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Abstract
Modern cultivated Citrus species and varieties result from interspecific hybridization between four ancestral taxa. Among them, Citrus maxima and Citrus reticulata, closely associated with the pummelo and mandarin horticultural groups, respectively, were particularly important as the progenitors of sour and sweet oranges (Citrus aurantium and Citrus sinensis), grapefruits (Citrus paradisi), and hybrid types resulting from modern breeding programs (tangors, tangelos, and orangelos). The differentiation between the four ancestral taxa and the phylogenomic structure of modern varieties widely drive the phenotypic diversity’s organization. In particular, strong phenotypic differences exist in the coloration and sweetness and represent important criteria for breeders. In this context, focusing on the genes of the sugar, carotenoid, and chlorophyll biosynthesis pathways, the aim of this work was to develop a set of diagnostic single-nucleotide polymorphism (SNP) markers to distinguish the ancestral haplotypes of C. maxima and C. reticulata and to provide information at the intraspecific diversity level (within C. reticulata or C. maxima). In silico analysis allowed the identification of 3,347 SNPs from selected genes. Among them, 1,024 were detected as potential differentiation markers between C. reticulata and C. maxima. A total of 115 SNPs were successfully developed using a competitive PCR technology. Their transferability among all Citrus species and the true citrus genera was very good, with only 0.87% of missing data. The ancestral alleles of the SNPs were identified, and we validated the usefulness of the developed markers for tracing the ancestral haplotype in large germplasm collections and sexually recombined progeny issued from the C. reticulata/C. maxima admixture gene pool. These markers will pave the way for targeted association studies based on ancestral haplotypes.
Highlights
Citrus is an important food crop worldwide, and its commercialization depends on two main markets: the fruitprocessing market and the fresh fruit market
Our work focuses on genes involved in specific metabolic pathways related to key traits of fruit quality: the carotenoid, sugar, and chlorophyll genes
Publicly available resequencing data of 10 modern varieties belonging to the C. reticulata/C. maxima gene pool were used to mine single-nucleotide polymorphism (SNP) and to infer haplotypic gene sequences for species and varieties having a parental relationship with clementine for which haplotypic data were available (Wu et al, 2014)
Summary
Citrus is an important food crop worldwide, and its commercialization depends on two main markets: the fruitprocessing market and the fresh fruit market. Brazil is the main orange producer at 17.3 million tons, followed by China, the European Union and the USA, at 7.2, 6.5, and 5.1 million tons, respectively (Usda, 2019). In parallel with the fruit juice industry, consumer demand for fresh citrus fruit has increased worldwide. Mandarins and other small citrus are highly consumed and exported from the Mediterranean region, while acid citrus (limes and lemons) and grapefruit reached record production in the last 2 years (2016–2018). In 2018, acid citrus production increased 5%, reaching 8.2 million tons, mainly from Mexico, Argentina, the European Union, and Turkey. Grapefruits showed significant increases in consumption and exports (3 and 8%, respectively), totaling 7 million tons/year due to crop investment in the USA and China (Usda, 2019)
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