The multi-allelic APRR2 Gene is associated with fruit pigment accumulation in melon and watermelon

Authors: OREN, ELAD - Israel Agricultural Research Organization (ARO); TZURI, GALIL - Israel Agricultural Research Organization (ARO); VEXLER, LEA 3 - Israel Agricultural Research Organization (ARO); DAFNA, ASAF - Israel Agricultural Research Organization (ARO); MEIR, AYALA - Israel Agricultural Research Organization (ARO); FAIGENBOIM, ADI - Israel Agricultural Research Organization (ARO); KENIGSWALD, MERAV - Israel Agricultural Research Organization (ARO); PORTNOY, VITALY - Israel Agricultural Research Organization (ARO); SCHAFFER, ARTHUR - Israel Agricultural Research Organization (ARO); Levi, Amnon; Buckler, Edward - Ed; KATZIR, NURIT - Israel Agricultural Research Organization (ARO); BURGER, JOSEPH - Israel Agricultural Research Organization (ARO); TADMOR, YAAKOV - Israel Agricultural Research Organization (ARO); GUR, AMIT - Israel Agricultural Research Organization (ARO)

Submitted to: Journal of Experimental Botany
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/11/2019
Publication Date: 4/24/2019
Citation: Oren, E., Tzuri, G., Vexler, L., Dafna, A., Meir, A., Faigenboim, A., Kenigswald, M., Portnoy, V., Schaffer, A.A., Levi, A., Buckler IV, E.S., Katzir, N., Burger, J., Tadmor, Y., Gur, A. 2019. The multi-allelic APRR2 Gene is associated with fruit pigment accumulation in melon and watermelon. Journal of Experimental Botany. https://doi.org/10.1093/jxb/erz182.
DOI: https://doi.org/10.1093/jxb/erz182

Interpretive Summary: Carotenoids are important vitamins and antioxidant molecules valuable in lowering the risk of cardiovascular diseases and cancer. Consumers have strong interest in melon and watermelon varieties rich in carotenoids. To date, there is limited knowledge with respect to genes controlling carotenoid production in melon and watermelon. In this study, Agricultural Research Service scientists at the U.S. Vegetable Laboratory, Charleston, South Carolina, and Cornell University collaborated with scientists at the Agricultural Research Organization (ARO) in Israel on using genomic technologies combined with genetic approaches to genetically map genes associated with carotenoid production in melon and watermelon. Through the collaborative study they identified a gene named “APRR2” which plays an important role in enhancing carotenoid production. The genetic and genomic information developed in this study should be useful for University researchers and seed company breeders aiming to enrich melon and watermelon with carotenoids and thus increase the nutritional value of these important cucurbit crops.

Technical Abstract: Color and pigment content are important aspects of fruit quality and consumer acceptance of cucurbit crops. Here, we describe the independent mapping and cloning of a common causative APRR2 gene regulating pigment accumulation in melon and watermelon. We initially show that the APRR2 transcription factor is causative for the qualitative difference between dark and light green rind in both crops. Further analyses establish the link between sequence or expression level variations in the CmAPRR2 gene and pigments content in the rind and flesh of mature melon fruits. Genome wide association (GWAS) of young fruit rind color in a panel composed of 177 diverse melon accessions did not result in any significant association, leading to an earlier assumption that multiple genes are involved in shaping the overall phenotypic variation at this trait. Through resequencing of 25 representative accessions and allelism tests between light rind accessions, we show that multiple independent Single nuclear polymorphisms (SNPs) in the CmAPRR2 gene are causative for the light rind phenotype. The multi-haplotypic nature of this gene explain the lack of detection power obtained through GBS-based GWAS and confirm the pivotal role of this gene in shaping fruit color variation in melon. This study demonstrates the power of combining bi- and multi-allelic designs with deep sequencing, to resolve lack of power due to high haplotypic diversity and low allele frequencies. Due to its central role and broad effect on pigment accumulation in fruits, the APRR2 gene is an attractive target for carotenoids bio-fortification of cucurbit crops.