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

文献类型： 外文期刊

作者： Li, Ming 3 ; Yang, Songtao 2 ; Xu, Wei 4 ; Pu, Zhigang 1 ; Feng, Junyan 1 ; Wang, Zhangying 5 ; Zhang, Cong 1 ; Peng, Mei 1 ;

作者机构： 1.Sichuan Acad Agr Sci, Inst Biotechnol & Nucl Technol, Chengdu 610061, Sichuan, Peoples R China

2.Sichuan Acad Agr Sci, Crop Res Inst, Chengdu 610066, Sichuan, Peoples R China

3.Sichuan Univ, Key Lab Bioresource & Ecoenvironm, Minist Educ, Coll Life Sci, Chengdu 610065, Sichuan, Peoples R China

4.Novogene Bioinformat Inst, Beijing 100083, Peoples R China

5.Guangdong Acad Agr Sci, Guangdong Prov Key Lab Crops Genet & Improvement, Crops Res Inst, Guangzhou 510640, Guangdong, Peoples R China

6.Montclair State Univ, Dept Biol, Montclair, NJ 07043 USA

关键词： Ipomoea trifida genome; Sweetpotato; Evolution; Storage root development; QTL; BMY11 (beta-amylase)

期刊名称：BMC PLANT BIOLOGY （ 影响因子：4.215； 五年影响因子：4.96 ）

ISSN： 1471-2229

年卷期： 2019 年 19 卷

页码：

收录情况： SCI

摘要： BackgroundSweetpotato (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.ResultsHere, 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.ConclusionsWe 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.

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