A molecular-marker linkage map has been constructed for perennial ryegrass (Lolium perenne L.) using a one-way pseudo-testcross population based on the mating of a multiple heterozygous individual with a doubled haploid genotype. RFLP, AFLP, isoenzyme, and EST data from four collaborating laboratories within the International Lolium Genome Initiative were combined to produce an integrated genetic map containing 240 loci covering 811 cM on seven linkage groups. The map contained 124 codominant markers, of which 109 were heterologous anchor RFLP probes from wheat, barley, oat, and rice, allowing comparative relationships between perennial ryegrass and other Poaceae species to be inferred. The genetic maps of perennial ryegrass and the Triticeae cereals are highly conserved in terms of synteny and colinearity. This observation was supported by the general agreement of the syntenic relationships between perennial ryegrass, oat, and rice and those between the Triticeae and these species. A lower level of synteny and colinearity was observed between perennial ryegrass and oat compared with the Triticeae, despite the closer taxonomic affinity between these species. It is proposed that the linkage groups of perennial ryegrass be numbered in accordance with these syntenic relationships, to correspond to the homoeologous groups of the Triticeae cereals.Key words: Lolium perenne, genetic linkage map, RFLP, AFLP, conserved synteny.Résumé : Une carte génétique composée de marqueurs moléculaires a été produite pour l'ivraie vivace (Lolium perenne L.) à l'aide d'une population issue d'un pseudo-testcross unidirectionnel. Les parents étaient, d'une part, un individu multiple hétérozygote et, d'autre part, un génotype haploïde doublé. Des données pour des marqueurs RFLP, AFLP, isoenzymatiques ainsi que des EST ont été contribuées par quatre laboratoires faisant partie du « International Lolium Genome Initiative (ILGI) ». Ces données ont été combinées pour produire une carte génétique intégrée comprenant 240 locus, formant sept groupes de liaison et s'étendant sur 811 cM. La carte compte 124 marqueurs codominants dont 169 sont des sondes-repères RFLP hétérologues provenant du blé, de l'orge, de l'avoine ou du riz. Ces sondes permettent d'examiner les relations entre l'ivraie vivace et d'autres espèces de graminées. Les cartes génétiques de l'ivraie vivace et des céréales de la tribu des hordées sont très conservées en termes de synténie et de colinéarité. Cette conclusion s'appuie sur une concordance générale au niveau des relations de synténie entre l'ivraie vivace, l'avoine et le riz ainsi qu'entre les hordées et ces espèces. Un plus faible niveau de synténie et de colinéarité a été observé entre l'ivraie vivace et l'avoine par rapport aux hordées, malgré la proximité taxinomique entre ces espèces. Il est suggéré que les groupes de liaison chez l'ivraie vivace soient numérotés en fonction des relations de synténie de façon à correspondre aux groupes d'homéologues chez les céréales.

Here we report the draft genome sequence of perennial ryegrass (Lolium perenne), an economically important forage and turf grass species that is widely cultivated in temperate regions worldwide. It is classified along with wheat, barley, oats and Brachypodium distachyon in the Pooideae sub-family of the grass family (Poaceae). Transcriptome data was used to identify 28,455 gene models, and we utilized macro-co-linearity between perennial ryegrass and barley, and synteny within the grass family, to establish a synteny-based linear gene order. The gametophytic self-incompatibility mechanism enables the pistil of a plant to reject self-pollen and therefore promote out-crossing. We have used the sequence assembly to characterize transcriptional changes in the stigma during pollination with both compatible and incompatible pollen. Characterization of the pollen transcriptome identified homologs to pollen allergens from a range of species, many of which were expressed to very high levels in mature pollen grains, and are potentially involved in the self-incompatibility mechanism. The genome sequence provides a valuable resource for future breeding efforts based on genomic prediction, and will accelerate the development of new varieties for more productive grasslands.

A key gene involved in plant senescence, mutations of which partially disable chlorophyll catabolism and confer stay-green leaf and cotyledon phenotypes, has been identified in Pisum sativum, Arabidopsis thaliana, and Festuca pratensis by using classical and molecular genetics and comparative genomics. A stay-green locus in F. pratensis is syntenically equivalent to a similar stay-green locus on rice chromosome 9. Functional testing in Arabidopsis of a homolog of the rice candidate gene revealed (i) senescence-associated gene expression and (ii) a stay-green phenotype after RNA interference silencing. Genetic mapping in pea demonstrated cosegregation with the yellow/green cotyledon polymorphism (I/i) first reported by Gregor Mendel in 1866.

As part of an initiative to develop Brachypodium distachyon as a genomic ''bridge'' species between rice and the temperate cereals and grasses, a BAC library has been constructed for the two diploid (2n ¼ 2x ¼ 10) genotypes, ABR1 and ABR5. The library consists of 9100 clones, with an approximate average insert size of 88 kb, representing 2.22 genome equivalents. To validate the usefulness of this species for comparative genomics and gene discovery in its larger genome relatives, the library was screened by PCR using primers designed on previously mapped rice and Poaceae sequences. Screening indicated a degree of synteny between these species and B. distachyon, which was confirmed by fluorescent in situ hybridization of the marker-selected BACs (BAC landing) to the 10 chromosome arms of the karyotype, with most of the BACs hybridizing as single loci on known chromosomes. Contiguous BACs colocalized on individual chromosomes, thereby confirming the conservation of genome synteny and proving that B. distachyon has utility as a temperate grass model species alternative to rice.

The genetic control of induction to flowering has been studied extensively in both model and crop species because of its fundamental biological and economic significance. An ultimate aim of many of these studies has been the application of the understanding of control of flowering that can be gained from the study of model species, to the improvement of crop species. The present study identifies a region of genetic synteny between rice and Lolium perenne, which contains the Hd3 heading-date QTL in rice and a major QTL, accounting for up to 70% of the variance associated with heading date in L. perenne. The identification of synteny between rice and L. perenne in this region demonstrates the direct applicability of the rice genome to the understanding of biological processes in other species. Specifically, this syntenic relationship will greatly facilitate the genetic dissection of aspects of heading-date induction by enabling the magnitude of the genetic component of the heading-date QTL in L. perenne to be combined with the sequencing and annotation information from the rice genome.

Molecular-marker loci were used to investigate the adaptation differences between highland and lowland tropical maize. An F2 population from the cross of two inbred lines independently derived from highland and lowland maize germplasm was developed, and extracted F3:4 lines were phenotype in replicated field trials at four thermally diverse tropical testing sites, ranging from lowland to extreme highland (mean growing season temperature range 13.2?24.6?C). Traits closely related with adaptation, such as biomass and grain yield, yield components, days from sowing to male and female flowering, total leaf number, plant height and number of primary tassel branches (TBN), were analyzed. A large line ? environment interaction was observed for most traits. The genetic basis of this interaction was reflected by significant, but systematic, changes from lowland to highland sites in the correlation between the trait value and genomic composition (designated by the proportion of marker alleles with the same origin). Joint analysis of quantitative trait loci (QTLs) over sites detected 5?8 QTLs for each trait (except disease scores, with data only from one site). With the exception of one QTL for TBN, none of these accounted for more than 15% of the total phenotypic variation. In total, detected QTLs accounted for 24?61% of the variation at each site on average. For yield, yield components and disease scores, alleles generally favored the site of origin. Highland-derived alleles had little effect at lowland sites, while lowland-derived alleles showed relatively broader adaptation. Gradual changes in the estimated QTL effects with increasing mean site temperature were observed, and paralleled the observed patterns of adaptation in highland and lowland germplasm. Several clusters of QTLs for different traits reflected the relative importance in the adaptation differences between the two germplasm types, and pleiotropy is suggested as the main cause for the clustering. Breeding for broad thermal adaptation should be possible by pooling genes showing adaptation to specific thermal regimes, though perhaps at the expense of reduced progress for adaptation to a specific site. Molecular marker-assisted selection would be an ideal tool for this task, since it could greatly reduce the linkage drag caused by the unintentional transfer of undesirable traits.Peer reviewe

Summary• Quantitative trait locus (QTL) mapping, which can be a useful tool for dissecting complex traits, has been used here to study the regulation of fructan metabolism in temperate forage grasses.• An F2 mapping family, derived from a high water-soluble carbohydrate (WSC) × low WSC cross, was used to map fructans and the other components of WSC (sucrose, glucose and fructose) in leaves and tiller bases of perennial ryegrass ( Lolium perenne ) in spring and autumn. To characterize regions of the genome that control basic carbohydrate metabolism, a strategy to minimize the impact of genotype (G) × environment (E), and E-effects on the characterization of G-effects, was adopted.• Most traits were highly variable within the family. There was also considerable year-to-year environmental variation. However, significant genetic effects were detected, and several traits had high broad-sense heritability. QTL were identified on chromosomes 1, 2, 5 and 6. Leaf and tiller base QTL did not coincide. Individual QTL explained between 8 and 59% of the total phenotypic variation in the traits.• Fructan turnover, metabolism and their genetic control, and the effect of environment, are discussed in the context of the results. Abbreviations AFLP, amplified fragment length polymorphism; DP, degree of polymerisation; G × E, genotype by environment; HPLC, high-performance liquid chromatography; LOD, log-odds score; QTL, quantitative trait locus (loci); RFLP, restriction fragment length polymorphism; SSR, simple sequence repeat; STS, sequence-tagged site; WSC, watersoluble carbohydrate.

Perennial ryegrass (Lolium perenne L.) is an outcrossing, wind-pollinated species exhibiting a gametophytic two-locus system of self-incompatibility (S and Z). The two incompatibility loci were genotyped in a cross between a doubled-haploid plant crossed as the female parent with a normal heterozygous plant. The S and Z loci were found to segregate in the expected 1:1 ratio and also segregated independently. The two loci were mapped to linkage groups one and two respectively, in accordance with the Triticeae consensus map. In addition, there were notable associations