The distribution, natural habitats and availability of wild cereals in relation to their domestication in the Near East: multiple events, multiple centres

In this article we examine the natural habitats and distribution of the six wild cereals: Triticum urartu (wild urartu wheat), T. boeoticum aegilopoides (single-grained wild einkorn), T. boeoticum thaoudar (two-grained wild einkorn), T. dicoccoides (wild emmer wheat), Secale spp. (wild ryes) and Hordeum spontaneum (wild barley). A comparison of late Pleistocene/early Holocene archaeobotanical assemblages in the Near East with present-day distributions of wild cereals shows a good correlation. The regional variation in the archaeobotanical cereal assemblages and the ensuing domestication provide evidence that different cereal species were domesticated independently in different areas. Some sites were not situated near wild cereal habitats and a few were located outside the limits of distribution, even accounting for moister climatic conditions. I argue here that current models which try to explain the shift to farming have tended to over-emphasize the effect of the Younger Dryas climatic change. First, it would have had only a minor effect on cereal availability. Secondly, agriculture appears to have been established after the Younger Dryas. Thirdly, there is no evidence for a single centre of origin; agriculture arose in widely separated geographic and climatic regions. And fourthly, agriculture depends on stable climatic conditions which were not established until after the Younger Dryas.     

Evidence of three maternal lineages in Near Eastern sheep supporting multiple domestication events

The variability of mtDNA was analysed in local sheep breeds reared throughout Turkey, for which a fragment of the D-loop region and the complete cytochrome b were sequenced. Phylogenetic analyses performed independently for the D-loop and the Cyt b gene revealed three clearly separated clusters indicating three major maternal lineages, two of which had been previously described as types B and A. The new type, C, was present in all the breeds analysed and showed considerable mtDNA variability. Divergence time was obtained on the basis of Cyt b gene and was estimated to be around 160,000-170,000 years ago for lineages B and A, whereas the divergence of lineage C proved to have occurred earlier (between 450,000 and 750,000 years ago). These times greatly predate domestication and suggest that the origin of modern sheep breeds was more complex than previously thought and that at least three independent sheep domestication events occurred. Our results, together with archaeological information and the current wild sheep populations in the Near East region support the high importance of this area in the sheep domestication process. Finally, the evidence of a third maternal lineage has important implications regarding the history of modern sheep.     

The climate of the Younger Dryas as a boundary for Einkorn domestication

The domestication of the Neolithic founder crops of the Near East has recently been a topic of debate particularly with respect to how rapidly the domestication of these crops occurred. One school of thought maintains that these processes lasted several thousand years (‘protracted model’ with ‘gathering’, ‘cultivation’ and ‘domestication’ as three stages of a continuum, each taking up to several thousand years), while another favors the view that domestication occurred much more quickly, over several hundred years at most (‘rapid transition’). Our study focuses on one of these crops, 1-grained domesticated Einkorn wheat, incorporating data from geology, vegetation history, and climate. In the Karacadağ region of southeastern Turkey, where 1-grained Einkorn wheat was domesticated, the climate was severe (i.e. cold and dry) during the Younger Dryas. The climate of the Younger Dryas acted as boundary during which a) conditions were not suitable for ‘cultivation’, and b) Einkorn would have retreated to refugia exhibiting more suitable moisture-bearing soils that would have made ‘gathering’ difficult. Around 11600 cal. b.p., the Younger Dryas ended and a very rapid climatic amelioration commenced at the beginning of the Early Holocene, enabling grasses to spread throughout the region. A ritual PPNA/PPNB site (G?bekli Tepe) and associated PPNB settlements such as Nevali ?ori and ?ay?nü were established at this time. In the settlements of Nevali ?ori and Cafer H?yük, the oldest domesticated Einkorn was found in the earliest archaeological layers. This confirms that the inhabitants made use of domesticated 1-grained Einkorn from the very beginning of settlement activity, although they continued to practice a mixed lifestyle as hunter-gatherers and farmers. For ?ay?nü the issue is more complex, but here domesticated Einkorn also appears around the same time. In summary, by 10400 cal. b.p. domesticated 1-grained Einkorn was present in large quantities at a variety of sites. This would give a maximum window of time lasting approximately 1,200 years and is therefore not in agreement with the ‘protracted’ model but would be consistent with a ‘rapid transition’. It is improbable that the ‘cultivation’ of wild Einkorn was practiced in the Karacadağ region, since wild Einkorn was plentiful during the favorable growing conditions following the Younger Dryas, making it more likely that ‘gathering’ would have been practiced. Because Einkorn has not been found in early settlements in the southern Levant, this crop cannot have been ‘gathered’ and ‘cultivated’ there but instead was ‘domesticated’ independently and solely in southeastern Turkey. Therefore, the YD acts as a boundary, providing a maximum time frame for 1-grained Einkorn domestication.     

Analysis of Triticum boeoticum and Triticum urartu seed defensins: To the problem of the origin of polyploid wheat genomes

The origin of polyploid wheat genomes has been the subject of numerous studies and is the key problem in wheat phylogeny. Different diploid species have been supposed to donate genomes to tetraploid and hexaploid wheat species. To shed light on phylogenetic relationships between the presumable A genome donors and hexaploid wheat species we have applied a new approach: the comparison of defensins from diploid Triticum species, Triticum boeoticum Boiss. and Triticum urartu Thum. ex Gandil., with previously characterized Triticum kiharae defensins [T.I. Odintsova et al., Biochimie 89 (2007) 605-612]. Defensins were isolated by acidic extraction of seeds followed by three-step chromatographic separation. Isolated defensins were identified by molecular masses using MALDI-TOF mass spectrometry and N-terminal sequencing. For the first time, we have shown that T. urartu defensins are more similar to those of the hexaploid wheat than T. boeoticum defensins, although variation among samples collected in different regions of the world was revealed. Our results clearly demonstrate that T. urartu of the Asian origin contributed the A genome to polyploid wheat species.     

Identification of a 5S rDNA spacer type specific Triticum urartu and wheats containing the T. urartu genome.

A PCR system was designed to amplify 5S spacer rDNA specifically from homeologous chromosome 1 in a variety of species representative of the Aegilops and Triticum genera. Two polymerase chain reaction (PCR) primer combinations were used, one of which appears to be apomorphic in nature and specific to chromosome 1A in Triticum urartu and tetraploid and hexaploid wheats containing the AA genome donated by T. urartu. The value of studying single repeat types to investigate the molecular evolution of 5S-rDNA arrays is considered.     

Identification and Characterization of the Expansin Genes in Triticum urartu in Response to Various Phytohormones

Russian Journal of Genetics - Expansins are ancient proteins involved in cell wall loosening during diverse biological processes in plants. They may participate inplant developmental processes and...     

Molecular diversity at 18 loci in 321 wild and 92 domesticate lines reveal no reduction of nucleotide diversity during Triticum monococcum (Einkorn) domestication: implications for the origin of agriculture

The diploid wheat Triticum monococcum L. (einkorn) was among the first crops domesticated by humans in the Fertile Crescent 10,000 years ago. During the last 5,000 years, it was replaced by tetraploid and hexaploid wheats and largely forgotten by modern breeders. Einkorn germplasm is thus devoid of breeding bottlenecks and has therefore preserved in unfiltered form the full spectrum of genetic variation that was present during its domestication. We investigated haplotype variation among >12 million nucleotides sequenced at 18 loci across 321 wild and 92 domesticate T. monococcum lines. In contrast to previous studies of cereal domestication, we sampled hundreds of wild lines, rather than a few dozen. Unexpectedly, our broad sample of wild lines reveals that wild einkorn underwent a process of natural genetic differentiation, most likely an incipient speciation, prior to domestication. That natural differentiation was previously overlooked within wild einkorn, but it bears heavily upon inferences concerning the domestication process because it brought forth 3 genetically, and to some extent morphologically, distinct wild einkorn races that we designate here as alpha, beta, and gamma. Only one of those natural races, beta, was exploited by humans for domestication. Nucleotide diversity and haplotype diversity in domesticate einkorn is higher than in its wild sister group, the einkorn beta race, indicating that einkorn underwent no reduction of diversity during domestication. This is in contrast to findings from previous studies of domestication history among more intensely bred crop species. Taken together with archaeological findings from the Fertile Crescent, the data indicate that a specific wild einkorn race that arose without human intervention was subjected to multiple independent domestication events.     

Basis of difference between reciprocal crosses involving Triticum boeoticum and T. urartu

Summary The boeoticum () X urartu () F₁ hybrids gave small, plump and viable seeds while the reciprocal crosses with T. urartu as the female parent had long, shrivelled and non-viable seeds. Reciprocal nuclear-substitution lines comprising the nucleus of one species into the cytoplasm of the other were developed through repeated backcrossing and were crossed as female parents with respective non-recurrent parents (the cytoplasm donors). The difference between the reciprocal crosses was presumably attributable to different boeoticum urartu genomic ratios in the triploid endosperm rather than to the cytoplasmic difference between the diploid wheats. The endosperm with two doses of the boeoticum and one of the urartu genome resulted in small, plump and viable seed while the endosperm of the reciprocal crosses with two doses of the urartu and one of the boeoticum genome led to large but shrivelled and non-viable seeds irrespective of the cytoplasmic type. One dose of the paternal genome in the triploid endosperm is probably not expressed in the presence of two doses of the maternal genome thereby leading to the difference between the reciprocal crosses. The results reported here indicate that difference between reciprocal crosses may not always be attributed to cytoplasmic difference between the parental species.     

Genetic variability of the wild diploid wheat Triticum urartu revealed by RFLP and RAPD markers

 Genetic variability among 49 accessions of Triticum urartu was estimated by RFLP and RAPD marker analyses, and the two data sets were compared. One T. timopheevii accession and two accessions of T. durum and T. aestivum, respectively, were included to identify T. urartu accessions closely related to these polyploid wheats. Twenty eight RFLP clones and 29 RAPD primers generated 451 and 155 polymorphic bands, respectively. The three accessions from Armenia clustered together and were well separated from all other accessions, which showed less pronounced geographical patterns. Genetic similarity and co-phenetic values calculated with RAPD markers were very similar to those calculated with RFLP markers for the intraspecific comparisons, but not for the interspecific comparisons. The identification of individual T. urartu accessions which are more related to polyploid wheats than others was not possible. Received: 14 May 1996 / Accepted: 13 September 1996     

Population phylogenomic analysis of mitochondrial DNA in wild boars and domestic pigs revealed multiple domestication events in East Asia

Background  

Previously reported evidence indicates that pigs were independently domesticated in multiple places throughout the world. However, a detailed picture of the origin and dispersal of domestic pigs in East Asia has not yet been reported.     

BAC libraries of Triticum urartu, Aegilops speltoides and Ae. tauschii, the diploid ancestors of polyploid wheat

Triticum urartu, Aegilops speltoides and Ae. tauschii are respectively the immediate diploid sources, or their closest relatives, of the A, B and D genomes of polyploid wheats. Here we report the construction and characterization of arrayed large-insert libraries in a bacterial artificial chromosome (BAC) vector, one for each of these diploid species. The libraries are equivalent to 3.7, 5.4 and 4.1 of the T. urartu, Ae. speltoides, Ae. tauschii genomes, respectively. The predicted levels of genome coverage were confirmed by library hybridization with single-copy genes. The libraries were used to estimate the proportion of known repeated nucleotide sequences and gene content in each genome by BAC-end sequencing. Repeated sequence families previously detected in Triticeae accounted for 57, 61 and 57% of the T. urartu, Ae. speltoides and Ae. tauschii genomes, and coding regions accounted for 5.8, 4.5 and 4.8%, respectively.     

Plant Domestication and Crop Evolution in the Near East: On Events and Processes

Reconstructing the evolutionary history of crop plants is fundamental for understanding their adaptation profile and the genetic basis of yield-limiting factors, which in turn are critical for future crop improvement. A major topic in this field is the recent claim for a millennia-long ‘protracted’ domestication process. Here we evaluate the evidence for the protracted domestication model in light of published archaeobotanical data, experimental evidence and the biology of the Near Eastern crops and their wild progenitors. The crux of our discussion is the differentiation between events or ‘domestication episodes’ and the later following crop evolutionary processes under domestication (frequently termed ‘crop improvement stage’), which are by definition, still ongoing. We argue that by assuming a protracted millennia-long domestication process, one needlessly opts to operate within an intellectual framework that does not allow differentiating between the decisive (critical) domestication traits and their respective loci, and those that have evolved later during the crop dissemination and improvement following the episodic domestication event. Therefore, in our view, apart from the lack of experimental evidence to support it, the protracted domestication assumption undermines the resolution power of the study of both plant domestication and crop evolution, from the cultural as well as from the biological perspectives.     

Desert rocks as plant refugia in the Near East

The outcrops of smooth-faced rocks in Near Eastern deserts function as refugia for plants that do not fit the present local climate. They have survived in the area from periods when the continuous extensions of the moister climate enabled their penetration from the Mediterranean zone. The largest Mediterranean enclave in Near Eastern deserts and steppes is the sandstone and limestone outcrops at the upper escarpments of the southwestern Jordanian plateau, between At Tafila and Ras en Naqb, including the famous Petra and Wadi Dana. Hundreds of Mediterranean relict species and dozens of endemic species coexist with steppe and desert species in the crevices of these rocks. In this article I discuss the ecology, phytogeography, and distribution of this special habitat in Jordan, the Sinai, and Israel; and I compare the influence on past and present floras of climatic oscillations during the Pleistocene and Holocene in the Near East and Africa.     

A proteomic analysis to identify cold acclimation associated proteins in wild wheat (Triticum urartu L.)

To gain a better understanding of cold acclimation process in wheat, we applied a 2-DE based proteomic approach to discover changes in proteome profile of a diploid wild wheat (Triticum urartu L.) during prolonged cold stress treatment. To this end, plants were grown in pots and the growing seedlings (4-leaf stage) were exposed to cold stress. After 4 weeks of cold acclimation (4–6 °C) and subsequent treatment for 12 h at ?2 °C, samples were collected from control and stressed plants and were subjected to proteome pattern analysis. Among approximately 450 reproducible protein spots displayed in each given 2-DE gels, 34 proteins changed significantly in abundance in response to cold stress. Among them, 25 and 9 proteins were up and down-regulated under stress condition, respectively. Analysis by matrix-assisted laser desorption ionization time of flight/time of flight mass spectrometry coupled with non-redundant protein database search allowed the identification of 20 cold-induced proteins. Integrated proteomic and database survey resulted in identification of several cold stress related proteins such as pathogenesis related protein, cold regulated protein, cold-responsive LEA/RAB-related COR protein, oxygen-evolving enhancer protein and oxalate oxidase. The presumed functions of the identified proteins were mostly related to cold acclimation, oxidative stress and photosynthesis. The possible implications of differentially accumulated proteins in acquiring systemic tolerance to freezing stress following exposure to prolonged low temperature will be discussed.     

乌拉尔图小麦(Triticum urartu)1Ay高分子量麦谷蛋白亚基基因编码区的克隆与鉴定(英文)

应用简并性引物和基因组PCR反应从乌拉尔图小麦(Triticum urartu)不同种质材料中获得并测定了表达型和沉默型1Ay高分子量麦谷蛋白亚基基因全长编码区的基因组DNA序列。表达型1Ay基因编码区的序列与前人已发表的y型高分子量麦谷蛋白亚基基因编码区的序列高度同源,由其推导的1Ay亚基的一级结构与已知的高分子量麦谷蛋白亚基相似。在细菌细胞中,表达型1Ay基因编码区的克隆序列可经诱导而产生1Ay蛋白,该蛋白与种子中1Ay亚基在电泳迁移率和抗原性上类似,表明所克隆的序列真实地代表了表达型1Ay基因的全长编码区。但是,本研究所克隆的沉默型1Ay基因的编码区序列因含有3个提前终止子而不能翻译成完整的1Ay蛋白。讨论了表达型1Ay基因在小麦籽粒加工品质改良中的潜在利用价值以及1Ay基因沉默的机制。     

The Druze: a population genetic refugium of the Near East

Background

Phylogenetic mitochondrial DNA haplogroups are highly partitioned across global geographic regions. A unique exception is the X haplogroup, which has a widespread global distribution without major regions of distinct localization.

Principal Findings

We have examined mitochondrial DNA sequence variation together with Y-chromosome-based haplogroup structure among the Druze, a religious minority with a unique socio-demographic history residing in the Near East. We observed a striking overall pattern of heterogeneous parental origins, consistent with Druze oral tradition, together with both a high frequency and a high diversity of the mitochondrial DNA (mtDNA) X haplogroup within a confined regional subpopulation. Furthermore demographic modeling indicated low migration rates with nearby populations.

Conclusions

These findings were enabled through the use of a paternal kindred based sampling approach, and suggest that the Galilee Druze represent a population isolate, and that the combination of a high frequency and diversity of the mtDNA X haplogroup signifies a phylogenetic refugium, providing a sample snapshot of the genetic landscape of the Near East prior to the modern age.