Somatic variations in the meiosis-specific gene CrMER3 confer seedlessness in a citrus bud sport

Seedlessness is a most valuable trait in fruit crops for fresh consumption and processing. The mutations in essential meiosis genes are known to confer sterility and seed abortion in plants. However, defects in meiosis have rarely been reported in fruit crops. Here, we found meiosis defects caused sterility in a seedless citrus bud sport cultivar, with massive unpaired univalents during diakinesis, indicating a disruption in crossover formation. A non-functional CrMER3A^-103 bp allele with a 103-bp deletion in the gene body, together with the other non-functional CrMER3a allele with a T deletion in exon, were identified in the seedless cultivar. The CrMER3 protein was undetectable at meiotic prophase I in the seedless cultivar, and knock out of CrMER3 resulted in sterility in precocious Mini-citrus. Therefore, the natural variation in CrMER3 is responsible for sterility and seedlessness in this bud sport cultivar. The CrMER3a allele originated from the primitive wild mandarin and was passed to cultivated mandarins. A Kompetitive Allele-Specific PCR (KASP) marker was developed to identify citrus germplasm with CrMER3a allele and to screen potential sterile and seedless hybrids in citrus cross breeding. Uncovering the natural mutations responsible for meiosis defects in citrus enhances our understanding of mechanisms controlling seedlessness in fruit crops and facilitates breeding of seedless varieties.