Genome-Wide Identification of Common Bean PvLTP Family Genes and Expression Profiling Analysis in Response to Drought Stress

Xue Dong; Huijun Zhu; Xiaopeng Hao; Yan Wang; Xiaolei Ma; Jiandong Zhao; Jianwu Chang

doi:10.3390/genes13122394

Genome-Wide Identification of Common Bean PvLTP Family Genes and Expression Profiling Analysis in Response to Drought Stress

Genes (Basel). 2022 Dec 16;13(12):2394. doi: 10.3390/genes13122394.

Authors

Xue Dong^{1

2

3

4}, Huijun Zhu⁵, Xiaopeng Hao^{1

2

3}, Yan Wang^{1

2

3}, Xiaolei Ma^{1

2

3}, Jiandong Zhao^{1

2

3}, Jianwu Chang^{1

2

3}

Affiliations

¹ Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan 030031, China.
² Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Taiyuan 030031, China.
³ Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Taiyuan 030031, China.
⁴ National Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, Taiyuan 030031, China.
⁵ College of Agriculture, Shanxi Agricultural University, Taiyuan 030031, China.

Abstract

Common bean is one of the most important legume crops for human consumption. Its yield is adversely affected by environmental stress. Plant non-specific lipid transfer proteins (nsLTPs) are essential for plant growth, development, and resistance to abiotic stress, such as salt, drought, and alkali. However, changes in nsLTP family genes responding to drought stress are less known. The PvLTP gene family in the common bean was identified by a comprehensive genome-wide analysis. Molecular weights, theoretical isoelectric points, phylogenetic tree, conserved motifs, gene structures, gene duplications, chromosome localization, and expression profiles were analyzed by SignalP 5.0, ExPASy, ClustalX 2.1, MEGA 7.0, NCBI-CDD, MEME, Weblogo, and TBtools 1.09876, respectively. Heatmap and qRT-PCR analyses were performed to validate the expression profiles of PvLTP genes in different organs. In addition, the expression patterns of nine PvLTP genes in common beans treated with drought stress were investigated by qRT-PCR. We obtained 58 putative PvLTP genes in the common bean genome via genome-wide analyses. Based on the diversity of the eight-cysteine motif (ECM), these genes were categorized into five types (I, II, IV, V, and VIII). The signal peptides of the PvLTP precursors were predicted to be from 16 to 42 amino acid residues. PvLTPs had a predicated theoretical isoelectric point of 3.94-10.34 and a molecular weight of 7.15-12.17 kDa. The phylogenetic analysis showed that PvLTPs were closer to AtLTPs than OsLTPs. Conserved motif and gene structure analyses indicated that PvLTPs were randomly distributed on all chromosomes except chromosome 9. In addition, 23 tandem duplicates of PvLTP genes were arranged in 10 gene clusters on chromosomes 1 and 2. The heatmap and qRT-PCR showed that PvLTP expression significantly varied in different tissues. Moreover, 9 PvLTP genes were up-regulated under drought treatment. Our results reveal that PvLTPs play potentially vital roles in plants and provide a comprehensive reference for studies on PvLTP genes and a theoretical basis for further analysis of regulatory mechanisms influencing drought tolerance in the common bean.

Keywords: common bean; drought stress; expression profile; lipid transfer protein; tandem duplicates.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Droughts
Genome-Wide Association Study
Humans
Multigene Family
Phaseolus* / genetics
Phaseolus* / metabolism
Phylogeny
Plant Proteins / metabolism
Plants / genetics

Substances

Plant Proteins

Grants and funding

This research was supported by the Shanxi Province Science Foundation for Youths (201901D211561), Shanxi Academy of Agricultural Science Doctoral Research Fund (YBSJJ2003), Research Program Sponsored by National Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding (in preparation) (202204010910001), China Agriculture Research System of MOF and MARA-Food Legumes (CARS-08), and the National Key Research and Development Program of China (2021YFD1600601).