In a nutshell: pistachio genome and kernel development

Abstract

Introduction

Tree nuts are the most carbon-efficient protein source of any food (Poore & Nemecek, 2018). Pistachios are also rich in unsaturated fatty acids, antioxidants, and vitamins (Tsantili et al., 2011; Marvinney et al., 2014; Noguera-Artiaga et al., 2019; Polari et al., 2019; Mandalari et al., 2021; Derbyshire et al., 2023). Given that pistachio trees are highly resilient to abiotic stress, particularly drought and salinity, they are projected to be an important source of sustainable nutrition in the face of climate change over the next century (Moazzam Jazi et al., 2016), with global production of pistachios having more than doubled over the past two decades (Food and Agricultural Organization; https://www.fao.org/faostat/en/#search/pistachio; Fig. 1a).

Fig. 1

Open in figure viewerPowerPoint

Pistachio nut development is categorized into four distinct stages. (a) Comparison of United States (US) pistachio (Pistacia vera) production to the world in the past 60 years (Food and Agricultural Organization; https://www.fao.org/faostat/en/#search/pistachio). Pistachios (‘Kerman’) at Stage III on a tree (b) and a branch, (c) with nut and kernel anatomy. (d) Pistachio development (whole nut, halved nut, and kernel) assessed from April to September 2019 in California and categorized into four stages represented by calendar time and accumulated heat units expressed as growing degree days (GDD) in °C. Bar, 1 cm. The new stages were defined by assessing (e) whole nut and kernel area growth (mm²), (f) dry weight (g) of the whole nut and kernel, (g) color changes in the hull measured in the L*a*b* color space (L*, or lightness, a* or redness, and b* or yellowness), (h) texture changes in the hull, shell, and kernel (kg of Force), (i) fat content in the kernel (g 100 g⁻¹ dry weight), and (j) kernel color changes measured in the L*a*b* color space. (e–j) Lines show fitted linear and linear mixed polynomial models as a function of heat accumulation (GDD). Error bars indicate SD from the means. (e–j) The stages are represented in a bar with distinct colors below the x-axes. Stage I, light green; Stage II, green; Stage III, yellow; Stage IV, pink.

Pistachio (Pistacia vera, 2n = 30) belongs to the Anacardiaceae family, along with cashew and mango, and is the only species in the genus Pistacia grown for its edible fruit. Pistachio trees are dioecious and wind-pollinated. Although commonly known as nuts, pistachio fruits are botanically dehiscent drupes consisting of three main tissues: a leathery exo-mesocarp (hull), a stony endocarp (shell), and an edible seed (kernel; Fig. 1b,c). Pistachio nut growth has been previously divided into three stages: (1) growth of the hull and shell; (2) shell lignification; and (3) kernel growth (Lin et al., 1984; Polito & Pinney, 1999; Goldhamer & Beede, 2004; Ferguson et al., 2005; Zhang et al., 2021). These stages, defined by biometric parameters like nut and kernel size, have guided research and agronomic management in the past; yet, a complete physiological assessment of pistachio development from fruit-set to harvest is lacking.

Also, a better understanding of the molecular mechanisms behind the composition of pistachio kernels can provide a robust foundation for breeding novel pistachio varieties with higher nutritional value and advancing management strategies to boost yield, cut costs, and enhance quality. Such insights provide transferable knowledge that will benefit the development of other hard-shelled nut crops, such as almonds and walnuts.

Here, we present foundational genomic resources for and research into nut development that are critically needed to support the rising demand for pistachio production. We have generated the first chromosome-scale reference-quality genome and annotation of P. vera ‘Kerman’, the most important female cultivar in the United States, leveraging this resource (available at https://pistachiomics.sf.ucdavis.edu/) to address outstanding questions about the molecular genomics of pistachio nut development. We combined transcriptomic and physiological data to uncover pathways and regulators behind the kernel's protein accumulation and high unsaturated fat content. Altogether, this work yields a new model of nut development to significantly expand the knowledge of hard-shelled fruit biology, link key molecular processes with the nutritional profile of pistachios, and support growers in decisions like harvest timing and irrigation.