Editing Botany (section)

== Genetics ==
{{Main|Plant genetics}}
{{plain image with caption|File:Punnett square mendel flowers.svg|A [[Punnett square]] depicting a cross between two pea plants [[heterozygous]] for purple (B) and white (b) blossoms|250px|left|bottom|triangle|#51e89e}}

Inheritance in plants follows the same fundamental principles of genetics as in other multicellular organisms. [[Gregor Mendel]] discovered the [[Mendelian inheritance|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, "[[transposon|jumping genes]]" were discovered by [[Barbara McClintock]] while she was studying maize.{{sfn|Ben-Menahem|2009|p = 5369}} 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 [[hybrid (biology)|hybrids]] are often possible. A familiar example is [[peppermint]], ''Mentha'' × ''piperita'', a [[Sterility (physiology)|sterile]] hybrid between ''[[Mentha aquatica]]'' and spearmint, ''[[Mentha spicata]]''.{{sfn|Stace|2010b|pp = 629–633}} The many cultivated varieties of wheat are the result of multiple inter- and intra-[[species|specific]] crosses between wild species and their hybrids.{{sfn|Hancock|2004|pp = 190–196}} [[Angiosperms]] with [[monoecious]] flowers often have [[Self-incompatibility in plants|self-incompatibility mechanisms]] that operate between the [[pollen]] and [[stigma (botany)|stigma]] so that the pollen either fails to reach the stigma or fails to [[germinate]] and produce male [[gamete]]s.{{sfn|Sobotka|Sáková|Curn|2000|pp = 103–112}} This is one of several methods used by plants to promote [[plant reproductive morphology|outcrossing]].{{sfn|Renner|Ricklefs|1995|pp = 596–606}} In many land plants the male and female gametes are produced by separate individuals. These species are said to be [[Plant reproductive morphology#Terminology|dioecious]] when referring to vascular plant [[sporophyte]]s and [[monoecious|dioicous]] when referring to [[bryophyte]] [[gametophyte]]s.{{sfn|Porley|Hodgetts|2005|pp = 2–3}}

Charles Darwin in his 1878 book The Effects of Cross and Self-Fertilization in the Vegetable Kingdom<ref>Darwin, C. R. 1878. The effects of cross and self fertilisation in the vegetable kingdom. London: John Murray". darwin-online.org.uk</ref> at the start of chapter XII noted "The first and most important of the conclusions which may be drawn from the observations given in this volume, is that generally cross-fertilisation is beneficial and self-fertilisation often injurious, at least with the plants on which I experimented." An important adaptive benefit of outcrossing is that it allows the masking of deleterious mutations in the genome of progeny. This beneficial effect is also known as hybrid vigor or heterosis. Once outcrossing is established, subsequent switching to inbreeding becomes disadvantageous since it allows expression of the previously masked deleterious recessive mutations, commonly referred to as inbreeding depression.

Unlike in higher animals, where [[parthenogenesis]] is rare, [[asexual reproduction]] may occur in plants by several different mechanisms. The formation of stem [[tuber]]s in potato is one example. Particularly in [[arctic]] or [[alpine climate|alpine]] habitats, where opportunities for fertilisation of flowers [[zoophily|by animals]] are rare, plantlets or [[bulbs]], may develop instead of flowers, replacing [[sexual reproduction]] with asexual reproduction and giving rise to [[cloning|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.{{sfn|Savidan|2000|pp = 13–86}}

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 [[hybridization event|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 [[sympatric speciation|species]].{{sfn|Campbell|Reece|Urry|Cain|2008|pp = 495–496}} Some otherwise sterile plant polyploids can still reproduce [[vegetative propagation|vegetatively]] or by seed apomixis, forming clonal populations of identical individuals.{{sfn|Campbell|Reece|Urry|Cain|2008|pp = 495–496}} [[Durum]] wheat is a fertile [[tetraploid]] allopolyploid, while [[common wheat|bread wheat]] is a fertile [[hexaploid]]. The commercial banana is an example of a sterile, seedless [[triploid]] hybrid. [[Taraxacum officinale|Common dandelion]] is a triploid that produces viable seeds by apomictic seed.

As in other eukaryotes, the inheritance of [[endosymbiotic]] organelles like [[mitochondria]] and [[chloroplast]]s in plants is non-[[Mendelian]]. Chloroplasts are inherited through the male parent in gymnosperms but often through the female parent in flowering plants.{{sfn|Morgensen|1996|pp = 383–384}}

=== Molecular genetics ===
{{Further|Molecular genetics}}
[[File:Arabidopsis thaliana inflorescencias.jpg|thumb|alt=Flowers of Arabidopsis thaliana, the most important model plant and the first to have its genome sequenced|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 organism#Plants|model plants]] such as the Thale cress, ''[[Arabidopsis thaliana]]'', a weedy species in the mustard family ([[Brassicaceae]]).{{sfn|Benderoth|Textor|Windsor|Mitchell-Olds|2006|pp = 9118–9123}} 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 plant]]s. ''Arabidopsis'' was the first plant to have its genome sequenced, in 2000.{{sfn|Arabidopsis Genome Initiative|2000|pp = 796–815}} The sequencing of some other relatively small genomes, of rice (''[[Oryza sativa]]''){{sfn|Devos|Gale|2000}} and ''[[Brachypodium distachyon]]'',{{sfn|University of California-Davis|2012}} has made them important model species for understanding the genetics, cellular and molecular biology of [[cereals]], [[grasses]] and [[monocots]] generally.

[[Model organism#Plants|Model plants]] such as ''Arabidopsis thaliana'' are used for studying the molecular biology of [[plant cell]]s 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|{{C4}} plants]].{{sfn|Russin|Evert|Vanderveer|Sharkey|1996|pp = 645–658}} The [[single celled]] [[green alga]] ''[[Chlamydomonas reinhardtii]]'', while not an [[embryophyte]] itself, contains a [[chlorophyll b|green-pigmented]] [[Chloroplast#Chloroplastida (green algae and plants)|chloroplast]] related to that of land plants, making it useful for study.{{sfn|Rochaix|Goldschmidt-Clermont|Merchant|1998|p = 550}} A [[red alga]] ''[[Cyanidioschyzon merolae]]'' has also been used to study some basic chloroplast functions.{{sfn|Glynn|Miyagishima|Yoder|Osteryoung|2007|pages = 451–461}} [[Spinach]],{{sfn|Possingham|Rose|1976|pp = 295–305}} [[peas]],{{sfn|Sun|Forouhar|Li Hm|Tu|2002|pp = 95–100}} [[soybeans]] and a moss ''[[Physcomitrella patens]]'' are commonly used to study plant cell biology.{{sfn|Heinhorst|Cannon|1993|pp = 1–9}}

''[[Agrobacterium tumefaciens]]'', a soil [[rhizosphere]] bacterium, can attach to plant cells and infect them with a [[Callus (cell biology)|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 [[Fabaceae|legumes]] and other plant species.{{sfn|Schell|Van Montagu|1977|pp = 159–179}} Today, genetic modification of the Ti plasmid is one of the main techniques for introduction of [[transgene]]s to plants and the creation of [[genetically modified crops]].

=== Epigenetics ===
{{Main|Epigenetics}}
[[Epigenetics]] is the study of heritable changes in [[gene expression|gene function]] that cannot be explained by changes in the underlying [[DNA sequence]]{{sfn|Bird|2007|pp = 396–398}} but cause the organism's genes to behave (or "express themselves") differently.{{sfn|Hunter|2008}} 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 (DNA)|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 division]]s for the remainder of the cell's life. Some epigenetic changes have been shown to be [[Heritability|heritable]],{{sfn|Spector|2012|p = 8}} while others are reset in the germ cells.

Epigenetic changes in [[Eukaryote|eukaryotic]] biology serve to regulate the process of [[cellular differentiation]]. During [[morphogenesis]], [[totipotent]] [[stem cells]] become the various [[pluripotent]] [[cell line]]s 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]], [[vessel element|xylem vessel elements]], [[phloem]] sieve tubes, [[guard cell]]s of the [[epidermis (botany)|epidermis]], etc. as it continues to [[mitosis|divide]]. The process results from the epigenetic activation of some genes and inhibition of others.{{sfn|Reik|2007|pp = 425–432}}

Unlike animals, many plant cells, particularly those of the [[ground tissue#Parenchyma|parenchyma]], do not terminally differentiate, remaining totipotent with the ability to give rise to a new individual plant. Exceptions include highly lignified cells, the [[ground tissue#Sclerenchyma|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 remodeling|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.{{sfn|Costa|Shaw|2007|pp = 101–106}}

Epigenetic changes can lead to [[paramutation]]s, 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.{{sfn|Cone|Vedova|2004}}