Mikeal L. Roose

Rapid advancements in technologies provide various tools to analyze fruit crop genomes to better understand genetic diversity and relationships and aid in breeding. Genome-wide single nucleotide polymorphism (SNP) genotyping arrays offer highly multiplexed assays at a relatively low cost per data point. We report the development and validation of 1.4M SNP Axiom® Citrus HD Genotyping Array (Citrus 15AX 1 and Citrus 15AX 2) and 58K SNP Axiom® Citrus Genotyping Arrays for Citrus and close relatives. SNPs represented were chosen from a citrus variant discovery panel consisting of 41 diverse whole-genome re-sequenced accessions of Citrus and close relatives, including eight progenitor citrus species. SNPs chosen mainly target putative genic regions of the genome and are accurately called in both Citrus and its closely related genera while providing good coverage of the nuclear and chloroplast genomes. Reproducibility of the arrays was nearly 100%, with a large majority of the SNPs classified as the most stringent class of markers, “PolyHighResolution” (PHR) polymorphisms. Concordance between SNP calls in sequence data and array data average 98%. Phylogenies generated with array data were similar to those with comparable sequence data and little affected by 3 to 5% genotyping error. Both arrays are publicly available.

This study utilized the Fourier-based method to analyze the morphology of over 4000 leaves from more than 190 accessions selected from the Givaudan Citrus Variety Collection at the University of California Riverside, one of the world’s most diverse collections of citrus and closely related genera. Our analysis revealed significant variations in leaf morphology among the major citrus species groups, and hybrid varieties produced through breeding exhibited intermediate leaf morphology compared to their parental citrus species. We found a positive correlation between leaf area in native citrus species and temperature in lower tropical latitudes, while negative/positive associations between aspect ratio and temperature/rainfall were also observed, respectively. These results suggest that citrus leaves may have evolved into larger but thinner leaves to increase their photosynthetic capacity per unit area while maintaining water balance by reducing water loss through transpiration. Our analysis also indicates that the existing biodiversity observed in citrus species can be attributed to their migrations across the foothills of the Himalayas, southward to the islands of Indonesia, and northward to the islands of Japan. Our study supports the hypothesis that citrus species have adapted to warm areas lacking extreme daily and nightly temperatures, where a large number of species of origin are found. Overall, this study presents a promising approach to investigate the morphological variation in citrus leaves, which could potentially aid in the selection and breeding of citrus cultivars with superior physiological traits and deepen our understanding of citrus diversity.