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Xiao S, Dai X, Zhao L, Zhou Z, Zhao L, Xu P, Gao B, Zhang A, Zhao D, Yuan R, Wang Y, Wang J, Li Q, Cao Q. Resequencing of sweetpotato germplasm resources reveals key loci associated with multiple agronomic traits. HORTICULTURE RESEARCH 2022; 10:uhac234. [PMID: 36643760 PMCID: PMC9832839 DOI: 10.1093/hr/uhac234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
Sweetpotato is an important crop that exhibits hexaploidy and high heterozygosity, which limits gene mining for important agronomic traits. Here, 314 sweetpotato germplasm resources were deeply resequenced, and 4 599 509 SNPs and 846 654 InDels were generated, among which 196 124 SNPs were nonsynonymous and 9690 InDels were frameshifted. Based on the Indels, genome-wide marker primers were designed, and 3219 of 40 366 primer pairs were selected to construct the core InDel marker set. The molecular ID of 104 sweetpotato samples verified the availability of these primers. The sweetpotato population structures were then assessed through multiple approaches using SNPs, and diverse approaches demonstrated that population stratification was not obvious for most Chinese germplasm resources. As many as 20 important agronomic traits were evaluated, and a genome-wide association study was conducted on these traits. A total of 19 high-confidence loci were detected in both models. These loci included several candidate genes, such as IbMYB1, IbZEP1, and IbYABBY1, which might be involved in anthocyanin metabolism, carotenoid metabolism, and leaf morphogenesis, respectively. Among them, IbZEP1 and IbYABBY1 were first reported in sweetpotato. The variants in the promoter and the expression levels of IbZEP1 were significantly correlated with flesh color (orange or not orange) in sweetpotato. The expression levels of IbYABBY1 were also correlated with leaf shape. These results will assist in genetic and breeding studies in sweetpotato.
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Affiliation(s)
| | | | | | - Zhilin Zhou
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, Chinese Agricultural Academy of Sciences, Xuzhou 221131, China
| | - Lukuan Zhao
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, Chinese Agricultural Academy of Sciences, Xuzhou 221131, China
| | - Pan Xu
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Bingqian Gao
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, Chinese Agricultural Academy of Sciences, Xuzhou 221131, China
| | - An Zhang
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, Chinese Agricultural Academy of Sciences, Xuzhou 221131, China
| | - Donglan Zhao
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, Chinese Agricultural Academy of Sciences, Xuzhou 221131, China
| | - Rui Yuan
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, Chinese Agricultural Academy of Sciences, Xuzhou 221131, China
| | - Yao Wang
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, Chinese Agricultural Academy of Sciences, Xuzhou 221131, China
| | - Jie Wang
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, Chinese Agricultural Academy of Sciences, Xuzhou 221131, China
| | - Qinglian Li
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, Chinese Agricultural Academy of Sciences, Xuzhou 221131, China
| | - Qinghe Cao
- Correspondence: Qinghe Cao (); Tel.: 086-0516-82189205; Fax: 086-0516-82189205
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Xiao S, Xu P, Deng Y, Dai X, Zhao L, Heider B, Zhang A, Zhou Z, Cao Q. Comparative analysis of chloroplast genomes of cultivars and wild species of sweetpotato (Ipomoea batatas [L.] Lam). BMC Genomics 2021; 22:262. [PMID: 33849443 PMCID: PMC8042981 DOI: 10.1186/s12864-021-07544-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 03/22/2021] [Indexed: 02/08/2023] Open
Abstract
Background Sweetpotato (Ipomoea batatas [L.] Lam.) is an important food crop. However, the genetic information of the nuclear genome of this species is difficult to determine accurately because of its large genome and complex genetic background. This drawback has limited studies on the origin, evolution, genetic diversity and other relevant studies on sweetpotato. Results The chloroplast genomes of 107 sweetpotato cultivars were sequenced, assembled and annotated. The resulting chloroplast genomes were comparatively analysed with the published chloroplast genomes of wild species of sweetpotato. High similarity and certain specificity were found among the chloroplast genomes of Ipomoea spp. Phylogenetic analysis could clearly distinguish wild species from cultivars. Ipomoea trifida and Ipomoea tabascana showed the closest relationship with the cultivars, and different haplotypes of ycf1 could be used to distinguish the cultivars from their wild relatives. The genetic structure was analyzed using variations in the chloroplast genome. Compared with traditional nuclear markers, the chloroplast markers designed based on the InDels on the chloroplast genome showed significant advantages. Conclusions Comparative analysis of chloroplast genomes of 107 cultivars and several wild species of sweetpotato was performed to help analyze the evolution, genetic structure and the development of chloroplast DNA markers of sweetpotato. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07544-y.
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Affiliation(s)
- Shizhuo Xiao
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, China Agricultural Academy of Sciences, Xuzhou, 221131, China
| | - Pan Xu
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Yitong Deng
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, China Agricultural Academy of Sciences, Xuzhou, 221131, China
| | - Xibin Dai
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, China Agricultural Academy of Sciences, Xuzhou, 221131, China
| | - Lukuan Zhao
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, China Agricultural Academy of Sciences, Xuzhou, 221131, China
| | - Bettina Heider
- International Potato Center, Av.La Molina 1895, La Molina, Lima, Peru
| | - An Zhang
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, China Agricultural Academy of Sciences, Xuzhou, 221131, China
| | - Zhilin Zhou
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, China Agricultural Academy of Sciences, Xuzhou, 221131, China
| | - Qinghe Cao
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, China Agricultural Academy of Sciences, Xuzhou, 221131, China.
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Isobe S, Shirasawa K, Hirakawa H. Current status in whole genome sequencing and analysis of Ipomoea spp. PLANT CELL REPORTS 2019; 38:1365-1371. [PMID: 31468128 PMCID: PMC6797701 DOI: 10.1007/s00299-019-02464-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/19/2019] [Indexed: 05/03/2023]
Abstract
The recent advances of next-generation sequencing have made it possible to construct reference genome sequences in divergent species. However, de novo assembly at the chromosome level remains challenging in polyploid species, due to the existence of more than two pairs of homoeologous chromosomes in one nucleus. Cultivated sweet potato (Ipomoea batatas (L.) Lam) is a hexaploid species with 90 chromosomes (2n = 6X = 90). Although the origin of sweet potato is also still under discussion, diploid relative species, I. trifida and I. triloba have been considered as one of the most possible progenitors. In this manuscript, we review the recent results and activities of whole-genome sequencing in the genus Ipomoea series Batatas, I. trifida, I. triloba and sweet potato (I. batatas). Most of the results of genome assembly suggest that the genomes of sweet potato consist of two pairs and four pairs of subgenomes, i.e., B1B1B2B2B2B2. The results also revealed the relation between sweet potato and other Ipomoea species. Together with the development of bioinformatics approaches, the large-scale publicly available genome and transcript sequence resources and international genome sequencing streams are expected to promote the genome sequence dissection in sweet potato.
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Affiliation(s)
- Sachiko Isobe
- Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba, Japan.
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba, Japan
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Kim HS, Yoon UH, Lee CJ, Kim SE, Ji CY, Kwak SS. Status of research on the sweetpotato biotechnology and prospects of the molecular breeding on marginal lands. ACTA ACUST UNITED AC 2018. [DOI: 10.5010/jpb.2018.45.3.196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Ho Soo Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Ung-Han Yoon
- Genomics Division, National Academy of Agricultural Science, Jeonju 54875, Korea
| | - Chan-Ju Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - So-Eun Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Chang Yoon Ji
- Research & Development Center, Korea Scientific Technique Industry Co., Ltd., 67, Saneop-ro 92, Gwonseon-gu, Suwon-si 16643, Korea
| | - Sang-Soo Kwak
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
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Isobe S, Shirasawa K, Hirakawa H. Challenges to genome sequence dissection in sweetpotato. BREEDING SCIENCE 2017; 67:35-40. [PMID: 28465666 PMCID: PMC5407923 DOI: 10.1270/jsbbs.16186] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/23/2017] [Indexed: 05/23/2023]
Abstract
The development of next generation sequencing (NGS) technologies has enabled the determination of whole genome sequences in many non-model plant species. However, genome sequencing in sweetpotato (Ipomoea batatas (L.) Lam) is still difficult because of the hexaploid genome structure. Previous studies suggested that a diploid wild relative, I. trifida (H.B.K.) Don., is the most possible ancestor of sweetpotato. Therefore, the genetic and genomic features of I. trifida have been studied as a potential reference for sweetpotato. Meanwhile, several research groups have begun the challenging task of directly sequencing the sweetpotato genome. In this manuscript, we review the recent results and activities of large-scale genome and transcriptome analysis related to genome sequence dissection in sweetpotato under the sections as follows: I. trifida genome and transcript sequencing, genome sequences of I. nil (Japanese morning glory), transcript sequences in sweetpotato, chloroplast sequences, transposable elements and transfer DNA. The recent international activities of de novo whole genome sequencing in sweetpotato are also described. The large-scale publically available genome and transcript sequence resources and the international genome sequencing streams are expected to promote the genome sequence dissection in sweetpotato.
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