Genome-wide identification and evolution of the PIN-FORMED (PIN) gene family in Glycine max

• Published in: Genome Vol. 60; no. 7; pp. 564 - 571
• Main Authors: Liu, Yuan, Wei, Haichao
• Format: Journal Article
• Language: English
• Published: Canada NRC Research Press 01.07.2017; Canadian Science Publishing NRC Research Press
• Subjects: artificial selection; Biological evolution; Crops, Agricultural - genetics; Databases, Genetic; duplication des GmPIN; Evolution, Molecular; Evolutionary genetics; expression génique; expression pattern; famille de gènes GmPIN; Gene duplication; Gene expression; Gene Expression Regulation, Plant; Gene sequencing; Genes; Genes, Plant; Genetic aspects; Genome-wide association studies; Genomes; Glycine max; Glycine max - classification; Glycine max - genetics; Glycine max - metabolism; GmPIN duplication; GmPIN gene family; Indoleacetic Acids - metabolism; Morphology; Multigene Family; Mutation; Nucleotide sequence; Phylogeny; Plant morphology; Plants (botany); Proteins; Reproduction (copying); Seed coats; Selection, Genetic; soya sauvage et cultivé; Soybean; Soybeans; Studies; sélection artificielle; Transport; wild and cultivated soybean; expression pattern; GmPIN duplication; soya sauvage et cultivé; expression génique; wild and cultivated soybean; sélection artificielle; GmPIN gene family; famille de gènes GmPIN; artificial selection; duplication des GmPIN
• ISSN: 0831-2796; 1480-3321
• DOI: 10.1139/gen-2016-0141

Soybean (Glycine max) is one of the most important crop plants. Wild and cultivated soybean varieties have significant differences worth further investigation, such as plant morphology, seed size, and seed coat development; these characters may be related to auxin biology. The PIN gene family encodes essential transport proteins in cell-to-cell auxin transport, but little research on soybean PIN genes (GmPIN genes) has been done, especially with respect to the evolution and differences between wild and cultivated soybean. In this study, we retrieved 23 GmPIN genes from the latest updated G. max genome database; six GmPIN protein sequences were changed compared with the previous database. Based on the Plant Genome Duplication Database, 18 GmPIN genes have been involved in segment duplication. Three pairs of GmPIN genes arose after the second soybean genome duplication, and six occurred after the first genome duplication. The duplicated GmPIN genes retained similar expression patterns. All the duplicated GmPIN genes experienced purifying selection (K a /K s < 1) to prevent accumulation of non-synonymous mutations and thus remained more similar. In addition, we also focused on the artificial selection of the soybean PIN genes. Five artificially selected GmPIN genes were identified by comparing the genome sequence of 17 wild and 14 cultivated soybean varieties. Our research provides useful and comprehensive basic information for understanding GmPIN genes.