Foxtail millet is an important crop in Northwest China; however, the mechanism responsible for regulating root adjustment, including water uptake, sugar transport, or metabolism, in foxtail millet remains unclear. Two millet cultivars (the drought-resistant Yugu1 [YG] and the drought-sensitive An04 [An]) were used to detect physiological, molecular, and agronomic traits under two different soil water conditions. Water use efficiency increased by 18.4% and 63.2% under drought stress in An and YG, respectively. Under drought stress, YG and An root exudation (RE) decreased by 66.7% and 89.0%, the photosynthesis rate decreased by 34.3% and 61.8%, and the grain yield decreased by 40.6% and 62.6%, respectively. An contained a high ratio of soluble sugar to starch, whereas YG remained consistent. RNA-seq data showed a lower expression of beta-amylase 2 in YG than in An. The expression levels of three SWEET genes involved in sugar transport and four plasma membrane intrinsic protein (PIP) genes were higher in YG than in An, allocating more photosynthetic sugar to the roots to prevent a significant elevation in the ratio of soluble sugar to starch. The high expression levels of SiPIPs also enhanced root water transport capacity. Based on the above-mentioned adaptations, millet maintains high RE, stomatal conductance, and net photosynthetic rate in drought stress conditions.

As an indispensable grain crop, foxtail millet (Setaria italica L.) is becoming a functional food in China because of its abundant nutrients. However, low rainfall and uneven precipitation limit its growth and production, especially in northwest China. Understanding the root phenotypic characteristics of foxtail millet is critical for utilizing its root characteristics to breed new millet varieties with improved resource-use efficiency and better adaptation to harsh environments. The present study characterized the variability of the root morphological traits at the seedling stage of 65 millet genotypes selected from four ecological regions across seven provinces in China. The plants were assessed after 21 days of growth in the germination pouches, and 48 root and shoot traits were measured. The results showed a large variation among the genotypes in the growth and functional traits. Among the measured traits, root dry mass, maximal root length, root surface area, and root tissue density contributed the most to the principal components. Root surface area ratio and root volume ratio were significantly correlated with root length ratio, respectively, while root length density and root weight density were negatively correlated with root diameter (p < 0.01). Shoot dry mass, root number, root length, root dry mass, and total dry mass were closely correlated with each other. Root length and root surface area in each 5-cm sections decreased from the top to the bottom along the root system. Among the four ecological regions, genotypes from the early maturing area of northwest China had the greatest root length, shoot dry mass, root dry mass, and root density, while those from the early maturing area of northwest China generally had the largest root system, with about 2.2 times more root length and dry weight than those from the early maturing area of northeast China (the shortest root system). The genotypic variability in root traits and correlations among shoot and root traits form a basis for breeding new millet cultivars.