Genome sequence analysis provides insights on genomic variation and late blight resistance genes in potato somatic hybrid (parents and progeny)
Wild Solanum species are the important resources for potato improvement. With the availability of potato genome and sequencing progress, knowledge about genomic resources is essential for novel genes discovery. Hence, the aim of this study was to decipher draft genome sequences of unique potato geno...
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| Veröffentlicht in: | Molecular biology reports 2021, Vol.48 (1), p.623-635 |
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| creator | Tiwari, Jagesh Kumar Rawat, Shashi Luthra, Satish K. Zinta, Rasna Sahu, Sarika Varshney, Shivangi Kumar, Vinod Dalamu, Dalamu Mandadi, Nagesh Kumar, Manoj Chakrabarti, Swarup K. Rao, Atmakuri R. Rai, Anil |
| description | Wild
Solanum
species are the important resources for potato improvement. With the availability of potato genome and sequencing progress, knowledge about genomic resources is essential for novel genes discovery. Hence, the aim of this study was to decipher draft genome sequences of unique potato genotypes i.e. somatic hybrid P8 (J1), wild species
S. pinnatisectum
(J2), progeny MSH/14-112 (P8 × cv. Kufri Jyoti) (J3), and
S. tuberosum
dihaploid C-13 (J4). Draft genome sequencing using Illumina platform and reference-based assemblies with the potato genome yielded genome assembly size of 725.01 Mb (J1), 724.95 Mb (J2), 725.01 Mb (J3), and 809.59 Mb (J4). Further, 39,260 (J1), 25,711 (J2), 39,730 (J3) and 30,241 (J4) genes were identified and 17,411 genes were found common in the genotypes particularly late blight resistance genes (
R3a
,
RGA2
,
RGA3
,
R1B-16
,
Rpi-blb2
,
Rpi
and
Rpi-vnt1
). Gene ontology (GO) analysis showed that molecular function was predominant and signal transduction was major KEGG pathways. Further, gene enrichment analysis revealed dominance of metabolic process (GO: 0008152) in all the samples. Phylogeny analysis showed relatedness with potato and other plant species. Heterozygous single nucleotide polymorphism (SNP) was more than homozygous, and SNP in genic region was more than inter-genic region. Copy number variation (CNV) analysis indicated greater number of deletions than duplications. Sequence diversity and conserved motifs analysis revealed variation for late blight resistance genes. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed differential expression of late blight resistance genes. Our study provides insights on genome sequence, structural variation and late blight resistance genes in potato somatic hybrid (parents and progeny) for future research. |
| doi_str_mv | 10.1007/s11033-020-06106-x |
| format | Article |
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Solanum
species are the important resources for potato improvement. With the availability of potato genome and sequencing progress, knowledge about genomic resources is essential for novel genes discovery. Hence, the aim of this study was to decipher draft genome sequences of unique potato genotypes i.e. somatic hybrid P8 (J1), wild species
S. pinnatisectum
(J2), progeny MSH/14-112 (P8 × cv. Kufri Jyoti) (J3), and
S. tuberosum
dihaploid C-13 (J4). Draft genome sequencing using Illumina platform and reference-based assemblies with the potato genome yielded genome assembly size of 725.01 Mb (J1), 724.95 Mb (J2), 725.01 Mb (J3), and 809.59 Mb (J4). Further, 39,260 (J1), 25,711 (J2), 39,730 (J3) and 30,241 (J4) genes were identified and 17,411 genes were found common in the genotypes particularly late blight resistance genes (
R3a
,
RGA2
,
RGA3
,
R1B-16
,
Rpi-blb2
,
Rpi
and
Rpi-vnt1
). Gene ontology (GO) analysis showed that molecular function was predominant and signal transduction was major KEGG pathways. Further, gene enrichment analysis revealed dominance of metabolic process (GO: 0008152) in all the samples. Phylogeny analysis showed relatedness with potato and other plant species. Heterozygous single nucleotide polymorphism (SNP) was more than homozygous, and SNP in genic region was more than inter-genic region. Copy number variation (CNV) analysis indicated greater number of deletions than duplications. Sequence diversity and conserved motifs analysis revealed variation for late blight resistance genes. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed differential expression of late blight resistance genes. Our study provides insights on genome sequence, structural variation and late blight resistance genes in potato somatic hybrid (parents and progeny) for future research.</description><identifier>ISSN: 0301-4851</identifier><identifier>EISSN: 1573-4978</identifier><identifier>DOI: 10.1007/s11033-020-06106-x</identifier><identifier>PMID: 33442830</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Animal Anatomy ; Animal Biochemistry ; Biomedical and Life Sciences ; Chromosome Mapping ; Conserved sequence ; Copy number ; Dihaploid ; Disease resistance ; Disease Resistance - genetics ; DNA Copy Number Variations - genetics ; Gene polymorphism ; Genes ; Genome, Plant - genetics ; Genomes ; Genomics ; Histology ; Late blight ; Life Sciences ; Morphology ; Nucleotide sequence ; Offspring ; Original Article ; Phylogeny ; Plant Diseases - genetics ; Plant Diseases - microbiology ; Plant Proteins - genetics ; Plant Somatic Embryogenesis Techniques ; Polymerase chain reaction ; Sequence analysis ; Signal transduction ; Single-nucleotide polymorphism ; Solanum pinnatisectum ; Solanum tuberosum ; Solanum tuberosum - genetics ; Solanum tuberosum - growth & development ; Species ; Variation</subject><ispartof>Molecular biology reports, 2021, Vol.48 (1), p.623-635</ispartof><rights>The Author(s), under exclusive licence to Springer Nature B.V. part of Springer Nature 2021</rights><rights>The Author(s), under exclusive licence to Springer Nature B.V. part of Springer Nature 2021.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c375t-e9790e0e571294ceaeb9fc1a901a0477dcfb8ad406bb8af04dc76c3c10aaefca3</citedby><cites>FETCH-LOGICAL-c375t-e9790e0e571294ceaeb9fc1a901a0477dcfb8ad406bb8af04dc76c3c10aaefca3</cites><orcidid>0000-0002-3936-1458</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s11033-020-06106-x$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s11033-020-06106-x$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27915,27916,41479,42548,51310</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33442830$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Tiwari, Jagesh Kumar</creatorcontrib><creatorcontrib>Rawat, Shashi</creatorcontrib><creatorcontrib>Luthra, Satish K.</creatorcontrib><creatorcontrib>Zinta, Rasna</creatorcontrib><creatorcontrib>Sahu, Sarika</creatorcontrib><creatorcontrib>Varshney, Shivangi</creatorcontrib><creatorcontrib>Kumar, Vinod</creatorcontrib><creatorcontrib>Dalamu, Dalamu</creatorcontrib><creatorcontrib>Mandadi, Nagesh</creatorcontrib><creatorcontrib>Kumar, Manoj</creatorcontrib><creatorcontrib>Chakrabarti, Swarup K.</creatorcontrib><creatorcontrib>Rao, Atmakuri R.</creatorcontrib><creatorcontrib>Rai, Anil</creatorcontrib><title>Genome sequence analysis provides insights on genomic variation and late blight resistance genes in potato somatic hybrid (parents and progeny)</title><title>Molecular biology reports</title><addtitle>Mol Biol Rep</addtitle><addtitle>Mol Biol Rep</addtitle><description>Wild
Solanum
species are the important resources for potato improvement. With the availability of potato genome and sequencing progress, knowledge about genomic resources is essential for novel genes discovery. Hence, the aim of this study was to decipher draft genome sequences of unique potato genotypes i.e. somatic hybrid P8 (J1), wild species
S. pinnatisectum
(J2), progeny MSH/14-112 (P8 × cv. Kufri Jyoti) (J3), and
S. tuberosum
dihaploid C-13 (J4). Draft genome sequencing using Illumina platform and reference-based assemblies with the potato genome yielded genome assembly size of 725.01 Mb (J1), 724.95 Mb (J2), 725.01 Mb (J3), and 809.59 Mb (J4). Further, 39,260 (J1), 25,711 (J2), 39,730 (J3) and 30,241 (J4) genes were identified and 17,411 genes were found common in the genotypes particularly late blight resistance genes (
R3a
,
RGA2
,
RGA3
,
R1B-16
,
Rpi-blb2
,
Rpi
and
Rpi-vnt1
). Gene ontology (GO) analysis showed that molecular function was predominant and signal transduction was major KEGG pathways. Further, gene enrichment analysis revealed dominance of metabolic process (GO: 0008152) in all the samples. Phylogeny analysis showed relatedness with potato and other plant species. Heterozygous single nucleotide polymorphism (SNP) was more than homozygous, and SNP in genic region was more than inter-genic region. Copy number variation (CNV) analysis indicated greater number of deletions than duplications. Sequence diversity and conserved motifs analysis revealed variation for late blight resistance genes. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed differential expression of late blight resistance genes. Our study provides insights on genome sequence, structural variation and late blight resistance genes in potato somatic hybrid (parents and progeny) for future research.</description><subject>Animal Anatomy</subject><subject>Animal Biochemistry</subject><subject>Biomedical and Life Sciences</subject><subject>Chromosome Mapping</subject><subject>Conserved sequence</subject><subject>Copy number</subject><subject>Dihaploid</subject><subject>Disease resistance</subject><subject>Disease Resistance - genetics</subject><subject>DNA Copy Number Variations - genetics</subject><subject>Gene polymorphism</subject><subject>Genes</subject><subject>Genome, Plant - genetics</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Histology</subject><subject>Late blight</subject><subject>Life Sciences</subject><subject>Morphology</subject><subject>Nucleotide sequence</subject><subject>Offspring</subject><subject>Original Article</subject><subject>Phylogeny</subject><subject>Plant Diseases - genetics</subject><subject>Plant Diseases - microbiology</subject><subject>Plant Proteins - genetics</subject><subject>Plant Somatic Embryogenesis Techniques</subject><subject>Polymerase chain reaction</subject><subject>Sequence analysis</subject><subject>Signal transduction</subject><subject>Single-nucleotide polymorphism</subject><subject>Solanum pinnatisectum</subject><subject>Solanum tuberosum</subject><subject>Solanum tuberosum - genetics</subject><subject>Solanum tuberosum - growth & development</subject><subject>Species</subject><subject>Variation</subject><issn>0301-4851</issn><issn>1573-4978</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9kcFO3DAQhq2qVdkufQEOlaVe6CFlHDvr5IgQ0EpIXOBsTZzJYpTYWzuL2KfoK-OwlEocOI1kf_8_sj_GjgT8FAD6JAkBUhZQQgErAavi8QNbiErLQjW6_sgWIEEUqq7EAfuS0j0AKKGrz-xASqXKWsKC_b0kH0biif5syVvi6HHYJZf4JoYH11Hizie3vpsSD56vZ9pZ_oDR4eTyCfqODzgRb4eZ4pFyeMK5KsPPcb4JE06BpzDmjOV3uza6jh9vMJLPvXNF3pbx3Y9D9qnHIdHXl7lktxfnN2e_iqvry99np1eFlbqaCmp0AwRUaVE2yhJS2_RWYAMCQWnd2b6tsVOwavPsQXVWr6y0AhCptyiX7Hjfmxfnl6fJjC5ZGgb0FLbJlErXILWQdUa_v0Hvwzbmb8pUpbVWetawZOWesjGkFKk3m-hGjDsjwMy6zF6XybrMsy7zmEPfXqq37Ujda-SfnwzIPZDylV9T_L_7ndoncxSkPA</recordid><startdate>2021</startdate><enddate>2021</enddate><creator>Tiwari, Jagesh Kumar</creator><creator>Rawat, Shashi</creator><creator>Luthra, Satish K.</creator><creator>Zinta, Rasna</creator><creator>Sahu, Sarika</creator><creator>Varshney, Shivangi</creator><creator>Kumar, Vinod</creator><creator>Dalamu, Dalamu</creator><creator>Mandadi, Nagesh</creator><creator>Kumar, Manoj</creator><creator>Chakrabarti, Swarup K.</creator><creator>Rao, Atmakuri R.</creator><creator>Rai, Anil</creator><general>Springer Netherlands</general><general>Springer Nature B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7TK</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-3936-1458</orcidid></search><sort><creationdate>2021</creationdate><title>Genome sequence analysis provides insights on genomic variation and late blight resistance genes in potato somatic hybrid (parents and progeny)</title><author>Tiwari, Jagesh Kumar ; Rawat, Shashi ; Luthra, Satish K. ; Zinta, Rasna ; Sahu, Sarika ; Varshney, Shivangi ; Kumar, Vinod ; Dalamu, Dalamu ; Mandadi, Nagesh ; Kumar, Manoj ; Chakrabarti, Swarup K. ; Rao, Atmakuri R. ; Rai, Anil</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c375t-e9790e0e571294ceaeb9fc1a901a0477dcfb8ad406bb8af04dc76c3c10aaefca3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Animal Anatomy</topic><topic>Animal Biochemistry</topic><topic>Biomedical and Life Sciences</topic><topic>Chromosome Mapping</topic><topic>Conserved sequence</topic><topic>Copy number</topic><topic>Dihaploid</topic><topic>Disease resistance</topic><topic>Disease Resistance - genetics</topic><topic>DNA Copy Number Variations - genetics</topic><topic>Gene polymorphism</topic><topic>Genes</topic><topic>Genome, Plant - genetics</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Histology</topic><topic>Late blight</topic><topic>Life Sciences</topic><topic>Morphology</topic><topic>Nucleotide sequence</topic><topic>Offspring</topic><topic>Original Article</topic><topic>Phylogeny</topic><topic>Plant Diseases - genetics</topic><topic>Plant Diseases - microbiology</topic><topic>Plant Proteins - genetics</topic><topic>Plant Somatic Embryogenesis Techniques</topic><topic>Polymerase chain reaction</topic><topic>Sequence analysis</topic><topic>Signal transduction</topic><topic>Single-nucleotide polymorphism</topic><topic>Solanum pinnatisectum</topic><topic>Solanum tuberosum</topic><topic>Solanum tuberosum - genetics</topic><topic>Solanum tuberosum - growth & development</topic><topic>Species</topic><topic>Variation</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Tiwari, Jagesh Kumar</creatorcontrib><creatorcontrib>Rawat, Shashi</creatorcontrib><creatorcontrib>Luthra, Satish K.</creatorcontrib><creatorcontrib>Zinta, Rasna</creatorcontrib><creatorcontrib>Sahu, Sarika</creatorcontrib><creatorcontrib>Varshney, Shivangi</creatorcontrib><creatorcontrib>Kumar, Vinod</creatorcontrib><creatorcontrib>Dalamu, Dalamu</creatorcontrib><creatorcontrib>Mandadi, Nagesh</creatorcontrib><creatorcontrib>Kumar, Manoj</creatorcontrib><creatorcontrib>Chakrabarti, Swarup K.</creatorcontrib><creatorcontrib>Rao, Atmakuri R.</creatorcontrib><creatorcontrib>Rai, Anil</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>ProQuest Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Biological Sciences</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>PML(ProQuest Medical Library)</collection><collection>ProQuest Science Journals</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>ProQuest Central Basic</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Molecular biology reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Tiwari, Jagesh Kumar</au><au>Rawat, Shashi</au><au>Luthra, Satish K.</au><au>Zinta, Rasna</au><au>Sahu, Sarika</au><au>Varshney, Shivangi</au><au>Kumar, Vinod</au><au>Dalamu, Dalamu</au><au>Mandadi, Nagesh</au><au>Kumar, Manoj</au><au>Chakrabarti, Swarup K.</au><au>Rao, Atmakuri R.</au><au>Rai, Anil</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome sequence analysis provides insights on genomic variation and late blight resistance genes in potato somatic hybrid (parents and progeny)</atitle><jtitle>Molecular biology reports</jtitle><stitle>Mol Biol Rep</stitle><addtitle>Mol Biol Rep</addtitle><date>2021</date><risdate>2021</risdate><volume>48</volume><issue>1</issue><spage>623</spage><epage>635</epage><pages>623-635</pages><issn>0301-4851</issn><eissn>1573-4978</eissn><abstract>Wild
Solanum
species are the important resources for potato improvement. With the availability of potato genome and sequencing progress, knowledge about genomic resources is essential for novel genes discovery. Hence, the aim of this study was to decipher draft genome sequences of unique potato genotypes i.e. somatic hybrid P8 (J1), wild species
S. pinnatisectum
(J2), progeny MSH/14-112 (P8 × cv. Kufri Jyoti) (J3), and
S. tuberosum
dihaploid C-13 (J4). Draft genome sequencing using Illumina platform and reference-based assemblies with the potato genome yielded genome assembly size of 725.01 Mb (J1), 724.95 Mb (J2), 725.01 Mb (J3), and 809.59 Mb (J4). Further, 39,260 (J1), 25,711 (J2), 39,730 (J3) and 30,241 (J4) genes were identified and 17,411 genes were found common in the genotypes particularly late blight resistance genes (
R3a
,
RGA2
,
RGA3
,
R1B-16
,
Rpi-blb2
,
Rpi
and
Rpi-vnt1
). Gene ontology (GO) analysis showed that molecular function was predominant and signal transduction was major KEGG pathways. Further, gene enrichment analysis revealed dominance of metabolic process (GO: 0008152) in all the samples. Phylogeny analysis showed relatedness with potato and other plant species. Heterozygous single nucleotide polymorphism (SNP) was more than homozygous, and SNP in genic region was more than inter-genic region. Copy number variation (CNV) analysis indicated greater number of deletions than duplications. Sequence diversity and conserved motifs analysis revealed variation for late blight resistance genes. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed differential expression of late blight resistance genes. Our study provides insights on genome sequence, structural variation and late blight resistance genes in potato somatic hybrid (parents and progeny) for future research.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><pmid>33442830</pmid><doi>10.1007/s11033-020-06106-x</doi><tpages>13</tpages><orcidid>https://orcid.org/0000-0002-3936-1458</orcidid></addata></record> |
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| ispartof | Molecular biology reports, 2021, Vol.48 (1), p.623-635 |
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| source | MEDLINE; SpringerLink Journals - AutoHoldings |
| subjects | Animal Anatomy Animal Biochemistry Biomedical and Life Sciences Chromosome Mapping Conserved sequence Copy number Dihaploid Disease resistance Disease Resistance - genetics DNA Copy Number Variations - genetics Gene polymorphism Genes Genome, Plant - genetics Genomes Genomics Histology Late blight Life Sciences Morphology Nucleotide sequence Offspring Original Article Phylogeny Plant Diseases - genetics Plant Diseases - microbiology Plant Proteins - genetics Plant Somatic Embryogenesis Techniques Polymerase chain reaction Sequence analysis Signal transduction Single-nucleotide polymorphism Solanum pinnatisectum Solanum tuberosum Solanum tuberosum - genetics Solanum tuberosum - growth & development Species Variation |
| title | Genome sequence analysis provides insights on genomic variation and late blight resistance genes in potato somatic hybrid (parents and progeny) |
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