Author:
Bohry Dieimes,Ramos Helaine Christine Cancela,dos Santos Pedro Henrique Dias,Boechat Marcela Santana Bastos,Arêdes Fernanda Abreu Santana,Pirovani Adriana Azevedo Vimercati,Pereira Messias Gonzaga
Abstract
AbstractPapaya is a tropical and climacteric fruit that is recognized for its nutritional benefits and medicinal applications. Its fruits ripen quickly and show a drastic fruit softening, leading to great post-harvest losses. To overcome this scenario, breeding programs of papaya must invest in exploring the available genetic variation to continue developing superior cultivars with improved fruit quality traits. The objective of this study was to perform a whole-genome genotyping (WGG) of papaya, predict the effects of the identified variants, and develop a list of ripening-related genes (RRGs) with linked variants. The Formosa elite lines of papaya Sekati and JS-12 were submitted to WGG with an Illumina Miseq platform. The effects of variants were predicted using the snpEff program. A total of 28,451 SNPs having Ts/Tv (Transition/Transversion) ratio of 2.45 and 1,982 small insertions/deletions (InDels) were identified. Most variant effects were predicted in non-coding regions, with only 2,104 and 138 effects placed in exons and splice site regions, respectively. A total of 106 RRGs were found to be associated with 460 variants, which may be converted into PCR markers to facilitate genetic mapping and diversity studies and to apply marker-assisted selection (MAS) for specific traits in papaya breeding programs.
Funder
Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
Publisher
Springer Science and Business Media LLC
Reference49 articles.
1. FAOSTAT. Food and Agriculture Organization of the United Nations (2020). http://www.fao.org/faostat/en/#data/QC/visualize. Accessed 13 April 2020.
2. Chandrika, U. G., Jansz, E. R., Wickramasinghe, S. M. D. N. & Warnasuriya, N. D. Carotenoids in yellow- and red-fleshed papaya (Carica papaya L.). J. Sci. Food Agric. 83, 1279–1282 (2003).
3. De Souza, L. M., Ferreira, K. S., Chaves, J. B. P. & Teixeira, S. L. L-ascorbic acid, B-carotene and lycopene content in papaya fruits (Carica papaya) with or without physiological skin freckles. Sci. Agric. 65, 246–250 (2008).
4. Lee, C. Y. et al. The development of functional mapping by three sex-related loci on the third whorl of different sex types of Carica papaya L.. PLoS ONE 13, 1–21 (2018).
5. Liao, Z., Yu, Q. & Ming, R. Development of male-specific markers and identification of sex reversal mutants in papaya. Euphytica 213, 1–12 (2017).