Genetics of Adaptation Graduate Seminar
Author: Kim Thompson
The tasty and productive rice we enjoy today has some wild relatives with big differences. First domesticated approximately 7000 years ago in China, rice is widely planted and also collected from the wild in Asia and Africa. Domesticated rice depends on humans to persist but wild types can grow un-aided in both swampy and seasonally dry areas in Southeastern Asia and India. Michael Grillo and colleagues from Michigan State University (Grillo et al. 2009) used quantitative trait loci (QTL), genetic regions associated with differences between two wild rice species from southeast Asia (Oryza nivara and Oryza rufipogon) to investigate how the rice we grow began its evolutionary trajectory from wild strains as an adaptation to a drier environment. Oryza nivara is an annual rice plant that lives in an environment that becomes dry for part of the year and Oryza rufipogon is a perennial living in an ever-wet environment, similar to the ancestral species (Figure 1).
Figure 1: Diagram of predicted evolution of Oryza nivara and the cultivar, Oryza sativa subspecies indica from an Oryza rufipogon-like ancestor. Blue background represents an ever-wet habitat; orange indicates a seasonally dry habitat. Although the indica cultivar may have arisen from Oryza nivara, introgression from Oryza rufipogon is also likely to have influenced its genetic composition (Li et al. 2007; Sang and Ge 2007). Diagram from Grillo et al. (2009) supporting information.
Researchers crossed Oryza nivara and Oryza rufipogon, creating a hybrid (F1) population. Oryza nivara is self-pollinated so individuals have less variation at each gene but Oryza rufipogon has high heterozygosity or genetic variability. Therefore two individuals that captured the most genetic diversity present in Oryza rufipogon were selected from the F1, self-pollinated, and grown for two years in a greenhouse, producing two F2 populations (labeled A and B). A total of four populations could then be compared: Oryza nivara, Oryza rufipogon, F2 (A) and F2 (B).
Figure 2: Physical differences between Oryza nivara and Oryza rufipogon rice plants grown under the same greenhouse conditions. (A) Oryza rufipogon has longer stems and more branching (tillering) (B) Oryza nivara has a more compact structure (C) Open flowering structure of Oryza rufipogon. (D) Compact flowering structure of Oryza nivara (figure from Grillo et al. 2009.
Differences in how fertilization occurs (mating system) and the timing of the flowering seasons relative to the amount of daylight they experience (photoperiod sensitivity) contribute to the success of a plant as either an annual or perennial. Therefore, features associated with these differences were measured in this study including: days to flowering after germination, sizes and positions of flowering parts (tiller length, anther length, panicle exsertion and shape, and spikelet number) and grain weight. Each of these is a quantitative trait resulting from the combined effects of multiple genetic and environmental factors, and significant differences are observed between the two study species (Figure 2). In order to measure the genetic differences, simple sequence repeats (SSRs), or microsatellites were used to detect differences among individuals and identify individuals for generating the F2 populations. Differences in SSRs between the species also helped the researchers detect QTL, sets of genes located together on a region of the chromosome and linked to a phenotype (Figure 3).
Figure 3: a) Two different parents (the Oryza species in this study) differ in a phenotype and become more divergent as they are inbred (self-pollinated) over many generations. b) The parental lines are crossed, providing different genetic and phenotypic combinations in the offspring. These traits can be measured and linked to genetic markers such as SSRs. c) The probability that a known marker is associated with a QTL is evaluated using statistical techniques to map the QTL on a chromosome and measure how strong is its effect on a particular phenotype. From Miles and Wayne (2008).
Figure 4: Chromosomes 1 and 6 of Oryza rufipogon with select QTL (quantitative trait loci) pictured (abbreviations defined above). Red and blue symbols indicate two different sets of Oryza rufipogon plants that vary in physical and genetic characteristics. Black symbols indicate a combined analysis of the Oryza rufipogon plants. The gene, Hd1 is located near DF6 on chromosome 6 (Grillo et al. 2009).
QTL that affect sizes of flower structures, days to flowering from germination, and length of flowering time were identified in the two wild rice species, Oryza nivara and Oryza rufipogon and in hybrids of the two. The QTL contain genes that are at least partly responsible for those changes (Figure 4). The largest effect observed in the QTL was for timing of flowering (photoperiod sensitivity) so this became the focus of the remainder of the investigation.
Near a QTL named DF6, scientists know that one gene, Hd1is associated with photoperiod sensitivity. This gene was sequenced from each of the original parents, Oryza nivara and Oryza rufipogon. A mutation in Hd1 was found in the annual rice Oryza nivara, which is photoperiod insensitive. An insertion into the first exon of the gene is thought to have interrupted the proper functioning of the gene so that Oryza nivara is no longer responsive to day-length changes and it continues flowering throughout its life. All second generation hybrids of the two plants (F2 population), were both perennial and sensitive to daily increases in light amount, suggesting that genes for these traits are dominant and that multiple genes are interacting.
If Hd1 is responsible for photoperiod sensitivity, then the original form of the gene, selected from Oryza rufipogon, when inserted into Oryza nivara should make it sensitive to changes in light conditions. However when such transgenic rice plants were developed and grown in long day conditions, they continued to flower, overlapping the normal flowering times of Oryza nivara. This was unexpected since Oryza rufipogon only flowers in short-days and the gene was expected to introduce this sensitivity to the transformed Oryza nivara. This type of transformation was observed in previous studies when the gene was introduced in cultivated rice varieties. Two other genes are suspected to be involved, acting in concert with Hd1 to create the lack of day-length sensitivity that is seen in Oryza nivara.
How did rice evolve into an annual crop that eventually was domesticated? Some changes may have occurred as it was colonizing a new environment that was drier than that of its ancestors or as a result of ancient climate changes. In order to be successful as an annual plant, rice would need to flower longer and produce an abundance of seeds before it died. Oryza nivara plants start to flower in the middle of the monsoon season, within four months after its seeds germinate, speeding its ability to produce new seeds before the ground dries up. A perennial ancestor would have put more energy into growing stems that persisted after flowering was finished. Its ancestor resembled Oryza rufipogon, which does not flower until the days grow shorter, at the end of the monsoons but which continues growing for many years in the swamps. The loss of sensitivity to seasonal light changes was important for Oryza nivara’s success in a dry environment, allowing it to produce numerous seeds before the rest of the plant perished. This study showed that loss of photoperiod sensitivity is a major factor in evolution from a perennial to an annual plant but that multiple genes interact to create this new phenotype.
Grillo, M. A., C. Li., A. M. Fowlkes, R. M. Briggeman, A. Zhou, D. W. Schemske and T. Sang. 2009. Genetic architecture for the adaptive origin of annual wild rice, Oryza nivara. Evolution 63: 870–883.
Li, C. B., A. L. Zhou and T. Sang. 2006. Genetic analysis of rice domestication syndrome with the wild annual species, Oryza nivara. New Phytologist 170:185–194.
Miles, C. and Wayne, M. 2008. Quantitative trait locus (QTL) analysis. Nature Education 1:1.
Sang, T. and S. Ge. 2007. The puzzle of rice domestication. Journal of Integrative Plant Biology 49:760–768.
Vaughan, D. A., B. Lu and N. Tomooka. 2008. The evolving story of rice evolution. Plant Science 174:394–408.