Pulse domestication and cereal domestication: How different are they?

Evidence is brought to indicate that the domestication of lentil and pea is not very different from that of wheat and barley. All these Near East crops are characterized by basically the same domestication traits the key elements of which are breakdown of the wild mode of seed dispersal and loss of germination regulation. It is argued that both in the pulses and in the cereals these traits evolved in the same way. The changes are best explained by assuming that mutations causing the loss of the wild-type adaptations were automatically selected for soon after people transferred the wild progenitors into a system of planting and reaping.     

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.     

A whole-genome snapshot of 454 sequences exposes the composition of the barley genome and provides evidence for parallel evolution of genome size in wheat and barley

The genomes of barley and wheat, two of the world's most important crops, are very large and complex due to their high content of repetitive DNA. In order to obtain a whole-genome sequence sample, we performed two runs of 454 (GS20) sequencing on genomic DNA of barley cv. Morex, which yielded approximately 1% of a haploid genome equivalent. Almost 60% of the sequences comprised known transposable element (TE) families, and another 9% represented novel repetitive sequences. We also discovered high amounts of low-complexity DNA and non-genic low-copy DNA. We identified almost 2300 protein coding gene sequences and more than 660 putative conserved non-coding sequences. Comparison of the 454 reads with previously published genomic sequences suggested that TE families are distributed unequally along chromosomes. This was confirmed by in situ hybridizations of selected TEs. A comparison of these data for the barley genome with a large sample of publicly available wheat sequences showed that several TE families that are highly abundant in wheat are absent from the barley genome. This finding implies that the TE composition of their genomes differs dramatically, despite their very similar genome size and their close phylogenetic relationship.     

Control of flowering time in temperate cereals: genes, domestication, and sustainable productivity

The control of flowering is central to reproductive success in plants, and has a major impact on grain yield in crop species. The global importance of temperate cereal crops such as wheat and barley has meant emphasis has long been placed on understanding the genetics of flowering in order to enhance yield. Leads gained from the dissection of the molecular genetics of model species have combined with comparative genetic approaches, recently resulting in the isolation of the first flowering time genes in wheat and barley. This paper reviews the genetics and genes involved in cereal flowering pathways and the current understanding of how two of the principal genes, Vrn and Ppd, have been involved in domestication and adaptation to local environments, and the implications for future breeding programmes are discussed.     

Seed traits and genes important for translational biology--highlights from recent discoveries

Seeds provide food, feed, fiber and fuel. They are also an important delivery system of genetic information, which is essential for the survival of wild species in ecosystems and the production of agricultural crops. In this review, seed traits and genes that are potentially important for agricultural applications are discussed. Over the long period of crop domestication, seed traits have been modified through intentional or unintentional selections. While most selections have led to seed traits favorable for agricultural consumption, such as larger seeds with higher nutritional value than the wild type, other manipulations in modern breeding sometimes led to negative traits, such as vivipary, precocious germination on the maternal plant or reduced seed vigor, as a side effect during the improvement of other characteristics. Greater effort is needed to overcome these problems that have emerged as a consequence of crop improvement. Seed biology researchers have characterized the function of many genes in the last decade, including those associated with seed domestication, which may be useful in addressing critical issues in modern agriculture, such as the prevention of vivipary and seed shattering or the enhancement of yields. Recent discoveries in seed biology research are highlighted in this review, with an emphasis on their potential for translational biology.     

A global barley panel revealing genomic signatures of breeding in modern Australian cultivars

The future of plant cultivar improvement lies in the evaluation of genetic resources from currently available germplasm. Today’s gene pool of crop genetic diversity has been shaped during domestication and more recently by breeding. Recent efforts in plant breeding have been aimed at developing new and improved varieties from poorly adapted crops to suit local environments. However, the impact of these breeding efforts is poorly understood. Here, we assess the contributions of both historical and recent breeding efforts to local adaptation and crop improvement in a global barley panel by analysing the distribution of genetic variants with respect to geographic region or historical breeding category. By tracing the impact that breeding had on the genetic diversity of Hordeum vulgare (barley) released in Australia, where the history of barley production is relatively young, we identify 69 candidate regions within 922 genes that were under selection pressure. We also show that modern Australian barley varieties exhibit 12% higher genetic diversity than historical cultivars. Finally, field-trialling and phenotyping for agriculturally relevant traits across a diverse range of Australian environments suggests that genomic regions under strong breeding selection and their candidate genes are closely associated with key agronomic traits. In conclusion, our combined data set and germplasm collection provide a rich source of genetic diversity that can be applied to understanding and improving environmental adaptation and enhanced yields.     

The improved assembly of 7DL chromosome provides insight into the structure and evolution of bread wheat

Wheat is one of the most important staple crops worldwide and also an excellent model species for crop evolution and polyploidization studies. The breakthrough of sequencing the bread wheat genome and progenitor genomes lays the foundation to decipher the complexity of wheat origin and evolutionary process as well as the genetic consequences of polyploidization. In this study, we sequenced 3286 BACs from chromosome 7DL of bread wheat cv. Chinese Spring and integrated the unmapped contigs from IWGSC v1 and available PacBio sequences to close gaps present in the 7DL assembly. In total, 8043 out of 12 825 gaps, representing 3 491 264 bp, were closed. We then used the improved assembly of 7DL to perform comparative genomic analysis of bread wheat (Ta7DL) and its D donor, Aegilops tauschii (At7DL), to identify domestication signatures. Results showed a strong syntenic relationship between Ta7DL and At7DL, although some small rearrangements were detected at the distal regions. A total of 53 genes appear to be lost genes during wheat polyploidization, with 23% (12 genes) as RGA (disease resistance gene analogue). Furthermore, 86 positively selected genes (PSGs) were identified, considered to be domestication‐related candidates. Finally, overlapping of QTLs obtained from GWAS analysis and PSGs indicated that TraesCS7D02G321000 may be one of the domestication genes involved in grain morphology. This study provides comparative information on the sequence, structure and organization between bread wheat and Ae. tauschii from the perspective of the 7DL chromosome, which contribute to better understanding of the evolution of wheat, and supports wheat crop improvement.     

Vegetable biology and breeding in the genomics era

Vegetable crops provide a rich source of essential nutrients for humanity and represent critical economic values to global rural societies. However, genetic studies of vegetable crops have lagged behind major food crops, such as rice, wheat and maize, thereby limiting the application of molecular breeding. In the past decades, genome sequencing technologies have been increasingly applied in genetic studies and breeding of vegetables. In this review, we recapitulate recent progress on reference genome construction, population genomics and the exploitation of multi-omics datasets in vegetable crops. These advances have enabled an in-depth understanding of their domestication and evolution, and facilitated the genetic dissection of numerous agronomic traits, which jointly expedites the exploitation of state-of-the-art biotechnologies in vegetable breeding. We further provide perspectives of further directions for vegetable genomics and indicate how the ever-increasing omics data could accelerate genetic, biological studies and breeding in vegetable crops.

     

Key Features of Cereal Genome Organization as Revealed by the Use of Cytosine Methylation-Sensitive Restriction Endonucleases

Unlike mammalian genomes, cereal (Gramineae) genomes exhibit little suppression of CpG dinucleotides. In cereal genomes, however, most of the numerous potential recognition sites for CpG methylation-sensitive restriction enzymes are methylated. Analysis of cereal genomic libraries and of regions flanking genes indicates that unmethylated NotI sites are useful landmarks for regions containing genes/single-copy sequences. Studies of a rye chromosome arm indicate that its pericentromeric region has a reduced density of unmethylated NotI (and MluI) sites and therefore of genes. Unmethylated MluI and NruI sites are distributed nonrandomly in the genomes of wheat, barley, and rice. Analysis of the genomic blocks defined by these sites in wheat and barley indicates that they are most likely to have arisen by amplification. These observations form the basis of a proposed model for the organization and evolution of the wheat, barley, and rice genomes.     

The development and application of molecular markers for abiotic stress tolerance in barley

This article represents some current thinking and objectives in the use of molecular markers to abiotic stress tolerance. Barley has been chosen for study as it is an important crop species, as well as a model for genetic and physiological studies. It is an important crop and, because of its well-studied genetics and physiology, is an excellent candidate in which to devise more efficient breeding methods. Abiotic stress work on cultivated gene pools of small grain cereals frequently shows that adaptive and developmental genes are strongly associated with responses. Developmental genes have strong pleiotropic effects on a number of performance traits, not just abiotic stresses. One concern is that much of the genetic variation for improving abiotic stress tolerance has been lost during domestication, selection and modern breeding, leaving pleiotropic effects of the selected genes for development and adaptation. Such genes are critical in matching cultivars to their target agronomic environment, and since there is little leverage in changing these, other sources of variation may be required. In barley, and many other crops, greater variation to abiotic stresses exists in primitive landraces and related wild species gene pools. Wild barley, Hordeum spontaneum C. Koch is the progenitor of cultivated barley, Hordeum vulgare L. and is easily hybridized to H. vulgare. Genetic fingerprinting of H. spontaneum has revealed genetic marker associations with site-of-origin ecogeographic factors and also experimentally imposed stresses. Genotypes and collection sites have been identified which show the desired variation for particular stresses. Doubled haploid and other segregating populations, including landrace derivatives have been used to map genetically the loci involved. These data can be used in molecular breeding approaches to improve the drought tolerance of barley. One strategy involves screening for genetic markers and physiological traits for drought tolerance, and the associated problem of drought relief-induced mildew susceptibility in naturally droughted fields of North Africa.     

Domestication of plants in the Americas: insights from Mendelian and molecular genetics

BACKGROUND: Plant domestication occurred independently in four different regions of the Americas. In general, different species were domesticated in each area, though a few species were domesticated independently in more than one area. The changes resulting from human selection conform to the familiar domestication syndrome, though different traits making up this syndrome, for example loss of dispersal, are achieved by different routes in crops belonging to different families. GENETIC AND MOLECULAR ANALYSES OF DOMESTICATION: Understanding of the genetic control of elements of the domestication syndrome is improving as a result of the development of saturated linkage maps for major crops, identification and mapping of quantitative trait loci, cloning and sequencing of genes or parts of genes, and discoveries of widespread orthologies in genes and linkage groups within and between families. As the modes of action of the genes involved in domestication and the metabolic pathways leading to particular phenotypes become better understood, it should be possible to determine whether similar phenotypes have similar underlying genetic controls, or whether human selection in genetically related but independently domesticated taxa has fixed different mutants with similar phenotypic effects. CONCLUSIONS: Such studies will permit more critical analysis of possible examples of multiple domestications and of the origin(s) and spread of distinctive variants within crops. They also offer the possibility of improving existing crops, not only major food staples but also minor crops that are potential export crops for developing countries or alternative crops for marginal areas.     

Diverse approaches to achieving grain yield in wheat

Artificial selection (domestication and breeding) leaves a strong footprint in plant genomes. Second generation high throughput DNA sequencing technologies make it possible to sequence the gene complement of a plant genome within 3 to 5 months, and the costs of doing so are declining very quickly. This makes it practical to identify genomic regions that have undergone very strong selection. Available reference sequences of important crops such as rice, maize, and sorghum will promote the wide use of re-sequencing strategies in these crops. Marker/trait associations, especially haplotype (or haplotype block) association analyses, will help the precise mapping of important genomic regions and location of favored alleles or haplotypes for breeding. This mini-review examines a genomics approach to defining yield traits in wheat.     

Wild barley: a source of genes for crop improvement in the 21st century?

The development of new barleys tolerant of abiotic and biotic stresses is an essential part of the continued improvement of the crop. The domestication of barley, as in many crops, resulted in a marked truncation of the genetical variation present in wild populations. This process is significant to agronomists and scientists because a lack of allelic variation will prevent the development of adapted cultivars and hinder the investigation of the genetic mechanisms underlying performance. Wild barley would be a useful source of new genetic variation for abiotic stress tolerance if surveys identify appropriate genetic variation and the development of marker-assisted selection allows efficient manipulation in cultivar development. There are many wild barley collections from all areas of its natural distribution, but the largest are derived from the Mediterranean region. The results of a range of assays designed to explore abiotic stress tolerance in barley are reported in this paper. The assays included; sodium chloride uptake in wild barley and a mapping population, effects for delta 13C and plant dry weight in wheat aneuploids, effects of photoperiod and vernalization in wild barley, and measurements of root length in wild barley given drought and nitrogen starvation treatments in hydroponic culture. There are examples of the use of wild barley in breeding programmes, for example, as a source of new disease resistance genes, but the further exploration of the differences between wild barley and cultivars is hampered by the lack of good genetic maps. In parallel to the need for genetic studies there is also a need for the development of good physiological models of crop responses to the environment. Given these tools, wild barley offers the prospect of a 'goldmine' of untapped genetic reserves.     

麦类作物遗传转化

麦类作物包括小麦(Triticum aestivum L.)、硬粒小麦(Triticum turgidum con v.durum Dest.e.m)、大麦(Hordeum vulgare L.)、黑麦(Secale cereal L.)、燕麦(Avena sativa L.)及小大麦(×Tritordeum Ascherson et Graebuer.).自从基因枪被发明以来,科学家们已经利用来自麦类作物的幼胚、 盾片、成熟种子胚、花粉粒、花药、幼穗、叶基组织、发芽种子幼苗的顶端分生组织及其愈伤组织或培养物作为外植体,通过基因枪、农杆菌介导、 PEG法、电激法、微注射法、硅化纤维素介导、幼穗注射法等技术先后将一些选择标记基因、报告基因和有用的目的基因如抗真菌、抗虫、 籽粒品质、抗干旱基因等转化到麦类作物中.转基因植物表现为抗性增强或籽粒的加工品质提高和营养成份增加.被转化的基因通常以单位点多拷贝的形式随机整合到受体细胞的基因组中,并以孟德尔规律遗传.整合位点一般分布在染色体的近端粒区域,整合的拷贝数大多为5～10个拷贝,最高可达到50个拷贝.在转化过程中,被转化的质粒上的片段包括选择标记基因、目标基因、甚至质粒的抗生素基因和其他无关序列,随机地连接并形成多个分子量大小不等,组成成分不同的分子簇,或首先由其中一个分子簇整合到植物基因组中,这会导致在整合位点附近产生"热点",易于其他分子簇在此处整合,从而完成两期整合;或被转化的质粒上的选择标记基因、目标基因、质粒的抗生素基因和其他无关序列、植物基因组DNA等片段共同形成各种不同类型的分子簇,当植物细胞染色体复制时,在复制叉处整合到植物基因组中.转基因可以在各种水平上表达,也会时常发生基因沉默,这会导致转基因植物DNA水平上表达但在蛋白质水平上不表达,后代偏向分离,沉默的转基因重新表达.转基因的位置效应、甲基化和启动子都会诱发转基因沉默.在麦类作物中,35S启动子易于导致转基因沉默,应尽量减少使用.转基因还导致被转化麦类作物在农艺性状和细胞学上的变异.目前,麦类作物遗传转化已经成为一种常规的技术,转基因麦类作物正开始进入商业应用阶段.相信多种转化新技术的应用和发展将会培育出高产、稳产、优质、低投入的各类品种和种质.     

麦类作物遗传转化(英)

麦类作物包括小麦 (TriticumaestivumL .)、硬粒小麦 (Triticumturgidumconv .durumDest.e.m)、大麦 (HordeumvulgareL .)、黑麦 (SecalecerealL .)、燕麦 (AvenasativaL .)及小大麦 (×TritordeumAschersonetGraebuer.)。自从基因枪被发明以来 ,科学家们已经利用来自麦类作物的幼胚、盾片、成熟种子胚、花粉粒、花药、幼穗、叶基组织、发芽种子幼苗的顶端分生组织及其愈伤组织或培养物作为外植体 ,通过基因枪、农杆菌介导、PEG法、电激法、微注射法、硅化纤维素介导、幼穗注射法等技术先后将一些选择标记基因、报告基因和有用的目的基因如抗真菌、抗虫、籽粒品质、抗干旱基因等转化到麦类作物中。转基因植物表现为抗性增强或籽粒的加工品质提高和营养成份增加。被转化的基因通常以单位点多拷贝的形式随机整合到受体细胞的基因组中 ,并以孟德尔规律遗传。整合位点一般分布在染色体的近端粒区域 ,整合的拷贝数大多为 5～ 10个拷贝 ,最高可达到 5 0个拷贝。在转化过程中 ,被转化的质粒上的片段包括选择标记基因、目标基因、甚至质粒的抗生素基因和其他无关序列 ,随机地连接并形成多个分子量大小不等 ,组成成分不同的分子簇 ,或首先由其中一个分子簇整合到植物基因组中 ,这会导致在整合位点附近产生“热点     

Molecular approaches to origin,ancestry and domestication history of crop plants: Barley and clover as examples

Knowledge of the origin and domestication history of crop plants is important for studies aiming at avoiding the erosion of genetic resources due to the loss of ecotypes and landraces and habitats and increased urbanization. Such knowledge also strengthens the capacity of modern farming system to develop and scale-up the domestication of high value potential crops that can be achieved by improving the knowledge that help to identify and select high value plant species within their locality, identify and apply the most appropriate propagation techniques for improving crops and integrate improved crop species into the farming systems. The study of domestication history and ancestry provide means for germplasm preservation through establishment of gene banks, largely as seed collections, and preservation of natural habitats. Information about crop evolution and specifically on patterns of genetic change generated by evolution prior, during, and after domestication, is important to develop sound genetic conservation programs of genetic resources of crop plants and also increases the efficiency of breeding programs. In recent years, molecular approaches have contributed to our understanding of the aspects of plant evolution and crops domestication. In this article, aspects of crops domestication are outlined and the role of molecular data in elucidating the ancestry and domestication of crop plants are outlined. Particular emphasis is given to the contribution of molecular approaches to the origin and domestication history of barley and the origin and ancestry of the Egyptian clover.