Domestication Reduces Plant Immune Receptor Gene Repertoires Across Lineages

Abstract

Plant domestication is sometimes associated with a reduction in the diversity of immune receptor genes, critical for pathogen recognition and defense. Yet, the extent and evolutionary forces driving this pattern remain unclear. Using a comparative genomics framework, we analyzed the immune receptor gene repertoires of 15 domesticated crop species and their wild relatives, representing nine plant families. We examined both cell surface pattern recognition receptors and intracellular nucleotide-binding leucine-rich repeat receptors. Our results show that five crops-grapes, mandarins, rice, barley, and yellow sarson-exhibited significantly reduced immune receptor gene repertoires compared to their wild counterparts; however, the overall rate of immune receptor gene loss reflected the background rate of gene loss. Despite this, there is a positive association between domestication duration and immune receptor gene loss. Together, these results suggest that domestication imposes a subtle, cumulative pressure, consistent with relaxed selection rather than a strong cost-of-resistance effect. This study provides insights into how domestication impacts plant immunity, with implications for future crop breeding strategies to enhance disease resistance.

Keywords: cost of resistance; crop evolution; evolutionary genomics; gene loss; plant immunity; relaxed selection.

Fig. 1.

a) Phylogenetic tree of crop species used in the study (see Materials and Methods). b) Proportional changes in each IRG classification between crops and their respective wild relatives. Significantly differing repertoires are marked by *. Proportional increases per IRG classification are marked by green circles and proportional decreases in red circles. c to f) Box plots linking the median to the interquartile range, with whiskers extending to the last points within 1.5 times the interquartile range showing the percentage of IRG orthogroup loss between c) all crops and wild relatives and d) crops with significantly reduced repertoires and their wild relatives. e) All crop IRG orthogroups compared to their own genome-wide (GW) orthogroups and f) crops with significantly reduced repertoires IRG orthogroups compared to their own genome-wide orthogroups. Box plots showing no significant differences are labeled with ns.

Fig. 2.

Results from bivariate a, b) and multivariate c) PGLS analysis showing each explanatory variable and their relationship to the percentage difference in IRG loss between crops and their respective wild relatives. The scientific and common species names of the crop species used in the study along with their abbreviations above each data point are as follows: B_o = broccoli/Brassica oleracea var. italica, B_r = yellow sarson/Brassica rapa var yellow sarson, C_l = watermelon/Citrullus lanatus subsp. vulgaris, C_r = mandarin/Citrus reticulata, F_e = buckwheat/Fagopyrum esculentum, H_v = barley/Hordeum vulgare subsp. vulgare, J_n = black walnut/Juglans nigra, S_b = sorghum/Sorghum bicolor, S_i = foxtail millet/Setaria italica, O_s = rice/Oryza sativa, Z_m = maize/Zea mays subsp. mays, P_p = peach/Prunus persica, S_l = tomato/Solanum lycopersicum, V_v = grape/Vitis vinifera subsp. vinifera, and S_t = potato/Solanum tuberosum.