Pinus balfouriana Raw sequence reads. Pinus balfouriana

Water availability is an important driver of the geographic distribution of many plant species, although its importance relative to other climatic variables varies across climate regimes and species. A common indirect measure of water-use efficiency (WUE) is the ratio of carbon isotopes (13C) fixed during photosynthesis, especially when analyzed in conjunction with a measure of leaf-level resource utilization (15N). Here, we test two hypotheses about the genetic architecture of WUE for foxtail pine (Pinus balfouriana Grev. & Balf.) using a novel mixture of double digest restriction site associated DNA sequencing, species distribution modeling, and quantitative genetics. First, we test the hypothesis that water availability is an important determinant of the geographical range of foxtail pine. Second, we test the hypothesis that variation in 13C and 15N is genetically based, differentiated between regional populations, and has genetic architectures that include loci of large effect. We show that precipitation-related variables structured the geographical range of foxtail pine, climate-based niches differed between regional populations, and 13C and 15N were heritable with moderate signals of differentiation between regional populations. A set of large-effect QTLs (n = 11 for 13C; n = 10 for 15N) underlying 13C and 15N variation, with little to no evidence of pleiotropy, was discovered using multiple-marker, half-sibling regression models. Our results represent a first approximation to the genetic architecture of these phenotypic traits, including documentation of several patterns consistent with 13C being a fitness-related trait affected by natural selection.