Genotyping marker density reduction is not an effective approach in long-term prediction-based breeding of cross-pollinated crops

Reductions of genotyping marker density have been extensively evaluated as potential strategies to reduce the genotyping costs of genomic selection (GS). Low-density marker panels are appealing in GS because they entail lower multicollinearity and computational time-consumption and allow more individuals to be genotyped for the same cost. However, statistical models used in GS are usually evaluated with empirical data, using "static" training sets and populations. This may be adequate for making predictions during a breeding program's initial cycles, but not for the long term. Moreover, to the best of our knowledge, no GS models consider the effect of dominance, which is particularly important for breeding outcomes in cross-pollinated crops. Hence, dominance effects are an important and unexplored issue in GS for long-term programs involving allogamous species. To address it, we employed two approaches: analysis of empirical maize datasets and simulations of long-term breeding applying phenotypic and genomic recurrent selection (intrapopulation and reciprocal schemes). In both schemes, we simulated twenty breeding cycles and assessed the effect of marker density reduction on the population mean, the best crosses, additive variance, selective accuracy, and response to selection with models (additive, additive-dominant, general (GCA), and specific combining ability (SCA)). Our results indicate that marker reduction based on linkage disequilibrium levels provides useful predictions only within a cycle, as accuracy significantly decreases over cycles. In the long-term, high-marker density provides the best responses to selection. The model to be used depends on the breeding scheme: additive for intrapopulation and additive-dominant or SCA for reciprocal.

Floral and reproductive biology of Matisia cordata (fam: malvaceae)

In Colombia there is a large diversity of promising fruit trees, one of them is Matisia cordata. Sapoti species is appreciated by the consumers, although it is produced in small volumes by traditional productors. The objective of this research is to describe the floral and reproductive biology of sapoti, including floral visitors that act as biotic pollination agents. The study was conducted in two farms, between February/2016 and July/2017. In the first farm, floral buds were marked to follow the stages until fruit formation, pollination mechanism was studied, and floral visitors were collected for identification. In the second farm, flowers were marked to measure the floral nectar production. The duration from floral bud to ripe fruit was 269 days, the 2.7% of the flowers reached the fruit stage. Twenty-five floral visitors were registered, seven of which contacted the sexual whorls, specially Meliponini bees, hummingbirds and bats from Artibeus and Glossophaga genus. M. cordata is a prevalently allogamous species, it attracts diurnal and nocturnal animals, which can contribute to the pollination process. The flowers produced 1.6 ml of nectar with a sugar content from 6.2 to 11 °Brix. The sapoti flowers constitute an abundant and valuable resource for animals from the region.

Study of the efficiency of creeping clover pollination (Trifolium repens L.) by honey bees (Apis mellifera L.)

The creeping clover (Trifolium repens L.) is a natural allotetraploid allogamous species and is characterized by an entomophilic xenogamous pollination method. One of the reasons for the low yield of clover seeds is the insufficient provision of its flowering grass stands with pollinating insects. The main pollinators are representatives of the order of hymenoptera insects (Himenoptera) from the family of true bees (Apidae) – the honey bee Apis mellifera L. and various species of bumblebees (Bombus). Studies have shown that in the conditions of the Central Non-Chernozem region of Russia, the role of bumblebees in the pollination of creeping clover did not exceed 12-13%. In the presence of bumblebees in different growing seasons in the amount of 30-80 to 110-170 indivi-duals/ha during the mass flowering of creeping clover, they -ensured the formation of seed yields of no more than 90 kg/ha. It is established that honey bees perform up to 87-88% of clover pollination. The highest collections of creeping clover seeds are formed at the flight density of bees of 18-21 thousand individuals per hectare. This makes it possible to form a biological clover yield over 720 kg/ha. To ensure such a rich flight of bees, it is necessary to have at least 2-3 strong bee colonies on clover crops.

Iterative allogamy–autogamy transitions drive actual and incipient speciation during the ongoing evolutionary radiation within the orchid genus Epipactis (Orchidaceae)

Background and Aims The terrestrial orchid genus Epipactis has become a model system for the study of speciation via transitions from allogamy to autogamy, but close phylogenetic relationships have proven difficult to resolve through Sanger sequencing. Methods We analysed with restriction site-associated sequencing (RAD-seq) 108 plants representing 29 named taxa that together span the genus, focusing on section Epipactis. Our filtered matrix of 12 543 single nucleotide polymorphisms was used to generate an unrooted network and a rooted, well-supported likelihood tree. We further inferred genetic structure through a co-ancestry heat map and admixture analysis, and estimated inbreeding coefficients per sample. Key Results The 27 named taxa of the ingroup were resolved as 11 genuine, geographically widespread species: four dominantly allogamous and seven dominantly autogamous. A single comparatively allogamous species, E. helleborine, is the direct ancestor of most of the remaining species, though one of the derived autogams has generated one further autogamous species. An assessment of shared ancestry suggested only sporadic hybridization between the re-circumscribed species. Taxa with the greatest inclination towards autogamy show less, if any, admixture, whereas the gene pools of more allogamous species contain a mixture alleles found in the autogams. Conclusions This clade is presently undergoing an evolutionary radiation driven by a wide spectrum of genotypic, phenotypic and environmental factors. Epipactis helleborine has also frequently generated many local variants showing inclinations toward autogamy (and occasionally cleistogamy), best viewed as incipient speciation from within the genetic background provided by E. helleborine, which thus becomes an example of a convincingly paraphyletic species. Autogams are often as widespread and ecologically successful as allogams.

Molecular genetic diversity and mating system in sacha inchi progenies1

ABSTRACT Sacha inchi (Plukenetia volubilis L.) is a species with nutraceutical benefits traditionally consumed by Amazonic indigenous and urban communities. Studies on the genetic diversity and mating system are required to preserve and make the best use of the genetic resources for this species. This study aimed to estimate the genetic diversity and mating system parameters of sacha inchi progenies using Amplified Fragment Length Polymorphism (AFLP) markers. A total of 360 progenies from 30 accessions of sacha inchi were analyzed using three AFLP primers combinations. The percentage variation between and within families and the crossing rate, among other parameters, were estimated. The AFLP markers were efficient in genetically differentiating progenies, revealing 251 (98.82 %) polymorphic fragments. The analysis of molecular variance showed that the strongest variation occurs between progenies (57.16 %). However, the genetic differentiation within progenies was considerable (42.84 %), and could be exploited in breeding programs. The estimated population outcrossing rate was high (0.957), indicating it is a predominantly allogamous species. On the other hand, 33.7 % of the crosses occurred between related individuals. The estimate for biparental crosses revealed that the progenies consisted mainly of half-siblings (66.9 %) and full-siblings (28.8 %). For purposes of breeding and ex situ genetic conservation, sacha inchi seeds should be collected from a large number of parent plants.

Recent advances on evolution of pollination systems and reproductive biology of Vanilloideae (Orchidaceae)

Vanilloideae as currently circumscribed comprises nine genera and two tribes: Vanilleae and Pogonieae. The pantropical genus Vanilla has been frequently assumed to be natural on the basis of its climbing habit and lateral inflorescences. However, the inclusion of the rare Dictyophyllaria dietschiana in phylogenetic analyses makes the genus Vanilla paraphyletic. Within Pogonieae, phylogenetic analyses show that inclusion of Pogoniopsis turns the tribe paraphyletic. All analyses reveal that Pogoniopsis is closely related to members of Epidendroideae. Members of Pogonieae are pollinated by several groups of solitary and social bees, two pollination systems being recognized: reward-producing and deceptive. Molecular phylogeny suggests that the common ancestor to Pogonieae gave rise to two evolutionary lineages: one tropical with a condition of reward production; and one predominantly temperate-invading line with deceptive flowers. Reward-producing flowers characterize South and Central American clade (= Cleistes), while deceptive pollination is prominent in the clade including North American-Asiatic taxa plus Amazonian Duckeella. Species of “orchid bees” have been recorded as pollinators of the genus Vanilla (V. planifolia group and V. pompona group) in the Neotropics. In species of the V. pompona group, these bees are attracted by the fragrance of the flowers. Hummingbirds have been reported to pollinate some species of Vanilla. Vanilla insignis, V. odorata and V. planifolia are known to be pollinated through generalized food deception. Some species of Vanilla yield fruits through spontaneous self-pollination. This form of autogamy has been reported for V. griffithii, V. palmarum, V. planifolia, V. savannarum and V. bicolor. In Brazil, data on the pollination biology of Vanilla are scarce, but conclusive data are available for V. edwallii, which is pollinated by Epicharis (Apidae: Centridini). This species is rewardless, but male Epicharis are attracted to its flowers by their fragrance. Additionally, the Brazilian V. dubia and E. sclerophyllum are pollinated by bees. The mentum region of V. dubia and V. edwallii is dry, whereas that of E. sclerophyllum presents a small quantity of nectar. Flowers of E. sclerophyllum are scentless, while those of V. dubia are odoriferous. Vanilla dubia and V. edwallii are self-compatible and need a pollinator to yield fruits. In contrast, Epistephium sclerophyllum sets fruits through spontaneous self-pollination, but biotic pollination also occurs. Both species are primarily adapted to pollination by euglossine bees. Pollination by Euglossini seems to have evolved at least twice along the evolution of Vanilleae. Furthermore, shifts between rewarding and rewardless flowers and between autogamous and allogamous species have been reported among vanillas.

The development rhythm of the flower-bud in some Papilionaceae species. III. Macrosporogenesis, microsporogenesis and early gametogenesis in several species of the Vicieae tribe

Each of the examined species of the tribe <em>Vicieae</em> (<em>Vicia</em> faba, V. sativa, V, villosa, Lathyrus silvester, L. <em>pratensis</em> and Pisum <em>sativum</em>) has its peculiar characteristic development rhythm of the bud. A similarity has been demonstrated between the development rhythms of flower buds of <em>Vicia</em> faba and <em>Pisum sativum</em>. It was found that mature flowers of autogamous species had long calyces, whereas those of the allogamous species were short as compared with the petals of the corolla.

Aspects of sexual reproduction in rare monoecious Populus nigra var. nigra trees

Individuals of the genus Populus are mostly dioecious, although deviations from strict dioecism occasionally occur. The aim of this study was to determine whether six, rare monoecious Populus nigra var. nigra trees, identified in trial plots, were fertile and capable of sexually reproducing. Controlled pollinations were carried out and compared with the results of open pollination. Viable seeds were obtained from all combinations of pollination possibilities, suggesting these monoecious trees could be used as either male or female parent and were self-fertile. However, no individuals produced by selfpollination were found among the offspring from openpollinated, monoecious trees. The parentage of some of the crosses was verified using microsatellite markers. The germination energy (GE) and germination capacity (GC) were in most cases higher for seeds produced from controlled pollinations than from open pollination. Furthermore, GE and GC were both higher when pollen from the monoecious trees was used. An association between GE and GC rates on the one hand, and the pollination method and year it took place on the other, was found in most crosses made. This study extends knowledge of the reproductive biology of P. nigra that could be utilized in conservation genetic of this endangered allogamous species.

Cultivar development of allogamous crops

Objectives of this review were to present the state of the art of the technologies used to develop cultivars in allogamous species, excluding the perennial and asexually propagated species. It was reviewed the genetic structure of these species and its relationship with the development of cultivars, the technologies used to develop hybrids and improved open-pollinated varieties and their F1´s, and the impact of the biotechnology and the mixed models on the development of cultivars. A summary of results from the researches developed in the maize breeding project at the Department of Genetics of the Agriculture College "Luiz de Queiroz" will be presented.

Determination of the mating system of Tucumã palm using microsatellite markers

The Amazonian Tucumã palm (Astrocaryum aculeatum) produces edible fruit, traditionally consumed in indigenous communities and increasingly in urban centers. The species is incipiently domesticated and little studied, despite its growing economic importance for smallholder farmers and gatherers. Studies on the mating system are required for the conservation and use of the species' genetic resources. Our objective was to estimate mating system parameters of the Tucumã palm using microsatellite markers. Plants of 11 progenies of a spontaneous population were genotyped with eight microsatellite loci and the mating system parameters estimated. The population outcrossing rate was estimated at 0.978, and ranged from 0.774 to 1at the family level. The estimates of the correlation of paternity (0.176 and 0.205) suggest a low probability of full-sibs within progenies. Tucumã palm is a predominantly allogamous species and the open-pollinated progenies consist predominantly of half-sibs.