QTL mapping of tree leaf shape in high and low altitude in the Qinghai-Tibetan plateau. Identification of quantitative trait loci for altitude adaptation for tree leaf shape in the Qinghai-Tibetan plateau

As an important functional organ of plants, leaves alter their shapes in response to a changing environment. The variation of leaf shape has long been an important evolutionary and developmental force in plants. Despite an increasing amount of investigations into the genetic controls of leaf morphology, few have systematically studied the genetic architecture controlling shape differences among distinct altitudes. Altitude denotes a comprehensive complex of environmental factors affecting plant growth in many aspects, e.g., UV-light radiation, temperature, and humidity. To reveal how genes affect leaf shape variations at low and high altitudes, we used Populus szechuanica var. tibetica growing on the Qinghai-Tibetan plateau. Usage of the Elliptic Fourier-based morphometric model allowed dissection of the pleiotropic expression of quantitative trait loci (QTL)-mediating altitude-derived leaf shape variation. For high and low altitudes, 122 and 155 significant single-nucleotide polymorphisms (SNPs) were identified. QTLs that affected leaf axis length and leaf width were expressed in high-altitude populations, while QTLs regulating “leaf tip” and “leaf base” were expressed in low-altitude populations. Pkinase, PRR2, and LETM1 were common significant genes in both types of populations. Auxin-related and differentiation-related genes included PIN1, CDK-like, and CAK1AT at high altitude, whereas they included NAP5, PIN-LIKES, and SCL1 at low altitude. The presence of stress-antifung genes in high-altitude populations suggested an interaction between genes and harsh environment in mediating leaf shape, while the senescence repression-related genes (EIN2 and JMJ18) in low-altitude populations suggested crucial roles in ecological adaptability. These data provide new information that strengthens the understanding of genetic control with respect to leaf shape and constitute an entirely novel perspective regarding leaf adaptation and development in plants.