Which plants are selectively bred

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Plant breeding can be broadly defined as alterations caused in plants as a result of their use by humans, ranging from unintentional changes resulting from the advent of agriculture to the application of molecular tools for precision breeding. The vast diversity of breeding methods can be simplified into three categories: i plant breeding based on observed variation by selection of plants based on natural variants appearing in nature or within traditional varieties; ii plant breeding based on controlled mating by selection of plants presenting recombination of desirable genes from different parents; and iii plant breeding based on monitored recombination by selection of specific genes or marker profiles, using molecular tools for tracking within-genome variation.

The continuous application of traditional breeding methods in a given species could lead to the narrowing of the gene pool from which cultivars are drawn, rendering crops vulnerable to biotic and abiotic stresses and hampering future progress. Several methods have been devised for introducing exotic variation into elite germplasm without undesirable effects. Cases in rice are given to illustrate the potential and limitations of different breeding approaches.

Figure 1. American A-genome wild rice Oryza glumaepatula. Abundant and wide angle tillering, open and shattering panicles, and small grains with awns are typical of wild rice species. Figure 2. Comparison of schematic rice plants representing typical traditional varieties, modern semidwarf cultivars, and the proposed new plant type.

Figure 3. Experimental plots showing the contrast between lines with and without the allele conferring submergence tolerance of the Sub1A gene. Plots without the tolerance gene have been almost completely eliminated after 15 days of flooding.

Food Chem. View Author Information. Fax: E-mail: [email protected]. Cite this: J. ACS AuthorChoice. Article Views Altmetric -. Citations Abstract High Resolution Image. Plant breeding can be considered a coevolutionary process between humans and edible plants.

People caused changes in the plants that were used for agriculture and, in turn, those new plant types allowed changes in human populations to take place. Civilization could not exist without agriculture, and agriculture could not sustain the civilized world without modern crop varieties. In industrialized countries, only a small portion of the population is engaged in agriculture. The vast majority of people rely on a tacit social pact for their survival, which assures that someone will provide food in exchange for some service or good.

This pact is so basic to modern life that people take for granted that food is available in the nearest supermarket. However, agriculture failure could cause a disruption of this pact, leaving people in a situation of food insecurity. Thus, protecting agriculture means warranting the foundation pact of modern civilization.

The core of plant breeding is the selection of better types among variants, in terms of yield and quality of edible parts; ease of cultivation, harvest, and processing; tolerance to environmental stresses; and resistance against pests. Each of these aspects of agronomic or food value can be dissected in many specific traits, each presenting its own range of variation.

Manipulating a single trait, disregarding all others, is relatively straightforward; however, this is unlikely to result in a useful variety. The challenge of plant breeding resides in improving all of the traits of interest simultaneously, a task made more difficult by the genetic correlations between different traits, which may be due to genes with pleiotropic effects , to physical linkage between genes in the chromosomes, or to population genetic structure.

Whether this assumption is reasonable or not is a matter of debate. The objective of this paper is to discuss plant breeding methods as an evolving technology, considering the increasing levels of knowledge of the underlying mechanisms and the control of the process of generating and selecting superior plant types. In this context, three main eras of plant breeding can be identified: i plant breeding based on the selection of observed variants, disregarding their origin; ii generation and selection of expanded variation by controlled mating; and iii monitoring the inheritance of within-genome variation and selection of specific recombinants.

The fourth stage of plant breeding, which is not discussed in this paper, can be considered the creation and introduction of novel variation into genomes through genetic engineering. The varieties resulting from the methods presented in this paper can be considered a reference against which transgenic plants are compared with regard to their food safety. Plant Breeding Based on Observed Variation. The most primitive form of plant breeding was the selection of naturally occurring variants in the wild and, later, in cultivated fields.

Genetic variation was continuously submitted to the selection pressure of food gathering or planting—harvesting cycles. In some cases, this process resulted in deep changes in plant phenotypes, as exemplified by the derivation of maize from teosinte. For a given gene, mutations are rare events, but considering the large numbers of plants in a field and of genes in a plant, mutations are quite frequent events in a population. However, some of these mutations may result in more favorable phenotypes either in terms of cultivation or in terms of food quality.

Some of those mutants were rescued by ancient farmers, who protected them against competition and established with those otherwise disabled plants a relationship of symbiosis. Unlike wild habitats, cultivated fields were environments in which those mutations conferred a selective advantage, thus becoming the predominant type through human selection. The accumulation of this type of mutation is the major cause of the domestication syndrome, a set of characteristics that made many cultivated species irreversibly dependent on humans for their survival.

The molecular variability in domesticated plants tends to be smaller than in related wild species, as a consequence of the founder effect during domestication. By strongly selecting for the rare mutant plants adapted to cultivation, early farmers dropped most of the variation present in the wild populations from which cultivated forms arose.

It is now clear that many valuable genes, especially those related to resistance to pests, were left out of the cultivated gene pool. Landraces are populations of plants that have been cultivated for many generations in a certain region, being shaped by biotic and abiotic stresses, crop management, seed handling, and eating preferences.

They are dynamic genetic entities: continuously changing as a consequence of intentional and unintentional selection, seed mixture, and pollen exchange. Landraces are shaped by a balance between stabilizing selection , which keeps the identity of the landrace in a given region, and mild directional selection , leading to slow adjustments to environmental changes. In some cases, quick changes can take place, especially when the landrace is taken to a different region or when new materials are cultivated in close proximity with the original landrace.

Landraces can still nowadays derive from modern cultivars, if certified seed production is discontinued and farmer-saved seeds are planted recurrently, without care for isolation against seed or pollen contamination. The major characteristics of landraces are 12 i high levels of genetic diversity within populations, characterized by a limited range of variation between individuals, with distinctive traits that make the landrace identifiable; ii adaptation to soil and climate conditions typical of the region, combined with resistance to common pests; iii edible parts that are valued by local people, normally shaping and being shaped by the local cuisine; and iv modest but stable yield, conferring food security to the local community under normal environmental variation.

Intuitive farmer selection has the virtue of shaping varieties for the actual and specific environment of use and for the local food preferences, serving well the case of subsistence agriculture, where most of the production is locally consumed.

However, when farmers select for one trait, genetic correlations may result in undesirable changes in other traits. For example, cereal landraces are normally tall plants, prone to lodging and presenting low harvest index , probably as a result of human selection for large edible parts panicles, ears, spikes. Nevertheless, for their wealth in genetic variability and adaptability to different environments, landraces are the most valuable genetic resources for long-term plant breeding programs and also prime targets for germplasm collections.

New systems of germplasm conservation have been built on social networks connecting people interested in the subject as a hobby e. Those networks take advantage of modern communication tools to replicate on a global scale what used to happen through personal contact in traditional communities. Notwithstanding, a large part of the variability that once existed in cultivated fields of annual plants may have been irreversibly lost during the introduction of modern, high-yielding cultivars.

In this sense, the same modern cultivars that saved millions from starving may have wiped out varieties that were the result of centuries of local intuitive selection by farmers and a valuable resource for future genetic improvement.

The earliest method of plant breeding based on an elementary knowledge of the laws of inheritance has been the selection of plants within landraces, based on the assumption that the progenies of the best individuals are expected to be superior to the progeny of a random sample of the population. This method was formally proposed by Louis de Vilmorin in , although there are mentions of the use of its principles by some farmers earlier in the 19th century.

From this point on, within-field heterogeneity was considered to be undesirable and both plant breeding and agronomy developed methods to achieve maximum spatial homogeneity e. In self-pollinating species, such as rice and wheat, landraces can be thought of as a mixture of pure lines, including some heterozygous individuals derived from a low frequency of cross-pollination. In this type of population, selecting single plants and deriving inbred progenies invariably result in some lines that outperform the original landrace for a given growing condition.

However, this superiority comes at a cost, because pure lines are normally less stable than diverse populations in the face of stresses, especially diseases, and have no capacity for long-term adaptation, because it is monomorphic for most genes. In the case of open-pollinated species, such as maize, landraces are populations of random mating individuals, approximating the Hardy—Weinberg equilibrium HWE , with some deviations due to mild selection.

Mass selection and recombination of the top-performing portion of the population result in a gradual increase in the frequency of favorable alleles.

Successive generations of selection on maize landraces resulted in improved open-pollinated varieties, which were the basis of corn production until the advent of hybrid maize. Plant Breeding Based on Controlled Mating. Despite the great spontaneous diversity that can be found in the landraces, simply applying selection on preexisting diversity is an eroding process that eventually comes to a limit. The true creative power of plant breeding resides in promoting recombination for shuffling favorable alleles.

One could conceivably start a commercial breeding program from a dozen well-adapted founding parents, with a clear focus on a specific target environment and evaluating large segregating progenies. Injection of novel variability might become necessary in the case of a significant change of the target environment, such as the emergence of new pests for which the founder materials had no resistance.

Given the myriad of possible genotypes resulting from crossing diverse parents, the limitation for genetic gains becomes the capacity of the breeding program to evaluate a large number of plants, derived from a large number of crosses. For this reason, plant breeding is frequently dubbed a numbers game, and large competitive programs in commodities invest heavily in high-throughput methods for seed handling, planting, evaluating, and harvesting. As genetic gains accumulate, the bar is gradually raised, and increasingly higher investments are required to keep a steady rate of genetic progress.

The limit of this escalation is the financial viability of returns in the seed market and associated business. The main methods developed for efficient use of resources in breeding programs are discussed next.

The vast majority of the released cultivars of self-pollinating species have been developed through the pedigree method. Pedigree breeding consists of crossing parents and generating segregating populations, which are conducted through generations of self-pollination and selection, until a set of derived lines that combines the good characteristics of both parents is obtained.

Because it is based on the complementation of traits, this method is efficient for breeding for qualitative traits, such as disease resistance, or easily classifiable traits, such as plant architecture or the color or shape of plant parts.

The pedigree method is appealing to breeders because it allows building better varieties by putting together, in the same plant, good characteristics that were present in different materials. Because all crossings are controlled, it is possible to know the genealogy of each cultivar. The main weakness of the pedigree method resides in the fact that yield is evaluated efficiently only at the end of the process, on inbred lines, when seed is available for replicated trials.

At this point, though, unless a large number of lines have been advanced, there is little room for improvement of yield potential. The ideotype breeding approach can be regarded as a strategy to improve the capacity of the pedigree method to promote gains for quantitative traits , especially yield.

It is based on the hypothesis that one can improve complex traits by changing simpler traits that are positively correlated with them.

Additionally, it is scientifically attractive to breeders, because they have a chance of changing paradigms in their favorite crop. However, it is important to keep in mind that unfavorable genetic correlations can offset the advantage brought by the traits that make up the ideotype.

Changing the ideotype of a crop often requires looking for variation beyond the boundaries of elite germplasm, which is normally of the current plant type. However, using landraces as parents in breeding programs normally results in marked reduction in yield. For this reason, backcross toward the elite materials is necessary to recover a competitive progeny.

To avoid undesirable effects of direct introduction of exotic materials into elite breeding populations, those materials are normally used first in a phase of prebreeding, when breeders try to break the association between useful and undesirable traits. Once the new trait needed to assemble the ideotype is inserted into an elite background, those vector lines can be transferred to the elite breeding program. The simplest version of population breeding is the mass selection method applied to cross-pollinated species, in which the improved population is directly used as a cultivar.

Later, more sophisticated schemes of population breeding have been designed, providing the framework for the development of the quantitative genetics theory. In modern population breeding, the objective is to increase the value of the population as a source of elite lines. Improving the mean quality of the population, while preserving the variation within it, results in top individuals that outperform previously existing lines.

Those lines can be used as cultivars, in the case of self-pollinated species, or as parents of hybrids, in the case of cross-pollinated species.

Population breeding is an open-ended scheme of consecutive rounds of selection and recombination, thus being also known as recurrent selection breeding. Recurrent selection requires an efficient crossing system, which can be a limitation for self-pollinating species. This scheme, when applied repeatedly on small populations, leads to depletion of genetic variation and slowing of genetic gains. However, even moderate population sizes e. This phenomenon releases hidden variation in latter generations down the process of recurrent selection, compensating for the loss of variation due to selection.

Breeders create new populations by intercrossing several lines, chosen as sources of favorable alleles for one or more traits. These synthetic populations under recurrent selection mimic the genetic events that used to take place in the landraces in the hands of traditional farmers, with the difference that the whole process is monitored and controlled, and selection pressure is intensified for faster gains.

The rate of genetic gain per unit of time can be increased by speeding up the selection—recombination cycles, by intensifying the selection pressure, by improving the evaluation precision thus increasing the heritability , or by any combination of those. The general scheme of population breeding is very flexible, allowing customization to specific needs and objectives of different species and breeding programs. The system can be formatted for rapid, short-term results, normally by applying strong selection pressure on genetically narrow-based populations, or for sustained, long-term results, by applying moderate selection pressure on genetically broad-based populations.

Population breeding can also be used as a prebreeding scheme, because its frequent crossing events promote recombination between exotic and elite genomes, purging unfavorable exotic genes from the population. Heterosis is the superiority of hybrid individuals compared to inbred individuals. For this reason, maize breeding programs nowadays are focused on developing competitive F1 hybrids , in which heterozygosis is at its maximum.

Two challenges are present in hybrid breeding programs: i the need to improve at least two populations toward agronomic adaptation, while keeping them genetically distant enough to express strong heterosis, and ii developing efficient seed production of selected hybrids, such that the cost of seed production does not offset the value of the additional yield resulting from heterosis.

In maize, the first problem led to the concept of heterotic groups , 26 splitting the elite gene pool into subsets, within which population breeding is applied. On the other hand, hybrids present great advantages from the business perspective. The seeds produced by hybrid plants are genetically heterogeneous due to the segregation of thousands of genes. If planted, the resulting crop would present a large variation in agronomic traits, plant architecture, and cycle duration, thus reducing yield and grain quality.

Hence, farmers must buy new seeds every year, resulting in a constant demand for hybrid seeds. Additionally, with the advent of the transgenics, hybrid seeds became preferential carriers of those valuable proprietary traits because they allow a better control of the event by the owner.

Plant Breeding Based on Monitored Recombination. Traditional breeding methods were based on the complementarity between parental characteristics. However, little or nothing was known about which part of the genome came from each parent. This situation changed with the advent and dissemination of molecular marker technologies, which made it possible to monitor the transmission of chromosome segments in the progeny.

Virtually any sequence variation between individuals can be used to design a marker that will allow the identification of the parent that contributed a specific segment of the chromosome in a recombinant line. Until recently, the most popular markers were the simple sequence repeats SSRs , also known as microsatellites.

Those markers were superseded by the single nucleotide polymorphisms SNPs , which are more abundant in the genome and more amenable to high-throughput genotyping. Molecular markers are essential tools for studying the genetic control of any trait of interest, eventually leading to the identification of the genes underlying the trait and the metabolic chains involved.

This venue can be broadly defined as molecular biology, which dominated the field of biological sciences in the past decades. However, in this paper we limit the discussion to the application of molecular markers as tools for plant breeding. When many molecular markers are genotyped in a set of plants derived from a single cross, the frequency of recombination between them can be used to infer their order and relative distance in the chromosomes, resulting in a genetic map.

If those plants, or their progeny, are evaluated for a quantitative trait, a statistical model can be built in which part of the phenotypic variance can be explained by some of the markers, which implies that those markers should be linked to the genes underlying the trait. This approach results in quantitative trait loci QTL maps, which are normally the first step toward understanding the genetic control of a quantitative trait.

In the case of large-effect QTLs, it may be possible to jump directly into marker-assisted selection, using the closest markers available in the map. However, in most cases a step of fine mapping, involving a larger population and denser marker spacing in the target genomic region, is necessary for developing useful selection tools. The ultimate result of this approach is the identification of the gene, and the polymorphism in its nucleotide sequence, responsible for the observed phenotypic differences.

The QTL mapping approach is effective for explaining contrasts between two parents, but is inefficient for exploring the wider genetic diversity for a trait in the germplasm. The association mapping approach offers a shortcut in this path and for this reason has strong appeal to breeders. Because the genealogical distance between the materials in the panel is large, those associations will remain significant only if the marker is tightly linked to the causative gene or if factors related to population genetics population structure create associations between unlinked loci.

For the latter case, estimating population structure and taking it into account explicitly in the statistical model can avoid the detection of false associations. Gene banks harbor thousands of accessions that are potentially useful for plant breeding. Those accessions include wild crop relatives and obsolete landraces.

Although presenting poor agronomic value, compared to modern cultivars, those materials are believed to have useful genes 33 that have not been captured from wild species in the process of domestication or from landraces in the early phases of scientific breeding.

Understanding the genetic diversity in germplasm collections is the first step toward better use of a broader gene pool in breeding programs.

Marker-assisted backcrossing allows identifying the rare recombinants in the vicinity of the introduced gene, trimming the chromosome segment as close as possible to the target gene. Collections of chromosome segment substitution lines CSSL libraries are a set of lines derived from an elite variety, in which each line has one chromosome segment replaced by the corresponding segment in the wild species of interest. The phenotypic effect of the set of genes in each bin can be evaluated against the original elite line, used as a check.

Aberdeen Angus cows have also been bred for their meat. Farmers selectively breed different types of cows with highly desirable characteristics in order to produce the best meat and dairy.

Characteristics can be chosen for usefulness or appearance. Desired characteristics in plants:. Desired characteristics in animals:. All rights reserved. Mutations Figure 2 are changes in the genetic makeup of a plant.

Mutations occur naturally and sometimes result in the development of new beneficial traits. In , plant breeders learned that they could make mutations happen faster with a process called mutagenesis. Radiation or chemicals are used to change the plant's DNA, the basic molecular system of all organisms' genetic material.

The goal is to cause changes in the sequence of the base pairs of DNA, which provide biochemical instructions for the development of plants. Resultant plants may possess new and desirable characteristics through this modification of their genetic material.

During this process, plant breeders must grow and evaluate each plant from each seed produced. Figure 2: The effects of genetic mutations in carrots. Induced mutation breeding was widely used in the United States during the 's, but today few varieties are produced using this technique.

As our understanding of genetics developed, so new technologies for plant variety development arose. Examples of these that are used today include genetic marker assisted breeding, where molecular markers associated with specific traits could be used to direct breeding programs, and genetic engineering.

Some of the significant steps leading to the current state of the art are explained below. Many different tools are available for increasing and improving agricultural production. These tools include methods to develop new varieties such as classical breeding and biotechnology. Traditional agricultural approaches are experiencing some resurgence today, with renewed interest in organic agriculture; an approach that does not embrace the use of genetically engineered crops.

The role that genetic engineering stands to play in sustainable agricultural development is an interesting topic for the future. American Association for the Advancement of Science. Annual meeting Land Grant Universities Can GM crops harm the environment? McLintock, B. The origin and behavior of mutable loci in maize. Pray, L. Nature Education Knowledge 1 , Thorpe, T.

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Enzymes 6. Cell Respiration 9. Photosynthesis 3: Genetics 1. Genes 2. Chromosomes 3. Meiosis 4. Inheritance 5. Genetic Modification 4: Ecology 1. Energy Flow 3.