Haplotype variations of sucrose phosphate synthase B gene among sugarcane accessions with different sucrose content.

Haplotypes Saccharum / genetics Sucrose Glucosyltransferases / genetics
Haplotype Sucrose Sucrose phosphate synthase B (SPSB) gene Sugarcane

Journal

BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258

Informations de publication

Date de publication:
25 Jan 2023
Historique:
received: 05 10 2022
accepted: 16 01 2023
entrez: 25 1 2023
pubmed: 26 1 2023
medline: 28 1 2023
Statut: epublish

Résumé

Sucrose phosphate synthase B (SPSB) gene encoding an important rate-limiting enzyme for sucrose synthesis in sugarcane is mainly expressed on leaves, where its alleles control sucrose synthesis. In this study, genetic variation of SPSB gene represented by different haplotypes in sugarcane was investigated in hybrid clones with high and low sugar content and various accessory species. A total of 39 haplotypes of SPSB gene with 2, 824 bp in size were identified from 18 sugarcane accessions. These haplotypes mainly distributed on Chr3B, Chr3C, and Chr3D according to the AP85-441 reference genome. Single nucleotide polymorphisms (SNPs) and insertion/deletion (InDels) were very dense (42 bp/sequence variation) including 44 transitional and 23 transversional SNPs among the 39 haplotypes. The sequence diversity related Hd, Eta, and Pi values were all lower in clones of high sucrose content (HS) than those in clones of low sucrose content (LS). The evolutionary network analysis showed that about half SPSB haplotypes (19 out of 39) were clustered into one group, including 6 (HAP4, HAP6, HAP7, HAP9, HAP17 and HAP20) haplotypes under positive selection in comparison to HAP26 identified in Badila (S. officinarum), an ancestry noble cane species and under purification selection (except HAP19 under neutral selection) in comparison to HAP18 identified from India1 (S. spontaneum), an ancestry species with low sugar content but high stress tolerance. The average number of haplotypes under positive selection in HS clones was twice as that in LS. Most of the SNPs and InDels sequence variation sites were positively correlated with sucrose and fiber content and negatively correlated with reducing sugar. A total of 39 haplotypes of SPSB gene were identified in this study. Haplotypes potentially associated with high sucrose synthesis efficiency were identified. The mutations of SPSB haplotypes in HS were favorable and tended to be selected and fixed. The results of this study are informative and beneficial to the molecular assisted breeding of sucrose synthesis in sugarcane in the future.

Sections du résumé

BACKGROUND BACKGROUND
Sucrose phosphate synthase B (SPSB) gene encoding an important rate-limiting enzyme for sucrose synthesis in sugarcane is mainly expressed on leaves, where its alleles control sucrose synthesis. In this study, genetic variation of SPSB gene represented by different haplotypes in sugarcane was investigated in hybrid clones with high and low sugar content and various accessory species.
RESULTS RESULTS
A total of 39 haplotypes of SPSB gene with 2, 824 bp in size were identified from 18 sugarcane accessions. These haplotypes mainly distributed on Chr3B, Chr3C, and Chr3D according to the AP85-441 reference genome. Single nucleotide polymorphisms (SNPs) and insertion/deletion (InDels) were very dense (42 bp/sequence variation) including 44 transitional and 23 transversional SNPs among the 39 haplotypes. The sequence diversity related Hd, Eta, and Pi values were all lower in clones of high sucrose content (HS) than those in clones of low sucrose content (LS). The evolutionary network analysis showed that about half SPSB haplotypes (19 out of 39) were clustered into one group, including 6 (HAP4, HAP6, HAP7, HAP9, HAP17 and HAP20) haplotypes under positive selection in comparison to HAP26 identified in Badila (S. officinarum), an ancestry noble cane species and under purification selection (except HAP19 under neutral selection) in comparison to HAP18 identified from India1 (S. spontaneum), an ancestry species with low sugar content but high stress tolerance. The average number of haplotypes under positive selection in HS clones was twice as that in LS. Most of the SNPs and InDels sequence variation sites were positively correlated with sucrose and fiber content and negatively correlated with reducing sugar.
CONCLUSIONS CONCLUSIONS
A total of 39 haplotypes of SPSB gene were identified in this study. Haplotypes potentially associated with high sucrose synthesis efficiency were identified. The mutations of SPSB haplotypes in HS were favorable and tended to be selected and fixed. The results of this study are informative and beneficial to the molecular assisted breeding of sucrose synthesis in sugarcane in the future.

Identifiants

DOI: 10.1186/s12864-023-09139-1 PMID: 36698074 PMC: PMC9875459
pubmed: 36698074
doi: 10.1186/s12864-023-09139-1
pii: 10.1186/s12864-023-09139-1
pmc: PMC9875459
doi:

Substances chimiques

sucrose-phosphate synthase EC 2.4.1.14
Sucrose 57-50-1
Glucosyltransferases EC 2.4.1.-

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

42

Subventions

Organisme : National Key Research and Development Program of China
ID : 2018YFD1000503
Organisme : NSFC
ID : 31760411
Organisme : Joint Special Project of Basic Agricultural Research of Yunnan Province
ID : 202101BD070001-025, 2017FG001-069
Organisme : The key research plan of Yunnan Province
ID : 202203AK140029

Informations de copyright

© 2023. The Author(s).

Références

BMC Genomics. 2017 Aug 9;18(1):594
pubmed: 28793856
BMC Genomics. 2016 Feb 01;17:88
pubmed: 26830680
Genome Biol Evol. 2017 Feb 1;9(2):266-278
pubmed: 28082603
DNA Cell Biol. 2004 May;23(5):311-24
pubmed: 15169610
Bioinformatics. 2009 Jun 1;25(11):1451-2
pubmed: 19346325
Funct Plant Biol. 2006 Jun;33(6):605-610
pubmed: 32689268
Proc Natl Acad Sci U S A. 2009 Aug 4;106(31):13118-23
pubmed: 19625620
BMC Genomics. 2013 May 10;14:314
pubmed: 23663250
Mol Biol Evol. 2013 Dec;30(12):2725-9
pubmed: 24132122
Cell Mol Life Sci. 2008 Apr;65(7-8):1176-85
pubmed: 18217203
Plant Physiol. 2017 Feb;173(2):1330-1341
pubmed: 27986867
Cell Res. 2017 Feb;27(2):226-240
pubmed: 27934869
J Comput Biol. 2000 Feb-Apr;7(1-2):203-14
pubmed: 10890397
Curr Opin Plant Biol. 2002 Apr;5(2):122-7
pubmed: 11856607
BMC Plant Biol. 2020 Sep 14;20(1):422
pubmed: 32928111
Nucleic Acids Res. 1994 Nov 11;22(22):4673-80
pubmed: 7984417
PLoS One. 2020 Jan 16;15(1):e0227716
pubmed: 31945094
BMC Plant Biol. 2019 Jun 28;19(1):285
pubmed: 31253103
Plant Physiol. 2011 Mar;155(3):1169-90
pubmed: 21205616
Plants (Basel). 2020 Feb 06;9(2):
pubmed: 32041093
Plant Cell Environ. 2006 Oct;29(10):1871-80
pubmed: 16930313
J Plant Physiol. 2007 Jul;164(7):923-33
pubmed: 16876912

Auteurs

Hongbo Liu (H)

Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan, 661699, China.
Agronomy Department, University of Florida, Gainesville, FL, 32610, USA.
Genetics Institute, Plant Molecular and Biology Program, University of Florida, Gainesville, FL, 32610, USA.
Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Guangxi, 530004, Kaiyuan, China.

Xiuqin Lin (X)

Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan, 661699, China.

Xujuan Li (X)

Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan, 661699, China.

Ziliang Luo (Z)

Agronomy Department, University of Florida, Gainesville, FL, 32610, USA.
Genetics Institute, Plant Molecular and Biology Program, University of Florida, Gainesville, FL, 32610, USA.

Xin Lu (X)

Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan, 661699, China.

Qian You (Q)

Agronomy Department, University of Florida, Gainesville, FL, 32610, USA.

Xiping Yang (X)

Agronomy Department, University of Florida, Gainesville, FL, 32610, USA.
Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Guangxi, 530004, Kaiyuan, China.

Chaohua Xu (C)

Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan, 661699, China.

Xinlong Liu (X)

Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan, 661699, China.

Jiayong Liu (J)

Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan, 661699, China.

Caiwen Wu (C)

Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan, 661699, China.

Jianping Wang (J)

Agronomy Department, University of Florida, Gainesville, FL, 32610, USA. wangjp@ufl.edu.
Genetics Institute, Plant Molecular and Biology Program, University of Florida, Gainesville, FL, 32610, USA. wangjp@ufl.edu.

Articles similaires

A meiotic driver hijacks an epigenetic reader to disrupt mitosis in noncarrier offspring.

Yu Hua, Jianxiu Zhang, Man-Yun Yang et al.
1.00
Schizosaccharomyces Meiosis Schizosaccharomyces pombe Proteins Mitosis Epigenesis, Genetic

Genetic analyses of Anisakis pegreffii (Nematoda: Anisakidae) from the East Asian finless porpoise Neophocaena asiaeorientalis sunameri (Cetacea: Phocoenidae) in Korean waters.

Sunmin Kim, Jong Yoon Jeon, Kyunglee Lee et al.
1.00
Animals Anisakis Genetic Variation Porpoises Anisakiasis

Genome-wide analysis of the Amorphophallus konjac AkCSLA gene family and its functional characterization in drought tolerance of transgenic arabidopsis.

Changxin Luo, Shicheng Luo, Zhe Chen et al.
1.00
Arabidopsis Amorphophallus Plants, Genetically Modified Phylogeny Droughts

Gliflozins, sucrose and flavonoids are allosteric activators of lecithin-cholesterol acyltransferase.

Akseli Niemelä, Laura Giorgi, Sirine Nouri et al.
1.00
Phosphatidylcholine-Sterol O-Acyltransferase Flavonoids Humans Allosteric Regulation Molecular Dynamics Simulation

Classifications MeSH

questionsmedicales.fr › Phénomènes génétiques › Génotype › Haplotypes › Haplotype variations of sucrose phosphate...
questionsmedicales.fr › Eucaryotes › Viridiplantae › Streptophyta › Embryophyta › Tracheobionta › Magnoliopsida › Poaceae › Saccharum › Haplotype variations of sucrose phosphate...
questionsmedicales.fr › Glucides › Sucres › Diholoside › Saccharose › Haplotype variations of sucrose phosphate...
questionsmedicales.fr › Enzymes et coenzymes › Enzymes › Transferases › Glycosyltransferase › Hexosyltransferases › Glucosyltransferases › Haplotype variations of sucrose phosphate...