alcoholic beverages come from fermentation of carbohydrate-rich plant products such as barley (beer), rice (sake) and grapes (wine). native americans have used various plants as ways of treating illness or disease for thousands of years. this knowledge native americans have on plants has been recorded by enthnobotanists and then in turn has been used by pharmaceutical companies as a way of drug discovery. plants can synthesise coloured dyes and pigments such as the anthocyanins responsible for the red colour of red wine, yellow weld and blue woad used together to produce lincoln green, indoxyl, source of the blue dye indigo traditionally used to dye denim and the artist's pigments gamboge and rose madder. sugar, starch, cotton, linen, hemp, some types of rope, wood and particle boards, papyrus and paper, vegetable oils, wax, and natural rubber are examples of commercially important materials made from plant tissues or their secondary products. charcoal, a pure form of carbon made by pyrolysis of wood, has a long history as a metal-smelting fuel, as a filter material and adsorbent and as an artist's material and is one of the three ingredients of gunpowder. cellulose, the world's most abundant organic polymer, can be converted into energy, fuels, materials and chemical feedstock. products made from cellulose include rayon and cellophane, wallpaper paste, biobutanol and gun cotton. sugarcane, rapeseed and soy are some of the plants with a highly fermentable sugar or oil content that are used as sources of biofuels, important alternatives to fossil fuels, such as biodiesel. sweetgrass was used by native americans to ward off bugs like mosquitoes. these bug repelling properties of sweetgrass were later found by the american chemical society in the molecules phytol and coumarin. plant ecology the nodules of medicago italica contain the nitrogen fixing bacterium sinorhizobium meliloti. the plant provides the bacteria with nutrients and an anaerobic environment, and the bacteria fix nitrogen for the plant. plant ecology is the science of the functional relationships between plants and their habitats – the environments where they complete their life cycles. plant ecologists study the composition of local and regional floras, their biodiversity, genetic diversity and fitness, the adaptation of plants to their environment, and their competitive or mutualistic interactions with other species. some ecologists even rely on empirical data from indigenous people that is gathered by ethnobotanists. this information can relay a great deal of information on how the land once was thousands of years ago and how it has changed over that time. the goals of plant ecology are to understand the causes of their distribution patterns, productivity, environmental impact, evolution, and responses to environmental change. plants depend on certain edaphic (soil) and climatic factors in their environment but can modify these factors too. for example, they can change their environment's albedo, increase runoff interception, stabilise mineral soils and develop their organic content, and affect local temperature. plants compete with other organisms in their ecosystem for resources. they interact with their neighbours at a variety of spatial scales in groups, populations and communities that collectively constitute vegetation. regions with characteristic vegetation types and dominant plants as well as similar abiotic and biotic factors, climate, and geography make up biomes like tundra or tropical rainforest. herbivores eat plants, but plants can defend themselves and some species are parasitic or even carnivorous. other organisms form mutually beneficial relationships with plants. for example, mycorrhizal fungi and rhizobia provide plants with nutrients in exchange for food, ants are recruited by ant plants to provide protection, honey bees, bats and other animals pollinate flowers and humans and other animals act as dispersal vectors to spread spores and seeds. plants, climate and environmental change plant responses to climate and other environmental changes can inform our understanding of how these changes affect ecosystem function and productivity. for example, plant phenology can be a useful proxy for temperature in historical climatology, and the biological impact of climate change and global warming. palynology, the analysis of fossil pollen deposits in sediments from thousands or millions of years ago allows the reconstruction of past climates. estimates of atmospheric co2 concentrations since the palaeozoic have been obtained from stomatal densities and the leaf shapes and sizes of ancient land plants. ozone depletion can expose plants to higher levels of ultraviolet radiation-b (uv-b), resulting in lower growth rates. moreover, information from studies of community ecology, plant systematics, and taxonomy is essential to understanding vegetation change, habitat destruction and species extinction. genetics a punnett square depicting a cross between two pea plants heterozygous for purple (b) and white (b) blossoms inheritance in plants follows the same fundamental principles of genetics as in other multicellular organisms. gregor mendel discovered the genetic laws of inheritance by studying inherited traits such as shape in pisum sativum (peas). what mendel learned from studying plants has had far-reaching benefits outside of botany. similarly, "jumping genes" were discovered by barbara mcclintock while she was studying maize. nevertheless, there are some distinctive genetic differences between plants and other organisms. species boundaries in plants may be weaker than in animals, and cross species hybrids are often possible. a familiar example is peppermint, mentha × piperita, a sterile hybrid between mentha aquatica and spearmint, mentha spicata. the many cultivated varieties of wheat are the result of multiple inter- and intra-specific crosses between wild species and their hybrids. angiosperms with monoecious flowers often have self-incompatibility mechanisms that operate between the pollen and stigma so that the pollen either fails to reach the stigma or fails to germinate and produce male gametes. this is one of several methods used by plants to promote outcrossing. in many land plants the male and female gametes are produced by separate individuals. these species are said to be dioecious when referring to vascular plant sporophytes and dioicous when referring to bryophyte gametophytes. unlike in higher animals, where parthenogenesis is rare, asexual reproduction may occur in plants by several different mechanisms. the formation of stem tubers in potato is one example. particularly in arctic or alpine habitats, where opportunities for fertilisation of flowers by animals are rare, plantlets or bulbs, may develop instead of flowers, replacing sexual reproduction with asexual reproduction and giving rise to clonal populations genetically identical to the parent. this is one of several types of apomixis that occur in plants. apomixis can also happen in a seed, producing a seed that contains an embryo genetically identical to the parent. most sexually reproducing organisms are diploid, with paired chromosomes, but doubling of their chromosome number may occur due to errors in cytokinesis. this can occur early in development to produce an autopolyploid or partly autopolyploid organism, or during normal processes of cellular differentiation to produce some cell types that are polyploid (endopolyploidy), or during gamete formation. an allopolyploid plant may result from a hybridisation event between two different species. both autopolyploid and allopolyploid plants can often reproduce normally, but may be unable to cross-breed successfully with the parent population because there is a mismatch in chromosome numbers. these plants that are reproductively isolated from the parent species but live within the same geographical area, may be sufficiently successful to form a new species. some otherwise sterile plant polyploids can still reproduce vegetatively or by seed apomixis, forming clonal populations of identical individuals. durum wheat is a fertile tetraploid allopolyploid, while bread wheat is a fertile hexaploid. the commercial banana is an example of a sterile, seedless triploid hybrid. common dandelion is a triploid that produces viable seeds by apomictic seed. as in other eukaryotes, the inheritance of endosymbiotic organelles like mitochondria and chloroplasts in plants is non-mendelian. chloroplasts are inherited through the male parent in gymnosperms but often through the female parent in flowering plants. molecular genetics thale cress, arabidopsis thaliana, the first plant to have its genome sequenced, remains the most important model organism. a considerable amount of new knowledge about plant function comes from studies of the molecular genetics of model plants such as the thale cress, arabidopsis thaliana, a weedy species in the mustard family (brassicaceae). the genome or hereditary information contained in the genes of this species is encoded by about 135 million base pairs of dna, forming one of the smallest genomes among flowering plants. arabidopsis was the first plant to have its genome sequenced, in 2000. the sequencing of some other relatively small genomes, of rice (oryza sativa) and brachypodium distachyon, has made them important model species for understanding the genetics, cellular and molecular biology of cereals, grasses and monocots generally. model plants such as arabidopsis thaliana are used for studying the molecular biology of plant cells and the chloroplast. ideally, these organisms have small genomes that are well known or completely sequenced, small stature and short generation times. corn has been used to study mechanisms of photosynthesis and phloem loading of sugar in c4 plants. the single celled green alga chlamydomonas reinhardtii, while not an embryophyte itself, contains a green-pigmented chloroplast related to that of land plants, making it useful for study. a red alga cyanidioschyzon merolae has also been used to study some basic chloroplast functions. spinach, peas, soybeans and a moss physcomitrella patens are commonly used to study plant cell biology. agrobacterium tumefaciens, a soil rhizosphere bacterium, can attach to plant cells and infect them with a callus-inducing ti plasmid by horizontal gene transfer, causing a callus infection called crown gall disease. schell and van montagu (1977) hypothesised that the ti plasmid could be a natural vector for introducing the nif gene responsible for nitrogen fixation in the root nodules of legumes and other plant species. today, genetic modification of the ti plasmid is one of the main techniques for introduction of transgenes to plants and the creation of genetically modified crops. epigenetics main article: epigenetics epigenetics is the study of heritable changes in gene function that cannot be explained by changes in the underlying dna sequence but cause the organism's genes to behave (or "express themselves") differently. one example of epigenetic change is the marking of the genes by dna methylation which determines whether they will be expressed or not. gene expression can also be controlled by repressor proteins that attach to silencer regions of the dna and prevent that region of the dna code from being expressed. epigenetic marks may be added or removed from the dna during programmed stages of development of the plant, and are responsible, for example, for the differences between anthers, petals and normal leaves, despite the fact that they all have the same underlying genetic code. epigenetic changes may be temporary or may remain through successive cell divisions for the remainder of the cell's life. some epigenetic changes have been shown to be heritable, while others are reset in the germ cells. epigenetic changes in eukaryotic biology serve to regulate the process of cellular differentiation. during morphogenesis, totipotent stem cells become the various pluripotent cell lines of the embryo, which in turn become fully differentiated cells. a single fertilised egg cell, the zygote, gives rise to the many different plant cell types including parenchyma, xylem vessel elements, phloem sieve tubes, guard cells of the epidermis, etc. as it continues to divide. the process results from the epigenetic activation of some genes and inhibition of others. unlike animals, many plant cells, particularly those of the parenchyma, do not terminally differentiate, remaining totipotent with the ability to give rise to a new individual plant. exceptions include highly lignified cells, the sclerenchyma and xylem which are dead at maturity, and the phloem sieve tubes which lack nuclei. while plants use many of the same epigenetic mechanisms as animals, such as chromatin remodelling, an alternative hypothesis is that plants set their gene expression patterns using positional information from the environment and surrounding cells to determine their developmental fate. epigenetic changes can lead to paramutations, which do not follow the mendelian heritage rules. these epigenetic marks are carried from one generation to the next, with one allele inducing a change on the other. plant evolution transverse section of a fossil stem of the devonian vascular plant rhynia gwynne-vaughani the chloroplasts of plants have a number of biochemical, structural and genetic similarities to cyanobacteria, (commonly but incorrectly known as "blue-green algae") and are thought to be derived from an ancient endosymbiotic relationship between an ancestral eukaryotic cell and a cyanobacterial resident. the algae are