in pea. A population consisting of 88 recombinant inbred lines (RILs) was developed from a cross between Carneval and MP1401. The RILs were evaluated in 11 environments across the provinces of Manitoba, Saskatchewan and Alberta, Canada in 1998, 1999 and 2000. One hundred and ninety two amplified fragment length polymorphism (AFLP) markers, 13 random amplified polymorphic DNA (RAPD) markers and one sequence tagged site (STS) marker were assigned to ten linkage groups (LGs) that covered 1,274 centi Morgans (cM) of the pea genome. Six of these LGs were aligned with the previous pea map. Two QTLs were identified for lodging resistance that collectively explained 58% of the total phenotypic variation in the mean environment. Three QTLs were identified each for plant height and resistance to mycosphaerella blight, which accounted for 65% and 36% of the total phenotypic variation, respectively, in the mean environment. These QTLs were relatively consistent across environments. The AFLP marker that was associated with the major locus for lodging resistance was converted into the sequence-characterized amplified-region (SCAR) marker. The presence or absence of the SCAR marker corresponded well with the lodging reaction of 50 commercial pea varieties.

We investigated the isozyme profiles of antioxidant enzymes in cultivars and lines with different seed productivity in cool climate conditions as a step towards understanding the physiological and genetical mechanisms underlying chilling tolerance in soybean. While no difference in superoxide dismutase, or catalase isozyme profiles was observed among the cultivars and lines tested, we found polymorphism in the ascorbate peroxidase isozyme profile; there were two types, with or without a cytosolic isoform (APX1). The cultivars and lines lacking APX1 proved more tolerant to chilling temperatures, as evaluated by yielding ability. The genotype-dependent deficiency of APX1 was consistent in plants and tissues under various oxidative stress conditions including the exposure to low-temperatures. In addition, the genetic analysis of progeny derived from crossing between cultivars differing in the isozyme profile indicated that the APX1 deficiency is controlled by a single recessive gene (apx1), and is inherited independently of the genes that have previously been identified for their association with chilling tolerance. Molecular and linkage analyses suggested that the variant gene of the APX1-absent genotype coding for a cytosolic APX, which contained a single nucleotide substitution and a single nucleotide deletion in the coding region, is responsible for the genotype-dependent deficiency of APX1. The association of APX1 deficiency with chilling tolerance is discussed in detail.

A complex ancestral resistance (R) gene cluster, localized at the end of linkage group B4, and referred to as the B4 R gene cluster, has been previously genetically characterized. The B4 R gene cluster existed prior to the separation of the two major gene pools of cultivated common bean and contains several resistance specificities effective against the fungus Colletotrichum lindemuthianum. In this paper we report the molecular analysis of four expressed resistance gene candidates (RGCs) that map at the B4 R-cluster and co-localize with R-specificities or R-QTLs effective against C. lindemuthianum. These RGCs have been isolated from two genotypes that are representative of the two major gene pools of common bean: the BA8 and BA11 RGCs originating from the Mesoamerican BAT93 genotype, and the JA71 and JA78 RGCs originating from the Andean JaloEEP558 genotype. These RGCs encode NBS-LRR resistance-like proteins that are closely similar to the tomato I2 R-protein. Based upon sequence comparisons and genetic localization, we established that these four bean RGCs belong to two different subfamilies of R-sequences independently of their gene pool of origin. No feature discriminating the four RGCs according to their gene pool of origin has been observed yet. Comparative sequence analyses of the full-length RGCs and their flanking genomic sequences confirmed the ancestral origin of the B4 R-cluster.

A BC2F2 population developed from an interspecific cross between Oryza sativa (cv IR64) and O. rufipogon (IRGC 105491) was used in an advanced backcross QTL analysis to identify and introduce agronomically useful genes from this wild relative into the cultivated gene pool. The objectives of this study were: (1) to identify putative yield and yield component QTLs that can be useful to improve the elite cultivar IR64; (2) to compare the QTLs within this study with previously reported QTLs in rice as the basis for identifying QTLs that are stable across different environments and genetic backgrounds; and (3) to compare the identified QTLs with previously reported QTLs from maize to examine the degree of QTL conservation across the grass family. Two hundred eighty-five families were evaluated in two field environments in Indonesia, with two replications each, for 12 agronomic traits. A total of 165 markers consisting of 131 SSRs and 34 RFLPs were used to construct the genetic linkage map. By employing interval mapping and composite interval mapping, 42 QTLs were identified. Despite its inferior performance, 33% of the QTL alleles originating from O. rufipogon had a beneficial effect for yield and yield components in the IR64 background. Twenty-two QTLs (53.4%) were located in similar regions as previously reported rice QTLs, suggesting the existence of stable QTLs across genetic backgrounds and environments. Twenty QTLs (47.6%) were exclusively detected in this study, uncovering potentially novel alleles from the wild, some of which might improve the performance of the tropical indica variety IR64. Additionally, several QTLs for plant height, grain weight, and flowering time detected in this study corresponded to homeologous regions in maize containing previously detected maize QTLs for these traits.

A differentially expressed OsIM1 gene was isolated from rice salt-tolerant mutant M-20 by differential display. Sequence analysis revealed that the amino-acid sequence of OsIM1 showed 66% and 62% identity with PTOX from tomato (Capsicum annuum) and AtIM from Arabidopsis, both of which encoded chloroplast-orientated terminal oxidase. Comparison of the nucleotide sequence of the OsIM1 cDNA with its genomic sequence revealed that OsIM1 genomic DNA contained nine exons and eight introns. A pseudo-transcript (OsIM2), which probably resulted from the abnormal splicing of the OsIM1 pre-mRNA, was also identified. Southern-blot analysis showed that there existed only one copy of the OsIM1 gene in the rice genome. RFLP analysis located it on rice chromosome 3. The Northern blot revealed that OsIM1 was up-regulated by NaCl and ABA treatment. RT-PCR analysis indicated that OsIM1 and OsIM2 co-existed in the OsIM transcript pool, and the ratio of OsIM1/OsIM2 was differentially regulated by salt stress in the salt-sensitive variety and the salt-tolerant varieties.

A new source of resistance to the highly virulent and widespread biotype L of the Hessian fly, Mayetiola destructor (Say), was identified in an accession of tetraploid durum wheat, Triticum turgidum Desf., and was introgressed into hexaploid common wheat, Triticum aestivum L. Genetic analysis and deletion mapping revealed that the common wheat line contained a single locus for resistance, H31, residing at the terminus of chromosome 5BS. H31 is the first Hessian fly-resistance gene to be placed on 5BS, making it unique from all previously reported sources of resistance. AFLP analysis identified two markers linked to the resistance locus. These markers were converted to highly specific sequence-tagged site markers. The markers are being applied to the development of cultivars carrying multiple genes for resistance to Hessian fly biotype L in order to test gene pyramiding as a strategy for extending the durability of deployed resistance.

Genetic diversity among 13 different cultivars of date palm (Phoenix dactylifera L.) of Saudi Arabia was studied using random amplified polymorphic DNA (RAPD) markers. The screening of 140 RAPD primers allowed selection of 37 primers which revealed polymorphism, and the results were reproducible. All 13 genotypes were distinguishable by their unique banding patterns produced by 37 selected primers. Cluster analysis by the unweighted paired group method of arithmetic mean (UPGMA) showed two main clusters. Cluster A consisted of five cultivars (Shehel, Om-Kobar, Ajwa, Om-Hammam and Bareem) with 0.59-0.89 Nei and Li's coefficient in the similarity matrix. Cluster B consisted of seven cultivars (Rabeeha, Shishi, Nabtet Saif, Sugai, Sukkary Asfar, Sukkary Hamra and Nabtet Sultan) with a 0.66-0.85 Nei and Li's similarity range. Om-Hammam and Bareem were the two most closely related cultivars among the 13 cultivars with the highest value in the similarity matrix for Nei and Li's coefficient (0.89). Ajwa was closely related with Om-Hammam and Bareem with the second highest value in the similarity matrix (0.86). Sukkary Hamra and Nabtet Sultan were also closely related, with the third highest value in the similarity matrix (0.85). The cultivar Barny did not belong to any of the cluster groups. It was 34% genetically similar to the rest of the 12 cultivars. The average similarity among the 13 cultivars was more than 50%. As expected, most of the cultivars have a narrow genetic base. The results of the analysis can be used for the selection of possible parents to generate a mapping population. The variation detected among the closely related genotypes indicates the efficiency of RAPD markers over the morphological and isozyme markers for the identification and construction of genetic linkage maps.

Although molecular methods are a major advance over phenological or root connectivity studies in the identification of clonal plants, there is still a level of ambiguity associated with two types of error: misidentification of genetically similar seedlings as clones and misidentification of dissimilar fingerprints from clones as genetically distinct individuals. We have addressed the second of these error types by determining the level of variation for AFLP fingerprints in Salix exigua, and then by developing a threshold value of Jaccard's similarity index for assigning individuals to clones or to siblings. Variation in AFLP banding patterns among clones was partitioned into three potential sources; clones, stems within-clones and foliage within-stems. Most of the variation was attributable to clones and then to stems within-clones. To provide an objective means of identifying clones, we developed a method for establishing a threshold similarity index to assign individuals to the same clone. Our method yielded a Jaccard similarity threshold of 0.983 that resulted in a potential pairwise error rate of 8.1% putative clone assigned to siblings and 1.5% sibling assigned to clones. The method was tested on independent clonal and sibling individuals resulting in the same threshold value and similar error rates. We applied our method to assign individuals to clones in a population of S. exigua along the Cosumnes River, California. A total of 11 clones were identified, with one clone including 43% of the individuals sampled. Our results show that this approach can be useful in the accurate identification of clones.