Analyses of <i>Ipomoea batatas</i> cultivated species and wild relatives based on mtDNA and cpDNA sequences

WANG Chong; WANG Lianjun; TIAN Xiaohai; LEI Jian; CHAI Shasha; JIAO Chunhai; YANG Xinsun

doi:10.7671/j.issn.1001-411X.202011026

Journal of South China Agricultural University > 2021 > 42(4): 25-32. > DOI: 10.7671/j.issn.1001-411X.202011026

WANG Chong, WANG Lianjun, TIAN Xiaohai, et al. Analyses of Ipomoea batatas cultivated species and wild relatives based on mtDNA and cpDNA sequences[J]. Journal of South China Agricultural University, 2021, 42(4): 25-32. DOI: 10.7671/j.issn.1001-411X.202011026

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Analyses of Ipomoea batatas cultivated species and wild relatives based on mtDNA and cpDNA sequences

WANG Chong^{1, 2, †,},
WANG Lianjun^{1, †,},
TIAN Xiaohai²,
LEI Jian¹,
CHAI Shasha¹,
JIAO Chunhai^3, ,,
YANG Xinsun^1, ,

1.
Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Resarch Center of Sweetpotato/Hubei Key Laboratory of Food Crop Germplasms and Genetic Improvement, Wuhan 430064, China
2.
College of Agriculture, Yangtze University, Jingzhou 434000, China
3.
Hubei Academy of Agricultural Sciences, Wuhan 430064, China

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Received Date: November 22, 2020
Available Online: May 17, 2023

Graphical Abstract

Abstract

Abstract

Objective
To conduct molecular identification and genetic relationship analysis of Ipomoea batatas cultivated species and wild relatives based on mitochondrial DNA (mtDNA) and chloroplast DNA (cpDNA) matK sequences, and provide theoretical bases for germplasm identification, protection, development and utilization.

Method
Three cultivated species and eight wild relatives were used as materials, from which total DNA was extracted by the CTAB method. Their mtDNA and cpDNA matK sequences were amplified by PCR. DnaSP 6.0 was used to analyze nucleotide diversity, haplotype diversity and other characteristics. The phylogenetic tree of three cultivated species and eight wild relatives was constructed based on the neighbor-joining method.

Result
The length of five mtDNA regions and one cpDNA region was 6 713 bp after sequencing, alignment and splicing, the GC proportion was 47.79%−48.31%, and the haplotype number, nucleotide diversity, variable site number, singleton variable site number, parsimony informative site number, insertion/deletion site number were 9, 0.003 25, 69, 39, 30, 111, respectively. The neutrality test showed there was no significant difference between Tajima’sD values at the level of P>0.10, which indicated that variation of those regions followed neutral theory of molecular evolution. The genetic distances among three cultivated species and eight wild relatives ranged from 0.000 00 to 0.005 84, with an average genetic distance of 0.003 26, indicating low genetic diversity. The phylogenetic tree divided the 11 species into two categories with close genetic relationship within the category.

Conclusion
The sequences used in this study can accurately identify I. batatas cultivated species and wild relatives, and provide references and theoretical guidance for the evolution and utilization of I. batatas wild relatives.
- Ipomoea batatas,
- mitochondrial DNA,
- matK sequence,
- phylogeny,
- genetic diversity

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References (34)

References

[1]	SHEKHAR S, MISHRA D, BURAGOHAIN A K, et al. Comparative analysis of phytochemicals and nutrient availability in two contrasting cultivars of sweet potato (Ipomoea batatas L.)[J]. Food Chemistry, 2015, 173: 957-965. doi: 10.1016/j.foodchem.2014.09.172
[2]	MOHANRAJ R, SIVASANKAR S. Sweet potato (Ipomoea batatas [L. ] Lam): A valuable medicinal food: A rievew[J]. Journal of Medicinal Food, 2014, 17(7): 733-741. doi: 10.1089/jmf.2013.2818
[3]	YANG Z, ZHU P, KANG H, et al. High-throughput deep sequencing reveals the important role that microRNAs play in the salt response in sweet potato (Ipomoea batatas L.)[J]. BMC Genomics, 2020, 21(1). doi: 10.1186/s12864-020-6567-3.
[4]	谢一芝, 郭小丁, 贾赵东, 等. 中国食用甘薯育种现状及展望[J]. 江苏农业学报, 2018, 34(6): 1419-1424. doi: 10.3969/j.issn.1000-4440.2018.06.030
[5]	胡玲, 李强, 王欣, 等. 甘薯地方品种和育成品种的遗传多样性[J]. 江苏农业学报, 2010, 26(5): 925-935. doi: 10.3969/j.issn.1000-4440.2010.05.006
[6]	李强, 刘庆昌, 马代夫. 甘薯近缘野生种研究利用现状及展望[J]. 分子植物育种, 2006, 4(6S): 105-110.
[7]	曹清河, 张安, 李鹏, 等. 甘薯近缘野生种的抗病性鉴定与新型种间杂种的获得[J]. 植物遗传资源学报, 2009, 10(2): 224-229.
[8]	GARRIDO-CARDENAS J A, MESA-VALLE C, MANZANO-AGUGLIARO F. Trends in plant research using molecular markers[J]. Planta, 2018, 247(3): 543-557. doi: 10.1007/s00425-017-2829-y
[9]	YANG X S, SU W J, WANG L J, et al. Molecular diversity and genetic structure of 380 sweetpotato accessions as revealed by SSR markers[J]. Journal of Integrative Agriculture, 2015, 14(4): 633-641. doi: 10.1016/S2095-3119(14)60794-2
[10]	苏一钧, 王娇, 戴习彬, 等. 303份甘薯地方种SSR遗传多样性与群体结构分析[J]. 植物遗传资源学报, 2018, 19(2): 243-251.
[11]	季志仙, 王美兴, 范宏环, 等. 基于ISSR指纹的甘薯食用品种的遗传多样性分析[J]. 核农学报, 2014, 28(7): 1197-1202. doi: 10.11869/j.issn.100-8551.2014.07.1197
[12]	王崇, 王连军, 苏文瑾, 等. 基于cpSSR标记的甘薯品种亲缘关系及遗传多样性分析[J]. 分子植物育种, 2020, 18(5): 1687-1696.
[13]	LEE K J, LEE G A, LEE J R, et al. Genetic diversity of sweet potato (Ipomoea batatas L. Lam) germplasms collected worldwide using chloroplast SSR markers[J]. Agronomy, 2019, 9(11): 725-740. doi: 10.3390/agronomy9110725
[14]	GUALBERTO J M, NEWTON K J. Plant mitochondrial genomes: Dynamics and mechanisms of mutation[M]//MERCHANT S S. Annual Review of Plant Biology: Vol 68. Palo alto: Annual Reviews. 2017: 225-252.
[15]	PELLETIER G, BUDAR F. The molecular biology of cytoplasmically inherited male sterility and prospects for its engineering[J]. Current Opinion in Biotechnology, 2007, 18(2): 121-125. doi: 10.1016/j.copbio.2006.12.002
[16]	LILLY J W, BARTOSZEWSKI G, MALEPSZY S, et al. A major deletion in the cucumber mitochondrial genome sorts with the MSC phenotype[J]. Current Genetics, 2001, 40(2): 144-151. doi: 10.1007/s002940100238
[17]	QIN Y J, BUAHOM N, KROSCH M N, et al. Genetic diversity and population structure in Bactrocera correcta (Diptera: Tephritidae) inferred from mtDNA cox1 and microsatellite markers[J]. Scientific Reports, 2016, 6: 38476. doi: 10.1038/srep38476.
[18]	BOUILLÉ M, SENNEVILLE S, BOUSQUET J. Discordant mtDNA and cpDNA phylogenies indicate geographic speciation and reticulation as driving factors for the diversification of the genus Picea[J]. Tree Genetics & Genomes, 2011, 7(3): 469-484.
[19]	GODBOUT J, JARAMILLO-CORREA J P, BEAULIEU J, et al. A mitochondrial DNA minisatellite reveals the postglacial history of jack pine (Pinus banksiana), a broad-range North American conifer[J]. Molecular Ecology, 2005, 14(11): 3497-3512. doi: 10.1111/j.1365-294X.2005.02674.x
[20]	HU D, LUO Z. Polymorphisms of amplified mitochondrial DNA non-coding regions in Diospyros spp.[J]. Scientia Horticulturae, 2006, 109(3): 275-281. doi: 10.1016/j.scienta.2006.02.027
[21]	马丽, 周玉亮, 郝兆祥, 等. 石榴种质资源的matK基因序列分析[J]. 分子植物育种, 2020, 18(16): 5274-5279.
[22]	DUMINIL J, PEMONGE M H, PETIT R J. A set of 35 consensus primer pairs amplifying genes and introns of plant mitochondrial DNA[J]. Molecular Ecology Notes, 2002, 2(4): 428-430. doi: 10.1046/j.1471-8286.2002.00263.x
[23]	DUMOLIN-LAPEGUE S, PEMONGE M H, PETIT R J. An enlarged set of consensus primers for the study of organelle DNA in plants[J]. Molecular Ecology, 1997, 6(4): 393-397. doi: 10.1046/j.1365-294X.1997.00193.x
[24]	SUN X Q, ZHU Y J, GUO J L, et al. DNA barcoding the Dioscorea in China, a vital group in the evolution of monocotyledon: Use of matK gene for species discrimination[J]. PLoS One, 2012, 7(2): e32057. doi: 10.1371/journal.pone.0032057
[25]	KUMAR S, STECHER G, LI M, et al. MEGA X: Molecular evolutionary genetics analysis across computing platforms[J]. Molecular Biology and Evolution, 2018, 35(6): 1547-1549. doi: 10.1093/molbev/msy096
[26]	ROZAS J, FERRER-MATA A, SÁNCHEZ-DELBARRIO J C, et al. DnaSP 6: DNA sequence polymorphism analysis of large data sets[J]. Molecular Biology and Evolution, 2017, 34(12): 3299-3302. doi: 10.1093/molbev/msx248
[27]	刘峥, 张汉尧. 旋花科植物ITS序列分析[J]. 西部林业科学, 2012, 41(4): 70-74. doi: 10.3969/j.issn.1672-8246.2012.04.012
[28]	俞立璇, 刘美艳, 曹清河, 等. 栽培种甘薯及其近缘野生种nrDNA ITS序列分析[J]. 植物科学学报, 2014, 32(1): 40-49.
[29]	JIN D P, LEE J H, XU B, et al. Phylogeography of East Asian Lespedeza buergeri (Fabaceae) based on chloroplast and nuclear ribosomal DNA sequence variations[J]. Journal of Plant Research, 2016, 129(5): 793-805. doi: 10.1007/s10265-016-0831-2
[30]	郭亚龙, 葛颂. 线粒体nad1基因内含子在稻族系统学研究中的价值: 兼论Porteresia的系统位置[J]. 植物分类学报, 2004, 42(4): 333-344.
[31]	陆佳妮, 赵志礼, 倪梁红, 等. 线粒体nad1/b-c及nad5/d-e在秦艽组植物中物种鉴定意义的评价[J]. 药物学报, 2019, 54(1): 166-172.
[32]	SNOUSSI H, DUVAL M F, GARCIA-LOR A, et al. Assessment of the genetic diversity of the Tunisian citrus rootstock germplasm[J]. BMC Genetics, 2012: 13. doi: 10.1186/1471-2156-13-16.
[33]	YANG J, VÁZQUEZ L, CHEN X D, et al. Development of chloroplast and nuclear DNA markers for Chinese Oaks (Quercus Subgenus Quercus) and assessment of their utility as DNA barcodes[J]. Frontiers in Plant Science, 2017: 8. doi: 10.3389/fpls.2017.00816.
[34]	KORNELIUSSEN T S, MOLTKE I, ALBRECHTSEN A, et al. Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data[J]. BMC Bioinformatics, 2013: 14. doi: 10.1186/1471-2105-14-289.

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Analyses of Ipomoea batatas cultivated species and wild relatives based on mtDNA and cpDNA sequences

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