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Allelic variation in shrunken2 gene affecting kernel sweetness in exotic-and indigenous-maize inbreds
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 (...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Public Library of Science
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9498942/ https://www.ncbi.nlm.nih.gov/pubmed/36136965 http://dx.doi.org/10.1371/journal.pone.0274732 |
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author | Chhabra, Rashmi Muthusamy, Vignesh Baveja, Aanchal Katral, Ashvinkumar Mehta, Brijesh Zunjare, Rajkumar U. Hossain, Firoz |
author_facet | Chhabra, Rashmi Muthusamy, Vignesh Baveja, Aanchal Katral, Ashvinkumar Mehta, Brijesh Zunjare, Rajkumar U. Hossain, Firoz |
author_sort | Chhabra, Rashmi |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-9498942 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-94989422022-09-23 Allelic variation in shrunken2 gene affecting kernel sweetness in exotic-and indigenous-maize inbreds Chhabra, Rashmi Muthusamy, Vignesh Baveja, Aanchal Katral, Ashvinkumar Mehta, Brijesh Zunjare, Rajkumar U. Hossain, Firoz PLoS One Research Article 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. Public Library of Science 2022-09-22 /pmc/articles/PMC9498942/ /pubmed/36136965 http://dx.doi.org/10.1371/journal.pone.0274732 Text en © 2022 Chhabra et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Chhabra, Rashmi Muthusamy, Vignesh Baveja, Aanchal Katral, Ashvinkumar Mehta, Brijesh Zunjare, Rajkumar U. Hossain, Firoz Allelic variation in shrunken2 gene affecting kernel sweetness in exotic-and indigenous-maize inbreds |
title | Allelic variation in shrunken2 gene affecting kernel sweetness in exotic-and indigenous-maize inbreds |
title_full | Allelic variation in shrunken2 gene affecting kernel sweetness in exotic-and indigenous-maize inbreds |
title_fullStr | Allelic variation in shrunken2 gene affecting kernel sweetness in exotic-and indigenous-maize inbreds |
title_full_unstemmed | Allelic variation in shrunken2 gene affecting kernel sweetness in exotic-and indigenous-maize inbreds |
title_short | Allelic variation in shrunken2 gene affecting kernel sweetness in exotic-and indigenous-maize inbreds |
title_sort | allelic variation in shrunken2 gene affecting kernel sweetness in exotic-and indigenous-maize inbreds |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9498942/ https://www.ncbi.nlm.nih.gov/pubmed/36136965 http://dx.doi.org/10.1371/journal.pone.0274732 |
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