The wild sweetpotato (Ipomoea trifida) genome provides insights into storage root development

Ming Li, Songtao Yang, Wei Xu, Zhigang Pu, Junyan Feng, Zhangying Wang, Cong Zhang, Meifang Peng, Chunguang Du, Feng Lin, Changhe Wei, Shuai Qiao, Hongda Zou, Lei Zhang, Yan Li, Huan Yang, Anzhong Liao, Wei Song, Zhongren Zhang, Ji Li & 5 others Kai Wang, Yizheng Zhang, Honghui Lin, Jinbo Zhang, Wenfang Tan

Research output: Contribution to journalArticleResearchpeer-review

Abstract

Background: Sweetpotato (Ipomoea batatas (L.) Lam.) is the seventh most important crop in the world and is mainly cultivated for its underground storage root (SR). The genetic studies of this species have been hindered by a lack of high-quality reference sequence due to its complex genome structure. Diploid Ipomoea trifida is the closest relative and putative progenitor of sweetpotato, which is considered a model species for sweetpotato, including genetic, cytological, and physiological analyses. Results: Here, we generated the chromosome-scale genome sequence of SR-forming diploid I. trifida var. Y22 with high heterozygosity (2.20%). Although the chromosome-based synteny analysis revealed that the I. trifida shared conserved karyotype with Ipomoea nil after the separation, I. trifida had a much smaller genome than I. nil due to more efficient eliminations of LTR-retrotransposons and lack of species-specific amplification bursts of LTR-RTs. A comparison with four non-SR-forming species showed that the evolution of the beta-amylase gene family may be related to SR formation. We further investigated the relationship of the key gene BMY11 (with identity 47.12% to beta-amylase 1) with this important agronomic trait by both gene expression profiling and quantitative trait locus (QTL) mapping. And combining SR morphology and structure, gene expression profiling and qPCR results, we deduced that the products of the activity of BMY11 in splitting starch granules and be recycled to synthesize larger granules, contributing to starch accumulation and SR swelling. Moreover, we found the expression pattern of BMY11, sporamin proteins and the key genes involved in carbohydrate metabolism and stele lignification were similar to that of sweetpotato during the SR development. Conclusions: We constructed the high-quality genome reference of the highly heterozygous I. trifida through a combined approach and this genome enables a better resolution of the genomics feature and genome evolutions of this species. Sweetpotato SR development genes can be identified in I. trifida and these genes perform similar functions and patterns, showed that the diploid I. trifida var. Y22 with typical SR could be considered an ideal model for the studies of sweetpotato SR development.

Original languageEnglish
Article number119
JournalBMC Plant Biology
Volume19
Issue number1
DOIs
StatePublished - 1 Apr 2019

Fingerprint

Ipomoea
genome
Ipomoea nil
beta-amylase
diploidy
genes
sporamin
chromosomes
gene expression
stele
Ipomoea batatas
lignification
retrotransposons
carbohydrate metabolism
starch granules
agronomic traits
karyotyping
granules
quantitative trait loci
heterozygosity

Keywords

  • BMY11 (beta-amylase)
  • Evolution
  • Ipomoea trifida genome
  • QTL
  • Storage root development
  • Sweetpotato

Cite this

Li, Ming ; Yang, Songtao ; Xu, Wei ; Pu, Zhigang ; Feng, Junyan ; Wang, Zhangying ; Zhang, Cong ; Peng, Meifang ; Du, Chunguang ; Lin, Feng ; Wei, Changhe ; Qiao, Shuai ; Zou, Hongda ; Zhang, Lei ; Li, Yan ; Yang, Huan ; Liao, Anzhong ; Song, Wei ; Zhang, Zhongren ; Li, Ji ; Wang, Kai ; Zhang, Yizheng ; Lin, Honghui ; Zhang, Jinbo ; Tan, Wenfang. / The wild sweetpotato (Ipomoea trifida) genome provides insights into storage root development. In: BMC Plant Biology. 2019 ; Vol. 19, No. 1.
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abstract = "Background: Sweetpotato (Ipomoea batatas (L.) Lam.) is the seventh most important crop in the world and is mainly cultivated for its underground storage root (SR). The genetic studies of this species have been hindered by a lack of high-quality reference sequence due to its complex genome structure. Diploid Ipomoea trifida is the closest relative and putative progenitor of sweetpotato, which is considered a model species for sweetpotato, including genetic, cytological, and physiological analyses. Results: Here, we generated the chromosome-scale genome sequence of SR-forming diploid I. trifida var. Y22 with high heterozygosity (2.20{\%}). Although the chromosome-based synteny analysis revealed that the I. trifida shared conserved karyotype with Ipomoea nil after the separation, I. trifida had a much smaller genome than I. nil due to more efficient eliminations of LTR-retrotransposons and lack of species-specific amplification bursts of LTR-RTs. A comparison with four non-SR-forming species showed that the evolution of the beta-amylase gene family may be related to SR formation. We further investigated the relationship of the key gene BMY11 (with identity 47.12{\%} to beta-amylase 1) with this important agronomic trait by both gene expression profiling and quantitative trait locus (QTL) mapping. And combining SR morphology and structure, gene expression profiling and qPCR results, we deduced that the products of the activity of BMY11 in splitting starch granules and be recycled to synthesize larger granules, contributing to starch accumulation and SR swelling. Moreover, we found the expression pattern of BMY11, sporamin proteins and the key genes involved in carbohydrate metabolism and stele lignification were similar to that of sweetpotato during the SR development. Conclusions: We constructed the high-quality genome reference of the highly heterozygous I. trifida through a combined approach and this genome enables a better resolution of the genomics feature and genome evolutions of this species. Sweetpotato SR development genes can be identified in I. trifida and these genes perform similar functions and patterns, showed that the diploid I. trifida var. Y22 with typical SR could be considered an ideal model for the studies of sweetpotato SR development.",
keywords = "BMY11 (beta-amylase), Evolution, Ipomoea trifida genome, QTL, Storage root development, Sweetpotato",
author = "Ming Li and Songtao Yang and Wei Xu and Zhigang Pu and Junyan Feng and Zhangying Wang and Cong Zhang and Meifang Peng and Chunguang Du and Feng Lin and Changhe Wei and Shuai Qiao and Hongda Zou and Lei Zhang and Yan Li and Huan Yang and Anzhong Liao and Wei Song and Zhongren Zhang and Ji Li and Kai Wang and Yizheng Zhang and Honghui Lin and Jinbo Zhang and Wenfang Tan",
year = "2019",
month = "4",
day = "1",
doi = "10.1186/s12870-019-1708-z",
language = "English",
volume = "19",
journal = "BMC Plant Biology",
issn = "1471-2229",
publisher = "BioMed Central Ltd.",
number = "1",

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Li, M, Yang, S, Xu, W, Pu, Z, Feng, J, Wang, Z, Zhang, C, Peng, M, Du, C, Lin, F, Wei, C, Qiao, S, Zou, H, Zhang, L, Li, Y, Yang, H, Liao, A, Song, W, Zhang, Z, Li, J, Wang, K, Zhang, Y, Lin, H, Zhang, J & Tan, W 2019, 'The wild sweetpotato (Ipomoea trifida) genome provides insights into storage root development', BMC Plant Biology, vol. 19, no. 1, 119. https://doi.org/10.1186/s12870-019-1708-z

The wild sweetpotato (Ipomoea trifida) genome provides insights into storage root development. / Li, Ming; Yang, Songtao; Xu, Wei; Pu, Zhigang; Feng, Junyan; Wang, Zhangying; Zhang, Cong; Peng, Meifang; Du, Chunguang; Lin, Feng; Wei, Changhe; Qiao, Shuai; Zou, Hongda; Zhang, Lei; Li, Yan; Yang, Huan; Liao, Anzhong; Song, Wei; Zhang, Zhongren; Li, Ji; Wang, Kai; Zhang, Yizheng; Lin, Honghui; Zhang, Jinbo; Tan, Wenfang.

In: BMC Plant Biology, Vol. 19, No. 1, 119, 01.04.2019.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - The wild sweetpotato (Ipomoea trifida) genome provides insights into storage root development

AU - Li, Ming

AU - Yang, Songtao

AU - Xu, Wei

AU - Pu, Zhigang

AU - Feng, Junyan

AU - Wang, Zhangying

AU - Zhang, Cong

AU - Peng, Meifang

AU - Du, Chunguang

AU - Lin, Feng

AU - Wei, Changhe

AU - Qiao, Shuai

AU - Zou, Hongda

AU - Zhang, Lei

AU - Li, Yan

AU - Yang, Huan

AU - Liao, Anzhong

AU - Song, Wei

AU - Zhang, Zhongren

AU - Li, Ji

AU - Wang, Kai

AU - Zhang, Yizheng

AU - Lin, Honghui

AU - Zhang, Jinbo

AU - Tan, Wenfang

PY - 2019/4/1

Y1 - 2019/4/1

N2 - Background: Sweetpotato (Ipomoea batatas (L.) Lam.) is the seventh most important crop in the world and is mainly cultivated for its underground storage root (SR). The genetic studies of this species have been hindered by a lack of high-quality reference sequence due to its complex genome structure. Diploid Ipomoea trifida is the closest relative and putative progenitor of sweetpotato, which is considered a model species for sweetpotato, including genetic, cytological, and physiological analyses. Results: Here, we generated the chromosome-scale genome sequence of SR-forming diploid I. trifida var. Y22 with high heterozygosity (2.20%). Although the chromosome-based synteny analysis revealed that the I. trifida shared conserved karyotype with Ipomoea nil after the separation, I. trifida had a much smaller genome than I. nil due to more efficient eliminations of LTR-retrotransposons and lack of species-specific amplification bursts of LTR-RTs. A comparison with four non-SR-forming species showed that the evolution of the beta-amylase gene family may be related to SR formation. We further investigated the relationship of the key gene BMY11 (with identity 47.12% to beta-amylase 1) with this important agronomic trait by both gene expression profiling and quantitative trait locus (QTL) mapping. And combining SR morphology and structure, gene expression profiling and qPCR results, we deduced that the products of the activity of BMY11 in splitting starch granules and be recycled to synthesize larger granules, contributing to starch accumulation and SR swelling. Moreover, we found the expression pattern of BMY11, sporamin proteins and the key genes involved in carbohydrate metabolism and stele lignification were similar to that of sweetpotato during the SR development. Conclusions: We constructed the high-quality genome reference of the highly heterozygous I. trifida through a combined approach and this genome enables a better resolution of the genomics feature and genome evolutions of this species. Sweetpotato SR development genes can be identified in I. trifida and these genes perform similar functions and patterns, showed that the diploid I. trifida var. Y22 with typical SR could be considered an ideal model for the studies of sweetpotato SR development.

AB - Background: Sweetpotato (Ipomoea batatas (L.) Lam.) is the seventh most important crop in the world and is mainly cultivated for its underground storage root (SR). The genetic studies of this species have been hindered by a lack of high-quality reference sequence due to its complex genome structure. Diploid Ipomoea trifida is the closest relative and putative progenitor of sweetpotato, which is considered a model species for sweetpotato, including genetic, cytological, and physiological analyses. Results: Here, we generated the chromosome-scale genome sequence of SR-forming diploid I. trifida var. Y22 with high heterozygosity (2.20%). Although the chromosome-based synteny analysis revealed that the I. trifida shared conserved karyotype with Ipomoea nil after the separation, I. trifida had a much smaller genome than I. nil due to more efficient eliminations of LTR-retrotransposons and lack of species-specific amplification bursts of LTR-RTs. A comparison with four non-SR-forming species showed that the evolution of the beta-amylase gene family may be related to SR formation. We further investigated the relationship of the key gene BMY11 (with identity 47.12% to beta-amylase 1) with this important agronomic trait by both gene expression profiling and quantitative trait locus (QTL) mapping. And combining SR morphology and structure, gene expression profiling and qPCR results, we deduced that the products of the activity of BMY11 in splitting starch granules and be recycled to synthesize larger granules, contributing to starch accumulation and SR swelling. Moreover, we found the expression pattern of BMY11, sporamin proteins and the key genes involved in carbohydrate metabolism and stele lignification were similar to that of sweetpotato during the SR development. Conclusions: We constructed the high-quality genome reference of the highly heterozygous I. trifida through a combined approach and this genome enables a better resolution of the genomics feature and genome evolutions of this species. Sweetpotato SR development genes can be identified in I. trifida and these genes perform similar functions and patterns, showed that the diploid I. trifida var. Y22 with typical SR could be considered an ideal model for the studies of sweetpotato SR development.

KW - BMY11 (beta-amylase)

KW - Evolution

KW - Ipomoea trifida genome

KW - QTL

KW - Storage root development

KW - Sweetpotato

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JO - BMC Plant Biology

JF - BMC Plant Biology

SN - 1471-2229

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