Reassessing domestication events in the Near East: Einkorn and Triticum urartu

To reassess domestication events in the Near East, accessions of Triticum urartu from a well-described sampling were combined with a representative sample covering the Karacada? Einkorn wheat domestication. The observed DNA separation between the two wheat species accounts for the main differentiation, but geographic variation within T. urartu is evident and so is the domestication scenario among wild, feral, and domesticated Einkorn. In contrast to the clear DNA differences, it is difficult to separate living T. urartu from wild Einkorn based on morphology. With archaeobotanical material a distinction of carbonized remains of these two wheats is considered to be impossible. We reviewed the differences concerning morphology and maturity and combined these observations with information about archaeological sites in the Near East. In conclusion, the excavation sites in the middle Euphrates may contain T. urartu rather than Einkorn wheat and T. urartu may underlie the reported occurrence of the extinct 2-grained domesticated "Einkorn" wheat. The first Einkorn wheat domestication sensu stricto seems to have happened around the Karacada?, as reported earlier. The human dimension shown by the excavation of G?bekli Tepe can explain why domesticated phenotypes might have spread quickly.     

A Gene Family Derived from Transposable Elements during Early Angiosperm Evolution Has Reproductive Fitness Benefits in Arabidopsis thaliana

The benefits of ever-growing numbers of sequenced eukaryotic genomes will not be fully realized until we learn to decipher vast stretches of noncoding DNA, largely composed of transposable elements. Transposable elements persist through self-replication, but some genes once encoded by transposable elements have, through a process called molecular domestication, evolved new functions that increase fitness. Although they have conferred numerous adaptations, the number of such domesticated transposable element genes remains unknown, so their evolutionary and functional impact cannot be fully assessed. Systematic searches that exploit genomic signatures of natural selection have been employed to identify potential domesticated genes, but their predictions have yet to be experimentally verified. To this end, we investigated a family of domesticated genes called MUSTANG (MUG), identified in a previous bioinformatic search of plant genomes. We show that MUG genes are functional. Mutants of Arabidopsis thaliana MUG genes yield phenotypes with severely reduced plant fitness through decreased plant size, delayed flowering, abnormal development of floral organs, and markedly reduced fertility. MUG genes are present in all flowering plants, but not in any non-flowering plant lineages, such as gymnosperms, suggesting that the molecular domestication of MUG may have been an integral part of early angiosperm evolution. This study shows that systematic searches can be successful at identifying functional genetic elements in noncoding regions and demonstrates how to combine systematic searches with reverse genetics in a fruitful way to decipher eukaryotic genomes.     

Use of Random Amplified Polymorphic DNA Analysis for Economically Important Food Crops

The objective of this review is to summarize numerous studies on the use of the random amplified polymorphic DNA （RAPD） technique on rice, corn, wheat, sorghum, barley, rye, and oats to examine its feasibility and validity for assessment of genetic variation, population genetics, mapping, linkage and marker assisted selection, phylogenetic analysis, and the detection of somaclonal variation. Also we discuss the advantages and limitations of RAPD. Molecular markers have entered the scene of genetic improvement in different fields of agricultural research. The simplicity of the RAPD technique made it ideal for genetic mapping, plant and animal breeding programs, and DNA fingerprinting, with particular utility in the field of population genetics.     

Wheat domestication: lessons for the future

Wheat was one of the first crops to be domesticated more than 10,000 years ago in the Middle East. Molecular genetics and archaeological data have allowed the reconstruction of plausible domestication scenarios leading to modern cultivars. For diploid einkorn and tetraploid durum wheat, a single domestication event has likely occurred in the Karacadag Mountains, Turkey. Following a cross between tetraploid durum and diploid T.?tauschii, the resultant hexaploid bread wheat was domesticated and disseminated around the Caucasian region. These polyploidisation events facilitated wheat domestication and created genetic bottlenecks, which excluded potentially adaptive alleles. With the urgent need to accelerate genetic progress to confront the challenges of climate change and sustainable agriculture, wild ancestors and old landraces represent a reservoir of underexploited genetic diversity that may be utilized through modern breeding methods. Understanding domestication processes may thus help identifying new strategies.     

Ancient plant DNA: review and prospects

Ancient DNA has received much attention since the mid-1980s, when the first sequence of an extinct animal species was recovered from a museum specimen. Since then, the majority of ancient DNA studies have focused predominantly on animal species, while studies in plant palaeogenetics have been rather limited, with the notable exception of cultivated species found in archaeological sites. Here, we outline the recent developments in the analysis of plant ancient DNA. We emphasize the trend from species identification to population-level investigation and highlight the potential and the difficulties in this field, related to DNA preservation and to risks of contamination. Further efforts towards the analysis of ancient DNA from the abundant store of fossil plant remains should provide new research opportunities in palaeoecology and phylogeography. In particular, intraspecific variation should be considered not only in cultivated plants but also in wild taxa if palaeogenetics is to become a fully emancipated field of plant research.     

家马的驯化起源与遗传演化特征

人类文明发展历史中, 家马(Equus ferus caballus)曾是推动文化交流、促进人类社会发展的主要动力。关于家马何时、何地被驯化以及在此过程中其遗传演化如何被人类影响等一直备受关注。近年来随着遗传学技术的发展, 人们对该问题有了更为深入的理解。本文回顾了近二十年来相关研究所取得的成果, 探讨了家马的驯化起源中心和驯化过程中的遗传演化特征, 并对未来的研究方向以及遗传资源保护提出了建议。分子标记遗传学和考古学研究认为家马可能来自多个驯化起源地种群, 然而最近的古DNA研究结果表明, 现代家马的驯化起源可能比之前人们所猜测的更加复杂, 古代博泰马被认为是最早被驯化的家马, 然而最近被证实并不是现代家马的直系祖先。如此复杂的驯化问题可能从多学科的层次才能解析清楚。人类社会活动直接或间接影响了家马的演化历程, 特别是工业革命以来家马的遗传基础发生了巨大变化, 其遗传多样性开始急剧衰退, 不少地方品种正逐渐走向衰落甚至灭绝。为确保农业生态安全不受威胁, 建议加强家马遗传资源保护与动物遗传学和文化地理之间的联系研究。     

Genomics at the origins of agriculture,part one

The causes and consequences of the Neolithic revolution represent a fundamental problem for anthropological inquiry. Traditional archeological evidence, ethnobotanical remains, artifacts, and settlement patterns have been used to infer the transition from foraging to primary food production. Recent advances in genomics (the study of the sequence, structure, and function of the genome) has enhanced our understanding of the process of plant and animal domestication, revealed the impact that adaptation to agriculture has had on human biology, and provided clues to the pathogens and parasites thought to have emerged during the Neolithic. Genomic analysis provides insights into the complexity of the process of domestication that may not be apparent from the physical remains of bones and seeds, and allows us to measure the impact that the shift to primary food production had on the human genome. Questions related to the location and the process of domestication can be answered more fully by analyzing the genomes of the plants and animals brought under human control. The spread of the agriculture package (plants, animals, and technology) by cultural diffusion or demic expansion can also be investigated through this approach. Whether dissemination by farmers or the diffusion of farming knowledge and technology was the source of the Neolithic expansion, this process should be revealed by the patterh of genetic and linguistic diversity and language found from centers of agricultural Neolithic development. In addition, a number of pathogens that were previously thought to have been transmitted from domesticated species to human now appear to have been present in foragers long before the agricultural revolution took place. Furthermore, we now have evidence that humans were the source of the transmission of some parasites to domesticated animals. For all of these reasons, data from genomic studies are providing a more complete understanding of the origins of agriculture, a critical hallmark in human evolution.     

古DNA 及其在生物系统与进化研究中的应用

古DNA是指从已经死亡的古代生物的遗体和遗迹中得到的DNA。本文回顾了近20年古DNA研究所经历的3个阶段, 从早期参与研究的科学家较少并主要利用克隆技术, 到后来由于PCR技术的出现以及提取化石DNA技术的成熟从而出现大量有关古DNA的报道; 近几年由于发现不少问题, 并引起激烈的争论, 科学家们因此而开始考虑古DNA的真实性问题, 并且提出了开展古DNA研究的严格标准。本文还讨论了古DNA在人类起源、系统发育重建、动植物驯化及考古研究中的重要意义以及现状, 表明古DNA的研究给某些原先的观点如人类的非洲起源说提供了重要证据, 也对某些观点提出了挑战; 古DNA研究还提供了某些已经灭绝生物的形态学和分子资料, 为从序列上确定古代材料的系统位置并有效地补充仅用现代DNA建立起来的谱系提供了来自古生物的依据。在动植物驯化及考古方面, 古DNA证据也为科学家提供了许多有价值的信息。最后, 本文还对古DNA研究的应用前景进行了展望。     

The Origins of Domesticated Cattle

The origin of domestic cattle has perplexed archaeologists for more than a century. Researchers have proposed various theories, which offer alternative spatial and chronological models for the origin and spread of domesticated cattle. One point of discussion is whether domestic cattle had a single or multiple origins; however, most authorities considered that the first steps towards cattle domestication were taken in southwest Asia and that domesticated cattle entered Europe with pastoralists migrating from this region. Domesticated taurine cattle were thought to have entered Africa in successive waves from southwest Asia, while zebu cattle migrated into Africa at a later date from Arabia and the Indian subcontinent. Analysis of mitochondrial DNA (mtDNA) shows that taurine and zebu cattle divergence before the Holocene and were probably domesticated independently. Recent mtDNA sequence data shows that African and European taurine cattle were probably domesticated independently, but that there was a process of genetic introgression between taurine and zebu cattle in Africa. Ancient DNA studies over the last 10 years suggest that Northern European aurochsens apparently contributed little or nothing to domestic cattle while Southern European aurochsens apparently made a significant input. However, Middle Eastern aurochsen, unfortunately not typed yet, are expected to be to be very similar to European breeds as well, both because archeological data suggest that the major center of domestication for European Bos taurus breeds was the Fertile Crescent (9), and also because a mtDNA sequence from a Syrian specimen dated at 8,000–9,000 years ago shows a typical European haplotype found both in modern breeds and the Italian aurochsen. Evidence seems to suggest that small to moderate levels of local gene flow from wild Bos primigenius females in selected breeds were either accepted or may be reinforced by Neolithic breeders.     

植物分子群体遗传学研究动态

分子群体遗传学是当代进化生物学研究的支柱学科, 也是遗传育种和关于遗传关联作图和连锁分析的基础理论学科。分子群体遗传学是在经典群体遗传的基础上发展起来的, 它利用大分子主要是DNA序列的变异式样来研究群体的遗传结构及引起群体遗传变化的因素与群体遗传结构的关系, 从而使得遗传学家能够从数量上精确地推知群体的进化演变, 不仅克服了经典的群体遗传学通常只能研究群体遗传结构短期变化的局限性, 而且可检验以往关于长期进化或遗传系统稳定性推论的可靠程度。同时, 对群体中分子序列变异式样的研究也使人们开始重新审视达尔文的以“自然选择”为核心的进化学说。到目前为止, 分子群体遗传学已经取得长足的发展, 阐明了许多重要的科学问题, 如一些重要农作物的DNA多态性式样、连锁不平衡水平及其影响因素、种群的变迁历史、基因进化的遗传学动力等, 更为重要的是, 在分子群体遗传学基础上建立起来的新兴的学科如分子系统地理学等也得到了迅速的发展。文中综述了植物分子群体遗传研究的内容及最新成果。     

Sequences From First Settlers Reveal Rapid Evolution in Icelandic mtDNA Pool

A major task in human genetics is to understand the nature of the evolutionary processes that have shaped the gene pools of contemporary populations. Ancient DNA studies have great potential to shed light on the evolution of populations because they provide the opportunity to sample from the same population at different points in time. Here, we show that a sample of mitochondrial DNA (mtDNA) control region sequences from 68 early medieval Icelandic skeletal remains is more closely related to sequences from contemporary inhabitants of Scotland, Ireland, and Scandinavia than to those from the modern Icelandic population. Due to a faster rate of genetic drift in the Icelandic mtDNA pool during the last 1,100 years, the sequences carried by the first settlers were better preserved in their ancestral gene pools than among their descendants in Iceland. These results demonstrate the inferential power gained in ancient DNA studies through the application of population genetics analyses to relatively large samples.     

古DNA及其在生物系统与进化研究中的应用

古DNA是指从已经死亡的古代生物的遗体和遗迹中得到的DNA.本文回顾了近20年古DNA研究所经历的3个阶段,从早期参与研究的科学家较少并主要利用克隆技术,到后来由于PCR技术的出现以及提取化石DNA技术的成熟从而出现大量有关古DNA的报道;近几年由于发现不少问题,并引起激烈的争论,科学家们因此而开始考虑古DNA的真实性问题,并且提出了开展古DNA研究的严格标准.本文还讨论了古DNA在人类起源、系统发育重建、动植物驯化及考古研究中的重要意义以及现状,表明古DNA的研究给某些原先的观点如人类的非洲起源说提供了重要证据,也对某些观点提出了挑战;古DNA研究还提供了某些已经灭绝生物的形态学和分子资料,为从序列上确定古代材料的系统位置并有效地补充仅用现代DNA建立起来的谱系提供了来自古生物的依据.在动植物驯化及考古方面,古DNA证据也为科学家提供了许多有价值的信息.最后,本文还对古DNA研究的应用前景进行了展望.     

The ripples of "The Big (agricultural) Bang": the spread of early wheat cultivation.

Demographic expansion and (or) migrations leave their mark in the pattern of DNA polymorphisms of the respective populations. Likewise, the spread of cultural phenomena can be traced by dating archaeological finds and reconstructing their direction and pace. A similar course of events is likely to have taken place following the "Big Bang" of the agricultural spread in the Neolithic Near East from its core area in southeastern Turkey. Thus far, no attempts have been made to track the movement of the founder genetic stocks of the first crop plants from their core area based on the genetic structure of living plants. In this minireview, we re-interpret recent wheat DNA polymorphism data to detect the genetic ripples left by the early wave of advance of Neolithic wheat farming from its core area. This methodology may help to suggest a model charting the spread of the first farming phase prior to the emergence of truly domesticated wheat types (and other such crops), thereby increasing our resolution power in studying this revolutionary period of human cultural, demographic, and social evolution.     

Ancient DNA applications for wildlife conservation

Ancient DNA analyses of historical, archaeological and paleontological remains can contribute important information for the conservation of populations and species that cannot be obtained any other way. In addition to ancient DNA analyses involving a single or few individuals, population level studies are now possible. Biases inherent in estimating population parameters and history from modern genetic diversity are exaggerated when populations are small or have been heavily impacted by recent events, as is common for many endangered species. Going directly back in time to study past populations removes many of the assumptions that undermine conclusions based only on recent populations. Accurate characterization of historic population size, levels of gene flow and relationships with other populations are fundamental to developing appropriate conservation and management plans. The incorporation of ancient DNA into conservation genetics holds a lot of potential, if it is employed responsibly.     

Domestication evolution,genetics and genomics in wheat

Domestication of plants and animals is the major factor underlying human civilization and is a gigantic evolutionary experiment of adaptation and speciation, generating incipient species. Wheat is one of the most important grain crops in the world, and consists mainly of two types: the hexaploid bread wheat (Triticum aestivum) accounting for about 95% of world wheat production, and the tetraploid durum wheat (T. durum) accounting for the other 5%. In this review, we summarize and discuss research on wheat domestication, mainly focusing on recent findings in genetics and genomics studies. T. aestivum originated from a cross between domesticated emmer wheat T. dicoccum and the goat grass Aegilops tauschii, most probably in the south and west of the Caspian Sea about 9,000 years ago. Wild emmer wheat has the same genome formula as durum wheat and has contributed two genomes to bread wheat, and is central to wheat domestication. Domestication has genetically not only transformed the brittle rachis, tenacious glume and non-free threshability, but also modified yield and yield components in wheat. Wheat domestication involves a limited number of chromosome regions, or domestication syndrome factors, though many relevant quantitative trait loci have been detected. On completion of the genome sequencing of diploid wild wheat (T. urartu or Ae. tauschii), domestication syndrome factors and other relevant genes could be isolated, and effects of wheat domestication could be determined. The achievements of domestication genetics and robust research programs in Triticeae genomics are of greatly help in conservation and exploitation of wheat germplasm and genetic improvement of wheat cultivars.     

From the cradle of agriculture a handful of lentils: History of domestication

Literature on lentil domestication is reviewed, particularly considering archeobotanical, phylogenetic, and molecular evidence. Lentils are one of the oldest crops cultivated and domesticated by man. Carbonized small lentil seeds have been found in several archaeological remains starting from the Neolithic. It is probable, however, that the most ancient remains refer to wild lentils; this is difficult to ascertain since seed size was probably selected after the establishment of a domesticated lentil. It is general opinion that cultivation occurred before domestication, but for how long is still an open question. It is now well accepted that the domestication of lentils was accomplished in the Near East, in an area called “the cradle of agriculture”. The genus Lens is very small, containing only 6 taxa. A wide range of morphological and molecular evidence supports the idea that the lentil wild progenitor is Lens culinaris ssp. orientalis. On the other hand, the most distantly related species within the genus appears to be L. nigricans, whose domestication was also attempted without success. The first characters involved in lentil domestication were pod dehiscence and seed dormancy. These traits are under a simple genetic control, and therefore mutants must have been fixed in a relatively short time. These and other morphological traits possibly involved in lentil domestication have been mapped in several linkage maps. However, generally these maps are not easily integrated since they are based on a limited number of markers. Newer maps, mainly built on different kinds of molecular markers, have been more recently produced. A consensus map is needed to fill the gap in lentil breeding and, at the same time, endow with deeper information on the genetics of lentil domestication, giving new insight into the origins of this crop, which present fragmented knowledge is unable.      

质粒DNA物理形态和其它因素对获得可育转基因小麦的影响

The applicability of hyperosmotic treatment and different configurations of plasmid DNA for stable transformation of wheat mediated by particle bombardment was investigated. Hyperosmotic treatment increased the frequency of transient expression and had also a positive effect on stable transformation. Denaturation of plasmid DNA prior to bombardment led to dramatic reduction of transient expression. However, there were no marked differences between single-stranded and double-stranded DNA in stable transformation. Single-stranded plasmid DNA, double-stranded plasmid DNA in linear state and double-stranded plasmid DNA in circular state could all be used to produce transgenic wheat plants. A total of 26 independent transgenic plants of winter wheat genotype Florida and 4 independent transgenic plants of spring wheat genotype Veery were obtained. Most transgenic plants have set seeds. T2 seeds of some spring wheat transgenic plants have also been harvested.     

The complex history of the domestication of rice

BACKGROUND: Rice has been found in archaeological sites dating to 8000 bc, although the date of rice domestication is a matter of continuing debate. Two species of domesticated rice, Oryza sativa (Asian) and Oryza glaberrima (African) are grown globally. Numerous traits separate wild and domesticated rices including changes in: pericarp colour, dormancy, shattering, panicle architecture, tiller number, mating type and number and size of seeds. SCOPE: Genetic studies using diverse methodologies have uncovered a deep population structure within domesticated rice. Two main groups, the indica and japonica subspecies, have been identified with several subpopulations existing within each group. The antiquity of the divide has been estimated at more than 100 000 years ago. This date far precedes domestication, supporting independent domestications of indica and japonica from pre-differentiated pools of the wild ancestor. Crosses between subspecies display sterility and segregate for domestication traits, indicating that different populations are fixed for different networks of alleles conditioning these traits. Numerous domestication QTLs have been identified in crosses between the subspecies and in crosses between wild and domesticated accessions of rice. Many of the QTLs cluster in the same genomic regions, suggesting that a single gene with pleiotropic effects or that closely linked clusters of genes underlie these QTL. Recently, several domestication loci have been cloned from rice, including the gene controlling pericarp colour and two loci for shattering. The distribution and evolutionary history of these genes gives insight into the domestication process and the relationship between the subspecies. CONCLUSIONS: The evolutionary history of rice is complex, but recent work has shed light on the genetics of the transition from wild (O. rufipogon and O. nivara) to domesticated (O. sativa) rice. The types of genes involved and the geographic and genetic distribution of alleles will allow scientists to better understand our ancestors and breed better rice for our descendents.     

质粒DNA物理形态和其它因素对获得可育转基因小麦的影响

本工作分析了不同形态质粒DNA和未成熟胚高渗透压处理对基因枪小麦转化体系的适用性.高渗处理对瞬间表达和转基因小麦的再生均有明显的促进作用.轰击之前对质粒DNA进行变性处理导致瞬间表达反应大幅度下降,但稳定转化频率(指从100个轰击未成熟胚得到的再生可育转基因植株数)与双链DNA相差不大.使用单链质粒DNA、线性双链质粒DNA和环状双链质粒DNA均可以得到转基因小麦植株.迄今已得到26个不同的转基因冬小麦株系和4个不同的转基因春小麦株系.这些转基因小麦大多数已产生种子,几个春小麦株系已获第二代种子.     

Starch granule size and the domestication of manioc (Manihot esculenta) and sweet potato (Ipomoea batatas)

Archaeological studies of plant remains have indicated that an increase in seed size is frequently correlated with both intensive cultivation and domestication of seed crop plants. To test if starch granules of domesticated root crops are significantly larger than those of wild or less intensively cultivated plants, archaeological and modern specimens of manioc and sweet potato were sampled for starch granules, and granule size was compared across a temporal sequence. The results indicate that a gross generalization can be made that modern specimens of both manioc and sweet potato yield larger starch granules than some archaeological specimens. It does appear, however, that modern domesticated manioc roots produce significantly larger-sized starch granules than those of its purported wild ancestor. Additionally, there exist two lines of evidence that the coastal Peruvian and lowland Neotropical regional types of manioc differ from one another and have been separate for several millennia. These findings indicate that manioc may have been domesticated more than once.