Allelic variation in shrunken2 gene affecting kernel sweetness in exotic-and indigenous-maize inbreds

Rashmi Chhabra; Vignesh Muthusamy; Aanchal Baveja; Ashvinkumar Katral; Brijesh Mehta; Rajkumar U Zunjare; Firoz Hossain

doi:10.1371/journal.pone.0274732

Allelic variation in shrunken2 gene affecting kernel sweetness in exotic-and indigenous-maize inbreds

PLoS One. 2022 Sep 22;17(9):e0274732. doi: 10.1371/journal.pone.0274732. eCollection 2022.

Authors

Rashmi Chhabra¹, Vignesh Muthusamy¹, Aanchal Baveja¹, Ashvinkumar Katral¹, Brijesh Mehta², Rajkumar U Zunjare¹, Firoz Hossain¹

Affiliations

¹ ICAR-Indian Agricultural Research Institute, New Delhi, India.
² ICAR-Indian Grassland and Fodder Research Institute, Jhansi, India.

Abstract

Sweet corn has become a popular food worldwide. It possesses six-times more sugar than field corn due to the presence of recessive shrunken2 (sh2) gene. Despite availability of diverse sweet corn germplasm, comprehensive characterization of sh2 has not been undertaken so far. Here, entire Sh2 gene (7320 bp) among five field corn-(Sh2Sh2) and six sweet corn-(sh2sh2) inbreds was sequenced. A total of 686 SNPs and 372 InDels were identified, of which three SNPs differentiated the wild-(Sh2) and mutant-(sh2) allele. Ten InDel markers were developed to assess sh2 gene-based diversity among 23 sweet corn and 25 field corn lines. Twenty-five alleles and 47 haplotypes of sh2 were identified among 48 inbreds. Among markers, MGU-InDel-2, MGU-InDel-3, MGU-InDel-5 and MGU-InDel-8 had PIC>0.5. Major allele frequency varied from 0.458-0.958. The gene sequence of these maize inbreds was compared with 25 orthologues of monocots. Sh2 gene possessed 15-18 exons with 6-225bp among maize, while it was 6-21 exons with 30-441bp among orthologues. While intron length across maize genotypes varied between 67-2069bp, the same among orthologues was 57-2713 bp. Sh2-encoded AGPase domain was more conserved than NTP transferase domain. Nucleotide and protein sequences of sh2 in maize and orthologues revealed that rice orthologue was closer to maize than other monocots. The study also provided details of motifs and domains present in sh2 gene, physicochemical properties and secondary structure of SH2 protein in maize inbreds and orthologues. This study reports detailed characterization and diversity analysis in sh2 gene of maize and related orthologues in various monocots.

Publication types

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

MeSH terms

Alleles
Nucleotides
Sugars*
Transferases / genetics
Zea mays* / genetics

Substances

Nucleotides
Sugars
Transferases

Grants and funding

RC acknowledges financial support from ‘Women Scientist-A Scheme’ (File No. WOS-A/LS-306/2018), Department of Science and Technology, Govt. of India, and ‘Young Scientists' Scheme’ [Sanction No. YSS/2015/001029], Science and Engineering Research Board (SERB). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.