Genome-Wide Characterization and Haplotypic Variation Analysis of the IDD Gene Family in Foxtail Millet (Setaria italica)

Author:

Wu Hongpo1,Zhang Renliang1,Diao Xianmin12

Affiliation:

1. Key Laboratory of Grain Crop Genetic Resources Evaluation and Utlization of Ministry of Agriculture and Rural Affairs and State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China

2. Zhongyuan Research Center, Chinese Academy of Agricultural Sciences, Xinxiang 453500, China

Abstract

The indeterminate domain proteins (IDD proteins) play essential roles in the growth and development of various plant tissues and organs across different developmental stages, but members of this gene family have not yet been characterized in foxtail millet (Setaria italica). To have a comprehensive understanding of the IDD gene family in foxtail millet, we performed a genome-wide characterization and haplotypic variation analysis of the IDD gene family in foxtail millet. In this study, sixteen IDD genes were identified across the reference genome of Yugu1, a foxtail millet cultivar. Phylogenetic analysis revealed that the Setaria italica IDD (SiIDD) proteins were clustered into four groups together with IDD proteins from Arabidopsis thaliana (dicot) and Oryza sativa (monocot). Conserved protein motif and gene structure analyses revealed that the closely clustered SiIDD genes were highly conserved within each subgroup. Furthermore, chromosomal location analysis showed that the SiIDD genes were unevenly distributed on nine chromosomes of foxtail millet and shared collinear relationships with IDD genes of other grass species. Transcriptional analysis revealed that the SiIDD genes differed greatly in their expression patterns, and paralogous genes shared similar expression patterns. In addition, superior haplotypes for two SiIDD genes (SiIDD8 and SiIDD14) were identified to correlate with traits of early heading date, and high thousand seed weight and molecular markers were designed for SiIDD8 and SiIDD14 to distinguish different haplotypes for breeding. Taken together, the results of this study provide useful information for further functional investigation of SiIDD genes, and the superior haplotypes of SiIDD8 and SiIDD14 will be particularly beneficial for improving heading date and yield of foxtail millet in breeding programs.

Funder

National Key Research and Development Program of China

National Natural Science Foundation of China

China Agricultural Research System

Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Technology Innovation Program of CAAS

Publisher

MDPI AG

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