Inquiry Question

How does reproduction ensure the continuity of a species?

Content Descriptor

Evaluate the impact of scientific knowledge on the manipulation of plant and animal reproduction in agriculture

Historical perspectives of agriculture

Archaeological evidence suggests that humans have been practising agriculture for more than 10,000 years and became established in many communities about 7,000 years ago. Indeed, agriculture was the driving force for the growth of civilisations. While hunter-gatherer societies relied on natural biological diversities for food, agricultural societies domesticated crops and animals. Over time, farmers began to select for desirable traits in crops and animals. Some desirable traits include disease and pest resistance, plant varieties with larger seeds and fruits, higher nutrient content, longer shelf lives and better adaptations to local environmental conditions.

Until the scientific discoveries of the 19th and 20th centuries, farmers engaged in agricultural improvements without an understanding of the underlying biology. Much of those attempts were 'hits-and-misses'. For example, crop rotations and the use of fertilisers improved yield. Selective breeding increased the frequency of plants and animals with desired traits. However, with the advent of scientific approaches to agriculture, systematic crop and animal enhancement processes were developed. Underpinning these are the advances in reproductive biology and genetics.

Understanding reproductive biology

Although far from complete, scientists have developed a good understanding of the essential processes that govern reproduction. Discoveries in genetics, physiology and biotechnology have enabled researchers to develop protocols to manipulate reproduction to achieve specific outcomes. It is important to remember that people have attempted to manipulate the reproduction of plants and animals since time immemorial. For example, the domestication of animals and the development of plant varieties for agriculture are examples of this. Modern scientific knowledge of reproductive biology has enhanced those processes to be more efficient and productive. While all organisms can acquire new traits through evolution, science allows us to 'speed up' the process of generating organisms with novel characteristics for agricultural and other purposes.

While the manipulation of reproduction has been used for many reasons (e.g. conservation, pest eradication, population control, disease management and treating human infertility), this discussion will explore how the manipulation of reproduction enhances agricultural outcomes.

The value of Australian agriculture

In 2018-9, the Australian agriculture industry produced a revenue of $62 billion. The top agricultural commodities include ((NFF)), ((ABS)):

Agricultural commodity	Revenue/$ ‘billions
Cattle and calves	9.485
Wool	4.159
Wheat	3.676

Other essential agricultural commodities are cotton, dairy, dried fruits, forestry, grains, rice, sheep meat and sugar. The Australian agricultural sector feeds the nation's population and contributes significantly to the world's food supply. In addition to food and fibre, other spin-offs from agricultural commodities are used to manufacture other materials our society needs.

Selective Breeding

Selective breeding is the selection of parents to produce the next generation. If one selects desirable animals or plants as parents, the offspring will be better than if the parents were not selected. Selective breeding frequently does not produce predictable results because the offspring receive a random half of the alleles of each parent, and there is a high level of heterozygosity in all species of domestic animals and plants. The problem is worse if the selected trait has low heritability or is sex-limited (sex-linked).

Why manipulate reproduction?

The manipulation of reproduction in agriculture is designed to improve the quality of the end products (e.g., the quality of animal stocks and crop varieties). The main thrust of these efforts is to improve the genetic quality of agricultural animals and plants. Enhancing genetic traits is accomplished by manipulating the reproductive biology of the organisms. This includes manipulating the production of the gametes (the sperm or eggs), ovulation, fertilisation, implantation, gestation (pregnancy) and birth (parturition).

Animal reproduction

Since the 19th century, there have been significant advances in the science of animal reproduction based on research on how animals grow and how yields can be influenced and protected. Biotechnology has further enhanced the application of this knowledge to benefit agriculture. Reproductive technology refers to all current and anticipated uses of technology in human and animal reproductions (Mapletoft and Hasler, 2005). Thus, advances in our understanding of endocrinology, reproductive physiology, cell biology and embryology have resulted in animal reproductive technologies such as oestrus synchronisation and induction, artificial insemination, Multiple Ovulation Induction and Embryo Transfer (MOET), In Vitro embryo Production (IVP) and cloning by Nuclear Transfer (NT). As a result, animal agriculture is well-placed to improve farm animals in large numbers genetically.

The domestication of cattle began around 10,000 years ago: Bos taurus in Europe and the Middle East and Bos indicus in India. Crossbreeding of these species is likely to have occurred in many communities.

Improvements in male animal reproduction ((Holland MK, McGowan M. Manipulation of fertility to enhance the productivity of cattle. The Biochemist. 2018;40(3):20-5.))

The first recorded use of artificial insemination occurred in 1780 (dog). Artificial insemination of cattle occurred in the early 20th century (in Russia). This method of reproductive manipulation quickly spread to Europe and America.
The 1930s: Electroejaculation was developed to extract semen from high-quality bulls.
'Extenders' were added to collected semen so that it may be diluted and used to inseminate multiple cows. In addition, antibiotics were added to the semen to extend its shelf-life.
1949: Techniques for cryopreservation of semen were developed, especially by mixing semen with glycerol. This allowed semen to be stored for long periods. One technique was using straws to store the semen, which allowed for easy transportation of semen across vast distances.
In-Vitro Fertilisation (IVF): development of IVF technology allowed in vitro embryo development. Embryos were allowed to develop to the blastocyst stage and then implanted into females. This improved the efficiency of the reproductive process, as the fertilisation of gametes is better controlled.
Sperm sexing: cytogenetic techniques were developed to identify sperm carrying X or Y chromosomes. This allows farmers to select the sex of the calves born, thus improving farm productivity.

Improvements in female animal reproduction

Detection of oestrous (developing techniques that allowed farmers to know when the cows are sexually receptive for insemination). Identifying females in oestrous is important for improving pregnancy rates through artificial semination.
Females are injected with gonadotropic hormones, which cause them to superovulate, thus increasing the chances of success of IVF. This protocol is called Multiple Ovulation and Embryo Transfer (MOET). The gonadotropic hormones also allow for synchronising the oestrous cycles of multiple females on a farm.
Techniques for detecting embryo quality—Various techniques can be used to determine the quality of embryos before they are implanted into females. However, this is an emerging field, and presently, embryo screening relies largely on cell morphology.
Detection of pregnancy using transrectal ultrasound can also be used to identify the sex of the fetus.

Farm animal cloning

A clone is an organism that has identical genetic material to its ancestor. This is usually achieved by:

Embryo splitting: splitting the embryo at an early (pluripotent) stage to produce identical twins
Somatic Cell Nuclear Transfer (SCNT): the somatic cell nucleus from a donor is transferred into the enucleated cytoplasm of a recipient oocyte. After this, the ovum is transferred to the womb of a surrogate mother for growth and development. The technique has been tested in cattle, rabbits, cats and pigs and was found to be successful (Sandoe, 2005)

Embryo splitting. Image credit: BioNinja.

Somatic Cell Nuclear Transfer. Image credit: BioNinja

Advantages and disadvantages of animal cloning

Advantages

1. Cloning preserves the breeding capacity of the genetically elite and protects against the loss of valuable genetic and characteristic features. With techniques such as artificial insemination, only half of the males' beneficial genetic traits will be transferred to the progeny—all the progeny are half-sibs.

2. Reduced flock time - 18 months for sheep (compared to 44 months with traditional breeding methods) and 33 months for cows (78 months with conventional breeding methods).

3. Embryos can be genetically manipulated using DNA microinjection techniques. This allows foreign DNA (from different species) to be inserted into the embryonic genome. Animals carrying foreign genes are referred to as transgenics, and the foreign gene is called a transgene. Many studies indicate that the transgenes are expressed in those animals as adults and can be transferred to their progeny.

4. In addition to improving agricultural outcomes, cloning also allows for the breeding of animals for human medical benefits, including understanding various diseases, producing therapeutic agents (e.g., pharmaceutical proteins—recombinant DNA products), and developing organs and xenotransplantation.

Disadvantages

Cloning techniques are inefficient and expensive. For example, 90% of embryos produced via SCNT are non-viable.
Studies have shown that, in cloned animals, about 4% of genes function abnormally. The abnormalities do not arise from gene mutations but from changes in the normal activation or expression of certain genes (Van Eenennaam et al., 2007). Other problems with farm animal cloning include placental abnormalities, fetal overgrowth, prolonged gestation, respiratory failure and circulatory problems, lack of post-natal vigour, malformations in the urogenital tract (hydronephrosis, testicular hypoplasia), malformations in liver and brain, immune dysfunction, lymphoid hypoplasia, anaemia, thymic atrophy and bacterial and viral infection.

Plant reproduction

Humans have manipulated plant reproduction for agricultural purposes for more than 10,000 years. For example, archaeological evidence suggests that wheat was cultivated 8,000 to 10,000 years ago in various civilisations. Modern wheat (T. aestivum) is believed to have been derived from crossing ancestral wheat (T. turgidum) with a type of grass (Ae. tauschii; goatgrass) about 8,000 years ago in the Middle East.

Improvements in plant reproduction

Before the 17th century, plant breeding was done 'unintentionally'. However, from the 17th century onwards, plant breeders developed specific techniques, such as artificial pollination, to develop superior-quality plant varieties. This approach took a giant leap forward with the work of Gregor Mendel. His discoveries of the Laws of Inheritance in plant breeding provided a genetic basis for improving agricultural varieties.

In Australia, William Farrar undertook experiments in wheat hybridisation, especially developing wheat varieties that thrived in Australian conditions (heat, water availability, diseases). One variety he created, known as Federation, was well-suited for mechanical harvesting - it became the dominant wheat variety cultivated by Australian farmers. Current wheat breeding research focuses on improving crop yields, disease resistance, tolerance to abiotic stress (heat and drought) and biofortification (enhanced nutrient content).

The middle panel shows the evolution of wheat through hybridization, allopolyploidization, domestication and mutation along with modification in spike size and spike threshability. The yellow panel on the left indicates the approximate time those events occurred, and the right panel shows the gradual changes in grain size and shape during evolution. Image credit: Rahman S, Islam S, Yu Z, She M, Nevo E, Ma W. Current progress in understanding and recovering the wheat genes lost in evolution and domestication. International journal of molecular sciences. 2020 Jan;21(16):5836. Distributed under a Creative Commons licence.

Wheat breeding experiments by William Farrer produced high-quality cultivars that performed well in Australian conditions. Image credit: this image was produced by the author.

Non-genetic approaches in plant breeding

Modern plant breeding relies heavily on genetic technologies and biotechnology. However, before this, techniques such as selective breeding, artificial pollination and vegetative propagation were used to produce plants with new traits. These methods are also currently used in agriculture.

Selective breeding

As indicated above, the crossing of closely related plants with different desirable traits can produce progeny with a combination of those qualities (e.g., breeding wheat). More extensive breeding can produce new crops for human consumption. For example, extensive selective breeding of wild mustard has produced various vegetables commonly used today.

Selective breeding enlarged desired traits of the wild mustard plant (Brassica oleracea) over hundreds of years, resulting in dozens of today's agricultural crops. Cabbage, kale, broccoli, and cauliflower are all cultivars of this plant. Image credit: Liwnoc. Distributed under a Creative Common 4.0 licence.

Another plant that has undergone extensive selective breeding is the carrot. Originally, carrots were black or dark purple in colour, but through various cross-breeding efforts, the modern orange-coloured variety was produced from the 17th century onwards.

Image showing the diversity of carrot colours (cultivars). Image credit: Anguskirk. Distributed under a Creative Commons 2.0 licence.

Artificial pollination

Pollination is the movement of pollen from the anthers of a flower to the stigma of the same or a different flower. In nature, pollination may be carried out by abiotic factors such as wind and water, or biotic factors such as insects and other animals. In natural systems, plants have evolved complex relationships with their pollinators. However, natural pollination systems are often inadequate for agriculture, as they do not 'scale up' efficiently. For example, in many parts of the world, plants that rely on bee pollinators are experiencing reduced reproduction rates because of declining bee populations. Another issue facing agriculture is that many crops are grown in areas where natural relationships between plants and their pollinators do not exist. Hence, agriculturalists rely on artificial pollination. At the simplest level, this involves hand-pollinating plants (the manual transfer of pollen from the stamen or male part of the flower to the pistil or female part). However, the agriculture industry is exploring using new technologies to increase the efficiency of artificial pollination, including mechanical pollination systems and drones. For more information, the following resources may be useful:

Hand pollination. Image credit: International Institute of Tropical Agriculture. Distributed under a Creative Commons 3.0 licence.

Vegetative propagation

Vegetative reproduction is a form of asexual reproduction in plants in which a new plant grows from a fragment or cutting of the parent plant. Both sexual and asexual reproduction strategies provide several benefits and/or advantages:

For some plant species, sexual reproduction may be quicker and more economical than asexual propagation. For others, the opposite is true.
Sexual reproduction may result in the production of new cultivars and vigorous hybrids. Generally, it is more difficult to produce new cultivars through asexual reproduction.
For some species, sexual reproduction may be the only way to perpetuate particular cultivars (they may be incapable of asexual reproduction). In some species, asexual reproduction maintains the juvenile or adult characteristics of certain cultivars (during sexual reproduction, plants alternate between juvenile and adult stages). It may more quickly result in a large plant (compared to one propagated by seed).
Sexual reproduction provides a way to avoid the transmission of particular diseases. It maintains genetic variation, which increases the potential for plants to adapt to environmental pressures. This is more difficult in asexually-reproducing plant populations.

The main advantage of vegetative propagation is that the new plants are essentially clones of the parent plant (true-breeding). Therefore, plants with the desirable traits can be grown indefinitely, assuming the same growth conditions are maintained. For farmers, this consistency of product quality, productivity and availability are important.

Some methods of vegetative propagation include:

Cuttings: a cutting is a severed piece of a parent plant (e.g. leaf, stem) that is planted to generate a new individual.
Budding and grafting: vegetative propagation methods that join parts of two or more different plants together so they unite and grow as one plant
Micropropagation: Micropropagation involves the use of tissue culture techniques to propagate plants from very small plant parts (parts of leaves, stems, shoot tips, root tips, single cells, and pollen grains). The initial stages of micropropagation are often conducted in laboratories under sterile conditions.

Food crops such as cassava, sweet potato, sugarcane, pineapple, banana, and onion are propagated vegetatively.

Plant tissue culture is a technique of growing cells, tissues or organs in sterilized nutrient media under controlled aseptic conditions. The plant material to be cultured may be cells, tissues or plant organs such as excised root tip, shoot tip, shoot bud, leaf petiole, inflorescence, anther, embryo, ovule or ovary. Image credit: Syed Sajidul Islam. Distributed under a Creative Commons 4.0 licence.

Plant hormones

In agriculture, hormones are used to improve yield and productivity. These hormones control or influence all aspects of plant growth and reproduction, including seed germination, growth of roots, stems and leaves, plant flowering, seed development, seed fill and seed dormancy. Some plant hormones and their effects are described next:

Abscisic acid
- Abscisic acid inhibits cell growth and promotes seed dormancy. Its levels increase when plants start to produce shoots and leaves.
Auxins
- Auxins are responsible for many aspects of plant growth, including cellular elongation and stimulating shoot growth. They are manufactured mostly in the shoot tips and in parts of developing flowers and seeds. Auxins control plant aging and senescence and play a role in seed dormancy. Synthetic auxins, such as 2,4-D, are used as herbicides to kill many types of broad-leaved plants.

Cytokinins
- Cytokinins and auxins tend to work together. The ratio of these two hormone groups affects growth throughout a plant’s lifecycle. As cytokinin levels increase and auxin levels decrease, the plant transitions into the reproductive growth stage.

Ethylene
- Ethylene is a gaseous hydrocarbon. Roots, senescing flowers and ripening seeds all produce ethylene. Ethylene production can be promoted by auxins.

Gibberellins
- Gibberellins initiate seed germination and promote the transition from vegetative to reproductive growth. A reduction of gibberellin reduces stem length between internodes to cause dwarf plants.

The future of plant breeding

Modern techniques in plant breeding focus on cytogenetic and molecular methods. Some of these methods include:

Mutagenesis (inducing mutations in a plant's genome and subsequently identifying mutants with desired characteristics). Presently, CRISPR/Cas9 is being used to introduce specific mutations in genomes, thus improving the control of the process.
Genetic markers (e.g. Quantitative Trait Loci (QTL) mapping and Marker-Assisted Selection (MAS)) are used to identify individuals who possess known genetic determinants of desired traits. Both of these methods are limited in that only a small number of markers can be studied at any one time. However, recent developments in Genome Sequencing and Genome-Wide Association Studies mean that researchers can rapidly identify and manipulate numerous genes simultaneously.
Meiotic recombination: scientists have manipulated the recombination system in wheat to promote additional recombination events, including those between non-homologous chromosomes, to produce gametes with novel gene combinations.
Speed breeding: this method allows selected cultivars to be grown out of season. It relies on manipulating photoperiod, light and temperature (artificially) in growth chambers and glasshouses. This method can produce up to six generations of wheat in a single year.
Other methods include using sensors to monitor plant development in real time, contributing to our understanding of key stages that may be manipulated. This is referred to as phenotype monitoring.

Development of plant breeding technology. Since the 1970s, techniques such as tissue culture, intra-specific hybridisation, molecular diversity, molecular marker analysis, interspecific hybridisation and mutation and the CRISPR-Cas system have revolutionised the manipulation of plant reproduction. Figure from Numan et al. (2021). ((Numan M, Khan AL, Asaf S, Salehin M, Beyene G, Tadele Z, Ligaba-Osena A. From Traditional Breeding to Genome Editing for Boosting Productivity of the Ancient Grain Tef [Eragrostis tef (Zucc.) Trotter]. Plants. 2021;10(4):628.)) Distributed under a Creative Commons by 4.0 licence