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SNP genotyping reveals major QTLs for plant architectural traits between A-genome peanut wild species

Molecular Genetics and Genomics volume 293, pages 1477–1491 (2018)Cite this article

Abstract

Key message

QTL mapping of important architectural traits was successfully applied to an A-genome diploid population using gene-specific variations.

Abstract

Peanut wild species are an important source of resistance to biotic and possibly abiotic stress; because these species differ from the cultigen in many traits, we have undertaken to identify QTLs for several plant architecture-related traits. In this study, we took recently identified SNPs, converted them into markers, and identified QTLs for architectural traits. SNPs from RNASeq data distinguishing two parents, A. duranensis (KSSc38901) and A. cardenasii (GKP10017), of a mapping population were identified using three references—A. duranensis V14167 genome sequence, and transcriptome sequences of A. duranensis KSSc38901 and OLin. More than 49,000 SNPs differentiated the parents, and 87.9% of the 190 SNP calls tested were validated. SNPs were then genotyped on 91 F2 lines using KASP chemistry on a Roche LightCycler 480 and a Fluidigm Biomark HD, and using SNPType chemistry on the Fluidigm Biomark HD. A linkage map was constructed having ten linkage groups, with 144 loci spanning a total map distance of 1040 cM. Comparison of the A-genome map to the A. duranensis genome sequence revealed a high degree of synteny. QTL analysis was also performed on the mapping population for important architectural traits. Fifteen definitive and 16 putative QTLs for petiole length, leaflet length and width, leaflet area, leaflet length/width ratio, main stem height, presence of flowers on the main stem, and seed mass were identified. Results demonstrate that SNPs identified from transcriptome sequencing could be converted to KASP or SNPType markers with a high success rate, and used to identify alleles with significant phenotypic effects, These could serve as information useful for introgression of alleles into cultivated peanut from wild species and have the potential to allow breeders to more easily fix these alleles using a marker-assisted backcrossing approach.

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References

  • Abdou YAM, Gregory WC, Cooper WE (1974) Sources and nature of resistance to Cercospora arachidicola Hori and Cercosporidium personatum (Berk. et Curtis) Deighton in Arachis species. Peanut Sci 1:6–11

    Article  Google Scholar 

  • Beavis WD (1998) QTL analyses: power, precision and accuracy. In: Paterson AH (ed) Molecular dissection of complex traits. CRC Press, Boca Raton, pp 145–162

    Google Scholar 

  • Bertioli DJ, Ozias-Akins P, Chu Y, Dantas KM, Santos SP, Gouvea E, Guimarães PM, Leal-Bertioli SCM, Knapp SJ, Moretzsohn MC (2014) The use of SNP markers for linkage mapping in diploid and tetraploid peanuts. G3 Genes Genomes Genet 4:89–96

    Google Scholar 

  • Bertioli DJ, Cannon SB, Froenicke L, Huang G, Farmer AD, Cannon EK, Liu X, Gao D, Clevenger J, Dash S, Ren L, Moretzsohn MC, Shirasawa K, Huang W, Vidigal B, Abernathy B, Chu Y, Niederhuth CE, Umale P, Araujo AC, Kozik A, Do Kim K, Burow MD, Varshney RK, Wang X, Zhang X, Barkley N, Guimaraes PM, Isobe S, Guo B, Liao B, Stalker HT, Schmitz RJ, Scheffler BE, Leal-Bertioli SCM, Xun X, Jackson SA, Michelmore R, Ozias-Akins P (2016) The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nat Genet 48:438–446

    CAS  Article  Google Scholar 

  • Blanc G, Wolfe KH (2004) Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16:1667–1678

    CAS  Article  Google Scholar 

  • Burow MD, Simpson CE, Paterson AH, Starr JL (1996) Identification of peanut (Arachis hypogaea) RAPD markers diagnostic of root-knot nematode (Meloidogyne arenaria (Neal) Chitwood) resistance. Mol Breed 2:307–319

    Article  Google Scholar 

  • Burow M, Simpson C, Starr J, Paterson A (2001) Transmission genetics of chromatin from a synthetic amphidiploid to cultivated peanut (Arachis hypogaea L.): broadening the gene pool of a monophyletic polyploid species. Genetics 159:823–837

    CAS  PubMed  PubMed Central  Google Scholar 

  • Burow M, Simpson C, Faries W, Starr J, Paterson A (2009) Molecular biogeography study of recently described B- and A-genome Arachis species, also providing new insights into the origins of cultivated peanut. Genome 52:107–119

    CAS  Article  Google Scholar 

  • Burow MD, Leal-Bertioli SCM, Simpson CE, Ozias-Akins P, Chu Y, Denwar N, Chagoya J, Starr JL, Moretzsohn MC, Pande MK, Varshney RK, Holbrook CC, Bertioli DJ (2013) Marker-assisted selection for biotic stress resistance in peanut. Chapter 13. In: Varshney RK, Tuberosa R (eds) Translational genomics for crop breeding, volume I: Biotic Stresses, 1st edn. Wiley, New York, pp 125–150

    Chapter  Google Scholar 

  • Burow M, Starr J, Park C-H, Simpson C, Paterson A (2014) Introgression of homoeologous quantitative trait loci (QTLs) for resistance to the root-knot nematode [Meloidogyne arenaria (Neal) Chitwood] in an advanced backcross-QTL population of peanut (Arachis hypogaea L.). Mol Breed 34:393–406

    CAS  Article  Google Scholar 

  • Byers RL, Harker DB, Yourstone SM, Maughan PJ, Udall JA (2012) Development and mapping of SNP assays in allotetraploid cotton. Theor Appl Genet (2012) 124:1201–1214

    CAS  Article  Google Scholar 

  • Chen ZJ (2010) Molecular mechanisms of polyploidy and hybrid vigor. Trends Plant Sci 15:57–71

    CAS  Article  Google Scholar 

  • Chen X, Li H, Pandey MK, Yang Q, Wang X, Garg V, Li H, Chi X, Doddamani D, Hong Y, Upadhyaya H, Guo H, Khan AW, Zhu F, Zhang X, Pan L, Pierce GJ, Zhou G, Krishnamohan K, Chen M, Zhong N, Agarwal G, Li S, Chitikineni A, Zhang G-Q, Sharma S, Chen N, Liu H, Janila P, Li S, Wang M, Wang T, Sun J, Li X, Li C, Wang M, Yu L, Wen S, Singh S, Yang Z, Zhao J, Zhang C, Yu Y, Bi J, Zhang X, Liu Z-J, Paterson AH, Wang S, Liang X, Varshney RK, Yu S (2016) Draft genome of the peanut A-genome progenitor (Arachis duranensis) provides insights into geocarpy, oil biosynthesis, and allergens. Proc Natl Acad Sci USA 113(24):6785–6790

    CAS  Article  Google Scholar 

  • Chopra R, Burow GB, Farmer A, Mudge JM, Simpson CE, Burow MD (2014) Comparisons of de novo transcriptome assemblers in diploid and polyploid species using peanut (Arachis spp.) RNA-Seq data. PLoS ONE 9(12):e115055

    Article  Google Scholar 

  • Chopra R, Burow G, Farmer A, Mudge J, Simpson CE, Wilkins TA, Baring MA, Puppala N, Chamberlin KD, Burow MD (2015) Next-generation transcriptome sequencing, SNP discovery and validation in four market classes of peanut, Arachis hypogaea L. Mol Genet Genom 290:1169–1180

    CAS  Article  Google Scholar 

  • Chopra R, Burow G, Simpson CE, Chagoya J, Mudge J, Burow MD (2016) Transcriptome sequencing of diverse peanut (Arachis) wild species and the cultivated species reveals a wealth of untapped genetic variability. G3 Genes Genomes Genet 6:3825–38360

    Google Scholar 

  • Church GT, Simpson CE, Burow MD, Paterson AH, Starr JL (2000) Use of RFLP markers for identification of individuals homozygous for resistance to Meloidogyne arenaria in peanut. Nematology 2:575–580

    CAS  Article  Google Scholar 

  • Clevenger J, Chu Y, Chavarro C, Agarwal G, Bertioli DJ, Leal-Bertioli SCM, Pandey MK, Vaughn J, Abernathy B, Barkley NA, Hovav R, Burow M, Nayak SN, Chitikineni A, Isleib TG, Holbrook CC, Jackson SA, Varshney RK, Ozias-Akins P (2017) Genome-wide SNP genotyping resolves signatures of selection and tetrasomic recombination in peanut. Mol Plant 10(2):309–322

    CAS  Article  Google Scholar 

  • Coffelt TA, Hammons RO (1972) Inheritance of sterile brachytic in an infraspecific cross of Arachis hypogaea L. Crop Sci 12:82–84

    Article  Google Scholar 

  • Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R (2011) The variant call format and VCFtools. Bioinformatics 27:2156–2158

    CAS  Article  Google Scholar 

  • DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43:491–498

    CAS  Article  Google Scholar 

  • Fonceka D, Tossim H-A, Rivallan R, Vignes H, Faye I, Ndoye O, Moretzsohn M, Bertioli D, Glaszmann J-C, Courtois B, Rami J-F (2012a) Fostered and left behind alleles in peanut: interspecific QTL mapping reveals footprints of domestication and useful natural variation for breeding. BMC Plant Biol 12:26

    Article  Google Scholar 

  • Fonceka D, Tossim HA, Rivallan R, Vignes H, Lacut E, de Bellis F, Faye I, Ndoye O, Leal-Bertioli SCM, Valls JFM, Bertioli DJ, Glaszmann J-C, Courtois B, Rami J-F (2012b) Construction of chromosome segment substitution lines in peanut (Arachis hypogaea L.) using a wild synthetic and QTL mapping for plant morphology. PLOS ONE 7(11):e48642

    CAS  Article  Google Scholar 

  • Garcia GM, Stalker HT, Shroeder E, Kochert G (1996) Identification of RAPD, SCAR, and RFLP markers tightly linked to nematode resistance genes introgressed from Arachis cardenasii into Arachis hypogaea. Genome 39:836–845

    CAS  Article  Google Scholar 

  • Gowda MVC, Motagi BN, Naidu GK, Diddimani SB, Sheshagiri R (2002) GPBD 4: a Spanish bunch groundnut genotype resistant to rust and late leaf spot. Int Arachis Newsl 22:29–32

    Google Scholar 

  • Halward T, Stalker H, Kochert G (1993) Development of an RFLP linkage map in diploid peanut species. Theor Appl Genet 87:379–384

    CAS  Article  Google Scholar 

  • Hammons RO (1971) Inheritance of inflorescences in main stem leaf axils in Arachis hypogaea L. Crop Sci 11:570–571

    Article  Google Scholar 

  • Holbrook CC, Timper P, Culbreath AK, Kvien CK (2008) Registration of ‘Tifguard’ peanut. J of Plant Regist 2:2

    Google Scholar 

  • Holbrook CC, Ozias-Akins P. Chu Y. Culbreath AK, Kvien C, Brenneman T (2017) Registration of ‘TifNV-high O/L’ peanut. J Plant Regist 11:228–230

    Article  Google Scholar 

  • Hu Y, Yan C, Hsu C-H, Chen Q-R, Niu K, Komatsoulis GA, Meerzaman D (2014) OmicCircos: a simple-to-use R package for the circular visualization of multidimensional omics data. Cancer Inform 13:13–20

    CAS  Article  Google Scholar 

  • Husted JR (1936) Cytological studies on the peanut. Arachis. 2. Chromosome number and morphology and behaviour and their application to the problem of origin of cultivated forms. Cytologia 7:396–423

    Article  Google Scholar 

  • Jia J, Zhao S, Kong X, Li Y, Zhao G, He W, Appels R, Pfeifer M, Tao Y, Zhang X, Jing R, Zhang C, Ma Y, Gao L, Gao C, Spannagl M, Mayer KF, Li D, Pan S, Zheng F, Hu Q, Xia X, Li J, Liang Q, Chen J, Wicker T, Gou C, Kuang H, He G, Luo Y, Keller B, Xia Q, Lu P, Wang J, Zou H, Zhang R, Xu J, Gao J, Middleton C, Quan Z, Liu G, Wang J, International Wheat Genome Sequencing Yang C, Liu H, He X, Mao Z, Wang L J (2013) Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 496:91–95

    CAS  Article  Google Scholar 

  • Kayam G, Brand Y, Faigenboim-Doron A, Patil A, Hedvat I, Hovav R (2017) Fine-mapping the branching habit trait in cultivated peanut by combining bulked segregant analysis and high-throughput sequencing. Front Plant Sci 8:467

    Article  Google Scholar 

  • Khedikar YP, Gowda MVC, Sarvamangala C, Patgar KV, Upadhyaya HD, Varshney RK (2010) A QTL study on late leaf spot and rust revealed one major QTL for molecular breeding for rust resistance in groundnut (Arachis hypogaea L.). Theor Appl Genet 121:971–984

    CAS  Article  Google Scholar 

  • Kirby JS, Melouk HA, Stevens TE Jr, Banks DJ, Sholar JR, Damicone JP, Jackson KE (1998) Registration of ‘Southwest Runner’ peanut. Crop Sci 1998 38:545–546

    Article  Google Scholar 

  • Kochert G, Stalker HT, Gimenes M, Galgaro L, Lopes CR, Moore K (1996) RFLP and cytogenetic evidence on the origin and evolution of allotetraploid domesticated peanut, Arachis hypogaea (Leguminosae). Am J Bot 83:1282–1291

    CAS  Article  Google Scholar 

  • Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newberg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181

    CAS  Article  Google Scholar 

  • Leal-Bertioli SCM, José ACVF, Alves-Freitas DMT, Moretzsohn MC, Guimarães PM, Nielen S, Vidigal BS, Pereira RW, Pike J, Fávero AP, Parniske M, Varshney RK, Bertioli DJ (2009) Identification of candidate genome regions controlling disease resistance in Arachis. BMC Plant Biol 9:112

    Article  Google Scholar 

  • Leal-Bertioli SCM, Bertioli DJ, Guimarães PM, Pereira TD, Galhardoa I, Silva JP, Brasileiro ACM, Oliveira RS, Silva PIT, Vadez V, Araujo ACG (2012) The effect of tetraploidization of wild Arachis on leaf morphology and other drought-related traits. Environ Exp Bot 84:17–24

    Article  Google Scholar 

  • Leal-Bertioli SCM, Cavalcante U, Gouvea EG, Ballén-Taborda C, Shirasawa K, Guimarães PM, Jackson SA, Bertioli DJ, Moretzsohn MC (2015a) Identification of QTLs for rust resistance in the peanut wild species Arachis magna and the development of KASP markers for marker assisted selection. G3 Genes Genomes Genet 5:1403–1413

    CAS  Google Scholar 

  • Leal-Bertioli S, Shirasawa K, Abernathy B, Moretzsohn M, Chavarro C, Clevenger J,J, Ozias-Akins P, Jackson S, and Bertioli D (2015b) Tetrasomic recombination is surprisingly frequent in allotetraploid Arachis. Genetics 199(4):1093–1105

    CAS  Article  Google Scholar 

  • Leal-Bertioli SCM, Moretzsohn MC, Roberts PA, Ballén-Taborda C, Borba TCO, Valdisser PA, Vianello RP, Araújo ACG, Guimarães PM, Bertioli DJ (2016) Genetic mapping of resistance to Meloidogyne arenaria in Arachis stenosperma: a new source of nematode resistance for peanut. G3 Genes Genomes Genet 6:377–390

    CAS  Google Scholar 

  • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754–1760

    CAS  Article  Google Scholar 

  • Mallikarjuna N, Shilpa K, Pandey M, Janila P, Varshney RK (2014) Groundnut. Chapter 8. In: Singh M et al (ed) Broadening the genetic base of grain legumes. Springer, India

    Google Scholar 

  • Maloof JN, Nozue K, Mumbach MR, Palmer CM (2013) LeafJ: An ImageJ plugin for semi-automated leaf shape measurement. J Vis Exp 71:50028

    Google Scholar 

  • Moretzsohn M, Leoi L, Proite K, Guimaraes P, Leal-Bertioli S, Gimenes M, Martins W, Valls J, Grattapaglia D, Bertioli D (2005) A microsatellite-based, gene-rich linkage map for the AA genome of Arachis (Fabaceae). Theor Appl Genet 111:1060–1071

    CAS  Article  Google Scholar 

  • Moretzsohn MC, Barbosa AVG, Alves-Freitas DMT, Teixeira C, Leal-Bertioli S, Guimares PM, Pereira RW, Lopes CR, Cavallari MM, Cavallari MM, Valls JFM (2009) A linkage map for the B-genome of Arachis (Fabaceae) and its synteny to the A-genome. BMC Plant Biol 9:40

    Article  Google Scholar 

  • Muñoz N, Liu A, Kan L, Li M-W, Lam H-M (2017) Potential uses of wild germplasms of grain legumes for crop improvement. Int J Mol Sci 18(2):328

    Article  Google Scholar 

  • Nagy ED, Guo Y, Tang S, Bowers JE, Okashah RA, Taylor CA, Zhang D, Khanal S, Heesacker AF, Khalilian N, Farmer AD, Carrasquilla-Garcia N, Penmetsa RV, Cook D, Stalker HT, Nielsen N, Ozias-Akins P, Knapp SJ (2012) A high-density genetic map of Arachis duranensis, a diploid ancestor of cultivated peanut. BMC Genom 13:469

    CAS  Article  Google Scholar 

  • Pandey MK, Agarwal G, Kale SM, Clevenger J, Nayak SN, Sriswathi M, Chitikineni A, Chavarro C, Chen X, Upadhyaya HD, Vishwakarma MK, Leal-Bertioli S, Liang X, Bertioli DJ, Guo B, Jackson SA, Ozias-Akins P, Varshney RK (2017) Development and evaluation of a high density genotyping ‘Axiom_Arachis’ array with 58 K SNPs for accelerating genetics and breeding in groundnut. Sci Rep 7:40577

    CAS  Article  Google Scholar 

  • Qin J, Jones RC, Ramakrishnan R (2008) Studying copy number variations using a nanofluidic platform. Nucleic Acids Res 36(18):e116

    Article  Google Scholar 

  • Schneider CA, Rasband WS, Eliceiri KW (2012) NIH image to ImageJ: 25 years of image analysis. Nat Methods 9:671–675

    CAS  Article  Google Scholar 

  • Shirasawa K, Bertioli DJ, Varshney RK, Moretzsohn MC, Leal-Bertioli SCM, Thudi M, Pandey MK, Rami J-F, Foncéka D, Gowda MVC, Qin H, Guo B, Hong Y, Liang X, Hirakawa H, Tabata S, Isobe S (2013) Integrated consensus map of cultivated peanut and wild relatives reveals structures of the A and B genomes of Arachis and divergence of the legume genomes. DNA Res 20:173–184

    CAS  Article  Google Scholar 

  • Simpson CE, Starr JL (2001) Registration of ‘COAN’ peanut. Crop Sci 41:918

    Article  Google Scholar 

  • Simpson CE, Nelson SC, Starr JL, Woodard KE, Smith OD (1993) Registration of TxAG-6 and TxAG-7 peanut germplasm lines. Crop Sci 33:1418–1418

    Article  Google Scholar 

  • Simpson CE, Starr JL, Church GT, Burow MD, Paterson AH (2003) Registration of NemaTAM peanut. Crop Sci 43:1561

    Article  Google Scholar 

  • Simpson CE, Starr JL, Baring MR, Burow MD, Cason J, Wilson JN (2013) Registration of ‘Webb’ peanut. J Plant Regist 7:265–268

    Article  Google Scholar 

  • Smartt J, Gregory W (1967) Interspecific cross-compatibility between the cultivated peanut and Arachis hypogaea L. and its behavior in backcrosses. Olèâgineux 22:455–459

    Google Scholar 

  • Soltis P, Soltis D (2009) The role of hybridization in plant speciation. Ann Rev Plant Biol 60:561–588

    CAS  Article  Google Scholar 

  • Stalker H (1984) Utilizing Arachis cardenasii as a source of Cercospora leafspot resistance for peanut improvement. Euphytica 33:529–538

    Article  Google Scholar 

  • Stalker HT (2017) Utilizing wild species for peanut improvement. Crop Sci 57:1102–1120

    Article  Google Scholar 

  • Stalker HT, Moss JP (1987) Speciation, cytogenetics and utilization of Arachis species. Adv Agron 41:1–39

    Article  Google Scholar 

  • Stalker HT, Simpson CE (1995) Germplasm resources in Arachis. In: Pattee HE, Stalker HT (eds) Advances in peanut science. Am. Peanut Res. and Educ. Soc., Stillwater, pp 14–53

    Google Scholar 

  • Sujay V, Gowda M, Pandey M, Bhat R, Khedikar Y, Nadaf H, Gautami B, Sarvamangala C, Lingaraju S, Radhakrishan T (2012) Quantitative trait locus analysis and construction of consensus genetic map for foliar disease resistance based on two recombinant inbred line populations in cultivated groundnut (Arachis hypogaea L.). Mol Breed 30:773–788

    CAS  Article  Google Scholar 

  • Tiwari S, Ghewandhe M, Mishra D (1984) Inheritance of resistance to rust and late leaf spot in groundnut (Arachis hypogaea). J Cytol Genet 19:97–101

    Google Scholar 

  • Upadhyaya HD (2008) Crop germplasm and wild relatives: a source of novel variation for crop improvement. Korean J Crop Sci 53:12–17

    Google Scholar 

  • Upadhyaya H, Sharma S, Dwivedi SL (2011) Arachis. Chapter 1. In: Cole C (ed) Wild crop relatives: genomic and breeding resources, legumes and forages. Springer, Berlin, pp 1–20

    Google Scholar 

  • Varshney RK, Pandey MK, Janila P, Nigam SN, Sudini H, Gowda MV (2014) Marker-assisted introgression of a QTL region to improve rust resistance in three elite and popular varieties of peanut (Arachis hypogaea L.). Theor Appl Genet 127:1771–1781

    Article  Google Scholar 

  • Voorrips RE (2002) MapChart Software for the Graphical Presentation of Linkage Maps and QTLs. J Hered 93:77–78

    CAS  Article  Google Scholar 

  • Wang J, Lin M, Crenshaw A, Hutchinson A, Hicks B, Yeager M, Berndt S, Huang W-Y, Hayes RB, Chanock SJ, Jones RC, Ramakrishnan R (2009) High-throughput single nucleotide polymorphism genotyping using nanofluidic dynamic arrays. BMC Genom 10:561

    Article  Google Scholar 

  • Wang S, Basten CJ, Zeng Z-B (2011) Windows QTL cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh

    Google Scholar 

  • Wilson JN, Chopra R, Baring MR, Selvaraj MG, Simpson CE, Chagoya J, Burow MD (2017) Advanced backcross quantitative trait loci (QTL) analysis of oil concentration and oil quality traits in peanut (Arachis hypogaea L.). Trop Plant Biol 10:1–17

    CAS  Article  Google Scholar 

  • Wynne JC (1975) Inheritance of branching pattern in Arachis hypogaea L. Peanut Sci 2:1–5

    Article  Google Scholar 

  • Zhou X, Xia Y, Ren X, Chen Y, Huang L, Huang S, Liao B, Lei Y, Yan L, Jian H (2014) Construction of a SNP-based genetic linkage map in cultivated peanut based on large scale marker development using next-generation double-digest restriction-site-associated DNA sequencing (ddRADseq). BMC Genom 15(1):351

    Article  Google Scholar 

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Acknowledgements

The authors wish to thank Jennifer Chagoya at Texas A&M AgriLife Research, Lubbock for technical support.

Funding

This work was supported by Grants from the National Peanut Board Grant #332/TX-99/1139 to MDB and #332/TX-99/1213 to MDB and CES, Peanut Foundation award 04-858-14 to MB and CES, Ogallala Aquifer program award IPM_12.06 to MDB and PP, Peanut and Mycotoxin Innovation Lab award RC299-430/4942356 to MDB and CES, and NIFA Hatch funding project number TEX08835 to MDB.

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Affiliations

  1. Department of Plant and Soil Sciences, Texas Tech University, Lubbock, TX, 79409, USA

    Ratan Chopra, Jyotsna Sharma & Mark D. Burow

  2. Texas A&M AgriLife Research, Stephenville, TX, 76401, USA

    Charles E. Simpson

  3. Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX, 77843, USA

    Andrew Hillhouse

  4. USDA-ARS-CSRL, Lubbock, TX, 79415, USA

    Paxton Payton

  5. Texas A&M AgriLife Research, Lubbock, TX, 79403, USA

    Mark D. Burow

Authors
  1. Ratan Chopra
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  2. Charles E. Simpson
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  3. Andrew Hillhouse
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  4. Paxton Payton
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  5. Jyotsna Sharma
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  6. Mark D. Burow
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Contributions

RC prepared the draft of manuscripts and performed bioinformatics analysis, genotyping and genetic mapping. CS developed the mapping population and co-wrote the manuscript. AH assisted with genotyping. JS and PP helped with reviewing the manuscript. MDB conceived the idea, assisted with genotyping, genetic analysis, and with revision of the manuscript. All the authors approved this submission.

Corresponding author

Correspondence to Mark D. Burow.

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Conflict of interest

All authors declare no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Data availability

Sequences for these two accessions are deposited at NCBI under biosample runs SRR4039015 and SRR1535034. SNP variant calls using the references will be made available upon acceptance of manuscript for publication, and have already been uploaded at Figshare at https://figshare.com/account/projects/26287/articles/5568220 and https://figshare.com/account/projects/26287/articles/5568229.

Additional information

Communicated by S. Hohmann.

Electronic supplementary material

Below is the link to the electronic supplementary material.

438_2018_1472_MOESM1_ESM.tif

Supplementary Figure 1: Differences in clustering patterns of KASP amplification on the Fluidigm Biomark HD based on amplification cycles. Panels A- 26 cycles, B- 36 cycles, and C- 46 cycles (TIF 7447 KB)

438_2018_1472_MOESM2_ESM.tif

Clustering of amplified markers which deviated from 1:2:1 ratio in F2 population. A-C plots are the SNPType assays on Fluidigm where A: two classes with a 3:1 ratio; B: three classes but fewer genotypes for parent B; and C: two classes scored by the software but could perhaps be classified as three. D-F plots are the assays on the LightCycler 480 where D- Spurious amplification and hard to classify due to high variability among accessions, could score accurately as three genotypes, E and F have one parent allele poorly amplified (TIF 5159 KB)

438_2018_1472_MOESM3_ESM.tif

Genotype data for an F2 intercross generated with 91 individuals and 144 markers. The genotypes A-Parent1, H-heterozygote, B-Parent2 are displayed in the colors red, blue, and green, respectively. In an intercross, if a 3:1 segregation ratio was observed, these are displayed in purple and orange, respectively. White pixels indicate missing data (TIF 3853 KB)

438_2018_1472_MOESM4_ESM.tif

Circos plot representing synteny between the genetic and physical maps. Chr1-Chr10 indicate the linkage groups (LG01-LG10) of the genetic map generated using SNP markers in this study and Chr11-Chr20 indicate the chromosomes of the genome sequence (AA01-AA10). Blue bar plots on Chr11-Chr20 of the physical map indicate the SNPs distribution on the genome sequence with the use of transcriptome data (TIF 14977 KB)

438_2018_1472_MOESM5_ESM.xlsx

Primer sequences for the markers used in validation of SNPs and genotyping the F2 mapping population derived from cross between A. duranensis (KSSc38901) and A. cardenasii (GKP10017) (XLSX 20 KB)

438_2018_1472_MOESM6_ESM.xlsx

Genotype and phenotype data on the mapping population obtained from allele calls of two different platforms (XLSX 96 KB)

438_2018_1472_MOESM7_ESM.xlsx

Chi-square test on segregation ratio of SNP markers and apparently dominant markers deviated in the F2 population. * - significantly departing for the expected ratio (XLSX 21 KB)

438_2018_1472_MOESM8_ESM.xlsx

Genome coordinates used from the genome assembly to evaluate the synteny between the linkage and physical map (XLSX 20 KB)

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Chopra, R., Simpson, C.E., Hillhouse, A. et al. SNP genotyping reveals major QTLs for plant architectural traits between A-genome peanut wild species. Mol Genet Genomics 293, 1477–1491 (2018). https://doi.org/10.1007/s00438-018-1472-z

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  • DOI: https://doi.org/10.1007/s00438-018-1472-z

Keywords

  • Arachis
  • Wild species
  • Domestication
  • QTLs
  • SNPs
  • Markers
  • KASP
  • Fluidigm
  • Peanut