This research aims to identify key factors contributing to the genetic differentiation within a species and the genetic mechanism underlying such differentiation. Using a North America native mustard plant species as model, preliminary study has found significant genotypic and phenotypic divergence between two subspecies. In order to study the genetic mechanism responsible for this differentiation, the investigators will generate a cross between the two subspecies and identify possible genes responsible for the phenotypic differentiation. Also, the direct contribution of genes and phenotypes to adaptation will be measured by growing the plants in their native environments. The investigators will further examine the genome-wide differentiation pattern between the two subspecies. Combining these results, the effect of local adaptation on the pattern of within-species genetic variation will be investigated empirically.
This proposed research will advance understanding of patterns of within-species genetic diversity. Understanding the extent and driving factors of genetic variation will provide valuable information in various applications, such as identifying genetic factors underlying important traits in various species, including agricultural plants. The proposed project will be one of the first studies identifying possible genes responsible for important phenotypes, investigating the adaptive effect of these genes and phenotypes, and unifying these results with the investigation of population genomic divergence patterns. The utilization of a plant species in this research enables direct experimental manipulation on studied individuals. Finally, several undergraduate students will be trained with the interdisciplinary knowledge of ecology, population genetics, and genomics in this project.
Tremendous amounts of biodiversity exists in the natural environment, and one major question in biology is: How is biodiversity created or maintained? The research field of 'speciation' is dedicated to answering this question. On one hand, individuals from the same or some close species hybridize to each other, homogenizing their genomes. On the other hand, geographic or environmental isolation may increase the divergence and promote the increase of biodiversity. The main goal of this proposal is focused on whether or how environmental isolation may promote speciation: If populations of the same species are locally adapted to different environments, the between-population immigrants or hybrids may be inferior to local individuals, and thus gene flow among populations is blocked by natural selection. To test this, we used Boechera stricta as model, a mustard plant native to the northern Rocky Mountains. We found that while a clinal pattern of genetic variation can be sufficiently explained by geographical isolation, environmental adaptation has high contribution to the discrete pattern of genetic differentiation between the two subspecies within B. stricta. Further greenhouse experiments support this conclusion and found environment-related trait differentiation among subspecies. Through quantitative trait loci (QTL) mapping,we also identified the genomic regions responsible for the adaptive traits or fitness in the natural environment. We also performed a population genomics study, using next generation sequencing to genotype tens of thousands of single nucleotide polymorphism (SNP) across the genome. Interestingly, a chromosomal inversion that previously showed to be locally adaptive also harbors more highly diverged loci than other places in the genome, consistent with other studies that inversion may play an important role in speciation. During this award we investigated how environmental adaptation may contribute to speciation. We also developed novel statistical methods to identify genomic regions controlling biological traits. These methods may be useful in the field of agricultural studies. This award has resulted in more than a dozen research articles published in high-profile academic journals and several presentations in international meetings.