Ecological and evolutionary drivers of phenotypic and genetic variation in the European crabapple [Malus sylvestris (L.) Mill.], a wild relative of the cultivated apple.

BACKGROUND AND AIMS: Studying the relationship between phenotypic and genetic variation in populations distributed across environmental gradients can help us to understand the ecological and evolutionary processes involved in population divergence. We investigated the patterns of genetic and phenotypic diversity in the European crabapple, Malus sylvestris, a wild relative of the cultivated apple (Malus domestica) that occurs naturally across Europe in areas subjected to different climatic conditions, to test for divergence among populations. METHODS: Growth rates and traits related to carbon uptake in seedlings collected across Europe were measured in controlled conditions and associated with the genetic status of the seedlings, which was assessed using 13 microsatellite loci and the Bayesian clustering method. Isolation-by-distance, isolation-by-climate and isolation-by-adaptation patterns, which can explain genetic and phenotypic differentiation among M. sylvestris populations, were also tested. KEY RESULTS: A total of 11.6 % of seedlings were introgressed by M. domestica, indicating that crop-wild gene flow is ongoing in Europe. The remaining seedlings (88.4 %) belonged to seven M. sylvestris populations. Significant phenotypic trait variation among M. sylvestris populations was observed. We did not observe significant isolation by adaptation; however, the significant association between genetic variation and the climate during the Last Glacial Maximum suggests that there has been local adaptation of M. sylvestris to past climates. CONCLUSIONS: This study provides insight into the phenotypic and genetic differentiation among populations of a wild relative of the cultivated apple. This might help us to make better use of its diversity and provide options for mitigating the impact of climate change on the cultivated apple through breeding.

Contrasted patterns of selection since maize domestication on duplicated genes encoding a starch pathway enzyme.

Maize domestication from teosinte (Zea mays ssp. parviglumis) was accompanied by an increase of kernel size in landraces. Subsequent breeding has led to a diversification of kernel size and starch content among major groups of inbred lines. We aim at investigating the effect of domestication on duplicated genes encoding a key enzyme of the starch pathway, the ADP-glucose pyrophosphorylase (AGPase). Three pairs of paralogs encode the AGPase small (SSU) and large (LSU) subunits mainly expressed in the endosperm, the embryo and the leaf. We first validated the putative sequence of LSU(leaf) through a comparative expression assay of the six genes. Second, we investigated the patterns of molecular evolution on a 2 kb coding region homologous among the six genes in three panels: teosintes, landraces, and inbred lines. We corrected for demographic effects by relying on empirical distributions built from 580 previously sequenced ESTs. We found contrasted patterns of selection among duplicates: three genes exhibit patterns of directional selection during domestication (SSU(end), LSU(emb)) or breeding (LSU(leaf)), two exhibit patterns consistent with diversifying (SSU(leaf)) and balancing selection (SSU(emb)) accompanying maize breeding. While patterns of linkage disequilibrium did not reveal sign of coevolution between genes expressed in the same organ, we detected an excess of non-synonymous substitutions in the small subunit functional domains highlighting their role in AGPase evolution. Our results offer a different picture on AGPase evolution than the one depicted at the Angiosperm level and reveal how genetic redundancy can provide flexibility in the response to selection.

Maize Sh2 gene is constrained by natural selection but escaped domestication.

In Zea mays L., we studied the molecular evolution of Shrunken2 (Sh2), a gene that encodes the large subunits of a major enzyme in endosperm starch biosynthesis, ADP-glucose pyrophosphorylase. We compared 4669 bp of the Sh2 coding region on 50 accessions of maize and teosinte. Very few nucleotide polymorphisms were found when compared with other genes in Z. mays, revealing an effect of purifying selection in the whole species that predates domestication. Additionally, the comparison of Sh2 sequences in all Z. mays subspecies and outgroups Z. diploperennis and Tripsacum dactyloides suggests the occurrence of an ancient selective sweep in the Sh2 3' region. The amount and nature of nucleotide diversity are similar in both maize and teosinte, confirming previous results that suggested that Sh2 has not been involved in maize domestication. The very low level of nucleotide diversity as well as the highly conserved protein sequence suggest that natural selection retained effective Sh2 allele(s) long before agriculture started, making human selection inefficient on this gene.

Characterization of novel proteins affected by the o2 mutation and expressed during maize endosperm development.

The effect of the o2 mutation on protein expression during grain development was examined by two-dimensional electrophoresis (2-D PAGE) in seven different pairs of near-isogenic maize lines. The aim was to identify a set of proteins that are consistently affected in mutants, and which could be the products of new genes that are direct or indirect targets of the transcriptional activator O2. The abundance of 36 polypeptides was found to be modified in the seven backgrounds. Seventeen polypeptides were present in greater amounts in wild types than in mutants, and most of these were affected early. The remaining polypeptides were expressed at higher levels in mutants than in the wild types and were generally affected later in development, suggesting that they might be products of indirect targets of O2. Products of known direct target genes such as zeins, b-32 protein and a pyruvate orthophospate dikinase were included in the first set of polypeptides. Microsequencing of internal stretches of 15 amino acids was performed for thirteen polypeptides and homologies with sequences stored in databases were found for nine of them. Enzymes belonging to various metabolic pathways were tentatively identified, most of which were not previously known to be affected by the o2 mutation. These results confirm that the O2 gene could act as a connecting regulatory gene for different pathways of grain metabolism.

Characterization of storage proteins in Daucus carota L.: two novel proteins display zygotic embryo specificity.

Although maturation-related proteins are well known in the endosperm of albuminous seeds, an important question is whether the zygotic embryo possesses its own maturation proteins. We report on the isolation and partial characterization of storage proteins of carrot (Daucus carota L. var Nandor) dry achenes and isolated zygotic embryos, using one- and two-dimensional electrophoresis techniques, HPLC and amino acid sequencing. The presence of a series of abundant polypeptides showing charge heterogeneity, that are rapidly degraded upon germination, was revealed in the endosperm. These proteins consisted of glycoproteins, the most abundant of which displayed a molecular mass (M(r)) of 58,000, albumins of M(r) 42,000 comprising at least one beta-1,3-glucanase, and two globulins of M(r) 90,000 and 50,000-55,000 respectively, the second being an oligomer composed of three subunits of M(r) 13,000, 20,000 and 30,000. None of these storage proteins identified in the endosperm were detected in zygotic embryos. In contrast, two novel proteins were isolated from zygotic embryos, namely a globulin family of M(r) 50,000 and pI 6.3-6.8, which was named "daucin", and a late embryogenesis abundant (LEA) protein family of M(r) 25,000 and pI 6.3-6.6, named "RAB25". Since the latter proteins are apparently absent of the endosperm, these results suggest that the maturation of carrot zygotic embryos requires its own specific set of storage and LEA proteins.

Somatic and zygotic embryos of Daucus carota L. display different protein patterns until conversion to plants.

Total protein patterns of different developmental stages of carrot zygotic and somatic embryos revealed by one- and two-dimensional gel electrophoresis were compared using statistical dissimilarity index matrix, and some major polypeptides were partially sequenced. In spite of similar morphology, the protein patterns of somatic embryos at the torpedo stage were clearly different from those of zygotic embryos. In particular, none of the proteins specific of zygotic embryos required for maturation, previously identified, were accumulated in somatic embryos, namely the daucin (a globulin-type storage protein), the RAB25 protein (a late embryogenesis abundant protein) (Dodeman et al. 1998), as well as a novel globulin of M(r) 30,000, that we proposed to name apiacin. Somatic plantlets and seedlings also showed different patterns. This discrepancy likely reflects culture conditions, since somatic embryos recover a protein pattern close to that of seedlings after conversion to plant and growth on a carbon-free medium.

Characterizing allelic proteins for genome mapping in maize.

Mapping cDNA probes in order to construct genetic linkage maps is becoming a widespread strategy for genome analysis and gene isolation, particularly in cultivated plant species. Nevertheless, almost all cDNAs reveal two or more unlinked loci, making it difficult to identify the gene(s) actually expressed. In a highly polymorphic species, such as maize, two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) of proteins may circumvent this limitation. With the analysis of various segregating populations, we previously showed that the apparent position shifts of proteins on the 2-D gels are monogenic and codominant. In this paper we compared allelic proteins on the basis of their high performance liquid chromatography (HPLC) profile and partial amino acid sequences. In a sample of 20 position shifts, the allelic proteins appeared to be similar in all but one case, strongly suggesting that polymorphism of structural genes is involved. Thus 2-D PAGE could prove to be a useful tool for genome mapping: when a cDNA probe detects several loci, a position shift of the encoded protein will allow the identification of the gene translated in the organ considered.