Mapping of a novel locus Ra conferring extreme resistance against potato virus A in cultivated potato (Solanum tuberosum L.).
Journal
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
ISSN: 1432-2242
Titre abrégé: Theor Appl Genet
Pays: Germany
ID NLM: 0145600
Informations de publication
Date de publication:
06 Aug 2024
06 Aug 2024
Historique:
received:
07
02
2024
accepted:
27
07
2024
medline:
7
8
2024
pubmed:
7
8
2024
entrez:
6
8
2024
Statut:
epublish
Résumé
The Ra extreme resistance against potato virus A was mapped to the upper of chromosome 4 in tetraploid potato. Potato virus A (PVA) is one of the major viruses affecting potato worldwide and can cause serious disease symptoms and yield losses. Previously, we determined that potato cultivar Barbara harbors Ry
Identifiants
pubmed: 39107580
doi: 10.1007/s00122-024-04705-x
pii: 10.1007/s00122-024-04705-x
doi:
Substances chimiques
Genetic Markers
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
198Subventions
Organisme : National Natural Science Foundation of China
ID : 31971989
Organisme : Chian Agriculture Research System
ID : CARS-09
Organisme : Modern Agricultural Industrial Technology System of Hubei Province
ID : HBHZD-ZB-2020-005
Informations de copyright
© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
Références
Andrews S (2014) FastQC a quality control tool for high throughput sequence data. Available at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Aronesty E (2011) Ea-utils: command-line tools for processing biological sequencing data. Available at: https://github.com/ExpressionAnalysis/ea-utils
Barker H (1996) Inheritance of resistance to potato viruses Y and A in progeny obtained from potato cultivars containing gene Ry: evidence for a new gene for extreme resistance to PVA. Theor Appl Genet 93:710–716. https://doi.org/10.1007/BF00224066
doi: 10.1007/BF00224066
Birch PRJ, Bryan G, Fenton B et al (2012) Crops that feed the world 8: potato: are the trends of increased global production sustainable? Food Secur 4:477–508. https://doi.org/10.1007/s12571-012-0220-1
doi: 10.1007/s12571-012-0220-1
Chen X, Lewandowska D, Armstrong MR et al (2018b) Identification and rapid mapping of a gene conferring broad-spectrum late blight resistance in the diploid potato species Solanum verrucosum through DNA capture technologies. Theor Appl Genet 131:1287–1297. https://doi.org/10.1007/s00122-018-3078-6
doi: 10.1007/s00122-018-3078-6
Chen N, Zhu W, Xu J et al (2018) Molecular marker development and primary physical map construction for the tuber shape Ro gene locus in diploid potato (Solanum tuberosum L.). Molecul Breed 39:6. https://doi.org/10.1007/s11032-018-0913-z
doi: 10.1007/s11032-018-0913-z
Cockerham G (1970) Genetical studies on resistance to potato viruses X and Y. Heredity 25:309–348
doi: 10.1038/hdy.1970.35
DePristo MA, Banks E, Poplin R et al (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43:491–498. https://doi.org/10.1038/ng.806
doi: 10.1038/ng.806
Endelman JB, Jansky SH (2016) Genetic mapping with an inbred line-derived F2 population in potato. Theor Appl Genet 129:935–943. https://doi.org/10.1007/s00122-016-2673-7
doi: 10.1007/s00122-016-2673-7
Fekih R, Takagi H, Tamiru M et al (2013) MutMap+: genetic mapping and mutant identification without crossing in rice. PLoS ONE 8:e68529. https://doi.org/10.1371/journal.pone.0068529
doi: 10.1371/journal.pone.0068529
Fuentes S, Gibbs A, Adams I et al (2021) Potato virus A isolates from three continents: their biological properties, phylogenetics, and prehistory. Phytopathology 111:217–216. https://doi.org/10.1094/PHYTO-08-20-0354-FI
doi: 10.1094/PHYTO-08-20-0354-FI
Giovannoni JJ, Wing RA, Ganal MW, Tanksley SD (1991) Isolation of molecular markers from specific chromosomal intervals using DNA pools from existing mapping populations. Nucleic Acids Res 19:6553–6568. https://doi.org/10.1093/nar/19.23.6553
doi: 10.1093/nar/19.23.6553
Grech-Baran M, Witek K, Szajko K et al (2020) Extreme resistance to Potato virus Y in potato carrying the Ry
doi: 10.1111/pbi.13230
Hackett CA, Milne I, Bradshaw JE et al (2007) TetraploidMap for windows: linkage map construction and QTL mapping in autotetraploid species. J Hered 98:727–729. https://doi.org/10.1093/jhered/esm086
doi: 10.1093/jhered/esm086
Hämäläinen JH, Gebhardt C, Watanabe KN et al (2000) Recessive and dominant genes interfere with the vascular transport of potato virus A in diploid potatoes. Mol Plant Microbe Iinteract 13:402–412. https://doi.org/10.1094/MPMI.2000.13.4.402
doi: 10.1094/MPMI.2000.13.4.402
He C, Zhang W, Hu X et al (2014) Molecular characterization of a Chinese isolate of potato virus A (PVA) and evidence of a genome recombination event between PVA variants at the 3′-proximal end of the genome. Arch Virol 159:2457–2462. https://doi.org/10.1007/s00705-014-2053-z
doi: 10.1007/s00705-014-2053-z
Huang W, Nie B, Tu Z et al (2021) Extreme resistance to potato virus A in potato cultivar Barbara is independently mediated by Ra and Ry
doi: 10.1094/PDIS-02-21-0233-SC
Illa-Berenguer E, Van Houten J, Huang Z et al (2015) Rapid and reliable identification of tomato fruit weight and locule number loci by QTL-seq. Theor Appl Genet 128:1329–1342. https://doi.org/10.1007/s00122-015-2509-x
doi: 10.1007/s00122-015-2509-x
Kage U, Kumar A, Dhokane D et al (2015) Functional molecular markers for crop improvement. Crit Rev Biotechnol 36:917–930. https://doi.org/10.3109/07388551.2015.1062743
doi: 10.3109/07388551.2015.1062743
Karki HS, Halterman DA, Endelman JB (2021) Characterization of a late blight resistance gene homologous to R2 in potato variety Payette Russet. Am J Potato Res 98:78–84. https://doi.org/10.1007/s12230-020-09811-2
doi: 10.1007/s12230-020-09811-2
Kreuz JF, Souza-Dias JAC, Jeevalatha A et al (2020) Viral diseases in potato. In: Hugo C, Ortiz O (eds) The Potato Crop its agricultural, nutritional and social contribution to humankind. Springer Nature, Berlin, pp 389–430. https://doi.org/10.1007/978-3-030-28683-5_11
doi: 10.1007/978-3-030-28683-5_11
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754–1760. https://doi.org/10.1093/bioinformatics/btp324
doi: 10.1093/bioinformatics/btp324
Li H, Handsaker B, Wysoker A et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079. https://doi.org/10.1093/bioinformatics/btp352
doi: 10.1093/bioinformatics/btp352
Li H, Ikram M, Xia Y et al (2022) Genome-wide identification and development of InDel markers in tobacco (Nicotiana tabacum L.) using RAD-seq. Physiol Mol Biol Plants 28:1077–1089. https://doi.org/10.1007/s12298-022-01187-3
doi: 10.1007/s12298-022-01187-3
Lohse M, Bolger AM, Nagel A et al (2012) RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Res 40:W622-627. https://doi.org/10.1093/nar/gks540
doi: 10.1093/nar/gks540
Lu H, Lin T, Klein J et al (2014) QTL-seq identifies an early flowering QTL located near flowering locus T in cucumber. Theor Appl Genet 127:1491–1499. https://doi.org/10.1007/s00122-014-2313-z
doi: 10.1007/s00122-014-2313-z
Lv Y, Liu Y, Zhao H (2016) mInDel: a high-throughput and efficient pipeline for genome-wide InDel marker development. BMC Genomics 17:290. https://doi.org/10.1186/s12864-016-2614-5
doi: 10.1186/s12864-016-2614-5
MacLachlan DS, Larson RH, Walker JC (1954) Potato Virus A. Am Potato J 31:67–72. https://doi.org/10.1007/BF02859999
doi: 10.1007/BF02859999
Makarova SS, Makarov VV, Taliansky ME et al (2017) Virus resistance in potato: current state and prospects. Rus J Genet: Appl Res 7:845–857. https://doi.org/10.1134/S2079059717050148
doi: 10.1134/S2079059717050148
Mansfeld BN, Grumet R (2018) QTLseqr: an R Package for bulk segregant analysis with next-generation sequencing. Plant Genome 11:180006. https://doi.org/10.3835/plantgenome2018.01.0006
doi: 10.3835/plantgenome2018.01.0006
McKenna A, Hanna M, Banks E et al (2010) The genome analysis toolkit: a mapreduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303. https://doi.org/10.1101/gr.107524.110
doi: 10.1101/gr.107524.110
Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 88:9828–9832. https://doi.org/10.1073/pnas.88.21.9828
doi: 10.1073/pnas.88.21.9828
Nie X, Sutherland D, Dickison V et al (2016) Development and validation of high-resolution melting markers derived from Ry
doi: 10.1094/PHYTO-05-16-0204-R
Pajaree S, Nganga ML, Lieberman MC et al (2024) A k-mer-based bulked segregant analysis approach to map seed traits in unphased heterozygous potato genomes. G3-Genes Genomes Genet 14(4):jkae35. https://doi.org/10.1093/g3journal/jkae035
doi: 10.1093/g3journal/jkae035
Pham GM, Hamilton JP, Wood JC et al (2020) Construction of a chromosome-scale long-read reference genome assembly for potato. GigaScience 9:giaa100. https://doi.org/10.1093/gigascience/giaa100
doi: 10.1093/gigascience/giaa100
Prodhomme C, Esselink D, Borm T et al (2019) Comparative subsequence sets analysis (CoSSA) is a robust approach to identify haplotype specific SNPs; mapping and pedigree analysis of a potato wart disease resistance gene Sen3. Plant Methods 15:60. https://doi.org/10.1186/s13007-019-0445-5
doi: 10.1186/s13007-019-0445-5
Saghai-Maroof MA, Soliman KM, Jorgensen RA et al (1985) Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA 81:8014–8018. https://doi.org/10.1073/pnas.81.24.8014
doi: 10.1073/pnas.81.24.8014
Schneeberger K, Ossowski S, Lanz C et al (2009) SHOREmap: simultaneous mapping and mutation identification by deep sequencing. Nat Methods 6:550–551. https://doi.org/10.1038/nmeth0809-550
doi: 10.1038/nmeth0809-550
Singh VK, Khan AW, Saxena RK et al (2017) Indel-seq: a fast-forward genetics approach for identification of trait-associated putative candidate genomic regions and its application in pigeonpea (Cajanus cajan). Plant Biotechnol J 15:906–914. https://doi.org/10.1111/pbi.12685
doi: 10.1111/pbi.12685
Song YS, Schwarzfischer A (2008) Development of STS markers for selection of extreme resistance (Ry
doi: 10.1007/s12230-008-9012-8
Sorensen PL, Christensen G, Karki HS (2023) A KASP marker for the potato late blight resistance gene RB/Rpi-blb1. BioRxiv. https://doi.org/10.1101/2023.02.22.529539
doi: 10.1101/2023.02.22.529539
Strachan SM, Armstrong MR, Kaur A et al (2019) Mapping the H2 resistance effective against Globodera pallida pathotype Pa1 in tetraploid potato. Theor Appl Genet 132:1283–1294. https://doi.org/10.1007/s00122-019-03278-4
doi: 10.1007/s00122-019-03278-4
Takagi H, Abe A, Yoshida K et al (2013) QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J 74:174–183. https://doi.org/10.1111/tpj.12105
doi: 10.1111/tpj.12105
Thomas-Sharma S, Abdurahman A, Ali S et al (2016) Seed degeneration in potato: the need for an integrated seed health strategy to mitigate the problem in developing countries. Plant Pathol. https://doi.org/10.1111/ppa.12439
doi: 10.1111/ppa.12439
Torrance L, Cowan GH, McLean K et al (2020) Natural resistance to Potato virus Y in Solanum tuberosum Group Phureja. Theor Appl Genet 133:967–980. https://doi.org/10.1007/s00122-019-03521-y
doi: 10.1007/s00122-019-03521-y
Valkonen J, Gebhardt C, Zimnoch-Guzowska E et al (2017) Resistance to potato virus Y in potato. In: Lacomme C, Glais L, Bellstedt DU (eds) Potato virus Y: biodiversity, pathogenicity, epidemiology and management. Springer International Publishing, Switzerland, pp 207–241. https://doi.org/10.1007/978-3-319-58860-5_8
doi: 10.1007/978-3-319-58860-5_8
Witek K, Jupe F, Witek AI et al (2016) Accelerated cloning of a potato late blight-resistance gene using RenSeq and SMRT sequencing. Nat Biotechnol 34:656–660. https://doi.org/10.1038/nbt.3540
doi: 10.1038/nbt.3540
Yamakawa H, Haque E, Tanaka M et al (2021) Polyploid QTL-seq towards rapid development of tightly linked DNA markers for potato and sweetpotato breeding through whole-genome resequencing. Plant Biotechnol J 19:2040–2051. https://doi.org/10.1111/pbi.13633
doi: 10.1111/pbi.13633