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An Early Season Perspective of Key Differentially Expressed Genes and Single Nucleotide Polymorphisms Involved in Sucrose Accumulation in Sugarcane

An Early Season Perspective of Key Differentially Expressed Genes and Single Nucleotide... Sucrose is the prime product of sugarcane and a significant variation has been observed among different sugarcane genotypes for the time taken to initiate sucrose accumulation. High sucrose accumulation in sugarcane at early crop phase is one of the most desirable traits, since it can help in reducing its long growth cycle. This study is based on a segregating population raised in sub-tropical India, where, sucrose accumulation starts at ~ 10-month crop stage. RNA-seq data of two extreme bulks from a segregating full-sib population and its parents were used to identify differential genes and single nucleotide polymorphisms (SNPs) associated with early season high sucrose accumulation. A total of 49 common significantly differential genes were identified between high- and low- sucrose parents and bulks among which chlorophyll a-b binding protein and psaK were observed as initial points of sucrose-mediated feedback regulation. The high sucrose accumulation during early season coincided with upregulation of transcription factors (TIFY10a and ERF), and genes related to arabinogalactans, glutaredoxin, ethylene and amino acid transporters as well as downregulation of genes for solute transport (PUP, STP) and hormones (ABA and IAA). Further, six of the identified early sucrose linked DEGs, viz., ethylene-responsive transcription factor 1 (AP 2), TIFY, YUCCA, Monosaccharide transporter 2, Photosystem I reaction center subunit psaK, and chlorophyll a-b binding protein were validated for similar patterns of differential expression in a panel of sugarcane genotypes comprising the two parents and three varieties each showing early season high and low sucrose accumulation. This study was further able to identify significantly differential SNPs located pre-dominantly on several transcription factors, receptor kinases, glucuronosyltransferase, callose synthase, microRNA biogenesis complex and phytohormone action. These preliminary results provide useful insights into the role of differential genes and allelic heterozygosity in early season sucrose accumulation in sugarcane. Further confirmation of the role of these genes in early sucrose accumulation is suggested and could assist in the production of early maturing sugarcane varieties. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Tropical Plant Biology Springer Journals

An Early Season Perspective of Key Differentially Expressed Genes and Single Nucleotide Polymorphisms Involved in Sucrose Accumulation in Sugarcane

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Publisher
Springer Journals
Copyright
Copyright © The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2022
ISSN
1935-9756
eISSN
1935-9764
DOI
10.1007/s12042-022-09311-z
Publisher site
See Article on Publisher Site

Abstract

Sucrose is the prime product of sugarcane and a significant variation has been observed among different sugarcane genotypes for the time taken to initiate sucrose accumulation. High sucrose accumulation in sugarcane at early crop phase is one of the most desirable traits, since it can help in reducing its long growth cycle. This study is based on a segregating population raised in sub-tropical India, where, sucrose accumulation starts at ~ 10-month crop stage. RNA-seq data of two extreme bulks from a segregating full-sib population and its parents were used to identify differential genes and single nucleotide polymorphisms (SNPs) associated with early season high sucrose accumulation. A total of 49 common significantly differential genes were identified between high- and low- sucrose parents and bulks among which chlorophyll a-b binding protein and psaK were observed as initial points of sucrose-mediated feedback regulation. The high sucrose accumulation during early season coincided with upregulation of transcription factors (TIFY10a and ERF), and genes related to arabinogalactans, glutaredoxin, ethylene and amino acid transporters as well as downregulation of genes for solute transport (PUP, STP) and hormones (ABA and IAA). Further, six of the identified early sucrose linked DEGs, viz., ethylene-responsive transcription factor 1 (AP 2), TIFY, YUCCA, Monosaccharide transporter 2, Photosystem I reaction center subunit psaK, and chlorophyll a-b binding protein were validated for similar patterns of differential expression in a panel of sugarcane genotypes comprising the two parents and three varieties each showing early season high and low sucrose accumulation. This study was further able to identify significantly differential SNPs located pre-dominantly on several transcription factors, receptor kinases, glucuronosyltransferase, callose synthase, microRNA biogenesis complex and phytohormone action. These preliminary results provide useful insights into the role of differential genes and allelic heterozygosity in early season sucrose accumulation in sugarcane. Further confirmation of the role of these genes in early sucrose accumulation is suggested and could assist in the production of early maturing sugarcane varieties.

Journal

Tropical Plant BiologySpringer Journals

Published: Jun 1, 2022

Keywords: Saccharum species hybrid; RNAseq; BSR-seq Early season sucrose

References