Plant Genetics and Crop Biodiversity PDF

Principles of Genetics PLANT GENETICS AND CROP BIODIVERSITY P R E PA R E D BY: A N G E L O E. E B O R A , L. A G R  Outline of Topics 1. Mechanisms of Genetic Variation in Plants 2. Conservation Strategies for Plant Genetic Resources 3. Role of Biodiversity in Crop Imp...

Principles of Genetics PLANT GENETICS AND CROP BIODIVERSITY P R E PA R E D BY: A N G E L O E. E B O R A , L. A G R  Outline of Topics 1. Mechanisms of Genetic Variation in Plants 2. Conservation Strategies for Plant Genetic Resources 3. Role of Biodiversity in Crop Improvement 4. Impact of Climate Change on Plant Genetic Diversity 5. Policy and Global Initiatives in Biodiversity Conservation 6. Future Directions in Plant Genetics and Biodiversity Research What is the genetic basis of variation in plants? The study of genes, genetic variation, and heredity in plants is known as plant genetics. Understanding the principles of plant genetics may be important in many activities involving crop breeding and conservation of plant genetic diversity. SOURCE: https://www.longdom.org/open-access/a-brief- note-on-plant-genetics-89814.html  Gregor Mendel looked into "trait inheritance," or how qualities are passed down from parents to offspring. He discovered that organisms (most notably pea plants) pass along features in separate " “units of inheritance. This word, which is still in use today, is an imprecise definition of what is known as a gene. Much of Mendel's plant research is still used in modern plant genetics. SOURCE: https://cales.arizona.edu/research/azalfalf/pdf_pubs/plant_genetics_primer.pdf What is the chromosomal basis of genetic inheritance and variation? Genes are the fundamental physical and functional units of inheritance. They are essentially segments of the molecule DNA, the chemical sequence of which is ultimately responsible for producing all growth and development processes of an organism. Particular genes usually occur at a specific location, referred to as a locus (plural loci), on chromosomes. Chromosomes are the threadlike DNA and protein- based structures in cells whose function is the orderly duplication and distribution of genes during cell division. SOURCE: https://cales.arizona.edu/research/azalfalf/pdf_pubs/plant_genetics_primer.pdf SOURSE: https://www.flickr.com/photos/mitopencourseware/4814933459 SOURCE: https://slideplayer.com/slide/6626218/#google_vignette Each species generally has a characteristic number of chromosomes within each of its body (somatic, nonreproductive) cells. Chromosome complements (a) and karyotype (b) of O. sativa ssp. indica cv. Twelve homologous pair of chromosomes were arranged according to their morphology and numbered according to their length in descending order. SOURCE: https://www.researchgate.net/figure/Chromosome- complements-a-and-karyotype-b-of-O-sativa-ssp-indica-cv- Twelve_fig1_5638165 SOURCE: https://agrinfobank.com.pk/list-of-some-agricultural-crops- and-animals-with-their-diploid-chromosome-number/ Collectively, the total chromosomal DNA of an organism is referred to as its genome with each set of chromosomes making up a single genome. A diploid organism, therefore, has two genomes, one from each parent. It is important to note that “genome” has also come to refer to the total chromosomal DNA of a species. SOURCE: https://cales.arizona.edu/research/azalfalf/pdf_pubs/plant_ge netics_primer.pdf  Reproductive cells, such as the sperm and the egg and the other cells in pollen and embryo sacs are haploid, meaning they contain half the number of chromosomes of a diploid cell. SOURCE: https://iastate.pressbooks.pub/cropimprovement/chapter /basic-principles-of-plant-breeding/  The specific composition of DNA at each gene is known as an allele. Alleles may differ between chromosomes in a diploid species or among chromosomes in polyploid species. Multiple alleles of a gene may be generated by mutations, which are structural or chemical changes in DNA. SOURCE: https://cales.arizona.edu/research/azalfalf/pdf_pubs/plant_genetics_p rimer.pdf  What causes genetic variation? Genetic variation (diversity) is the result of differences among individuals in a group; it is ultimately a function of allelic differences resulting from mutations, and the random assortment of alleles during meiosis. Meiosis is a special type of cell division that ultimately leads to the production of sperm and egg. SOURCE: https://cales.arizona.edu/research/azalfalf/pdf_pubs/plant_genetics_p rimer.pdf An individual’s genotype is the set of alleles it possesses at a certain locus or over particular loci. Genotype can be expanded to reflect allelic constitution over all of the loci in the individual. In contrast, the appearance or performance of an individual is known as its phenotype. SOURCE: https://cales.arizona.edu/research/azalfalf/pdf_pubs/plant_genetics _primer.pdf If different alleles exist at a locus in an individual, the locus is considered heterozygous and the individual is a heterozygote for that locus. If alleles at a locus are the same, the locus is homozygous and the organism is a homozygote. SOURCE: https://cales.arizona.edu/research/azalfalf/pdf_p ubs/plant_genetics_primer.pdf How is assessment of genotype done? It is often useful to describe the genotype of a particular individual or of individuals in a population and a number of methods now exist to do so. The simplest method uses morphological markers. A morphological marker is an easily observable genetically determined trait that identifies, or marks, different genotypes. Flower and fruit or seed color are commonly used morphological markers in plants. Although morphological markers are generally easy to use, their usefulness is limited by their availability. That is, there are typically insufficient morphological markers in a particular species to be able to uniquely identify individual genotypes. Most well characterized morphological markers are only available in cultivated species that have been intensively studied genetically. What are molecular markers? Molecular markers identify differences in the genetic code (DNA) among individuals. The process of using molecular markers to identify individuals is known commonly as DNA fingerprinting. There are many techniques used to fingerprint, however, the basic concept is the same for most approaches.  Plant DNA is segmented by certain enzymes called restriction endonucleases. Different endonucleases recognize different segments of the DNA code. When a particular endonuclease finds its DNA code segment in the plant DNA, it makes a cut. After the DNA has been cut, the DNA segments, now called fragments, are separated by gel electrophoresis  Electrophoresis separates the fragments by size with the largest fragment appearing at the top of the gel and successively smaller fragments. A stain is added to the gel that reacts with the DNA fragments causing the DNA to become visible. SOURCE: https://byjus.com/chemistry/types-of- electrophoresis/ SOURCE: https://www.technologynetworks.com/analysis/articles/agaros e-gel-electrophoresis-how-it-works-and-its-uses-358161 https://link.springer.com/chapter/10.1007/978-94-017- 9996-6_2  How can mating system affect genetic variation? Plant species exhibit great variability in sexual reproduction and this has significant effects on the genetic constitution of individuals, specially the average heterozygosity or homozygosity that they possess. https://www.researchgate.net/publication/221879768_Shifts_in_reproductive_assurance_strateg ies_and_inbreeding_costs_associated_with_habitat_fragmentation_in_Central_American_maho gany Reproduction may range from complete self-pollination, where seeds are derived from pollen that has come only from the same plant, to complete cross- pollination, where pollen that leads to seed is received only from different plants. Individuals in self-pollinated species tend to be highly homozygous. When heterozygosity does occur, either as a result of mutation or cross-pollination between genetically different individuals, repeated self-pollination tends to rapidly reduce the amount of heterozygosity present within offspring of a given individual. Alternatively, in species that tend to exhibit more cross- pollination, heterozygosity is typically much more common and is generally preserved over generations of sexual reproduction. More than 400 plant species, including many grasses and members of the sunflower and rose families exhibit apomixis, which is an asexual reproductive process where seeds are not derived from the union of sperm and egg (fertilization) but result from the development of a body cell into an embryo. Plants derived from seeds produced by means of apomixis are genetically equal to the parental plant that produced them. In apomictic species, a single genotype may occupy very large areas and therefore populations may contain relatively little genetic variation. Inbreeding results from matings between individuals that are related to each other and therefore possess alleles derived from a common ancestor(s). Self-pollination is the most extreme example of such a mating, but cross- pollination between other kinds of relatives will also lead to inbreeding. In many cross-pollinated species, inbreeding may lead to an overall decline in plant performance that is known as inbreeding depression Species that are predominately self-pollinated typically do not display significant inbreeding depression. Heterosis, or hybrid vigor, can be thought of as the opposite of inbreeding depression. Heterosis is observed when the performance of offspring from a mating far exceeds that of the parents. Typically, heterosis is observed in offspring produced from matings between 2 genetically different parents that will tend to produce highly heterozygous offspring.  Figure 1 The manifestation of heterosis with respect to different phenotypic traits of maize SOURCE: https://www.cell.com/current-biology/fulltext/S0960- 9822%2818%2930832-7 What is the role of genetic variation in evolution? Genetic variation that exists among plants within and among populations is ultimately due to actions of evolution, a collection of processes that results in a change in allele frequencies over time. Evolution leading to local adaptation is primarily the result of natural selection. Natural selection is based on fitness, which is measured by the tendency for an individual and its offspring to survive. Fitness may be associated with a plant’s longevity, fertility, and its ability to produce highly viable offspring.  If variation for a trait associated with fitness is genetically based or “heritable” (heritability > 0), then individuals with higher fitness will leave more offspring on average than those with lower fitness. This will result in the genetic constitution of the population becoming more similar to that of the more fit individuals.  In many ways, artificial selection as practiced in plant breeding programs is directly analogous to evolution through natural selection. Plant breeders select (retain) plants with desired phenotypes or genotypes and these individuals contribute alleles to the next generation. Over generations, the frequencies of alleles associated with the desired phenotypes therefore increase within the population. SOURCE: https://evolution.berkeley.edu/wp- content/uploads/2021/03/brassica_artificial_selection.jpg What other processes other than natural selection can result in genetic changes in plant populations? One of the most common of these encountered in many plant collection and propagation activities is genetic (random) drift. This occurs when particular alleles are very rare or when population size becomes very small, as may occur with a near extinction event or during seed collection. If a small sample, say of only 10 plants, is randomly taken from this population, then chances are quite high that at least one of the 10 alleles will be completely excluded from the sample and that the frequencies of the other alleles will differ markedly from 0.1 simply by chance alone. SOURCE: https://www.croptrust.org/mission/why-we-need-crop-diversity/ SOURCE: https://www.computomics.com/news-reader/genius- genes-unlocking-genetic-diversity.html Securing the world’s crop diversity is a global concern and a prerequisite for future food and nutrition security. Only by safeguarding crop diversity in perpetuity, and making it available for use by researchers, plant breeders and farmers, can we adapt agriculture to the climate crisis, reduce environmental degradation, improve livelihoods, and feed everyone adequately. Plant breeders and scientists use crop diversity to develop new, more resilient and productive varieties that consumers want to eat, that are nutritious and tasty, and that are adapted to local preferences, environments and challenges. SOURCE: https://www.croptrust.org/mission/why-we-need-crop-diversity/ And once an heirloom variety or wild crop relative is lost, it is gone forever. How do we secure our food supply? Out of 20,000 edible plants, and 6,000 that have historically been used as food, fewer than 200 now make a major contribution to food production, and just 9 account for two thirds of food production, according to FAO’s State of the World’s Biodiversity for Food and Agriculture.  It is only through conserving and using crop diversity to adapt agriculture to the effects of climate change that we will meet one of humanity’s greatest challenges: sustainably producing sufficient and sufficiently nutritious food for an increasing global population in the face of multiple crises. SOURCE: https://www.croptrust.org/mission/why-we-need-crop-diversity/ SOURCE: https://agricultureandfoodsecurity.biomedcentral.com/articles/10.1186/s40066-024- 00478-0 The biodiversity of grain legumes has a great important role in food and nutritional security worldwide. Grain legumes are a vital component of the human diet and also increased in demand past few years due to its other nutritional and health benefits over the main crop grains. SOURCE: https://link.springer.com/chapter/10.1007/978-981-99-5245-8_3 SOURCE: https://link.springer.com/chapter/10.1007/978-981-99-5245-8_3 Plant breeders and scientists use crop diversity to develop new, more resilient and productive varieties that consumers want to eat, that are nutritious and tasty, and that are adapted to local preferences, environments and challenges. SOURCE: https://www.discovery.co.za/corporate/nutrition-love-legumes  It is only through conserving and using crop diversity to adapt agriculture to the effects of climate change that we will meet one of humanity’s greatest challenges: sustainably producing sufficient and sufficiently nutritious food for an increasing global population in the face of multiple crises. Source: https://www.croptrust.org/mission/why-we-need-crop-diversity/ What are the threats to crop diversity? SOURCE: https://www.croptrust.org/mission/why-we-need- crop-diversity/ We are losing the diversity of crops and their wild relatives at an alarming rate. This erosion of crop diversity is undermining the resilience of food systems. Increasingly rapid environmental, technological and social changes, including extreme weather events, changes in agricultural practices, the emergence and spread of new pests and diseases, and conflict, are causing crop diversity to disappear in many places around the world. What is genetic erosion? Genetic erosion refers to the loss of genetic diversity, sometimes used in a narrow sense, that is, the loss of genes or alleles, as well as more broadly, referring to the loss of varieties, and crop species, mainly because of the replacement of traditional landraces by modern, high-yielding cultivars, natural devastations, and large-scale destruction and modification of natural habitats sheltering wild species. SOURCE: https://www.sciencedirect.com/topics/agricultural-and- biological-sciences/genetic erosion#:~:text=Genetic%20erosion%20refers%20to%20the,%2C%2 0high%2Dyielding%20cultivars%2C%20natural In the current setting, a handful of multinational companies supply most commercial seeds. These companies only invest in a limited variety of seeds and, therefore, decide what is on offer. Kinver (2014). “Crop diversity decline 'threatens food security’”. A US study found that out of 544 different kinds of cabbage in 1903, only 28 survived until 1983. Out of 307 maize varieties, only 12 were left in 1903, and 408 pea varieties were reduced to just 25. Some of the lost species might still exist in somebody’s garden or are stored in a dusty seed jar in some basement. But they disappeared from the seed catalogues and are not available for commercial farming anymore file:///C:/Users/ADOLFO/Downloads/dempewolf-et-al-2023-our-shared-global- responsibility-safeguarding-crop-diversity-for-future-generations.pdf