Solanum pinnatisectum 엽록체 전장유전체 구명 및 특이적 분자마커의 개발
Completion of chloroplast genome sequence and development of PCR-based markers for Solanum pinnatisectum
2
조회
0
다운로드
0
인용
0
참고문헌
키워드
초록
Solanum pinnatisectum, originating from Mexico, is a wild potato species valued for its resistance to various insects and pathogens, including the Colorado potato beetle, potato tuber moth, Phytophthora infestans, and Erwinia carotovorum. Despite its advantageous traits, S. pinnatisectum is diploid with an endosperm balanced number (EBN) of one, presenting sexual reproduction barriers with cultivated potatoes. Cell fusion methods can be employed to circumvent these barriers and integrate beneficial traits from S. pinnatisectum into cultivated potatoes. In this study, therefore, the chloroplast genome sequence of S. pinnatisectum was completed using next-generation sequencing (NGS) tech- nology and compared with those of ten other Solanum species to develop specific PCR markers for S. pinnatisectum. The complete chloroplast genome of S. pinnatisectum is 155,597 bp in length and exhibits structural organization similar to those of other Solanum species. Sequence alignment of the complete chloroplast genomes sequences of eleven Solanum species, including S. pinnatisectum, identified 216 SNPs and 26 InDels unique to S. pinnatisectum. Based on these InDels and SNPs, six PCR-based markers were developed to identify the plastid genotype of S. pinnatisectum. The results of this study will be instrumental in distinguishing S. pinnatisectum from other Solanum species, selecting suitable genotypes for potato breeding through somatic hybridization, and accelerating the breeding program using S. pinnatisectum.
Abstract
Solanum pinnatisectum, originating from Mexico, is a wild potato species valued for its resistance to various insects and pathogens, including the Colorado potato beetle, potato tuber moth, Phytophthora infestans, and Erwinia carotovorum. Despite its advantageous traits, S. pinnatisectum is diploid with an endosperm balanced number (EBN) of one, presenting sexual reproduction barriers with cultivated potatoes. Cell fusion methods can be employed to circumvent these barriers and integrate beneficial traits from S. pinnatisectum into cultivated potatoes. In this study, therefore, the chloroplast genome sequence of S. pinnatisectum was completed using next-generation sequencing (NGS) tech- nology and compared with those of ten other Solanum species to develop specific PCR markers for S. pinnatisectum. The complete chloroplast genome of S. pinnatisectum is 155,597 bp in length and exhibits structural organization similar to those of other Solanum species. Sequence alignment of the complete chloroplast genomes sequences of eleven Solanum species, including S. pinnatisectum, identified 216 SNPs and 26 InDels unique to S. pinnatisectum. Based on these InDels and SNPs, six PCR-based markers were developed to identify the plastid genotype of S. pinnatisectum. The results of this study will be instrumental in distinguishing S. pinnatisectum from other Solanum species, selecting suitable genotypes for potato breeding through somatic hybridization, and accelerating the breeding program using S. pinnatisectum.
참고문헌 (43)
- Chen L, "Nuclear and cytoplasmic genome components of Solanum tuberosum + S. chacoense somatic hybrids and three SSR alleles related to bacterial wilt resistance", Theor Appl Genet, 126, pp.1861~1872 (2013)
- Chen Q, "Identification of late blight, Colorado potato beetle, and blackleg resistance in three Mexican and two south American wild 2x(1EBN)Solanum species", Am J Potato Res, 80, pp.919~ (2003)
- Chen Q, "Construction of two BAC libraries from the wild Mexican diploid potato, Solanum pinnatisectum, and the identification of clones near the late blight and Colorado potato beetle resistance loci", Theor Appl Genet, 108, pp.1002~1009 (2004)
- Cho HM, "Influence of endosperm balance number(EBN)in interploidal and interspecific crosses between Solanum tuberosum dihaploids and wild species", Korean J Breed, 29, pp.154~161 (1997)
- Cho KS, "Complete chloroplast genome sequences of Solanum commersonii and its application to chloroplast genotype in somatic hybrids with Solanum tuberosum", Plant Cell Rep, 35, pp.2113~2123 (2016)
- Cho KS, "Chloroplast genome sequence of Solanum demissum, a wild tuber-bearing species was completed", Mitochondr DNA Part B, 4, pp.1800~1802 (2019)
- Cho KS, "Potato breeding via protoplast fusion", J Plant Biotechnol, 41, pp.65~72 (2014)
- Cho KS, "Complete chloroplast genome sequence of Solanum nigrum and Development of markers for the discrimination of S. nigrum", Hort Environ Biotechnol, 57, pp.69~78 (2016)
- Cho KS, "Complete chloroplast genome sequence of tartary Buckwheat (Fagopyrum tataricum) and comparative analysis with common Buckwheat (F. esculentum)", PloS One, 10, pp.e0125332~ (2015)
- Daniell H, "Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes", Theor Appl Genet, 112, pp.1503~1518 (2006)
- Gargano D, "The complete nucleotide sequence genome of potato (Solanum tuberosum cv. Desiree) chloroplast DNA", the abstract of the 2nd Solanaceae Genome Workshop, pp.107~ (2005)
- Hawkes JG, "The potato : Evolution, biodiversity and genetic resources" (1990), Belhaven Press
- Jansky S, "Overcoming hybridization barriers in potato", Plant breeding, 125, pp.1~12 (2006)
- Kim S, "Development of PCR-based markers for discriminating Solanum berthaultii using its complete chloroplast genome species", J Plant Biotechnol, 45, pp.207~216 (2018)
- Kim S, "PCR-based markers developed by comparison of complete chloroplast genome sequences discriminate Solanum chacoense from other Solanum species", J Plant Bioechnol, 46, pp.79~87 (2019)
- Kim S, "Comparison of the complete chloroplast genome sequences of Solanum stoloniferum with other Solanum species generate PCR-based markers specific for Solanum stoloniferum", J Plant Bioechnol, 47, pp.131~140 (2020)
- Kim S, "Development of Solanum hougasiispecific markers using the complete chloroplast genome sequences of Solanum species", J Plant Bioechnol, 47, pp.141~149 (2020)
- Konovalov F, "A CAPS marker set for mapping in linkage group III of pea (Pisum sativum L.)", Cell Mol Biol Lett, 10, pp.163~171 (2005)
- Kuhl J-C, "Characterization and mapping of Rpi1, a late-blight resistance locus from diploid(1EBN)mexican Solanum pinnatisectum", Mol Genet Genomics, 265, pp.977~985 (2001)
- Lee J, "A CAPS marker associated with the partial restoration of cytoplasmic male sterility in chili pepper (Capsicum annuum L.)", Mol Breeding, 21, pp.95~104 (2008)
- Lohse M, "OrganellarGenomeDRAW(OGDRAW) : a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes", Curr Genet, 52, pp.267~274 (2007)
- Lössl A, "Molecular markers for cytoplasm in potato : male sterility and contribution of different plastid-mitochondrial configurations to starch production", Euphytica, 116, pp.221~230 (2000)
- Machida-Hirano R, "Diversity of potato genetic resources", Breed Sci, 65, pp.26~40 (2015)
- Menke U, "Somatic hybrids between the cultivated potato Solanum tuberosum L. and the 1EBN wild species Solanum pinnatisectum Dun : morphological and molecular characterization", Theor Appl Genet, 92, pp.617~626 (1996)
- Mohapatra T, "Random chloroplast segregation and mitochondrial genome recombination in somatic hybrid plants of diplotaxis cathollica + Brassica Juncea", Plant Cell Rep, 17, pp.814~818 (1998)
- Park T-H, "Complete chloroplast genome sequence of the wild diploid potato relative, Solanum acaule", Mitochondr DNA Part B, 6, pp.1189~1191 (2021)
- Park T-H, "PCR-based markers for discriminating Solanum demissum were developed by comparison of complete chloroplast genome sequences of Solanum species", J Plant Biotechnol, 48, pp.18~25 (2021)
- Park T-H, "Development of PCR-based markers specific to Solanum brevicaule by using the complete chloroplast genome sequences of Solanum species", J Plant Biotechnol, 49, pp.30~38 (2022)
- Park T-H, "PCR-based markers to select plastid genotypes of Solanum acaule", J Plant Biotechnol, 49, pp.178~186 (2022)
- Park T-H, "Development of PCR-based markers for selecting plastid genotypes of Solanum hjertingii", J Plant Biotechnol, 50, pp.34~44 (2023)
- Park T-H, "Chloroplast genome sequence and PCR-based markers for S. cardiophyllum", J Plant Biotechnol, 50, pp.45~55 (2023)
- Pettenkofer T, "Development of novel Quercus rubra chloroplast genome CAPS markers for haplotype indentification", Silvae Genetica, 69, pp.78~85 (2020)
- Schwartz S, "Human-mouse alignments with BLASTZ", Genome Res, 13, pp.103~107 (2003)
- Smilde WD, "Solanum mochiquense chromosome IX carries a novel late blight resistance gene Rpi-moc1", Theor Appl Genet, 110, pp.252~258 (2005)
- Smyda-Dajmund P, "Genetic composition of interspecific potato somatic hybrids and autofused 4x plants evaluated by DArT and cytoplasmic DNA markers", Plant Cell Rep, 35, pp.1345~1358 (2016)
- Srivastava A, "Potato diversity and its genetic enhancement", Gene Pool Divers Crop Im, pp.187~226 (2016)
- Tamura K, "MEGA6 : molecular evolutionary genetic analysis version 6. 0", Mol Biol Evol, 30, pp.2725~2729 (2013)
- Tillich M, "GeSeq-versatile and accurate annotation of organelle genomes", Nucleic Acids Res, 45, pp.W6~W11 (2017)
- Uncu AT, "Development of a SNP-based CAPS assay for the Me1 gene conferring resistance to root knot nematode in pepper", Euphytica, 206, pp.393~399 (2015)
- van der Voort JR, "Tight physical linkage of the nematode resistance gene Gpa2 and the virus resistance gene Rx on a single segment introgressed from the wild species Solanum tuberosum subsp. andigena CPC 1673 into cultivated potato", Mol Plant-Microb Interact, 18, pp.722~729 (1999)
- Wang GX, "Production and characterization of interspecific somatic hybrids between Brassica oleracea var. botrytis and B. nigra and their progenies for the selection of advanced pre-breeding materials", Plant Cell Rep, 30, pp.1811~1821 (2011)
- Xiang F, "Regeneration of somatic hybrids in relation to the nuclear and cytoplasmic genomes of wheat and Setaria italica", Genome, 47, pp.680~688 (2004)
- Yurina NP, "Comparative structural organization of plant chloroplast and mitochondrial genomes", Russ J Genet, 34, pp.5~22 (1998)
