Fine Mapping and Candidate Gene Prediction of Tuber Shape Controlling Ro Locus Based on Integrating Genetic and Transcriptomic Analyses in Potato

Tuber shape is one of the most important quality traits in potato appearance. Since poor or irregular shape results in higher costs for processing and influences the consumers’ willingness to purchase, breeding for shape uniformity and shallow eye depth is highly important. Previous studies showed t...

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Autores principales: Fan, Guiyan, Wang, Qianru, Xu, Jianfei, Chen, Na, Zhu, Wenwen, Duan, Shaoguang, Yang, Xiaohui, De Jong, Walter S., Guo, Yangdong, Jin, Liping, Li, Guangcun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
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Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8836246/
https://www.ncbi.nlm.nih.gov/pubmed/35163389
http://dx.doi.org/10.3390/ijms23031470
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author Fan, Guiyan
Wang, Qianru
Xu, Jianfei
Chen, Na
Zhu, Wenwen
Duan, Shaoguang
Yang, Xiaohui
De Jong, Walter S.
Guo, Yangdong
Jin, Liping
Li, Guangcun
author_facet Fan, Guiyan
Wang, Qianru
Xu, Jianfei
Chen, Na
Zhu, Wenwen
Duan, Shaoguang
Yang, Xiaohui
De Jong, Walter S.
Guo, Yangdong
Jin, Liping
Li, Guangcun
author_sort Fan, Guiyan
collection PubMed
description Tuber shape is one of the most important quality traits in potato appearance. Since poor or irregular shape results in higher costs for processing and influences the consumers’ willingness to purchase, breeding for shape uniformity and shallow eye depth is highly important. Previous studies showed that the major round tuber shape controlling locus, the Ro locus, is located on chromosome 10. However, fine mapping and cloning of tuber shape genes have not been reported. In this study, the analyses of tissue sectioning and transcriptome sequencing showed that the developmental differences between round and elongated tuber shapes begin as early as the hook stage of the stolon. To fine map tuber shape genes, a high-density genetic linkage map of the Ro region on chromosome 10 based on a diploid segregating population was constructed. The total length of the genetic linkage map was 25.8 cM and the average marker interval was 1.98 cM. Combined with phenotypic data collected from 2014 to 2017, one major quantitative trait locus (QTL) for tuber shape was identified, which explained 61.7–72.9% of the tuber shape variation. Through the results of genotyping and phenotypic investigation of recombinant individuals, Ro was fine mapped in a 193.43 kb interval, which contained 18 genes. Five candidate genes were preliminarily predicted based on tissue sections and transcriptome sequencing. This study provides an important basis for cloning Ro gene(s).
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spelling pubmed-88362462022-02-12 Fine Mapping and Candidate Gene Prediction of Tuber Shape Controlling Ro Locus Based on Integrating Genetic and Transcriptomic Analyses in Potato Fan, Guiyan Wang, Qianru Xu, Jianfei Chen, Na Zhu, Wenwen Duan, Shaoguang Yang, Xiaohui De Jong, Walter S. Guo, Yangdong Jin, Liping Li, Guangcun Int J Mol Sci Article Tuber shape is one of the most important quality traits in potato appearance. Since poor or irregular shape results in higher costs for processing and influences the consumers’ willingness to purchase, breeding for shape uniformity and shallow eye depth is highly important. Previous studies showed that the major round tuber shape controlling locus, the Ro locus, is located on chromosome 10. However, fine mapping and cloning of tuber shape genes have not been reported. In this study, the analyses of tissue sectioning and transcriptome sequencing showed that the developmental differences between round and elongated tuber shapes begin as early as the hook stage of the stolon. To fine map tuber shape genes, a high-density genetic linkage map of the Ro region on chromosome 10 based on a diploid segregating population was constructed. The total length of the genetic linkage map was 25.8 cM and the average marker interval was 1.98 cM. Combined with phenotypic data collected from 2014 to 2017, one major quantitative trait locus (QTL) for tuber shape was identified, which explained 61.7–72.9% of the tuber shape variation. Through the results of genotyping and phenotypic investigation of recombinant individuals, Ro was fine mapped in a 193.43 kb interval, which contained 18 genes. Five candidate genes were preliminarily predicted based on tissue sections and transcriptome sequencing. This study provides an important basis for cloning Ro gene(s). MDPI 2022-01-27 /pmc/articles/PMC8836246/ /pubmed/35163389 http://dx.doi.org/10.3390/ijms23031470 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Fan, Guiyan
Wang, Qianru
Xu, Jianfei
Chen, Na
Zhu, Wenwen
Duan, Shaoguang
Yang, Xiaohui
De Jong, Walter S.
Guo, Yangdong
Jin, Liping
Li, Guangcun
Fine Mapping and Candidate Gene Prediction of Tuber Shape Controlling Ro Locus Based on Integrating Genetic and Transcriptomic Analyses in Potato
title Fine Mapping and Candidate Gene Prediction of Tuber Shape Controlling Ro Locus Based on Integrating Genetic and Transcriptomic Analyses in Potato
title_full Fine Mapping and Candidate Gene Prediction of Tuber Shape Controlling Ro Locus Based on Integrating Genetic and Transcriptomic Analyses in Potato
title_fullStr Fine Mapping and Candidate Gene Prediction of Tuber Shape Controlling Ro Locus Based on Integrating Genetic and Transcriptomic Analyses in Potato
title_full_unstemmed Fine Mapping and Candidate Gene Prediction of Tuber Shape Controlling Ro Locus Based on Integrating Genetic and Transcriptomic Analyses in Potato
title_short Fine Mapping and Candidate Gene Prediction of Tuber Shape Controlling Ro Locus Based on Integrating Genetic and Transcriptomic Analyses in Potato
title_sort fine mapping and candidate gene prediction of tuber shape controlling ro locus based on integrating genetic and transcriptomic analyses in potato
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8836246/
https://www.ncbi.nlm.nih.gov/pubmed/35163389
http://dx.doi.org/10.3390/ijms23031470
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