MORPHOLOGICAL DIFFERENTIATION OF PROBOSCIDEA PARVIFLORA SSP. PARVIFLORA (MARTYNIACEAE) UNDER DOMESTICATION

Aboriginal groups in the southwestern United States have grown Proboscidea parviflora ssp. parviflora for basketry fiber. It has been hypothesized that cultivated plants of this subspecies with white seeds and long-clawed fruit (which provide the fiber) have been domesticated. Cluster, multiple discriminant, and unvariate statistical analyses presented here show that the putative domesticate is indeed morphologically distinct from “wild” plants. It has clearly been domesticated, and has diverged from wild populations to the extent that a new variety, var. Hohokamiana, is proposed for the domesticate. Wild and domesticated varieties differ especially in seed color, rostrum, crest, style, and anther lengths. Most characteristics of the wild variety seem to be genetically dominant to those of the domesticate, which may account for absence of a weedy form intermediate between the wild and domesticated varieties. The wild variety is morphologically more variable than the domesticate, probably because of its broader geographical range and its intergradation with another subspecies. Ethnological data and the variational patterns reported here suggest that the domesticate originated in southern Arizonanorthern Sonora, but probably not north of that region.     

Genomic variation in tomato,from wild ancestors to contemporary breeding accessions

Background

Domestication modifies the genomic variation of species. Quantifying this variation provides insights into the domestication process, facilitates the management of resources used by breeders and germplasm centers, and enables the design of experiments to associate traits with genes. We described and analyzed the genetic diversity of 1,008 tomato accessions including Solanum lycopersicum var. lycopersicum (SLL), S. lycopersicum var. cerasiforme (SLC), and S. pimpinellifolium (SP) that were genotyped using 7,720 SNPs. Additionally, we explored the allelic frequency of six loci affecting fruit weight and shape to infer patterns of selection.

Results

Our results revealed a pattern of variation that strongly supported a two-step domestication process, occasional hybridization in the wild, and differentiation through human selection. These interpretations were consistent with the observed allele frequencies for the six loci affecting fruit weight and shape. Fruit weight was strongly selected in SLC in the Andean region of Ecuador and Northern Peru prior to the domestication of tomato in Mesoamerica. Alleles affecting fruit shape were differentially selected among SLL genetic subgroups. Our results also clarified the biological status of SLC. True SLC was phylogenetically positioned between SP and SLL and its fruit morphology was diverse. SLC and “cherry tomato” are not synonymous terms. The morphologically-based term “cherry tomato” included some SLC, contemporary varieties, as well as many admixtures between SP and SLL. Contemporary SLL showed a moderate increase in nucleotide diversity, when compared with vintage groups.

Conclusions

This study presents a broad and detailed representation of the genomic variation in tomato. Tomato domestication seems to have followed a two step-process; a first domestication in South America and a second step in Mesoamerica. The distribution of fruit weight and shape alleles supports that domestication of SLC occurred in the Andean region. Our results also clarify the biological status of SLC as true phylogenetic group within tomato. We detect Ecuadorian and Peruvian accessions that may represent a pool of unexplored variation that could be of interest for crop improvement.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1444-1) contains supplementary material, which is available to authorized users.     

QTL mapping of domestication and diversifying selection related traits in round-fruited semi-wild Xishuangbanna cucumber (<Emphasis Type="Italic">Cucumis sativus</Emphasis> L. var. <Emphasis Type="Italic">xishuangbannanesis</Emphasis>)

Key message

QTL analysis revealed 11 QTL underlying flowering time and fruit size variation in the semi-wild Xishuangbanna cucumber, of which, FT6.2 and FS5.2 played the most important roles in determining photoperiod-dependent flowering time and round-fruit shape, respectively.

Abstract

Flowering time and fruit size are two important traits in domestication and diversifying selection in cucumber, but their genetic basis is not well understood. Here we reported QTL mapping results on flowering time and fruit size with F₂ and F_2:3 segregating populations derived from the cross between WI7200, a small fruited, early flowering primitive cultivated cucumber and WI7167, a round-fruited, later flowering semi-wild Xishuangbanna (XIS) cucumber. A linkage map with 267 microsatellite marker loci was developed with 138 F₂ plants. Phenotypic data of male and female flowering time, fruit length and diameter and three other traits (mature fruit weight and number, and seedling hypocotyl length) were collected in multiple environments. Three flowering time QTL, FT1.1, FT5.1 and FT6.2 were identified, in which FT6.2 played the most important role in conferring less photoperiod sensitive early flowering during domestication whereas FT1.1 seemed more influential in regulating flowering time within the cultivated cucumber. Eight consensus fruit size QTL distributed in 7 chromosomes were detected, each of which contributed to both longitudinal and radial growth in cucumber fruit development. Among them, FS5.2 on chromosome 5 exhibited the largest effect on the determination of round fruit shape that was characteristic of the WI7167 XIS cucumber. Possible roles of these flowering time and fruit size QTL in domestication of cucumber and crop evolution of the semi-wild XIS cucumber, as well as the genetic basis of round fruit shape in cucumber are discussed.

     

Genetic variation for domestication-related traits revealed in a cultivated rice,Nipponbare (<Emphasis Type="Italic">Oryza sativa ssp. japonica</Emphasis>) × ancestral rice, <Emphasis Type="Italic">O. nivara</Emphasis>, mapping population

Oryza nivara is the ancestral species of cultivated rice (Oryza sativa). It has been the source of novel alleles for resistance to biotic and abiotic stresses, as well as yield improvement, lost during the course of domestication. To determine the molecular changes that occurred during domestication, the O. sativa ssp. japonica variety, Nipponbare, from which a reference sequence (RefSeq) was developed, was crossed with the O. nivara accession (IRGC100897), from which BAC-end sequences (BES) were derived. The mapping population composed of 279 F₂ progeny lines derived from this cross was phenotyped for 19 traits important to domestication and yield improvement, including basal sheath and culm color, culm angle, days to heading, plant height, seed shattering, flag leaf length and width, panicle type and length, awn length and color, pericarp color, and seed color, length, width, length to width ratio, volume and surface area. The population was genotyped using 95 SSR markers and 114 single nucleotide variation (SNV) markers, selected by comparing the Nipponbare RefSeq and O. nivara BES. At least one major QTL was identified for each trait evaluated, and for 28 of the 46 QTL, the trait increase was attributed to the allele contributed by the O. nivara parent. Candidate genes were identified in 37 of the QTL regions. This study validated SNV markers that can be used for mapping in populations with a wild species parent. In the future, SNVs could be used for marker-assisted selection to incorporate desirable, novel alleles for stress resistance and yield improvement, identified in rice wild species like O. nivara into elite, adapted O. sativa varieties.     

Barnacle Goose (Branta leucopsis) feeding ecology and trophic relationships on Kolguev Island: The usage patterns of nutritional resources in tundra and seashore habitats

Insight into colonization of new areas by invasive species and their relationships with aboriginal species is a major challenge in ecology, allowing for prediction of the outcome of biological invasions. In this context, the current expansion of the Barnacle Goose (Branta leucopsis) is of great interest. The seasonal dynamics of Barnacle Goose feeding and the structure of its diet on Kolguev Island during the nesting and postnesting periods (May 27–July 29) have been examined. The diet structures of the invasive Barnacle Goose and the aboriginal species White-fronted goose (Anser albifrons) and Bean goose (A. fabalis) have been compared. The probability of interspecific competition and the ecological advantages in the diet patterns of these species have been estimated. If the Barnacle Goose population on Kolguev Island continues to increase, this may led to a decline in the population of aboriginal species of geese on the island.     

Determination of morphological variation in subspecies of Isatis glauca Aucher ex Boiss. from Central Anatolia

Isatis glauca Aucher ex Boiss. has four subspecies: glauca, galatica Y?ld?r?ml?, sivasica (Davis) Y?ld?r?ml? and iconia (Boiss.) Davis, naturally growing in Turkey. In this study, 77 accessions from nine I. glauca ssp. populations were characterised in terms of variation in morphological characters, including the number of branches per plant, plant height, diameter of stem base, diameter of middle stem, diameter of apical stem, width and length of fruit, length of fruit stalk, fruit shape, fruit base shape, fruit apices shape, loculus, ondulation, apical process of fruit, fruit weight, basal length of fruit, apical length of fruit, wing width of fruit, loculus length, loculus width, length of seed, dorsal width of seed, lateral width of seed and seed weight. The number of branches had the highest value of coefficient of variation (CV), 0.21–0.86, while the fruit width had the lowest value of CV 0.08–0.20. According to Pearson’s correlation and multiple regression analyses, eco-geographical factors had a substantial effect on morphological variation. A principal component analysis explained 90.61 % of morphological variation through the study of five extracted components. A dendrogram, which was constructed according to the between-group linkages method, based on squared Euclidean distances, represented a hierarchical cluster analysis of 77 accessions. The results of the principal coordinate analysis, which showed differentiation according to morphological characters between nine populations, were consistent with the dendrogram. Consequently, morphological variation of I. glauca ssp. and the significant effects of eco-geographical factors on its morphological variation were discussed.     

Ancient Chinese literature reveals pathways of eggplant domestication

Background and Aims

Changes in key traits occurring during the processes of plant domestication have long been subjects of debate. Only in the case of genetic analysis or with extensive plant remains can specific sets of changes be documented. Historical details of the plant domestication processes are rare and other evidence of morphological change can be difficult to obtain, especially for those vegetables that lack a substantial body of archaeological data. Botanical records chronicled in the ancient literature of established ancient civilizations, such as that of China, are invaluable resources for the study and understanding of the process of plant domestication. Here, the considerable body of ancient Chinese literature is used to explore the domestication process that has occurred with the eggplant (Solanum melongena), an important vegetable in Old World.

Methods

Information about eggplant domestication in the ancient Chinese literature was retrieved using a variety of methods. The information obtained was then sorted by taxon, examined and taxonomic identifications verified.

Key Results

It was found that the earliest record of the eggplant documented in ancient Chinese literature was in a work from 59 bc. As far as is known, this is the earliest reliable and accurately dated record of eggplant in cultivation. The analysis reveals that the process of domestication of the eggplant in China involved three principal aspects of fruit quality: size, shape and taste. These traits were actively and gradually selected; fruit size changed from small to large, taste changed from not palatable to what was termed at the time sweetish, and that over time, a wider variety of fruit shapes was cultivated.

Conclusions

The results indicate that, in addition to data gleaned from archaeology and genetics, evidence as to changes in key traits occurring during the process of plant domestication and selective forces responsible for these changes can be traced through the ancient literature in some civilizations.Key words: Solanum melongena, ancient Chinese literature, domestication process, domestication traits, selective forces     

Molecular diversity of small balsam populations in relation to site characteristics

Climatic shifts within recent decades created favorable conditions for invasive species flourishing in more Northern parts of Europe. Our study was aimed at evaluation of genetic variability and habitat features of Impatiens parviflora populations growing in Lithuania. Twenty one populations were selected and analysed using simple sequence repeat (SSR) and randomly amplified polymorphic DNA (RAPD) assays. Evaluated by SSRs, 315 individuals were all monomorphic and homozygous at 4 loci and heterozygous at 1 locus. RAPD analyses revealed that the percentage of polymorphic DNA loci (% P) per population ranged from 7 to 39% and genetic differentiation between populations was Φ_PT=0.790 (P<0.01). Genetic distances among populations (0.135–0.426) correlated significantly with geographical distances (r=0.183; P<0.008). Populations in overmoistured soil contained higher % P (28.3) when compared to drier soil (18.7; P<0.05). All recorded populations were close to roads; their % P did not depend on proximity to buildings, light intensity or population size. Our RAPD analyses indicate multiple introductions of this species in Lithuania. Analyses of I. parviflora at SSR and RAPD loci show that the invasion process is reflected in genetic structure.     

A synopsis of the South American taxa of Fabronia (Fabroniaceae)

The genusFabronia in South America is found to represent five taxa:F. ciliaris var.ciliaris, F. ciliaris var.wrightii,F. ciliaris var.polycarpa,F. macroblepharis andF. jamesonii. Synonymy, brief discussion, illustrations and a key are provided.Fabronia enervis Herz., hom. illeg., is the basis for the new genusMahua.     

Contributions to the genus phytophthora de bary from india

The paper deals with some of the contributions made from India by various research workers towards our knowledge of the fungus genusPhytophthora de Bary, in the fields of morphology, disease production, occurrence and distribution of species, host range, physiology, taxonomy and control measures. Out of the total of fifteen species and five varieties ofPhytophthora reported from India, five species (viz.,P. arecae, P. palmivora, P. colocasiae, P. parasitica andP. infestans, and four varieties ofP. parasitica, viz.,P. parasitica var.macrospora, var.sesami, var.piperina and var.nicotianae) assume considerable parasitic roles inciting serious diseases like seedling-blights, wilts, cottoney-leaks, foot-rots, blights, budrot and rots of fruits, nuts, tubers and corms etc. They are widely distributed in various parts of this country, and are mostly prevalent in rainy seasons.Phytophthora palmivora, andP. parasitica were found to have a wide host range.     

Chenopodium pumilio in Czechoslovakia: Its strategy of dispersal and domestication

The paper deals with dispersal and domestication ofChenopodium pumilio R. Br. in Czechoslovakia. Tabulated habitats point out the predominant dispersal of this species by various kinds of hemorochory, while autochory, chamaechory, endochory and epichory are other possible means of dispersal. Successfull domestication ofChenopodium pumilio is facilitated by abundance of viable fruits possessing an efficient dormancy mechanism that prevents them germinating in adverse seasons of the year. Naturalization of this species is further supported by prolonged viability of the fruits, and by favourable periodicity of dissemination.     

Craniometric allometry in the thicktailed bushbabyOtolemur Crassicaudatus

Static adult craniometric allometry was evaluated in a sample of 66Otolemur crassicaudatus skulls (34 males, 32 females). Although cranial measures were equally well correlated to skull length in males and females, there were noteworthy differences in the exponential values between the sexes. These results underlined the need for caution when allometric analyses are based on pooled data. From the cranial allometric analyses it is concluded that the longer the skull, the shorter and the narrower the maxilla, and the broader the bizygomatic distance. Although cranial length increased proportionately to the increase in skull length, the cranial width in females was positively allometric whilst in males it was negatively allometric. Allometric analyses of mandibular dimensions suggest that larger animals will have proportionately longer mandibulae, which will, in turn, be relatively wider across the gonia, yet shallower behind the first molars. It is postulated that the disproportionate widening of the zygomata might be related to the widening across the gonia.     

Description of the oöcysts of Eimeria beccari n. sp. (Apicomplexa: Eimeriidae) from Varanus prasinus beccari (Reptilia: Varanidae)

Eimeria beccari n. sp. is described from the faecal contents of Varanus prasinus beccari (Reptilia: Varanidae), originally from the Aru Islands northwest of New Guinea. Oöcysts are cylindroid, 33.7 × 19.1 (29–36 × 18–21) µm, often with one end narrowing; shape index (length/width) 1.76 (1.6–1.9). A micropyle and oöcyst residuum are absent but a polar granule is present in most oöcysts. Sporocysts are ellipsoid, 12.0 × 7.7 (11–13.5 × 7–8) µm; shape index 1.56 (1.5–1.7). Stieda and substieda bodies are absent. Sporozoites are elongate, 10.4 × 2.8 (9–12 × 2.5–3) µm, and contain a posterior refractile body.     

中国特有植物艾比湖沙拐枣(Calligonum ebi-nuricum)居群内果实性状的变异

以中国荒漠特有植物艾比湖沙拐枣(Calligonum ebi-nuricum)果实形态特征为研究对象,对分布于原产区的同一居群12个样株的果实进行形态特征比较研究。通过每株30粒果实的喙长、果实长度、果实宽度、果实形状、瘦果长度、瘦果宽度、瘦果形状、刺毛长度、头部刺毛长度、两肋间距、两刺间距11个性状指标的数值分析表明：在株内与株间均有变异,株间果实性状变异较株内果实性状变异大;代表果实和瘦果大小指标正相关性极显著（p＜0.01）;两肋间距与瘦果形状呈负相关（r=-0.297**,p＜0.01）。研究结果证明：其果实形状和瘦果形状（长度、宽度及长宽比）较为稳定,可作为艾比湖沙拐枣的分种依据,而其它果实性状可塑性较大,只能作为分类的参考。该研究结果可供沙拐枣属其它种的准确分类参考。     

New species and other notes in the Malvaceae

The following species are described as new: Herissantia dressleri, Hibiscus longifilus, and Pavonia gentryi from Mexico, and Hibiscuswilsonii from Brazil. The comparative morphology and distribution of the MexicanPavonia melanommata Robins. & Seat. var.melanommata and ofP. melanommata var.pringleana R. E. Fries are discussed.     

Potato virus X induces DNA damage in leaf nuclei of the host plant Nicotiana tabacum L. var. xanthi

We employed the comet assay (single cell gel electrophoresis) to evaluate induced DNA damage in nuclei isolated from tobacco leaves (Nicotiana tabacum var. xanthi) inoculated with Potato virus X (PVX). The highest DNA damage, expressed by the tail moment value, was observed in the inoculated leaves and decreased in the 1^st to 4^th systemic leaves. DNA damage increased with the time after the inoculation (from day 3 to day 21) and was higher in nuclei isolated from a part of the leaf at the petiole compared to nuclei isolated from the leaf tip. A Pearson moment correlation (r = 0.94) between the induced DNA damage and the PVX titres expressed by ELISA absorbance values was observed. The PVX infection did not induce a significant increase in the rate of somatic mutations evaluated by appearance of dark green, yellow, and double green/yellow sectors on the heterozygous pale green leaves of N. tabacum var. xanthi.     

Round fruit shape in WI7239 cucumber is controlled by two interacting quantitative trait loci with one putatively encoding a tomato <Emphasis Type="Italic">SUN</Emphasis> homolog

Key message

QTL analysis revealed two interacting loci, FS1.2 and FS2.1, underlying round fruit shape in WI7239 cucumber; CsSUN , a homolog of tomato fruit shape gene SUN , was a candidate for FS1.2.

Abstract

Fruit size is an important quality and yield trait in cucumber, but its genetic basis remains poorly understood. Here we reported QTL mapping results on fruit size with segregating populations derived from the cross between WI7238 (long fruit) and WI7239 (round fruit) inbred cucumber lines. Phenotypic data of fruit length and diameter were collected at anthesis, immature and mature fruit stages in four environments. Ten major-effect QTL were detected for six traits; synthesis of information from these QTL supported two genes, FS1.2 and FS2.1, underlying fruit size variation in the examined populations. Under the two-gene model, deviation from expected segregation ratio in fruit length and diameter among segregating populations was observed, which could be explained mainly by the interactions between FS1.2 and FS2.1, and segregation distortion in the FS2.1 region. Genome-wide candidate gene search identified CsSUN, a homolog of the tomato fruit shape gene SUN, as the candidate for FS1.2. The round-fruited WI7239 had a 161-bp deletion in the first exon of CsSUN, and its expression in WI7239 was significantly lower than that in WI7238. A marker derived from this deletion was mapped at the peak location of FS1.2 in QTL analysis. Comparative analysis suggested the melon gene CmSUN-14, a homolog of CsSUN as a candidate of the fl2/fd2/fw2 QTL in melon. This study revealed the unique genetic architecture of round fruit shape in WI7239 cucumber. It also highlights the power of QTL analysis for traits with a simple genetic basis but their expression is complicated by other factors.

     

Phenotypic differentiation between wild and domesticated varieties of <Emphasis Type="Italic">Crescentia cujete</Emphasis>L. and culturally relevant uses of their fruits as bowls in the Yucatan Peninsula,Mexico

Background

Selection criteria are important for analyzing domestication of perennial plant species, which experience a selection pressure throughout several human generations. We analyze the preferred morphological characteristics of Crescentia cujete fruits, which are used as bowls by the Maya of Yucatan, according to the uses they are given and the phenotypic consequences of artificial selection between one wild and three domesticated varieties.

Methods

We performed 40 semi-structured interviews in seven communities. We calculated Sutrop’s salience index (S) of five classes of ceremonial and daily life uses, and of each item from the two most salient classes. We sampled 238 bowls at homes of people interviewed and compared their shape, volume and thickness with 139 fruits collected in homegardens and 179 from the wild. Morphology of varieties was assessed in fruit (n?=?114 trees) and vegetative characters (n?=?136 trees). Differences between varieties were evaluated through linear discriminant analysis (LDA).

Results

Use of bowls as containers for the Day of the Dead offerings was the most salient class (S?=?0.489) with chocolate as its most salient beverage (S?=?0.491), followed by consumption of daily beverages (S?=?0.423), especially maize-based pozol (S?=?0.412). The sacred saka’ and balche' are offered in different sized bowls during agricultural and domestic rituals. Roundness was the most relevant character for these uses, as bowls from households showed a strong selection towards round shapes compared with wild and homegarden fruits. Larger fruits from domesticated varieties were also preferred over small wild fruits, although in the household different sizes of the domesticated varieties are useful. LDA separated wild from domesticated trees (p?<?0.001) according to both fruit and vegetative variables, but domesticated varieties were not different among themselves.

Conclusions

The association between C. cujete bowls and traditional beverages in ritual and daily life situations has driven for centuries the selection of preferred fruit morphology in this tree. Selection of fruit roundness and volume has allowed for the differentiation between the wild variety and the three domesticated ones, counteracting gene flow among them. By choosing the best fruits from domesticated varieties propagated in homegardens, the Maya people model the domestication process of this important tree in their culture.

     

Floral and mating system divergence in secondary sympatry: testing an alternative hypothesis to reinforcement in Clarkia

Background and Aims

Reproductive character displacement (RCD) is often an important signature of reinforcement when partially cross-compatible taxa meet in secondary sympatry. In this study, floral evolution is examined during the Holocene range expansion of Clarkia xantiana subsp. parviflora from eastern Pleistocene refugia to a western zone of sympatry with its sister taxon, subsp. xantiana. Floral divergence between the two taxa is greater in sympatry than allopatry. The goal was to test an alternative hypothesis to reinforcement – that floral divergence of sympatric genotypes is simply a by-product of adaptation to pollination environments that differ between the allopatric and sympatric portions of the subspecies'' range.

Methods

Floral trait data from two common garden studies were used to examine floral divergence between sympatric and allopatric regions and among phylogeographically defined lineages. In natural populations of C. x. parviflora, the magnitude of pollen limitation and reproductive assurance were quantified across its west-to-east range. Potted sympatric and allopatric genotypes were also reciprocally translocated between geographical regions to distinguish between the effects of floral phenotype versus contrasting pollinator environments on reproductive ecology.

Key Results

Sympatric populations are considerably smaller flowered with reduced herkogamy. Pollen limitation and the reproductive assurance value of selfing are greater in sympatric than in allopatric populations. Most significantly, reciprocal translocation experiments showed these differences in reproductive ecology cannot be attributed to contrasting pollinator environments between the sympatric and allopatric regions, but instead reflect the effects of flower size on pollinator attraction.

Conclusions

Floral evolution occurred during the westward range expansion of parviflora, particularly in the zone of sympatry with xantiana. No evidence was found that strongly reduced flower size in sympatric parviflora (and RCD between parviflora and xantiana) is due to adaptation to limited pollinator availability. Rather, floral divergence appears to have been driven by other factors, such as interactions with congenerics in secondary sympatry.     

Two shrubby novelties in Eriogonum (Polygonaceae) from the deserts of Utah and Arizona

Two desert shrubs belonging toEriogonum subgen.Eucycla sect.Corymbosa are described from southern Utah and northern Arizona.Eriogonum mortonianum, endemic to red clay hills southwest of Fredonia, in extreme northeastern Mohave County, Arizona, is most closely related toE. smithii, a species endemic to the San Rafael Desert of Emery County, Utah, but differs in having wider leaves, a much more branched inflorescence, and smaller, pale-yellow or white flowers.Eriogonum leptocladon var.papiliunculi, found in central Garfield and eastern Kane counties, Utah, southward into northern Coconino and Navajo counties, Arizona, is distinguished from var.leptocladon by its white flowers and from var.ramosissimum by its glabrous stems.