Reproductive allocation of biomass and nitrogen in annual and perennial Lesquerella crops

* BACKGROUND AND AIMS: The use of perennial crops could contribute to increase agricultural sustainability. However, almost all of the major grain crops are herbaceous annuals and opportunities to replace them with more long-lived perennials have been poorly explored. This follows the presumption that the perennial life cycle is associated with a lower potential yield, due to a reduced allocation of biomass to grains. The hypothesis was tested that allocation to perpetuation organs in the perennial L. mendocina would not be directly related to a lower allocation to seeds. * METHODS: Two field experiments were carried on with the annual Lesquerella fendleri and the iteroparous perennial L. mendocina, two promising oil-seed crops for low-productivity environments, subjected to different water and nitrogen availability. * KEY RESULTS: Seed biomass allocation was similar for both species, and unresponsive to water and nitrogen availability. Greater root and vegetative shoot allocation in the perennial was counterbalanced by a lower allocation to other reproductive structures compared with the annual Lesquerella. Allometric relationships revealed that allocation differences between the annual and the perennial increased linearly with plant size. The general allocation patterns for nitrogen did not differ from those of biomass. However, nitrogen concentrations were higher in the vegetative shoot and root of L. mendocina than of L. fendleri but remained stable in seeds of both species. * CONCLUSIONS: It is concluded that vegetative organs are more hierarchically important sinks in L. mendocina than in the annual L. fendleri, but without disadvantages in seed hierarchy.     

European plant science: a field of opportunities

Plants have a pivotal role in eco- and agricultural systems.Genomics is driving a rapid expansion of our understanding ofhow genes, individually and in networks, determine plant function.Technological developments in breeding and genomics are providingstrategies to translate this knowledge into crop improvement.The possibilities range from improvement of existing crops andthe systematic use of natural diversity through to the domesticationof completely new species. As examples of possible goals, itis discussed how profiling of composition will integrate plantbreeding and agronomic practice with emerging knowledge aboutnutrition and health, how improved and novel crops will contributeto the creation of new bio-based economies revolving aroundplant products, and how advances in our knowledge about plant–environmentand plant–pathogen interactions will provide novel strategiesto stabilize agricultural yield in a fluctuating environmentand contribute to integrated approaches in which modern agricultureis carried out in concert with the environment. In addition,knowledge generated by plant science will be needed to monitor,understand, and cope with climate change and its impact on agricultureand ecosystems. Realization of these goals will require closeinteractions with related disciplines including agronomy andecology. Further, it will be important to continue and deepenopen support for research in the developing world. Key words: Agronomic practice, biodiversity, domestication, ecosystems, environment, genomics, novel crops, plant breeding, plant products, yield     

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.     

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.     

Leveraging natural diversity: back through the bottleneck

Plant breeders have long recognized the existence of useful genetic variation in the wild ancestors of our domesticated crop species. In cultivated rice (Oryza sativa), crosses between high-yielding elite cultivars and low-yielding wild accessions often give rise to superior offspring, with wild alleles conferring increased performance in the context of the elite cultivar genetic background. Because the breeding value of wild germplasm cannot be determined by examining the performance of wild accessions, a phylogenetic approach is recommended to determine which interspecific combinations are most likely to be useful in a breeding program. As we deepen our understanding of how genetic diversity is partitioned within and between cultivated and wild gene pools of Oryza, breeders will have increased power to make predictions about the most efficient strategies for utilizing wild germplasm for rice improvement.     

Native cover crops suppress exotic annuals and favor native perennials in a greenhouse competition experiment

In a greenhouse experiment, we examined the effectiveness of four native cover crops for controlling four exotic, invasive species and increasing success of four western North American grassland species. Planting the annual cover crops, annual ragweed (Ambrosia artemisiifolia) and common sunflower (Helianthus annuus), reduced the biomass of the exotic species cheatgrass (Bromus tectorum), Japanese brome (Bromus japonicus), Canada thistle (Cirsium arvense), and whitetop (Cardaria draba). The annual cover crops also reduced the desired species biomass in competition with the perennial exotics, but either increased or did not affect the desired species biomass in competition with the annual exotics. Planting the perennial cover crops, Canada goldenrod (Solidago canadensis) and littleleaf pussytoes (Antennaria microphylla), rarely inhibited exotic species, but did increase the desired species biomass. Field experiments are needed to test the cover crops under more ecologically relevant conditions, but our results suggested that the annual cover crops may be effective for controlling invasive annuals and for facilitating native perennials.     

Facilitated by nature and agriculture: performance of a specialist herbivore improves with host-plant life history evolution, domestication, and breeding

Plant defenses against herbivores are predicted to change as plant lineages diversify, and with domestication and subsequent selection and breeding in the case of crop plants. We addressed whether defense against a specialist herbivore declined coincidently with life history evolution, domestication, and breeding within the grass genus Zea (Poaceae). For this, we assessed performance of corn leafhopper (Dalbulus maidis) following colonization of one of four Zea species containing three successive transitions: the evolutionary transition from perennial to annual life cycle, the agricultural transition from wild annual grass to primitive crop cultivar, and the agronomic transition from primitive to modern crop cultivar. Performance of corn leafhopper was measured through seven variables relevant to development speed, survivorship, fecundity, and body size. The plants included in our study were perennial teosinte (Zea diploperennis), Balsas teosinte (Zea mays parviglumis), a landrace maize (Zea mays mays), and a hybrid maize. Perennial teosinte is a perennial, iteroparous species, and is basal in Zea; Balsas teosinte is an annual species, and the progenitor of maize; the landrace maize is a primitive, genetically diverse cultivar, and is ancestral to the hybrid maize; and, the hybrid maize is a highly inbred, modern cultivar. Performance of corn leafhopper was poorest on perennial teosinte, intermediate on Balsas teosinte and landrace maize, and best on hybrid maize, consistent with our expectation of declining defense from perennial teosinte to hybrid maize. Overall, our results indicated that corn leafhopper performance increased most with the agronomic transition, followed by the life history transition, and least with the domestication transition.     

Pod shattering in grain legumes: emerging genetic and environment-related patterns

A reduction in pod shattering is one of the main components of grain legume domestication. Despite this, many domesticated legumes suffer serious yield losses due to shattering, particularly under arid conditions. Mutations related to pod shattering modify the twisting force of pod walls or the structural strength of the dehiscence zone in pod sutures. At a molecular level, a growing body of evidence indicates that these changes are controlled by a relatively small number of key genes that have been selected in parallel across grain legume species, supporting partial molecular convergence. Legume homologs of Arabidopsis thaliana silique shattering genes play only minor roles in legume pod shattering. Most domesticated grain legume species contain multiple shattering-resistance genes, with mutants of each gene typically showing only partial shattering resistance. Hence, crosses between varieties with different genes lead to transgressive segregation of shattering alleles, producing plants with either enhanced shattering resistance or atavistic susceptibility to the trait. The frequency of these resistance pod-shattering alleles is often positively correlated with environmental aridity. The continued development of pod-shattering-related functional information will be vital for breeding crops that are suited to the increasingly arid conditions expected in the coming decades.

Recent genetic, genomic, and phenotypic studies of pod shattering in grain legumes lay the foundation for breeding crops suited for increasingly arid conditions.     

The domestication of American wildrice

The expansion in wildrice (Zizania palustris) production and the associated research efforts represent the largest modern effort to domesticate a cereal grain. Wildrice growers brought the species under cultivation, but plant breeding and agronomic research have accelerated the domestication process. The domestication and commercialization of this diploid (2n = 30), protogynous, cross-pollinated, annual, aquatic cereal present an opportunity to examine crop evolution and domestication theory. Traits associated with the domesticated cereal grains are shattering resistance, tiller synchrony, and increased seed size. This syndrome of traits may result from automatic selection, the selective force applied by repeated cycles of planting of harvested seed. Positive responses from deliberate selection for these traits in wildrice populations indicate that a domestication ideotype is attainable through plant breeding and that founder effect in this diploid species may be negligible. Continued commercial production of wildrice in the Great Lakes region is not likely to further the domestication process, whereas automatic selection may be initiated in the emerging California wildrice industry.     

A microRNA allele that emerged prior to apple domestication may underlie fruit size evolution

The molecular genetic mechanisms underlying fruit size remain poorly understood in perennial crops, despite size being an important agronomic trait. Here we show that the expression level of a microRNA gene (miRNA172) influences fruit size in apple. A transposon insertional allele of miRNA172 showing reduced expression associates with large fruit in an apple breeding population, whereas over‐expression of miRNA172 in transgenic apple significantly reduces fruit size. The transposon insertional allele was found to be co‐located with a major fruit size quantitative trait locus, fixed in cultivated apples and their wild progenitor species with relatively large fruit. This finding supports the view that the selection for large size in apple fruit was initiated prior to apple domestication, likely by large mammals, before being subsequently strengthened by humans, and also helps to explain why signatures of genetic bottlenecks and selective sweeps are normally weaker in perennial crops than in annual crops.     

Breeding system evolution in Tarasa (Malvaceae) and selection for reduced pollen grain size in the polyploid species

Polyploidy, primarily allopolyploidy, has played a major role throughout flowering plant evolution with an estimated 30-80% of all extant angiosperms carrying traces of ancient or recent polyploidy. One immediate and seemingly invariant phenotypic consequence of genome doubling is larger cell size in polyploids relative to their diploid progenitors. In plants, increases in pollen grain and guard cell sizes exemplify this rule and are often used as surrogate evidence for polyploidy. Tarasa (Malvaceae), a genus of 27 species primarily distributed in the high (>3000 m) Andes, has numerous independently generated tetraploid species, most of which have pollen grains smaller than their putative diploid parents. The tetraploids are also unusual because they are annual, rather than perennial, in habit. Data correlate these apparent anomalies to a change in the breeding system within the genus from xenogamy (outcrossing) in the diploid species to autogamy (inbreeding) in the tetraploids, leading to a convergence in reduced floral morphology. The harsh environment of the high-elevation Andean habitats in which all the tetraploid annuals are found is implicated as a critical factor in shaping the evolution of these unusual polyploids.     

No Evidence for Enforced Alloparental Care in a Cooperatively Breeding Parrot

In cooperatively breeding species, in which non‐breeding helpers assist in rearing the offspring of breeding individuals, conflicts of interest commonly occur between breeders and helpers over their respective contributions to offspring care. During such conflicts, breeders might use aggressive behavior to enforce contributions of helpers to offspring care, especially if helpers are not related to the breeders and their offspring and thus do not stand to gain indirect fitness benefits by helping. Using a combination of behavioral and genetic data, we investigated in the cooperatively breeding El Oro parakeet Pyrrhura orcesi (i) whether breeders are commonly dominant over helpers, (ii) whether they use aggressive behavior toward helpers to enforce offspring provisioning, and (iii) whether the relatedness of helpers to the nestlings affects the frequency of—or the reaction of helpers to—such aggressions. Even though breeders were generally dominant over helpers, we found no evidence for the enforcement of alloparental care. This finding was independent of the relatedness between helpers and nestlings, even though distantly related helpers overall contributed little to offspring care. We suggest that the inability of breeders to properly assess the work rates of their helpers at least partly explains the absence of enforcement. More generally, our results add to a body of evidence suggesting that enforcement might be an exceptional rather than a general mechanism underlying the expression of alloparental care in cooperatively breeding species.     

Cooperative breeding among Chinese passerines: inference from social behavior,diet, and migratory status

Recent estimates suggest that 9% of bird species are cooperative breeders. However, little is known about the breeding behavior of many species, particularly those in the Indomalayan and Neotropical regions. Our objective was to provide an overview of the prevalence of cooperative breeding among Chinese songbirds. Examination of the social behavior, diet, and migratory status of 55 known cooperative‐breeding species of songbirds in China revealed that 90.9% live in small groups, 89.1% are residents in at least one or all their subspecies, 81.8% are insectivores, and 14.5% are omnivores. In contrast, 58.2% of the 55 species are resident insectivores that live in small groups, 10.9% are resident omnivores that live in small groups, and 12.7% include subspecies that are resident insectivores. We used these combinations of traits of known cooperative breeders and phylogenetic relationships to infer that an additional 106 species of songbirds in China are probable cooperative breeders and 22 species are possible cooperative breeders. Our analysis suggests that a maximum of 27.2% (183 of 674 species) of Chinese passerines are cooperative breeders, with more occurring in subtropical southern China than in temperate northern China. Cooperative breeding is the main breeding system of species in the families Corvidae, Pycnonotidae, and, especially, Timaliidae (105 of 183 species, 57%). Based on our analyses, cooperative breeding might be more common than previously assumed, particularly among species in the families Timaliidae, Corvidae, and Sturnidae, and species in southern, subtropical China. Because most cooperative‐breeding species in our study were either inferred cooperative breeders or possible cooperative breeders, additional study of these species is needed to confirm our results. A better understanding of the prevalence of cooperative breeding in birds will improve our insight into the evolutionary and ecological factors that select for cooperative breeding.     

Perennial polypores as indicators of annual and red-listed polypores

Many polypores are specialized in their requirements for substrate and environment, and they have been suggested to indicate the continuity of coarse woody debris or naturalness of a forest stand. However, the use of polypores as indicators of conservation value is restricted by the temporally limited appearance of annual fruit bodies. We studied whether the species richness of perennial polypores (perennials) can be used to predict the species richness of annual or annual red-listed polypores (annuals). Our data included 1471 separate datasets (sample plots or larger inventoried areas) in different parts of Finland and Russian Karelia, ranging from the southern to northern boreal zone. At the large scale (the whole area) the number of perennials explained about 70% of the variation in the number of annuals, and about 67% in the number of red-listed annuals. A minimum set of 40–60 perennial occurrences gave a reliable estimate on the species richness of annuals, and 60–80 occurrences on the species richness of red-listed annuals. The richness of perennials predicted the richness of annuals and, in particular, richness of red-listed annuals, better than the size of inventoried area. According to our results, perennial polypores can be used as a surrogate for overall polypore species richness in natural and seminatural boreal forests, but the predictive power is weaker in managed forests. In addition, the relationship between the perennial and annual species seems to differ in different vegetation zones, management types and forest types. Due to this variation direct application of the indicator values derived from different vegetation zones and management or forest types are not recommended. Since perennials are easier to identify than annuals, detectable throughout the year, and have much smaller year-to-year variation, their use as an indicator group seems to offer advantages regarding the timing and cost-efficiency of inventories.     

Abiotic stress and control of grain number in cereals

Grain number is the only yield component that is directly associated with increased grain yield in important cereal crops like wheat. Historical yield studies show that increases in grain yield are always accompanied by an increase in grain number. Adverse weather conditions can cause severe fluctuations in grain yield and substantial yield losses in cereal crops. The problem is global and despite its impact on world food production breeding and selection approaches have only met with limited success. A specific period during early reproductive development, the young microspore stage of pollen development, is extremely vulnerable to abiotic stress in self-fertilising cereals (wheat, rice, barley, sorghum). A better understanding of the physiological and molecular processes that lead to stress-induced pollen abortion may provide us with the key to finding solutions for maintaining grain number under abiotic stress conditions. Due to the complexity of the problem, stress-proofing our main cereal crops will be a challenging task and will require joint input from different research disciplines.     

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.     

植被覆盖度的时间变化及其防风蚀效应

 在防治风蚀过程中过去人们只关注植被覆盖度的空间特性,但对其随时间变化的特性未引起足够的重视。该文着重强调了植被覆盖度随时间变化的特性,并对不同类型植物覆盖度的动态变化特征进行了研究。通过调查研究与理论分析,在土壤风蚀量与植被覆盖度及风蚀气候侵蚀因子三者之间建立了随时间变化的定量关系,并利用该公式计算和比较了不同类型植物防风治沙性能的动态差异、总植被覆盖度及相应的总土壤风蚀量的动态变化。结果表明在防风蚀的作用效应中灌木＞多年生牧草＞林木＞作物＞一年生牧草;总时空植被覆盖度与总土壤风蚀量呈“反相位”的动态变化;风蚀季节总植被覆盖度较低,介于0.11～0.14之间,低于20%的临界覆盖度,这也是该地区风蚀危害严重的一个重要原因所在。     

Comparative population genomics reveals the domestication history of the peach,Prunus persica,and human influences on perennial fruit crops

Background

Recently, many studies utilizing next generation sequencing have investigated plant evolution and domestication in annual crops. Peach, Prunus persica, is a typical perennial fruit crop that has ornamental and edible varieties. Unlike other fruit crops, cultivated peach includes a large number of phenotypes but few polymorphisms. In this study, we explore the genetic basis of domestication in peach and the influence of humans on its evolution.

Results

We perform large-scale resequencing of 10 wild and 74 cultivated peach varieties, including 9 ornamental, 23 breeding, and 42 landrace lines. We identify 4.6 million SNPs, a large number of which could explain the phenotypic variation in cultivated peach. Population analysis shows a single domestication event, the speciation of P. persica from wild peach. Ornamental and edible peach both belong to P. persica, along with another geographically separated subgroup, Prunus ferganensis.We identify 147 and 262 genes under edible and ornamental selection, respectively. Some of these genes are associated with important biological features. We perform a population heterozygosity analysis in different plants that indicates that free recombination effects could affect domestication history. By applying artificial selection during the domestication of the peach and facilitating its asexual propagation, humans have caused a sharp decline of the heterozygote ratio of SNPs.

Conclusions

Our analyses enhance our knowledge of the domestication history of perennial fruit crops, and the dataset we generated could be useful for future research on comparative population genomics.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0415-1) contains supplementary material, which is available to authorized users.