AFLP diversity in the common vetch ( Vicia sativa L.) on the world scale

Incorporating the pedigree information in multi-environment trial analyses for improving common vetch

Common vetch is one of the most profitable forage legumes due to its versatility in end-use which includes grain, hay, green manure, and silage. Furthermore, common vetch is one of the best crops to rotate with cereals as it can increase soil fertility which results in higher yield in cereal crops. The National Vetch Breeding Program located in South Australia is focused on developing new vetch varieties with higher grain and dry matter yields, better resistance to major diseases, and wider adaptability to Australian cropping environments. As part of this program, a study was conducted with 35 field trials from 2015 to 2021 in South Australia, Western Australia, Victoria, and New South Wales with the objective of determining the best parents for future crosses and the vetch lines with highest commercial value in terms of grain yield production. A total of 392 varieties were evaluated. The individual field trials were combined in a multi-environment trial data, where each trial is identified as an environment. Multiplicative mixed models were used to analyze the data and a factor analytic approach to model the genetic by environment interaction effects. The pedigree of the lines was then assembled and incorporated into the analysis. This approach allowed to partition the total effects into additive and non-additive components. The total and additive genetic effects were inspected across and within environments for broad and specific selections of the lines with the best commercial value and the best parents. Summary measures of overall performance and stability were used to aid with selection of parents. To the best of our knowledge, this is the first study which used the pedigree information to breed common vetch. In this paper, the application of this statistical methodology has been successfully implemented with the inclusion of the pedigree improving the fit of the models to the data with most of the total genetic variation explained by the additive heritable component. The results of this study have shown the importance of including the pedigree information for common vetch breeding programs and have improved the ability of breeders to select superior commercial lines and parents.

Optimizing Sample Size to Assess the Genetic Diversity in Common Vetch (Vicia sativa L.) Populations Using Start Codon Targeted (SCoT) Markers

Common vetch (Vicia sativa subsp. sativa L.) is a self-pollinating annual forage legume with worldwide importance. Here, we investigate the optimal number of individuals that may represent the genetic diversity of a single population, using Start Codon Targeted (SCoT) markers. Two cultivated varieties and two wild accessions were evaluated using five SCoT primers, also testing different sampling sizes: 1, 2, 3, 5, 8, 10, 20, 30, 40, 50, and 60 individuals. The results showed that the number of alleles and the Polymorphism Information Content (PIC) were different among the four accessions. Cluster analysis by Unweighted Pair Group Method with Arithmetic Mean (UPGMA) and STRUCTURE placed the 240 individuals into four distinct clusters. The Expected Heterozygosity (H_E) and PIC increased along with an increase in sampling size from 1 to 10 plants but did not change significantly when the sample sizes exceeded 10 individuals. At least 90% of the genetic variation in the four germplasms was represented when the sample size was 10. Finally, we concluded that 10 individuals could effectively represent the genetic diversity of one vetch population based on the SCoT markers. This study provides theoretical support for genetic diversity, cultivar identification, evolution, and marker-assisted selection breeding in common vetch.

Systematics, biogeography, and character evolution of the legume tribe Fabeae with special focus on the middle-Atlantic island lineages

BACKGROUND

Tribe Fabeae comprises about 380 legume species, including some of the most ancient and important crops like lentil, pea, and broad bean. Breeding efforts in legume crops rely on a detailed knowledge of closest wild relatives and geographic origin. Relationships within the tribe, however, are incompletely known and previous molecular results conflicted with the traditional morphology-based classification. Here we analyse the systematics, biogeography, and character evolution in the tribe based on plastid and nuclear DNA sequences.

RESULTS

Phylogenetic analyses including c. 70% of the species in the tribe show that the genera Vicia and Lathyrus in their current circumscription are not monophyletic: Pisum and Vavilovia are nested in Lathyrus, the genus Lens is nested in Vicia. A small, well-supported clade including Vicia hirsuta, V. sylvatica, and some Mediterranean endemics, is the sister group to all remaining species in the tribe. Fabeae originated in the East Mediterranean region in the Miocene (23-16 million years ago (Ma)) and spread at least 39 times into Eurasia, seven times to the Americas, twice to tropical Africa and four times to Macaronesia. Broad bean (V. faba) and its sister V. paucijuga originated in Asia and might be sister to V. oroboides. Lentil (Lens culinaris ssp. culinaris) is of Mediterranean origin and together with eight very close relatives forms a clade that is nested in the core Vicia, where it evolved c. 14 Ma. The Pisum clade is nested in Lathyrus in a grade with the Mediterranean L. gloeosperma, L. neurolobus, and L. nissolia. The extinct Azorean endemic V. dennesiana belongs in section Cracca and is nested among Mediterranean species. According to our ancestral character state reconstruction results, ancestors of Fabeae had a basic chromosome number of 2n=14, an annual life form, and evenly hairy, dorsiventrally compressed styles.

CONCLUSIONS

Fabeae evolved in the Eastern Mediterranean in the middle Miocene and spread from there across Eurasia, into Tropical Africa, and at least seven times to the Americas. The middle-Atlantic islands were colonized four times but apparently did not serve as stepping-stones for Atlantic crossings. Long-distance dispersal events are relatively common in Fabeae (seven per ten million years). Current generic and infrageneric circumscriptions in Fabeae do not reflect monophyletic groups and should be revised. Suggestions for generic level delimitation are offered.

Identification and genetic analysis of the APOSPORY locus in Hypericum perforatum L

The introduction of apomixis - seed formation without fertilization - into crop plants is a long-held goal of breeding research, since it would allow for the ready fixation of heterozygosity. The genetic basis of apomixis, whether of the aposporous or the diplosporous type, is still only poorly understood. Hypericum perforatum (St John's wort), a plant with a small genome and a short generation time, can be aposporous and/or parthenogenetic, and so represents an interesting model dicot for apomixis research. Here we describe a genetic analysis which first defined and then isolated a locus (designated HAPPY for Hypericum APOSPORY) associated with apospory. Amplified fragment length polymorphism (AFLP) profiling was used to generate a cleaved amplified polymorphic sequence (CAPS) marker for HAPPY which co-segregated with apospory but not with parthenogenesis, showing that these two components of apomixis are independently controlled. Apospory was inherited as a dominant simplex gene at the tetraploid level. Part of the HAPPY sequence is homologous to the Arabidopsis thaliana gene ARI7 encoding the ring finger protein ARIADNE7. This protein is predicted to be involved in various regulatory processes, including ubiquitin-mediated protein degradation. While the aposporous and sexual alleles of the HAPPY component HpARI were co-expressed in many parts of the plant, the gene product of the apomict's allele is truncated. Cloning HpARI represents the first step towards the full characterization of HAPPY and the elucidation of the molecular mechanisms underlying apomixis in H. perforatum.

Two extinct diploid progenitors were involved in allopolyploid formation in the Hordeum murinum (Poaceae: Triticeae) taxon complex

Wall barley (Hordeum murinum) occurs with three subspecies, naturally distributed from southern Central Asia through the Mediterranean region to northwestern Europe, but now is an invasive weed in many parts of the world. Subspecies glaucum is diploid, while subspp. murinum and leporinum are tetraploids, the latter also occurring with a hexaploid cytotype. Earlier analyses were inconclusive regarding auto- or allopolyploid origins of subspp. murinum and leporinum. We analyzed the phylogeny of the taxon group using amplified fragment length polymorphisms (AFLP), sequences of cloned PCR products of the nuclear ribosomal DNA internal transcribed spacer region (ITS), a part of the nuclear single-copy gene topoisomerase 6 (Topo6) spanning two introns, and sequences of the chloroplast trnL-F region together with length variation at six chloroplast microsatellite loci, including multiple individuals of each subspecies and cytotype, covering the entire natural distribution area of the species. Phylogenetic analyses with all used markers differentiate diploid and polyploids. Sequences of both nuclear regions indicated that diploid subsp. glaucum was involved in tetraploid formation together with a now extinct species belonging to the same Hordeum genome group (Xu). Furthermore, AFLP and ITS analyses suggest that a third, though closely related extinct taxon contributed to hexaploid formation. No method was able to discern tetraploid subspp. murinum and leporinum, which we attribute to the young age of subsp. murinum. None of the used molecular markers revealed a strong geographic pattern of genetic variation that would allow comprehensive phylogeographic analysis, most probably due to the very effective seed dispersal of the taxa.

Use of AFLP for differentiation of Metschnikowia pulcherrima strains for postharvest disease biological control

Metschnikowia pulcherrima occurs naturally on fruits, buds and floral parts of apple trees. Some strains are effective as biocontrol agents against postharvest decay of apples and other fruits. The usefulness of the amplified fragment length polymorphism (AFLP) technique was evaluated for the genetic analysis of 26 strains of M. pulcherrima, isolated from different sources in different geographical regions. With six AFLP primer pairs, 729 polymorphic bands were scored. The technique showed a high discriminatory power. Genetic relationships between strains were also estimated using AFLP. All the isolates from the carposphere of apple, previously tested as biocontrol agents, were grouped in a single cluster with a high bootstrap value (97), indicating robustness and reproducibility. AFLP patterns could clearly distinguish the different strains and research is in progress to use some putative specific bands for single tag sequence (STS) conversion to develop isolate-specific markers.

Isozyme evidence on the specific distinctness and phylogenetic position of Vicia incisa (Fabaceae)

Vicia incisa is a taxonomically controversial species that has been also treated as a subspecies of V. sativa because of a great morphological similarity. The phylogenetic position of V. incisa is uncertain because various DNA markers have provided contradictory results. Isozymes of V. incisa encoded by 15 loci and resolved with the use of polyacrylamide gel electrophoresis (PAGE) are described and compared with those of seven related species belonging to sections Vicia, Sepium, Lathyroides and Pseudolathyrus in order to get new evidence about its taxonomic rank and phylogenetic position. Phylogenetic relationships are analyzed with maximum parsimony and neighbour joining methods. Vicia incisa is shown to differ from all three subspecies of V. sativa including, sativa, cordata and nigra, by alternate variants of ten isozymes out of 15 analysed. Instead, V. incisa has much more similarity to V. grandiflora and V. sepium by sharing eight isozyme variants which differ from the subspecies of V. sativa. The most parsimony and neighbour joining analyses of the isozyme variation placed V. incisa as basally linked to the V. grandiflora and V. sepium species couple in the clade of section Sepium (= sect. Atossa), while the subspecies of V. sativa together with V. lathyroides formed a separate clade of section Vicia. The isozyme data provide further support to the species status of V. incisa.

Genetic divergence of climatically marginal populations of Vicia pisiformis on the Scandinavian Peninsula

Vicia pisiformis L. is a perennial leguminous plant with a main distribution in broadleaved forest-steppes of eastern Europe. The species is classified as endangered (EN) according to the IUCN red-lists in both Norway and Sweden, due to severe fragmentation, small population sizes and continuing population decline. The populations on the Scandinavian Peninsula constitute the northern limit of the species distribution and are mostly restricted to warm stony slopes with predominantly southern aspects. In this study we used the AFLP method, which is a high-resolution genetic fingerprint method. Samples were collected from 22 Scandinavian populations. The overall genetic structure was analysed in an AMOVA, in a Mantel test and through constrained correspondence analysis (CCA). The ordination scores representing non-geographic genetic divergence were extracted from the CCA and analysed in a linear model using habitat variables and population size as explanatory variables. We found (i) a strong geographic structure, (ii) significant genetic divergence between populations, (iii) that this genetic divergence remained significant even after removing the effect of geography in a partial CCA and (iv) that the remaining non-geographic part of genetic divergence (distance from the ordination centre) was associated with aspect, populations with a northern aspect were more genetically divergent. Aspect explains more variation than population size and is the only variable retained in the minimal adequate model. We suggest that local adaptation has caused this divergence from an expected geographical pattern of genetic variation. This explanation is further supported by the association between aspect and specific AFLP fragments.

Phylogenetic analyses within three sections of the genus Vicia

The averaged genomic similarities based on multilocus randomly amplified polymorphic DNA (RAPD) were calculated for eight species representing three sections of the genus Vicia: faba, bithynica and narbonensis. The frequency of appearance of the sequences corresponding to 25 decamers selected at random from genomes of different Fabace species was checked, and a high correlation with the frequency observed for Vicia allowed us to assume their similar weight in typing Vicia species. The RAPD-based similarity coefficients compared with those related to whole genome hybridization with barley rDNA and those based on restriction fragment length polymorphism (RFLP) revealed similar interspecies relationships. The averaged RAPD-based similarity coefficient (Pearson's) was 0.68 for all the species, and was sectionspecific: 0.43 (bithynica), 0.50 (faba) and 0.73 (narbonensis). The averaged similarity coefficient for V. serratifolia (0.63) placed it apart from the rest (0.75) of its section. The results correspond to the interspecies relationships built upon non-genetic data. The averaged similarity coefficient for particular RAPD was related to the presence and type of tandemly repeated motif in a primer: 0.7-0.8 for heterodimers (GC, AG, CA, GT, CT), 0.5-0.6 for homodimers (CC, GG) and 0.6 for no repeat, indicating the sensitivity of diversity range to the type of target sequences.

Differentiation in a geographical mosaic of plants coevolving with ants: phylogeny of the Leonardoxa africana complex (Fabaceae: Caesalpinioideae) using amplified fragment length polymorphism markers

Comprising four allopatric subspecies that exhibit various grades of ant-plant interactions, from diffuse to obligate and symbiotic associations, the Leonardoxa africana complex (Fabaceae, Caesalpinioideae) provides a good opportunity to investigate the evolutionary history of ant-plant mutualisms. A previous study of the L. africana complex based on chloroplast DNA noncoding sequences revealed a lack of congruence between clades suggested by morphological and plastid characters. In this study, we analysed phylogenetic relationships within the L. africana complex using a Bayesian probability approach on amplified fragment length polymorphism markers. The results reported permit partial validation of the four subspecies of L. africana previously defined by morphological and ecological markers. Incongruences between phylogenies based on chloroplast DNA and amplified fragment length polymorphism markers are discussed in the light of morphological and ecological data, and confronted with hypotheses of convergence, lineage sorting and introgression.