title: Genome-wide identification, characterization and expression profiling of LIM family genes in Solanum lycopersicum L.
abstract: LIM domain proteins, some of which have been shown to be actin binding proteins, are involved in various developmental activities and cellular processes in plants. To date, the molecular defense-related functions of LIM family genes have not been investigated in any solanaceous vegetable crop species. In this study, we identified 15 LIM family genes in tomato (Solanum lycopersicum L.) through genome-wide analysis and performed expression profiling in different organs of tomato, including fruits at six different developmental stages. We also performed expression profiling of selected tomato LIM genes in plants under ABA, drought, cold, NaCl and heat stress treatment. The encoded proteins of the 15 tomato LIM genes were classified into two main groups, i.e., proteins similar to cysteine-rich proteins and plant-specific DAR proteins, based on differences in functional domains and variability in their C-terminal regions. The DAR proteins contain a so far poorly characterized zinc-finger-like motif that we propose to call DAR-ZF. Six of the 15 LIM genes were expressed only in flowers, indicating that they play flower-specific roles in plants. The other nine genes were expressed in all organs and at various stages of fruit development. SlβLIM1b was expressed relatively highly at the later stage of fruit development, but three other genes, SlWLIM2a, SlDAR2 and SlDAR4, were expressed at the early stage of fruit development. Seven genes were induced by ABA, five by cold, seven by drought, eight by NaCl and seven by heat treatment respectively, indicating their possible roles in abiotic stress tolerance. Our results will be useful for functional analysis of LIM genes during fruit development in tomato plants under different abiotic stresses.
authors.affiliation: Department of Agricultural Industry Economy and Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea. Electronic address: kkr@pstu.ac.bd.
authors.forename: Khadiza
authors.initials: K
authors.lastname: Khatun
authors.affiliation: Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea. Electronic address: gpb21bau@bau.edu.bd.
authors.forename: Arif Hasan Khan
authors.initials: AHK
authors.lastname: Robin
authors.affiliation: Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea. Electronic address: jipark@sunchon.ac.kr.
authors.forename: Jong-In
authors.initials: JI
authors.lastname: Park
authors.affiliation: Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali, Bangladesh. Electronic address: nasargpb@yahoo.com.
authors.forename: Nasar Uddin
authors.initials: NU
authors.lastname: Ahmed
authors.affiliation: Department of Horticultural Science, Kyungpook National University, Daegu, 702-701, Republic of Korea. Electronic address: ckkim@knu.ac.kr.
authors.forename: Chang Kil
authors.initials: CK
authors.lastname: Kim
authors.affiliation: Department of Horticultural Science, Kyungpook National University, Daegu, 702-701, Republic of Korea. Electronic address: kblim@knu.ac.kr.
authors.forename: Ki-Byung
authors.initials: KB
authors.lastname: Lim
authors.affiliation: Department of Agricultural Industry Economy and Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea; Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea. Electronic address: salt@sunchon.ac.kr.
authors.forename: Min-Bae
authors.initials: MB
authors.lastname: Kim
authors.affiliation: Department of Agricultural Industry Economy and Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea; Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea. Electronic address: djlee@sunchon.ac.kr.
authors.forename: Do-Jin
authors.initials: DJ
authors.lastname: Lee
authors.affiliation: Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea. Electronic address: nis@sunchon.ac.kr.
authors.forename: Ill Sup
authors.initials: IS
authors.lastname: Nou
authors.affiliation: Department of Agricultural Industry Economy and Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea; Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea. Electronic address: queen@sunchon.ac.kr.
authors.forename: Mi-Young
authors.initials: MY
authors.lastname: Chung
mesh_terms: D032461:Chromosomes, Plant; D035264:Flowers / Q000235:genetics; D005638:Fruit / Q000235:genetics / Q000254:growth & development; D020440:Gene Duplication; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D018551:Solanum lycopersicum / Q000235:genetics*; D005810:Multigene Family; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D013312:Stress, Physiological / Q000235:genetics
chemical_list: D010940:Plant Proteins
keywords: Abiotic stress; Expression profiling; Fruit development; LIM genes; Solanum lycopersicum