Plant breeding programs consist of several steps that are usually conducted as reiterative procedures:
1. hire talented and cooperative scientists (e.g., plant breeder, scientists in other disciplines, and technical staff)
2. understand the ecology of the plant, the target environment, the system of crop production, and the consumers
3. define the target environment for crop production (e.g., Where and how are the crops grown? What is the prevailing ecology therein?)
4. assemble and maintain the necessary physical resources
5. identify clear goals for selection regarding the type of cultivar, the traits, and their expression
6. select or create testing environments representative of the target environment
7. survey and choose germplasm to serve as parents and sources of genes (the crop and other species, cultivars, accessions [individual samples of seed] from germplasm reserves, and genes)
8. identify and create genetic variation among the parents and their progeny by evaluating the parents, mating the parents, and evaluating their progeny and occasionally by modifying the parents' genome or introducing genes through genetic engineering and transformation
9. evaluate and select the progeny that optimize production in the target environment.
When practiced on a continuous basis, these steps have achieved impressive results for several species and target environments.
Plant breeding programs negotiate numerous challenges along the path of improvement. The reproductive biology and growth habit of the plant are primary factors that dictate breeding methods, their implementation, progress from selection, and the type of cultivar (e.g., hybrid, pure line, clonal, population, or other). Some important considerations include the mode of reproduction (sexual, vegetative, or both), flower structure (perfect or imperfect), prevailing type of pollination (e.g., autogamous [self] or al-logamous [other], wind, or insect), and methods to induce flowering, make controlled matings between the selected parents, and produce an adequate supply of progeny for evaluation and distribution. Considerations of the growth habit would include the length of the juvenile period (especially with trees) and if the species has an annual or perennial habit in the target environment.
The organization of the plant's genome also affects breeding strategy and the rate of progress. The plant genome is partitioned into the nucleus, mitochondrion (mt), and plastid (pt; e.g., chloroplast). The mt and pt genomes contain relatively few genes (hundreds) and in most angiosperm species are transmitted to the progeny exclusively through the cytoplasm of the female gametes (the egg cell in the embryo sac). The maternal inheritance of those genomes may dictate which parents are used as males and females. Plant nuclear genomes contain tens of thousands of genes as parts of several independent chromosomes, are inherited biparentally through the male (sperm nuclei in the generative cell of the pollen grain) and female gametes, and often contain more than two complete sets of chromosomes (polypoidy). For example, maize (Zea mays L.) and rice (Oryza sativa L.) are diploid because the nuclei of their somatic cells contain two complete sets of chromosomes, one each from the maternal and paternal parents. In contrast, cultivated alflalfa (Medicago sativa L.) and bread wheat (Triticum aes-tivum L.) are autotetraploid and allohexaploid because their somatic cells hybrid a mix of two species population a group of organisms of a single species that exist in the same region and interbreed angiosperm a flowering plant diploid having two sets of chromosomes, versus having one (haploid)
diploid having two sets of chromosomes, versus having one (haploid)
domesticate to tame an organism to live with and to be of use to humans
progenitor parent or ancestor polyploidy having multiple sets of chromosomes domesticate to tame an organism to live with and to be of use to humans contain four (from the same species) and six (from three different progenitor species) complete sets of chromosomes, respectively. Polyploidy challenges breeders because it leads to more complex inheritance patterns and may hinder identification of desirable progeny in segregating populations.
The ecology of the target environment and the plant affect the evaluation and selection of parents and progeny in myriad ways (e.g., climate, soil, organic diversity, and the subsequent stress on crop production). The relative merit of the germplasm (e.g., parent, progeny, or cultivar) may vary greatly and depend upon certain elements of the environment (i.e., genotype and environment interaction, GxE). For example, a disease-resistant cultivar may have superior productivity when evaluated in a disease-laden environment but the same cultivar may be inferior when tested in a disease-free environment. GxE is a major challenge for every plant-breeding program because so many factors could influence the plant's growth and productivity during its life cycle. GxE is managed by testing germplasm in samples of relatively few environments and treatments intended to resemble the prevailing conditions of the target environment. Inadequate testing may result in a poor choice of genotypes, less genetic progress, and, sometimes, truly inferior cultivars.
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