Genome-wide characterization and sequence polymorphism analyses of cysteine-rich poly comb-like protein in Glycine max

Tayyaba Nisar; Muhammad Hammad Nadeem Tahir; Shahid Iqbal; Muhammad Sajjad; Muhammad Azhar Nadeem; Ghulam Qanmber; Ayesha Baig; Zulqurnain Khan; Zhengyun Zhao; Zhide Geng; Shoaib Ur Rehman

doi:10.3389/fpls.2022.996265

Genome-wide characterization and sequence polymorphism analyses of cysteine-rich poly comb-like protein in Glycine max

Front Plant Sci. 2022 Sep 20:13:996265. doi: 10.3389/fpls.2022.996265. eCollection 2022.

Affiliations

¹ Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef (MNS) University of Agriculture, Multan, Pakistan.
² Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South (COMSATS) University Islamabad, Islamabad, Pakistan.
³ Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey.
⁴ State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, China.
⁵ Department of Biotechnology, Commission on Science and Technology for Sustainable Development in the South (COMSATS), University Islamabad, Abbottabad Campus, Abbottabad, Pakistan.
⁶ Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, China.

Abstract

Cysteine-rich poly comb-like protein (CPP) is a member of cysteine-rich transcription factors that regulates plant growth and development. In the present work, we characterized twelve CPP transcription factors encoding genes in soybean (Glycine max). Phylogenetic analyses classified CPP genes into six clades. Sequence logos analyses between G. max and G. soja amino acid residues exhibited high conservation. The presence of growth and stress-related cis-acting elements in the upstream regions of GmCPPs highlight their role in plant development and tolerance against abiotic stress. Ka/Ks levels showed that GmCPPs experienced limited selection pressure with limited functional divergence arising from segmental or whole genome duplication events. By using the PAN-genome of soybean, a single nucleotide polymorphism was identified in GmCPP-6. To perform high throughput genotyping, a kompetitive allele-specific PCR (KASP) marker was developed. Association analyses indicated that GmCPP-6-T allele of GmCPP-6 (in exon region) was associated with higher thousand seed weight under both water regimes (well-water and water-limited). Taken together, these results provide vital information to further decipher the biological functions of CPP genes in soybean molecular breeding.

Keywords: GmCPP; association analyses; drought; kompetitive allele specific PCR; phylogenetic analyses; soybean.