Genetic analysis of agronomic traits in a cross between sugarcane (Saccharum officinarum L.) and its presumed progenitor (S. robustum Brandes & Jesw. ex Grassl)

Saccharum robustum Brandes & Jesw. ex Grassl has been suggested as the immediate progenitor species of cultivated sugarcane (S. officinarum L.) [4]. Chromosome pairing and assortment in these two species were previously studied by genetic analysis of single-dose DNA markers in parents in and 44 F₁ progeny of a cross between euploid, meiotically regular 2n=80S. officinarum LA Purple andS. robustum Mol 5829 [2]. This same population was subsequently clonally propagated and evaluated in replicated trials for quantitative traits important to sugarcane breeders. Numbers of stalks, tasseled stalks, and stalks with smut, and the average diameter of two stalks were determined one day prior to harvest. At harvest, plant material from each plot was weighed and evaluated for pol (sucrose content) and fiber percentages. Clones were significantly different (P<0.01) for all traits analyzed. Associations of 83 single-dose arbitrarily primed PCR genetic markers with quantitative trait loci (QTL) of recorded traits was determined by single-factor ANOVA, and multiple regression. QTL analysis revealed markers significantly (P<0.05) associated with the expression of each trait analyzed. Markers associated with QTL after multiple regression were tested for digenic linear × linear epistatic interactions. The various multilocus models explained between 23% and 58% of the total phenotypic variation and 32% and 76% of the genotypic variation for the various traits. Digenic interactions were uncommon. Implications for marker-assisted selection in sugarcane and sugarcane domestication are discussed.     

鸡枞的驯化栽培现状

本文论述了当前鸡枞菌驯化栽培的两种模式即:以培养鸡枞菌为重心的腐生菌模式、以扩繁鸡枞菌共生白蚁为重心的原生态模式,并对其驯化栽培过程中所面临的问题及其可能的解决方案进行了阐述。     

卵孢侧耳野生菌株人工栽培及营养成分分析

采自西藏日喀则地区的两份野生蘑菇标本及其分离菌株,通过形态学及基于ITS序列的分子系统发育分析鉴定为卵孢侧耳Pleurotus placentodes。该物种在2016年首次报道于中国。人工驯化栽培试验表明卵孢侧耳可以在人工条件下出菇,生长周期80-95d;初步的营养成分分析表明,卵孢侧耳蛋白质、粗多糖、氨基酸含量比香菇、糙皮侧耳（平菇）、金针菇、柱状田头菇（茶树菇）等都高,尤其含有较高的组氨酸和丰富的矿物质,如铁、钙、锌等。卵孢侧耳可作为新的食用菌进行开发利用。     

Centennial olive trees as a reservoir of genetic diversity

Background and Aims

Genetic characterization and phylogenetic analysis of the oldest trees could be a powerful tool both for germplasm collection and for understanding the earliest origins of clonally propagated fruit crops. The olive tree (Olea europaea L.) is a suitable model to study the origin of cultivars due to its long lifespan, resulting in the existence of both centennial and millennial trees across the Mediterranean Basin.

Methods

The genetic identity and diversity as well as the phylogenetic relationships among the oldest wild and cultivated olives of southern Spain were evaluated by analysing simple sequence repeat markers. Samples from both the canopy and the roots of each tree were analysed to distinguish which trees were self-rooted and which were grafted. The ancient olives were also put into chronological order to infer the antiquity of traditional olive cultivars.

Key Results

Only 9·6 % out of 104 a priori cultivated ancient genotypes matched current olive cultivars. The percentage of unidentified genotypes was higher among the oldest olives, which could be because they belong to ancient unknown cultivars or because of possible intra-cultivar variability. Comparing the observed patterns of genetic variation made it possible to distinguish which trees were grafted onto putative wild olives.

Conclusions

This study of ancient olives has been fruitful both for germplasm collection and for enlarging our knowledge about olive domestication. The findings suggest that grafting pre-existing wild olives with olive cultivars was linked to the beginnings of olive growing. Additionally, the low number of genotypes identified in current cultivars points out that the ancient olives from southern Spain constitute a priceless reservoir of genetic diversity.     

Architectural evolution and its implications for domestication in grasses

BACKGROUND: The cereal crops domesticated from grasses provide a large percentage of the calories consumed by humans. Domestication and breeding in individual cereals has historically occurred in isolation, although this is rapidly changing with comparative genomics of the sequenced or soon-to-be sequenced genomes of rice, sorghum, maize and Brachypodium. Genetic information transferred through genomic comparisons is helping our understanding of genetically less tractable crops such as the hexaploid wheats and polyploid sugarcane, as well as the approx. 10 000 species of wild grasses. In turn, phylogenetic analysis helps put our knowledge of the morphology of cereal crops into an evolutionary context. GRASS ARCHITECTURE: Domestication often involves a change in the pattern and timing of branching, which affects both vegetative and inflorescence architecture, and ultimately yield. Cereal grasses exhibit two main forms of vegetative architecture: the pooid and erhartoid cereals such as wheat and rice have multiple basal tillers, while panicoid cereals such as maize, sorghum and the millets have few tillers or even only a single main stem. These differences are reflected in the differences between the wild species of pooid and some erhartoid grasses, which emphasize basal branching over axillary branching, and the panicoid grasses, where axillary branching is more frequently found. A combination of phylogenetic and genomic analysis is beginning to reveal the similarities and differences between different cereal crops, and relate these to the diversity of wild grasses to which they are related. Recent work on genes controlling branching emphasizes that developmental genetics needs to be viewed in both an evolutionary and ecological framework, if it is to be useful in understanding how morphology evolves. Increasingly, exploring the phylogenetic context of the crop grasses will suggest new ways to identify and create combinations of morphological traits that will best suit our future needs.     

Mutualism breakdown in breadfruit domestication

During the process of plant domestication, below-ground communities are rarely considered. Some studies have attempted to understand the changes in root symbionts owing to domestication, but little is known about how it influences mycorrhizal response in domesticated crops. We hypothesized that selection for above-ground traits may also result in decreased mycorrhizal abundance in roots. Breadfruit (Artocarpus sp.) has a long domestication history, with a strong geographical movement of cultivars from west to east across the Melanesian and Polynesian islands. Our results clearly show a decrease in arbuscular mycorrhizas (AMs) along a domestication gradient from wild to recently derived cultivars. We showed that the vesicular and arbuscular colonization rate decreased significantly in more recently derived breadfruit cultivars. In addition, molecular analyses of breadfruit roots indicated that AM fungal species richness also responded along the domestication gradient. These results suggest that human-driven selection for plant cultivars can have unintended effects on below-ground mutualists, with potential impacts on the stress tolerance of crops and long-term food security.     

Evidence for indigenous selection and distribution of the shea tree, Vitellaria paradoxa, and its potential significance to prevailing parkland savanna tree patterns in sub-Saharan Africa north of the equator

Aim Woody vegetation patterns in African savannas north of the equator are closely connected to human presence, but the distinctions between natural and anthropogenic landscapes have not been clear to many observers. Criteria for identifying savanna landscapes on a continuum of intensity of anthropic impact are explored. Methods A key savanna tree species, Vitellaria paradoxa (Sapotaceae), was used as model for evaluating anthropic impact. Fruits harvested from tree populations across the species range were analysed for variation in traits valued by indigenous peoples. A simple selection index was used to scale tree populations from a hypothetical wild state to a hypothetical domesticated state. Index values were compared with trait values along climate zone gradients and evaluated in the context of indigenous savanna management practices and historical species distribution reports. Results Trait values such as fruit size and shape, pulp sweetness, and kernel fat content show a significant influence of temperature and rainfall. At the same time, the mean values of groups of traits vary perpendicular to the general climatic zone gradient. Selection index values between Vitellaria populations vary up to sixfold, with highest values in central Burkina Faso. Comparison of present day Vitellaria distribution with historical range limits show range expansion by human migration. Main conclusions The prevalence of major economic tree species in the savannas of Africa north of the equator is a strong indicator of human involvement in tree dispersal. This conclusion is supported by paleobotanical evidence and by recent Vitellaria range expansion as a result of human migration. The presence of high mean values of several Vitellaria fruit traits in central Burkina Faso suggests that selection for desired characteristics has occurred. The impact of indigenous savanna peoples on woody species composition and spatial distribution is probably much greater than usually thought and is the result of a deliberate strategy of altering the landscape to provide needed human resources.     

Origins of domestic dog in southern East Asia is supported by analysis of Y-chromosome DNA

Global mitochondrial DNA (mtDNA) data indicates that the dog originates from domestication of wolf in Asia South of Yangtze River (ASY), with minor genetic contributions from dog-wolf hybridisation elsewhere. Archaeological data and autosomal single nucleotide polymorphism data have instead suggested that dogs originate from Europe and/or South West Asia but, because these datasets lack data from ASY, evidence pointing to ASY may have been overlooked. Analyses of additional markers for global datasets, including ASY, are therefore necessary to test if mtDNA phylogeography reflects the actual dog history and not merely stochastic events or selection. Here, we analyse 14,437 bp of Y-chromosome DNA sequence in 151 dogs sampled worldwide. We found 28 haplotypes distributed in five haplogroups. Two haplogroups were universally shared and included three haplotypes carried by 46% of all dogs, but two other haplogroups were primarily restricted to East Asia. Highest genetic diversity and virtually complete phylogenetic coverage was found within ASY. The 151 dogs were estimated to originate from 13-24 wolf founders, but there was no indication of post-domestication dog-wolf hybridisations. Thus, Y-chromosome and mtDNA data give strikingly similar pictures of dog phylogeography, most importantly that roughly 50% of the gene pools are shared universally but only ASY has nearly the full range of genetic diversity, such that the gene pools in all other regions may derive from ASY. This corroborates that ASY was the principal, and possibly sole region of wolf domestication, that a large number of wolves were domesticated, and that subsequent dog-wolf hybridisation contributed modestly to the dog gene pool.