Citrus and related genera, members of the Rutaceae family, are cultivated in over 145 countries within the monsoon region. In 2020, global citrus fruit production reached 158 million tons, highlighting its popularity due to its energizing scent, high vitamin C content, and health-promoting properties. However, the complex taxonomy of citrus, influenced by its unique reproduction methods, extensive cross-compatibility, and high frequency of bud mutations, complicates conventional breeding processes, which can take 3 to 8 years to complete due to the long juvenile stage.
Molecular breeding offers an effective strategy for improving scion and rootstock by enabling pre-selection from many individuals to discover and introduce precise genetic sequences that can impart desired attributes. Microsatellites, or Simple Sequence Repeats (SSRs), are widely used in genomic/genetic and molecular breeding studies due to their multi-allelic variation, excellent repeatability, co-dominant inheritance, and high-frequency polymorphism.
In a recent study published in the popular scientific journal Nature, researchers conducted a comprehensive genome-wide identification and validation of SSRs in Citrus sinensis and Citrus maxima. Due to their global importance, these species were chosen as model genotypes for citrus genomic research. Sweet orange (C. sinensis) is appreciated for its sweet taste, delicate aroma, ascorbic acid, and hesperidin. At the same time, Pummelo (C. maxima) is known for its large size and is a good source of vitamin C, iron, potassium, and calcium.
The researchers identified 1,08,833 and 1,29,321 perfect SSRs in C. sinensis and C. maxima, respectively, compared to 494,611 and 608,896 imperfect SSRs. The mononucleotide repeats were the most abundant in both citrus species. The genome-wide characterization and production of the first set of chromosome-specific highly polymorphic SSR markers in citrus were made possible by the chromosome-level assembly of these citrus species.
The study aimed to develop and validate SSRs in C. sinensis and C. maxima and to analyze the population structure and genetic variability of 181 citrus germplasms based on chromosome-wise highly variable SSR markers. The results could have significant utility for citriculture and molecular breeding, including cultivar identification, Genome-wide association studies (GWAS), and Marker Assisted Selection (MAS).