QTL involved in the modification of cyanidin compounds in black and red raspberry fruit.

Fruit from Rubus species are highly valued for their flavor and nutritive qualities. Anthocyanin content contributes to these qualities, and although many studies have been conducted to identify and quantify the major anthocyanin compounds from various Rubus species, the genetic control of the accumulation of these complex traits in Rubus is not yet well understood. The identification of the regions of the genome involved in the production of anthocyanins is an important first step in identifying the genes underlying their expression. In this study, ultra and high-performance liquid chromatography (UHPLC and HPLC) and two newly developed Rubus linkage maps were used to conduct QTL analyses to explore the presence of associations between concentrations of five anthocyanins in fruit and genotype. In total, 27 QTL were identified on the Rubus linkage maps, four of which are associated with molecular markers designed from transcription factors and three of which are associated with molecular markers designed from anthocyanin biosynthetic pathway candidate genes. The results of this study suggest that, while QTL for anthocyanin accumulation have been identified on six of seven Rubus linkage groups (RLG), the QTL on RLG2 and RLG7 may be very important for genetic control of cyanidin modification in Rubus.

Natural variation in GL1 and its effects on trichome density in Arabidopsis thaliana.

The ultimate understanding of how biological diversity arises, is maintained, and lost depends on identifying the genes responsible. Although a good deal has been discovered about gene function over the past few decades, far less is understood about gene effects, that is, how natural variation in a gene contributes to natural variation in phenotypes. Trichome density in Arabidopsis thaliana is an ideal trait for studies of natural molecular and phenotypic variation, as trichome initiation is genetically well-characterized and trichome density is highly variable in and among natural populations. Here, we show that variation at GLABRA1 (GL1), an R2R3 MYB transcription factor gene, which has a role in trichome initiation, has qualitative and likely quantitative effects on trichome density in natural accessions of A. thaliana. Specifically, we characterize four independent loss-of-function alleles for GL1, each of which yields a glabrous phenotype. Further, we find that a pattern of common polymorphisms confined to the GL1 locus is associated with quantitative variation for trichome density. While mutations resulting in a glabrous phenotype are primarily coding changes, the pattern resulting in quantitative variation spans both coding and regulatory regions. These data show that GL1 is an important source of trichome density variation within A. thaliana and, along with recent reports, suggest that the TTG1 epidermal cell fate pathway generally may be the key molecular genetic source of natural trichome density variation and an important model for the study of molecular evolution.

Construction of black (Rubus occidentalis) and red (R. idaeus) raspberry linkage maps and their comparison to the genomes of strawberry, apple, and peach.

The genus Rubus belongs to the Rosaceae and is comprised of 600-800 species distributed world-wide. To date, genetic maps of the genus consist largely of non-transferable markers such as amplified fragment length polymorphisms. An F(1) population developed from a cross between an advanced breeding selection of Rubus occidentalis (96395S1) and R. idaeus 'Latham' was used to construct a new genetic map consisting of DNA sequence-based markers. The genetic linkage maps presented here are constructed of 131 markers on at least one of the two parental maps. The majority of the markers are orthologous, including 14 Rosaceae conserved orthologous set markers, and 60 new gene-based markers developed for raspberry. Thirty-four published raspberry simple sequence repeat markers were used to align the new maps to published raspberry maps. The 96395S1 genetic map consists of six linkage groups (LG) and covers 309 cM with an average of 10 cM between markers; the 'Latham' genetic map consists of seven LG and covers 561 cM with an average of 5 cM between markers. We used BLAST analysis to align the orthologous sequences used to design primer pairs for Rubus genetic mapping with the genome sequences of Fragaria vesca 'Hawaii 4', Malus × domestica 'Golden Delicious', and Prunus 'Lovell'. The alignment of the orthologous markers designed here suggests that the genomes of Rubus and Fragaria have a high degree of synteny and that synteny decreases with phylogenetic distance. Our results give unprecedented insights into the genome evolution of raspberry from the putative ancestral genome of the single ancestor common to Rosaceae.

Arabidopsis seed coat development: morphological differentiation of the outer integument.

A morphological description of the differentiation of the outer integument of the Arabidopsis thaliana seed is presented. The period covered starts at about the octant embryo stage, extends to the mature seed, and concludes beyond that at the initial stages of seed imbibition. During this period the two-cell-layered outer integument goes through a dramatic differentiation process. The outer cell layer secretes mucilage in a ring between the plasma membrane and the outer cell wall at the corners of the cell. This secretion forces the cytoplasm into a columnar shape in the center of the cell. Before and during this process, starch granules are produced, initially at the center of the outer wall and later within the column. Late in differentiation, the starch granules are degraded as the cell produces a highly reinforced wall surrounding the columnar protoplast and at the radial walls between adjacent cells. This results in a cell containing large amounts of mucilage surrounding and completely outside of a highly reinforced columella. The mucilage and outer wall then dehydrate to leave the columella and radial walls visible as the epidermal plateau and reticulations visible on the mature seed. The inner cell layer of the outer integument also produces and degrades starch granules concomitantly with the outer layer but produces no mucilage. In the mature dry seed the collapsed outer wall remains connected to the top of the columella and the radial walls, but these connections are rapidly broken as the mucilage fully hydrates.