title: Evolution of DUF1313 family members across plant species and their association with maize photoperiod sensitivity.
abstract: Proteins of the DUF1313 family contain a highly conserved domain and are only found in plants; they play important roles in most plant functions. In this study, 269 DUF1313 genes from 81 photoautotrophic species were identified; they were classified into three major types based on the amino acid substitutions in the conserved region: IARV, I(S/T/F)(K/R)V, and IRRV. Phylogenic tree constructed from 51 DUF1313 genes from graminoids revealed three clades: A, B1, and B2. Clade B1 was found to have undergone episodic positive selection after a gene duplication event and included four amino acid sites under positive selection. The association between DUF1313 family members and traits investigated in maize indicated that three of four genes (GRMZM2G025646, GRMZM5G877647, GRMZM2G359322, and GRMZM2G382774) were associated with the target traits such as days to silking, days to tasselling, and plant height. The nucleotide diversity of the most primitive and highly conserved DUF1313 gene, ELF4-like4, was the highest in Tripsacum and the lowest in maize. Tajima's D and Fu and Li's D tests revealed that significant purifying selection had occurred in the coding sequence region of this DUF1313 gene in teosinte and maize. No significant signal was detected in the 5'-untranslated region of this gene in each of the three species (maize, teosinte, and Tripsacum) or in any gene regions of Tripsacum. Phylogenetic analyses revealed that the 103 accessions of maize, teosinte, and Tripsacum can be grouped into four clades based on the ELF4-like4 gene sequence similarity. Thus, this gene can be used to determine the relationships between maize and its relatives, and the DUF1313 family members and alleles identified in this study might be valuable genetic resources for molecular marker-assisted breeding in maize.
authors.affiliation: Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China.
authors.forename: Jia
authors.initials: J
authors.lastname: Li
authors.affiliation: Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China.
authors.forename: Erliang
authors.initials: E
authors.lastname: Hu
authors.affiliation: Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China.
authors.forename: Xueying
authors.initials: X
authors.lastname: Chen
authors.affiliation: Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Xu
authors.affiliation: Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China.
authors.forename: Hai
authors.initials: H
authors.lastname: Lan
authors.affiliation: Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China.
authors.forename: Chuan
authors.initials: C
authors.lastname: Li
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
authors.forename: Yaodong
authors.initials: Y
authors.lastname: Hu
authors.affiliation: Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China. Electronic address: yanli.lu82@hotmail.com.
authors.forename: Yanli
authors.initials: Y
authors.lastname: Lu
mesh_terms: D001947:Breeding; D019143:Evolution, Molecular; D020440:Gene Duplication; D018506:Gene Expression Regulation, Plant; D014644:Genetic Variation; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics; D017440:Photoperiod; D010802:Phylogeny; D010940:Plant Proteins / Q000096:biosynthesis* / Q000235:genetics; D012641:Selection, Genetic; D003313:Zea mays / Q000235:genetics
chemical_list: D010940:Plant Proteins
keywords: Association analysis; DUF1313 family; Maize; Phylogenetic analysis; Selection pressure