Gene prediction for leaf margin phenotype and fruit flesh color in pineapple (Ananas comosus) using haplotype-resolved genome sequencing.

Autor: Nashima K; College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, 252-0880, Japan., Shirasawa K; Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0813, Japan., Isobe S; Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0813, Japan., Urasaki N; Okinawa Prefectural Agricultural Research Center, Itoman, Okinawa, 901-0336, Japan., Tarora K; Okinawa Prefectural Agricultural Research Center, Itoman, Okinawa, 901-0336, Japan., Irei A; Okinawa Prefectural Agricultural Research Center, Itoman, Okinawa, 901-0336, Japan., Shoda M; Okinawa Prefectural Agricultural Research Center Nago Branch, Nago, Okinawa, 905-0012, Japan., Takeuchi M; Okinawa Prefectural Agricultural Research Center Nago Branch, Nago, Okinawa, 905-0012, Japan., Omine Y; Okinawa Prefectural Agricultural Research Center Nago Branch, Nago, Okinawa, 905-0012, Japan., Nishiba Y; Kyushu Okinawa Agricultural Research Center, NARO, Koshi, Kumamoto, 861-1192, Japan., Sugawara T; Kyushu Okinawa Agricultural Research Center, NARO, Koshi, Kumamoto, 861-1192, Japan., Kunihisa M; Institute of Fruit Tree and Tea Science, NARO, Tsukuba, Ibaraki, 305-0852, Japan., Nishitani C; Institute of Fruit Tree and Tea Science, NARO, Tsukuba, Ibaraki, 305-0852, Japan., Yamamoto T; Institute of Fruit Tree and Tea Science, NARO, Tsukuba, Ibaraki, 305-0852, Japan.
Jazyk: angličtina
Zdroj: The Plant journal : for cell and molecular biology [Plant J] 2022 May; Vol. 110 (3), pp. 720-734. Date of Electronic Publication: 2022 Mar 18.
DOI: 10.1111/tpj.15699
Abstrakt: Pineapple (Ananas comosus (L.) Merr.) is one of the most economically important tropical fruit species. The major aim of the breeding programs in several countries, including Japan, is quality improvement, mainly for the fresh market. ‘Yugafu’, a Japanese cultivar with distinctive pipe-type leaf margin phenotype and white flesh color, is popular for fresh consumption. Therefore, genome sequencing of ‘Yugafu’ is expected to assist pineapple breeding. Here, we developed a haplotype-resolved assembly for the heterozygous genome of ‘Yugafu’ using long-read sequencing technology and obtained a pair of 25 pseudomolecule sequences inherited from the parental accessions ‘Cream pineapple’ and ‘HI101’. The causative genes for leaf margin and fruit flesh color were identified. Fine mapping revealed a 162-kb region on CLG23 for the leaf margin phenotype. In this region, 20 kb of inverted repeat was specifically observed in the ‘Cream pineapple’ derived allele, and the WUSCHEL-related homeobox 3 (AcWOX3) gene was predicted as the key gene for leaf margin morphogenesis. Dominantly repressed AcWOX3 via RNAi was suggested to be the cause of the pipe-type leaf margin phenotype. Quantitative trait locus (QTL) analysis revealed that the terminal region of CLG08 contributed to white flesh and low carotenoid content. Carotenoid cleaved dioxygenase 4 (AcCCD4), a key gene for carotenoid degradation underlying this QTL, was predicted as the key gene for white flesh color through expression analysis. These findings could assist in modern pineapple breeding and facilitate marker-assisted selection for important traits.
(© 2022 Society for Experimental Biology and John Wiley & Sons Ltd.)
Databáze: MEDLINE
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